diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index 52b99edef8..721ea10ca1 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -1,22 +1,22 @@ { - "name": "nf-core.astro", - "build": { - "dockerfile": "Dockerfile", - "context": ".." - }, - "portsAttributes": { - "4321": { - "label": "Astro Dev Server", - "onAutoForward": "openPreview" + "name": "nf-core.astro", + "build": { + "dockerfile": "Dockerfile", + "context": ".." + }, + "portsAttributes": { + "4321": { + "label": "Astro Dev Server", + "onAutoForward": "openPreview" + } + }, + "customizations": { + "vscode": { + "extensions": ["astro-build.astro-vscode", "editorconfig.editorconfig", "esbenp.prettier-vscode"] + } + }, + "waitFor": "onCreateCommand", + "postAttachCommand": { + "server": "npm run dev --workspace sites/main-site -- --host" } - }, - "customizations": { - "vscode": { - "extensions": ["astro-build.astro-vscode", "editorconfig.editorconfig", "esbenp.prettier-vscode"] - } - }, - "waitFor": "onCreateCommand", - "postAttachCommand": { - "server": "npm run dev --workspace sites/main-site -- --host" - } } diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 110337b405..290b8f789d 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -9,4 +9,4 @@ repos: - prettier@3.8.3 - prettier-plugin-svelte@3.5.1 - prettier-plugin-astro@0.14.1 - files: \.(astro|svelte|mdx|md|yml|yaml)$ + files: \.(astro|svelte|mdx|md|yml|yaml|json)$ diff --git a/.vscode/settings.json b/.vscode/settings.json index 6fa4f86d44..5b167cf3ff 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -1,18 +1,16 @@ { - "markdown.styles": [ - "public/vscode_markdown.css" - ], - "cSpell.words": [ - "bioconda", - "bioinformatics", - "colab", - "condacolab", - "nextflow", - "Zenodo", - "helpdesk", - "Slurm", - "slurm", - "Biocontainer", - "Hackmd" - ] + "markdown.styles": ["public/vscode_markdown.css"], + "cSpell.words": [ + "bioconda", + "bioinformatics", + "colab", + "condacolab", + "nextflow", + "Zenodo", + "helpdesk", + "Slurm", + "slurm", + "Biocontainer", + "Hackmd" + ] } diff --git a/bin/params.json.js b/bin/params.json.js new file mode 100644 index 0000000000..5fe10e1d1b --- /dev/null +++ b/bin/params.json.js @@ -0,0 +1,192 @@ +#! /usr/bin/env node +import { getGitHubFile, getCurrentRateLimitRemaining } from '../sites/main-site/src/components/octokit.js'; +import { readFileSync, writeFileSync, existsSync } from 'fs'; +import path from 'path'; +import ProgressBar from 'progress'; + +const __dirname = path.resolve(); + +const args = process.argv.slice(2); +const singlePipelineName = args[0] || null; +const singleVersion = args[1] || null; + +if (singleVersion && !singlePipelineName) { + console.error('A pipeline name must be provided when specifying a version'); + process.exit(1); +} + +console.log(await getCurrentRateLimitRemaining()); + +// Internal key combining param name + type so same-named params with different types stay separate. +const internalKey = (name, type) => `${name}|${type ?? ''}`; + +// Convert the grouped output format { paramName: [{type, pipelines}] } +// back into the flat internal map { "paramName|type": {name, type, pipelines} }. +function ungroupParams(grouped) { + const flat = {}; + for (const [name, variants] of Object.entries(grouped)) { + for (const { type, pipelines } of variants) { + flat[internalKey(name, type)] = { name, type, pipelines }; + } + } + return flat; +} + +// Convert the flat internal map into the grouped output format. +function groupParams(flat) { + const grouped = {}; + for (const { name, type, pipelines } of Object.values(flat)) { + if (!grouped[name]) grouped[name] = []; + grouped[name].push({ type, pipelines }); + } + // Sort each variant list by type name, then sort params alphabetically by key. + return Object.fromEntries( + Object.keys(grouped) + .sort() + .map((name) => [ + name, + grouped[name] + .sort((a, b) => (a.type ?? '').localeCompare(b.type ?? '')) + .map(({ type, pipelines }) => ({ + type, + pipelines: pipelines.sort( + (a, b) => a.name.localeCompare(b.name) || a.version.localeCompare(b.version), + ), + })), + ]), + ); +} + +export const writeParamsJson = async () => { + const pipelinesJson = readFileSync(path.join(__dirname, '/public/pipelines.json')); + const pipelines = JSON.parse(pipelinesJson); + + const paramsJsonPath = path.join(__dirname, '/public/params.json'); + + // Internal map keyed by "paramName|type" + let params = {}; + + if (singlePipelineName) { + if (existsSync(paramsJsonPath)) { + params = ungroupParams(JSON.parse(readFileSync(paramsJsonPath))); + } + // Remove existing entries for the targeted pipeline+version before re-processing + for (const key of Object.keys(params)) { + params[key].pipelines = params[key].pipelines.filter((p) => { + if (p.name !== singlePipelineName) return true; + return singleVersion ? p.version !== singleVersion : false; + }); + if (params[key].pipelines.length === 0) { + delete params[key]; + } + } + + const pipelineEntry = pipelines.remote_workflows.find((p) => p.name === singlePipelineName); + if (!pipelineEntry) { + console.error(`Pipeline ${singlePipelineName} not found in pipelines.json`); + process.exit(1); + } + if (singleVersion && !pipelineEntry.releases.some((r) => r.tag_name === singleVersion)) { + console.error(`Version ${singleVersion} not found for pipeline ${singlePipelineName} in pipelines.json`); + process.exit(1); + } + console.log(`Processing parameters for: ${singlePipelineName}${singleVersion ? `@${singleVersion}` : ''}`); + } + + const pipelinesToProcess = singlePipelineName + ? pipelines.remote_workflows.filter((p) => p.name === singlePipelineName) + : pipelines.remote_workflows; + + // Build a set of already-processed {pipeline@version} pairs so re-runs skip unchanged releases + const processed = new Set(); + if (!singlePipelineName) { + for (const { pipelines: pipelineList } of Object.values(params)) { + for (const { name, version } of pipelineList) { + processed.add(`${name}@${version}`); + } + } + } + + const CONCURRENCY_LIMIT = 10; + const bar = new ProgressBar(' fetching schemas [:bar] :percent :etas', { total: pipelinesToProcess.length }); + + const processPipeline = async (pipeline) => { + const targetRelease = singleVersion + ? pipeline.releases?.find((r) => r.tag_name === singleVersion && r.has_schema) + : (pipeline.releases?.find((r) => r.tag_name !== 'dev' && r.has_schema) ?? + pipeline.releases?.find((r) => r.tag_name === 'dev' && r.has_schema)); + + if (!targetRelease) { + if (singleVersion) { + console.error(`Version ${singleVersion} not found or has no schema for ${pipeline.name}`); + } + bar.tick(); + return; + } + + // Skip if this exact release was already parsed into params.json + if (processed.has(`${pipeline.name}@${targetRelease.tag_name}`)) { + bar.tick(); + return; + } + + const schemaContent = await getGitHubFile(pipeline.name, 'nextflow_schema.json', targetRelease.tag_name); + + if (!schemaContent) { + bar.tick(); + return; + } + + let schema; + try { + schema = JSON.parse(schemaContent); + } catch { + bar.tick(); + return; + } + + // Collect param names + types from definitions (draft-07) or $defs (draft 2020-12) + const defs = schema.definitions || schema['$defs'] || {}; + const paramMap = new Map(); // paramName -> type + + for (const def of Object.values(defs)) { + if (def.properties) { + for (const [paramName, propValue] of Object.entries(def.properties)) { + const t = propValue.type ?? null; + paramMap.set(paramName, Array.isArray(t) ? t.filter((x) => x !== 'null')[0] ?? t[0] ?? null : t); + } + } + } + + // Top-level properties that aren't $ref pointers to definition groups + if (schema.properties) { + for (const [paramName, propValue] of Object.entries(schema.properties)) { + if (!propValue.$ref) { + const t = propValue.type ?? null; + paramMap.set(paramName, Array.isArray(t) ? t.filter((x) => x !== 'null')[0] ?? t[0] ?? null : t); + } + } + } + + const entry = { name: pipeline.name, version: targetRelease.tag_name }; + for (const [paramName, type] of paramMap) { + const key = internalKey(paramName, type); + if (!params[key]) { + params[key] = { name: paramName, type, pipelines: [] }; + } + params[key].pipelines.push(entry); + } + + bar.tick(); + }; + + for (let i = 0; i < pipelinesToProcess.length; i += CONCURRENCY_LIMIT) { + const batch = pipelinesToProcess.slice(i, i + CONCURRENCY_LIMIT); + await Promise.all(batch.map(processPipeline)); + } + + console.log(' writing params.json'); + writeFileSync(paramsJsonPath, JSON.stringify(groupParams(params), null, 2)); +}; + +writeParamsJson(); diff --git a/package.json b/package.json index bb96fe2647..3b36de742f 100644 --- a/package.json +++ b/package.json @@ -4,9 +4,10 @@ "private": true, "type": "module", "scripts": { - "build-cache": "npm run build-pipeline-json && npm run build-component-json", + "build-cache": "npm run build-pipeline-json && npm run build-component-json && npm run build-params-json", "build-pipeline-json": "node bin/pipelines.json.js", "build-component-json": "node bin/components.json.js", + "build-params-json": "node bin/params.json.js", "update": "npx npm-check-updates --interactive --format group --workspaces", "test-all": "for dir in sites/*; do (cd $dir && npm run test); done" }, diff --git a/public/components.json b/public/components.json index e73914ac1a..ee19128132 100644 --- a/public/components.json +++ b/public/components.json @@ -1,350219 +1,327455 @@ { - "modules": [ - { - "name": "abacas", - "path": "modules/nf-core/abacas/meta.yml", - "type": "module", - "meta": { - "name": "abacas", - "description": "Contiguate draft genome assembly", - "keywords": [ - "genome", - "assembly", - "contiguate" - ], - "tools": [ - { - "abacas": { - "description": "ABACAS is intended to rapidly contiguate (align, order, orientate),\nvisualize and design primers to close gaps on shotgun assembled\ncontigs based on a reference sequence.\n", - "homepage": "http://abacas.sourceforge.net/documentation.html", - "documentation": "http://abacas.sourceforge.net/documentation.html", - "doi": "10.1093/bioinformatics/btp347", - "licence": [ - "GPL v2-or-later" - ], - "identifier": "biotools:abacas" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "scaffold": { - "type": "file", - "description": "Fasta file containing scaffold", - "pattern": "*.{fasta,fa}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing genome information\ne.g. [ id:'fasta' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA reference file", - "pattern": "*.{fasta,fa}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ], - "output": { - "results": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "${prefix}.*": { - "type": "file", - "description": "List containing abacas output files\n[ '*.abacas.bin', '*.abacas.fasta', '*.abacas.gaps',\n'*.abacas.gaps.tab', '*.abacas.nucmer.delta',\n'*.abacas.nucmer.filtered.delta', '*.abacas.nucmer.tiling',\n'*.abacas.tab', '*.abacas.unused.contigs.out',\n'*.abacas.MULTIFASTA.fa' ]\n", - "pattern": "${prefix}.*", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - ], - "versions_abacas": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "abacas": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "abacas.pl --version 2>&1 | grep 'ABACAS\\.' | sed 's/ABACAS\\.//' || true": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "abacas": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "abacas.pl --version 2>&1 | grep 'ABACAS\\.' | sed 's/ABACAS\\.//' || true": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@joseespinosa", - "@drpatelh" - ], - "maintainers": [ - "@joseespinosa", - "@drpatelh" - ] - }, - "pipelines": [ - { - "name": "viralrecon", - "version": "3.0.0" - } - ] - }, - { - "name": "abra2", - "path": "modules/nf-core/abra2/meta.yml", - "type": "module", - "meta": { - "name": "abra2", - "description": "Assembly Based ReAligner for next-generation sequencing data", - "keywords": [ - "alignment", - "realignment", - "indels", - "bam", - "dna", - "rna", - "splice-junctions", - "assembly" - ], - "tools": [ - { - "abra2": { - "description": "Assembly Based ReAligner for next-generation sequencing data", - "homepage": "https://github.com/mozack/abra2", - "documentation": "https://github.com/mozack/abra2", - "tool_dev_url": "https://github.com/mozack/abra2", - "doi": "10.1093/bioinformatics/btz033", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "bams": { - "type": "file", - "description": "Input BAM file - must be coordinate sorted", - "pattern": "*.bam", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - }, - { - "bais": { - "type": "file", - "description": "BAM index file", - "pattern": "*.bai", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3327" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. `[ id:'genome' ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome FASTA file", - "pattern": "*.{fa,fasta,fna}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference index information\ne.g. `[ id:'genome' ]`\n" - } - }, - { - "fai": { - "type": "file", - "description": "Reference genome FASTA index file", - "pattern": "*.{fai}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3326" - } - ] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing target regions information\ne.g. `[ id:'targets' ]`\n" - } - }, - { - "targets": { - "type": "file", - "description": "BED file containing target regions for realignment (optional)", - "pattern": "*.{bed}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3003" - } - ] - } - } - ], - [ - { - "meta5": { - "type": "map", - "description": "Groovy Map containing GTF annotation information\ne.g. `[ id:'annotation' ]`\n" - } - }, - { - "gtf": { - "type": "file", - "description": "GTF annotation file for RNA-seq data (optional)", - "pattern": "*.{gtf}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2306" - } - ] - } - } - ], - [ - { - "meta6": { - "type": "map", - "description": "Groovy Map containing known indels information\ne.g. `[ id:'known_indels' ]`\n" - } - }, - { - "known_indels": { - "type": "file", - "description": "VCF file containing known indels (optional)", - "pattern": "*.{vcf,vcf.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - } - ] - } - } - ] - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "Realigned BAM file", - "pattern": "*.abra.bam", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - } - ] - ], - "bai": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.bam.bai": { - "type": "file", - "description": "BAM index file (optional)", - "pattern": "*.abra.bam.bai", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3327" - } - ] - } - } - ] - ], - "versions_abra2": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "abra2": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "abra2 2>&1 | sed -n 's/.*Abra version: //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "abra2": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "abra2 2>&1 | sed -n 's/.*Abra version: //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@adamrtalbot" - ], - "maintainers": [ - "@adamrtalbot" - ] - } - }, - { - "name": "abricate_run", - "path": "modules/nf-core/abricate/run/meta.yml", - "type": "module", - "meta": { - "name": "abricate_run", - "description": "Screen assemblies for antimicrobial resistance against multiple databases", - "keywords": [ - "bacteria", - "assembly", - "antimicrobial resistance" - ], - "tools": [ - { - "abricate": { - "description": "Mass screening of contigs for antibiotic resistance genes", - "homepage": "https://github.com/tseemann/abricate", - "documentation": "https://github.com/tseemann/abricate", - "tool_dev_url": "https://github.com/tseemann/abricate", - "licence": [ - "GPL v2" - ], - "identifier": "biotools:ABRicate" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "assembly": { - "type": "file", - "description": "FASTA, GenBank or EMBL formatted file", - "pattern": "*.{fa,fasta,fna,fa.gz,fasta.gz,fna.gz,gbk,gbk.gz,embl,embl.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - }, - { - "edam": "http://edamontology.org/format_1936" - }, - { - "edam": "http://edamontology.org/format_2204" - } - ] - } - } - ], - { - "databasedir": { - "type": "directory", - "description": "Optional location of local copy of database files, possibly with custom databases set up with `abricate --setupdb`", - "pattern": "*/" - } - } - ], - "output": { - "report": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.txt": { - "type": "file", - "description": "Tab-delimited report of results", - "pattern": "*.{txt}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2330" - } - ] - } - } - ] - ], - "versions_abricate": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "abricate": { - "type": "string", - "description": "The tool name" - } - }, - { - "abricate --version | sed 's/^.* //' ": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "abricate": { - "type": "string", - "description": "The tool name" - } - }, - { - "abricate --version | sed 's/^.* //' ": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@rpetit3" - ], - "maintainers": [ - "@rpetit3" - ] - }, - "pipelines": [ - { - "name": "funcscan", - "version": "3.0.0" - } - ] - }, - { - "name": "abricate_summary", - "path": "modules/nf-core/abricate/summary/meta.yml", - "type": "module", - "meta": { - "name": "abricate_summary", - "description": "Screen assemblies for antimicrobial resistance against multiple databases", - "keywords": [ - "bacteria", - "assembly", - "antimicrobial reistance" - ], - "tools": [ - { - "abricate": { - "description": "Mass screening of contigs for antibiotic resistance genes", - "homepage": "https://github.com/tseemann/abricate", - "documentation": "https://github.com/tseemann/abricate", - "tool_dev_url": "https://github.com/tseemann/abricate", - "licence": [ - "GPL v2" - ], - "identifier": "biotools:ABRicate" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reports": { - "type": "file", - "description": "FASTA, GenBank or EMBL formatted file", - "pattern": "*.{fa,fasta,fna,fa.gz,fasta.gz,fna.gz,gbk,gbk.gz,embl,embl.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - }, - { - "edam": "http://edamontology.org/format_1936" - }, - { - "edam": "http://edamontology.org/format_2204" - } - ] - } - } - ] - ], - "output": { - "report": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.txt": { - "type": "file", - "description": "Tab-delimited report of aggregated results", - "pattern": "*.{txt}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2330" - } - ] - } - } - ] - ], - "versions_abricate_summary": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "abricate": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "abricate --version 2>&1 | sed 's/^.*abricate //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "abricate": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "abricate --version 2>&1 | sed 's/^.*abricate //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - 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} - } + "pipelines": [ + { + "name": "viralrecon", + "version": "3.0.0" + } ] - ] - }, - "authors": [ - "@rpetit3" - ], - "maintainers": [ - "@rpetit3", - "@sateeshperi" - ] - } - }, - { - "name": "abyss_abysspe", - "path": "modules/nf-core/abyss/abysspe/meta.yml", - "type": "module", - "meta": { - "name": "abyss_abysspe", - "description": "ABySS is a de novo sequence assembler intended for short paired-end reads and genomes of all sizes.", - "keywords": [ - "genome", - "assembly", - "genome assembler", - "short reads", - "de novo assembler" - ], - "tools": [ - { - "abyss": { - "description": "Assembly By Short Sequences - a de novo, parallel, paired-end short read sequence assembler.", - "homepage": "https://github.com/bcgsc/abyss/blob/v2.3.10/README.md", - "documentation": "https://github.com/bcgsc/abyss/blob/v2.3.10/README.md", - "tool_dev_url": "https://github.com/bcgsc/abyss", - "doi": "10.1101/gr.214346.116", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:abyss" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input paired-end FastQ files (R1 and R2).\nMust be paired-end reads; ABySS requires paired reads for assembly.\n", - "pattern": "*.{fastq.gz,fastq,fq.gz,fq}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - }, - { - "merged": { - "type": "file", - "description": "Optional merged/overlapping paired-end reads or supplementary single-end reads.\nUse empty list `[]` if not available.\n", - "pattern": "*.{fastq.gz,fastq,fq.gz,fq}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ], - { - "kmersize": { - "type": "integer", - "description": "K-mer size for assembly. Must be an odd number.\n" + }, + { + "name": "abra2", + "path": "modules/nf-core/abra2/meta.yml", + "type": "module", + "meta": { + "name": "abra2", + "description": "Assembly Based ReAligner for next-generation sequencing data", + "keywords": ["alignment", "realignment", "indels", "bam", "dna", "rna", "splice-junctions", "assembly"], + "tools": [ + { + "abra2": { + "description": "Assembly Based ReAligner for next-generation sequencing data", + "homepage": "https://github.com/mozack/abra2", + "documentation": "https://github.com/mozack/abra2", + "tool_dev_url": "https://github.com/mozack/abra2", + "doi": "10.1093/bioinformatics/btz033", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "bams": { + "type": "file", + "description": "Input BAM file - must be coordinate sorted", + "pattern": "*.bam", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + }, + { + "bais": { + "type": "file", + "description": "BAM index file", + "pattern": "*.bai", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3327" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. `[ id:'genome' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference genome FASTA file", + "pattern": "*.{fa,fasta,fna}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference index information\ne.g. `[ id:'genome' ]`\n" + } + }, + { + "fai": { + "type": "file", + "description": "Reference genome FASTA index file", + "pattern": "*.{fai}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3326" + } + ] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing target regions information\ne.g. `[ id:'targets' ]`\n" + } + }, + { + "targets": { + "type": "file", + "description": "BED file containing target regions for realignment (optional)", + "pattern": "*.{bed}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3003" + } + ] + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing GTF annotation information\ne.g. `[ id:'annotation' ]`\n" + } + }, + { + "gtf": { + "type": "file", + "description": "GTF annotation file for RNA-seq data (optional)", + "pattern": "*.{gtf}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2306" + } + ] + } + } + ], + [ + { + "meta6": { + "type": "map", + "description": "Groovy Map containing known indels information\ne.g. `[ id:'known_indels' ]`\n" + } + }, + { + "known_indels": { + "type": "file", + "description": "VCF file containing known indels (optional)", + "pattern": "*.{vcf,vcf.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + } + ] + } + } + ] + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Realigned BAM file", + "pattern": "*.abra.bam", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + } + ] + ], + "bai": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.bam.bai": { + "type": "file", + "description": "BAM index file (optional)", + "pattern": "*.abra.bam.bai", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3327" + } + ] + } + } + ] + ], + "versions_abra2": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "abra2": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "abra2 2>&1 | sed -n 's/.*Abra version: //p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "abra2": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "abra2 2>&1 | sed -n 's/.*Abra version: //p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@adamrtalbot"], + "maintainers": ["@adamrtalbot"] } - 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] - } - } - ] - ], - "stats": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*-stats": { - "type": "file", - "description": "Assembly statistics file", - "pattern": "*-stats", - "ontologies": [] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*-abyss.log": { - "type": "file", - "description": "ABySS assembly log file", - "pattern": "*-abyss.log", - "ontologies": [] - } - } - ] - ], - "versions_abyss": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "abyss": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "abyss-pe version | grep abyss | cut -d\" \" -f3": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - 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"identifier": "biotools:adapterremoval" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + ], + "output": { + "report": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "Tab-delimited report of results", + "pattern": "*.{txt}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + } + ] + ], + "versions_abricate": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "abricate": { + "type": "string", + "description": "The tool name" + } + }, + { + "abricate --version | sed 's/^.* //' ": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "abricate": { + "type": "string", + "description": "The tool name" + } + }, + { + "abricate --version | sed 's/^.* //' ": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@rpetit3"], + "maintainers": ["@rpetit3"] }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", - "pattern": "*.{fq,fastq,fq.gz,fastq.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ], - { - "adapterlist": { - "type": "file", - "description": "Optional text file containing list of adapters to look for for removal with one adapter per line. Otherwise will look for default adapters (see AdapterRemoval man page), or can be modified to remove user-specified adapters via ext.args.", - "ontologies": [ + "pipelines": [ { - "edam": "http://edamontology.org/format_2330" + "name": "funcscan", + "version": "3.0.0" } - ] + ] + }, + { + "name": "abricate_summary", + "path": "modules/nf-core/abricate/summary/meta.yml", + "type": "module", + "meta": { + "name": "abricate_summary", + "description": "Screen assemblies for antimicrobial resistance against multiple databases", + "keywords": ["bacteria", "assembly", "antimicrobial reistance"], + "tools": [ + { + "abricate": { + "description": "Mass screening of contigs for antibiotic resistance genes", + "homepage": "https://github.com/tseemann/abricate", + "documentation": "https://github.com/tseemann/abricate", + "tool_dev_url": "https://github.com/tseemann/abricate", + "licence": ["GPL v2"], + "identifier": "biotools:ABRicate" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reports": { + "type": "file", + "description": "FASTA, GenBank or EMBL formatted file", + "pattern": "*.{fa,fasta,fna,fa.gz,fasta.gz,fna.gz,gbk,gbk.gz,embl,embl.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + }, + { + "edam": "http://edamontology.org/format_1936" + }, + { + "edam": "http://edamontology.org/format_2204" + } + ] + } + } + ] + ], + "output": { + "report": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "Tab-delimited report of aggregated results", + "pattern": "*.{txt}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + } + ] + ], + "versions_abricate_summary": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "abricate": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "abricate --version 2>&1 | sed 's/^.*abricate //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "abricate": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "abricate --version 2>&1 | sed 's/^.*abricate //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@rpetit3"], + "maintainers": ["@rpetit3"] } - } - ], - "output": { - "singles_truncated": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "${prefix}.truncated.fastq.gz": { - "type": "file", - "description": "Adapter trimmed FastQ files of either single-end reads, or singleton\n'orphaned' reads from merging of paired-end data (i.e., one of the pair\nwas lost due to filtering thresholds).\n", - "pattern": "*.truncated.fastq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - }, - { - "edam": "http://edamontology.org/format_3989" + }, + { + "name": "abritamr_run", + "path": "modules/nf-core/abritamr/run/meta.yml", + "type": "module", + "meta": { + "name": "abritamr_run", + "description": "A NATA accredited tool for reporting the presence of antimicrobial resistance genes in bacterial genomes", + "keywords": ["bacteria", "fasta", "antibiotic resistance"], + "tools": [ + { + "abritamr": { + "description": "A pipeline for running AMRfinderPlus and collating results into functional classes", + "homepage": "https://github.com/MDU-PHL/abritamr", + "documentation": "https://github.com/MDU-PHL/abritamr", + "tool_dev_url": "https://github.com/MDU-PHL/abritamr", + "doi": "10.1038/s41467-022-35713-4", + "licence": ["GPL v3"], + "identifier": "biotools:abritamr" + } } - ] - } - } - ] - ], - "discarded": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "${prefix}.discarded.fastq.gz": { - "type": "file", - "description": "Adapter trimmed FastQ files of reads that did not pass filtering\nthresholds.\n", - "pattern": "*.discarded.fastq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - }, - { - "edam": "http://edamontology.org/format_3989" + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Assembled contigs in FASTA format", + "pattern": "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ] + ], + "output": { + "matches": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.summary_matches.txt": { + "type": "file", + "description": "Tab-delimited file, with a row per sequence, and columns representing functional drug classes", + "pattern": "*.summary_matches.txt", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + } + ] + ], + "partials": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.summary_partials.txt": { + "type": "file", + "description": "Tab-delimited file, with a row per sequence, and columns representing partial hits to functional drug classes", + "pattern": "*.summary_partials.txt", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + } + ] + ], + "virulence": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.summary_virulence.txt": { + "type": "string", + "description": "Tab-delimited file, with a row per sequence, and columns representing AMRFinderPlus virulence gene classification", + "pattern": "*.summary_virulence.txt", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + } + ] + ], + "out": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.amrfinder.out": { + "type": "string", + "description": "raw output from AMRFinder plus (per sequence)", + "pattern": "*.amrfinder.txt", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + } + ] + ], + "txt": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.abritamr.txt": { + "type": "string", + "description": "Tab-delimited file, combining non-empty summary files", + "pattern": "*.abritamr.txt", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + } + ] + ], + "versions_abritamr": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "abritamr": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "abritamr --version 2>&1 | sed 's/^.*abritamr \\([0-9.]*\\).*/\\1/'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "abritamr": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "abritamr --version 2>&1 | sed 's/^.*abritamr \\([0-9.]*\\).*/\\1/'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@rpetit3"], + "maintainers": ["@rpetit3", "@sateeshperi"] + } + }, + { + "name": "abyss_abysspe", + "path": "modules/nf-core/abyss/abysspe/meta.yml", + "type": "module", + "meta": { + "name": "abyss_abysspe", + "description": "ABySS is a de novo sequence assembler intended for short paired-end reads and genomes of all sizes.", + "keywords": ["genome", "assembly", "genome assembler", "short reads", "de novo assembler"], + "tools": [ + { + "abyss": { + "description": "Assembly By Short Sequences - a de novo, parallel, paired-end short read sequence assembler.", + "homepage": "https://github.com/bcgsc/abyss/blob/v2.3.10/README.md", + "documentation": "https://github.com/bcgsc/abyss/blob/v2.3.10/README.md", + "tool_dev_url": "https://github.com/bcgsc/abyss", + "doi": "10.1101/gr.214346.116", + "licence": ["GPL v3"], + "identifier": "biotools:abyss" + } } - ] - } - } - ] - ], - "paired_truncated": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "${prefix}.pair{1,2}.truncated.fastq.gz": { - "type": "file", - "description": "Adapter trimmed R{1,2} FastQ files of paired-end reads that did not merge\nwith their respective R{1,2} pair due to long templates. The respective pair\nis stored in 'pair{1,2}_truncated'.\n", - "pattern": "*.pair{1,2}.truncated.fastq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "collapsed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "${prefix}.collapsed.fastq.gz": { - "type": "file", - "description": "Collapsed FastQ of paired-end reads that successfully merged with their\nrespective R1 pair but were not trimmed.\n", - "pattern": "*.collapsed.fastq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - }, + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input paired-end FastQ files (R1 and R2).\nMust be paired-end reads; ABySS requires paired reads for assembly.\n", + "pattern": "*.{fastq.gz,fastq,fq.gz,fq}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + }, + { + "merged": { + "type": "file", + "description": "Optional merged/overlapping paired-end reads or supplementary single-end reads.\nUse empty list `[]` if not available.\n", + "pattern": "*.{fastq.gz,fastq,fq.gz,fq}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ], { - "edam": "http://edamontology.org/format_3989" + "kmersize": { + "type": "integer", + "description": "K-mer size for assembly. Must be an odd number.\n" + } } - ] - } - } - ] - ], - "collapsed_truncated": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "${prefix}.collapsed.truncated.fastq.gz": { - "type": "file", - "description": "Collapsed FastQ of paired-end reads that successfully merged with their\nrespective R1 pair and were trimmed of adapter due to sufficient overlap.\n", - "pattern": "*.collapsed.truncated.fastq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - }, - { - "edam": "http://edamontology.org/format_3989" + ], + "output": { + "contigs": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*-contigs.fa.gz": { + "type": "file", + "description": "Assembled contigs in FASTA format", + "pattern": "*-contigs.fa.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/data_0925" + }, + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ] + ], + "scaffolds": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*-scaffolds.fa.gz": { + "type": "file", + "description": "Assembled scaffolds in FASTA format", + "pattern": "*-scaffolds.fa.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/data_0925" + }, + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ] + ], + "stats": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*-stats": { + "type": "file", + "description": "Assembly statistics file", + "pattern": "*-stats", + "ontologies": [] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*-abyss.log": { + "type": "file", + "description": "ABySS assembly log file", + "pattern": "*-abyss.log", + "ontologies": [] + } + } + ] + ], + "versions_abyss": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "abyss": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "abyss-pe version | grep abyss | cut -d\" \" -f3": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "abyss": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "abyss-pe version | grep abyss | cut -d\" \" -f3": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@LiaOb21"], + "maintainers": ["@LiaOb21"] + } + }, + { + "name": "adapterremoval", + "path": "modules/nf-core/adapterremoval/meta.yml", + "type": "module", + "meta": { + "name": "adapterremoval", + "description": "Trim sequencing adapters and collapse overlapping reads", + "keywords": ["trimming", "adapters", "merging", "fastq"], + "tools": [ + { + "adapterremoval": { + "description": "The AdapterRemoval v2 tool for merging and clipping reads.", + "homepage": "https://github.com/MikkelSchubert/adapterremoval", + "documentation": "https://adapterremoval.readthedocs.io", + "licence": ["GPL v3"], + "identifier": "biotools:adapterremoval" + } } - ] - } - } - ] - ], - "paired_interleaved": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "${prefix}.paired.fastq.gz": { - "type": "file", - "description": "Write paired-end reads to a single file, interleaving mate 1 and mate 2 reads\n", - "pattern": "*.paired.fastq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - }, - { - "edam": "http://edamontology.org/format_3989" + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", + "pattern": "*.{fq,fastq,fq.gz,fastq.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ], + { + "adapterlist": { + "type": "file", + "description": "Optional text file containing list of adapters to look for for removal with one adapter per line. Otherwise will look for default adapters (see AdapterRemoval man page), or can be modified to remove user-specified adapters via ext.args.", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } } - ] + ], + "output": { + "singles_truncated": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "${prefix}.truncated.fastq.gz": { + "type": "file", + "description": "Adapter trimmed FastQ files of either single-end reads, or singleton\n'orphaned' reads from merging of paired-end data (i.e., one of the pair\nwas lost due to filtering thresholds).\n", + "pattern": "*.truncated.fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "discarded": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "${prefix}.discarded.fastq.gz": { + "type": "file", + "description": "Adapter trimmed FastQ files of reads that did not pass filtering\nthresholds.\n", + "pattern": "*.discarded.fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "paired_truncated": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "${prefix}.pair{1,2}.truncated.fastq.gz": { + "type": "file", + "description": "Adapter trimmed R{1,2} FastQ files of paired-end reads that did not merge\nwith their respective R{1,2} pair due to long templates. The respective pair\nis stored in 'pair{1,2}_truncated'.\n", + "pattern": "*.pair{1,2}.truncated.fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ] + ], + "collapsed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "${prefix}.collapsed.fastq.gz": { + "type": "file", + "description": "Collapsed FastQ of paired-end reads that successfully merged with their\nrespective R1 pair but were not trimmed.\n", + "pattern": "*.collapsed.fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "collapsed_truncated": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "${prefix}.collapsed.truncated.fastq.gz": { + "type": "file", + "description": "Collapsed FastQ of paired-end reads that successfully merged with their\nrespective R1 pair and were trimmed of adapter due to sufficient overlap.\n", + "pattern": "*.collapsed.truncated.fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "paired_interleaved": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "${prefix}.paired.fastq.gz": { + "type": "file", + "description": "Write paired-end reads to a single file, interleaving mate 1 and mate 2 reads\n", + "pattern": "*.paired.fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "settings": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.settings": { + "type": "file", + "description": "AdapterRemoval log file", + "pattern": "*.settings", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + } + ] + ], + "versions_adapterremoval": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "AdapterRemoval": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "AdapterRemoval --version 2>&1 | sed -e \"s/AdapterRemoval ver. //g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "AdapterRemoval": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "AdapterRemoval --version 2>&1 | sed -e \"s/AdapterRemoval ver. //g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@maxibor", "@jfy133"], + "maintainers": ["@maxibor", "@jfy133"] + }, + "pipelines": [ + { + "name": "mag", + "version": "5.4.2" + }, + { + "name": "taxprofiler", + "version": "2.0.0" } - } ] - ], - "settings": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*.settings": { - "type": "file", - "description": "AdapterRemoval log file", - "pattern": "*.settings", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2330" - } - ] - } - } - ] - ], - "versions_adapterremoval": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "AdapterRemoval": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "AdapterRemoval --version 2>&1 | sed -e \"s/AdapterRemoval ver. //g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "AdapterRemoval": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "AdapterRemoval --version 2>&1 | sed -e \"s/AdapterRemoval ver. //g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] }, - "authors": [ - "@maxibor", - "@jfy133" - ], - "maintainers": [ - "@maxibor", - "@jfy133" - ] - }, - "pipelines": [ { - "name": "mag", - "version": "5.4.2" + "name": "adapterremovalfixprefix", + "path": "modules/nf-core/adapterremovalfixprefix/meta.yml", + "type": "module", + "meta": { + "name": "adapterremovalfixprefix", + "description": "Fixes prefixes from AdapterRemoval2 output to make sure no clashing read names are in the output. For use with DeDup.", + "keywords": ["adapterremoval", "fastq", "dedup"], + "tools": [ + { + "adapterremovalfixprefix": { + "description": "Fixes adapter removal prefixes to make sure no clashing read names are in the output.", + "homepage": "https://github.com/apeltzer/AdapterRemovalFixPrefix", + "tool_dev_url": "https://github.com/apeltzer/AdapterRemovalFixPrefix", + "doi": "10.1186/s13059-016-0918-z", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fastq": { + "type": "file", + "description": "FASTQ file from AdapterRemoval2", + "pattern": "*.{fq.gz,fastq.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ] + ], + "output": { + "fixed_fastq": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fq.gz": { + "type": "file", + "description": "FASTQ file with fixed read prefixes for DeDup", + "pattern": "*.{fq.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ] + ], + "versions_adapterremovalfixprefix": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "adapterremovalfixprefix": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "echo 0.0.5": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "adapterremovalfixprefix": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "echo 0.0.5": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@jfy133"], + "maintainers": ["@jfy133"] + } }, { - "name": "taxprofiler", - "version": "2.0.0" - } - ] - }, - { - "name": "adapterremovalfixprefix", - "path": "modules/nf-core/adapterremovalfixprefix/meta.yml", - "type": "module", - "meta": { - "name": "adapterremovalfixprefix", - "description": "Fixes prefixes from AdapterRemoval2 output to make sure no clashing read names are in the output. For use with DeDup.", - "keywords": [ - "adapterremoval", - "fastq", - "dedup" - ], - "tools": [ - { - "adapterremovalfixprefix": { - "description": "Fixes adapter removal prefixes to make sure no clashing read names are in the output.", - "homepage": "https://github.com/apeltzer/AdapterRemovalFixPrefix", - "tool_dev_url": "https://github.com/apeltzer/AdapterRemovalFixPrefix", - "doi": "10.1186/s13059-016-0918-z", - "licence": [ - "GPL v3" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fastq": { - "type": "file", - "description": "FASTQ file from AdapterRemoval2", - "pattern": "*.{fq.gz,fastq.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "output": { - "fixed_fastq": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.fq.gz": { - "type": "file", - "description": "FASTQ file with fixed read prefixes for DeDup", - "pattern": "*.{fq.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "versions_adapterremovalfixprefix": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "adapterremovalfixprefix": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "echo 0.0.5": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "adapterremovalfixprefix": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "echo 0.0.5": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@jfy133" - ], - "maintainers": [ - "@jfy133" - ] - } - }, - { - "name": "admixture", - "path": "modules/nf-core/admixture/meta.yml", - "type": "module", - "meta": { - "name": "admixture", - "description": "ADMIXTURE is a program for estimating ancestry in a model-based manner from large autosomal SNP genotype datasets, where the individuals are unrelated (for example, the individuals in a case-control association study).", - "keywords": [ - "ancestry", - "population genetics", - "admixture", - "reference panels", - "gwas" - ], - "tools": [ - { - "admixture": { - "description": "ADMIXTURE is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets.", - "homepage": "https://dalexander.github.io/admixture/", - "documentation": "https://dalexander.github.io/admixture/admixture-manual.pdf", - "doi": "10.1101/gr.094052.109", - "licence": [ - "Free for Academic Use" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bed_ped_geno": { - "type": "file", - "description": "One of PLINK \".bed\" file or PLINK \".ped\" or EIGENSTRAT \".geno\" file. If you provide \".bed\" then you need to provide \".bim\" and \"fam\" files. If you provide \".ped\" or \".geno\" then you need to provide a \".map\" file and an empty channel.", - "pattern": "*.{bed}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3586" - } - ] - } - }, - { - "bim_map": { - "type": "file", - "description": "Mandatory accompanying file. One of PLINK \".bim\" file or PLINK \".map\" file. Provide \".bim\" if \".bed\" is the input. Provide \".map\" if \".ped\" or \".geno\" is the input.", - "pattern": "*.{bim}", - "ontologies": [] - } - }, - { - "fam": { - "type": "file", - "description": "PLINK \".fam\" file. Mandatory if you provide \".bed\" as input. Replace with an empty channel if input is \".ped\" or \".geno\".", - "pattern": "*.{fam}", - "ontologies": [] - } - } - ], - { - "K": { - "type": "integer", - "description": "Belief of the number of ancestral populations.", - "pattern": "{*}" - } - } - ], - "output": { - "ancestry_fractions": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.Q": { - "type": "file", - "description": "Space-delimited files containing ancestry fractions. The output filenames have the number of populations (K) that was assumed for the analysis.", - "pattern": "*.{Q}", - "ontologies": [] - } - } - ] - ], - "allele_frequencies": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.P": { - "type": "file", - "description": "Space-delimited files containing the allele frequencies of the inferred ancestral populations. The output filenames have the number of populations (K) that was assumed for the analysis.", - "pattern": "*.{P}", - "ontologies": [] - } - } - ] - ], - "versions_admixture": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "admixture": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "admixture --version | tail -n 1": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "admixture": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "admixture --version | tail -n 1": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@atrigila" - ], - "maintainers": [ - "@atrigila", - "@gallvp" - ] - } - }, - { - "name": "affy_justrma", - "path": "modules/nf-core/affy/justrma/meta.yml", - "type": "module", - "meta": { - "name": "affy_justrma", - "description": "Read CEL files into an ExpressionSet and generate a matrix", - "keywords": [ - "affy", - "microarray", - "expression", - "matrix" - ], - "tools": [ - { - "affy": { - "description": "Methods for Affymetrix Oligonucleotide Arrays", - "homepage": "https://www.bioconductor.org/packages/release/bioc/html/affy.html", - "documentation": "https://www.bioconductor.org/packages/release/bioc/html/affy.html", - "tool_dev_url": "https://github.com/Bioconductor/affy", - "doi": "10.1093/bioinformatics/btg405", - "licence": [ - "LGPL >=2.0" - ], - "identifier": "biotools:affy" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "samplesheet": { - "type": "file", - "description": "CSV or TSV format sample sheet with sample metadata and CEL file names\n", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - }, - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - }, - { - "celfiles_dir": { - "type": "list", - "description": "Path to a directory containing CEL files", - "pattern": "*.{CEL,CEL.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1638" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "description": { - "type": "file", - "description": "Optional description file in MIAME format\n", - "ontologies": [] - } - } - ] - ], - "output": { - "rds": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.rds": { - "type": "file", - "description": "Serialised ExpressionSet object", - "pattern": "*.rds", - "ontologies": [] - } - } - ] - ], - "expression": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*matrix.tsv": { - "type": "file", - "description": "TSV-format intensity matrix", - "pattern": "matrix.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "annotation": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.annotation.tsv": { - "type": "file", - "description": "TSV-format annotation table", - "pattern": "*.annotation.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_affy": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "topics": { - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@pinin4fjords" - ], - "maintainers": [ - "@pinin4fjords" - ] - }, - "pipelines": [ - { - "name": "differentialabundance", - "version": "1.5.0" - } - ] - }, - { - "name": "agat_convertbed2gff", - "path": "modules/nf-core/agat/convertbed2gff/meta.yml", - "type": "module", - "meta": { - "name": "agat_convertbed2gff", - "description": "Takes a bed12 file and converts to a GFF3 file\n", - "keywords": [ - "genome", - "bed", - "gff", - "conversion" - ], - "tools": [ - { - "agat": { - "description": "AGAT is a toolkit for manipulation and getting information from GFF/GTF files", - "homepage": "https://github.com/NBISweden/AGAT", - "documentation": "https://agat.readthedocs.io/", - "tool_dev_url": "https://github.com/NBISweden/AGAT", - "doi": "10.5281/zenodo.3552717", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:AGAT" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "bed": { - "type": "file", - "description": "Input bed12 file", - "pattern": "*.bed", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3586" - } - ] - } - } - ] - ], - "output": { - "gff": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*.gff": { - "type": "file", - "description": "Output GFF3 file", - "pattern": "*.{gff}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1975" - } - ] - } - } - ] - ], - "versions_agat": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "agat": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "agat --version | sed 's/v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "agat": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "agat --version | sed 's/v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@GallVp" - ], - "maintainers": [ - "@GallVp" - ] - }, - "pipelines": [ - { - "name": "circrna", - "version": "dev" - } - ] - }, - { - "name": "agat_convertgff2bed", - "path": "modules/nf-core/agat/convertgff2bed/meta.yml", - "type": "module", - "meta": { - "name": "agat_convertgff2bed", - "description": "Takes a GFF3 file and converts to a bed12 file", - "keywords": [ - "genome", - "bed", - "gff", - "conversion" - ], - "tools": [ - { - "agat": { - "description": "Another Gff Analysis Toolkit (AGAT). Suite of tools to handle gene annotations in any GTF/GFF format.", - "homepage": "https://agat.readthedocs.io/en/latest/", - "documentation": "https://agat.readthedocs.io/en/latest/", - "tool_dev_url": "https://github.com/NBISweden/AGAT", - "doi": "10.5281/zenodo.3552717", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:AGAT" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "gff": { - "type": "file", - "description": "Input GFF3 file", - "pattern": "*.{gff}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1975" - } - ] - } - } - ] - ], - "output": { - "bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.bed": { - "type": "file", - "description": "Output bed12 file", - "pattern": "*.bed", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3586" - } - ] - } - } - ] - ], - "versions_agat": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "agat": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "agat --version | sed 's/v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "agat": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "agat --version | sed 's/v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@atrigila" - ], - "maintainers": [ - "@atrigila" - ] - }, - "pipelines": [ - { - "name": "rnafusion", - "version": "4.1.2" - } - ] - }, - { - "name": "agat_convertspgff2gtf", - "path": "modules/nf-core/agat/convertspgff2gtf/meta.yml", - "type": "module", - "meta": { - "name": "agat_convertspgff2gtf", - "description": "Converts a GFF/GTF file into a proper GTF file\n", - "keywords": [ - "genome", - "gff", - "gtf", - "conversion" - ], - "tools": [ - { - "agat": { - "description": "AGAT is a toolkit for manipulation and getting information from GFF/GTF files", - "homepage": "https://github.com/NBISweden/AGAT", - "documentation": "https://agat.readthedocs.io/", - "tool_dev_url": "https://github.com/NBISweden/AGAT", - "doi": "10.5281/zenodo.3552717", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:AGAT" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "gff": { - "type": "file", - "description": "Annotation file in GFF3/GTF format", - "pattern": "*.{gff, gtf}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1975" - }, - { - "edam": "http://edamontology.org/format_2306" - } - ] - } - } - ] - ], - "output": { - "output_gtf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*.agat.gtf": { - "type": "file", - "description": "Annotation file in GTF format", - "pattern": "*.{gtf}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2306" - } - ] - } - } - ] - ], - "versions_agat": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "agat": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "agat --version | sed 's/v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "agat": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "agat --version | sed 's/v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@toniher" - ], - "maintainers": [ - "@toniher", - "@gallvp" - ] - } - }, - { - "name": "agat_convertspgff2tsv", - "path": "modules/nf-core/agat/convertspgff2tsv/meta.yml", - "type": "module", - "meta": { - "name": "agat_convertspgff2tsv", - "description": "Converts a GFF/GTF file into a TSV file\n", - "keywords": [ - "genome", - "gff", - "gtf", - "conversion", - "tsv" - ], - "tools": [ - { - "agat": { - "description": "AGAT is a toolkit for manipulation and getting information from GFF/GTF files", - "homepage": "https://github.com/NBISweden/AGAT", - "documentation": "https://agat.readthedocs.io/", - "tool_dev_url": "https://github.com/NBISweden/AGAT", - "doi": "10.5281/zenodo.3552717", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:AGAT" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "gff": { - "type": "file", - "description": "Annotation file in GFF3/GTF format", - "pattern": "*.{gff, gtf}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1975" - }, - { - "edam": "http://edamontology.org/format_2306" - } - ] - } - } - ] - ], - "output": { - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*.tsv": { - "type": "file", - "description": "Annotation file in TSV format", - "pattern": "*.{gtf}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2306" - } - ] - } - } - ] - ], - "versions_agat": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "agat": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "agat --version | sed 's/v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "agat": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "agat --version | sed 's/v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@rannick" - ], - "maintainers": [ - "@gallvp" - ] - }, - "pipelines": [ - { - "name": "rnafusion", - "version": "4.1.2" - } - ] - }, - { - "name": "agat_convertspgxf2gxf", - "path": "modules/nf-core/agat/convertspgxf2gxf/meta.yml", - "type": "module", - "meta": { - "name": "agat_convertspgxf2gxf", - "description": "Fixes and standardizes GFF/GTF files and outputs a cleaned GFF/GTF file\n", - "keywords": [ - "genome", - "gff", - "gtf", - "conversion" - ], - "tools": [ - { - "agat": { - "description": "AGAT is a toolkit for manipulation and getting information from GFF/GTF files", - "homepage": "https://github.com/NBISweden/AGAT", - "documentation": "https://agat.readthedocs.io/", - "tool_dev_url": "https://github.com/NBISweden/AGAT", - "doi": "10.5281/zenodo.3552717", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:AGAT" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "gxf": { - "type": "file", - "description": "Annotation file in GFF3/GTF format", - "pattern": "*.{gff, gtf}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1975" - }, - { - "edam": "http://edamontology.org/format_2306" - } - ] - } - } - ] - ], - "output": { - "output_gff": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*.agat.gff": { - "type": "file", - "description": "Cleaned annotation file in GFF3 format", - "pattern": "*.{gff}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1975" - } - ] - } - } - ] - ], - "versions_agat": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "agat": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "agat --version | sed 's/v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "agat": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "agat --version | sed 's/v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@toniher" - ], - "maintainers": [ - "@toniher" - ] - }, - "pipelines": [ - { - "name": "genomeqc", - "version": "dev" - } - ] - }, - { - "name": "agat_spaddintrons", - "path": "modules/nf-core/agat/spaddintrons/meta.yml", - "type": "module", - "meta": { - "name": "agat_spaddintrons", - "description": "Add intron features to gtf/gff file without intron features.", - "keywords": [ - "gtf", - "gff", - "introns" - ], - "tools": [ - { - "agat": { - "description": "Another Gff Analysis Toolkit (AGAT). Suite of tools to handle gene annotations in any GTF/GFF format.", - "homepage": "https://agat.readthedocs.io/en/latest/", - "documentation": "https://agat.readthedocs.io/en/latest/", - "tool_dev_url": "https://github.com/NBISweden/AGAT", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:AGAT" + "name": "admixture", + "path": "modules/nf-core/admixture/meta.yml", + "type": "module", + "meta": { + "name": "admixture", + "description": "ADMIXTURE is a program for estimating ancestry in a model-based manner from large autosomal SNP genotype datasets, where the individuals are unrelated (for example, the individuals in a case-control association study).", + "keywords": ["ancestry", "population genetics", "admixture", "reference panels", "gwas"], + "tools": [ + { + "admixture": { + "description": "ADMIXTURE is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets.", + "homepage": "https://dalexander.github.io/admixture/", + "documentation": "https://dalexander.github.io/admixture/admixture-manual.pdf", + "doi": "10.1101/gr.094052.109", + "licence": ["Free for Academic Use"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bed_ped_geno": { + "type": "file", + "description": "One of PLINK \".bed\" file or PLINK \".ped\" or EIGENSTRAT \".geno\" file. If you provide \".bed\" then you need to provide \".bim\" and \"fam\" files. If you provide \".ped\" or \".geno\" then you need to provide a \".map\" file and an empty channel.", + "pattern": "*.{bed}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3586" + } + ] + } + }, + { + "bim_map": { + "type": "file", + "description": "Mandatory accompanying file. One of PLINK \".bim\" file or PLINK \".map\" file. Provide \".bim\" if \".bed\" is the input. Provide \".map\" if \".ped\" or \".geno\" is the input.", + "pattern": "*.{bim}", + "ontologies": [] + } + }, + { + "fam": { + "type": "file", + "description": "PLINK \".fam\" file. Mandatory if you provide \".bed\" as input. Replace with an empty channel if input is \".ped\" or \".geno\".", + "pattern": "*.{fam}", + "ontologies": [] + } + } + ], + { + "K": { + "type": "integer", + "description": "Belief of the number of ancestral populations.", + "pattern": "{*}" + } + } + ], + "output": { + "ancestry_fractions": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.Q": { + "type": "file", + "description": "Space-delimited files containing ancestry fractions. The output filenames have the number of populations (K) that was assumed for the analysis.", + "pattern": "*.{Q}", + "ontologies": [] + } + } + ] + ], + "allele_frequencies": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.P": { + "type": "file", + "description": "Space-delimited files containing the allele frequencies of the inferred ancestral populations. The output filenames have the number of populations (K) that was assumed for the analysis.", + "pattern": "*.{P}", + "ontologies": [] + } + } + ] + ], + "versions_admixture": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "admixture": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "admixture --version | tail -n 1": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "admixture": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "admixture --version | tail -n 1": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@atrigila"], + "maintainers": ["@atrigila", "@gallvp"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + }, + { + "name": "affy_justrma", + "path": "modules/nf-core/affy/justrma/meta.yml", + "type": "module", + "meta": { + "name": "affy_justrma", + "description": "Read CEL files into an ExpressionSet and generate a matrix", + "keywords": ["affy", "microarray", "expression", "matrix"], + "tools": [ + { + "affy": { + "description": "Methods for Affymetrix Oligonucleotide Arrays", + "homepage": "https://www.bioconductor.org/packages/release/bioc/html/affy.html", + "documentation": "https://www.bioconductor.org/packages/release/bioc/html/affy.html", + "tool_dev_url": "https://github.com/Bioconductor/affy", + "doi": "10.1093/bioinformatics/btg405", + "licence": ["LGPL >=2.0"], + "identifier": "biotools:affy" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "samplesheet": { + "type": "file", + "description": "CSV or TSV format sample sheet with sample metadata and CEL file names\n", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + }, + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, + { + "celfiles_dir": { + "type": "list", + "description": "Path to a directory containing CEL files", + "pattern": "*.{CEL,CEL.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1638" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "description": { + "type": "file", + "description": "Optional description file in MIAME format\n", + "ontologies": [] + } + } + ] + ], + "output": { + "rds": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.rds": { + "type": "file", + "description": "Serialised ExpressionSet object", + "pattern": "*.rds", + "ontologies": [] + } + } + ] + ], + "expression": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*matrix.tsv": { + "type": "file", + "description": "TSV-format intensity matrix", + "pattern": "matrix.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "annotation": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.annotation.tsv": { + "type": "file", + "description": "TSV-format annotation table", + "pattern": "*.annotation.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_affy": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "topics": { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@pinin4fjords"], + "maintainers": ["@pinin4fjords"] }, - { - "gff": { - "type": "file", - "description": "Input gtf/gff file", - "pattern": "*.{gff,gff3,gtf}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2305" - }, - { - "edam": "http://edamontology.org/format_1975" - }, - { - "edam": "http://edamontology.org/format_2306" - } - ] - } - } - ], - { - "config": { - "type": "file", - "description": "Optional input agat config file", - "pattern": "*.{yaml,yml}", - "ontologies": [ + "pipelines": [ { - "edam": "http://edamontology.org/format_3750" + "name": "differentialabundance", + "version": "1.5.0" } - ] - } - } - ], - "output": { - "gff": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "${output}": { - "type": "file", - "description": "Output gff3 file with introns", - "pattern": "*.gff", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1975" - } - ] - } - } - ] - ], - "versions_agat": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "agat": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "agat --version | sed 's/v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "agat": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "agat --version | sed 's/v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } ] - ] - }, - "authors": [ - "@anoronh4" - ], - "maintainers": [ - "@anoronh4", - "@gallvp" - ] - }, - "pipelines": [ - { - "name": "circrna", - "version": "dev" - } - ] - }, - { - "name": "agat_spextractsequences", - "path": "modules/nf-core/agat/spextractsequences/meta.yml", - "type": "module", - "meta": { - "name": "agat_spextractsequences", - "description": "This script extracts sequences in fasta format according to features described\nin a gff file.\n", - "keywords": [ - "genomics", - "gff", - "extract", - "fasta", - "sequence", - "feature" - ], - "tools": [ - { - "agat": { - "description": "Another Gff Analysis Toolkit (AGAT). Suite of tools to handle gene annotations in any GTF/GFF format.", - "homepage": "https://agat.readthedocs.io/en/latest/", - "documentation": "https://agat.readthedocs.io/en/latest/tools/agat_sp_extract_sequences.html", - "tool_dev_url": "https://github.com/NBISweden/AGAT", - "doi": "10.5281/zenodo.3552717", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:AGAT" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } + }, + { + "name": "agat_convertbed2gff", + "path": "modules/nf-core/agat/convertbed2gff/meta.yml", + "type": "module", + "meta": { + "name": "agat_convertbed2gff", + "description": "Takes a bed12 file and converts to a GFF3 file\n", + "keywords": ["genome", "bed", "gff", "conversion"], + "tools": [ + { + "agat": { + "description": "AGAT is a toolkit for manipulation and getting information from GFF/GTF files", + "homepage": "https://github.com/NBISweden/AGAT", + "documentation": "https://agat.readthedocs.io/", + "tool_dev_url": "https://github.com/NBISweden/AGAT", + "doi": "10.5281/zenodo.3552717", + "licence": ["GPL v3"], + "identifier": "biotools:AGAT" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "bed": { + "type": "file", + "description": "Input bed12 file", + "pattern": "*.bed", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3586" + } + ] + } + } + ] + ], + "output": { + "gff": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.gff": { + "type": "file", + "description": "Output GFF3 file", + "pattern": "*.{gff}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1975" + } + ] + } + } + ] + ], + "versions_agat": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "agat": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "agat --version | sed 's/v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "agat": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "agat --version | sed 's/v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@GallVp"], + "maintainers": ["@GallVp"] }, - { - "gxf": { - "type": "file", - "description": "Input GFF3/GTF file", - "pattern": "*.{gff,gff3,gtf}", - "ontologies": [] - } - } - ], - { - "fasta": { - "type": "file", - "description": "Input FASTA file", - "pattern": "*.{fa,fsa,faa,fasta}", - "ontologies": [] - } - }, - { - "config": { - "type": "file", - "description": "Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: \"agat config --expose\". The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently).\n", - "pattern": "*.yaml", - "ontologies": [ + "pipelines": [ { - "edam": "http://edamontology.org/format_3750" + "name": "circrna", + "version": "dev" } - ] - } - } - ], - "output": { - "fasta": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]\n" - } - }, - { - "*.fasta": { - "type": "file", - "description": "Output FASTA file.", - "pattern": "*.fasta", - "ontologies": [] - } - } - ] - ], - "versions_agat": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "agat": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "agat --version | sed 's/v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "agat": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "agat --version | sed 's/v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@GallVp" - ], - "maintainers": [ - "@GallVp" - ] - } - }, - { - "name": "agat_spfilterbyorfsize", - "path": "modules/nf-core/agat/spfilterbyorfsize/meta.yml", - "type": "module", - "meta": { - "name": "agat_spfilterbyorfsize", - "description": "The script reads a gff annotation file, and create two output files, one contains the gene models with ORF passing the test, the other contains the rest. By default the test is \"> 100\" that means all gene models that have ORF longer than 100 Amino acids, will pass the test.", - "keywords": [ - "genomics", - "GFF/GTF", - "filter", - "annotation" - ], - "tools": [ - { - "agat": { - "description": "Another Gff Analysis Toolkit (AGAT). Suite of tools to handle gene annotations in any GTF/GFF format.", - "homepage": "https://agat.readthedocs.io/en/latest/", - "documentation": "https://agat.readthedocs.io/en/latest/", - "tool_dev_url": "https://github.com/NBISweden/AGAT", - "doi": "10.5281/zenodo.3552717", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:AGAT" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } + }, + { + "name": "agat_convertgff2bed", + "path": "modules/nf-core/agat/convertgff2bed/meta.yml", + "type": "module", + "meta": { + "name": "agat_convertgff2bed", + "description": "Takes a GFF3 file and converts to a bed12 file", + "keywords": ["genome", "bed", "gff", "conversion"], + "tools": [ + { + "agat": { + "description": "Another Gff Analysis Toolkit (AGAT). Suite of tools to handle gene annotations in any GTF/GFF format.", + "homepage": "https://agat.readthedocs.io/en/latest/", + "documentation": "https://agat.readthedocs.io/en/latest/", + "tool_dev_url": "https://github.com/NBISweden/AGAT", + "doi": "10.5281/zenodo.3552717", + "licence": ["GPL v3"], + "identifier": "biotools:AGAT" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "gff": { + "type": "file", + "description": "Input GFF3 file", + "pattern": "*.{gff}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1975" + } + ] + } + } + ] + ], + "output": { + "bed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "Output bed12 file", + "pattern": "*.bed", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3586" + } + ] + } + } + ] + ], + "versions_agat": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "agat": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "agat --version | sed 's/v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "agat": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "agat --version | sed 's/v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@atrigila"], + "maintainers": ["@atrigila"] }, - { - "gxf": { - "type": "file", - "description": "Input GFF3/GTF file", - "pattern": "*.{gff,gff3,gtf}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2305" - }, - { - "edam": "http://edamontology.org/format_1975" - }, - { - "edam": "http://edamontology.org/format_2306" - } - ] - } - } - ], - { - "config": { - "type": "file", - "description": "Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any,\notherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: \"agat config --expose\".\nThe --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently).\n", - "pattern": "*.{yaml}", - "ontologies": [ + "pipelines": [ { - "edam": "http://edamontology.org/format_3750" + "name": "rnafusion", + "version": "4.1.2" } - ] - } - } - ], - "output": { - "passed_gff": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]\n", - "ontologies": [] - } - }, - { - "*.passed.gff": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]\n", - "pattern": "*.passed.{gff}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2305" - } - ] - } - } - ] - ], - "failed_gff": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]\n", - "ontologies": [] - } - }, - { - "*.failed.gff": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]\n", - "pattern": "*.failed.{gff}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2305" - } - ] - } - } ] - ], - "versions_agat": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "agat": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "agat --version | sed 's/v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "agat": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "agat --version | sed 's/v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@GallVp" - ], - "maintainers": [ - "@GallVp" - ] - } - }, - { - "name": "agat_spfilterfeaturefromkilllist", - "path": "modules/nf-core/agat/spfilterfeaturefromkilllist/meta.yml", - "type": "module", - "meta": { - "name": "agat_spfilterfeaturefromkilllist", - "description": "The script aims to remove features based on a kill list. The default behaviour is to look at the features's ID.\nIf the feature has an ID (case insensitive) listed among the kill list it will be removed. /!\\ Removing a level1\nor level2 feature will automatically remove all linked subfeatures, and removing all children of a feature will\nautomatically remove this feature too.\n", - "keywords": [ - "genomics", - "gff", - "remove", - "feature" - ], - "tools": [ - { - "agat": { - "description": "Another Gff Analysis Toolkit (AGAT). Suite of tools to handle gene annotations in any GTF/GFF format.", - "homepage": "https://agat.readthedocs.io/en/latest/", - "documentation": "https://agat.readthedocs.io/en/latest/tools/agat_sp_filter_feature_from_kill_list.html", - "tool_dev_url": "https://github.com/NBISweden/AGAT", - "doi": "10.5281/zenodo.3552717", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:AGAT" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "gff": { - "type": "file", - "description": "Input GFF3 file that will be read", - "pattern": "*.{gff,gff3}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2305" - }, - { - "edam": "http://edamontology.org/format_1975" - } - ] - } - } - ], - { - "kill_list": { - "type": "file", - "description": "Kill list. One value per line.", - "pattern": "*.txt", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2330" - } - ] - } - }, - { - "config": { - "type": "file", - "description": "Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the original agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: \"agat config --expose\". The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently).\n", - "pattern": "*.yaml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ], - "output": { - "gff": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]\n" - } - }, - { - "*.gff": { - "type": "file", - "description": "Output GFF file.", - "pattern": "*.gff", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2305" - }, - { - "edam": "http://edamontology.org/format_1975" + }, + { + "name": "agat_convertspgff2gtf", + "path": "modules/nf-core/agat/convertspgff2gtf/meta.yml", + "type": "module", + "meta": { + "name": "agat_convertspgff2gtf", + "description": "Converts a GFF/GTF file into a proper GTF file\n", + "keywords": ["genome", "gff", "gtf", "conversion"], + "tools": [ + { + "agat": { + "description": "AGAT is a toolkit for manipulation and getting information from GFF/GTF files", + "homepage": "https://github.com/NBISweden/AGAT", + "documentation": "https://agat.readthedocs.io/", + "tool_dev_url": "https://github.com/NBISweden/AGAT", + "doi": "10.5281/zenodo.3552717", + "licence": ["GPL v3"], + "identifier": "biotools:AGAT" + } } - ] - } - } - ] - ], - "versions_agat": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "agat": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "agat --version | sed 's/v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "agat": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "agat --version | sed 's/v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@GallVp" - ], - "maintainers": [ - "@GallVp" - ] - } - }, - { - "name": "agat_spflagshortintrons", - "path": "modules/nf-core/agat/spflagshortintrons/meta.yml", - "type": "module", - "meta": { - "name": "agat_spflagshortintrons", - "description": "The script flags the short introns with the attribute . Is is usefull to avoid ERROR when submiting the data to EBI.\n(Typical EBI error message: ********ERROR: Intron usually expected to be at least 10 nt long. Please check the accuracy)\n", - "keywords": [ - "genomics", - "gtf", - "gff", - "intron", - "short", - "annotation" - ], - "tools": [ - { - "agat": { - "description": "Another Gff Analysis Toolkit (AGAT). Suite of tools to handle gene annotations in any GTF/GFF format.", - "homepage": "https://agat.readthedocs.io/en/latest/", - "documentation": "https://agat.readthedocs.io/en/latest/", - "tool_dev_url": "https://github.com/NBISweden/AGAT", - "doi": "10.5281/zenodo.3552717", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:AGAT" + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "gff": { + "type": "file", + "description": "Annotation file in GFF3/GTF format", + "pattern": "*.{gff, gtf}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1975" + }, + { + "edam": "http://edamontology.org/format_2306" + } + ] + } + } + ] + ], + "output": { + "output_gtf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.agat.gtf": { + "type": "file", + "description": "Annotation file in GTF format", + "pattern": "*.{gtf}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2306" + } + ] + } + } + ] + ], + "versions_agat": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "agat": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "agat --version | sed 's/v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "agat": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "agat --version | sed 's/v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@toniher"], + "maintainers": ["@toniher", "@gallvp"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } + }, + { + "name": "agat_convertspgff2tsv", + "path": "modules/nf-core/agat/convertspgff2tsv/meta.yml", + "type": "module", + "meta": { + "name": "agat_convertspgff2tsv", + "description": "Converts a GFF/GTF file into a TSV file\n", + "keywords": ["genome", "gff", "gtf", "conversion", "tsv"], + "tools": [ + { + "agat": { + "description": "AGAT is a toolkit for manipulation and getting information from GFF/GTF files", + "homepage": "https://github.com/NBISweden/AGAT", + "documentation": "https://agat.readthedocs.io/", + "tool_dev_url": "https://github.com/NBISweden/AGAT", + "doi": "10.5281/zenodo.3552717", + "licence": ["GPL v3"], + "identifier": "biotools:AGAT" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "gff": { + "type": "file", + "description": "Annotation file in GFF3/GTF format", + "pattern": "*.{gff, gtf}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1975" + }, + { + "edam": "http://edamontology.org/format_2306" + } + ] + } + } + ] + ], + "output": { + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.tsv": { + "type": "file", + "description": "Annotation file in TSV format", + "pattern": "*.{gtf}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2306" + } + ] + } + } + ] + ], + "versions_agat": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "agat": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "agat --version | sed 's/v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "agat": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "agat --version | sed 's/v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@rannick"], + "maintainers": ["@gallvp"] }, - { - "gxf": { - "type": "file", - "description": "Input GFF3/GTF file", - "pattern": "*.{gff,gff3,gtf}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2305" - }, - { - "edam": "http://edamontology.org/format_1975" - }, - { - "edam": "http://edamontology.org/format_2306" - } - ] - } - } - ], - { - "config": { - "type": "file", - "description": "Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any,\notherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: \"agat config --expose\".\nThe --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently).\n", - "pattern": "*.{yaml}", - "ontologies": [ + "pipelines": [ { - "edam": "http://edamontology.org/format_3750" + "name": "rnafusion", + "version": "4.1.2" } - ] - } - } - ], - "output": { - "gff": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]\n" - } - }, - { - "*.gff": { - "type": "file", - "description": "Output GFF file.", - "pattern": "*.{gff}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2305" - } - ] - } - } - ] - ], - "versions_agat": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "agat": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "agat --version | sed 's/v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "agat": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "agat --version | sed 's/v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } ] - ] - }, - "authors": [ - "@GallVp" - ], - "maintainers": [ - "@GallVp" - ] - } - }, - { - "name": "agat_spkeeplongestisoform", - "path": "modules/nf-core/agat/spkeeplongestisoform/meta.yml", - "type": "module", - "meta": { - "name": "agat_spkeeplongestisoform", - "description": "Filters GFF records to keep only the longest isoform per gene", - "keywords": [ - "gff", - "gtf", - "filter", - "isoform", - "gene", - "longest", - "agat" - ], - "tools": [ - { - "agat": { - "description": "Another Gff Analysis Toolkit (AGAT). Suite of tools to handle gene annotations in any GTF/GFF format.", - "homepage": "https://agat.readthedocs.io/en/latest/", - "documentation": "https://agat.readthedocs.io/en/latest/", - "tool_dev_url": "https://github.com/NBISweden/AGAT", - "doi": "10.5281/zenodo.3552717", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:AGAT" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } + }, + { + "name": "agat_convertspgxf2gxf", + "path": "modules/nf-core/agat/convertspgxf2gxf/meta.yml", + "type": "module", + "meta": { + "name": "agat_convertspgxf2gxf", + "description": "Fixes and standardizes GFF/GTF files and outputs a cleaned GFF/GTF file\n", + "keywords": ["genome", "gff", "gtf", "conversion"], + "tools": [ + { + "agat": { + "description": "AGAT is a toolkit for manipulation and getting information from GFF/GTF files", + "homepage": "https://github.com/NBISweden/AGAT", + "documentation": "https://agat.readthedocs.io/", + "tool_dev_url": "https://github.com/NBISweden/AGAT", + "doi": "10.5281/zenodo.3552717", + "licence": ["GPL v3"], + "identifier": "biotools:AGAT" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "gxf": { + "type": "file", + "description": "Annotation file in GFF3/GTF format", + "pattern": "*.{gff, gtf}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1975" + }, + { + "edam": "http://edamontology.org/format_2306" + } + ] + } + } + ] + ], + "output": { + "output_gff": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.agat.gff": { + "type": "file", + "description": "Cleaned annotation file in GFF3 format", + "pattern": "*.{gff}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1975" + } + ] + } + } + ] + ], + "versions_agat": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "agat": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "agat --version | sed 's/v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "agat": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "agat --version | sed 's/v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@toniher"], + "maintainers": ["@toniher"] }, - { - "gxf": { - "type": "file", - "description": "Annotation file in GFF/GTF format", - "pattern": "*.{gff, gtf}", - "ontologies": [] - } - } - ], - { - "config": { - "type": "file", - "description": "Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any,\notherwise it takes the original agat_config.yaml shipped with AGAT. To get the agat_config.yaml\nlocally type: \"agat config --expose\". The --config option gives you the possibility to use your\nown AGAT config file (located elsewhere or named differently).\n", - "pattern": "*.yaml", - "ontologies": [ + "pipelines": [ { - "edam": "http://edamontology.org/format_3750" + "name": "genomeqc", + "version": "dev" } - ] - } - } - ], - "output": { - "gff": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n", - "pattern": "*.gff" - } - }, - { - "${output}": { - "type": "file", - "description": "Output GFF3 file", - "pattern": "*.longest.gff", - "ontologies": [] - } - } - ] - ], - "versions_agat": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "agat": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "agat --version | sed 's/v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "agat": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "agat --version | sed 's/v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@Juke34" - ], - "maintainers": [ - "@Juke34" - ] - }, - "pipelines": [ - { - "name": "genomeqc", - "version": "dev" - } - ] - }, - { - "name": "agat_spmergeannotations", - "path": "modules/nf-core/agat/spmergeannotations/meta.yml", - "type": "module", - "meta": { - "name": "agat_spmergeannotations", - "description": "This script merge different gff annotation files in one. It uses the AGAT parser that takes care of duplicated names and fixes other oddities met in those files.\n", - "keywords": [ - "genomics", - "gff", - "merge", - "combine" - ], - "tools": [ - { - "agat": { - "description": "Another Gff Analysis Toolkit (AGAT). Suite of tools to handle gene annotations in any GTF/GFF format.", - "homepage": "https://agat.readthedocs.io/en/latest/", - "documentation": "https://agat.readthedocs.io/en/latest/tools/agat_sp_merge_annotations.html", - "tool_dev_url": "https://github.com/NBISweden/AGAT", - "doi": "10.5281/zenodo.3552717", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:AGAT" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } + }, + { + "name": "agat_spaddintrons", + "path": "modules/nf-core/agat/spaddintrons/meta.yml", + "type": "module", + "meta": { + "name": "agat_spaddintrons", + "description": "Add intron features to gtf/gff file without intron features.", + "keywords": ["gtf", "gff", "introns"], + "tools": [ + { + "agat": { + "description": "Another Gff Analysis Toolkit (AGAT). Suite of tools to handle gene annotations in any GTF/GFF format.", + "homepage": "https://agat.readthedocs.io/en/latest/", + "documentation": "https://agat.readthedocs.io/en/latest/", + "tool_dev_url": "https://github.com/NBISweden/AGAT", + "licence": ["GPL v3"], + "identifier": "biotools:AGAT" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "gff": { + "type": "file", + "description": "Input gtf/gff file", + "pattern": "*.{gff,gff3,gtf}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2305" + }, + { + "edam": "http://edamontology.org/format_1975" + }, + { + "edam": "http://edamontology.org/format_2306" + } + ] + } + } + ], + { + "config": { + "type": "file", + "description": "Optional input agat config file", + "pattern": "*.{yaml,yml}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ], + "output": { + "gff": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "${output}": { + "type": "file", + "description": "Output gff3 file with introns", + "pattern": "*.gff", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1975" + } + ] + } + } + ] + ], + "versions_agat": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "agat": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "agat --version | sed 's/v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "agat": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "agat --version | sed 's/v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@anoronh4"], + "maintainers": ["@anoronh4", "@gallvp"] }, - { - "gffs": { - "type": "list", - "description": "A list of GFFs to merge", - "pattern": "[ *.{gff,gff3} ]", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2305" - } - ] - } - } - ], - { - "config": { - "type": "file", - "description": "Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any,\notherwise it takes the original agat_config.yaml shipped with AGAT. To get the agat_config.yaml\nlocally type: \"agat config --expose\". The --config option gives you the possibility to use your\nown AGAT config file (located elsewhere or named differently).\n", - "pattern": "*.yaml", - "ontologies": [ + "pipelines": [ { - "edam": "http://edamontology.org/format_3750" + "name": "circrna", + "version": "dev" } - ] - } - } - ], - "output": { - "gff": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.gff": { - "type": "file", - "description": "Output GFF file.", - "pattern": "*.gff", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2305" - } - ] - } - } ] - ], - "versions_agat": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "agat": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "agat --version | sed 's/v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "agat": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "agat --version | sed 's/v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@GallVp" - ], - "maintainers": [ - "@GallVp" - ] - } - }, - { - "name": "agat_spstatistics", - "path": "modules/nf-core/agat/spstatistics/meta.yml", - "type": "module", - "meta": { - "name": "agat_spstatistics", - "description": "Provides different type of statistics in text format from a GFF/GTF annotation file\n", - "keywords": [ - "genome", - "gff", - "gtf", - "statistics" - ], - "tools": [ - { - "agat": { - "description": "AGAT is a toolkit for manipulation and getting information from GFF/GTF files", - "homepage": "https://github.com/NBISweden/AGAT", - "documentation": "https://agat.readthedocs.io/", - "tool_dev_url": "https://github.com/NBISweden/AGAT", - "doi": "10.5281/zenodo.3552717", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:AGAT" + }, + { + "name": "agat_spextractsequences", + "path": "modules/nf-core/agat/spextractsequences/meta.yml", + "type": "module", + "meta": { + "name": "agat_spextractsequences", + "description": "This script extracts sequences in fasta format according to features described\nin a gff file.\n", + "keywords": ["genomics", "gff", "extract", "fasta", "sequence", "feature"], + "tools": [ + { + "agat": { + "description": "Another Gff Analysis Toolkit (AGAT). Suite of tools to handle gene annotations in any GTF/GFF format.", + "homepage": "https://agat.readthedocs.io/en/latest/", + "documentation": "https://agat.readthedocs.io/en/latest/tools/agat_sp_extract_sequences.html", + "tool_dev_url": "https://github.com/NBISweden/AGAT", + "doi": "10.5281/zenodo.3552717", + "licence": ["GPL v3"], + "identifier": "biotools:AGAT" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "gxf": { + "type": "file", + "description": "Input GFF3/GTF file", + "pattern": "*.{gff,gff3,gtf}", + "ontologies": [] + } + } + ], + { + "fasta": { + "type": "file", + "description": "Input FASTA file", + "pattern": "*.{fa,fsa,faa,fasta}", + "ontologies": [] + } + }, + { + "config": { + "type": "file", + "description": "Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: \"agat config --expose\". The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently).\n", + "pattern": "*.yaml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ], + "output": { + "fasta": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]\n" + } + }, + { + "*.fasta": { + "type": "file", + "description": "Output FASTA file.", + "pattern": "*.fasta", + "ontologies": [] + } + } + ] + ], + "versions_agat": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "agat": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "agat --version | sed 's/v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "agat": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "agat --version | sed 's/v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@GallVp"], + "maintainers": ["@GallVp"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "gff": { - "type": "file", - "description": "Annotation file in GFF3/GTF format", - "pattern": "*.{gff, gtf}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1975" - }, - { - "edam": "http://edamontology.org/format_2306" - } - ] - } + }, + { + "name": "agat_spfilterbyorfsize", + "path": "modules/nf-core/agat/spfilterbyorfsize/meta.yml", + "type": "module", + "meta": { + "name": "agat_spfilterbyorfsize", + "description": "The script reads a gff annotation file, and create two output files, one contains the gene models with ORF passing the test, the other contains the rest. By default the test is \"> 100\" that means all gene models that have ORF longer than 100 Amino acids, will pass the test.", + "keywords": ["genomics", "GFF/GTF", "filter", "annotation"], + "tools": [ + { + "agat": { + "description": "Another Gff Analysis Toolkit (AGAT). Suite of tools to handle gene annotations in any GTF/GFF format.", + "homepage": "https://agat.readthedocs.io/en/latest/", + "documentation": "https://agat.readthedocs.io/en/latest/", + "tool_dev_url": "https://github.com/NBISweden/AGAT", + "doi": "10.5281/zenodo.3552717", + "licence": ["GPL v3"], + "identifier": "biotools:AGAT" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "gxf": { + "type": "file", + "description": "Input GFF3/GTF file", + "pattern": "*.{gff,gff3,gtf}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2305" + }, + { + "edam": "http://edamontology.org/format_1975" + }, + { + "edam": "http://edamontology.org/format_2306" + } + ] + } + } + ], + { + "config": { + "type": "file", + "description": "Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any,\notherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: \"agat config --expose\".\nThe --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently).\n", + "pattern": "*.{yaml}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ], + "output": { + "passed_gff": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]\n", + "ontologies": [] + } + }, + { + "*.passed.gff": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]\n", + "pattern": "*.passed.{gff}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2305" + } + ] + } + } + ] + ], + "failed_gff": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]\n", + "ontologies": [] + } + }, + { + "*.failed.gff": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]\n", + "pattern": "*.failed.{gff}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2305" + } + ] + } + } + ] + ], + "versions_agat": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "agat": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "agat --version | sed 's/v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "agat": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "agat --version | sed 's/v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@GallVp"], + "maintainers": ["@GallVp"] } - ] - ], - "output": { - "stats_txt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*.txt": { - "type": "file", - "description": "Output of Statistics execution", - "pattern": "*.{txt}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2330" - } - ] - } - } - ] - ], - "versions_agat": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "agat": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "agat --version | sed 's/v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "agat": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "agat --version | sed 's/v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@toniher" - ], - "maintainers": [ - "@toniher", - "@gallvp" - ] - }, - "pipelines": [ - { - "name": "genomeqc", - "version": "dev" - } - ] - }, - { - "name": "agat_sqstatbasic", - "path": "modules/nf-core/agat/sqstatbasic/meta.yml", - "type": "module", - "meta": { - "name": "agat_sqstatbasic", - "description": "Provides basic statistics in text format from a GFF/GTF annotation file\n", - "keywords": [ - "genome", - "gff", - "gtf", - "statistics" - ], - "tools": [ - { - "agat": { - "description": "AGAT is a toolkit for manipulation and getting information from GFF/GTF annotation files", - "homepage": "https://github.com/NBISweden/AGAT", - "documentation": "https://agat.readthedocs.io/", - "tool_dev_url": "https://github.com/NBISweden/AGAT", - "doi": "10.5281/zenodo.3552717", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:AGAT" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "gff": { - "type": "file", - "description": "Annotation file in GFF3/GTF format", - "pattern": "*.{gff, gtf}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1975" - }, - { - "edam": "http://edamontology.org/format_2306" - } - ] - } - } - ] - ], - "output": { - "stats_txt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*.txt": { - "type": "file", - "description": "Output of Statistics execution", - "pattern": "*.{txt}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2330" - } - ] - } - } - ] - ], - "versions_agat": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "agat": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "agat --version | sed 's/v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "agat": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "agat --version | sed 's/v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@toniher" - ], - "maintainers": [ - "@toniher", - "@gallvp" - ] - } - }, - { - "name": "agrvate", - "path": "modules/nf-core/agrvate/meta.yml", - "type": "module", - "meta": { - "name": "agrvate", - "description": "Rapid identification of Staphylococcus aureus agr locus type and agr operon variants", - "keywords": [ - "fasta", - "virulence", - "Staphylococcus aureus" - ], - "tools": [ - { - "agrvate": { - "description": "Rapid identification of Staphylococcus aureus agr locus type and agr operon variants.", - "homepage": "https://github.com/VishnuRaghuram94/AgrVATE", - "documentation": "https://github.com/VishnuRaghuram94/AgrVATE", - "tool_dev_url": "https://github.com/VishnuRaghuram94/AgrVATE", - "licence": [ - "MIT" - ], - "identifier": "biotools:agrvate" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "A Staphylococcus aureus fasta file.", - "pattern": "*.fasta", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ], - "output": { - "summary": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${fasta.baseName}-results/${fasta.baseName}-summary.tab": { - "type": "file", - "description": "A summary of the agrvate assessment", - "pattern": "*-summary.tab", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "results_dir": [ - { - "${fasta.baseName}-results": { - "type": "directory", - "description": "Results of the agrvate assessment", - "pattern": "*-results" - } - } - ], - "versions_agrvate": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "agrvate": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "agrvate --version | sed 's/[^0-9.]//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "agrvate": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "agrvate --version | sed 's/[^0-9.]//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@abhi18av" - ], - "maintainers": [ - "@abhi18av" - ] - } - }, - { - "name": "ale", - "path": "modules/nf-core/ale/meta.yml", - "type": "module", - "meta": { - "name": "ale", - "description": "ALE: assembly likelihood estimator.", - "keywords": [ - "reference-independent", - "assembly", - "evaluation" - ], - "tools": [ - { - "ale": { - "description": "ALE is a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies.", - "documentation": "https://portal.nersc.gov/dna/RD/Adv-Seq/ALE-doc/index.html#document-install", - "tool_dev_url": "https://github.com/sc932/ALE", - "doi": "10.1093/bioinformatics/bts723", - "licence": [ - "NCSA" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "asm": { - "type": "file", - "description": "Assembly in FASTA format", - "pattern": "*.{fasta,fa}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - }, - { - "bam": { - "type": "file", - "description": "BAM file containing sorted read mappings", - "pattern": "*.{bam}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - } - ] - ], - "output": { - "ale": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*_ALEoutput.txt": { - "type": "file", - "description": "Output TXT file containing ALE results", - "pattern": "*_ALEoutput.{txt}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2330" - } - ] - } - } - ] - ], - "versions_ale": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "ALE": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "20180904": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "ALE": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "20180904": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@rodtheo" - ], - "maintainers": [ - "@rodtheo" - ] - }, - "pipelines": [ - { - "name": "mag", - "version": "5.4.2" - } - ] - }, - { - "name": "alignoth", - "path": "modules/nf-core/alignoth/meta.yml", - "type": "module", - "meta": { - "name": "alignoth", - "description": "Creating alignment plots from bam files", - "keywords": [ - "genomics", - "alignment", - "visualization", - "pileup", - "plotting" - ], - "tools": [ - { - "alignoth": { - "description": "A tool for creating alignment plots from bam files.", - "homepage": "https://github.com/alignoth/alignoth/blob/v1.4.6/README.md", - "documentation": "https://github.com/alignoth/alignoth/blob/v1.4.6/README.md", - "tool_dev_url": "https://github.com/alignoth/alignoth", - "doi": "10.1093/bioinformatics/btaf663", - "licence": [ - "MIT" - ], - "identifier": "biotools:alignoth" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM/CRAM/SAM file to be visualized", - "pattern": "*.{bam,cram,sam}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - }, - { - "edam": "http://edamontology.org/format_2573" - }, - { - "edam": "http://edamontology.org/format_3462" - } - ] - } - }, - { - "bai": { - "type": "file", - "description": "Index file for the BAM/CRAM/SAM file", - "pattern": "*.{bai,crai}", - "ontologies": [] - } - }, - { - "fasta": { - "type": "file", - "description": "Reference fasta file", - "pattern": "*.{fa,fasta}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - }, - { - "fai": { - "type": "file", - "description": "Index file for the reference fasta file", - "pattern": "*.{fa,fasta}.fai", - "ontologies": [] - } - }, - { - "bed": { - "type": "file", - "description": "Bed file with regions to be visualized (optional)", - "pattern": "*.bed", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3003" - } - ] - } - }, - { - "vcf": { - "type": "file", - "description": "VCF file with variants to be highlighted (optional)", - "pattern": "*.vcf", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - } - ] - } - }, - { - "tbi": { - "type": "file", - "description": "Index file for the VCF file", - "pattern": "*.vcf.tbi", - "ontologies": [] - } + }, + { + "name": "agat_spfilterfeaturefromkilllist", + "path": "modules/nf-core/agat/spfilterfeaturefromkilllist/meta.yml", + "type": "module", + "meta": { + "name": "agat_spfilterfeaturefromkilllist", + "description": "The script aims to remove features based on a kill list. The default behaviour is to look at the features's ID.\nIf the feature has an ID (case insensitive) listed among the kill list it will be removed. /!\\ Removing a level1\nor level2 feature will automatically remove all linked subfeatures, and removing all children of a feature will\nautomatically remove this feature too.\n", + "keywords": ["genomics", "gff", "remove", "feature"], + "tools": [ + { + "agat": { + "description": "Another Gff Analysis Toolkit (AGAT). Suite of tools to handle gene annotations in any GTF/GFF format.", + "homepage": "https://agat.readthedocs.io/en/latest/", + "documentation": "https://agat.readthedocs.io/en/latest/tools/agat_sp_filter_feature_from_kill_list.html", + "tool_dev_url": "https://github.com/NBISweden/AGAT", + "doi": "10.5281/zenodo.3552717", + "licence": ["GPL v3"], + "identifier": "biotools:AGAT" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "gff": { + "type": "file", + "description": "Input GFF3 file that will be read", + "pattern": "*.{gff,gff3}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2305" + }, + { + "edam": "http://edamontology.org/format_1975" + } + ] + } + } + ], + { + "kill_list": { + "type": "file", + "description": "Kill list. One value per line.", + "pattern": "*.txt", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + }, + { + "config": { + "type": "file", + "description": "Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the original agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: \"agat config --expose\". The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently).\n", + "pattern": "*.yaml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ], + "output": { + "gff": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]\n" + } + }, + { + "*.gff": { + "type": "file", + "description": "Output GFF file.", + "pattern": "*.gff", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2305" + }, + { + "edam": "http://edamontology.org/format_1975" + } + ] + } + } + ] + ], + "versions_agat": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "agat": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "agat --version | sed 's/v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "agat": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "agat --version | sed 's/v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@GallVp"], + "maintainers": ["@GallVp"] } - ] - ], - "output": { - "html": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}.html": { - "type": "file", - "description": "HTML file with the alignment plot", - "pattern": "*.html", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2331" - } - ] - } - } - ] - ], - "output": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}": { - "type": "directory", - "description": "Output directory with the alignment plot and all intermediate files", - "pattern": "*" - } - } - ] - ], - "vl_json": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}.vl.json": { - "type": "file", - "description": "Vega-Lite JSON file with the alignment plot", - "pattern": "*.vl.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "versions_alignoth": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "alignoth": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "alignoth --version | sed 's/alignoth //g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "alignoth": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "alignoth --version | sed 's/alignoth //g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@famosab" - ], - "maintainers": [ - "@famosab" - ] - } - }, - { - "name": "allelecounter", - "path": "modules/nf-core/allelecounter/meta.yml", - "type": "module", - "meta": { - "name": "allelecounter", - "description": "Generates a count of coverage of alleles", - "keywords": [ - "allele", - "count", - "coverage" - ], - "tools": [ - { - "allelecounter": { - "description": "Takes a file of locations and a [cr|b]am file and generates a count of coverage of each allele at that location (given any filter settings)", - "homepage": "https://github.com/cancerit/alleleCount", - "documentation": "https://github.com/cancerit/alleleCount", - "tool_dev_url": "https://github.com/cancerit/alleleCount", - "licence": [ - "GPL 3.0" - ], - "identifier": "" + }, + { + "name": "agat_spflagshortintrons", + "path": "modules/nf-core/agat/spflagshortintrons/meta.yml", + "type": "module", + "meta": { + "name": "agat_spflagshortintrons", + "description": "The script flags the short introns with the attribute . Is is usefull to avoid ERROR when submiting the data to EBI.\n(Typical EBI error message: ********ERROR: Intron usually expected to be at least 10 nt long. Please check the accuracy)\n", + "keywords": ["genomics", "gtf", "gff", "intron", "short", "annotation"], + "tools": [ + { + "agat": { + "description": "Another Gff Analysis Toolkit (AGAT). Suite of tools to handle gene annotations in any GTF/GFF format.", + "homepage": "https://agat.readthedocs.io/en/latest/", + "documentation": "https://agat.readthedocs.io/en/latest/", + "tool_dev_url": "https://github.com/NBISweden/AGAT", + "doi": "10.5281/zenodo.3552717", + "licence": ["GPL v3"], + "identifier": "biotools:AGAT" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "gxf": { + "type": "file", + "description": "Input GFF3/GTF file", + "pattern": "*.{gff,gff3,gtf}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2305" + }, + { + "edam": "http://edamontology.org/format_1975" + }, + { + "edam": "http://edamontology.org/format_2306" + } + ] + } + } + ], + { + "config": { + "type": "file", + "description": "Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any,\notherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: \"agat config --expose\".\nThe --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently).\n", + "pattern": "*.{yaml}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ], + "output": { + "gff": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]\n" + } + }, + { + "*.gff": { + "type": "file", + "description": "Output GFF file.", + "pattern": "*.{gff}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2305" + } + ] + } + } + ] + ], + "versions_agat": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "agat": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "agat --version | sed 's/v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "agat": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "agat --version | sed 's/v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@GallVp"], + "maintainers": ["@GallVp"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - }, - { - "edam": "http://edamontology.org/format_3462" - }, - { - "edam": "http://edamontology.org/format_2573" - } - ] - } + }, + { + "name": "agat_spkeeplongestisoform", + "path": "modules/nf-core/agat/spkeeplongestisoform/meta.yml", + "type": "module", + "meta": { + "name": "agat_spkeeplongestisoform", + "description": "Filters GFF records to keep only the longest isoform per gene", + "keywords": ["gff", "gtf", "filter", "isoform", "gene", "longest", "agat"], + "tools": [ + { + "agat": { + "description": "Another Gff Analysis Toolkit (AGAT). Suite of tools to handle gene annotations in any GTF/GFF format.", + "homepage": "https://agat.readthedocs.io/en/latest/", + "documentation": "https://agat.readthedocs.io/en/latest/", + "tool_dev_url": "https://github.com/NBISweden/AGAT", + "doi": "10.5281/zenodo.3552717", + "licence": ["GPL v3"], + "identifier": "biotools:AGAT" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "gxf": { + "type": "file", + "description": "Annotation file in GFF/GTF format", + "pattern": "*.{gff, gtf}", + "ontologies": [] + } + } + ], + { + "config": { + "type": "file", + "description": "Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any,\notherwise it takes the original agat_config.yaml shipped with AGAT. To get the agat_config.yaml\nlocally type: \"agat config --expose\". The --config option gives you the possibility to use your\nown AGAT config file (located elsewhere or named differently).\n", + "pattern": "*.yaml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ], + "output": { + "gff": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n", + "pattern": "*.gff" + } + }, + { + "${output}": { + "type": "file", + "description": "Output GFF3 file", + "pattern": "*.longest.gff", + "ontologies": [] + } + } + ] + ], + "versions_agat": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "agat": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "agat --version | sed 's/v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "agat": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "agat --version | sed 's/v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@Juke34"], + "maintainers": ["@Juke34"] }, - { - "input_index": { - "type": "file", - "description": "BAM/CRAM/SAM index file", - "pattern": "*.{bai,crai,sai}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3327" - }, - { - "edam": "http://edamontology.org/format_3462" - } - ] - } - } - ], - { - "loci": { - "type": "file", - "description": "loci file ", - "pattern": "*.{tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - }, - { - "fasta": { - "type": "file", - "description": "Input genome fasta file. Required when passing CRAM files.", - "ontologies": [ + "pipelines": [ { - "edam": "http://edamontology.org/format_1929" + "name": "genomeqc", + "version": "dev" } - ] - } - } - ], - "output": { - "allelecount": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.alleleCount": { - "type": "file", - "description": "Allele count file", - "pattern": "*.{alleleCount}", - "ontologies": [] - } - } - ] - ], - "versions_allelecounter": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "alleleCounter": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "alleleCounter --version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "alleleCounter": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "alleleCounter --version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@fullama", - "@fbdtemme" - ], - "maintainers": [ - "@fullama", - "@fbdtemme" - ] - } - }, - { - "name": "ampcombi", - "path": "modules/nf-core/ampcombi/meta.yml", - "type": "module", - "meta": { - "name": "ampcombi", - "description": "A tool to parse and summarise results from antimicrobial peptides tools and present functional classification.", - "deprecated": true, - "keywords": [ - "antimicrobial peptides", - "amps", - "parsing", - "reporting", - "align", - "macrel", - "amplify", - "hmmsearch", - "neubi", - "ampir", - "DRAMP" - ], - "tools": [ - { - "ampcombi": { - "description": "This tool parses the results of amp prediction tools into a single table and aligns the hits against a reference database of antimicrobial peptides for functional classifications.", - "homepage": "https://github.com/Darcy220606/AMPcombi", - "documentation": "https://github.com/Darcy220606/AMPcombi", - "tool_dev_url": "https://github.com/Darcy220606/AMPcombi/tree/dev", - "licence": [ - "MIT" - ], - "identifier": "" + }, + { + "name": "agat_spmergeannotations", + "path": "modules/nf-core/agat/spmergeannotations/meta.yml", + "type": "module", + "meta": { + "name": "agat_spmergeannotations", + "description": "This script merge different gff annotation files in one. It uses the AGAT parser that takes care of duplicated names and fixes other oddities met in those files.\n", + "keywords": ["genomics", "gff", "merge", "combine"], + "tools": [ + { + "agat": { + "description": "Another Gff Analysis Toolkit (AGAT). Suite of tools to handle gene annotations in any GTF/GFF format.", + "homepage": "https://agat.readthedocs.io/en/latest/", + "documentation": "https://agat.readthedocs.io/en/latest/tools/agat_sp_merge_annotations.html", + "tool_dev_url": "https://github.com/NBISweden/AGAT", + "doi": "10.5281/zenodo.3552717", + "licence": ["GPL v3"], + "identifier": "biotools:AGAT" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "gffs": { + "type": "list", + "description": "A list of GFFs to merge", + "pattern": "[ *.{gff,gff3} ]", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2305" + } + ] + } + } + ], + { + "config": { + "type": "file", + "description": "Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any,\notherwise it takes the original agat_config.yaml shipped with AGAT. To get the agat_config.yaml\nlocally type: \"agat config --expose\". The --config option gives you the possibility to use your\nown AGAT config file (located elsewhere or named differently).\n", + "pattern": "*.yaml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ], + "output": { + "gff": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.gff": { + "type": "file", + "description": "Output GFF file.", + "pattern": "*.gff", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2305" + } + ] + } + } + ] + ], + "versions_agat": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "agat": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "agat --version | sed 's/v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "agat": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "agat --version | sed 's/v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@GallVp"], + "maintainers": ["@GallVp"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + }, + { + "name": "agat_spstatistics", + "path": "modules/nf-core/agat/spstatistics/meta.yml", + "type": "module", + "meta": { + "name": "agat_spstatistics", + "description": "Provides different type of statistics in text format from a GFF/GTF annotation file\n", + "keywords": ["genome", "gff", "gtf", "statistics"], + "tools": [ + { + "agat": { + "description": "AGAT is a toolkit for manipulation and getting information from GFF/GTF files", + "homepage": "https://github.com/NBISweden/AGAT", + "documentation": "https://agat.readthedocs.io/", + "tool_dev_url": "https://github.com/NBISweden/AGAT", + "doi": "10.5281/zenodo.3552717", + "licence": ["GPL v3"], + "identifier": "biotools:AGAT" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "gff": { + "type": "file", + "description": "Annotation file in GFF3/GTF format", + "pattern": "*.{gff, gtf}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1975" + }, + { + "edam": "http://edamontology.org/format_2306" + } + ] + } + } + ] + ], + "output": { + "stats_txt": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.txt": { + "type": "file", + "description": "Output of Statistics execution", + "pattern": "*.{txt}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + } + ] + ], + "versions_agat": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "agat": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "agat --version | sed 's/v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "agat": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "agat --version | sed 's/v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@toniher"], + "maintainers": ["@toniher", "@gallvp"] }, - { - "amp_input": { - "type": "list", - "description": "The path to the directory containing the results for the AMP tools for each sample processed or a list of files corresponding to each file generated by AMP tools.", - "pattern": "[*amptool.tsv, *amptool.tsv]", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - { - "faa_input": { - "type": "file", - "description": "The path to the file corresponding to the respective protein fasta files with '.faa' extension. File names have to contain the corresponding sample name, i.e. sample_1.faa", - "pattern": "*.faa", - "ontologies": [ + "pipelines": [ { - "edam": "http://edamontology.org/format_1929" + "name": "genomeqc", + "version": "dev" } - ] - } - }, - { - "opt_amp_db": { - "type": "directory", - "description": "The path to the folder containing the fasta and tsv database files.", - "pattern": "*/" - } - } - ], - "output": { - "sample_dir": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${meta.id}/": { - "type": "directory", - "description": "The output directory that contains the summary output and related alignment files for one sample.", - "pattern": "/*" - } - } - ] - ], - "txt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${meta.id}/*diamond_matches.txt": { - "type": "file", - "description": "An alignment file containing the results from the DIAMOND alignment step done on all AMP hits.", - "pattern": "/*/*_diamond_matches.txt", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2330" - } - ] - } - } ] - ], - "csv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${meta.id}/*ampcombi.csv": { - "type": "file", - "description": "A file containing the summary report of all predicted AMP hits from all AMP tools given as input and the corresponding taxonomic and functional classification from the alignment step.", - "pattern": "/*/*_ampcombi.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "faa": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${meta.id}/*amp.faa": { - "type": "file", - "description": "A fasta file containing the amino acid sequences of all predicted AMP hits.", - "pattern": "/*/*_amp.faa", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ], - "summary_csv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "AMPcombi_summary.csv": { - "type": "file", - "description": "A file that concatenates all samples ampcombi summaries. This is activated with `--complete_summary true`.", - "pattern": "AMPcombi_summary.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "summary_html": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "AMPcombi_summary.html": { - "type": "file", - "description": "A file that concatenates all samples ampcombi summaries. This is activated with `--complete_summary true`.", - "pattern": "AMPcombi_summary.html", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2331" - } - ] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.log": { - "type": "file", - "description": "A log file that captures the standard output ina log file. Can be activated by `--log`.", - "pattern": "*.log", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2330" - } - ] - } - } - ] - ], - "results_db": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "amp_ref_database/": { - "type": "directory", - "description": "If the AMP reference database is not provided by the user using the flag `--amp_database', by default the DRAMP database will be downloaded, filtered and stored in this folder.", - "pattern": "/amp_ref_database" - } - } - ] - ], - "results_db_dmnd": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "amp_ref_database/*.dmnd": { - "type": "file", - "description": "AMP reference database converted to DIAMOND database format.", - "pattern": "/amp_ref_database/*.dmnd", - "ontologies": [] - } - } - ] - ], - "results_db_fasta": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "amp_ref_database/*.clean.fasta": { - "type": "file", - "description": "AMP reference database fasta file, cleaned of diamond-incompatible characters.", - "pattern": "/amp_ref_database/*.clean.fasta", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ], - "results_db_tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "amp_ref_database/*.tsv": { - "type": "file", - "description": "AMP reference database in tsv-format with two columns containing header and sequence.", - "pattern": "/amp_ref_database/*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_ampcombi": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "ampcombi": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "0.1.7": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "ampcombi": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "0.1.7": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@darcy220606", - "@louperelo" - ], - "maintainers": [ - "@darcy220606", - "@louperelo" - ] - } - }, - { - "name": "ampcombi2_cluster", - "path": "modules/nf-core/ampcombi2/cluster/meta.yml", - "type": "module", - "meta": { - "name": "ampcombi2_cluster", - "description": "A submodule that clusters the merged AMP hits generated from ampcombi2/parsetables and ampcombi2/complete using MMseqs2 cluster.", - "keywords": [ - "antimicrobial peptides", - "amps", - "parsing", - "reporting", - "align", - "clustering", - "mmseqs2" - ], - "tools": [ - { - "ampcombi2/cluster": { - "description": "A tool for clustering all AMP hits found across many samples and supporting many AMP prediction tools.", - "homepage": "https://github.com/paleobiotechnology/AMPcombi", - "documentation": "https://ampcombi.readthedocs.io", - "tool_dev_url": "https://github.com/paleobiotechnology/AMPcombi/tree/dev", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - { - "summary_file": { - "type": "file", - "description": "A file corresponding to the Ampcombi_summary.tsv that is generated by running 'ampcombi complete'. It is a file containing all the merged AMP results from all samples and all tools.", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - "output": { - "cluster_tsv": [ - { - "Ampcombi_summary_cluster.tsv": { - "type": "file", - "description": "A file containing all the results from the merged input table 'Ampcombi_summary.tsv', but also including the cluster id number. The clustering is done using MMseqs2 cluster.", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - "rep_cluster_tsv": [ - { - "Ampcombi_summary_cluster_representative_seq.tsv": { - "type": "file", - "description": "A file containing the representative sequences of the clusters estimated by the tool. The clustering is done using MMseqs2 cluster.", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - "log": [ - { - "Ampcombi_cluster.log": { - "type": "file", - "description": "A log file that captures the standard output for the entire process in a log file. Can be activated by `--log`.", - "pattern": "*.log", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2330" - } - ] - } - } - ], - "versions_ampcombi": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "ampcombi": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "ampcombi --version | sed 's/ampcombi //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "ampcombi": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "ampcombi --version | sed 's/ampcombi //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@darcy220606" - ], - "maintainers": [ - "@darcy220606", - "@jasmezz" - ] - }, - "pipelines": [ - { - "name": "funcscan", - "version": "3.0.0" - } - ] - }, - { - "name": "ampcombi2_complete", - "path": "modules/nf-core/ampcombi2/complete/meta.yml", - "type": "module", - "meta": { - "name": "ampcombi2_complete", - "description": "A submodule that merges all output summary tables from ampcombi/parsetables in one summary file.", - "keywords": [ - "antimicrobial peptides", - "amps", - "parsing", - "reporting", - "align", - "macrel", - "amplify", - "hmmsearch", - "neubi", - "ampir", - "ampgram", - "amptransformer", - "DRAMP" - ], - "tools": [ - { - "ampcombi2/complete": { - "description": "This merges the per sample AMPcombi summaries generated by running 'ampcombi2/parsetables'.", - "homepage": "https://github.com/paleobiotechnology/AMPcombi", - "documentation": "https://ampcombi.readthedocs.io", - "tool_dev_url": "https://github.com/paleobiotechnology/AMPcombi/tree/dev", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - { - "summaries": { - "type": "list", - "description": "The path to the list of files corresponding to each sample as generated by ampcombi2/parsetables.", - "pattern": "[*_ampcombi.tsv, *_ampcombi.tsv]", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - "output": { - "tsv": [ - { - "Ampcombi_summary.tsv": { - "type": "file", - "description": "A file containing the complete AMPcombi summaries from all processed samples.", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - "log": [ - { - "Ampcombi_complete.log": { - "type": "file", - "description": "A log file that captures the standard output for the entire process in a log file. Can be activated by `--log`.", - "pattern": "*.log", - "ontologies": [] - } + }, + { + "name": "agat_sqstatbasic", + "path": "modules/nf-core/agat/sqstatbasic/meta.yml", + "type": "module", + "meta": { + "name": "agat_sqstatbasic", + "description": "Provides basic statistics in text format from a GFF/GTF annotation file\n", + "keywords": ["genome", "gff", "gtf", "statistics"], + "tools": [ + { + "agat": { + "description": "AGAT is a toolkit for manipulation and getting information from GFF/GTF annotation files", + "homepage": "https://github.com/NBISweden/AGAT", + "documentation": "https://agat.readthedocs.io/", + "tool_dev_url": "https://github.com/NBISweden/AGAT", + "doi": "10.5281/zenodo.3552717", + "licence": ["GPL v3"], + "identifier": "biotools:AGAT" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "gff": { + "type": "file", + "description": "Annotation file in GFF3/GTF format", + "pattern": "*.{gff, gtf}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1975" + }, + { + "edam": "http://edamontology.org/format_2306" + } + ] + } + } + ] + ], + "output": { + "stats_txt": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.txt": { + "type": "file", + "description": "Output of Statistics execution", + "pattern": "*.{txt}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + } + ] + ], + "versions_agat": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "agat": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "agat --version | sed 's/v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "agat": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "agat --version | sed 's/v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@toniher"], + "maintainers": ["@toniher", "@gallvp"] } - ], - "versions_ampcombi": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "ampcombi": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "ampcombi --version | sed 's/ampcombi //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "ampcombi": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "ampcombi --version | sed 's/ampcombi //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@darcy220606" - ], - "maintainers": [ - "@darcy220606", - "@jasmezz" - ] - }, - "pipelines": [ - { - "name": "funcscan", - "version": "3.0.0" - } - ] - }, - { - "name": "ampcombi2_parsetables", - "path": "modules/nf-core/ampcombi2/parsetables/meta.yml", - "type": "module", - "meta": { - "name": "ampcombi2_parsetables", - "description": "A submodule that parses and standardizes the results from various antimicrobial peptide identification tools.", - "keywords": [ - "antimicrobial peptides", - "amps", - "parsing", - "reporting", - "align", - "macrel", - "amplify", - "hmmsearch", - "neubi", - "ampir", - "ampgram", - "amptransformer", - "DRAMP", - "MMseqs2", - "InterProScan" - ], - "tools": [ - { - "ampcombi2/parsetables": { - "description": "A parsing tool to convert and summarise the outputs from multiple AMP detection tools in a standardized format.", - "homepage": "https://github.com/paleobiotechnology/AMPcombi", - "documentation": "https://ampcombi.readthedocs.io", - "tool_dev_url": "https://github.com/paleobiotechnology/AMPcombi/tree/dev", - "licence": [ - "MIT" - ], - "identifier": "" + }, + { + "name": "agrvate", + "path": "modules/nf-core/agrvate/meta.yml", + "type": "module", + "meta": { + "name": "agrvate", + "description": "Rapid identification of Staphylococcus aureus agr locus type and agr operon variants", + "keywords": ["fasta", "virulence", "Staphylococcus aureus"], + "tools": [ + { + "agrvate": { + "description": "Rapid identification of Staphylococcus aureus agr locus type and agr operon variants.", + "homepage": "https://github.com/VishnuRaghuram94/AgrVATE", + "documentation": "https://github.com/VishnuRaghuram94/AgrVATE", + "tool_dev_url": "https://github.com/VishnuRaghuram94/AgrVATE", + "licence": ["MIT"], + "identifier": "biotools:agrvate" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "A Staphylococcus aureus fasta file.", + "pattern": "*.fasta", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ] + ], + "output": { + "summary": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${fasta.baseName}-results/${fasta.baseName}-summary.tab": { + "type": "file", + "description": "A summary of the agrvate assessment", + "pattern": "*-summary.tab", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "results_dir": [ + { + "${fasta.baseName}-results": { + "type": "directory", + "description": "Results of the agrvate assessment", + "pattern": "*-results" + } + } + ], + "versions_agrvate": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "agrvate": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "agrvate --version | sed 's/[^0-9.]//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "agrvate": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "agrvate --version | sed 's/[^0-9.]//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@abhi18av"], + "maintainers": ["@abhi18av"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } + }, + { + "name": "ale", + "path": "modules/nf-core/ale/meta.yml", + "type": "module", + "meta": { + "name": "ale", + "description": "ALE: assembly likelihood estimator.", + "keywords": ["reference-independent", "assembly", "evaluation"], + "tools": [ + { + "ale": { + "description": "ALE is a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies.", + "documentation": "https://portal.nersc.gov/dna/RD/Adv-Seq/ALE-doc/index.html#document-install", + "tool_dev_url": "https://github.com/sc932/ALE", + "doi": "10.1093/bioinformatics/bts723", + "licence": ["NCSA"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "asm": { + "type": "file", + "description": "Assembly in FASTA format", + "pattern": "*.{fasta,fa}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + }, + { + "bam": { + "type": "file", + "description": "BAM file containing sorted read mappings", + "pattern": "*.{bam}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + } + ] + ], + "output": { + "ale": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*_ALEoutput.txt": { + "type": "file", + "description": "Output TXT file containing ALE results", + "pattern": "*_ALEoutput.{txt}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + } + ] + ], + "versions_ale": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "ALE": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "20180904": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "ALE": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "20180904": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@rodtheo"], + "maintainers": ["@rodtheo"] }, - { - "amp_input": { - "type": "list", - "description": "The path to the directory containing the results for the AMP tools for each processed sample or a list of files corresponding to each file generated by AMP tools.", - "pattern": "[*amptool.tsv, *amptool.tsv]", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - { - "faa_input": { - "type": "file", - "description": "The path to the file corresponding to the respective protein fasta files with '.faa' extension. File names have to contain the corresponding sample name, i.e. sample_1.faa", - "pattern": "*.faa", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - }, - { - "gbk_input": { - "type": "file", - "description": "The path to the file corresponding to the respective annotated files with either '.gbk' or '.gbff' extensions. File names must contain the corresponding sample name, i.e. sample_1.faa where \"sample_1\" is the sample name.", - "pattern": "*.gbk", - "ontologies": [ + "pipelines": [ { - "edam": "http://edamontology.org/format_1936" + "name": "mag", + "version": "5.4.2" } - ] + ] + }, + { + "name": "alignoth", + "path": "modules/nf-core/alignoth/meta.yml", + "type": "module", + "meta": { + "name": "alignoth", + "description": "Creating alignment plots from bam files", + "keywords": ["genomics", "alignment", "visualization", "pileup", "plotting"], + "tools": [ + { + "alignoth": { + "description": "A tool for creating alignment plots from bam files.", + "homepage": "https://github.com/alignoth/alignoth/blob/v1.4.6/README.md", + "documentation": "https://github.com/alignoth/alignoth/blob/v1.4.6/README.md", + "tool_dev_url": "https://github.com/alignoth/alignoth", + "doi": "10.1093/bioinformatics/btaf663", + "licence": ["MIT"], + "identifier": "biotools:alignoth" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "bam": { + "type": "file", + "description": "Sorted BAM/CRAM/SAM file to be visualized", + "pattern": "*.{bam,cram,sam}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + }, + { + "edam": "http://edamontology.org/format_2573" + }, + { + "edam": "http://edamontology.org/format_3462" + } + ] + } + }, + { + "bai": { + "type": "file", + "description": "Index file for the BAM/CRAM/SAM file", + "pattern": "*.{bai,crai}", + "ontologies": [] + } + }, + { + "fasta": { + "type": "file", + "description": "Reference fasta file", + "pattern": "*.{fa,fasta}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + }, + { + "fai": { + "type": "file", + "description": "Index file for the reference fasta file", + "pattern": "*.{fa,fasta}.fai", + "ontologies": [] + } + }, + { + "bed": { + "type": "file", + "description": "Bed file with regions to be visualized (optional)", + "pattern": "*.bed", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3003" + } + ] + } + }, + { + "vcf": { + "type": "file", + "description": "VCF file with variants to be highlighted (optional)", + "pattern": "*.vcf", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + } + ] + } + }, + { + "tbi": { + "type": "file", + "description": "Index file for the VCF file", + "pattern": "*.vcf.tbi", + "ontologies": [] + } + } + ] + ], + "output": { + "html": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}.html": { + "type": "file", + "description": "HTML file with the alignment plot", + "pattern": "*.html", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2331" + } + ] + } + } + ] + ], + "output": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}": { + "type": "directory", + "description": "Output directory with the alignment plot and all intermediate files", + "pattern": "*" + } + } + ] + ], + "vl_json": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}.vl.json": { + "type": "file", + "description": "Vega-Lite JSON file with the alignment plot", + "pattern": "*.vl.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "versions_alignoth": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "alignoth": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "alignoth --version | sed 's/alignoth //g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "alignoth": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "alignoth --version | sed 's/alignoth //g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@famosab"], + "maintainers": ["@famosab"] } - }, - { - "opt_amp_db": { - "type": "string", - "description": "The name of the database to download and set up. This can either be 'DRAMP', 'APD' or 'UniRef100'.", - "pattern": "DRAMP|APD|UniRef100" + }, + { + "name": "allelecounter", + "path": "modules/nf-core/allelecounter/meta.yml", + "type": "module", + "meta": { + "name": "allelecounter", + "description": "Generates a count of coverage of alleles", + "keywords": ["allele", "count", "coverage"], + "tools": [ + { + "allelecounter": { + "description": "Takes a file of locations and a [cr|b]am file and generates a count of coverage of each allele at that location (given any filter settings)", + "homepage": "https://github.com/cancerit/alleleCount", + "documentation": "https://github.com/cancerit/alleleCount", + "tool_dev_url": "https://github.com/cancerit/alleleCount", + "licence": ["GPL 3.0"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + }, + { + "edam": "http://edamontology.org/format_3462" + }, + { + "edam": "http://edamontology.org/format_2573" + } + ] + } + }, + { + "input_index": { + "type": "file", + "description": "BAM/CRAM/SAM index file", + "pattern": "*.{bai,crai,sai}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3327" + }, + { + "edam": "http://edamontology.org/format_3462" + } + ] + } + } + ], + { + "loci": { + "type": "file", + "description": "loci file ", + "pattern": "*.{tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, + { + "fasta": { + "type": "file", + "description": "Input genome fasta file. Required when passing CRAM files.", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + "output": { + "allelecount": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.alleleCount": { + "type": "file", + "description": "Allele count file", + "pattern": "*.{alleleCount}", + "ontologies": [] + } + } + ] + ], + "versions_allelecounter": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "alleleCounter": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "alleleCounter --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "alleleCounter": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "alleleCounter --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@fullama", "@fbdtemme"], + "maintainers": ["@fullama", "@fbdtemme"] } - }, - { - "opt_amp_db_dir": { - "type": "directory", - "description": "The path to the folder containing the fasta and tsv database files.", - "pattern": "path/to/amp_*_database" + }, + { + "name": "ampcombi", + "path": "modules/nf-core/ampcombi/meta.yml", + "type": "module", + "meta": { + "name": "ampcombi", + "description": "A tool to parse and summarise results from antimicrobial peptides tools and present functional classification.", + "deprecated": true, + "keywords": [ + "antimicrobial peptides", + "amps", + "parsing", + "reporting", + "align", + "macrel", + "amplify", + "hmmsearch", + "neubi", + "ampir", + "DRAMP" + ], + "tools": [ + { + "ampcombi": { + "description": "This tool parses the results of amp prediction tools into a single table and aligns the hits against a reference database of antimicrobial peptides for functional classifications.", + "homepage": "https://github.com/Darcy220606/AMPcombi", + "documentation": "https://github.com/Darcy220606/AMPcombi", + "tool_dev_url": "https://github.com/Darcy220606/AMPcombi/tree/dev", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "amp_input": { + "type": "list", + "description": "The path to the directory containing the results for the AMP tools for each sample processed or a list of files corresponding to each file generated by AMP tools.", + "pattern": "[*amptool.tsv, *amptool.tsv]", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + { + "faa_input": { + "type": "file", + "description": "The path to the file corresponding to the respective protein fasta files with '.faa' extension. File names have to contain the corresponding sample name, i.e. sample_1.faa", + "pattern": "*.faa", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + }, + { + "opt_amp_db": { + "type": "directory", + "description": "The path to the folder containing the fasta and tsv database files.", + "pattern": "*/" + } + } + ], + "output": { + "sample_dir": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${meta.id}/": { + "type": "directory", + "description": "The output directory that contains the summary output and related alignment files for one sample.", + "pattern": "/*" + } + } + ] + ], + "txt": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${meta.id}/*diamond_matches.txt": { + "type": "file", + "description": "An alignment file containing the results from the DIAMOND alignment step done on all AMP hits.", + "pattern": "/*/*_diamond_matches.txt", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + } + ] + ], + "csv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${meta.id}/*ampcombi.csv": { + "type": "file", + "description": "A file containing the summary report of all predicted AMP hits from all AMP tools given as input and the corresponding taxonomic and functional classification from the alignment step.", + "pattern": "/*/*_ampcombi.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "faa": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${meta.id}/*amp.faa": { + "type": "file", + "description": "A fasta file containing the amino acid sequences of all predicted AMP hits.", + "pattern": "/*/*_amp.faa", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ] + ], + "summary_csv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "AMPcombi_summary.csv": { + "type": "file", + "description": "A file that concatenates all samples ampcombi summaries. This is activated with `--complete_summary true`.", + "pattern": "AMPcombi_summary.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "summary_html": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "AMPcombi_summary.html": { + "type": "file", + "description": "A file that concatenates all samples ampcombi summaries. This is activated with `--complete_summary true`.", + "pattern": "AMPcombi_summary.html", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2331" + } + ] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "A log file that captures the standard output ina log file. Can be activated by `--log`.", + "pattern": "*.log", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + } + ] + ], + "results_db": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "amp_ref_database/": { + "type": "directory", + "description": "If the AMP reference database is not provided by the user using the flag `--amp_database', by default the DRAMP database will be downloaded, filtered and stored in this folder.", + "pattern": "/amp_ref_database" + } + } + ] + ], + "results_db_dmnd": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "amp_ref_database/*.dmnd": { + "type": "file", + "description": "AMP reference database converted to DIAMOND database format.", + "pattern": "/amp_ref_database/*.dmnd", + "ontologies": [] + } + } + ] + ], + "results_db_fasta": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "amp_ref_database/*.clean.fasta": { + "type": "file", + "description": "AMP reference database fasta file, cleaned of diamond-incompatible characters.", + "pattern": "/amp_ref_database/*.clean.fasta", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ] + ], + "results_db_tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "amp_ref_database/*.tsv": { + "type": "file", + "description": "AMP reference database in tsv-format with two columns containing header and sequence.", + "pattern": "/amp_ref_database/*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_ampcombi": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "ampcombi": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "0.1.7": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "ampcombi": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "0.1.7": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@darcy220606", "@louperelo"], + "maintainers": ["@darcy220606", "@louperelo"] } - }, - { - "opt_interproscan": { - "type": "directory", - "description": "A path to a file corresponding to the respective tsv files containing protein classifications of the annotated CDSs. The file must be the raw output from InterProScan.", - "pattern": "*.tsv", - "ontologies": [ + }, + { + "name": "ampcombi2_cluster", + "path": "modules/nf-core/ampcombi2/cluster/meta.yml", + "type": "module", + "meta": { + "name": "ampcombi2_cluster", + "description": "A submodule that clusters the merged AMP hits generated from ampcombi2/parsetables and ampcombi2/complete using MMseqs2 cluster.", + "keywords": [ + "antimicrobial peptides", + "amps", + "parsing", + "reporting", + "align", + "clustering", + "mmseqs2" + ], + "tools": [ + { + "ampcombi2/cluster": { + "description": "A tool for clustering all AMP hits found across many samples and supporting many AMP prediction tools.", + "homepage": "https://github.com/paleobiotechnology/AMPcombi", + "documentation": "https://ampcombi.readthedocs.io", + "tool_dev_url": "https://github.com/paleobiotechnology/AMPcombi/tree/dev", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + { + "summary_file": { + "type": "file", + "description": "A file corresponding to the Ampcombi_summary.tsv that is generated by running 'ampcombi complete'. It is a file containing all the merged AMP results from all samples and all tools.", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + "output": { + "cluster_tsv": [ + { + "Ampcombi_summary_cluster.tsv": { + "type": "file", + "description": "A file containing all the results from the merged input table 'Ampcombi_summary.tsv', but also including the cluster id number. The clustering is done using MMseqs2 cluster.", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + "rep_cluster_tsv": [ + { + "Ampcombi_summary_cluster_representative_seq.tsv": { + "type": "file", + "description": "A file containing the representative sequences of the clusters estimated by the tool. The clustering is done using MMseqs2 cluster.", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + "log": [ + { + "Ampcombi_cluster.log": { + "type": "file", + "description": "A log file that captures the standard output for the entire process in a log file. Can be activated by `--log`.", + "pattern": "*.log", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + } + ], + "versions_ampcombi": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "ampcombi": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "ampcombi --version | sed 's/ampcombi //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "ampcombi": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "ampcombi --version | sed 's/ampcombi //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@darcy220606"], + "maintainers": ["@darcy220606", "@jasmezz"] + }, + "pipelines": [ { - "edam": "http://edamontology.org/format_3475" + "name": "funcscan", + "version": "3.0.0" } - ] - } - } - ], - "output": { - "sample_dir": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "${prefix}/": { - "type": "directory", - "description": "The output directory that contains the summary output and related alignment files for one sample.", - "pattern": "/*" - } - } - ] - ], - "full_log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "Ampcombi_parse_tables.log": { - "type": "file", - "description": "A log file that captures the standard output for the entire process in a log file. Can be activated by `--log`.", - "pattern": "Ampcombi_parse_tables.log", - "ontologies": [] - } - } - ] - ], - "db": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "amp_${opt_amp_db}_database/": { - "type": "directory", - "description": "If the AMP reference database ID is not provided by the user using the flag `--amp_database', by default the DRAMP database will be downloaded, filtered and stored in this folder.", - "pattern": "/amp_*_database" - } - } - ] - ], - "versions_ampcombi": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "ampcombi": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "ampcombi --version | sed 's/ampcombi //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "ampcombi": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "ampcombi --version | sed 's/ampcombi //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } ] - ] - }, - "authors": [ - "@darcy220606" - ], - "maintainers": [ - "@darcy220606", - "@jasmezz" - ] - }, - "pipelines": [ - { - "name": "funcscan", - "version": "3.0.0" - } - ] - }, - { - "name": "ampir", - "path": "modules/nf-core/ampir/meta.yml", - "type": "module", - "meta": { - "name": "ampir", - "description": "A fast and user-friendly method to predict antimicrobial peptides (AMPs) from any given size protein dataset. ampir uses a supervised statistical machine learning approach to predict AMPs.", - "keywords": [ - "ampir", - "amp", - "antimicrobial peptide prediction" - ], - "tools": [ - { - "ampir": { - "description": "A toolkit to predict antimicrobial peptides from protein sequences on a genome-wide scale.", - "homepage": "https://github.com/Legana/ampir", - "documentation": "https://cran.r-project.org/web/packages/ampir/index.html", - "tool_dev_url": "https://github.com/Legana/ampir", - "doi": "10.1093/bioinformatics/btaa653", - "licence": [ - "GPL v2" - ], - "identifier": "biotools:ampir" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + }, + { + "name": "ampcombi2_complete", + "path": "modules/nf-core/ampcombi2/complete/meta.yml", + "type": "module", + "meta": { + "name": "ampcombi2_complete", + "description": "A submodule that merges all output summary tables from ampcombi/parsetables in one summary file.", + "keywords": [ + "antimicrobial peptides", + "amps", + "parsing", + "reporting", + "align", + "macrel", + "amplify", + "hmmsearch", + "neubi", + "ampir", + "ampgram", + "amptransformer", + "DRAMP" + ], + "tools": [ + { + "ampcombi2/complete": { + "description": "This merges the per sample AMPcombi summaries generated by running 'ampcombi2/parsetables'.", + "homepage": "https://github.com/paleobiotechnology/AMPcombi", + "documentation": "https://ampcombi.readthedocs.io", + "tool_dev_url": "https://github.com/paleobiotechnology/AMPcombi/tree/dev", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + { + "summaries": { + "type": "list", + "description": "The path to the list of files corresponding to each sample as generated by ampcombi2/parsetables.", + "pattern": "[*_ampcombi.tsv, *_ampcombi.tsv]", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + "output": { + "tsv": [ + { + "Ampcombi_summary.tsv": { + "type": "file", + "description": "A file containing the complete AMPcombi summaries from all processed samples.", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + "log": [ + { + "Ampcombi_complete.log": { + "type": "file", + "description": "A log file that captures the standard output for the entire process in a log file. Can be activated by `--log`.", + "pattern": "*.log", + "ontologies": [] + } + } + ], + "versions_ampcombi": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "ampcombi": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "ampcombi --version | sed 's/ampcombi //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "ampcombi": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "ampcombi --version | sed 's/ampcombi //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@darcy220606"], + "maintainers": ["@darcy220606", "@jasmezz"] }, - { - "faa": { - "type": "file", - "description": "FASTA file containing amino acid sequences", - "pattern": "*.{faa,fasta}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - { - "model": { - "type": "string", - "description": "Built-in model for AMP prediction", - "pattern": "{precursor,mature}" - } - }, - { - "min_length": { - "type": "integer", - "description": "Minimum protein length for which predictions will be generated", - "pattern": "[0-9]+" - } - }, - { - "min_probability": { - "type": "float", - "description": "Cut-off for AMP prediction", - "pattern": "[0-9].[0-9]+" - } - } - ], - "output": { - "amps_faa": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.faa": { - "type": "file", - "description": "File containing AMP predictions in amino acid FASTA format", - "pattern": "*.{faa}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ], - "amps_tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "File containing AMP predictions in TSV format", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_ampir": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "ampir": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "Rscript -e \"library(ampir); cat(paste((unlist(packageVersion('ampir'))), collapse = '.'))\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "ampir": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "Rscript -e \"library(ampir); cat(paste((unlist(packageVersion('ampir'))), collapse = '.'))\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "funcscan", + "version": "3.0.0" + } ] - ] - }, - "authors": [ - "@jasmezz" - ], - "maintainers": [ - "@jasmezz" - ] - }, - "pipelines": [ - { - "name": "funcscan", - "version": "3.0.0" - } - ] - }, - { - "name": "amplify_predict", - "path": "modules/nf-core/amplify/predict/meta.yml", - "type": "module", - "meta": { - "name": "amplify_predict", - "description": "AMPlify is an attentive deep learning model for antimicrobial peptide prediction.", - "keywords": [ - "antimicrobial peptides", - "AMPs", - "prediction", - "model" - ], - "tools": [ - { - "amplify": { - "description": "Attentive deep learning model for antimicrobial peptide prediction", - "homepage": "https://github.com/bcgsc/AMPlify", - "documentation": "https://github.com/bcgsc/AMPlify", - "tool_dev_url": "https://github.com/bcgsc/AMPlify", - "doi": "10.1186/s12864-022-08310-4", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:amplify" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + }, + { + "name": "ampcombi2_parsetables", + "path": "modules/nf-core/ampcombi2/parsetables/meta.yml", + "type": "module", + "meta": { + "name": "ampcombi2_parsetables", + "description": "A submodule that parses and standardizes the results from various antimicrobial peptide identification tools.", + "keywords": [ + "antimicrobial peptides", + "amps", + "parsing", + "reporting", + "align", + "macrel", + "amplify", + "hmmsearch", + "neubi", + "ampir", + "ampgram", + "amptransformer", + "DRAMP", + "MMseqs2", + "InterProScan" + ], + "tools": [ + { + "ampcombi2/parsetables": { + "description": "A parsing tool to convert and summarise the outputs from multiple AMP detection tools in a standardized format.", + "homepage": "https://github.com/paleobiotechnology/AMPcombi", + "documentation": "https://ampcombi.readthedocs.io", + "tool_dev_url": "https://github.com/paleobiotechnology/AMPcombi/tree/dev", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "amp_input": { + "type": "list", + "description": "The path to the directory containing the results for the AMP tools for each processed sample or a list of files corresponding to each file generated by AMP tools.", + "pattern": "[*amptool.tsv, *amptool.tsv]", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + { + "faa_input": { + "type": "file", + "description": "The path to the file corresponding to the respective protein fasta files with '.faa' extension. File names have to contain the corresponding sample name, i.e. sample_1.faa", + "pattern": "*.faa", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + }, + { + "gbk_input": { + "type": "file", + "description": "The path to the file corresponding to the respective annotated files with either '.gbk' or '.gbff' extensions. File names must contain the corresponding sample name, i.e. sample_1.faa where \"sample_1\" is the sample name.", + "pattern": "*.gbk", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1936" + } + ] + } + }, + { + "opt_amp_db": { + "type": "string", + "description": "The name of the database to download and set up. This can either be 'DRAMP', 'APD' or 'UniRef100'.", + "pattern": "DRAMP|APD|UniRef100" + } + }, + { + "opt_amp_db_dir": { + "type": "directory", + "description": "The path to the folder containing the fasta and tsv database files.", + "pattern": "path/to/amp_*_database" + } + }, + { + "opt_interproscan": { + "type": "directory", + "description": "A path to a file corresponding to the respective tsv files containing protein classifications of the annotated CDSs. The file must be the raw output from InterProScan.", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + "output": { + "sample_dir": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}/": { + "type": "directory", + "description": "The output directory that contains the summary output and related alignment files for one sample.", + "pattern": "/*" + } + } + ] + ], + "full_log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "Ampcombi_parse_tables.log": { + "type": "file", + "description": "A log file that captures the standard output for the entire process in a log file. Can be activated by `--log`.", + "pattern": "Ampcombi_parse_tables.log", + "ontologies": [] + } + } + ] + ], + "db": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "amp_${opt_amp_db}_database/": { + "type": "directory", + "description": "If the AMP reference database ID is not provided by the user using the flag `--amp_database', by default the DRAMP database will be downloaded, filtered and stored in this folder.", + "pattern": "/amp_*_database" + } + } + ] + ], + "versions_ampcombi": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "ampcombi": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "ampcombi --version | sed 's/ampcombi //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "ampcombi": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "ampcombi --version | sed 's/ampcombi //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@darcy220606"], + "maintainers": ["@darcy220606", "@jasmezz"] }, - { - "faa": { - "type": "file", - "description": "amino acid sequences fasta", - "pattern": "*.{fa,fa.gz,faa,faa.gz,fasta,fasta.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - { - "model_dir": { - "type": "directory", - "description": "Directory of where models are stored (optional)" - } - } - ], - "output": { - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "amino acid sequences with prediction (AMP, non-AMP) and probability scores", - "pattern": "*.{tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_amplify": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "AMPlify": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "AMPlify --help 2>&1 | sed -n 's/AMPlify v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "AMPlify": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "AMPlify --help 2>&1 | sed -n 's/AMPlify v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@louperelo" - ], - "maintainers": [ - "@louperelo" - ] - }, - "pipelines": [ - { - "name": "funcscan", - "version": "3.0.0" - } - ] - }, - { - "name": "amps", - "path": "modules/nf-core/amps/meta.yml", - "type": "module", - "meta": { - "name": "amps", - "description": "Post-processing script of the MaltExtract component of the HOPS package", - "keywords": [ - "malt", - "MaltExtract", - "HOPS", - "amps", - "alignment", - "metagenomics", - "ancient DNA", - "aDNA", - "palaeogenomics", - "archaeogenomics", - "microbiome", - "authentication", - "damage", - "edit distance", - "post Post-processing", - "visualisation" - ], - "tools": [ - { - "amps": { - "description": "Post-processing script of the MaltExtract tool for ancient metagenomics", - "homepage": "https://github.com/rhuebler/HOPS", - "documentation": "https://github.com/keyfm/amps", - "tool_dev_url": "https://github.com/keyfm/amps", - "doi": "10.1186/s13059-019-1903-0", - "licence": [ - "GPL >=3" - ], - "identifier": "" - } - } - ], - "input": [ - { - "maltextract_results": { - "type": "directory", - "description": "MaltExtract output directory", - "pattern": "results/" - } - }, - { - "taxon_list": { - "type": "file", - "description": "List of target taxa to evaluate used in MaltExtract", - "pattern": "*.txt", - "ontologies": [ + "pipelines": [ { - "edam": "http://edamontology.org/format_2330" + "name": "funcscan", + "version": "3.0.0" } - ] - } - }, - { - "filter": { - "type": "string", - "description": "The filter mode used in MaltExtract", - "pattern": "def_anc|default|scan|ancient|crawl", - "ontologies": [] - } - } - ], - "output": { - "json": [ - { - "results/heatmap_overview_Wevid.json": { - "type": "file", - "description": "Candidate summary heatmap in MultiQC compatible JSON format", - "pattern": "heatmap_overview_Wevid.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ], - "summary_pdf": [ - { - "results/heatmap_overview_Wevid.pdf": { - "type": "file", - "description": "Candidate summary heatmap in PDF format", - "pattern": "heatmap_overview_Wevid.pdf", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3508" - } - ] - } - } - ], - "tsv": [ - { - "results/heatmap_overview_Wevid.tsv": { - "type": "file", - "description": "Candidate summary heatmap in TSV format", - "pattern": "heatmap_overview_Wevid.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - "candidate_pdfs": [ - { - "results/pdf_candidate_profiles/": { - "type": "directory", - "description": "Directory of per sample output PDFs organised by reference", - "pattern": "pdf_candidate_profiles/" - } - } - ], - "versions_hops": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "hops": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "hops --version 2>&1 | sed 's/HOPS version//' ": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "hops": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "hops --version 2>&1 | sed 's/HOPS version//' ": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } ] - ] - }, - "authors": [ - "@jfy133" - ], - "maintainers": [ - "@jfy133" - ] - } - }, - { - "name": "amrfinderplus_run", - "path": "modules/nf-core/amrfinderplus/run/meta.yml", - "type": "module", - "meta": { - "name": "amrfinderplus_run", - "description": "Identify antimicrobial resistance in gene or protein sequences", - "keywords": [ - "bacteria", - "fasta", - "antibiotic resistance" - ], - "tools": [ - { - "amrfinderplus": { - "description": "AMRFinderPlus finds antimicrobial resistance and other genes in protein or nucleotide sequences.", - "homepage": "https://github.com/ncbi/amr/wiki", - "documentation": "https://github.com/ncbi/amr/wiki", - "tool_dev_url": "https://github.com/ncbi/amr", - "doi": "10.1038/s41598-021-91456-0", - "licence": [ - "Public Domain" - ], - "identifier": "biotools:amrfinderplus" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + }, + { + "name": "ampir", + "path": "modules/nf-core/ampir/meta.yml", + "type": "module", + "meta": { + "name": "ampir", + "description": "A fast and user-friendly method to predict antimicrobial peptides (AMPs) from any given size protein dataset. ampir uses a supervised statistical machine learning approach to predict AMPs.", + "keywords": ["ampir", "amp", "antimicrobial peptide prediction"], + "tools": [ + { + "ampir": { + "description": "A toolkit to predict antimicrobial peptides from protein sequences on a genome-wide scale.", + "homepage": "https://github.com/Legana/ampir", + "documentation": "https://cran.r-project.org/web/packages/ampir/index.html", + "tool_dev_url": "https://github.com/Legana/ampir", + "doi": "10.1093/bioinformatics/btaa653", + "licence": ["GPL v2"], + "identifier": "biotools:ampir" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "faa": { + "type": "file", + "description": "FASTA file containing amino acid sequences", + "pattern": "*.{faa,fasta}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + { + "model": { + "type": "string", + "description": "Built-in model for AMP prediction", + "pattern": "{precursor,mature}" + } + }, + { + "min_length": { + "type": "integer", + "description": "Minimum protein length for which predictions will be generated", + "pattern": "[0-9]+" + } + }, + { + "min_probability": { + "type": "float", + "description": "Cut-off for AMP prediction", + "pattern": "[0-9].[0-9]+" + } + } + ], + "output": { + "amps_faa": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.faa": { + "type": "file", + "description": "File containing AMP predictions in amino acid FASTA format", + "pattern": "*.{faa}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ] + ], + "amps_tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "File containing AMP predictions in TSV format", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_ampir": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "ampir": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "Rscript -e \"library(ampir); cat(paste((unlist(packageVersion('ampir'))), collapse = '.'))\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "ampir": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "Rscript -e \"library(ampir); cat(paste((unlist(packageVersion('ampir'))), collapse = '.'))\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@jasmezz"], + "maintainers": ["@jasmezz"] }, - { - "fasta": { - "type": "file", - "description": "Nucleotide or protein sequences in FASTA format", - "pattern": "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - { - "db": { - "type": "file", - "description": "A compressed tarball of the AMRFinderPlus database to query", - "pattern": "*.tar.gz", - "ontologies": [ + "pipelines": [ { - "edam": "http://edamontology.org/format_3981" + "name": "funcscan", + "version": "3.0.0" + } + ] + }, + { + "name": "amplify_predict", + "path": "modules/nf-core/amplify/predict/meta.yml", + "type": "module", + "meta": { + "name": "amplify_predict", + "description": "AMPlify is an attentive deep learning model for antimicrobial peptide prediction.", + "keywords": ["antimicrobial peptides", "AMPs", "prediction", "model"], + "tools": [ + { + "amplify": { + "description": "Attentive deep learning model for antimicrobial peptide prediction", + "homepage": "https://github.com/bcgsc/AMPlify", + "documentation": "https://github.com/bcgsc/AMPlify", + "tool_dev_url": "https://github.com/bcgsc/AMPlify", + "doi": "10.1186/s12864-022-08310-4", + "licence": ["GPL v3"], + "identifier": "biotools:amplify" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "faa": { + "type": "file", + "description": "amino acid sequences fasta", + "pattern": "*.{fa,fa.gz,faa,faa.gz,fasta,fasta.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + { + "model_dir": { + "type": "directory", + "description": "Directory of where models are stored (optional)" + } + } + ], + "output": { + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "amino acid sequences with prediction (AMP, non-AMP) and probability scores", + "pattern": "*.{tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_amplify": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "AMPlify": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "AMPlify --help 2>&1 | sed -n 's/AMPlify v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "AMPlify": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "AMPlify --help 2>&1 | sed -n 's/AMPlify v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] }, + "authors": ["@louperelo"], + "maintainers": ["@louperelo"] + }, + "pipelines": [ { - "edam": "http://edamontology.org/format_3989" + "name": "funcscan", + "version": "3.0.0" } - ] - } - } - ], - "output": { - "report": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.tsv": { - "type": "file", - "description": "AMRFinder+ final report", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "mutation_report": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}-mutations.tsv": { - "type": "file", - "description": "Report of organism-specific point-mutations", - "pattern": "*-mutations.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "tool_version": [ - { - "VER": { - "type": "string", - "description": "The version of the tool in string format (useful for downstream tools such as hAMRronization)" - } - } - ], - "db_version": [ - { - "DBVER": { - "type": "string", - "description": "The version of the used database in string format (useful for downstream tools such as hAMRronization)" - } - } - ], - "versions_amrfinderplus": [ - [ - { - "${task.process}": { - "type": "string", - "description": "Process name" - } - }, - { - "amrfinderplus": { - "type": "string", - "description": "Tool name" - } - }, - { - "amrfinder --version": { - "type": "string", - "description": "Tool version command" - } - } - ] - ], - "versions_amrfinderplus_database": [ - [ - { - "${task.process}": { - "type": "string", - "description": "Process name" - } - }, - { - "amrfinderplus_database": { - "type": "string", - "description": "Database name" - } - }, - { - "amrfinder --database amrfinderdb --database_version 2>&1 | grep -oE '[0-9]{4}-[0-9]{2}-[0-9]{2}\\.[0-9]+' | tail -1": { - "type": "string", - "description": "Database version command" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "Process name" - } - }, - { - "amrfinderplus": { - "type": "string", - "description": "Tool name" - } - }, - { - "amrfinder --version": { - "type": "string", - "description": "Tool version command" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "Process name" - } - }, - { - "amrfinderplus_database": { - "type": "string", - "description": "Database name" - } - }, - { - "amrfinder --database amrfinderdb --database_version 2>&1 | grep -oE '[0-9]{4}-[0-9]{2}-[0-9]{2}\\.[0-9]+' | tail -1": { - "type": "string", - "description": "Database version command" - } - } - ] - ] - }, - "authors": [ - "@rpetit3", - "@louperelo", - "@jfy133" - ], - "maintainers": [ - "@rpetit3", - "@louperelo", - "@jfy133" - ] - }, - "pipelines": [ - { - "name": "funcscan", - "version": "3.0.0" - } - ] - }, - { - "name": "amrfinderplus_update", - "path": "modules/nf-core/amrfinderplus/update/meta.yml", - "type": "module", - "meta": { - "name": "amrfinderplus_update", - "description": "Identify antimicrobial resistance in gene or protein sequences", - "keywords": [ - "bacteria", - "fasta", - "antibiotic resistance" - ], - "tools": [ - { - "amrfinderplus": { - "description": "AMRFinderPlus finds antimicrobial resistance and other genes in protein or nucleotide sequences.", - "homepage": "https://github.com/ncbi/amr/wiki", - "documentation": "https://github.com/ncbi/amr/wiki", - "tool_dev_url": "https://github.com/ncbi/amr", - "doi": "10.1038/s41598-021-91456-0", - "licence": [ - "Public Domain" - ], - "identifier": "biotools:amrfinderplus" - } - } - ], - "input": [], - "output": { - "db": [ - { - "amrfinderdb.tar.gz": { - "type": "file", - "description": "The latest AMRFinder+ database in a compressed tarball", - "pattern": "*.tar.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3981" - }, - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ], - "versions_amrfinder": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "amrfinder": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "amrfinder --version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "amrfinder": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "amrfinder --version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } ] - ] - }, - "authors": [ - "@rpetit3" - ], - "maintainers": [ - "@rpetit3" - ] - }, - "pipelines": [ - { - "name": "funcscan", - "version": "3.0.0" - } - ] - }, - { - "name": "amulety_antiberta2", - "path": "modules/nf-core/amulety/antiberta2/meta.yml", - "type": "module", - "meta": { - "name": "amulety_antiberta2", - "description": "A module to create antiberta2 embeddings of antibody (BCR) amino acid sequences using amulety.", - "deprecated": true, - "keywords": [ - "embeddings", - "BCR", - "antibody", - "GPU-accelerated", - "immunoinformatics", - "immunology" - ], - "tools": [ - { - "amulety": { - "description": "Python package to create embeddings of BCR and TCR amino acid sequences.", - "homepage": "https://amulety.readthedocs.io/en/latest/", - "documentation": "https://amulety.readthedocs.io/en/latest/", - "tool_dev_url": "https://github.com/immcantation/amulety", - "doi": "10.1101/2025.03.21.644583", - "licence": [ - "GPL v3" - ], - "identifier": "" + }, + { + "name": "amps", + "path": "modules/nf-core/amps/meta.yml", + "type": "module", + "meta": { + "name": "amps", + "description": "Post-processing script of the MaltExtract component of the HOPS package", + "keywords": [ + "malt", + "MaltExtract", + "HOPS", + "amps", + "alignment", + "metagenomics", + "ancient DNA", + "aDNA", + "palaeogenomics", + "archaeogenomics", + "microbiome", + "authentication", + "damage", + "edit distance", + "post Post-processing", + "visualisation" + ], + "tools": [ + { + "amps": { + "description": "Post-processing script of the MaltExtract tool for ancient metagenomics", + "homepage": "https://github.com/rhuebler/HOPS", + "documentation": "https://github.com/keyfm/amps", + "tool_dev_url": "https://github.com/keyfm/amps", + "doi": "10.1186/s13059-019-1903-0", + "licence": ["GPL >=3"], + "identifier": "" + } + } + ], + "input": [ + { + "maltextract_results": { + "type": "directory", + "description": "MaltExtract output directory", + "pattern": "results/" + } + }, + { + "taxon_list": { + "type": "file", + "description": "List of target taxa to evaluate used in MaltExtract", + "pattern": "*.txt", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + }, + { + "filter": { + "type": "string", + "description": "The filter mode used in MaltExtract", + "pattern": "def_anc|default|scan|ancient|crawl", + "ontologies": [] + } + } + ], + "output": { + "json": [ + { + "results/heatmap_overview_Wevid.json": { + "type": "file", + "description": "Candidate summary heatmap in MultiQC compatible JSON format", + "pattern": "heatmap_overview_Wevid.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ], + "summary_pdf": [ + { + "results/heatmap_overview_Wevid.pdf": { + "type": "file", + "description": "Candidate summary heatmap in PDF format", + "pattern": "heatmap_overview_Wevid.pdf", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3508" + } + ] + } + } + ], + "tsv": [ + { + "results/heatmap_overview_Wevid.tsv": { + "type": "file", + "description": "Candidate summary heatmap in TSV format", + "pattern": "heatmap_overview_Wevid.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + "candidate_pdfs": [ + { + "results/pdf_candidate_profiles/": { + "type": "directory", + "description": "Directory of per sample output PDFs organised by reference", + "pattern": "pdf_candidate_profiles/" + } + } + ], + "versions_hops": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "hops": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "hops --version 2>&1 | sed 's/HOPS version//' ": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "hops": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "hops --version 2>&1 | sed 's/HOPS version//' ": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@jfy133"], + "maintainers": ["@jfy133"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } + }, + { + "name": "amrfinderplus_run", + "path": "modules/nf-core/amrfinderplus/run/meta.yml", + "type": "module", + "meta": { + "name": "amrfinderplus_run", + "description": "Identify antimicrobial resistance in gene or protein sequences", + "keywords": ["bacteria", "fasta", "antibiotic resistance"], + "tools": [ + { + "amrfinderplus": { + "description": "AMRFinderPlus finds antimicrobial resistance and other genes in protein or nucleotide sequences.", + "homepage": "https://github.com/ncbi/amr/wiki", + "documentation": "https://github.com/ncbi/amr/wiki", + "tool_dev_url": "https://github.com/ncbi/amr", + "doi": "10.1038/s41598-021-91456-0", + "licence": ["Public Domain"], + "identifier": "biotools:amrfinderplus" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Nucleotide or protein sequences in FASTA format", + "pattern": "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + { + "db": { + "type": "file", + "description": "A compressed tarball of the AMRFinderPlus database to query", + "pattern": "*.tar.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3981" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ], + "output": { + "report": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.tsv": { + "type": "file", + "description": "AMRFinder+ final report", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "mutation_report": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}-mutations.tsv": { + "type": "file", + "description": "Report of organism-specific point-mutations", + "pattern": "*-mutations.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "tool_version": [ + { + "VER": { + "type": "string", + "description": "The version of the tool in string format (useful for downstream tools such as hAMRronization)" + } + } + ], + "db_version": [ + { + "DBVER": { + "type": "string", + "description": "The version of the used database in string format (useful for downstream tools such as hAMRronization)" + } + } + ], + "versions_amrfinderplus": [ + [ + { + "${task.process}": { + "type": "string", + "description": "Process name" + } + }, + { + "amrfinderplus": { + "type": "string", + "description": "Tool name" + } + }, + { + "amrfinder --version": { + "type": "string", + "description": "Tool version command" + } + } + ] + ], + "versions_amrfinderplus_database": [ + [ + { + "${task.process}": { + "type": "string", + "description": "Process name" + } + }, + { + "amrfinderplus_database": { + "type": "string", + "description": "Database name" + } + }, + { + "amrfinder --database amrfinderdb --database_version 2>&1 | grep -oE '[0-9]{4}-[0-9]{2}-[0-9]{2}\\.[0-9]+' | tail -1": { + "type": "string", + "description": "Database version command" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "Process name" + } + }, + { + "amrfinderplus": { + "type": "string", + "description": "Tool name" + } + }, + { + "amrfinder --version": { + "type": "string", + "description": "Tool version command" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "Process name" + } + }, + { + "amrfinderplus_database": { + "type": "string", + "description": "Database name" + } + }, + { + "amrfinder --database amrfinderdb --database_version 2>&1 | grep -oE '[0-9]{4}-[0-9]{2}-[0-9]{2}\\.[0-9]+' | tail -1": { + "type": "string", + "description": "Database version command" + } + } + ] + ] + }, + "authors": ["@rpetit3", "@louperelo", "@jfy133"], + "maintainers": ["@rpetit3", "@louperelo", "@jfy133"] }, - { - "tsv": { - "type": "file", - "description": "TSV with BCR/TCR nucleotide sequences in AIRR rearrangement format", - "pattern": "*.{tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - { - "chain": { - "type": "string", - "description": "The chain to use for the embeddings. Can be either 'H' (heavy) or 'HL' (heavy + light, for single-cell data).\n" - } - } - ], - "output": { - "embedding": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "TSV with antiberta2 embeddings.", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } + "pipelines": [ + { + "name": "funcscan", + "version": "3.0.0" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@ggabernet" - ], - "maintainers": [ - "@ggabernet" - ] - } - }, - { - "name": "amulety_antiberty", - "path": "modules/nf-core/amulety/antiberty/meta.yml", - "type": "module", - "meta": { - "name": "amulety_antiberty", - "description": "A module to create antiberty embeddings of antibody (BCR) amino acid sequences using amulety.", - "deprecated": true, - "keywords": [ - "embeddings", - "BCR", - "antibody", - "GPU-accelerated", - "immunoinformatics", - "immunology" - ], - "tools": [ - { - "amulety": { - "description": "Python package to create embeddings of BCR and TCR amino acid sequences.", - "homepage": "https://amulety.readthedocs.io/en/latest/", - "documentation": "https://amulety.readthedocs.io/en/latest/", - "tool_dev_url": "https://github.com/immcantation/amulety", - "doi": "10.1101/2025.03.21.644583", - "licence": [ - "GPL v3" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } + }, + { + "name": "amrfinderplus_update", + "path": "modules/nf-core/amrfinderplus/update/meta.yml", + "type": "module", + "meta": { + "name": "amrfinderplus_update", + "description": "Identify antimicrobial resistance in gene or protein sequences", + "keywords": ["bacteria", "fasta", "antibiotic resistance"], + "tools": [ + { + "amrfinderplus": { + "description": "AMRFinderPlus finds antimicrobial resistance and other genes in protein or nucleotide sequences.", + "homepage": "https://github.com/ncbi/amr/wiki", + "documentation": "https://github.com/ncbi/amr/wiki", + "tool_dev_url": "https://github.com/ncbi/amr", + "doi": "10.1038/s41598-021-91456-0", + "licence": ["Public Domain"], + "identifier": "biotools:amrfinderplus" + } + } + ], + "input": [], + "output": { + "db": [ + { + "amrfinderdb.tar.gz": { + "type": "file", + "description": "The latest AMRFinder+ database in a compressed tarball", + "pattern": "*.tar.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3981" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ], + "versions_amrfinder": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "amrfinder": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "amrfinder --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "amrfinder": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "amrfinder --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@rpetit3"], + "maintainers": ["@rpetit3"] }, - { - "tsv": { - "type": "file", - "description": "TSV with BCR/TCR nucleotide sequences in AIRR rearrangement format", - "pattern": "*.{tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - { - "chain": { - "type": "string", - "description": "The chain to use for the embeddings. Can be either 'H' (heavy) or 'HL' (heavy + light, for single-cell data).\n" - } - } - ], - "output": { - "embedding": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "TSV with Antiberty embeddings.", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } + "pipelines": [ + { + "name": "funcscan", + "version": "3.0.0" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } + }, + { + "name": "amulety_antiberta2", + "path": "modules/nf-core/amulety/antiberta2/meta.yml", + "type": "module", + "meta": { + "name": "amulety_antiberta2", + "description": "A module to create antiberta2 embeddings of antibody (BCR) amino acid sequences using amulety.", + "deprecated": true, + "keywords": ["embeddings", "BCR", "antibody", "GPU-accelerated", "immunoinformatics", "immunology"], + "tools": [ + { + "amulety": { + "description": "Python package to create embeddings of BCR and TCR amino acid sequences.", + "homepage": "https://amulety.readthedocs.io/en/latest/", + "documentation": "https://amulety.readthedocs.io/en/latest/", + "tool_dev_url": "https://github.com/immcantation/amulety", + "doi": "10.1101/2025.03.21.644583", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "tsv": { + "type": "file", + "description": "TSV with BCR/TCR nucleotide sequences in AIRR rearrangement format", + "pattern": "*.{tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + { + "chain": { + "type": "string", + "description": "The chain to use for the embeddings. Can be either 'H' (heavy) or 'HL' (heavy + light, for single-cell data).\n" + } + } + ], + "output": { + "embedding": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "TSV with antiberta2 embeddings.", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@ggabernet"], + "maintainers": ["@ggabernet"] } - ] - }, - "authors": [ - "@ggabernet" - ], - "maintainers": [ - "@ggabernet" - ] - } - }, - { - "name": "amulety_balmpaired", - "path": "modules/nf-core/amulety/balmpaired/meta.yml", - "type": "module", - "meta": { - "name": "amulety_balmpaired", - "description": "A module to create BALM paired embeddings of antibody (BCR) amino acid sequences using amulety.", - "deprecated": true, - "keywords": [ - "embeddings", - "BCR", - "antibody", - "GPU-accelerated", - "immunoinformatics", - "immunology" - ], - "tools": [ - { - "amulety": { - "description": "Python package to create embeddings of BCR and TCR amino acid sequences.", - "homepage": "https://amulety.readthedocs.io/en/latest/", - "documentation": "https://amulety.readthedocs.io/en/latest/", - "tool_dev_url": "https://github.com/immcantation/amulety", - "doi": "10.1101/2025.03.21.644583", - "licence": [ - "GPL v3" - ], - "identifier": "" + }, + { + "name": "amulety_antiberty", + "path": "modules/nf-core/amulety/antiberty/meta.yml", + "type": "module", + "meta": { + "name": "amulety_antiberty", + "description": "A module to create antiberty embeddings of antibody (BCR) amino acid sequences using amulety.", + "deprecated": true, + "keywords": ["embeddings", "BCR", "antibody", "GPU-accelerated", "immunoinformatics", "immunology"], + "tools": [ + { + "amulety": { + "description": "Python package to create embeddings of BCR and TCR amino acid sequences.", + "homepage": "https://amulety.readthedocs.io/en/latest/", + "documentation": "https://amulety.readthedocs.io/en/latest/", + "tool_dev_url": "https://github.com/immcantation/amulety", + "doi": "10.1101/2025.03.21.644583", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "tsv": { + "type": "file", + "description": "TSV with BCR/TCR nucleotide sequences in AIRR rearrangement format", + "pattern": "*.{tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + { + "chain": { + "type": "string", + "description": "The chain to use for the embeddings. Can be either 'H' (heavy) or 'HL' (heavy + light, for single-cell data).\n" + } + } + ], + "output": { + "embedding": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "TSV with Antiberty embeddings.", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@ggabernet"], + "maintainers": ["@ggabernet"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "tsv": { - "type": "file", - "description": "TSV with BCR/TCR nucleotide sequences in AIRR rearrangement format", - "pattern": "*.{tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - { - "chain": { - "type": "string", - "description": "The chain to use for the embeddings. Can be either 'H' (heavy) or 'HL' (heavy + light, for single-cell data).\n" - } - } - ], - "output": { - "embedding": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "TSV with BALM paired embeddings.", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@ggabernet" - ], - "maintainers": [ - "@ggabernet" - ] - } - }, - { - "name": "amulety_embed", - "path": "modules/nf-core/amulety/embed/meta.yml", - "type": "module", - "meta": { - "name": "amulety_embed", - "description": "A module to create embeddings of B-cell receptor (BCR) or T-cell receptor (TCR) amino acid sequences using amulety.", - "keywords": [ - "embeddings", - "BCR", - "antibody", - "GPU-accelerated", - "immunoinformatics", - "immunology" - ], - "tools": [ - { - "amulety": { - "description": "Python package to create embeddings of BCR and TCR amino acid sequences.", - "homepage": "https://amulety.readthedocs.io/en/latest/", - "documentation": "https://amulety.readthedocs.io/en/latest/", - "tool_dev_url": "https://github.com/immcantation/amulety", - "doi": "10.1101/2025.03.21.644583", - "licence": [ - "GPL v3" - ], - "identifier": "" + }, + { + "name": "amulety_balmpaired", + "path": "modules/nf-core/amulety/balmpaired/meta.yml", + "type": "module", + "meta": { + "name": "amulety_balmpaired", + "description": "A module to create BALM paired embeddings of antibody (BCR) amino acid sequences using amulety.", + "deprecated": true, + "keywords": ["embeddings", "BCR", "antibody", "GPU-accelerated", "immunoinformatics", "immunology"], + "tools": [ + { + "amulety": { + "description": "Python package to create embeddings of BCR and TCR amino acid sequences.", + "homepage": "https://amulety.readthedocs.io/en/latest/", + "documentation": "https://amulety.readthedocs.io/en/latest/", + "tool_dev_url": "https://github.com/immcantation/amulety", + "doi": "10.1101/2025.03.21.644583", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "tsv": { + "type": "file", + "description": "TSV with BCR/TCR nucleotide sequences in AIRR rearrangement format", + "pattern": "*.{tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + { + "chain": { + "type": "string", + "description": "The chain to use for the embeddings. Can be either 'H' (heavy) or 'HL' (heavy + light, for single-cell data).\n" + } + } + ], + "output": { + "embedding": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "TSV with BALM paired embeddings.", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@ggabernet"], + "maintainers": ["@ggabernet"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } + }, + { + "name": "amulety_embed", + "path": "modules/nf-core/amulety/embed/meta.yml", + "type": "module", + "meta": { + "name": "amulety_embed", + "description": "A module to create embeddings of B-cell receptor (BCR) or T-cell receptor (TCR) amino acid sequences using amulety.", + "keywords": ["embeddings", "BCR", "antibody", "GPU-accelerated", "immunoinformatics", "immunology"], + "tools": [ + { + "amulety": { + "description": "Python package to create embeddings of BCR and TCR amino acid sequences.", + "homepage": "https://amulety.readthedocs.io/en/latest/", + "documentation": "https://amulety.readthedocs.io/en/latest/", + "tool_dev_url": "https://github.com/immcantation/amulety", + "doi": "10.1101/2025.03.21.644583", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "tsv": { + "type": "file", + "description": "TSV with BCR/TCR nucleotide sequences in AIRR rearrangement format", + "pattern": "*.{tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + { + "chain": { + "type": "string", + "description": "The chain to use for the embeddings. Can be either 'H' (high diversity chain: BCR heavy or TCR beta or delta),\n'L' (low diversity chain: BCR light or TCR alpha or gamma) or 'HL'/'LH' (BCR heavy + light, and TCR alpha + beta or gamma + delta).\n", + "enum": ["L", "H", "HL", "LH"] + } + }, + { + "model": { + "type": "string", + "description": "The embedding model to use. Options are detailed on the amulety documentation.\n" + } + } + ], + "output": { + "embedding": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${task.ext.prefix ?: meta.id}.tsv": { + "type": "file", + "description": "TSV with embeddings of BCR or TCR amino acid sequences.", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "embedding_metadata": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*metadata.tsv": { + "type": "file", + "description": "TSV with metadata about the embeddings.", + "pattern": "*metadata.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_amulety": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "amulety": { + "type": "string", + "description": "The tool name" + } + }, + { + "amulety --help 2>&1 | grep -o 'version [0-9\\.]\\+' | grep -o '[0-9\\.]\\+'": { + "type": "eval", + "description": "The command used to generate the version of the tool" + } + } + ] + ], + "versions_python": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "python": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python --version 2>&1 | grep -o 'Python [0-9\\.]\\+' | grep -o '[0-9\\.]\\+'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_pytorch": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "pytorch": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python -c 'import torch; print(torch.__version__)'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_transformers": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "transformers": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python -c 'import transformers; print(transformers.__version__)'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "amulety": { + "type": "string", + "description": "The tool name" + } + }, + { + "amulety --help 2>&1 | grep -o 'version [0-9\\.]\\+' | grep -o '[0-9\\.]\\+'": { + "type": "eval", + "description": "The command used to generate the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "python": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python --version 2>&1 | grep -o 'Python [0-9\\.]\\+' | grep -o '[0-9\\.]\\+'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "pytorch": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python -c 'import torch; print(torch.__version__)'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "transformers": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python -c 'import transformers; print(transformers.__version__)'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@ggabernet"], + "maintainers": ["@ggabernet"] }, - { - "tsv": { - "type": "file", - "description": "TSV with BCR/TCR nucleotide sequences in AIRR rearrangement format", - "pattern": "*.{tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - { - "chain": { - "type": "string", - "description": "The chain to use for the embeddings. Can be either 'H' (high diversity chain: BCR heavy or TCR beta or delta),\n'L' (low diversity chain: BCR light or TCR alpha or gamma) or 'HL'/'LH' (BCR heavy + light, and TCR alpha + beta or gamma + delta).\n", - "enum": [ - "L", - "H", - "HL", - "LH" - ] - } - }, - { - "model": { - "type": "string", - "description": "The embedding model to use. Options are detailed on the amulety documentation.\n" - } - } - ], - "output": { - "embedding": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "${task.ext.prefix ?: meta.id}.tsv": { - "type": "file", - "description": "TSV with embeddings of BCR or TCR amino acid sequences.", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "embedding_metadata": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*metadata.tsv": { - "type": "file", - "description": "TSV with metadata about the embeddings.", - "pattern": "*metadata.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_amulety": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "amulety": { - "type": "string", - "description": "The tool name" - } - }, - { - "amulety --help 2>&1 | grep -o 'version [0-9\\.]\\+' | grep -o '[0-9\\.]\\+'": { - "type": "eval", - "description": "The command used to generate the version of the tool" - } - } - ] - ], - "versions_python": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "python": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python --version 2>&1 | grep -o 'Python [0-9\\.]\\+' | grep -o '[0-9\\.]\\+'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_pytorch": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "pytorch": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python -c 'import torch; 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print(torch.__version__)'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "transformers": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python -c 'import transformers; print(transformers.__version__)'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "airrflow", + "version": "5.0.0" + } ] - ] - }, - "authors": [ - "@ggabernet" - ], - "maintainers": [ - "@ggabernet" - ] - }, - "pipelines": [ - { - "name": "airrflow", - "version": "5.0.0" - } - ] - }, - { - "name": "amulety_esm2", - "path": "modules/nf-core/amulety/esm2/meta.yml", - "type": "module", - "meta": { - "name": "amulety_esm2", - "description": "A module to create esm2 embeddings of antibody (BCR) amino acid sequences using amulety.", - "deprecated": true, - "keywords": [ - "embeddings", - "BCR", - "antibody", - "GPU-accelerated", - "immunoinformatics", - "immunology" - ], - "tools": [ - { - "amulety": { - "description": "Python package to create embeddings of BCR and TCR amino acid sequences.", - "homepage": "https://amulety.readthedocs.io/en/latest/", - "documentation": "https://amulety.readthedocs.io/en/latest/", - "tool_dev_url": "https://github.com/immcantation/amulety", - "doi": "10.1101/2025.03.21.644583", - "licence": [ - "GPL v3" - ], - "identifier": "" + }, + { + "name": "amulety_esm2", + "path": "modules/nf-core/amulety/esm2/meta.yml", + "type": "module", + "meta": { + "name": "amulety_esm2", + "description": "A module to create esm2 embeddings of antibody (BCR) amino acid sequences using amulety.", + "deprecated": true, + "keywords": ["embeddings", "BCR", "antibody", "GPU-accelerated", "immunoinformatics", "immunology"], + "tools": [ + { + "amulety": { + "description": "Python package to create embeddings of BCR and TCR amino acid sequences.", + "homepage": "https://amulety.readthedocs.io/en/latest/", + "documentation": "https://amulety.readthedocs.io/en/latest/", + "tool_dev_url": "https://github.com/immcantation/amulety", + "doi": "10.1101/2025.03.21.644583", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "tsv": { + "type": "file", + "description": "TSV with BCR/TCR nucleotide sequences in AIRR rearrangement format", + "pattern": "*.{tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + { + "chain": { + "type": "string", + "description": "The chain to use for the embeddings. Can be either 'H' (heavy) or 'HL' (heavy + light, for single-cell data).\n" + } + } + ], + "output": { + "embedding": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "TSV with esm2 embeddings.", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@ggabernet"], + "maintainers": ["@ggabernet"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } + }, + { + "name": "amulety_translate", + "path": "modules/nf-core/amulety/translate/meta.yml", + "type": "module", + "meta": { + "name": "amulety_translate", + "description": "A module to translate BCR and TCR nucleotide sequences into amino acid sequences using amulety and igblast.", + "keywords": [ + "immunology", + "BCR", + "TCR", + "translation", + "amino acid", + "nucleotide", + "immunoinformatics" + ], + "tools": [ + { + "amulety": { + "description": "Python package to create embeddings of BCR and TCR amino acid sequences.", + "homepage": "https://amulety.readthedocs.io/en/latest/", + "documentation": "https://amulety.readthedocs.io/en/latest/", + "tool_dev_url": "https://github.com/immcantation/amulety", + "doi": "10.1101/2025.03.21.644583", + "licence": ["GPL v3"], + "identifier": "" + } + }, + { + "igblast": { + "description": "A tool for immunoglobulin (IG, BCR) and T cell receptor (TCR) V domain sequences blasting.", + "homepage": "https://www.ncbi.nlm.nih.gov/igblast/", + "documentation": "https://ncbi.github.io/igblast/", + "tool_dev_url": "https://github.com/ncbi/igblast", + "doi": "10.1093/nar/gkt382", + "licence": ["United States Government Work"], + "identifier": "biotools:igblast" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "tsv": { + "type": "file", + "description": "TSV with BCR/TCR nucleotide sequences in AIRR rearrangement format", + "pattern": "*.{tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + { + "reference_igblast": { + "type": "file", + "description": "Built reference databases for igblast", + "ontologies": [] + } + } + ], + "output": { + "repertoire_translated": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*_translated.tsv": { + "type": "file", + "description": "TSV with BCR/TCR amino acid sequences in AIRR rearrangement format", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_amulety": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "amulety": { + "type": "string", + "description": "The tool name" + } + }, + { + "amulety --help 2>&1 | grep -o 'version [0-9\\.]\\+' | grep -o '[0-9\\.]\\+'": { + "type": "eval", + "description": "The command used to generate the version of the tool" + } + } + ] + ], + "versions_igblastn": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "igblastn": { + "type": "string", + "description": "The tool name" + } + }, + { + "igblastn -version | grep -o 'igblast[0-9\\. ]\\+' | grep -o '[0-9\\. ]\\+'": { + "type": "eval", + "description": "The command used to generate the version of the tool" + } + } + ] + ], + "versions_python": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "python": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python --version 2>&1 | grep -o 'Python [0-9\\.]\\+' | grep -o '[0-9\\.]\\+'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_pytorch": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "pytorch": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python -c 'import torch; print(torch.__version__)'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_transformers": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "transformers": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python -c 'import transformers; print(transformers.__version__)'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "amulety": { + "type": "string", + "description": "The tool name" + } + }, + { + "amulety --help 2>&1 | grep -o 'version [0-9\\.]\\+' | grep -o '[0-9\\.]\\+'": { + "type": "eval", + "description": "The command used to generate the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "igblastn": { + "type": "string", + "description": "The tool name" + } + }, + { + "igblastn -version | grep -o 'igblast[0-9\\. ]\\+' | grep -o '[0-9\\. ]\\+'": { + "type": "eval", + "description": "The command used to generate the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "python": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python --version 2>&1 | grep -o 'Python [0-9\\.]\\+' | grep -o '[0-9\\.]\\+'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "pytorch": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python -c 'import torch; print(torch.__version__)'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "transformers": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python -c 'import transformers; print(transformers.__version__)'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@ggabernet"], + "maintainers": ["@ggabernet"] }, - { - "tsv": { - "type": "file", - "description": "TSV with BCR/TCR nucleotide sequences in AIRR rearrangement format", - "pattern": "*.{tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - { - "chain": { - "type": "string", - "description": "The chain to use for the embeddings. Can be either 'H' (heavy) or 'HL' (heavy + light, for single-cell data).\n" - } - } - ], - "output": { - "embedding": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "TSV with esm2 embeddings.", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } + "pipelines": [ + { + "name": "airrflow", + "version": "5.0.0" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@ggabernet" - ], - "maintainers": [ - "@ggabernet" - ] - } - }, - { - "name": "amulety_translate", - "path": "modules/nf-core/amulety/translate/meta.yml", - "type": "module", - "meta": { - "name": "amulety_translate", - "description": "A module to translate BCR and TCR nucleotide sequences into amino acid sequences using amulety and igblast.", - "keywords": [ - "immunology", - "BCR", - "TCR", - "translation", - "amino acid", - "nucleotide", - "immunoinformatics" - ], - "tools": [ - { - "amulety": { - "description": "Python package to create embeddings of BCR and TCR amino acid sequences.", - "homepage": "https://amulety.readthedocs.io/en/latest/", - "documentation": "https://amulety.readthedocs.io/en/latest/", - "tool_dev_url": "https://github.com/immcantation/amulety", - "doi": "10.1101/2025.03.21.644583", - "licence": [ - "GPL v3" - ], - "identifier": "" - } - }, - { - "igblast": { - "description": "A tool for immunoglobulin (IG, BCR) and T cell receptor (TCR) V domain sequences blasting.", - "homepage": "https://www.ncbi.nlm.nih.gov/igblast/", - "documentation": "https://ncbi.github.io/igblast/", - "tool_dev_url": "https://github.com/ncbi/igblast", - "doi": "10.1093/nar/gkt382", - "licence": [ - "United States Government Work" - ], - "identifier": "biotools:igblast" + }, + { + "name": "anarcii", + "path": "modules/nf-core/anarcii/meta.yml", + "type": "module", + "meta": { + "name": "anarcii", + "description": "A language model for antigen receptor numbering", + "keywords": ["annotate", "antibody", "TCR", "immunology"], + "tools": [ + { + "anarcii": { + "description": "A language model for antigen receptor numbering", + "homepage": "https://github.com/oxpig/ANARCII", + "documentation": "https://github.com/oxpig/ANARCII/wiki", + "tool_dev_url": "https://github.com/oxpig/ANARCII", + "doi": "10.5281/zenodo.15274840", + "licence": ["BSD 3-Clause License"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Fasta file with full receptor sequences", + "pattern": "*.fasta", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ] + ], + "output": { + "anarcii": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.csv": { + "type": "file", + "description": "File containing per-base numbering", + "pattern": "*.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "versions_anarcii": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "anarcii": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "anarcii --version | sed \"s/^anarcii //\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "anarcii": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "anarcii --version | sed \"s/^anarcii //\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@Clara0611"], + "maintainers": ["@Clara0611"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "tsv": { - "type": "file", - "description": "TSV with BCR/TCR nucleotide sequences in AIRR rearrangement format", - "pattern": "*.{tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } + }, + { + "name": "angsd_contamination", + "path": "modules/nf-core/angsd/contamination/meta.yml", + "type": "module", + "meta": { + "name": "angsd_contamination", + "description": "A tool to estimate nuclear contamination in males based on heterozygosity in the female chromosome.", + "keywords": ["angsd", "population genetics", "nuclear contamination estimate"], + "tools": [ + { + "angsd": { + "description": "ANGSD: Analysis of next generation Sequencing Data", + "homepage": "http://www.popgen.dk/angsd/", + "documentation": "http://www.popgen.dk/angsd/", + "tool_dev_url": "https://github.com/ANGSD/angsd", + "doi": "10.1186/s12859-014-0356-4", + "licence": ["GPL v3", "MIT"], + "identifier": "biotools:angsd" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "icounts": { + "type": "file", + "description": "Internal format for dumping binary single chrs. Useful for ANGSD contamination", + "pattern": "*.icnts.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing information related to the hapmap_file.\ne.g. [ id:'test' ]\n" + } + }, + { + "hapmap_file": { + "type": "file", + "description": "A list of variable sites to look for heterozygosity.", + "ontologies": [] + } + } + ] + ], + "output": { + "txt": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "Contamination estimation output.", + "pattern": "*.txt", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + } + ] + ], + "versions_angsd": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "angsd": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "angsd 2>&1 | sed '1!d;s/.*version: //;s/ .*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "angsd": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "angsd 2>&1 | sed '1!d;s/.*version: //;s/ .*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@jbv2"], + "maintainers": ["@jbv2"] } - ], - { - "reference_igblast": { - "type": "file", - "description": "Built reference databases for igblast", - "ontologies": [] + }, + { + "name": "angsd_docounts", + "path": "modules/nf-core/angsd/docounts/meta.yml", + "type": "module", + "meta": { + "name": "angsd_docounts", + "description": "Calculates base frequency statistics across reference positions from BAM.", + "keywords": ["angsd", "population genetics", "allele counts", "doCounts"], + "tools": [ + { + "angsd": { + "description": "ANGSD: Analysis of next generation Sequencing Data", + "homepage": "http://www.popgen.dk/angsd/", + "documentation": "http://www.popgen.dk/angsd/", + "tool_dev_url": "https://github.com/ANGSD/angsd", + "doi": "10.1186/s12859-014-0356-4", + "licence": ["GPL v3, MIT"], + "identifier": "biotools:angsd" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "A list of BAM or CRAM files", + "pattern": "*.{bam,cram}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + }, + { + "edam": "http://edamontology.org/format_3462" + } + ] + } + }, + { + "bai": { + "type": "file", + "description": "List of BAM/CRAM index files", + "pattern": "*.{bai,csi}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3327" + } + ] + } + }, + { + "minqfile": { + "type": "file", + "description": "File with individual quality score thresholds", + "pattern": "*", + "ontologies": [] + } + } + ] + ], + "output": { + "depth_sample": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.depthSample": { + "type": "file", + "description": "Distribution of sequencing depths", + "pattern": "*.depthSample", + "ontologies": [] + } + } + ] + ], + "depth_global": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.depthGlobal": { + "type": "file", + "description": "Distribution of sequencing depths", + "pattern": "*.depthGlobal", + "ontologies": [] + } + } + ] + ], + "qs": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.qs": { + "type": "file", + "description": "Distribution of scores", + "pattern": "*.qs", + "ontologies": [] + } + } + ] + ], + "pos": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.pos.gz": { + "type": "file", + "description": "Various types of depth statistics (depending on value for -dumpCounts)", + "pattern": "*.pos.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3675" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "counts": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.counts.gz": { + "type": "file", + "description": "Various types of statistics (related to pos.gz)", + "pattern": "*.counts.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "icounts": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.icnts.gz": { + "type": "file", + "description": "Internal format for dumping binary single chrs. 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} - } - ] - ], - "versions_transformers": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "transformers": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python -c 'import transformers; print(transformers.__version__)'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "amulety": { - "type": "string", - "description": "The tool name" - } - }, - { - "amulety --help 2>&1 | grep -o 'version [0-9\\.]\\+' | grep -o '[0-9\\.]\\+'": { - "type": "eval", - "description": "The command used to generate the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "igblastn": { - "type": "string", - "description": "The tool name" - } - }, - { - "igblastn -version | grep -o 'igblast[0-9\\. ]\\+' | grep -o '[0-9\\. ]\\+'": { - "type": "eval", - "description": "The command used to generate the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "python": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python --version 2>&1 | grep -o 'Python [0-9\\.]\\+' | grep -o '[0-9\\.]\\+'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "pytorch": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python -c 'import torch; print(torch.__version__)'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - 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} - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } + }, + { + "name": "anndata_barcodes", + "path": "modules/nf-core/anndata/barcodes/meta.yml", + "type": "module", + "meta": { + "name": "anndata_barcodes", + "description": "Module to subset AnnData object to cells with matching barcodes from the csv file", + "keywords": ["single-cell", "barcodes", "anndata", "subsetting", "transcriptomics"], + "tools": [ + { + "anndata": { + "description": "An annotated data matrix.", + "homepage": "https://anndata.readthedocs.io", + "documentation": "https://anndata.readthedocs.io", + "tool_dev_url": "https://github.com/theislab/anndata", + "doi": "10.21105/joss.04371", + "licence": ["BSD-3-clause"], + "identifier": "biotools:anndata" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "h5ad": { + "type": "file", + "description": "Anndata object as H5AD file", + "pattern": "*.h5ad", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3590" + } + ] + } + }, + { + "barcodes": { + "type": "file", + "description": "CSV file containing barcodes. Barcodes are written in plain text. One column, no header\n", + "pattern": "*.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "output": { + "h5ad": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n", + "pattern": "*.h5ad" + } + }, + { + "*.h5ad": { + "type": "file", + "description": "AnnData file containing all cells with barcodes that match those in the input barcodes csv file\n", + "pattern": "*.h5ad", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3590" + } + ] + } + } + ] + ], + "versions_anndata": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "topics": { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@nictru", "@chaochaowong", "@LeonHafner"], + "maintainers": ["@nictru", "@LeonHafner"] }, - { - "fasta": { - "type": "file", - "description": "Fasta file with full receptor sequences", - "pattern": "*.fasta", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ], - "output": { - "anarcii": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.csv": { - "type": "file", - "description": "File containing per-base numbering", - "pattern": "*.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "versions_anarcii": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "anarcii": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "anarcii --version | sed \"s/^anarcii //\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "anarcii": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "anarcii --version | sed \"s/^anarcii //\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "scdownstream", + "version": "dev" + }, + { + "name": "scrnaseq", + "version": "4.1.0" + } ] - ] - }, - "authors": [ - "@Clara0611" - ], - "maintainers": [ - "@Clara0611" - ] - } - }, - { - "name": "angsd_contamination", - "path": "modules/nf-core/angsd/contamination/meta.yml", - "type": "module", - "meta": { - "name": "angsd_contamination", - "description": "A tool to estimate nuclear contamination in males based on heterozygosity in the female chromosome.", - "keywords": [ - "angsd", - "population genetics", - "nuclear contamination estimate" - ], - "tools": [ - { - "angsd": { - "description": "ANGSD: Analysis of next generation Sequencing Data", - "homepage": "http://www.popgen.dk/angsd/", - "documentation": "http://www.popgen.dk/angsd/", - "tool_dev_url": "https://github.com/ANGSD/angsd", - "doi": "10.1186/s12859-014-0356-4", - "licence": [ - "GPL v3", - "MIT" - ], - "identifier": "biotools:angsd" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "icounts": { - "type": "file", - "description": "Internal format for dumping binary single chrs. Useful for ANGSD contamination", - "pattern": "*.icnts.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing information related to the hapmap_file.\ne.g. [ id:'test' ]\n" - } + }, + { + "name": "anndata_getsize", + "path": "modules/nf-core/anndata/getsize/meta.yml", + "type": "module", + "meta": { + "name": "anndata_getsize", + "description": "Get the size (n_cells or n_genes) of an anndata object stored as a h5ad file", + "keywords": ["anndata", "single-cell", "scanpy"], + "tools": [ + { + "anndata": { + "description": "An annotated data matrix.", + "homepage": "http://anndata.rtfd.io", + "documentation": "http://anndata.rtfd.io", + "tool_dev_url": "https://github.com/theislab/anndata", + "doi": "10.21105/joss.04371", + "licence": ["BSD-3-clause"], + "identifier": "biotools:anndata" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "h5ad": { + "type": "file", + "description": "H5AD file of anndata object", + "pattern": "*.h5ad", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3590" + } + ] + } + } + ], + { + "size_type": { + "type": "string", + "description": "either 'cells', 'genes', 'obs', or 'var'" + } + } + ], + "output": { + "size": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "text file containing the requested size", + "pattern": "*.txt", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + } + ] + ], + "versions_anndata": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "topics": { + "versions": [ + { + "versions.yml": { + "type": "string", + "description": "The name of the process" + } + } + ] + }, + "authors": ["@LeonHafner"], + "maintainers": ["@LeonHafner"] }, - { - "hapmap_file": { - "type": "file", - "description": "A list of variable sites to look for heterozygosity.", - "ontologies": [] - } - } - ] - ], - "output": { - "txt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.txt": { - "type": "file", - "description": "Contamination estimation output.", - "pattern": "*.txt", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2330" - } - ] - } - } - ] - ], - "versions_angsd": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "angsd": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "angsd 2>&1 | sed '1!d;s/.*version: //;s/ .*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "angsd": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "angsd 2>&1 | sed '1!d;s/.*version: //;s/ .*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "scdownstream", + "version": "dev" + } ] - ] - }, - "authors": [ - "@jbv2" - ], - "maintainers": [ - "@jbv2" - ] - } - }, - { - "name": "angsd_docounts", - "path": "modules/nf-core/angsd/docounts/meta.yml", - "type": "module", - "meta": { - "name": "angsd_docounts", - "description": "Calculates base frequency statistics across reference positions from BAM.", - "keywords": [ - "angsd", - "population genetics", - "allele counts", - "doCounts" - ], - "tools": [ - { - "angsd": { - "description": "ANGSD: Analysis of next generation Sequencing Data", - "homepage": "http://www.popgen.dk/angsd/", - "documentation": "http://www.popgen.dk/angsd/", - "tool_dev_url": "https://github.com/ANGSD/angsd", - "doi": "10.1186/s12859-014-0356-4", - "licence": [ - "GPL v3, MIT" - ], - "identifier": "biotools:angsd" + }, + { + "name": "annosine", + "path": "modules/nf-core/annosine/meta.yml", + "type": "module", + "meta": { + "name": "annosine", + "description": "Accelerating de novo SINE annotation in plant and animal genomes", + "keywords": ["genomics", "SINE", "annotation", "plant"], + "tools": [ + { + "annosine": { + "description": "AnnoSINE_v2 - SINE Annotation Tool for Plant and Animal Genomes", + "homepage": "https://github.com/liaoherui/AnnoSINE_v2", + "documentation": "https://github.com/liaoherui/AnnoSINE_v2", + "tool_dev_url": "https://github.com/liaoherui/AnnoSINE_v2", + "doi": "10.1101/2024.03.01.582874", + "licence": ["MIT"], + "identifier": "biotools:annosine" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input genome assembly", + "pattern": "*.{fasta,fa,fsa}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + { + "mode": { + "type": "integer", + "description": "Choose the running mode of the program.\n1--Homology-based method;\n2--Structure-based method;\n3--Hybrid of homology-based and structure-based method.\n" + } + } + ], + "output": { + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}.log": { + "type": "file", + "description": "AnnoSINE_v2 log file\n", + "pattern": "*.{log}", + "ontologies": [] + } + } + ] + ], + "fa": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}.fa": { + "type": "map", + "description": "Non-redundant SINE library with serial number\n", + "pattern": "*.{fa}" + } + } + ] + ], + "versions_annosine": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "annosine": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pip show annosine2 | sed -n 's/Version: //p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "annosine": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pip show annosine2 | sed -n 's/Version: //p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@GallVp"], + "maintainers": ["@GallVp"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "A list of BAM or CRAM files", - "pattern": "*.{bam,cram}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - }, - { - "edam": "http://edamontology.org/format_3462" - } - ] - } - }, - { - "bai": { - "type": "file", - "description": "List of BAM/CRAM index files", - "pattern": "*.{bai,csi}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3327" - } - ] - } + }, + { + "name": "annotsv_annotsv", + "path": "modules/nf-core/annotsv/annotsv/meta.yml", + "type": "module", + "meta": { + "name": "annotsv_annotsv", + "description": "Annotation and Ranking of Structural Variation", + "keywords": ["annotation", "structural variants", "vcf", "bed", "tsv"], + "tools": [ + { + "annotsv": { + "description": "Annotation and Ranking of Structural Variation", + "homepage": "https://lbgi.fr/AnnotSV/", + "documentation": "https://lbgi.fr/AnnotSV/", + "tool_dev_url": "https://github.com/lgmgeo/AnnotSV", + "doi": "10.1093/bioinformatics/bty304", + "licence": ["GPL-3.0"], + "identifier": "biotools:AnnotSV" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "sv_vcf": { + "type": "file", + "description": "A VCF or BED file containing the structural variants to be annotated", + "pattern": "*.{bed,vcf,vcf.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3003" + }, + { + "edam": "http://edamontology.org/format_3016" + } + ] + } + }, + { + "sv_vcf_index": { + "type": "file", + "description": "OPTIONAL - The index for gzipped VCF files", + "pattern": "*.tbi", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, + { + "candidate_small_variants": { + "type": "file", + "description": "OPTIONAL - A file containing candidate small variants", + "pattern": "*.{vcf,vcf.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing annotations information\n" + } + }, + { + "annotations": { + "type": "directory", + "description": "The directory containing the annotations (URL to download this will be made available soon)\nFor now this can be downloaded in the way defined in the repo (https://github.com/lgmgeo/AnnotSV#quick-installation)\n" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing candidate genes information\n" + } + }, + { + "candidate_genes": { + "type": "file", + "description": "OPTIONAL - A file containing genes (either space-separated, tab-separated or line-break-separated)", + "pattern": "*.txt", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing candidate false positive SNV information\n" + } + }, + { + "false_positive_snv": { + "type": "file", + "description": "OPTIONAL - A VCF file containing small variant candidates", + "pattern": "*.{vcf,vcf.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + } + ] + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing candidate gene transcripts information\n" + } + }, + { + "gene_transcripts": { + "type": "file", + "description": "OPTIONAL - A file containing the preferred gene transcripts to be used in priority during annotation (either space-separated or tab-separated)", + "pattern": "*.txt", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + } + ] + ], + "output": { + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.tsv": { + "type": "file", + "description": "A TSV file containing the annotated variants", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "unannotated_tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.unannotated.tsv": { + "type": "file", + "description": "OPTIONAL - TSV file containing the unannotated variants", + "pattern": "*.unannotated.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf": { + "type": "file", + "description": "OPTIONAL - A VCF file containing the annotated variants (created when `-vcf 1` is specified in the args)\n", + "pattern": "*.vcf", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + } + ] + } + } + ] + ], + "versions_annotsv": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "annotsv": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "AnnotSV --version | sed 's/AnnotSV //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "annotsv": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "AnnotSV --version | sed 's/AnnotSV //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@nvnieuwk"], + "maintainers": ["@nvnieuwk"] }, - { - "minqfile": { - "type": "file", - "description": "File with individual quality score thresholds", - "pattern": "*", - "ontologies": [] - } - } - ] - ], - "output": { - "depth_sample": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.depthSample": { - "type": "file", - "description": "Distribution of sequencing depths", - "pattern": "*.depthSample", - "ontologies": [] - } - } - ] - ], - "depth_global": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.depthGlobal": { - "type": "file", - "description": "Distribution of sequencing depths", - "pattern": "*.depthGlobal", - "ontologies": [] - } - } + "pipelines": [ + { + "name": "pacsomatic", + "version": "dev" + } ] - ], - "qs": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.qs": { - "type": "file", - "description": "Distribution of scores", - "pattern": "*.qs", - "ontologies": [] - } - } + }, + { + "name": "annotsv_installannotations", + "path": "modules/nf-core/annotsv/installannotations/meta.yml", + "type": "module", + "meta": { + "name": "annotsv_installannotations", + "description": "Install the AnnotSV annotations", + "keywords": ["annotation", "download", "installation", "structural variants"], + "tools": [ + { + "annotsv": { + "description": "Annotation and Ranking of Structural Variation", + "homepage": "https://lbgi.fr/AnnotSV/", + "documentation": "https://lbgi.fr/AnnotSV/", + "tool_dev_url": "https://github.com/lgmgeo/AnnotSV", + "licence": ["GPL v3"], + "identifier": "biotools:AnnotSV" + } + } + ], + "input": [], + "output": { + "annotations": [ + { + "AnnotSV_annotations": { + "type": "file", + "description": "A folder containing the annotations", + "pattern": "AnnotSV_annotations", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ], + "versions_annotsv": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "annotsv": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "AnnotSV --version | sed 's/AnnotSV //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "annotsv": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "AnnotSV --version | sed 's/AnnotSV //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@nvnieuwk"], + "maintainers": ["@nvnieuwk"] + }, + "pipelines": [ + { + "name": "pacsomatic", + "version": "dev" + } ] - 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"${prefix}/knownclusterblastoutput.txt": { + "type": "file", + "description": "Raw BLAST output of known clusters of the MIBiG database", + "pattern": "knownclusterblastoutput.txt", + "ontologies": [] + } + } + ] + ], + "versions_antismash": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "antismash": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "antismash --version | sed 's/antiSMASH //;s/-.*//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "antismash": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "antismash --version | sed 's/antiSMASH //;s/-.*//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@jasmezz"], + "maintainers": ["@jasmezz", "@jfy133"] + }, + "pipelines": [ + { + "name": "funcscan", + "version": "3.0.0" } - } - ] - ], - "counts": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.counts.gz": { - "type": "file", - "description": "Various types of statistics (related to pos.gz)", - "pattern": "*.counts.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } ] - ], - "icounts": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.icnts.gz": { - "type": "file", - "description": "Internal format for dumping binary single chrs. Useful for ANGSD contamination", - "pattern": "*.icnts.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "versions_angsd": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "angsd": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "angsd 2>&1 | sed '1!d;s/.*version: //;s/ .*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "angsd": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "angsd 2>&1 | sed '1!d;s/.*version: //;s/ .*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@jfy133" - ], - "maintainers": [ - "@jfy133" - ] - } - }, - { - "name": "angsd_gl", - "path": "modules/nf-core/angsd/gl/meta.yml", - "type": "module", - "meta": { - "name": "angsd_gl", - "description": "Calculated genotype likelihoods from BAM files.", - "keywords": [ - "angsd", - "genotype likelihood", - "genomics" - ], - "tools": [ - { - "angsd": { - "description": "ANGSD: Analysis of next generation Sequencing Data", - "homepage": "http://www.popgen.dk/angsd/", - "documentation": "http://www.popgen.dk/angsd/", - "tool_dev_url": "https://github.com/ANGSD/angsd", - "doi": "10.1186/s12859-014-0356-4", - "licence": [ - "GPL v3", - "MIT" - ], - "identifier": "biotools:angsd" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "A list of BAM or CRAM files", - "pattern": "*.{bam,cram}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - }, - { - "edam": "http://edamontology.org/format_3462" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "A reference genome in FASTA format", - "pattern": "*.fasta", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + }, + { + "name": "antismash_antismashdownloaddatabases", + "path": "modules/nf-core/antismash/antismashdownloaddatabases/meta.yml", + "type": "module", + "meta": { + "name": "antismash_antismashdownloaddatabases", + "description": "antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters. This module downloads the antiSMASH databases for conda and docker/singularity runs.", + "keywords": [ + "secondary metabolites", + "BGC", + "biosynthetic gene cluster", + "genome mining", + "NRPS", + "RiPP", + "antibiotics", + "prokaryotes", + "bacteria", + "eukaryotes", + "fungi", + "antismash", + "database" + ], + "tools": [ + { + "antismash": { + "description": "antiSMASH - the antibiotics and Secondary Metabolite Analysis SHell", + "homepage": "https://docs.antismash.secondarymetabolites.org", + "documentation": "https://docs.antismash.secondarymetabolites.org", + "tool_dev_url": "https://github.com/antismash/antismash", + "doi": "10.1093/nar/gkab335", + "licence": ["AGPL v3"], + "identifier": "biotools:antismash" + } + } + ], + "input": [], + "output": { + "database": [ + { + "antismash_db": { + "type": "directory", + "description": "Download directory for antiSMASH databases", + "pattern": "antismash_db" + } + } + ], + "versions_antismash": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "antismash": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "antismash --version | sed 's/antiSMASH //;s/-.*//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "antismash": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "antismash --version | sed 's/antiSMASH //;s/-.*//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@jasmezz"], + "maintainers": ["@jasmezz", "@jfy133"] }, - { - "error_file": { - "type": "file", - "description": "A file containing information about type specific errors.", - "pattern": "*.error.chunkunordered", - "ontologies": [] - } - } - ] - ], - "output": { - "genotype_likelihood": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.{glf,beagle}.gz": { - "type": "file", - "description": "File containing genotype likelihoods per sample", - "pattern": "*.{glf,beagle}.gz", - "ontologies": [] - } - } - ] - ], - "versions_angsd": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "angsd": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "angsd 2>&1 | sed '1!d;s/.*version: //;s/ .*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "angsd": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "angsd 2>&1 | sed '1!d;s/.*version: //;s/ .*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "funcscan", + "version": "3.0.0" + } ] - ] - }, - "authors": [ - "@apeltzer", - "@TCLamnidis" - ], - "maintainers": [ - "@apeltzer", - "@TCLamnidis" - ] - } - }, - { - "name": "anndata_barcodes", - "path": "modules/nf-core/anndata/barcodes/meta.yml", - "type": "module", - "meta": { - "name": "anndata_barcodes", - "description": "Module to subset AnnData object to cells with matching barcodes from the csv file", - "keywords": [ - "single-cell", - "barcodes", - "anndata", - "subsetting", - "transcriptomics" - ], - "tools": [ - { - "anndata": { - "description": "An annotated data matrix.", - "homepage": "https://anndata.readthedocs.io", - "documentation": "https://anndata.readthedocs.io", - "tool_dev_url": "https://github.com/theislab/anndata", - "doi": "10.21105/joss.04371", - "licence": [ - "BSD-3-clause" - ], - "identifier": "biotools:anndata" + }, + { + "name": "antismash_antismashlite", + "path": "modules/nf-core/antismash/antismashlite/meta.yml", + "type": "module", + "meta": { + "name": "antismash_antismashlite", + "description": "antiSMASH allows the rapid genome-wide identification, annotation\nand analysis of secondary metabolite biosynthesis gene clusters.\n", + "deprecated": true, + "keywords": [ + "secondary metabolites", + "BGC", + "biosynthetic gene cluster", + "genome mining", + "NRPS", + "RiPP", + "antibiotics", + "prokaryotes", + "bacteria", + "eukaryotes", + "fungi", + "antismash" + ], + "tools": [ + { + "antismashlite": { + "description": "antiSMASH - the antibiotics and Secondary Metabolite Analysis SHell", + "homepage": "https://docs.antismash.secondarymetabolites.org", + "documentation": "https://docs.antismash.secondarymetabolites.org", + "tool_dev_url": "https://github.com/antismash/antismash", + "doi": "10.1093/nar/gkab335", + "licence": ["AGPL v3"], + "identifier": "biotools:antismash" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "sequence_input": { + "type": "file", + "description": "nucleotide sequence file (annotated)", + "pattern": "*.{gbk, gb, gbff, genbank, embl, fasta, fna}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + }, + { + "edam": "http://edamontology.org/format_1936" + }, + { + "edam": "http://edamontology.org/format_1927" + } + ] + } + } + ], + { + "databases": { + "type": "directory", + "description": "Downloaded AntiSMASH databases (e.g. in the AntiSMASH installation directory\n\"data/databases\")\n", + "pattern": "*/" + } + }, + { + "antismash_dir": { + "type": "directory", + "description": "A local copy of an AntiSMASH installation folder. This is required when running with\ndocker and singularity (not required for conda), due to attempted 'modifications' of\nfiles during database checks in the installation directory, something that cannot\nbe done in immutable docker/singularity containers. Therefore, a local installation\ndirectory needs to be mounted (including all modified files from the downloading step)\nto the container as a workaround.\n", + "pattern": "*/" + } + } + ], + "output": { + "html_accessory_files": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/{css,images,js}": { + "type": "directory", + "description": "Accessory files for the HTML output", + "pattern": "{css/,images/,js/}" + } + } + ] + ], + "gbk_input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/*.gbk": { + "type": "file", + "description": "Nucleotide sequence and annotations in GenBank format; converted from input file", + "pattern": "*.gbk", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1936" + } + ] + } + } + ] + ], + "json_results": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/*.json": { + "type": "file", + "description": "Nucleotide sequence and annotations in JSON format; converted from GenBank file (gbk_input)", + "pattern": "*.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/*.log": { + "type": "file", + "description": "Contains all the logging output that antiSMASH produced during its run", + "pattern": "*.log", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + } + ] + ], + "zip": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/*.zip": { + "type": "file", + "description": "Contains a compressed version of the output folder in zip format", + "pattern": "*.zip", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3987" + } + ] + } + } + ] + ], + "html": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/index.html": { + "type": "file", + "description": "Graphical web view of results in HTML format", + "patterN": "index.html", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2331" + } + ] + } + } + ] + ], + "json_sideloading": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/regions.js": { + "type": "file", + "description": "Sideloaded annotations of protoclusters and/or subregions (see antiSMASH documentation \"Annotation sideloading\")", + "pattern": "regions.js", + "ontologies": [] + } + } + ] + ], + "clusterblast_file": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/clusterblast/*_c*.txt": { + "type": "file", + "description": "Output of ClusterBlast algorithm", + "pattern": "clusterblast/*_c*.txt", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + } + ] + ], + "knownclusterblast_html": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/knownclusterblast/region*/ctg*.html": { + "type": "file", + "description": "Tables with MIBiG hits in HTML format", + "pattern": "knownclusterblast/region*/ctg*.html", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2331" + } + ] + } + } + ] + ], + "knownclusterblast_dir": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/knownclusterblast/": { + "type": "directory", + "description": "Directory with MIBiG hits", + "pattern": "knownclusterblast/" + } + } + ] + ], + "knownclusterblast_txt": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/knownclusterblast/*_c*.txt": { + "type": "file", + "description": "Tables with MIBiG hits", + "pattern": "knownclusterblast/*_c*.txt", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + } + ] + ], + "svg_files_clusterblast": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/svg/clusterblast*.svg": { + "type": "file", + "description": "SVG images showing the % identity of the aligned hits against their queries", + "pattern": "svg/clusterblast*.svg", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3604" + } + ] + } + } + ] + ], + "svg_files_knownclusterblast": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/svg/knownclusterblast*.svg": { + "type": "file", + "description": "SVG images showing the % identity of the aligned hits against their queries", + "pattern": "svg/knownclusterblast*.svg", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3604" + } + ] + } + } + ] + ], + "gbk_results": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/*region*.gbk": { + "type": "file", + "description": "Nucleotide sequence and annotations in GenBank format; one file per antiSMASH hit", + "pattern": "*region*.gbk", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1936" + } + ] + } + } + ] + ], + "clusterblastoutput": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/clusterblastoutput.txt": { + "type": "file", + "description": "Raw BLAST output of known clusters previously predicted by antiSMASH using the built-in ClusterBlast algorithm", + "pattern": "clusterblastoutput.txt", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + } + ] + ], + "knownclusterblastoutput": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/knownclusterblastoutput.txt": { + "type": "file", + "description": "Raw BLAST output of known clusters of the MIBiG database", + "pattern": "knownclusterblastoutput.txt", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + } + ] + ], + "versions_antismash": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "antismash-lite": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "antismash --version | sed 's/antiSMASH //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "antismash-lite": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "antismash --version | sed 's/antiSMASH //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@jasmezz"], + "maintainers": ["@jasmezz"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "h5ad": { - "type": "file", - "description": "Anndata object as H5AD file", - "pattern": "*.h5ad", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3590" - } - ] - } - }, - { - "barcodes": { - "type": "file", - "description": "CSV file containing barcodes. Barcodes are written in plain text. One column, no header\n", - "pattern": "*.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } + }, + { + "name": "antismash_antismashlitedownloaddatabases", + "path": "modules/nf-core/antismash/antismashlitedownloaddatabases/meta.yml", + "type": "module", + "meta": { + "name": "antismash_antismashlitedownloaddatabases", + "description": "antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters. This module downloads the antiSMASH databases for conda and docker/singularity runs.", + "deprecated": true, + "keywords": [ + "secondary metabolites", + "BGC", + "biosynthetic gene cluster", + "genome mining", + "NRPS", + "RiPP", + "antibiotics", + "prokaryotes", + "bacteria", + "eukaryotes", + "fungi", + "antismash", + "database" + ], + "tools": [ + { + "antismash": { + "description": "antiSMASH - the antibiotics and Secondary Metabolite Analysis SHell", + "homepage": "https://docs.antismash.secondarymetabolites.org", + "documentation": "https://docs.antismash.secondarymetabolites.org", + "tool_dev_url": "https://github.com/antismash/antismash", + "doi": "10.1093/nar/gkab335", + "licence": ["AGPL v3"], + "identifier": "biotools:antismash" + } + } + ], + "input": [ + { + "database_css": { + "type": "directory", + "description": "antismash/outputs/html/css folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.\n", + "pattern": "css", + "ontologies": [] + } + }, + { + "database_detection": { + "type": "directory", + "description": "antismash/detection folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.\n", + "pattern": "detection", + "ontologies": [] + } + }, + { + "database_modules": { + "type": "directory", + "description": "antismash/modules folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.\n", + "pattern": "modules", + "ontologies": [] + } + } + ], + "output": { + "database": [ + { + "antismash_db": { + "type": "directory", + "description": "Download directory for antiSMASH databases", + "pattern": "antismash_db", + "ontologies": [] + } + } + ], + "antismash_dir": [ + { + "antismash_dir": { + "type": "directory", + "description": "antismash installation folder which is being modified during the antiSMASH database downloading step. The modified files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database and installation folder in pipelines.\n", + "pattern": "antismash_dir", + "ontologies": [] + } + } + ], + "versions_antismash": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "antismash-lite": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "antismash --version | sed 's/antiSMASH //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "antismash-lite": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "antismash --version | sed 's/antiSMASH //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@jasmezz"], + "maintainers": ["@jasmezz"] } - ] - ], - "output": { - "h5ad": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n", - "pattern": "*.h5ad" - } - }, - { - "*.h5ad": { - "type": "file", - "description": "AnnData file containing all cells with barcodes that match those in the input barcodes csv file\n", - "pattern": "*.h5ad", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3590" - } - ] - } - } - ] - ], - "versions_anndata": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } + }, + { + "name": "any2fasta", + "path": "modules/nf-core/any2fasta/meta.yml", + "type": "module", + "meta": { + "name": "any2fasta", + "description": "Convert various sequence formats (GenBank, GFF, FASTQ, FASTA, CLUSTAL, Stockholm, GFA) to FASTA format. Input files may be gzip, bzip2, zip, or zstd compressed.", + "keywords": ["fasta", "conversion", "sequences", "format", "genomics"], + "tools": [ + { + "any2fasta": { + "description": "Convert various sequence formats to FASTA", + "homepage": "https://github.com/tseemann/any2fasta", + "documentation": "https://github.com/tseemann/any2fasta", + "tool_dev_url": "https://github.com/tseemann/any2fasta", + "licence": ["GPL-3.0"], + "identifier": "biotools:any2fasta" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "sequence": { + "type": "file", + "description": "Input sequence file in any supported format (GenBank, GFF, FASTQ, FASTA,\nCLUSTAL, Stockholm, GFA). May be gzip, bzip2, zip, or zstd compressed. GFF3 must include a FASTA inside.\n", + "pattern": "*.{gb,gbk,fa,fasta,fna,fq,fastq,gff,gfa,clw,sth,gb.gz,gbk.gz,fa.gz,fasta.gz,fq.gz,fastq.gz}" + } + } + ] + ], + "output": { + "fasta": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.fasta": { + "type": "file", + "description": "Output sequences in FASTA format", + "pattern": "*.fasta" + } + } + ] + ], + "versions_any2fasta": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "any2fasta": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "any2fasta -v 2>&1 | head -1 | sed 's/any2fasta //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "any2fasta": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "any2fasta -v 2>&1 | head -1 | sed 's/any2fasta //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@cwoodside1278"], + "maintainers": ["@cwoodside1278"] } - ] - }, - "topics": { - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } + }, + { + "name": "apbs", + "path": "modules/nf-core/apbs/meta.yml", + "type": "module", + "meta": { + "name": "apbs", + "description": "Compute biomolecular electrostatics by solving the Poisson-Boltzmann equation\nusing APBS (Adaptive Poisson-Boltzmann Solver). Produces electrostatic potential\nmaps and solvation energy values for large biomolecular assemblages.\n", + "keywords": [ + "electrostatics", + "poisson-boltzmann", + "solvation", + "structural-biology", + "biophysics", + "computational-chemistry" + ], + "tools": [ + { + "apbs": { + "description": "APBS (Adaptive Poisson-Boltzmann Solver) is a software package for modelling\nbiomolecular solvation through solution of the Poisson-Boltzmann equation.\nIt computes electrostatic solvation energies and potentials for large\nbiomolecular assemblages and is widely used in structural biology and\ncomputational biophysics.\n", + "homepage": "https://www.poissonboltzmann.org/", + "documentation": "https://apbs.readthedocs.io/en/latest/", + "tool_dev_url": "https://github.com/Electrostatics/apbs", + "licence": ["Custom"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "apbs_input": { + "type": "file", + "description": "APBS input configuration file specifying the electrostatics calculation,\nincluding paths to molecular structure files (PQR/PDB) and calculation\nparameters. The file extension is typically `.in` but `.inp` is also\naccepted for legacy purposes.\n", + "pattern": "*.{in,inp}", + "ontologies": [] + } + }, + { + "pqr": { + "type": "file", + "description": "One or more PQR molecular structure files referenced by the input\nconfiguration file. PQR files contain atomic coordinates, charges, and\nradii used by APBS for electrostatics calculations.\n", + "pattern": "*.pqr", + "ontologies": [ + { + "edam": "http://edamontology.org/format_4035" + } + ] + } + } + ] + ], + "output": { + "dx": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.dx": { + "type": "file", + "description": "OpenDX format volumetric electrostatic potential map file output by APBS.\nOptional: this output is only produced when the input configuration file\ncontains a `write pot dx ` directive.\n", + "pattern": "*.dx", + "ontologies": [] + } + } + ] + ], + "mc": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "io.mc": { + "type": "file", + "description": "APBS multigrid calculation output file containing energy and force\ninformation from the finite difference solver.\n", + "pattern": "io.mc", + "ontologies": [] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}.log": { + "type": "file", + "description": "APBS standard output log file containing calculation results, including\nelectrostatic solvation energies and run diagnostics.\n", + "pattern": "*.log", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + } + ] + ], + "versions_apbs": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "apbs": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "apbs --version 2>&1 | sed '6!d;s|^.*Version APBS ||; s| .*\\$||'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "apbs": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "apbs --version 2>&1 | sed '6!d;s|^.*Version APBS ||; s| .*\\$||'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@vagkaratzas"], + "maintainers": ["@vagkaratzas"] } - ] - }, - "authors": [ - "@nictru", - "@chaochaowong", - "@LeonHafner" - ], - "maintainers": [ - "@nictru", - "@LeonHafner" - ] - }, - "pipelines": [ - { - "name": "scdownstream", - "version": "dev" - }, - { - "name": "scrnaseq", - "version": "4.1.0" - } - ] - }, - { - "name": "anndata_getsize", - "path": "modules/nf-core/anndata/getsize/meta.yml", - "type": "module", - "meta": { - "name": "anndata_getsize", - "description": "Get the size (n_cells or n_genes) of an anndata object stored as a h5ad file", - "keywords": [ - "anndata", - "single-cell", - "scanpy" - ], - "tools": [ - { - "anndata": { - "description": "An annotated data matrix.", - "homepage": "http://anndata.rtfd.io", - "documentation": "http://anndata.rtfd.io", - "tool_dev_url": "https://github.com/theislab/anndata", - "doi": "10.21105/joss.04371", - "licence": [ - "BSD-3-clause" - ], - "identifier": "biotools:anndata" + }, + { + "name": "arcashla_extract", + "path": "modules/nf-core/arcashla/extract/meta.yml", + "type": "module", + "meta": { + "name": "arcashla_extract", + "description": "Extracts reads mapped to chromosome 6 and any HLA decoys or chromosome 6 alternates.", + "keywords": ["HLA", "genotype", "RNA-seq"], + "tools": [ + { + "arcashla": { + "description": "arcasHLA performs high resolution genotyping for HLA class I and class II genes from RNA sequencing, supporting both paired and single-end samples.", + "homepage": "https://github.com/RabadanLab/arcasHLA", + "documentation": "https://github.com/RabadanLab/arcasHLA", + "tool_dev_url": "https://github.com/RabadanLab/arcasHLA", + "doi": "10.1093/bioinformatics/btz474", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file. If the BAM file is not indexed, this tool will run samtools index before extracting reads.", + "pattern": "*.bam", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + } + ] + ], + "output": { + "extracted_reads_fastq": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fq.gz": { + "type": "file", + "description": "FASTQ file(s) containing chromosome 6 reads and related HLA sequences", + "pattern": "*.fq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "log": [ + { + "*.log": { + "type": "file", + "description": "Log file for run summary", + "pattern": "*.log", + "ontologies": [] + } + } + ], + "intermediate_sam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "temp_files/**.sam": { + "type": "file", + "description": "Optional intermediate SAM file", + "pattern": "*.sam", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2573" + } + ] + } + } + ] + ], + "intermediate_bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "temp_files/**.bam": { + "type": "file", + "description": "Optional intermediate BAM file", + "pattern": "*.bam", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + } + ] + ], + "intermediate_sorted_bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "temp_files/**.sorted.bam": { + "type": "file", + "description": "Optional intermediate sorted BAM file", + "pattern": "*.sorted.bam", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + } + ] + ], + "versions_arcashla": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "arcashla": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "echo 0.5.0": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "arcashla": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "echo 0.5.0": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@christopher-mohr"], + "maintainers": ["@christopher-mohr"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } + }, + { + "name": "argnorm", + "path": "modules/nf-core/argnorm/meta.yml", + "type": "module", + "meta": { + "name": "argnorm", + "description": "Normalize antibiotic resistance genes (ARGs) using the ARO ontology (developed by CARD).", + "keywords": [ + "amr", + "antimicrobial resistance", + "arg", + "antimicrobial resistance genes", + "genomics", + "metagenomics", + "normalization", + "drug categorization" + ], + "tools": [ + { + "argnorm": { + "description": "Normalize antibiotic resistance genes (ARGs) using the ARO ontology (developed by CARD).", + "homepage": "https://argnorm.readthedocs.io/en/latest/", + "documentation": "https://argnorm.readthedocs.io/en/latest/", + "tool_dev_url": "https://github.com/BigDataBiology/argNorm", + "licence": ["MIT"], + "identifier": "biotools:argnorm" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "input_tsv": { + "type": "file", + "description": "ARG annotation output", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + { + "tool": { + "type": "string", + "description": "ARG annotation tool used", + "pattern": "argsoap|abricate|deeparg|resfinder|amrfinderplus" + } + }, + { + "db": { + "type": "string", + "description": "Database used for ARG annotation", + "pattern": "sarg|ncbi|resfinder|deeparg|megares|argannot|resfinderfg" + } + } + ], + "output": { + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "Normalized argNorm output", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_argnorm": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "argnorm": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "argnorm --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "argnorm": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "argnorm --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@Vedanth-Ramji"], + "maintainers": ["@Vedanth-Ramji"] }, - { - "h5ad": { - "type": "file", - "description": "H5AD file of anndata object", - "pattern": "*.h5ad", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3590" - } - ] - } - } - ], - { - "size_type": { - "type": "string", - "description": "either 'cells', 'genes', 'obs', or 'var'" - } - } - ], - "output": { - "size": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.txt": { - "type": "file", - "description": "text file containing the requested size", - "pattern": "*.txt", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2330" - } - ] - } - } + "pipelines": [ + { + "name": "funcscan", + "version": "3.0.0" + } ] - ], - "versions_anndata": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "topics": { - "versions": [ - { - "versions.yml": { - "type": "string", - "description": "The name of the process" - } - } - ] - }, - "authors": [ - "@LeonHafner" - ], - "maintainers": [ - "@LeonHafner" - ] - }, - "pipelines": [ - { - "name": "scdownstream", - "version": "dev" - } - ] - }, - { - "name": "annosine", - "path": "modules/nf-core/annosine/meta.yml", - "type": "module", - "meta": { - "name": "annosine", - "description": "Accelerating de novo SINE annotation in plant and animal genomes", - "keywords": [ - "genomics", - "SINE", - "annotation", - "plant" - ], - "tools": [ - { - "annosine": { - "description": "AnnoSINE_v2 - SINE Annotation Tool for Plant and Animal Genomes", - "homepage": "https://github.com/liaoherui/AnnoSINE_v2", - "documentation": "https://github.com/liaoherui/AnnoSINE_v2", - "tool_dev_url": "https://github.com/liaoherui/AnnoSINE_v2", - "doi": "10.1101/2024.03.01.582874", - "licence": [ - "MIT" - ], - "identifier": "biotools:annosine" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } + }, + { + "name": "aria2", + "path": "modules/nf-core/aria2/meta.yml", + "type": "module", + "meta": { + "name": "aria2", + "description": "CLI Download utility", + "keywords": ["download", "utility", "http(s)"], + "tools": [ + { + "aria2": { + "description": "aria2 is a lightweight multi-protocol & multi-source, cross platform download utility operated in command-line. It supports HTTP/HTTPS, FTP, SFTP, BitTorrent and Metalink.", + "homepage": "https://aria2.github.io/", + "documentation": "https://aria2.github.io/manual/en/html/index.html", + "tool_dev_url": "https://github.com/aria2/aria2/", + "licence": ["GPL v2"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "source_url": { + "type": "string", + "description": "Source URL to be downloaded", + "pattern": "{http,https}*", + "ontologies": [ + { + "edam": "http://edamontology.org/data_1052" + } + ] + } + } + ] + ], + "output": { + "downloaded_file": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "$downloaded_file": { + "type": "file", + "description": "Downloaded file from source", + "pattern": "*.*", + "ontologies": [] + } + } + ] + ], + "versions_aria2": [ + [ + { + "${task.process}": { + "type": "string", + "description": "Process name" + } + }, + { + "aria2": { + "type": "string", + "description": "Tool name" + } + }, + { + "aria2c --version 2>&1 | sed -n 's/^aria2 version \\([^ ]*\\).*/\\1/p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "Process name" + } + }, + { + "aria2": { + "type": "string", + "description": "Tool name" + } + }, + { + "aria2c --version 2>&1 | sed -n 's/^aria2 version \\([^ ]*\\).*/\\1/p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@JoseEspinosa", "@leoisl"], + "maintainers": ["@JoseEspinosa", "@leoisl"] }, - { - "fasta": { - "type": "file", - "description": "Input genome assembly", - "pattern": "*.{fasta,fa,fsa}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - { - "mode": { - "type": "integer", - "description": "Choose the running mode of the program.\n1--Homology-based method;\n2--Structure-based method;\n3--Hybrid of homology-based and structure-based method.\n" - } - } - ], - "output": { - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}.log": { - "type": "file", - "description": "AnnoSINE_v2 log file\n", - "pattern": "*.{log}", - "ontologies": [] - } - } - ] - ], - "fa": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}.fa": { - "type": "map", - "description": "Non-redundant SINE library with serial number\n", - "pattern": "*.{fa}" - } - } - ] - ], - "versions_annosine": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "annosine": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pip show annosine2 | sed -n 's/Version: //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "annosine": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pip show annosine2 | sed -n 's/Version: //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "proteinannotator", + "version": "1.1.0" + }, + { + "name": "proteinfold", + "version": "2.0.0" + } ] - ] - }, - "authors": [ - "@GallVp" - ], - "maintainers": [ - "@GallVp" - ] - } - }, - { - "name": "annotsv_annotsv", - "path": "modules/nf-core/annotsv/annotsv/meta.yml", - "type": "module", - "meta": { - "name": "annotsv_annotsv", - "description": "Annotation and Ranking of Structural Variation", - "keywords": [ - "annotation", - "structural variants", - "vcf", - "bed", - "tsv" - ], - "tools": [ - { - "annotsv": { - "description": "Annotation and Ranking of Structural Variation", - "homepage": "https://lbgi.fr/AnnotSV/", - "documentation": "https://lbgi.fr/AnnotSV/", - "tool_dev_url": "https://github.com/lgmgeo/AnnotSV", - "doi": "10.1093/bioinformatics/bty304", - "licence": [ - "GPL-3.0" - ], - "identifier": "biotools:AnnotSV" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "sv_vcf": { - "type": "file", - "description": "A VCF or BED file containing the structural variants to be annotated", - "pattern": "*.{bed,vcf,vcf.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3003" - }, - { - "edam": "http://edamontology.org/format_3016" - } - ] - } - }, - { - "sv_vcf_index": { - "type": "file", - "description": "OPTIONAL - The index for gzipped VCF files", - "pattern": "*.tbi", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - }, - { - "candidate_small_variants": { - "type": "file", - "description": "OPTIONAL - A file containing candidate small variants", - "pattern": "*.{vcf,vcf.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing annotations information\n" - } - }, - { - "annotations": { - "type": "directory", - "description": "The directory containing the annotations (URL to download this will be made available soon)\nFor now this can be downloaded in the way defined in the repo (https://github.com/lgmgeo/AnnotSV#quick-installation)\n" - } + }, + { + "name": "ariba_getref", + "path": "modules/nf-core/ariba/getref/meta.yml", + "type": "module", + "meta": { + "name": "ariba_getref", + "description": "Download and prepare database for Ariba analysis", + "keywords": ["fastq", "assembly", "resistance", "virulence"], + "tools": [ + { + "ariba": { + "description": "ARIBA: Antibiotic Resistance Identification By Assembly", + "homepage": "https://sanger-pathogens.github.io/ariba/", + "documentation": "https://sanger-pathogens.github.io/ariba/", + "tool_dev_url": "https://github.com/sanger-pathogens/ariba", + "doi": "10.1099/mgen.0.000131", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "db_name": { + "type": "string", + "description": "A database to setup up for Ariba" + } + } + ] + ], + "output": { + "db": [ + [ + { + "meta": { + "type": "file", + "description": "An Ariba prepared database", + "pattern": "*.tar.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + }, + { + "${db_name}.tar.gz": { + "type": "file", + "description": "An Ariba prepared database", + "pattern": "*.tar.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "versions_ariba": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "ariba": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "ariba version | sed -nE \"s/ARIBA version: //p\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "ariba": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "ariba version | sed -nE \"s/ARIBA version: //p\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@rpetit3"], + "maintainers": ["@rpetit3"] } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing candidate genes information\n" - } - }, - { - "candidate_genes": { - "type": "file", - "description": "OPTIONAL - A file containing genes (either space-separated, tab-separated or line-break-separated)", - "pattern": "*.txt", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2330" - } - ] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing candidate false positive SNV information\n" - } - }, - { - "false_positive_snv": { - "type": "file", - "description": "OPTIONAL - A VCF file containing small variant candidates", - "pattern": "*.{vcf,vcf.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - } - ] - } - } - ], - [ - { - "meta5": { - "type": "map", - "description": "Groovy Map containing candidate gene transcripts information\n" - } - }, - { - "gene_transcripts": { - "type": "file", - "description": "OPTIONAL - A file containing the preferred gene transcripts to be used in priority during annotation (either space-separated or tab-separated)", - "pattern": "*.txt", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2330" - } - ] - } - } - ] - ], - "output": { - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.tsv": { - "type": "file", - "description": "A TSV file containing the annotated variants", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "unannotated_tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.unannotated.tsv": { - "type": "file", - "description": "OPTIONAL - TSV file containing the unannotated variants", - "pattern": "*.unannotated.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.vcf": { - "type": "file", - "description": "OPTIONAL - A VCF file containing the annotated variants (created when `-vcf 1` is specified in the args)\n", - "pattern": "*.vcf", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - } - ] - } - } - ] - ], - "versions_annotsv": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "annotsv": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "AnnotSV --version | sed 's/AnnotSV //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "annotsv": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "AnnotSV --version | sed 's/AnnotSV //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@nvnieuwk" - ], - "maintainers": [ - "@nvnieuwk" - ] - }, - "pipelines": [ - { - "name": "pacsomatic", - "version": "dev" - } - ] - }, - { - "name": "annotsv_installannotations", - "path": "modules/nf-core/annotsv/installannotations/meta.yml", - "type": "module", - "meta": { - "name": "annotsv_installannotations", - "description": "Install the AnnotSV annotations", - "keywords": [ - "annotation", - "download", - "installation", - "structural variants" - ], - "tools": [ - { - "annotsv": { - "description": "Annotation and Ranking of Structural Variation", - "homepage": "https://lbgi.fr/AnnotSV/", - "documentation": "https://lbgi.fr/AnnotSV/", - "tool_dev_url": "https://github.com/lgmgeo/AnnotSV", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:AnnotSV" - } - } - ], - "input": [], - "output": { - "annotations": [ - { - "AnnotSV_annotations": { - "type": "file", - "description": "A folder containing the annotations", - "pattern": "AnnotSV_annotations", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ], - "versions_annotsv": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "annotsv": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "AnnotSV --version | sed 's/AnnotSV //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "annotsv": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "AnnotSV --version | sed 's/AnnotSV //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@nvnieuwk" - ], - "maintainers": [ - "@nvnieuwk" - ] - }, - "pipelines": [ - { - "name": "pacsomatic", - "version": "dev" - } - ] - }, - { - "name": "anota2seq_anota2seqrun", - "path": "modules/nf-core/anota2seq/anota2seqrun/meta.yml", - "type": "module", - "meta": { - "name": "anota2seq_anota2seqrun", - "description": "Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq", - "keywords": [ - "riboseq", - "rnaseq", - "translation", - "differential" - ], - "tools": [ - { - "anota2seq": { - "description": "Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq", - "homepage": "https://bioconductor.org/packages/release/bioc/html/anota2seq.html", - "documentation": "https://bioconductor.org/packages/release/bioc/vignettes/anota2seq/inst/doc/anota2seq.pdf", - "doi": "10.18129/B9.bioc.anota2seq", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:anota2seq" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing contrast information. e.g. [ id:'contrast1',\nblocking:'patient' ]\n" - } - }, - { - "sample_treatment_col": { - "type": "string", - "description": "The column in the sample sheet that should be used to define groups for\ncomparison\n" - } - }, - { - "reference": { - "type": "string", - "description": "The value within the contrast_variable column of the sample sheet that\nshould be used to derive the reference samples\n" - } - }, - { - "target": { - "type": "string", - "description": "The value within the contrast_variable column of the sample sheet that\nshould be used to derive the target samples\n" - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy map containing study-wide metadata related to the sample sheet\nand matrix\n" - } - }, - { - "samplesheet": { - "type": "file", - "description": "CSV or TSV format sample sheet with sample metadata\n", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - }, - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - }, - { - "counts": { - "type": "file", - "description": "Raw TSV or CSV format expression matrix\n", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - }, - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "output": { - "translated_mrna": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing contrast information. e.g. [ id:'contrast1',\nblocking:'patient' ]\n" - } - }, - { - "*.translated_mRNA.anota2seq.results.tsv": { - "type": "file", - "description": "anota2seq results for the 'translated mRNA' analysis, describing differences in RNA levels across conditions for Ribo-seq samples. See https://rdrr.io/bioc/anota2seq/man/anota2seqGetOutput.html for description of output columns.", - "pattern": ".translated_mRNA.anota2seq.results.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "total_mrna": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing contrast information. e.g. [ id:'contrast1',\nblocking:'patient' ]\n" - } - }, - { - "*.total_mRNA.anota2seq.results.tsv": { - "type": "file", - "description": "anota2seq results for the 'translated mRNA' analysis, describing differences in RNA levels across conditions for RNA-seq samples. See https://rdrr.io/bioc/anota2seq/man/anota2seqGetOutput.html for description of output columns.", - "pattern": ".total_mRNA.anota2seq.results.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "translation": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing contrast information. e.g. [ id:'contrast1',\nblocking:'patient' ]\n" - } - }, - { - "*.translation.anota2seq.results.tsv": { - "type": "file", - "description": "anota2seq results for the 'translated mRNA' analysis, describing differences in translation across conditions, being differences in translated RNA levels not explained by total RNA levels. See https://rdrr.io/bioc/anota2seq/man/anota2seqGetOutput.html for description of output columns.", - "pattern": ".translation.anota2seq.results.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "buffering": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing contrast information. e.g. [ id:'contrast1',\nblocking:'patient' ]\n" - } - }, - { - "*.buffering.anota2seq.results.tsv": { - "type": "file", - "description": "anota2seq results for the 'translated mRNA' analysis, describing buffering across conditions, being stable levels of translated RNA (from riboseq samples) across conditions, despite changes in total mRNA. See https://rdrr.io/bioc/anota2seq/man/anota2seqGetOutput.html for description of output columns.", - "pattern": ".buffering.anota2seq.results.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "mrna_abundance": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing contrast information. e.g. [ id:'contrast1',\nblocking:'patient' ]\n" - } - }, - { - "*.mRNA_abundance.anota2seq.results.tsv": { - "type": "file", - "description": "anota2seq results for the 'mRNA abunance' analysis, describing changes across conditions consistent between total mRNA and translated RNA (RNA-seq and Riboseq samples). See https://rdrr.io/bioc/anota2seq/man/anota2seqGetOutput.html for description of output columns.", - "pattern": ".mRNA_abundance.anota2seq.results.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "rdata": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing contrast information. e.g. [ id:'contrast1',\nblocking:'patient' ]\n" - } - }, - { - "*.Anota2seqDataSet.rds": { - "type": "file", - "description": "Serialised Anota2seqDataSet object", - "pattern": ".Anota2seqDataSet.rds", - "ontologies": [] - } - } - ] - ], - "fold_change_plot": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing contrast information. e.g. [ id:'contrast1',\nblocking:'patient' ]\n" - } - }, - { - "*.fold_change.png": { - "type": "file", - "description": "A fold change plot in PNG format, from anota2seq's anota2seqPlotFC()\nmethod.\n", - "pattern": ".fold_change.png", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3603" - } - ] - } - } - ] - ], - "interaction_p_distribution_plot": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing contrast information. e.g. [ id:'contrast1',\nblocking:'patient' ]\n" - } - }, - { - "*.interaction_p_distribution.pdf": { - "type": "file", - "description": "The distribution of p-values and adjusted p-values for the omnibus\ninteraction (both using densities and histograms). The second page of\nthe pdf displays the same plots but for the RVM statistics if RVM is\nused.\n", - "pattern": ".interaction_p_distribution.pdf", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3508" - } - ] - } - } - ] - ], - "residual_distribution_summary_plot": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing contrast information. e.g. [ id:'contrast1',\nblocking:'patient' ]\n" - } - }, - { - "*.residual_distribution_summary.jpeg": { - "type": "file", - "description": "Summary plot for assessing normal distribution of regression residuals.\n", - "pattern": ".residual_distribution_summary.jpeg", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3579" - } - ] - } - } - ] - ], - "residual_vs_fitted_plot": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing contrast information. e.g. [ id:'contrast1',\nblocking:'patient' ]\n" - } - }, - { - "*.residual_vs_fitted.jpeg": { - "type": "file", - "description": "QC plot showing residuals against fitted values.\n", - "pattern": ".residual_vs_fitted.jpeg", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3579" - } - ] - } - } - ] - ], - "rvm_fit_for_all_contrasts_group_plot": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing contrast information. e.g. [ id:'contrast1',\nblocking:'patient' ]\n" - } - }, - { - "*.rvm_fit_for_all_contrasts_group.jpg": { - "type": "file", - "description": "QC plot showing the CDF of variance (theoretical vs empirical), all\ncontrasts.\n", - "pattern": ".rvm_fit_for_all_contrasts_group.jpg", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3579" - } - ] - } - } - ] - ], - "rvm_fit_for_interactions_plot": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing contrast information. e.g. [ id:'contrast1',\nblocking:'patient' ]\n" - } - }, - { - "*.rvm_fit_for_interactions.jpg": { - "type": "file", - "description": "QC plot showing the CDF of variance (theoretical vs empirical), for\ninteractions.\n", - "pattern": ".rvm_fit_for_interactions.jpg", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3579" - } - ] - } - } - ] - ], - "rvm_fit_for_omnibus_group_plot": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing contrast information. e.g. [ id:'contrast1',\nblocking:'patient' ]\n" - } - }, - { - "*.rvm_fit_for_omnibus_group.jpg": { - "type": "file", - "description": "QC plot showing the CDF of variance (theoretical vs empirical), for\nomnibus group.\n", - "pattern": ".rvm_fit_for_omnibus_group.jpg", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3579" - } - ] - } - } - ] - ], - "simulated_vs_obt_dfbetas_without_interaction_plot": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing contrast information. e.g. [ id:'contrast1',\nblocking:'patient' ]\n" - } - }, - { - "*.simulated_vs_obt_dfbetas_without_interaction.pdf": { - "type": "file", - "description": "Bar graphs of the frequencies of outlier dfbetas using different\ndfbetas thresholds.\n", - "pattern": ".simulated_vs_obt_dfbetas_without_interaction.pdf", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3508" - } - ] - } - } - ] - ], - "session_info": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing contrast information. e.g. [ id:'contrast1',\nblocking:'patient' ]\n" - } - }, - { - "*.R_sessionInfo.log": { - "type": "file", - "description": "dump of R SessionInfo", - "pattern": "*.log", - "ontologies": [ - { - "edam": "http://edamontology.org/data_1678" - } - ] - } - } - ] - ], - "versions_anota2seq": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "topics": { - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@pinin4fjords" - ], - "maintainers": [ - "@pinin4fjords" - ] - }, - "pipelines": [ - { - "name": "riboseq", - "version": "1.2.0" - } - ] - }, - { - "name": "antismash_antismash", - "path": "modules/nf-core/antismash/antismash/meta.yml", - "type": "module", - "meta": { - "name": "antismash_antismash", - "description": "antiSMASH allows the rapid genome-wide identification, annotation\nand analysis of secondary metabolite biosynthesis gene clusters.\n", - "keywords": [ - "secondary metabolites", - "BGC", - "biosynthetic gene cluster", - "genome mining", - "NRPS", - "RiPP", - "antibiotics", - "prokaryotes", - "bacteria", - "eukaryotes", - "fungi", - "antismash" - ], - "tools": [ - { - "antismash": { - "description": "antiSMASH - the antibiotics and Secondary Metabolite Analysis SHell", - "homepage": "https://docs.antismash.secondarymetabolites.org", - "documentation": "https://docs.antismash.secondarymetabolites.org", - "tool_dev_url": "https://github.com/antismash/antismash", - "doi": "10.1093/nar/gkab335", - "licence": [ - "AGPL v3" - ], - "identifier": "biotools:antismash" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "sequence_input": { - "type": "file", - "description": "Nucleotide sequence file (annotated)", - "pattern": "*.{gbk, gb, gbff, genbank, embl, fasta, fna}", - "ontologies": [] - } - } - ], - { - "databases": { - "type": "directory", - "description": "Downloaded AntiSMASH databases (e.g. in the AntiSMASH installation directory\n\"data/databases\")\n", - "pattern": "*/" - } - }, - { - "gff": { - "type": "file", - "description": "Optional GFF3 file containing premade annotations of the input sequence", - "pattern": "*.gff", - "ontologies": [] - } - } - ], - "output": { - "html_accessory_files": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "${prefix}/{css,images,js}": { - "type": "directory", - "description": "Accessory files for the HTML output", - "pattern": "{css/,images/,js/}" - } - } - ] - ], - "gbk_input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "${prefix}/*.gbk": { - "type": "file", - "description": "Nucleotide sequence and annotations in GenBank format; converted from input file", - "pattern": "*.gbk", - "ontologies": [] - } - } - ] - ], - "json_results": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "${prefix}/*.json": { - "type": "file", - "description": "Nucleotide sequence and annotations in JSON format; converted from GenBank file (gbk_input)", - "pattern": "*.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "${prefix}/*.log": { - "type": "file", - "description": "Contains all the logging output that antiSMASH produced during its run", - "pattern": "*.log", - "ontologies": [] - } - } - ] - ], - "zip": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "${prefix}/*.zip": { - "type": "file", - "description": "Contains a compressed version of the output folder in zip format", - "pattern": "*.zip", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3987" - } - ] - } - } - ] - ], - "html": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "${prefix}/index.html": { - "type": "file", - "description": "Graphical web view of results in HTML format", - "patterN": "index.html", - "ontologies": [] - } - } - ] - ], - "json_sideloading": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "${prefix}/regions.js": { - "type": "file", - "description": "Sideloaded annotations of protoclusters and/or subregions (see antiSMASH documentation \"Annotation sideloading\")", - "pattern": "regions.js", - "ontologies": [] - } - } - ] - ], - "clusterblast_file": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "${prefix}/clusterblast/*_c*.txt": { - "type": "file", - "description": "Output of ClusterBlast algorithm", - "pattern": "clusterblast/*_c*.txt", - "ontologies": [] - } - } - ] - ], - "knownclusterblast_html": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "${prefix}/knownclusterblast/region*/ctg*.html": { - "type": "file", - "description": "Tables with MIBiG hits in HTML format", - "pattern": "knownclusterblast/region*/ctg*.html", - "ontologies": [] - } - } - ] - ], - "knownclusterblast_dir": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "${prefix}/knownclusterblast/": { - "type": "directory", - "description": "Directory with MIBiG hits", - "pattern": "knownclusterblast/" - } - } - ] - ], - "knownclusterblast_txt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "${prefix}/knownclusterblast/*_c*.txt": { - "type": "file", - "description": "Tables with MIBiG hits", - "pattern": "knownclusterblast/*_c*.txt", - "ontologies": [] - } - } - ] - ], - "svg_files_clusterblast": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "${prefix}/svg/clusterblast*.svg": { - "type": "file", - "description": "SVG images showing the % identity of the aligned hits against their queries", - "pattern": "svg/clusterblast*.svg", - "ontologies": [] - } - } - ] - ], - "svg_files_knownclusterblast": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "${prefix}/svg/knownclusterblast*.svg": { - "type": "file", - "description": "SVG images showing the % identity of the aligned hits against their queries", - "pattern": "svg/knownclusterblast*.svg", - "ontologies": [] - } - } - ] - ], - "gbk_results": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "${prefix}/*region*.gbk": { - "type": "file", - "description": "Nucleotide sequence and annotations in GenBank format; one file per antiSMASH hit", - "pattern": "*region*.gbk", - "ontologies": [] - } - } - ] - ], - "clusterblastoutput": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "${prefix}/clusterblastoutput.txt": { - "type": "file", - "description": "Raw BLAST output of known clusters previously predicted by antiSMASH using the built-in ClusterBlast algorithm", - "pattern": "clusterblastoutput.txt", - "ontologies": [] - } - } - ] - ], - "knownclusterblastoutput": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "${prefix}/knownclusterblastoutput.txt": { - "type": "file", - "description": "Raw BLAST output of known clusters of the MIBiG database", - "pattern": "knownclusterblastoutput.txt", - "ontologies": [] - } - } - ] - ], - "versions_antismash": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "antismash": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "antismash --version | sed 's/antiSMASH //;s/-.*//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "antismash": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "antismash --version | sed 's/antiSMASH //;s/-.*//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@jasmezz" - ], - "maintainers": [ - "@jasmezz", - "@jfy133" - ] - }, - "pipelines": [ - { - "name": "funcscan", - "version": "3.0.0" - } - ] - }, - { - "name": "antismash_antismashdownloaddatabases", - "path": "modules/nf-core/antismash/antismashdownloaddatabases/meta.yml", - "type": "module", - "meta": { - "name": "antismash_antismashdownloaddatabases", - "description": "antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters. This module downloads the antiSMASH databases for conda and docker/singularity runs.", - "keywords": [ - "secondary metabolites", - "BGC", - "biosynthetic gene cluster", - "genome mining", - "NRPS", - "RiPP", - "antibiotics", - "prokaryotes", - "bacteria", - "eukaryotes", - "fungi", - "antismash", - "database" - ], - "tools": [ - { - "antismash": { - "description": "antiSMASH - the antibiotics and Secondary Metabolite Analysis SHell", - "homepage": "https://docs.antismash.secondarymetabolites.org", - "documentation": "https://docs.antismash.secondarymetabolites.org", - "tool_dev_url": "https://github.com/antismash/antismash", - "doi": "10.1093/nar/gkab335", - "licence": [ - "AGPL v3" - ], - "identifier": "biotools:antismash" - } - } - ], - "input": [], - "output": { - "database": [ - { - "antismash_db": { - "type": "directory", - "description": "Download directory for antiSMASH databases", - "pattern": "antismash_db" - } - } - ], - "versions_antismash": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "antismash": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "antismash --version | sed 's/antiSMASH //;s/-.*//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "antismash": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "antismash --version | sed 's/antiSMASH //;s/-.*//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@jasmezz" - ], - "maintainers": [ - "@jasmezz", - "@jfy133" - ] - }, - "pipelines": [ - { - "name": "funcscan", - "version": "3.0.0" - } - ] - }, - { - "name": "antismash_antismashlite", - "path": "modules/nf-core/antismash/antismashlite/meta.yml", - "type": "module", - "meta": { - "name": "antismash_antismashlite", - "description": "antiSMASH allows the rapid genome-wide identification, annotation\nand analysis of secondary metabolite biosynthesis gene clusters.\n", - "deprecated": true, - "keywords": [ - "secondary metabolites", - "BGC", - "biosynthetic gene cluster", - "genome mining", - "NRPS", - "RiPP", - "antibiotics", - "prokaryotes", - "bacteria", - "eukaryotes", - "fungi", - "antismash" - ], - "tools": [ - { - "antismashlite": { - "description": "antiSMASH - the antibiotics and Secondary Metabolite Analysis SHell", - "homepage": "https://docs.antismash.secondarymetabolites.org", - "documentation": "https://docs.antismash.secondarymetabolites.org", - "tool_dev_url": "https://github.com/antismash/antismash", - "doi": "10.1093/nar/gkab335", - "licence": [ - "AGPL v3" - ], - "identifier": "biotools:antismash" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "sequence_input": { - "type": "file", - "description": "nucleotide sequence file (annotated)", - "pattern": "*.{gbk, gb, gbff, genbank, embl, fasta, fna}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - }, - { - "edam": "http://edamontology.org/format_1936" - }, - { - "edam": "http://edamontology.org/format_1927" - } - ] - } - } - ], - { - "databases": { - "type": "directory", - "description": "Downloaded AntiSMASH databases (e.g. in the AntiSMASH installation directory\n\"data/databases\")\n", - "pattern": "*/" - } - }, - { - "antismash_dir": { - "type": "directory", - "description": "A local copy of an AntiSMASH installation folder. This is required when running with\ndocker and singularity (not required for conda), due to attempted 'modifications' of\nfiles during database checks in the installation directory, something that cannot\nbe done in immutable docker/singularity containers. Therefore, a local installation\ndirectory needs to be mounted (including all modified files from the downloading step)\nto the container as a workaround.\n", - "pattern": "*/" - } - } - ], - "output": { - "html_accessory_files": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/{css,images,js}": { - "type": "directory", - "description": "Accessory files for the HTML output", - "pattern": "{css/,images/,js/}" - } - } - ] - ], - "gbk_input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/*.gbk": { - "type": "file", - "description": "Nucleotide sequence and annotations in GenBank format; converted from input file", - "pattern": "*.gbk", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1936" - } - ] - } - } - ] - ], - "json_results": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/*.json": { - "type": "file", - "description": "Nucleotide sequence and annotations in JSON format; converted from GenBank file (gbk_input)", - "pattern": "*.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/*.log": { - "type": "file", - "description": "Contains all the logging output that antiSMASH produced during its run", - "pattern": "*.log", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2330" - } - ] - } - } - ] - ], - "zip": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/*.zip": { - "type": "file", - "description": "Contains a compressed version of the output folder in zip format", - "pattern": "*.zip", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3987" - } - ] - } - } - ] - ], - "html": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/index.html": { - "type": "file", - "description": "Graphical web view of results in HTML format", - "patterN": "index.html", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2331" - } - ] - } - } - ] - ], - "json_sideloading": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/regions.js": { - "type": "file", - "description": "Sideloaded annotations of protoclusters and/or subregions (see antiSMASH documentation \"Annotation sideloading\")", - "pattern": "regions.js", - "ontologies": [] - } - } - ] - ], - "clusterblast_file": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/clusterblast/*_c*.txt": { - "type": "file", - "description": "Output of ClusterBlast algorithm", - "pattern": "clusterblast/*_c*.txt", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2330" - } - ] - } - } - ] - ], - "knownclusterblast_html": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/knownclusterblast/region*/ctg*.html": { - "type": "file", - "description": "Tables with MIBiG hits in HTML format", - "pattern": "knownclusterblast/region*/ctg*.html", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2331" - } - ] - } - } - ] - ], - "knownclusterblast_dir": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/knownclusterblast/": { - "type": "directory", - "description": "Directory with MIBiG hits", - "pattern": "knownclusterblast/" - } - } - ] - ], - "knownclusterblast_txt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/knownclusterblast/*_c*.txt": { - "type": "file", - "description": "Tables with MIBiG hits", - "pattern": "knownclusterblast/*_c*.txt", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2330" - } - ] - } - } - ] - ], - "svg_files_clusterblast": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/svg/clusterblast*.svg": { - "type": "file", - "description": "SVG images showing the % identity of the aligned hits against their queries", - "pattern": "svg/clusterblast*.svg", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3604" - } - ] - } - } - ] - ], - "svg_files_knownclusterblast": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/svg/knownclusterblast*.svg": { - "type": "file", - "description": "SVG images showing the % identity of the aligned hits against their queries", - "pattern": "svg/knownclusterblast*.svg", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3604" - } - ] - } - } - ] - ], - "gbk_results": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/*region*.gbk": { - "type": "file", - "description": "Nucleotide sequence and annotations in GenBank format; one file per antiSMASH hit", - "pattern": "*region*.gbk", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1936" - } - ] - } - } - ] - ], - "clusterblastoutput": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/clusterblastoutput.txt": { - "type": "file", - "description": "Raw BLAST output of known clusters previously predicted by antiSMASH using the built-in ClusterBlast algorithm", - "pattern": "clusterblastoutput.txt", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2330" - } - ] - } - } - ] - ], - "knownclusterblastoutput": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/knownclusterblastoutput.txt": { - "type": "file", - "description": "Raw BLAST output of known clusters of the MIBiG database", - "pattern": "knownclusterblastoutput.txt", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2330" - } - ] - } - } - ] - ], - "versions_antismash": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "antismash-lite": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "antismash --version | sed 's/antiSMASH //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "antismash-lite": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "antismash --version | sed 's/antiSMASH //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@jasmezz" - ], - "maintainers": [ - "@jasmezz" - ] - } - }, - { - "name": "antismash_antismashlitedownloaddatabases", - "path": "modules/nf-core/antismash/antismashlitedownloaddatabases/meta.yml", - "type": "module", - "meta": { - "name": "antismash_antismashlitedownloaddatabases", - "description": "antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters. This module downloads the antiSMASH databases for conda and docker/singularity runs.", - "deprecated": true, - "keywords": [ - "secondary metabolites", - "BGC", - "biosynthetic gene cluster", - "genome mining", - "NRPS", - "RiPP", - "antibiotics", - "prokaryotes", - "bacteria", - "eukaryotes", - "fungi", - "antismash", - "database" - ], - "tools": [ - { - "antismash": { - "description": "antiSMASH - the antibiotics and Secondary Metabolite Analysis SHell", - "homepage": "https://docs.antismash.secondarymetabolites.org", - "documentation": "https://docs.antismash.secondarymetabolites.org", - "tool_dev_url": "https://github.com/antismash/antismash", - "doi": "10.1093/nar/gkab335", - "licence": [ - "AGPL v3" - ], - "identifier": "biotools:antismash" - } - } - ], - "input": [ - { - "database_css": { - "type": "directory", - "description": "antismash/outputs/html/css folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.\n", - "pattern": "css", - "ontologies": [] - } - }, - { - "database_detection": { - "type": "directory", - "description": "antismash/detection folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.\n", - "pattern": "detection", - "ontologies": [] - } - }, - { - "database_modules": { - "type": "directory", - "description": "antismash/modules folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.\n", - "pattern": "modules", - "ontologies": [] - } - } - ], - "output": { - "database": [ - { - "antismash_db": { - "type": "directory", - "description": "Download directory for antiSMASH databases", - "pattern": "antismash_db", - "ontologies": [] - } - } - ], - "antismash_dir": [ - { - "antismash_dir": { - "type": "directory", - "description": "antismash installation folder which is being modified during the antiSMASH database downloading step. The modified files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database and installation folder in pipelines.\n", - "pattern": "antismash_dir", - "ontologies": [] - } - } - ], - "versions_antismash": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "antismash-lite": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "antismash --version | sed 's/antiSMASH //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "antismash-lite": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "antismash --version | sed 's/antiSMASH //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@jasmezz" - ], - "maintainers": [ - "@jasmezz" - ] - } - }, - { - "name": "any2fasta", - "path": "modules/nf-core/any2fasta/meta.yml", - "type": "module", - "meta": { - "name": "any2fasta", - "description": "Convert various sequence formats (GenBank, GFF, FASTQ, FASTA, CLUSTAL, Stockholm, GFA) to FASTA format. Input files may be gzip, bzip2, zip, or zstd compressed.", - "keywords": [ - "fasta", - "conversion", - "sequences", - "format", - "genomics" - ], - "tools": [ - { - "any2fasta": { - "description": "Convert various sequence formats to FASTA", - "homepage": "https://github.com/tseemann/any2fasta", - "documentation": "https://github.com/tseemann/any2fasta", - "tool_dev_url": "https://github.com/tseemann/any2fasta", - "licence": [ - "GPL-3.0" - ], - "identifier": "biotools:any2fasta" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "sequence": { - "type": "file", - "description": "Input sequence file in any supported format (GenBank, GFF, FASTQ, FASTA,\nCLUSTAL, Stockholm, GFA). May be gzip, bzip2, zip, or zstd compressed. GFF3 must include a FASTA inside.\n", - "pattern": "*.{gb,gbk,fa,fasta,fna,fq,fastq,gff,gfa,clw,sth,gb.gz,gbk.gz,fa.gz,fasta.gz,fq.gz,fastq.gz}" - } - } - ] - ], - "output": { - "fasta": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.fasta": { - "type": "file", - "description": "Output sequences in FASTA format", - "pattern": "*.fasta" - } - } - ] - ], - "versions_any2fasta": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "any2fasta": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "any2fasta -v 2>&1 | head -1 | sed 's/any2fasta //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "any2fasta": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "any2fasta -v 2>&1 | head -1 | sed 's/any2fasta //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@cwoodside1278" - ], - "maintainers": [ - "@cwoodside1278" - ] - } - }, - { - "name": "apbs", - "path": "modules/nf-core/apbs/meta.yml", - "type": "module", - "meta": { - "name": "apbs", - "description": "Compute biomolecular electrostatics by solving the Poisson-Boltzmann equation\nusing APBS (Adaptive Poisson-Boltzmann Solver). Produces electrostatic potential\nmaps and solvation energy values for large biomolecular assemblages.\n", - "keywords": [ - "electrostatics", - "poisson-boltzmann", - "solvation", - "structural-biology", - "biophysics", - "computational-chemistry" - ], - "tools": [ - { - "apbs": { - "description": "APBS (Adaptive Poisson-Boltzmann Solver) is a software package for modelling\nbiomolecular solvation through solution of the Poisson-Boltzmann equation.\nIt computes electrostatic solvation energies and potentials for large\nbiomolecular assemblages and is widely used in structural biology and\ncomputational biophysics.\n", - "homepage": "https://www.poissonboltzmann.org/", - "documentation": "https://apbs.readthedocs.io/en/latest/", - "tool_dev_url": "https://github.com/Electrostatics/apbs", - "licence": [ - "Custom" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "apbs_input": { - "type": "file", - "description": "APBS input configuration file specifying the electrostatics calculation,\nincluding paths to molecular structure files (PQR/PDB) and calculation\nparameters. The file extension is typically `.in` but `.inp` is also\naccepted for legacy purposes.\n", - "pattern": "*.{in,inp}", - "ontologies": [] - } - }, - { - "pqr": { - "type": "file", - "description": "One or more PQR molecular structure files referenced by the input\nconfiguration file. PQR files contain atomic coordinates, charges, and\nradii used by APBS for electrostatics calculations.\n", - "pattern": "*.pqr", - "ontologies": [ - { - "edam": "http://edamontology.org/format_4035" - } - ] - } - } - ] - ], - "output": { - "dx": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.dx": { - "type": "file", - "description": "OpenDX format volumetric electrostatic potential map file output by APBS.\nOptional: this output is only produced when the input configuration file\ncontains a `write pot dx ` directive.\n", - "pattern": "*.dx", - "ontologies": [] - } - } - ] - ], - "mc": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "io.mc": { - "type": "file", - "description": "APBS multigrid calculation output file containing energy and force\ninformation from the finite difference solver.\n", - "pattern": "io.mc", - "ontologies": [] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}.log": { - "type": "file", - "description": "APBS standard output log file containing calculation results, including\nelectrostatic solvation energies and run diagnostics.\n", - "pattern": "*.log", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2330" - } - ] - } - } - ] - ], - "versions_apbs": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "apbs": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "apbs --version 2>&1 | sed '6!d;s|^.*Version APBS ||; s| .*\\$||'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "apbs": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "apbs --version 2>&1 | sed '6!d;s|^.*Version APBS ||; s| .*\\$||'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@vagkaratzas" - ], - "maintainers": [ - "@vagkaratzas" - ] - } - }, - { - "name": "arcashla_extract", - "path": "modules/nf-core/arcashla/extract/meta.yml", - "type": "module", - "meta": { - "name": "arcashla_extract", - "description": "Extracts reads mapped to chromosome 6 and any HLA decoys or chromosome 6 alternates.", - "keywords": [ - "HLA", - "genotype", - "RNA-seq" - ], - "tools": [ - { - "arcashla": { - "description": "arcasHLA performs high resolution genotyping for HLA class I and class II genes from RNA sequencing, supporting both paired and single-end samples.", - "homepage": "https://github.com/RabadanLab/arcasHLA", - "documentation": "https://github.com/RabadanLab/arcasHLA", - "tool_dev_url": "https://github.com/RabadanLab/arcasHLA", - "doi": "10.1093/bioinformatics/btz474", - "licence": [ - "GPL v3" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file. If the BAM file is not indexed, this tool will run samtools index before extracting reads.", - "pattern": "*.bam", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } + }, + { + "name": "ariba_run", + "path": "modules/nf-core/ariba/run/meta.yml", + "type": "module", + "meta": { + "name": "ariba_run", + "description": "Query input FASTQs against Ariba formatted databases", + "keywords": ["fastq", "assembly", "resistance", "virulence"], + "tools": [ + { + "ariba": { + "description": "ARIBA: Antibiotic Resistance Identification By Assembly", + "homepage": "https://sanger-pathogens.github.io/ariba/", + "documentation": "https://sanger-pathogens.github.io/ariba/", + "tool_dev_url": "https://github.com/sanger-pathogens/ariba", + "doi": "10.1099/mgen.0.000131", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "Paired-end reads in FASTQ format", + "pattern": "*_R[1|2].{fastq.gz,fq.gz}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "db": { + "type": "file", + "description": "An Ariba prepared database", + "pattern": "*.tar.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "output": { + "results": [ + [ + { + "meta": { + "type": "file", + "description": "A directory of Ariba analysis outputs", + "pattern": "*", + "ontologies": [] + } + }, + { + "${prefix}/*": { + "type": "file", + "description": "A directory of Ariba analysis outputs", + "pattern": "*", + "ontologies": [] + } + } + ] + ], + "versions_ariba": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "ariba": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "ariba version 2>&1 | sed '1!d;s/ARIBA version: //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "ariba": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "ariba version 2>&1 | sed '1!d;s/ARIBA version: //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@rpetit3"], + "maintainers": ["@rpetit3"] } - ] - ], - "output": { - "extracted_reads_fastq": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.fq.gz": { - "type": "file", - "description": "FASTQ file(s) containing chromosome 6 reads and related HLA sequences", - "pattern": "*.fq.gz", - "ontologies": [ + }, + { + "name": "arriba_arriba", + "path": "modules/nf-core/arriba/arriba/meta.yml", + "type": "module", + "meta": { + "name": "arriba_arriba", + "description": "Arriba is a command-line tool for the detection of gene fusions from RNA-Seq data.", + "keywords": ["fusion", "arriba", "detection", "RNA-Seq"], + "tools": [ + { + "arriba": { + "description": "Fast and accurate gene fusion detection from RNA-Seq data", + "homepage": "https://github.com/suhrig/arriba", + "documentation": "https://arriba.readthedocs.io/en/latest/", + "tool_dev_url": "https://github.com/suhrig/arriba", + "doi": "10.1101/gr.257246.119", + "licence": ["MIT"], + "identifier": "biotools:Arriba" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Assembly FASTA file", + "pattern": "*.{fasta}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "gtf": { + "type": "file", + "description": "Annotation GTF file", + "pattern": "*.{gtf}", + "ontologies": [] + } + } + ], + { + "blacklist": { + "type": "file", + "description": "Blacklist file", + "pattern": "*.{tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, { - "edam": "http://edamontology.org/format_1930" + "known_fusions": { + "type": "file", + "description": "Known fusions file", + "pattern": "*.{tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, + { + "cytobands": { + "type": "file", + "description": "Cytobands file", + "pattern": "*.{tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } }, { - "edam": "http://edamontology.org/format_3989" + "protein_domains": { + "type": "file", + "description": "Protein domains file", + "pattern": "*.{gff3}", + "ontologies": [] + } } - ] - } - } - ] - ], - "log": [ - { - "*.log": { - "type": "file", - "description": "Log file for run summary", - "pattern": "*.log", - "ontologies": [] - } - } - ], - "intermediate_sam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "temp_files/**.sam": { - "type": "file", - "description": "Optional intermediate SAM file", - "pattern": "*.sam", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2573" - } - ] - } - } - ] - ], - "intermediate_bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "temp_files/**.bam": { - "type": "file", - "description": "Optional intermediate BAM file", - "pattern": "*.bam", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - } - ] - ], - "intermediate_sorted_bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "temp_files/**.sorted.bam": { - "type": "file", - "description": "Optional intermediate sorted BAM file", - "pattern": "*.sorted.bam", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - } - ] - ], - "versions_arcashla": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "arcashla": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "echo 0.5.0": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "arcashla": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "echo 0.5.0": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@christopher-mohr" - ], - "maintainers": [ - "@christopher-mohr" - ] - } - }, - { - "name": "argnorm", - "path": "modules/nf-core/argnorm/meta.yml", - "type": "module", - "meta": { - "name": "argnorm", - "description": "Normalize antibiotic resistance genes (ARGs) using the ARO ontology (developed by CARD).", - "keywords": [ - "amr", - "antimicrobial resistance", - "arg", - "antimicrobial resistance genes", - "genomics", - "metagenomics", - "normalization", - "drug categorization" - ], - "tools": [ - { - "argnorm": { - "description": "Normalize antibiotic resistance genes (ARGs) using the ARO ontology (developed by CARD).", - "homepage": "https://argnorm.readthedocs.io/en/latest/", - "documentation": "https://argnorm.readthedocs.io/en/latest/", - "tool_dev_url": "https://github.com/BigDataBiology/argNorm", - "licence": [ - "MIT" - ], - "identifier": "biotools:argnorm" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "input_tsv": { - "type": "file", - "description": "ARG annotation output", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - { - "tool": { - "type": "string", - "description": "ARG annotation tool used", - "pattern": "argsoap|abricate|deeparg|resfinder|amrfinderplus" - } - }, - { - "db": { - "type": "string", - "description": "Database used for ARG annotation", - "pattern": "sarg|ncbi|resfinder|deeparg|megares|argannot|resfinderfg" - } - } - ], - "output": { - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "Normalized argNorm output", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_argnorm": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "argnorm": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "argnorm --version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "argnorm": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "argnorm --version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@Vedanth-Ramji" - ], - "maintainers": [ - "@Vedanth-Ramji" - ] - }, - "pipelines": [ - { - "name": "funcscan", - "version": "3.0.0" - } - ] - }, - { - "name": "aria2", - "path": "modules/nf-core/aria2/meta.yml", - "type": "module", - "meta": { - "name": "aria2", - "description": "CLI Download utility", - "keywords": [ - "download", - "utility", - "http(s)" - ], - "tools": [ - { - "aria2": { - "description": "aria2 is a lightweight multi-protocol & multi-source, cross platform download utility operated in command-line. 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This information is used to draw ideograms", + "pattern": ".tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + "protein_domains": [ + { + "protein_domains*${genome}*.gff3": { + "type": "file", + "description": "Protein domain annotations", + "pattern": "*.gff3", + "ontologies": [] + } + } + ], + "known_fusions": [ + { + "known_fusions*${genome}*.tsv.gz": { + "type": "file", + "description": "Arriba is more sensitive to those fusions to improve the detection rate of expected or highly relevant events, such as recurrent fusions", + "pattern": "*.tsv.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ], + "versions_arriba": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "arriba": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "arriba -h | grep \"Version:\" 2>&1 | sed \"s/Version:\\s//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "arriba": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "arriba -h | grep \"Version:\" 2>&1 | sed \"s/Version:\\s//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@peterpru"] + } }, { - 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} + "name": "arriba_visualisation", + "path": "modules/nf-core/arriba/visualisation/meta.yml", + "type": "module", + "meta": { + "name": "arriba_visualisation", + "description": "Arriba is a command-line tool for the detection of gene fusions from RNA-Seq data.", + "keywords": ["visualisation", "arriba", "fusion", "RNA-Seq"], + "tools": [ + { + "arriba": { + "description": "Fast and accurate gene fusion detection from RNA-Seq data", + "homepage": "https://github.com/suhrig/arriba", + "documentation": "https://arriba.readthedocs.io/en/latest/", + "tool_dev_url": "https://github.com/suhrig/arriba", + "doi": "10.1101/gr.257246.119", + "licence": ["MIT"], + "identifier": "biotools:Arriba" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + }, + { + "edam": "http://edamontology.org/format_3462" + }, + { + "edam": "http://edamontology.org/format_2573" + } + ] + } + }, + { + "bai": { + "type": "file", + "description": "BAM index file", + "pattern": "*.bai", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3327" + } + ] + } + }, + { + "fusions": { + "type": "file", + "description": "Arriba fusions file", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "gtf": { + "type": "file", + "description": "Annotation GTF file", + "pattern": "*.gtf", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2306" + } + ] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "protein_domains": { + "type": "file", + "description": "Protein domain annotation files", + "pattern": "*.gff3", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1975" + } + ] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "cytobands": { + "type": "file", + "description": "Coordinates of the Giemsa staining bands needed to draw ideograms", + "pattern": ".tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "output": { + "pdf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.pdf": { + "type": "file", + "description": "File contains fusions visualisation", + "pattern": "*.pdf", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3508" + } + ] + } + } + ] + ], + "versions_arriba": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "arriba": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "arriba -h | grep \"Version:\" 2>&1 | sed \"s/Version:\\s//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "arriba": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "arriba -h | grep \"Version:\" 2>&1 | sed \"s/Version:\\s//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@rannick"] }, - 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ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. 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"type": "file", + "description": "BAM file", + "pattern": "*.{sorted.bam}", + "ontologies": [] + } + } + ] + ], + "bai": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.sorted.bam.bai": { + "type": "file", + "description": "BAM index file", + "pattern": "*.{sorted.bai}", + "ontologies": [] + } + } + ] + ], + "bam_trimmed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.trimmed.rg.sorted.bam": { + "type": "file", + "description": "BAM file with the primers left on", + "pattern": "*.{trimmed.rg.sorted.bam}", + "ontologies": [] + } + } + ] + ], + "bai_trimmed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.trimmed.rg.sorted.bam.bai": { + "type": "file", + "description": "BAM index file of bam_trimmed", + "pattern": "*.{sorted.bai}", + "ontologies": [] + } + } + ] + ], + "bam_primertrimmed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.primertrimmed.rg.sorted.bam": { + "type": "file", + "description": "BAM containing reads after primer-binding site trimming", + "pattern": "*.{trimmed.rg.sorted.bam}", + "ontologies": [] + } + } + ] + ], + "bai_primertrimmed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.primertrimmed.rg.sorted.bam.bai": { + "type": "file", + "description": "BAM index file of bam_primertrimmed", + "pattern": "*.{primertrimmed.rg.sorted.bam.bai}", + "ontologies": [] + } + } + ] + ], + "fasta": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.consensus.fasta": { + "type": "file", + "description": "FAST file with consensus sequence", + "pattern": "*.{consensus.fasta}", + "ontologies": [] + } + } + ] + ], + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.pass.vcf.gz": { + "type": "file", + "description": "VCF file containing detected variants passing quality filter", + "pattern": "*.{pass.vcf.gz}", + "ontologies": [] + } + } + ] + ], + "tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.pass.vcf.gz.tbi": { + "type": "file", + "description": "VCF index", + "pattern": "*.{pass.vcf.gz.tbi}", + "ontologies": [] + } + } + ] + ], + "json": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.json": { + "type": "file", + "description": "JSON file for MultiQC", + "pattern": "*.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "versions_artic": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "artic": { + "type": "string", + "description": "The tool name" + } + }, + { + "artic -v 2>&1 | sed 's/^.*artic //; s/ .*\\$//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "artic": { + "type": "string", + "description": "The tool name" + } + }, + { + "artic -v 2>&1 | sed 's/^.*artic //; s/ .*\\$//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@joseespinosa", "@drpatelh"], + "maintainers": ["@joseespinosa", "@drpatelh"] }, - { - "fasta": { - "type": "file", - "description": "FASTA file of input DNA/RNA reference", - "pattern": "*.{fasta,fa}", - "ontologies": [] - } - } - ], - { - "sequencing_system": { - "type": "string", - "description": "The name of Illumina sequencing system of the built-in profile used for simulation" - } - }, - { - "fold_coverage": { - "type": "integer", - "description": "The fold of read coverage to be simulated or number of reads/read pairs generated for each amplicon" - } - }, - { - "read_length": { - "type": "integer", - "description": "The length of reads to be simulated" - } - } - ], - "output": { - "fastq": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.fq.gz": { - "type": "file", - "description": "Simulated reads", - "pattern": "*.fq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "aln": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.aln": { - "type": "file", - "description": "OPTIONAL Alignment file of the simulated reads. Enabled by default, to disable, use -na/--noALN.", - "pattern": "*.aln", - "ontologies": [] - } - } - ] - ], - "sam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.sam": { - "type": "file", - "description": "OPTIONAL Alignment file in SAM format of the simulated reads. Enabled with -sam/--samout.", - "pattern": "*.sam", - "ontologies": [] - } - } - ] - ], - "versions_art_illumina": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "art": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "2016.06.05": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "art": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "2016.06.05": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "viralrecon", + "version": "3.0.0" + } ] - ] - }, - "authors": [ - "@MarieLataretu" - ], - "maintainers": [ - "@MarieLataretu", - "@gallvp" - ] - }, - "pipelines": [ - { - "name": "readsimulator", - "version": "1.0.1" - } - ] - }, - { - "name": "artic_aligntrim", - "path": "modules/nf-core/artic/aligntrim/meta.yml", - "type": "module", - "meta": { - "name": "artic_aligntrim", - "description": "Standalone version of fieldbioinformatics aligntrim. Soft clips amplicon scheme primer sites in BAM/SAM files.", - "keywords": [ - "artic", - "primer trimming", - "amplicon", - "genomics", - "sequencing", - "nanopore", - "illumina" - ], - "tools": [ - { - "align_trim": { - "description": "ARTIC align_trim: A tool for trimming amplicon sequencing primers from aligned reads.", - "homepage": "https://github.com/artic-network/align_trim", - "documentation": "https://github.com/artic-network/align_trim/blob/master/README.md", - "tool_dev_url": "https://github.com/artic-network/align_trim", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "samfile": { - "type": "file", - "description": "BAM or SAM file containing aligned reads", - "pattern": "*.{bam,sam}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - }, - { - "edam": "http://edamontology.org/format_2573" - } - ] - } - }, - { - "scheme_bed": { - "type": "file", - "description": "BED file containing amplicon scheme primer locations", - "pattern": "*.bed", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3617" - } - ] - } + }, + { + "name": "ascat", + "path": "modules/nf-core/ascat/meta.yml", + "type": "module", + "meta": { + "name": "ascat", + "description": "copy number profiles of tumour cells.", + "keywords": ["bam", "copy number", "cram"], + "tools": [ + { + "ascat": { + "description": "ASCAT is a method to derive copy number profiles of tumour cells, accounting for normal cell admixture and tumour aneuploidy. ASCAT infers tumour purity (the fraction of tumour cells) and ploidy (the amount of DNA per tumour cell), expressed as multiples of haploid genomes from SNP array or massively parallel sequencing data, and calculates whole-genome allele-specific copy number profiles (the number of copies of both parental alleles for all SNP loci across the genome).", + "documentation": "https://github.com/VanLoo-lab/ascat/tree/master/man", + "tool_dev_url": "https://github.com/VanLoo-lab/ascat", + "doi": "10.1093/bioinformatics/btaa538", + "licence": ["GPL v3"], + "identifier": "biotools:ascat" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input_normal": { + "type": "file", + "description": "BAM/CRAM file, must adhere to chr1, chr2, ...chrX notation For modifying chromosome notation in bam files please follow https://josephcckuo.wordpress.com/2016/11/17/modify-chromosome-notation-in-bam-file/.", + "pattern": "*.{bam,cram}", + "ontologies": [] + } + }, + { + "index_normal": { + "type": "file", + "description": "index for normal_bam/cram", + "pattern": "*.{bai,crai}", + "ontologies": [] + } + }, + { + "input_tumor": { + "type": "file", + "description": "BAM/CRAM file, must adhere to chr1, chr2, ...chrX notation", + "pattern": "*.{bam,cram}", + "ontologies": [] + } + }, + { + "index_tumor": { + "type": "file", + "description": "index for tumor_bam/cram", + "pattern": "*.{bai,crai}", + "ontologies": [] + } + } + ], + { + "allele_files": { + "type": "file", + "description": "allele files for ASCAT WGS. Can be downloaded here https://github.com/VanLoo-lab/ascat/tree/master/ReferenceFiles/WGS", + "ontologies": [] + } + }, + { + "loci_files": { + "type": "file", + "description": "loci files for ASCAT WGS. Loci files without chromosome notation can be downloaded here https://github.com/VanLoo-lab/ascat/tree/master/ReferenceFiles/WGS Make sure the chromosome notation matches the bam/cram input files. To add the chromosome notation to loci files (hg19/hg38) if necessary, you can run this command `if [[ $(samtools view | head -n1 | cut -f3)\\\" == *\\\"chr\\\"* ]]; then for i in {1..22} X; do sed -i 's/^/chr/' G1000_loci_hg19_chr_${i}.txt; done; fi`", + "ontologies": [] + } + }, + { + "bed_file": { + "type": "file", + "description": "Bed file for ASCAT WES (optional, but recommended for WES)", + "ontologies": [] + } + }, + { + "fasta": { + "type": "file", + "description": "Reference fasta file (optional)", + "ontologies": [] + } + }, + { + "gc_file": { + "type": "file", + "description": "GC correction file (optional) - Used to do logR correction of the tumour sample(s) with genomic GC content", + "ontologies": [] + } + }, + { + "rt_file": { + "type": "file", + "description": "replication timing correction file (optional, provide only in combination with gc_file)", + "ontologies": [] + } + } + ], + "output": { + "allelefreqs": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*alleleFrequencies_chr*.txt": { + "type": "file", + "description": "Files containing allee frequencies per chromosome", + "pattern": "*{alleleFrequencies_chr*.txt}", + "ontologies": [] + } + } + ] + ], + "bafs": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*BAF.txt": { + "type": "file", + "description": "BAF file", + "ontologies": [] + } + } + ] + ], + "cnvs": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*cnvs.txt": { + "type": "file", + "description": "CNV file", + "ontologies": [] + } + } + ] + ], + "logrs": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*LogR.txt": { + "type": "file", + "description": "LogR file", + "ontologies": [] + } + } + ] + ], + "metrics": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*metrics.txt": { + "type": "file", + "description": "File containing quality metrics", + "pattern": "*.{metrics.txt}", + "ontologies": [] + } + } + ] + ], + "png": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*png": { + "type": "file", + "description": "ASCAT plots", + "pattern": "*.{png}", + "ontologies": [] + } + } + ] + ], + "purityploidy": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*purityploidy.txt": { + "type": "file", + "description": "File with purity and ploidy data", + "pattern": "*.{purityploidy.txt}", + "ontologies": [] + } + } + ] + ], + "segments": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*segments.txt": { + "type": "file", + "description": "File with segments data", + "pattern": "*.{segments.txt}", + "ontologies": [] + } + } + ] + ], + "versions_ascat": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bioconductor-ascat": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "Rscript -e \"library(ASCAT); cat(as.character(packageVersion('ASCAT')))\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_allelecounter": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "alleleCounter": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "alleleCounter --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bioconductor-ascat": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "Rscript -e \"library(ASCAT); cat(as.character(packageVersion('ASCAT')))\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "alleleCounter": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "alleleCounter --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@aasNGC", "@lassefolkersen", "@FriederikeHanssen", "@maxulysse", "@SusiJo"], + "maintainers": ["@aasNGC", "@lassefolkersen", "@FriederikeHanssen", "@maxulysse", "@SusiJo"] }, - { - "normalise_depth": { - "type": "integer", - "description": "Normalise the read depth to this value" - } - } - ], - { - "sort_bam": { - "type": "boolean", - "description": "Optionally sort the BAM file after trimming" - } - } - ], - "output": { - "primertrimmed_bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.primertrimmed*.bam": { - "type": "file", - "description": "BAM file with primer sequences soft clipped", - "pattern": "*.primertrimmed*.bam", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - } - ] - ], - "align_trim_report": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + "pipelines": [ + { + "name": "sarek", + "version": "3.8.1" } - }, - { - "*.align_trim_report.tsv": { - "type": "file", - "description": "TSV report containing full details of primer trimming for each read / read pair", - "pattern": "*.align_trim_report.tsv", - "ontologies": [ + ] + }, + { + "name": "ashlar", + "path": "modules/nf-core/ashlar/meta.yml", + "type": "module", + "meta": { + "name": "ashlar", + "description": "Alignment by Simultaneous Harmonization of Layer/Adjacency Registration", + "keywords": ["image_processing", "alignment", "registration"], + "tools": [ + { + "ashlar": { + "description": "Alignment by Simultaneous Harmonization of Layer/Adjacency Registration", + "homepage": "https://labsyspharm.github.io/ashlar/", + "documentation": "https://labsyspharm.github.io/ashlar/", + "doi": "10.1093/bioinformatics/btac544", + "licence": ["MIT"], + "identifier": "biotools:ASHLAR" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "images": { + "type": "file", + "description": "Overlapping tile image data in formats from most commercial microscopes", + "pattern": "*.{ome.tiff,ome.tif,rcpnl,btf,nd2,tiff,tif,czi}", + "ontologies": [] + } + } + ], { - "edam": "http://edamontology.org/format_3750" + "opt_dfp": { + "type": "file", + "description": "Optional dark field image data", + "ontologies": [] + } }, { - "edam": "http://edamontology.org/format_3475" + "opt_ffp": { + "type": "file", + "description": "Optional flat field image data", + "ontologies": [] + } } - ] + ], + "output": { + "tif": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.ome.tif": { + "type": "file", + "description": "A pyramidal, tiled OME-TIFF file created from input images.", + "pattern": "*.ome.tif", + "ontologies": [] + } + } + ] + ], + "versions_ashlar": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "ashlar": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "ashlar --version | sed 's/^.*ashlar //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "ashlar": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "ashlar --version | sed 's/^.*ashlar //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@RobJY", "@jmuhlich"], + "maintainers": ["@RobJY", "@jmuhlich"] + }, + "pipelines": [ + { + "name": "mcmicro", + "version": "dev" } - } ] - ], - "amp_depth_report": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + }, + { + "name": "assemblyscan", + "path": "modules/nf-core/assemblyscan/meta.yml", + "type": "module", + "meta": { + "name": "assemblyscan", + "description": "Assembly summary statistics in JSON format", + "keywords": ["assembly", "statistics", "summary", "json"], + "tools": [ + { + "assemblyscan": { + "description": "Assembly summary statistics in JSON format", + "homepage": "https://github.com/rpetit3/assembly-scan", + "documentation": "https://github.com/rpetit3/assembly-scan", + "tool_dev_url": "https://github.com/rpetit3/assembly-scan", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "assembly": { + "type": "file", + "description": "FASTA file for a given assembly", + "pattern": "*.fasta", + "ontologies": [] + } + } + ] + ], + "output": { + "report": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{json,tsv}": { + "type": "file", + "description": "Assembly statistics in tsv or JSON format", + "pattern": "*.{json,tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + }, + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "versions_assemblyscan": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "assemblyscan": { + "type": "string", + "description": "The tool name" + } + }, + { + "assembly-scan --version 2>&1 | sed 's/^.*assembly-scan //; s/Using.*\\$//'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "assemblyscan": { + "type": "string", + "description": "The tool name" + } + }, + { + "assembly-scan --version 2>&1 | sed 's/^.*assembly-scan //; s/Using.*\\$//'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@sateeshperi", "@mjcipriano", "@eit-maxlcummins", "@charles-plessy"], + "maintainers": ["@sateeshperi", "@mjcipriano", "@eit-maxlcummins"] + }, + "pipelines": [ + { + "name": "pairgenomealign", + "version": "2.2.3" } - }, - { - "*.amp_depth_report.tsv": { - "type": "file", - "description": "TSV report containing mean depth per amplicon", - "pattern": "*.amp_depth_report.tsv", - "ontologies": [ + ] + }, + { + "name": "ataqv_ataqv", + "path": "modules/nf-core/ataqv/ataqv/meta.yml", + "type": "module", + "meta": { + "name": "ataqv_ataqv", + "description": "ataqv function of a corresponding ataqv tool", + "keywords": ["ATAC-seq", "qc", "ataqv"], + "tools": [ + { + "ataqv": { + "description": "ataqv is a toolkit for measuring and comparing ATAC-seq results. It was written to help understand how well ATAC-seq assays have worked, and to make it easier to spot differences that might be caused by library prep or sequencing.", + "homepage": "https://github.com/ParkerLab/ataqv/blob/master/README.rst", + "documentation": "https://github.com/ParkerLab/ataqv/blob/master/README.rst", + "tool_dev_url": "https://github.com/ParkerLab/ataqv", + "doi": "10.1016/j.cels.2020.02.009", + "licence": ["GPL v3"], + "identifier": "biotools:ataqv" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file", + "pattern": "*.bam", + "ontologies": [] + } + }, + { + "bai": { + "type": "file", + "description": "BAM index file with the same prefix as bam file. Required if tss_file input is provided.", + "pattern": "*.bam.bai", + "ontologies": [] + } + }, + { + "peak_file": { + "type": "file", + "description": "A BED file of peaks called for alignments in the BAM file", + "pattern": "*.bed", + "ontologies": [] + } + } + ], + { + "organism": { + "type": "string", + "description": "The subject of the experiment, which determines the list of autosomes (see \"Reference Genome Configuration\" section at https://github.com/ParkerLab/ataqv)." + } + }, { - "edam": "http://edamontology.org/format_3750" + "mito_name": { + "type": "string", + "description": "Name of the mitochondrial sequence." + } + }, + { + "tss_file": { + "type": "file", + "description": "A BED file of transcription start sites for the experiment organism. If supplied, a TSS enrichment score will be calculated according to the ENCODE data standards. This calculation requires that the BAM file of alignments be indexed.", + "pattern": "*.bed", + "ontologies": [] + } }, { - "edam": "http://edamontology.org/format_3475" + "excl_regs_file": { + "type": "file", + "description": "A BED file containing excluded regions. Peaks or TSS overlapping these will be ignored.", + "pattern": "*.bed", + "ontologies": [] + } + }, + { + "autosom_ref_file": { + "type": "file", + "description": "A file containing autosomal reference names, one per line. The names must match the reference names in the alignment file exactly, or the metrics based on counts of autosomal alignments will be wrong.", + "ontologies": [] + } } - ] + ], + "output": { + "json": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.ataqv.json": { + "type": "file", + "description": "The JSON file to which metrics will be written.", + "ontologies": [] + } + } + ] + ], + "problems": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.problems": { + "type": "file", + "description": "If given, problematic reads will be logged to a file per read group, with names derived from the read group IDs, with \".problems\" appended. If no read groups are found, the reads will be written to one file named after the BAM file.", + "pattern": "*.problems", + "ontologies": [] + } + } + ] + ], + "versions_ataqv": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "ataqv": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "echo \\$(ataqv --version)": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "ataqv": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "echo \\$(ataqv --version)": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@i-pletenev"], + "maintainers": ["@i-pletenev"] + }, + "pipelines": [ + { + "name": "atacseq", + "version": "2.1.2" } - } - ] - ], - "versions_align_trim": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "align_trim": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "align_trim --version | sed 's/align_trim //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "align_trim": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "align_trim --version | sed 's/align_trim //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@BioWilko" - ], - "maintainers": [ - "@BioWilko" - ] - } - }, - { - "name": "artic_guppyplex", - "path": "modules/nf-core/artic/guppyplex/meta.yml", - "type": "module", - "meta": { - "name": "artic_guppyplex", - "description": "Aggregates fastq files with demultiplexed reads", - "keywords": [ - "artic", - "aggregate", - "demultiplexed reads" - ], - "tools": [ - { - "artic": { - "description": "ARTIC pipeline - a bioinformatics pipeline for working with virus sequencing data sequenced with nanopore", - "homepage": "https://artic.readthedocs.io/en/latest/", - "documentation": "https://artic.readthedocs.io/en/latest/", - "tool_dev_url": "https://github.com/artic-network/fieldbioinformatics", - "licence": [ - "MIT" - ], - "identifier": "biotools:artic" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + }, + { + "name": "ataqv_mkarv", + "path": "modules/nf-core/ataqv/mkarv/meta.yml", + "type": "module", + "meta": { + "name": "ataqv_mkarv", + "description": "mkarv function of a corresponding ataqv tool", + "keywords": ["ataqv", "ATAC-seq", "qc", "mkarv"], + "tools": [ + { + "ataqv": { + "description": "ataqv is a toolkit for measuring and comparing ATAC-seq results. It was written to help understand how well ATAC-seq assays have worked, and to make it easier to spot differences that might be caused by library prep or sequencing.", + "homepage": "https://github.com/ParkerLab/ataqv/blob/master/README.rst", + "documentation": "https://github.com/ParkerLab/ataqv/blob/master/README.rst", + "tool_dev_url": "https://github.com/ParkerLab/ataqv", + "licence": ["GPL v3"], + "identifier": "biotools:ataqv" + } + } + ], + "input": [ + { + "jsons/*": { + "type": "file", + "description": "JSON files", + "pattern": "*.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ], + "output": { + "html": [ + { + "html": { + "type": "directory", + "description": "Web application to visualize results in HTML format", + "pattern": "*.html" + } + } + ], + "versions_ataqv": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "ataqv": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "echo \\$(ataqv --version)": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_mkarv": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "mkarv": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "mkarv --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "ataqv": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "echo \\$(ataqv --version)": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "mkarv": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "mkarv --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@bjlang"], + "maintainers": ["@bjlang"] }, - { - "fastq_dir": { - "type": "directory", - "description": "Directory containing the fastq files with demultiplexed reads", - "pattern": "*" - } - } - ] - ], - "output": { - "fastq": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.fastq.gz": { - "type": "file", - "description": "Aggregated FastQ files", - "pattern": "*.{fastq.gz}", - "ontologies": [] - } - } - ] - ], - "versions_artic": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "artic": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "artic -v 2>&1 | sed \"s/^.*artic //; s/ .*$//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "artic": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "artic -v 2>&1 | sed \"s/^.*artic //; s/ .*$//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "atacseq", + "version": "2.1.2" + } ] - ] - }, - "authors": [ - "@joseespinosa", - "@drpatelh" - ], - "maintainers": [ - "@joseespinosa", - "@drpatelh" - ] - }, - "pipelines": [ - { - "name": "viralrecon", - "version": "3.0.0" - } - ] - }, - { - "name": "artic_minion", - "path": "modules/nf-core/artic/minion/meta.yml", - "type": "module", - "meta": { - "name": "artic_minion", - "description": "Run the alignment/variant-call/consensus logic of the artic pipeline\n", - "keywords": [ - "artic", - "aggregate", - "demultiplexed reads" - ], - "tools": [ - { - "artic": { - "description": "ARTIC pipeline - a bioinformatics pipeline for working with virus sequencing data sequenced with nanopore", - "homepage": "https://artic.readthedocs.io/en/latest/", - "documentation": "https://artic.readthedocs.io/en/latest/", - "tool_dev_url": "https://github.com/artic-network/fieldbioinformatics", - "licence": [ - "MIT" - ], - "identifier": "biotools:artic" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fastq": { - "type": "file", - "description": "FastQ file containing reads", - "pattern": "*.{fastq.gz}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing model information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "model_dir": { - "type": "directory", - "description": "Path containing clair3 models, defaults to models packaged with conda installation", - "pattern": "*" - } - }, - { - "model": { - "type": "string", - "description": "The model to use for clair3, if not provided the pipeline will try to figure\nit out the appropriate model from the read fastq\n" - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing scheme information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Scheme reference fasta file", - "pattern": "*.{fasta}", - "ontologies": [] - } - }, - { - "bed": { - "type": "file", - "description": "Scheme BED file", - "pattern": "*.{bed}", - "ontologies": [] - } - } - ], - { - "hdf5_plugin_path": { - "type": "directory", - "description": "Optional path to HDF5 plugin library" - } - } - ], - "output": { - "results": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.*": { - "type": "file", - "description": "Aggregated FastQ files", - "pattern": "*.fastq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.sorted.bam": { - "type": "file", - "description": "BAM file", - "pattern": "*.{sorted.bam}", - "ontologies": [] - } - } - ] - ], - "bai": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.sorted.bam.bai": { - "type": "file", - "description": "BAM index file", - "pattern": "*.{sorted.bai}", - "ontologies": [] - } - } - ] - ], - "bam_trimmed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.trimmed.rg.sorted.bam": { - "type": "file", - "description": "BAM file with the primers left on", - "pattern": "*.{trimmed.rg.sorted.bam}", - "ontologies": [] - } - } - ] - ], - "bai_trimmed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.trimmed.rg.sorted.bam.bai": { - "type": "file", - "description": "BAM index file of bam_trimmed", - "pattern": "*.{sorted.bai}", - "ontologies": [] - } - } - ] - ], - "bam_primertrimmed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.primertrimmed.rg.sorted.bam": { - "type": "file", - "description": "BAM containing reads after primer-binding site trimming", - "pattern": "*.{trimmed.rg.sorted.bam}", - "ontologies": [] - } - } - ] - ], - "bai_primertrimmed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.primertrimmed.rg.sorted.bam.bai": { - "type": "file", - "description": "BAM index file of bam_primertrimmed", - "pattern": "*.{primertrimmed.rg.sorted.bam.bai}", - "ontologies": [] - } - } - ] - ], - "fasta": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.consensus.fasta": { - "type": "file", - "description": "FAST file with consensus sequence", - "pattern": "*.{consensus.fasta}", - "ontologies": [] - } - } - ] - ], - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.pass.vcf.gz": { - "type": "file", - "description": "VCF file containing detected variants passing quality filter", - "pattern": "*.{pass.vcf.gz}", - "ontologies": [] - } - } - ] - ], - "tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.pass.vcf.gz.tbi": { - "type": "file", - "description": "VCF index", - "pattern": "*.{pass.vcf.gz.tbi}", - "ontologies": [] - } - } - ] - ], - "json": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.json": { - "type": "file", - "description": "JSON file for MultiQC", - "pattern": "*.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "versions_artic": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "artic": { - "type": "string", - "description": "The tool name" - } - }, - { - "artic -v 2>&1 | sed 's/^.*artic //; s/ .*\\$//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "artic": { - "type": "string", - "description": "The tool name" - } - }, - { - "artic -v 2>&1 | sed 's/^.*artic //; s/ .*\\$//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@joseespinosa", - "@drpatelh" - ], - "maintainers": [ - "@joseespinosa", - "@drpatelh" - ] - }, - "pipelines": [ - { - "name": "viralrecon", - "version": "3.0.0" - } - ] - }, - { - "name": "ascat", - "path": "modules/nf-core/ascat/meta.yml", - "type": "module", - "meta": { - "name": "ascat", - "description": "copy number profiles of tumour cells.", - "keywords": [ - "bam", - "copy number", - "cram" - ], - "tools": [ - { - "ascat": { - "description": "ASCAT is a method to derive copy number profiles of tumour cells, accounting for normal cell admixture and tumour aneuploidy. ASCAT infers tumour purity (the fraction of tumour cells) and ploidy (the amount of DNA per tumour cell), expressed as multiples of haploid genomes from SNP array or massively parallel sequencing data, and calculates whole-genome allele-specific copy number profiles (the number of copies of both parental alleles for all SNP loci across the genome).", - "documentation": "https://github.com/VanLoo-lab/ascat/tree/master/man", - "tool_dev_url": "https://github.com/VanLoo-lab/ascat", - "doi": "10.1093/bioinformatics/btaa538", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:ascat" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input_normal": { - "type": "file", - "description": "BAM/CRAM file, must adhere to chr1, chr2, ...chrX notation For modifying chromosome notation in bam files please follow https://josephcckuo.wordpress.com/2016/11/17/modify-chromosome-notation-in-bam-file/.", - "pattern": "*.{bam,cram}", - "ontologies": [] - } - }, - { - "index_normal": { - "type": "file", - "description": "index for normal_bam/cram", - "pattern": "*.{bai,crai}", - "ontologies": [] - } - }, - { - "input_tumor": { - "type": "file", - "description": "BAM/CRAM file, must adhere to chr1, chr2, ...chrX notation", - "pattern": "*.{bam,cram}", - "ontologies": [] - } - }, - { - "index_tumor": { - "type": "file", - "description": "index for tumor_bam/cram", - "pattern": "*.{bai,crai}", - "ontologies": [] - } - } - ], - { - "allele_files": { - "type": "file", - "description": "allele files for ASCAT WGS. Can be downloaded here https://github.com/VanLoo-lab/ascat/tree/master/ReferenceFiles/WGS", - "ontologies": [] - } - }, - { - "loci_files": { - "type": "file", - "description": "loci files for ASCAT WGS. Loci files without chromosome notation can be downloaded here https://github.com/VanLoo-lab/ascat/tree/master/ReferenceFiles/WGS Make sure the chromosome notation matches the bam/cram input files. To add the chromosome notation to loci files (hg19/hg38) if necessary, you can run this command `if [[ $(samtools view | head -n1 | cut -f3)\\\" == *\\\"chr\\\"* ]]; then for i in {1..22} X; do sed -i 's/^/chr/' G1000_loci_hg19_chr_${i}.txt; done; fi`", - "ontologies": [] - } - }, - { - "bed_file": { - "type": "file", - "description": "Bed file for ASCAT WES (optional, but recommended for WES)", - "ontologies": [] - } - }, - { - "fasta": { - "type": "file", - "description": "Reference fasta file (optional)", - "ontologies": [] - } - }, - { - "gc_file": { - "type": "file", - "description": "GC correction file (optional) - Used to do logR correction of the tumour sample(s) with genomic GC content", - "ontologies": [] - } - }, - { - "rt_file": { - "type": "file", - "description": "replication timing correction file (optional, provide only in combination with gc_file)", - "ontologies": [] - } - } - ], - "output": { - "allelefreqs": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*alleleFrequencies_chr*.txt": { - "type": "file", - "description": "Files containing allee frequencies per chromosome", - "pattern": "*{alleleFrequencies_chr*.txt}", - "ontologies": [] - } - } - ] - ], - "bafs": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*BAF.txt": { - "type": "file", - "description": "BAF file", - "ontologies": [] - } - } - ] - ], - "cnvs": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*cnvs.txt": { - "type": "file", - "description": "CNV file", - "ontologies": [] - } - } - ] - ], - "logrs": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*LogR.txt": { - "type": "file", - "description": "LogR file", - "ontologies": [] - } - } - ] - ], - "metrics": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*metrics.txt": { - "type": "file", - "description": "File containing quality metrics", - "pattern": "*.{metrics.txt}", - "ontologies": [] - } - } - ] - ], - "png": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*png": { - "type": "file", - "description": "ASCAT plots", - "pattern": "*.{png}", - "ontologies": [] - } - } - ] - ], - "purityploidy": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*purityploidy.txt": { - "type": "file", - "description": "File with purity and ploidy data", - "pattern": "*.{purityploidy.txt}", - "ontologies": [] - } - } - ] - ], - "segments": [ - [ - { - "meta": { - "type": "map", - 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"edam": "http://edamontology.org/format_3475" + "known_alleles": { + "type": "file", + "description": "Optional tab separated text file containing 1-based list of known alleles. See atlas call documentation.", + "pattern": "*.{txt.tsv}", + "ontologies": [] + } }, { - "edam": "http://edamontology.org/format_3464" + "method": { + "type": "string", + "description": "Which variant calling algorithm to use. Some may require additional parameters supplied via ext.args. Check atlas documentation.", + "pattern": "MLE|Bayesian|allelePresence|randomBase|majorityBase" + } } - ] - } - } - ] - ], - "versions_assemblyscan": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "assemblyscan": { - "type": "string", - "description": "The tool name" - } - }, - { - "assembly-scan --version 2>&1 | sed 's/^.*assembly-scan //; s/Using.*\\$//'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "assemblyscan": { - "type": "string", - "description": "The tool name" - } - }, - { - "assembly-scan --version 2>&1 | sed 's/^.*assembly-scan //; s/Using.*\\$//'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@sateeshperi", - "@mjcipriano", - "@eit-maxlcummins", - "@charles-plessy" - ], - "maintainers": [ - "@sateeshperi", - "@mjcipriano", - "@eit-maxlcummins" - ] - }, - "pipelines": [ - { - "name": "pairgenomealign", - "version": "2.2.3" - } - ] - }, - { - "name": "ataqv_ataqv", - "path": "modules/nf-core/ataqv/ataqv/meta.yml", - "type": "module", - "meta": { - "name": "ataqv_ataqv", - "description": "ataqv function of a corresponding ataqv tool", - "keywords": [ - "ATAC-seq", - "qc", - "ataqv" - ], - "tools": [ - { - "ataqv": { - "description": "ataqv is a toolkit for measuring and comparing ATAC-seq results. 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See atlas call documentation.", - "pattern": "*.{txt.tsv}", - "ontologies": [] - } - }, - { - "method": { - "type": "string", - "description": "Which variant calling algorithm to use. Some may require additional parameters supplied via ext.args. Check atlas documentation.", - "pattern": "MLE|Bayesian|allelePresence|randomBase|majorityBase" - } - } - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.vcf.gz": { - "type": "file", - "description": "VCF file with variant calls", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "versions_atlas": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "atlas": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "(atlas 2>&1) | grep Atlas | head -n 1 | sed -e 's/^[[:space:]]*Atlas //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "atlas": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "(atlas 2>&1) | grep Atlas | head -n 1 | sed -e 's/^[[:space:]]*Atlas //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@jfy133" - ], - "maintainers": [ - "@jfy133" - ] - } - }, - { - "name": "atlas_pmd", - "path": "modules/nf-core/atlas/pmd/meta.yml", - "type": "module", - "meta": { - "name": "atlas_pmd", - "description": "Estimate the post-mortem damage patterns of DNA", - "keywords": [ - "ancient DNA", - "post mortem damage", - "bam" - ], - "tools": [ - { - "atlas": { - "description": "ATLAS, a suite of methods to accurately genotype and estimate genetic diversity", - "homepage": "https://bitbucket.org/wegmannlab/atlas/wiki/Home", - "documentation": "https://bitbucket.org/wegmannlab/atlas/wiki/Home", - "tool_dev_url": "https://bitbucket.org/wegmannlab/atlas", - "doi": "10.1101/105346", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:atlas_db" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "Single input BAM file", - "pattern": "*.bam", - "ontologies": [] - } - }, - { - "bai": { - "type": "file", - "description": "The BAI file for the input BAM file", - "pattern": "*.bai", - "ontologies": [] - } - }, - { - "pool_rg_txt": { - "type": "file", - "description": "Optional. Provide the names of read groups that should be merged for PMD estimation.\nAll read groups that should be pooled listed on one line, separated by any white space.\nOther read groups will be recalibrated separately.\n", - "pattern": "*.txt", - "ontologies": [] - } + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "VCF file with variant calls", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "versions_atlas": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "atlas": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "(atlas 2>&1) | grep Atlas | head -n 1 | sed -e 's/^[[:space:]]*Atlas //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "atlas": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "(atlas 2>&1) | grep Atlas | head -n 1 | sed -e 's/^[[:space:]]*Atlas //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@jfy133"], + "maintainers": ["@jfy133"] } - ], - { - "fasta": { - "type": "file", - "description": "The reference genome provided as FASTA file", - "pattern": "*.fasta", - "ontologies": [] + }, + { + "name": "atlas_pmd", + "path": "modules/nf-core/atlas/pmd/meta.yml", + "type": "module", + "meta": { + "name": "atlas_pmd", + "description": "Estimate the post-mortem damage patterns of DNA", + "keywords": ["ancient DNA", "post mortem damage", "bam"], + "tools": [ + { + "atlas": { + "description": "ATLAS, a suite of methods to accurately genotype and estimate genetic diversity", + "homepage": "https://bitbucket.org/wegmannlab/atlas/wiki/Home", + "documentation": "https://bitbucket.org/wegmannlab/atlas/wiki/Home", + "tool_dev_url": "https://bitbucket.org/wegmannlab/atlas", + "doi": "10.1101/105346", + "licence": ["GPL v3"], + "identifier": "biotools:atlas_db" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "Single input BAM file", + "pattern": "*.bam", + "ontologies": [] + } + }, + { + "bai": { + "type": "file", + "description": "The BAI file for the input BAM file", + "pattern": "*.bai", + "ontologies": [] + } + }, + { + "pool_rg_txt": { + "type": "file", + "description": "Optional. Provide the names of read groups that should be merged for PMD estimation.\nAll read groups that should be pooled listed on one line, separated by any white space.\nOther read groups will be recalibrated separately.\n", + "pattern": "*.txt", + "ontologies": [] + } + } + ], + { + "fasta": { + "type": "file", + "description": "The reference genome provided as FASTA file", + "pattern": "*.fasta", + "ontologies": [] + } + }, + { + "fai": { + "type": "file", + "description": "The FAI file for the reference genome FASTA file", + "pattern": "*.fai", + "ontologies": [] + } + } + ], + "output": { + "empiric": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_PMD_input_Empiric.txt": { + "type": "file", + "description": "A list of pmd patterns estimated with the empirical method for each readgroup", + "pattern": "*_PMD_input_Empiric.txt", + "ontologies": [] + } + } + ] + ], + "exponential": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_PMD_input_Exponential.txt": { + "type": "file", + "description": "A list of pmd patterns estimated with the exponential method for each readgroup", + "pattern": "*_PMD_input_Exponential.txt", + "ontologies": [] + } + } + ] + ], + "counts": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_PMD_Table_counts.txt": { + "type": "file", + "description": "The counts of all possible transitions for each read position\n(or up to a certain position, see specific command length)\n", + "pattern": "*_PMD_Table_counts.txt", + "ontologies": [] + } + } + ] + ], + "table": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_PMD_Table.txt": { + "type": "file", + "description": "For all possible transitions the ratio of the transition counts,\nwhich are taken from the _counts.txt table, over the total amount\nof the base that was mutated, for each position and readgroup\n", + "pattern": "*_PMD_Table.txt", + "ontologies": [] + } + } + ] + ], + "versions_atlas": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "atlas": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "atlas | sed -e \"2!d;s/.*Atlas //\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "atlas": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "atlas | sed -e \"2!d;s/.*Atlas //\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@maxibor", "@merszym"], + "maintainers": ["@maxibor", "@merszym"] } - }, - { - "fai": { - "type": "file", - "description": "The FAI file for the reference genome FASTA file", - "pattern": "*.fai", - "ontologies": [] + }, + { + "name": "atlas_recal", + "path": "modules/nf-core/atlas/recal/meta.yml", + "type": "module", + "meta": { + "name": "atlas_recal", + "description": "Gives an estimation of the sequencing bias based on known invariant sites", + "keywords": ["sequencing_bias", "ATLAS", "bias"], + "tools": [ + { + "atlas": { + "description": "ATLAS, a suite of methods to accurately genotype and estimate genetic diversity", + "homepage": "https://bitbucket.org/wegmannlab/atlas/wiki/Home", + "documentation": "https://bitbucket.org/wegmannlab/atlas/wiki/Home", + "doi": "10.1101/105346", + "licence": ["GPL v3"], + "identifier": "biotools:atlas_db" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file", + "pattern": "*.bam", + "ontologies": [] + } + }, + { + "bai": { + "type": "file", + "description": "BAI file", + "pattern": "*.bai", + "ontologies": [] + } + }, + { + "empiric": { + "type": "file", + "description": "Optional txt file from PMD estimations (atlas/pmd)", + "pattern": "*.txt", + "ontologies": [] + } + }, + { + "readgroups": { + "type": "file", + "description": "read groups", + "ontologies": [] + } + } + ], + { + "alleles": { + "type": "file", + "description": "Optional bed file with known alleles", + "pattern": "*.bed", + "ontologies": [] + } + }, + { + "invariant_sites": { + "type": "file", + "description": "Optional bed file with invariant site coordinates", + "pattern": "*.bed", + "ontologies": [] + } + } + ], + "output": { + "recal_patterns": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "file containing the sequencing bias for each of the Read Group pools", + "pattern": "*.txt", + "ontologies": [] + } + } + ] + ], + "versions_atlas": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "atlas": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "((atlas 2>&1) | grep Atlas | head -n 1 | sed -e 's/^[ \t]*Atlas //')": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "atlas": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "((atlas 2>&1) | grep Atlas | head -n 1 | sed -e 's/^[ \t]*Atlas //')": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@ltcrod"], + "maintainers": ["@ltcrod"] } - } - ], - "output": { - "empiric": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_PMD_input_Empiric.txt": { - "type": "file", - "description": "A list of pmd patterns estimated with the empirical method for each readgroup", - "pattern": "*_PMD_input_Empiric.txt", - "ontologies": [] - } - } - ] - ], - "exponential": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_PMD_input_Exponential.txt": { - "type": "file", - "description": "A list of pmd patterns estimated with the exponential method for each readgroup", - "pattern": "*_PMD_input_Exponential.txt", - "ontologies": [] - } - } - ] - ], - "counts": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_PMD_Table_counts.txt": { - "type": "file", - "description": "The counts of all possible transitions for each read position\n(or up to a certain position, see specific command length)\n", - "pattern": "*_PMD_Table_counts.txt", - "ontologies": [] - } - } - ] - ], - "table": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_PMD_Table.txt": { - "type": "file", - "description": "For all possible transitions the ratio of the transition counts,\nwhich are taken from the _counts.txt table, over the total amount\nof the base that was mutated, for each position and readgroup\n", - "pattern": "*_PMD_Table.txt", - "ontologies": [] - } - } - ] - ], - "versions_atlas": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "atlas": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "atlas | sed -e \"2!d;s/.*Atlas //\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "atlas": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "atlas | sed -e \"2!d;s/.*Atlas //\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@maxibor", - "@merszym" - ], - "maintainers": [ - "@maxibor", - "@merszym" - ] - } - }, - { - "name": "atlas_recal", - "path": "modules/nf-core/atlas/recal/meta.yml", - "type": "module", - "meta": { - "name": "atlas_recal", - "description": "Gives an estimation of the sequencing bias based on known invariant sites", - "keywords": [ - "sequencing_bias", - "ATLAS", - "bias" - ], - "tools": [ - { - "atlas": { - "description": "ATLAS, a suite of methods to accurately genotype and estimate genetic diversity", - "homepage": "https://bitbucket.org/wegmannlab/atlas/wiki/Home", - "documentation": "https://bitbucket.org/wegmannlab/atlas/wiki/Home", - "doi": "10.1101/105346", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:atlas_db" + }, + { + "name": "atlas_splitmerge", + "path": "modules/nf-core/atlas/splitmerge/meta.yml", + "type": "module", + "meta": { + "name": "atlas_splitmerge", + "description": "split single end read groups by length and merge paired end reads", + "keywords": ["split", "merge", "bam", "read group"], + "tools": [ + { + "atlas": { + "description": "ATLAS, a suite of methods to accurately genotype and estimate genetic diversity", + "homepage": "https://bitbucket.org/wegmannlab/atlas/wiki/Home", + "documentation": "https://bitbucket.org/wegmannlab/atlas/wiki/Home", + "tool_dev_url": "https://bitbucket.org/wegmannlab/atlas", + "doi": "10.1101/105346", + "licence": ["GPL v3"], + "identifier": "biotools:atlas_db" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "Single input BAM file.", + "pattern": "*.bam", + "ontologies": [] + } + }, + { + "bai": { + "type": "file", + "description": "The BAI file for the input BAM file", + "pattern": "*.bai", + "ontologies": [] + } + }, + { + "read_group_settings": { + "type": "file", + "description": "TXT file containing the split and merge settings for\neach readgroup. Each line consist of one readgroup,\nsingle/double identifier and the maximum cycle number\nof the sequencer. e.g. \"RG1 single 100\"\n", + "pattern": "*.txt", + "ontologies": [] + } + }, + { + "blacklist": { + "type": "file", + "description": "blacklist.txt (optional), A txt file with blacklisted read names\nthat should be ignored and just written to file, each on a new line\n", + "pattern": "*.txt", + "ontologies": [] + } + } + ] + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_mergedReads.bam": { + "type": "file", + "description": "A BAM file with suffix_mergedReads.bam", + "pattern": "*_mergedReads.bam", + "ontologies": [] + } + } + ] + ], + "txt": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt.gz": { + "type": "file", + "description": "A file listing all reads that were filtered out in the merging process with suffix_ignoredReads.txt.gz", + "pattern": "*.txt.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "versions_atlas": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "atlas": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "atlas | sed -e '2!d;s/.*Atlas //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "atlas": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "atlas | sed -e '2!d;s/.*Atlas //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@merszym"], + "maintainers": ["@merszym"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file", - "pattern": "*.bam", - "ontologies": [] - } - }, - { - "bai": { - "type": "file", - "description": "BAI file", - "pattern": "*.bai", - "ontologies": [] - } - }, - { - "empiric": { - "type": "file", - "description": "Optional txt file from PMD estimations (atlas/pmd)", - "pattern": "*.txt", - "ontologies": [] - } + }, + { + "name": "atlasgeneannotationmanipulation_gtf2featureannotation", + "path": "modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/meta.yml", + "type": "module", + "meta": { + "name": "atlasgeneannotationmanipulation_gtf2featureannotation", + "description": "Generate tables of feature metadata from GTF files", + "keywords": ["gtf", "gene", "annotation"], + "tools": [ + { + "atlasgeneannotationmanipulation": { + "description": "Scripts for manipulating gene annotation", + "homepage": "https://github.com/ebi-gene-expression-group/atlas-gene-annotation-manipulation", + "documentation": "https://github.com/ebi-gene-expression-group/atlas-gene-annotation-manipulation", + "tool_dev_url": "https://github.com/ebi-gene-expression-group/atlas-gene-annotation-manipulation", + "licence": ["Apache-2.0"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information on input GTF file\ne.g. [ id:'test' ]\n" + } + }, + { + "gtf": { + "type": "file", + "description": "gtf annotation file", + "pattern": "*.{gtf}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing information in input FASTA file\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "An optional cDNA file for extracting meta info and/or filtering.\n", + "pattern": "*.{gtf}", + "ontologies": [] + } + } + ] + ], + "output": { + "feature_annotation": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.anno.tsv": { + "type": "file", + "description": "TSV file with feature annotation", + "pattern": "*.{tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "filtered_cdna": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.fa.gz": { + "type": "file", + "description": "Where --parse-cdnas is specified in ext.args and an input fasta file is\nprovided, filtered sequences are output to the specified file. No file\nwill be output if this is not specified (for example for use of\n--dummy-from-cdnas only). See documentation at\nhttps://github.com/ebi-gene-expression-group/atlas-gene-annotation-manipulation.\n", + "pattern": "*.{tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_atlasgeneannotationmanipulation": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "atlas-gene-annotation-manipulation": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "1.1.1": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "atlas-gene-annotation-manipulation": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "1.1.1": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@pinin4fjords"], + "maintainers": ["@pinin4fjords"] }, - { - "readgroups": { - "type": "file", - "description": "read groups", - "ontologies": [] - } - } - ], - { - "alleles": { - "type": "file", - "description": "Optional bed file with known alleles", - "pattern": "*.bed", - "ontologies": [] - } - }, - { - "invariant_sites": { - "type": "file", - "description": "Optional bed file with invariant site coordinates", - "pattern": "*.bed", - "ontologies": [] - } - } - ], - "output": { - "recal_patterns": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.txt": { - "type": "file", - "description": "file containing the sequencing bias for each of the Read Group pools", - "pattern": "*.txt", - "ontologies": [] - } - } - ] - ], - "versions_atlas": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "atlas": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "((atlas 2>&1) | grep Atlas | head -n 1 | sed -e 's/^[ \t]*Atlas //')": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "atlas": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "((atlas 2>&1) | grep Atlas | head -n 1 | sed -e 's/^[ \t]*Atlas //')": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "differentialabundance", + "version": "1.5.0" + } ] - ] - }, - "authors": [ - "@ltcrod" - ], - "maintainers": [ - "@ltcrod" - ] - } - }, - { - "name": "atlas_splitmerge", - "path": "modules/nf-core/atlas/splitmerge/meta.yml", - "type": "module", - "meta": { - "name": "atlas_splitmerge", - "description": "split single end read groups by length and merge paired end reads", - "keywords": [ - "split", - "merge", - "bam", - "read group" - ], - "tools": [ - { - "atlas": { - 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} - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "Single input BAM file.", - "pattern": "*.bam", - "ontologies": [] - } - }, - { - "bai": { - "type": "file", - "description": "The BAI file for the input BAM file", - "pattern": "*.bai", - "ontologies": [] - } - }, - { - "read_group_settings": { - "type": "file", - "description": "TXT file containing the split and merge settings for\neach readgroup. Each line consist of one readgroup,\nsingle/double identifier and the maximum cycle number\nof the sequencer. e.g. \"RG1 single 100\"\n", - "pattern": "*.txt", - "ontologies": [] - } + }, + { + "name": "autocycler_cluster", + "path": "modules/nf-core/autocycler/cluster/meta.yml", + "type": "module", + "meta": { + "name": "autocycler_cluster", + "description": "Cluster replicons in compressed assemblies with Autocycler.", + "keywords": ["autocycler", "genome-assembly", "clustering", "long-read"], + "tools": [ + { + "autocycler": { + "description": "A tools for generating consensus long-read assemblies for bacterial genomes.", + "homepage": "https://github.com/rrwick/Autocycler/wiki", + "documentation": "https://github.com/rrwick/Autocycler/wiki", + "tool_dev_url": "https://github.com/rrwick/Autocycler", + "doi": "10.1093/bioinformatics/btaf474", + "licence": ["GPL-3.0"] + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "gfa": { + "type": "file", + "description": "Assembly graph files produced by the compression step.\n", + "pattern": "*/*.gfa" + } + } + ] + ], + "output": { + "clusters": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "clustering/$prefix/qc_pass/*/*.gfa": { + "type": "file", + "description": "Aassembly graphs of clustered contigs.", + "pattern": "clustering/*/qc_pass/*/*.gfa", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3975" + } + ] + } + } + ] + ], + "clusterstats": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "clustering/$prefix/qc_pass/*/*.yaml": { + "type": "file", + "description": "Per-cluster metrics reported by Autocycler.", + "pattern": "clustering/*/qc_pass/*/*.yaml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + ], + "newick": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "clustering/$prefix/*.newick": { + "type": "file", + "description": "Newick tree relating contigs.", + "pattern": "clustering/*/*.newick" + } + } + ] + ], + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "clustering/$prefix/*.tsv": { + "type": "file", + "description": "Tabular summary of cluster relationships.", + "pattern": "clustering/*/*.tsv" + } + } + ] + ], + "pairwisedistances": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "clustering/$prefix/*.phylip": { + "type": "file", + "description": "Pairwise distance matrix in PHYLIP format.", + "pattern": "clustering/*/*.phylip" + } + } + ] + ], + "stats": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "clustering/$prefix/*.yaml": { + "type": "file", + "description": "Run-level statistics for the clustering step.", + "pattern": "clustering/*/*.yaml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + ], + "versions_autocycler": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "autocycler": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "autocycler --version | sed 's/^[^ ]* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "autocycler": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "autocycler --version | sed 's/^[^ ]* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@dwells-eit", "@eit-maxlcummins"], + "maintainers": ["@dwells-eit"] }, - { - "blacklist": { - "type": "file", - "description": "blacklist.txt (optional), A txt file with blacklisted read names\nthat should be ignored and just written to file, each on a new line\n", - "pattern": "*.txt", - "ontologies": [] - } - } - ] - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_mergedReads.bam": { - "type": "file", - "description": "A BAM file with suffix_mergedReads.bam", - "pattern": "*_mergedReads.bam", - "ontologies": [] - } - } - ] - ], - "txt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.txt.gz": { - "type": "file", - "description": "A file listing all reads that were filtered out in the merging process with suffix_ignoredReads.txt.gz", - "pattern": "*.txt.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "versions_atlas": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "atlas": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "atlas | sed -e '2!d;s/.*Atlas //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "atlas": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "atlas | sed -e '2!d;s/.*Atlas //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "bacass", + "version": "2.6.0" + } ] - ] - }, - "authors": [ - "@merszym" - ], - "maintainers": [ - "@merszym" - ] - } - }, - { - "name": "atlasgeneannotationmanipulation_gtf2featureannotation", - "path": "modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/meta.yml", - "type": "module", - "meta": { - "name": "atlasgeneannotationmanipulation_gtf2featureannotation", - "description": "Generate tables of feature metadata from GTF files", - "keywords": [ - "gtf", - "gene", - "annotation" - ], - "tools": [ - { - "atlasgeneannotationmanipulation": { - "description": "Scripts for manipulating gene annotation", - "homepage": "https://github.com/ebi-gene-expression-group/atlas-gene-annotation-manipulation", - "documentation": "https://github.com/ebi-gene-expression-group/atlas-gene-annotation-manipulation", - "tool_dev_url": "https://github.com/ebi-gene-expression-group/atlas-gene-annotation-manipulation", - "licence": [ - "Apache-2.0" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing information on input GTF file\ne.g. [ id:'test' ]\n" - } - }, - { - "gtf": { - "type": "file", - "description": "gtf annotation file", - "pattern": "*.{gtf}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing information in input FASTA file\ne.g. [ id:'test' ]\n" - } + }, + { + "name": "autocycler_combine", + "path": "modules/nf-core/autocycler/combine/meta.yml", + "type": "module", + "meta": { + "name": "autocycler_combine", + "description": "Merge resolved cluster assemblies into final consensus outputs with Autocycler.", + "keywords": ["autocycler", "genome-assembly", "consensus", "long-read"], + "tools": [ + { + "autocycler": { + "description": "A tools for generating consensus long-read assemblies for bacterial genomes.", + "homepage": "https://github.com/rrwick/Autocycler/wiki", + "documentation": "https://github.com/rrwick/Autocycler/wiki", + "tool_dev_url": "https://github.com/rrwick/Autocycler", + "doi": "10.1093/bioinformatics/btaf474", + "licence": ["GPL-3.0"] + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "clusters": { + "type": "file", + "description": "Final cluster assembly graphs (GFA) to be combined into consensus sequences.\n", + "pattern": "*.gfa" + } + } + ] + ], + "output": { + "fasta": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "combine/${prefix}/consensus_assembly.fasta": { + "type": "file", + "description": "Consensus genome sequence generated by Autocycler.", + "pattern": "combine/*/consensus_assembly.fasta", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ] + ], + "gfa": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "combine/${prefix}/consensus_assembly.gfa": { + "type": "file", + "description": "Consensus assembly graph generated by Autocycler.", + "pattern": "combine/*/consensus_assembly.gfa", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3975" + } + ] + } + } + ] + ], + "stats": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "combine/${prefix}/consensus_assembly.yaml": { + "type": "file", + "description": "Run statistics for the combine step.", + "pattern": "combine/*/consensus_assembly.yaml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + ], + "versions_autocycler": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "autocycler": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "autocycler --version | sed 's/^[^ ]* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "autocycler": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "autocycler --version | sed 's/^[^ ]* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@dwells-eit", "@eit-maxlcummins"], + "maintainers": ["@dwells-eit"] }, - { - "fasta": { - "type": "file", - "description": "An optional cDNA file for extracting meta info and/or filtering.\n", - "pattern": "*.{gtf}", - "ontologies": [] - } - } - ] - ], - "output": { - "feature_annotation": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*.anno.tsv": { - "type": "file", - "description": "TSV file with feature annotation", - "pattern": "*.{tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "filtered_cdna": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*.fa.gz": { - "type": "file", - "description": "Where --parse-cdnas is specified in ext.args and an input fasta file is\nprovided, filtered sequences are output to the specified file. No file\nwill be output if this is not specified (for example for use of\n--dummy-from-cdnas only). 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{ - "gfa": { - "type": "file", - "description": "Trimmed assembly graph in GFA format from the previous step.\n", - "pattern": "*.gfa" - } - } - ] - ], - "output": { - "bridged": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "resolve/${prefix}/${prefix}_3_bridged.gfa": { - "type": "file", - "description": "Assembly graph with bridges resolved.", - "pattern": "resolve/*/*_3_bridged.gfa", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3975" - } - ] - } - } - ] - ], - "merged": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "resolve/${prefix}/${prefix}_4_merged.gfa": { - "type": "file", - "description": "Merged assembly graph after bridging.", - "pattern": "resolve/*/*_4_merged.gfa", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3975" - } - ] - } - } - ] - ], - "resolved": [ - 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"type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "mcmicro", + "version": "dev" + } ] - ] - }, - "authors": [ - "@dwells-eit", - "@eit-maxlcummins" - ], - "maintainers": [ - "@dwells-eit" - ] - }, - "pipelines": [ - { - "name": "bacass", - "version": "2.6.0" - } - ] - }, - { - "name": "autocycler_subsample", - "path": "modules/nf-core/autocycler/subsample/meta.yml", - "type": "module", - "meta": { - "name": "autocycler_subsample", - "description": "Downsample long-read sequencing data to the requested coverage using Autocycler.", - "keywords": [ - "autocycler", - "subsampling", - "long-read" - ], - "tools": [ - { - "autocycler": { - "description": "A tools for generating consensus long-read assemblies for bacterial genomes.", - "homepage": "https://github.com/rrwick/Autocycler/wiki", - "documentation": "https://github.com/rrwick/Autocycler/wiki", - "tool_dev_url": "https://github.com/rrwick/Autocycler", - "doi": "10.1093/bioinformatics/btaf474", - 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Must have amrfinderplus database directory already installed within it (in a directory called 'amrfinderplus-db/').\n", + "ontologies": [ + { + "edam": "http://edamontology.org/data_1049" + } + ] + } + }, + { + "proteins": { + "type": "file", + "description": "FASTA/GenBank file of trusted proteins to first annotate from (optional)", + "pattern": "*.{fa,fas,fna,fasta,faa}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + }, { - "edam": "http://edamontology.org/format_1930" + "prodigal_tf": { + "type": "file", + "description": "Training file to use for Prodigal for CDS prediction(optional)", + "pattern": "*.{tf,trn}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2333" + } + ] + } + }, + { + "regions": { + "type": "file", + "description": "GFF3 or GenBank file of pre-annotated regions (optional)", + "pattern": "*.{gbff,gff3}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2206" + } + ] + } }, { - "edam": 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"ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "hypotheticals_faa": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.hypotheticals.faa": { - "type": "file", - "description": "hypothetical protein CDS amino acid sequences as FASTA", - "pattern": "*.hypotheticals.faa", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } ] - ], - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.tsv": { - "type": "file", - "description": "annotations as simple human readable tab separated values", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "txt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.txt": { - "type": "file", - "description": "genome statistics and annotation summary", - "pattern": "*.txt", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_bakta": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bakta": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bakta --version 2>&1 | sed 's/bakta //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bakta": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bakta --version 2>&1 | sed 's/bakta //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] }, - "authors": [ - "@rpetit3", - "@oschwengers", - "@jfy133" - ], - "maintainers": [ - "@rpetit3", - "@oschwengers", - "@jfy133" - ] - }, - "pipelines": [ { - "name": "bacass", - "version": "2.6.0" + "name": "bam2fastx_bam2fastq", + "path": "modules/nf-core/bam2fastx/bam2fastq/meta.yml", + "type": "module", + "meta": { + "name": "bam2fastx_bam2fastq", + "description": "Conversion of PacBio BAM files into gzipped fastq files, including splitting of barcoded data", + "deprecated": true, + "keywords": ["bam2fastx", "bam2fastq", "pacbio"], + "tools": [ + { + "bam2fastx": { + "description": "Converting and demultiplexing of PacBio BAM files into gzipped fasta and fastq files", + "homepage": "https://github.com/PacificBiosciences/bam2fastx", + "documentation": "https://github.com/PacificBiosciences/bam2fastx", + "tool_dev_url": "https://github.com/PacificBiosciences/bam2fastx", + "licence": ["BSD-3-clause-Clear"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "PacBio BAM file", + "pattern": "*.bam", + "ontologies": [] + } + }, + { + "index": { + "type": "file", + "description": "PacBio BAM file index (.pbi)", + "pattern": "*.pbi", + "ontologies": [] + } + } + ] + ], + "output": { + "fastq": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fastq.gz": { + "type": "file", + "description": "Gzipped FASTQ file", + "pattern": "*.fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "versions_bam2fastx": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bam2fastx": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bam2fastq --version 2>&1) | sed 's/^.*bam2fastq //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bam2fastx": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bam2fastq --version 2>&1) | sed 's/^.*bam2fastq //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@priyanka-surana"], + "maintainers": ["@priyanka-surana", "@muffato"] + } }, { - "name": "funcscan", - "version": "3.0.0" + "name": "bamaligncleaner", + "path": "modules/nf-core/bamaligncleaner/meta.yml", + "type": "module", + "meta": { + "name": "bamaligncleaner", + "description": "removes unused references from header of sorted BAM/CRAM files.", + "keywords": ["bam", "clean", "align"], + "tools": [ + { + "bamaligncleaner": { + "description": "Removes unaligned references in aligned BAM alignment file", + "homepage": "https://github.com/maxibor/bamAlignCleaner", + "documentation": "https://github.com/maxibor/bamAlignCleaner", + "tool_dev_url": "https://github.com/maxibor/bamAlignCleaner", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM file", + "pattern": "*.{bam,cram}", + "ontologies": [] + } + } + ] + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Sorted BAM/CRAM file", + "pattern": "*.{bam,cram}", + "ontologies": [] + } + } + ] + ], + "versions_bamaligncleaner": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bamaligncleaner": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bamAlignCleaner --version | sed 's/.*version //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bamaligncleaner": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bamAlignCleaner --version | sed 's/.*version //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@jfy133"], + "maintainers": ["@jfy133"] + } }, { - "name": "pathogensurveillance", - "version": "1.1.0" - } - ] - }, - { - "name": "bakta_baktadbdownload", - "path": "modules/nf-core/bakta/baktadbdownload/meta.yml", - "type": "module", - "meta": { - "name": "bakta_baktadbdownload", - "description": "Downloads BAKTA database from Zenodo", - "keywords": [ - "bakta", - "annotation", - "fasta", - "bacteria", - "database", - "download" - ], - "tools": [ - { - "bakta": { - "description": "Rapid & standardized annotation of bacterial genomes, MAGs & plasmids", - "homepage": "https://github.com/oschwengers/bakta", - "documentation": "https://github.com/oschwengers/bakta", - "tool_dev_url": "https://github.com/oschwengers/bakta", - "doi": "10.1099/mgen.0.000685", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:bakta" - } - } - ], - "input": [], - "output": { - "db": [ - { - "db*": { - "type": "directory", - "description": "BAKTA database directory", - "pattern": "db*/" - } + "name": "bamclipper", + "path": "modules/nf-core/bamclipper/meta.yml", + "type": "module", + "meta": { + "name": "bamclipper", + "description": "This module is used to clip primer sequences from your alignments.", + "keywords": ["primer", "clipping", "genomics", "bam"], + "tools": [ + { + "bamclipper": { + "description": "BAMClipper: removing primers from alignments to minimize false-negative mutations in amplicon next-generation sequencing", + "homepage": "https://github.com/tommyau/bamclipper", + "documentation": "https://github.com/tommyau/bamclipper", + "tool_dev_url": "https://github.com/tommyau/bamclipper", + "doi": "10.1038/s41598-017-01703-6", + "license": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information `[ id:'sample1']`\n" + } + }, + { + "bam": { + "type": "file", + "description": "Sorted BAM file", + "pattern": "*.bam", + "ontologies": [] + } + }, + { + "bai": { + "type": "file", + "description": "BAI index of the input BAM file", + "pattern": "*.bam.bai", + "ontologies": [] + } + }, + { + "bedpe": { + "type": "file", + "description": "BEDPE file of primer pair locations", + "pattern": "*.bed", + "ontologies": [] + } + } + ] + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information `[ id:'sample1']`\n" + } + }, + { + "*.primerclipped.bam": { + "type": "file", + "description": "Sorted BAM file containing clipped query sequences according to the given primer pair locations", + "pattern": "*.primerclipped.bam", + "ontologies": [] + } + } + ] + ], + "bai": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information `[ id:'sample1']`\n" + } + }, + { + "*.primerclipped.bam.bai": { + "type": "file", + "description": "BAI index of the output BAM file", + "pattern": "*.primerclipped.bam.bai", + "ontologies": [] + } + } + ] + ], + "versions_bamclipper": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bamclipper": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "1.0.0": { + "type": "string", + "description": "The hardcoded version of the tool" + } + } + ] + ], + "versions_samtools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "samtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "samtools version | sed '1!d;s/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bamclipper": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "1.0.0": { + "type": "string", + "description": "The hardcoded version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "samtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "samtools version | sed '1!d;s/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@krannich479"], + "maintainers": ["@krannich479"] } - ], - "versions_bakta": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bakta": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bakta --version 2>&1 | sed 's/bakta //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bakta": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bakta --version 2>&1 | sed 's/bakta //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] }, - "authors": [ - "@jfy133", - "@jasmezz" - ], - "maintainers": [ - "@jfy133", - "@jasmezz" - ] - }, - "pipelines": [ { - "name": "bacass", - "version": "2.6.0" + "name": "bamcmp", + "path": "modules/nf-core/bamcmp/meta.yml", + "type": "module", + "meta": { + "name": "bamcmp", + "description": "Bamcmp (Bam Compare) is a tool for assigning reads between a primary genome and a contamination genome. For instance, filtering out mouse reads from patient derived xenograft mouse models (PDX).", + "keywords": ["filter", "xenograft", "host", "graft", "contamination", "mouse"], + "tools": [ + { + "bamcmp": { + "description": "Bamcmp is a tool for deconvolving host and graft reads, using two bam files. Reads should be mapped to two genomes, and the mapped, sorted bam files supplied to the tool. It is highly recommended to use the \"-s as\" option not the \"-s mapq\" option, else reads which multimap to the contamination genome will be spuriously kept.", + "homepage": "https://github.com/CRUKMI-ComputationalBiology/bamcmp", + "documentation": "https://github.com/CRUKMI-ComputationalBiology/bamcmp", + "tool_dev_url": "https://github.com/CRUKMI-ComputationalBiology/bamcmp", + "doi": "10.1158/1541-7786.MCR-16-0431", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "primary_aligned_bam": { + "type": "file", + "description": "BAM/CRAM/SAM file with the reads aligned to the primary genome (the one you want to keep)", + "pattern": "*.{bam,cram,sam}", + "ontologies": [] + } + }, + { + "contaminant_aligned_bam": { + "type": "file", + "description": "BAM/CRAM/SAM file with the reads aligned to the contaminant genome (the one you want to filter out)", + "pattern": "*.{bam,cram,sam}", + "ontologies": [] + } + } + ] + ], + "output": { + "primary_filtered_bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "${prefix}.bam": { + "type": "file", + "description": "Bam file containing the reads which align better to the primary genome.", + "pattern": "*.{bam,cram,sam}", + "ontologies": [] + } + } + ] + ], + "contamination_bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "${prefix2}.bam": { + "type": "file", + "description": "Bam file containing the reads which align better to the contaminant genome.", + "pattern": "*.{bam,cram,sam}", + "ontologies": [] + } + } + ] + ], + "versions_bamcmp": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bamcmp": { + "type": "string", + "description": "The tool name" + } + }, + { + "echo 2.2": { + "type": "string", + "description": "The version used (constant)" + } + } + ] + ], + "versions_samtools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "samtools": { + "type": "string", + "description": "The tool name" + } + }, + { + "samtools version | sed '1!d;s/.* //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bamcmp": { + "type": "string", + "description": "The tool name" + } + }, + { + "echo 2.2": { + "type": "string", + "description": "The version used (constant)" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "samtools": { + "type": "string", + "description": "The tool name" + } + }, + { + "samtools version | sed '1!d;s/.* //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@kmurat1", "@sppearce"], + "maintainers": ["@sppearce"] + } }, { - "name": "funcscan", - "version": "3.0.0" + "name": "bamreadcount", + "path": "modules/nf-core/bamreadcount/meta.yml", + "type": "module", + "meta": { + "name": "bamreadcount", + "description": "bam-readcount is a utility that runs on a BAM or CRAM file and generates low-level information about sequencing data at specific nucleotide positions. Its outputs include observed bases, readcounts, summarized mapping and base qualities, strandedness information, mismatch counts, and position within the reads.", + "keywords": ["BAM", "CRAM", "metrics", "genomics"], + "tools": [ + { + "bamreadcount": { + "description": "bam-readcount generates metrics at single nucleotide positions.", + "homepage": "https://github.com/genome/bam-readcount/blob/master/README.md", + "documentation": "https://github.com/genome/bam-readcount/blob/master/README.md", + "tool_dev_url": "https://github.com/genome/bam-readcount", + "doi": "10.21105/joss.03722", + "licence": ["MIT"], + "identifier": "biotools:bam-readcount" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "bam": { + "type": "file", + "description": "Sorted BAM/CRAM file", + "pattern": "*.{bam,cram}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + }, + { + "edam": "http://edamontology.org/format_2573" + } + ] + } + }, + { + "bai": { + "type": "file", + "description": "BAM/CRAM index file", + "pattern": "*.{bai,crai}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2574" + }, + { + "edam": "http://edamontology.org/format_2575" + } + ] + } + } + ], + { + "reference": { + "type": "file", + "description": "Reference genome FASTA file", + "pattern": "*.{fa,fasta,fa.gz,fasta.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1922" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + }, + { + "bed": { + "type": "file", + "description": "BED file with regions to analyze", + "pattern": "*.bed", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1920" + } + ] + } + } + ], + "output": { + "rc": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.rc": { + "type": "file", + "description": "Readcount file with metrics", + "pattern": "*.rc", + "ontologies": [] + } + } + ] + ], + "versions_bamreadcount": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bamreadcount": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bam-readcount --version | awk -F'version: ' '{print \\$2}' | awk -F'-' '{print \\$1}'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bamreadcount": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bam-readcount --version | awk -F'version: ' '{print \\$2}' | awk -F'-' '{print \\$1}'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@vmelichar"], + "maintainers": ["@vmelichar"] + } }, { - "name": "pathogensurveillance", - "version": "1.1.0" - } - ] - }, - { - "name": "bam2fastx_bam2fastq", - "path": "modules/nf-core/bam2fastx/bam2fastq/meta.yml", - "type": "module", - "meta": { - "name": "bam2fastx_bam2fastq", - "description": "Conversion of PacBio BAM files into gzipped fastq files, including splitting of barcoded data", - "deprecated": true, - "keywords": [ - "bam2fastx", - "bam2fastq", - "pacbio" - ], - "tools": [ - { - "bam2fastx": { - "description": "Converting and demultiplexing of PacBio BAM files into gzipped fasta and fastq files", - "homepage": "https://github.com/PacificBiosciences/bam2fastx", - "documentation": "https://github.com/PacificBiosciences/bam2fastx", - "tool_dev_url": "https://github.com/PacificBiosciences/bam2fastx", - "licence": [ - "BSD-3-clause-Clear" - ], - "identifier": "" + "name": "bamstats_generalstats", + "path": "modules/nf-core/bamstats/generalstats/meta.yml", + "type": "module", + "meta": { + "name": "bamstats_generalstats", + "description": "write your description here", + "keywords": ["bam", "statistics", "genomics"], + "tools": [ + { + "bamstats": { + "description": "A command line tool to compute mapping statistics from a BAM file", + "homepage": "https://github.com/guigolab/bamstats/", + "documentation": "https://github.com/guigolab/bamstats/", + "tool_dev_url": "https://github.com/guigolab", + "licence": ["BSD-3-clause"], + "identifier": "biotools:bamstats-ip" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "bam": { + "type": "file", + "description": "Sorted BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}", + "ontologies": [] + } + } + ] + ], + "output": { + "json": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.json": { + "type": "file", + "description": "json containing bam statistics", + "pattern": "*.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "versions_bamstats": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bamstats": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bamstats --version | grep \"version: \" | sed -e s\"/version: //\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bamstats": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bamstats --version | grep \"version: \" | sed -e s\"/version: //\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@johnoooh"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "PacBio BAM file", - "pattern": "*.bam", - "ontologies": [] - } - }, - { - "index": { - "type": "file", - "description": "PacBio BAM file index (.pbi)", - "pattern": "*.pbi", - "ontologies": [] - } + }, + { + "name": "bamtofastq10x", + "path": "modules/nf-core/bamtofastq10x/meta.yml", + "type": "module", + "meta": { + "name": "bamtofastq10x", + "description": "Tool for converting 10x BAMs produced by Cell Ranger, Space Ranger, Cell Ranger ATAC, Cell Ranger DNA, and Long Ranger back to FASTQ files that can be used as inputs to re-run analysis", + "keywords": ["bam", "convert", "fastq", "10x"], + "tools": [ + { + "bamtofastq10x": { + "description": "Tool for converting 10x BAMs produced by Cell Ranger, Space Ranger, Cell Ranger ATAC, Cell Ranger DNA, and Long Ranger back to FASTQ files that can be used as inputs to re-run analysis", + "homepage": "https://github.com/10XGenomics/bamtofastq", + "documentation": "https://github.com/10XGenomics/bamtofastq", + "tool_dev_url": "https://github.com/10XGenomics/bamtofastq", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file", + "pattern": "*.bam", + "ontologies": [] + } + } + ] + ], + "output": { + "fastq": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "**/*.fastq.gz": { + "type": "file", + "description": "fastq compressed file", + "pattern": "**/*.fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "versions_bamtofastq10x": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bamtofastq10x": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bamtofastq --version |& sed \"1!d ; s/bamtofastq //\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bamtofastq10x": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bamtofastq --version |& sed \"1!d ; s/bamtofastq //\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@BlueBicycleBlog"], + "maintainers": ["@BlueBicycleBlog"] } - ] - ], - "output": { - "fastq": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.fastq.gz": { - "type": "file", - "description": "Gzipped FASTQ file", - "pattern": "*.fastq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } + }, + { + "name": "bamtools_convert", + "path": "modules/nf-core/bamtools/convert/meta.yml", + "type": "module", + "meta": { + "name": "bamtools_convert", + "description": "BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.", + "keywords": [ + "bamtools", + "bamtools/convert", + "bam", + "convert", + "bed", + "fasta", + "fastq", + "json", + "pileup", + "sam", + "yaml" + ], + "tools": [ + { + "bamtools": { + "description": "C++ API & command-line toolkit for working with BAM data", + "homepage": "http://github.com/pezmaster31/bamtools", + "documentation": "https://github.com/pezmaster31/bamtools/wiki", + "tool_dev_url": "http://github.com/pezmaster31/bamtools", + "licence": ["MIT"], + "identifier": "biotools:bamtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file", + "pattern": "*.bam", + "ontologies": [] + } + } + ] + ], + "output": { + "data": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{bed,fasta,fastq,json,pileup,sam,yaml}": { + "type": "file", + "description": "Output file", + "pattern": "*.{bed,fasta,fastq,json,pileup,sam,yaml}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + }, + { + "edam": "http://edamontology.org/format_3464" + }, + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + ], + "versions_bamtools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bamtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bamtools --version | sed '2!d;s/bamtools //g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@sguizard"], + "maintainers": ["@sguizard"], + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bamtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bamtools --version | sed '2!d;s/bamtools //g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + } + }, + "pipelines": [ + { + "name": "isoseq", + "version": "2.0.0" + } ] - 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] - }, - "authors": [ - "@priyanka-surana" - ], - "maintainers": [ - "@priyanka-surana", - "@muffato" - ] - } - }, - { - "name": "bamaligncleaner", - "path": "modules/nf-core/bamaligncleaner/meta.yml", - "type": "module", - "meta": { - "name": "bamaligncleaner", - "description": "removes unused references from header of sorted BAM/CRAM files.", - "keywords": [ - "bam", - "clean", - "align" - ], - "tools": [ - { - "bamaligncleaner": { - "description": "Removes unaligned references in aligned BAM alignment file", - "homepage": "https://github.com/maxibor/bamAlignCleaner", - "documentation": "https://github.com/maxibor/bamAlignCleaner", - "tool_dev_url": "https://github.com/maxibor/bamAlignCleaner", - "licence": [ - "GPL v3" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM file", - "pattern": "*.{bam,cram}", - "ontologies": [] - } + }, + { + "name": "bamutil_clipoverlap", + "path": "modules/nf-core/bamutil/clipoverlap/meta.yml", + "type": "module", + "meta": { + "name": "bamutil_clipoverlap", + "description": "clips overlapping read pairs. When two mates overlap, this tool will clip the record's whose clipped region would have the lowest average quality.", + "keywords": ["bam", "clipping", "clipOverlap", "bamUtil"], + "tools": [ + { + "bamutil": { + "description": "Programs that perform operations on SAM/BAM files, all built into a single executable, bam.", + "homepage": "https://genome.sph.umich.edu/wiki/BamUtil", + "documentation": "https://genome.sph.umich.edu/wiki/BamUtil:_clipOverlap", + "tool_dev_url": "https://github.com/statgen/bamUtil", + "doi": "10.1101/gr.176552.114", + "licence": ["GPL v3"], + "identifier": "biotools:bamutil" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "bam": { + "type": "file", + "description": "Coordinate/ReadName sorted BAM/SAM/uncompressedBAM file", + "pattern": "*.{bam,sam,ubam}", + "ontologies": [] + } + } + ] + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Coordinate/ReadName sorted BAM/SAM/uncompressedBAM file", + "pattern": "*.{bam}", + "ontologies": [] + } + } + ] + ], + "stats_log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.log": { + "type": "file", + "description": "basic overlap statistics when unabled with --stats", + "pattern": "*.{log}", + "ontologies": [] + } + } + ] + ], + "versions_bamutil": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bamutil": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bam clipOverlap 2>&1 | grep '^Version:' | sed 's/^Version: //;s/;.*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bamutil": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bam clipOverlap 2>&1 | grep '^Version:' | sed 's/^Version: //;s/;.*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@Y-Pei"], + "maintainers": ["@Y-Pei"] } - ] - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "Sorted BAM/CRAM file", - "pattern": "*.{bam,cram}", - "ontologies": [] - } - } - ] - ], - "versions_bamaligncleaner": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bamaligncleaner": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bamAlignCleaner --version | sed 's/.*version //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bamaligncleaner": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bamAlignCleaner --version | sed 's/.*version //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@jfy133" - ], - "maintainers": [ - "@jfy133" - ] - } - }, - { - "name": "bamclipper", - "path": "modules/nf-core/bamclipper/meta.yml", - "type": "module", - "meta": { - "name": "bamclipper", - "description": "This module is used to clip primer sequences from your alignments.", - "keywords": [ - "primer", - "clipping", - "genomics", - "bam" - ], - "tools": [ - { - "bamclipper": { - "description": "BAMClipper: removing primers from alignments to minimize false-negative mutations in amplicon next-generation sequencing", - "homepage": "https://github.com/tommyau/bamclipper", - "documentation": "https://github.com/tommyau/bamclipper", - "tool_dev_url": "https://github.com/tommyau/bamclipper", - "doi": "10.1038/s41598-017-01703-6", - "license": [ - "MIT" - ], - "identifier": "" + }, + { + "name": "bamutil_trimbam", + "path": "modules/nf-core/bamutil/trimbam/meta.yml", + "type": "module", + "meta": { + "name": "bamutil_trimbam", + "description": "trims the end of reads in a SAM/BAM file, changing read ends to ‘N’ and quality to ‘!’, or by soft clipping", + "keywords": ["bam", "trim", "clipping", "bamUtil", "trimBam"], + "tools": [ + { + "bamutil": { + "description": "Programs that perform operations on SAM/BAM files, all built into a single executable, bam.", + "homepage": "https://genome.sph.umich.edu/wiki/BamUtil", + "documentation": "https://genome.sph.umich.edu/wiki/BamUtil:_trimBam", + "tool_dev_url": "https://github.com/statgen/bamUtil", + "doi": "10.1101/gr.176552.114", + "licence": ["GPL v3"], + "identifier": "biotools:bamutil" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file", + "pattern": "*.bam", + "ontologies": [] + } + }, + { + "trim_left": { + "type": "integer", + "description": "Number of bases to trim off the right-hand side of a read. Reverse strands are reversed before trimming." + } + }, + { + "trim_right": { + "type": "integer", + "description": "Number of bases to trim off the right-hand side of a read. Reverse strands are reversed before trimming." + } + } + ] + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Trimmed but unsorted BAM file", + "pattern": "*.bam", + "ontologies": [] + } + } + ] + ], + "versions_bamutil": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bamutil": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bam trimBam 2>&1 | head -1 | sed 's/^Version: //;s/;.*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bamutil": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bam trimBam 2>&1 | head -1 | sed 's/^Version: //;s/;.*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@jfy133"], + "maintainers": ["@jfy133"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information `[ id:'sample1']`\n" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM file", - "pattern": "*.bam", - "ontologies": [] - } - }, - { - "bai": { - "type": "file", - "description": "BAI index of the input BAM file", - "pattern": "*.bam.bai", - "ontologies": [] - } + }, + { + "name": "bandage_image", + "path": "modules/nf-core/bandage/image/meta.yml", + "type": "module", + "meta": { + "name": "bandage_image", + "description": "Render an assembly graph in GFA 1.0 format to PNG and SVG image formats", + "keywords": ["gfa", "graph", "assembly", "visualisation"], + "tools": [ + { + "bandage": { + "description": "Bandage - a Bioinformatics Application for Navigating De novo Assembly Graphs Easily\n", + "homepage": "https://github.com/rrwick/Bandage", + "documentation": "https://github.com/rrwick/Bandage", + "licence": ["GPL-3.0-or-later"], + "identifier": "biotools:bandage" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "gfa": { + "type": "file", + "description": "Assembly graph in GFA 1.0 format", + "pattern": "*.gfa", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3975" + } + ] + } + } + ] + ], + "output": { + "png": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.png": { + "type": "file", + "description": "Bandage image in PNG format", + "pattern": "*.png", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3603" + } + ] + } + } + ] + ], + "svg": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.svg": { + "type": "file", + "description": "Bandage image in SVG format", + "pattern": "*.svg", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3604" + } + ] + } + } + ] + ], + "versions_bandage": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bandage": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "export QT_QPA_PLATFORM=offscreen; Bandage --version 2>&1| grep Version | sed \"s/^Version: //\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bandage": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "export QT_QPA_PLATFORM=offscreen; Bandage --version 2>&1| grep Version | sed \"s/^Version: //\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@heuermh"], + "maintainers": ["@heuermh"] }, - { - "bedpe": { - "type": "file", - "description": "BEDPE file of primer pair locations", - "pattern": "*.bed", - "ontologies": [] - } - } - ] - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information `[ id:'sample1']`\n" - } - }, - { - "*.primerclipped.bam": { - "type": "file", - "description": "Sorted BAM file containing clipped query sequences according to the given primer pair locations", - "pattern": "*.primerclipped.bam", - "ontologies": [] - } - } - ] - ], - "bai": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information `[ id:'sample1']`\n" - } - }, - { - "*.primerclipped.bam.bai": { - "type": "file", - "description": "BAI index of the output BAM file", - "pattern": "*.primerclipped.bam.bai", - "ontologies": [] - } - } - ] - ], - "versions_bamclipper": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bamclipper": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "1.0.0": { - "type": "string", - "description": "The hardcoded version of the tool" - } - } - ] - ], - "versions_samtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bamclipper": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "1.0.0": { - "type": "string", - "description": "The hardcoded version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "viralrecon", + "version": "3.0.0" + } ] - ] - }, - "authors": [ - "@krannich479" - ], - "maintainers": [ - "@krannich479" - ] - } - }, - { - "name": "bamcmp", - "path": "modules/nf-core/bamcmp/meta.yml", - "type": "module", - "meta": { - "name": "bamcmp", - "description": "Bamcmp (Bam Compare) is a tool for assigning reads between a primary genome and a contamination genome. For instance, filtering out mouse reads from patient derived xenograft mouse models (PDX).", - "keywords": [ - "filter", - "xenograft", - "host", - "graft", - "contamination", - "mouse" - ], - "tools": [ - { - "bamcmp": { - "description": "Bamcmp is a tool for deconvolving host and graft reads, using two bam files. Reads should be mapped to two genomes, and the mapped, sorted bam files supplied to the tool. It is highly recommended to use the \"-s as\" option not the \"-s mapq\" option, else reads which multimap to the contamination genome will be spuriously kept.", - "homepage": "https://github.com/CRUKMI-ComputationalBiology/bamcmp", - "documentation": "https://github.com/CRUKMI-ComputationalBiology/bamcmp", - "tool_dev_url": "https://github.com/CRUKMI-ComputationalBiology/bamcmp", - "doi": "10.1158/1541-7786.MCR-16-0431", - "licence": [ - "GPL v3" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "primary_aligned_bam": { - "type": "file", - "description": "BAM/CRAM/SAM file with the reads aligned to the primary genome (the one you want to keep)", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } + }, + { + "name": "barrnap", + "path": "modules/nf-core/barrnap/meta.yml", + "type": "module", + "meta": { + "name": "barrnap", + "description": "barrnap uses a hmmer profile to find rrnas in reads or contig fasta files", + "keywords": ["rrna", "sequences", "removal"], + "tools": [ + { + "barrnap": { + "description": "Barrnap predicts the location of ribosomal RNA genes in genomes (bacteria, archaea, metazoan mitochondria and eukaryotes).", + "homepage": "https://github.com/tseemann/barrnap", + "documentation": "https://github.com/tseemann/barrnap", + "tool_dev_url": "https://github.com/tseemann/barrnap", + "licence": ["GPL v3"], + "identifier": "biotools:barrnap" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "fasta file", + "pattern": "*.fasta", + "ontologies": [] + } + }, + { + "dbname": { + "type": "string", + "description": "database to use(bacteria, archaea, eukaryota, metazoan mitochondria)" + } + } + ] + ], + "output": { + "gff": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.gff": { + "type": "file", + "description": "gff file containing coordinates of genes", + "pattern": "*.gff", + "ontologies": [] + } + } + ] + ], + "versions_barrnap": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "barrnap": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "barrnap --version 2>&1 | sed \"s/barrnap //g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "barrnap": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "barrnap --version 2>&1 | sed \"s/barrnap //g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@danilodileo", "@srisarya"], + "maintainers": ["@danilodileo"] }, - { - "contaminant_aligned_bam": { - "type": "file", - "description": "BAM/CRAM/SAM file with the reads aligned to the contaminant genome (the one you want to filter out)", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } - } - ] - ], - "output": { - "primary_filtered_bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "${prefix}.bam": { - "type": "file", - "description": "Bam file containing the reads which align better to the primary genome.", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } - } - ] - ], - "contamination_bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "${prefix2}.bam": { - "type": "file", - "description": "Bam file containing the reads which align better to the contaminant genome.", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } - } - ] - ], - "versions_bamcmp": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bamcmp": { - "type": "string", - "description": "The tool name" - } - }, - { - "echo 2.2": { - "type": "string", - "description": "The version used (constant)" - } - } - ] - ], - "versions_samtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "samtools": { - "type": "string", - "description": "The tool name" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } + "pipelines": [ + { + "name": "seqsubmit", + "version": "dev" + } ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bamcmp": { - "type": "string", - "description": "The tool name" - } - }, - { - "echo 2.2": { - "type": "string", - "description": "The version used (constant)" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "samtools": { - "type": "string", - "description": "The tool name" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } + }, + { + "name": "bases2fastq", + "path": "modules/nf-core/bases2fastq/meta.yml", + "type": "module", + "meta": { + "name": "bases2fastq", + "description": "Demultiplex Element Biosciences bases files", + "keywords": ["demultiplex", "element", "fastq"], + "tools": [ + { + "bases2fastq": { + "description": "Demultiplexes sequencing data and converts base calls into FASTQ files for secondary analysis", + "homepage": "https://go.elementbiosciences.com/bases2fastq-download", + "documentation": "https://www.elementbiosciences.com/resources/user-guides/workflow/bases2fastq", + "licence": ["http://go.elembio.link/eula"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "run_manifest": { + "type": "file", + "description": "RunManifest file", + "pattern": "*.{csv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + }, + { + "run_dir": { + "type": "directory", + "description": "Input run directory containing optionally containing a RunManifest.json if run_manifest is not supplied" + } + } + ] + ], + "output": { + "sample_fastq": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/Samples/**/*_R*.fastq.gz": { + "type": "file", + "description": "Demultiplexed sample FASTQ files", + "pattern": "${prefix}/Samples/*/*_R*.fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "sample_json": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/Samples/**/*_stats.json": { + "type": "file", + "description": "Demultiplexed sample stats", + "pattern": "${prefix}/Samples/*/*.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "qc_report": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/*_QC.html": { + "type": "file", + "description": "QC HTML report", + "pattern": "${prefix}//*_QC.html", + "ontologies": [] + } + } + ] + ], + "multiqc_report": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/multiqc_report.html": { + "type": "file", + "description": "Multiqc HTML report", + "pattern": "${prefix}/multiqc_report.html", + "ontologies": [] + } + } + ] + ], + "run_stats": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/RunStats.json": { + "type": "file", + "description": "QC HTML report", + "pattern": "${prefix}/*.html", + "ontologies": [] + } + } + ] + ], + "generated_run_manifest": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/RunManifest.json": { + "type": "file", + "description": "Updated Run Manifest JSON from the run_manifest csv", + "pattern": "${prefix}/RunManifest.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "metrics": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/Metrics.csv": { + "type": "file", + "description": "Sample metrics", + "pattern": "${prefix}/Metrics.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "unassigned": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/UnassignedSequences.csv": { + "type": "file", + "description": "Unassigned Sequences", + "pattern": "${prefix}/UnassignedSequences.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "versions_bases2fastq": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + 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sourceforge.net/projects/bbmap/"], + "identifier": "biotools:bbmap" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fastq": { + "type": "file", + "description": "fastq file", + "pattern": "*.{fastq,fq}(.gz)?", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ] + ], + "output": { + "fastq": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fastq.gz": { + "type": "file", + "description": "fastq file", + "pattern": "*.{fastq, fq}.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "log file", + "pattern": "*.log", + "ontologies": [] + } + } + ] + ], + "versions_bbmap": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bbmap": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bbversion.sh | grep -v \"Duplicate cpuset\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bbmap": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bbversion.sh | grep -v \"Duplicate cpuset\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@danilodileo"], + "maintainers": ["@danilodileo"] }, - { - "bam": { - "type": "file", - "description": "Sorted BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } - } - ] - ], - "output": { - "json": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*.json": { - "type": "file", - "description": "json containing bam statistics", - "pattern": "*.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "versions_bamstats": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bamstats": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bamstats --version | grep \"version: \" | sed -e s\"/version: //\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bamstats": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bamstats --version | grep \"version: \" | sed -e s\"/version: //\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "mag", + "version": "5.4.2" + }, + { + "name": "metatdenovo", + "version": "1.3.0" + } ] - ] - }, - "authors": [ - "@johnoooh" - ] - } - }, - { - "name": "bamtofastq10x", - "path": "modules/nf-core/bamtofastq10x/meta.yml", - "type": "module", - "meta": { - "name": "bamtofastq10x", - "description": "Tool for converting 10x BAMs produced by Cell Ranger, Space Ranger, Cell Ranger ATAC, Cell Ranger DNA, and Long Ranger back to FASTQ files that can be used as inputs to re-run analysis", - "keywords": [ - "bam", - "convert", - "fastq", - "10x" - ], - "tools": [ - { - "bamtofastq10x": { - "description": "Tool for converting 10x BAMs produced by Cell Ranger, Space Ranger, Cell Ranger ATAC, Cell Ranger DNA, and Long Ranger back to FASTQ files that can be used as inputs to re-run analysis", - "homepage": "https://github.com/10XGenomics/bamtofastq", - "documentation": "https://github.com/10XGenomics/bamtofastq", - "tool_dev_url": "https://github.com/10XGenomics/bamtofastq", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } + }, + { + "name": "bbmap_bbsplit", + "path": "modules/nf-core/bbmap/bbsplit/meta.yml", + "type": "module", + "meta": { + "name": "bbmap_bbsplit", + "description": "Split sequencing reads by mapping them to multiple references simultaneously", + "keywords": ["align", "map", "fastq", "genome", "reference"], + "tools": [ + { + "bbmap": { + "description": "BBMap is a short read aligner, as well as various other bioinformatic tools.", + "homepage": "https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/", + "documentation": "https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/", + "licence": ["UC-LBL license (see package)"], + "identifier": "biotools:bbmap" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", + "ontologies": [] + } + } + ], + { + "index": { + "type": "directory", + "description": "Directory to place generated index", + "pattern": "*" + } + }, + { + "primary_ref": { + "type": "file", + "description": "Path to the primary reference", + "pattern": "*", + "ontologies": [] + } + }, + [ + { + "other_ref_names": { + "type": "list", + "description": "List of other reference ids apart from the primary" + } + }, + { + "other_ref_paths": { + "type": "list", + "description": "Path to other references paths corresponding to \"other_ref_names\"" + } + } + ], + { + "only_build_index": { + "type": "string", + "description": "true = only build index; false = mapping" + } + } + ], + "output": { + "index": [ + { + "bbsplit_index": { + "type": "directory", + "description": "Directory with index files", + "pattern": "bbsplit_index" + } + } + ], + "primary_fastq": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*primary*fastq.gz": { + "type": "file", + "description": "Output reads that map to the primary reference", + "pattern": "*primary*fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "all_fastq": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*fastq.gz": { + "type": "file", + "description": "All reads mapping to any of the references", + "pattern": "*fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "stats": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*txt": { + "type": "file", + "description": "Tab-delimited text file containing mapping statistics", + "pattern": "*.txt", + "ontologies": [] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "Log file", + "pattern": "*.log", + "ontologies": [] + } + } + ] + ], + "versions_bbmap": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bbmap": { + "type": "string", + "description": "The tool name" + } + }, + { + "bbversion.sh | grep -v \"Duplicate cpuset\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bbmap": { + "type": "string", + "description": "The tool name" + } + }, + { + "bbversion.sh | grep -v \"Duplicate cpuset\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@joseespinosa", "@drpatelh", "@pinin4fjords"], + "maintainers": ["@joseespinosa", "@drpatelh", "@pinin4fjords"] }, - { - "bam": { - "type": "file", - "description": "BAM file", - "pattern": "*.bam", - "ontologies": [] - } - } - ] - ], - "output": { - "fastq": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "**/*.fastq.gz": { - "type": "file", - "description": "fastq compressed file", - "pattern": "**/*.fastq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "versions_bamtofastq10x": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bamtofastq10x": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bamtofastq --version |& sed \"1!d ; s/bamtofastq //\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bamtofastq10x": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bamtofastq --version |& sed \"1!d ; s/bamtofastq //\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "lncpipe", + "version": "dev" + }, + { + "name": "references", + "version": "0.1" + }, + { + "name": "riboseq", + "version": "1.2.0" + }, + { + "name": "rnaseq", + "version": "3.26.0" + }, + { + "name": "sarek", + "version": "3.8.1" + } ] - ] - }, - "authors": [ - "@BlueBicycleBlog" - ], - "maintainers": [ - "@BlueBicycleBlog" - ] - } - }, - { - "name": "bamtools_convert", - "path": "modules/nf-core/bamtools/convert/meta.yml", - "type": "module", - "meta": { - "name": "bamtools_convert", - "description": "BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.", - "keywords": [ - "bamtools", - "bamtools/convert", - "bam", - "convert", - "bed", - "fasta", - "fastq", - 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And remove duplicates", + "keywords": ["clumping fastqs", "smaller fastqs", "deduping", "fastq"], + "tools": [ + { + "bbmap": { + "description": "BBMap is a short read aligner, as well as various other bioinformatic tools.", + "homepage": "https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/clumpify-guide/", + "documentation": "https://www.biostars.org/p/225338/", + "licence": ["UC-LBL license (see package)"], + "identifier": "biotools:bbmap" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", + "ontologies": [] + } + } + ] + ], + "output": { + "reads": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fastq.gz": { + "type": "file", + "description": "The reordered/clumped (and if necessary deduped) fastq reads", + "pattern": "*.clumped.fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "Clumpify log file", + "pattern": "*clumpify.log", + "ontologies": [] + } + } + ] + ], + "versions_bbmap": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bbmap": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bbversion.sh | grep -v \"Duplicate cpuset\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bbmap": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bbversion.sh | grep -v \"Duplicate cpuset\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@tamuanand"], + "maintainers": ["@tamuanand"] } - ] - ], - "output": { - "data": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.{bed,fasta,fastq,json,pileup,sam,yaml}": { - "type": "file", - "description": "Output file", - "pattern": "*.{bed,fasta,fastq,json,pileup,sam,yaml}", - "ontologies": [ + }, + { + "name": "bbmap_filterbyname", + "path": "modules/nf-core/bbmap/filterbyname/meta.yml", + "type": "module", + "meta": { + "name": "bbmap_filterbyname", + "description": "Filter out sequences by sequence header name(s)", + "keywords": ["fastq", "fasta", "filter"], + "tools": [ + { + "bbmap": { + "description": "BBMap is a short read aligner, as well as various other bioinformatic tools.", + "homepage": "https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/clumpify-guide/", + "documentation": "https://www.biostars.org/p/225338/", + "licence": ["UC-LBL license (see package)"], + "identifier": "biotools:bbmap" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and\npaired-end data, respectively.\n", + "ontologies": [] + } + } + ], { - "edam": "http://edamontology.org/format_1930" + "names_to_filter": { + "type": "string", + "description": "String containing names of reads to filter out of the fastq files.\n" + } }, { - "edam": "http://edamontology.org/format_3464" + "output_format": { + "type": "string", + "description": "String with the format of the output file, e.g. fastq.gz, fasta, fasta.bz2\n" + } }, { - "edam": "http://edamontology.org/format_3750" + "interleaved_output": { + "type": "boolean", + "description": "Whether to produce an interleaved fastq output file\n" + } } - ] + ], + "output": { + "reads": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.${output_format}": { + "type": "file", + "description": "The trimmed/modified fastq reads", + "pattern": "*${output_format}", + "ontologies": [] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "filterbyname.sh log file", + "pattern": "*.filterbyname.log", + "ontologies": [] + } + } + ] + ], + "versions_bbmap": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bbmap": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bbversion.sh | grep -v \"Duplicate cpuset\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bbmap": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bbversion.sh | grep -v \"Duplicate cpuset\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@tokarevvasily", "@sppearce"], + "maintainers": ["@sppearce"] + }, + "pipelines": [ + { + "name": "detaxizer", + "version": "1.3.0" } - } - ] - ], - "versions_bamtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bamtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bamtools --version | sed '2!d;s/bamtools //g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } ] - ] - }, - "authors": [ - "@sguizard" - ], - "maintainers": [ - "@sguizard" - ], - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bamtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bamtools --version | sed '2!d;s/bamtools //g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - } - }, - "pipelines": [ + }, { - "name": "isoseq", - "version": "2.0.0" - } - ] - }, - { - "name": "bamtools_split", - "path": "modules/nf-core/bamtools/split/meta.yml", - "type": "module", - "meta": { - "name": "bamtools_split", - "description": "BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.", - "keywords": [ - "bamtools", - "bamtools/split", - "bam", - "split", - "chunk" - ], - "tools": [ - { - "bamtools": { - "description": "C++ API & command-line toolkit for working with BAM data", - "homepage": "http://github.com/pezmaster31/bamtools", - "documentation": "https://github.com/pezmaster31/bamtools/wiki", - "tool_dev_url": "http://github.com/pezmaster31/bamtools", - "licence": [ - "MIT" - ], - "identifier": "biotools:bamtools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + "name": "bbmap_index", + "path": "modules/nf-core/bbmap/index/meta.yml", + "type": "module", + "meta": { + "name": "bbmap_index", + "description": "Creates an index from a fasta file, ready to be used by bbmap.sh in mapping mode.", + "keywords": ["map", "index", "fasta"], + "tools": [ + { + "bbmap": { + "description": "BBMap is a short read aligner, as well as various other bioinformatic tools.", + "homepage": "https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/", + "documentation": "https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/", + "licence": ["UC-LBL license (see package)"], + "identifier": "biotools:bbmap" + } + } + ], + "input": [ + { + "fasta": { + "type": "file", + "description": "fasta formatted file with nucleotide sequences", + "pattern": "*.{fna,fa,fasta}", + "ontologies": [] + } + } + ], + "output": { + "index": [ + { + "ref": { + "type": "directory", + "description": "Directory containing the index files" + } + } + ], + "versions_bbmap": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bbmap": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bbversion.sh | grep -v \"Duplicate cpuset\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bbmap": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bbversion.sh | grep -v \"Duplicate cpuset\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@erikrikarddaniel"], + "maintainers": ["@erikrikarddaniel"] }, - { - "bam": { - "type": "file", - "description": "A list of one or more BAM files to merge and then split", - "pattern": "*.bam", - "ontologies": [] - } - } - ] - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "Several Bam files", - "pattern": "*.bam", - "ontologies": [] - } - } - ] - ], - "versions_bamtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bamtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bamtools --version | sed '2!d;s/bamtools //g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@sguizard", - "@matthdsm" - ], - "maintainers": [ - "@sguizard", - "@matthdsm" - ], - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bamtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bamtools --version | sed '2!d;s/bamtools //g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "magmap", + "version": "1.0.0" + }, + { + "name": "metatdenovo", + "version": "1.3.0" + } ] - ] - } - }, - "pipelines": [ + }, { - "name": "scnanoseq", - "version": "1.2.2" - } - ] - }, - { - "name": "bamtools_stats", - "path": "modules/nf-core/bamtools/stats/meta.yml", - "type": "module", - "meta": { - "name": "bamtools_stats", - "description": "BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.", - "keywords": [ - "bamtools", - "stats", - "bam" - ], - "tools": [ - { - "bamtools": { - "description": "C++ API & command-line toolkit for working with BAM data", - "homepage": "http://github.com/pezmaster31/bamtools", - "documentation": "https://github.com/pezmaster31/bamtools/wiki", - "tool_dev_url": "http://github.com/pezmaster31/bamtools", - "licence": [ - "MIT" - ], - "identifier": "biotools:bamtools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + "name": "bbmap_pileup", + "path": "modules/nf-core/bbmap/pileup/meta.yml", + "type": "module", + "meta": { + "name": "bbmap_pileup", + "description": "Calculates per-scaffold or per-base coverage information from an unsorted sam or bam file.", + "keywords": ["fasta", "genome", "coverage"], + "tools": [ + { + "bbmap": { + "description": "BBMap is a short read aligner, as well as various other bioinformatic tools.", + "homepage": "https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/", + "documentation": "https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/", + "tool_dev_url": "https://github.com/BioInfoTools/BBMap/blob/master/sh/pileup.sh", + "licence": ["UC-LBL license (see package)"], + "identifier": "biotools:bbmap" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}", + "ontologies": [] + } + } + ] + ], + "output": { + "covstats": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.stats.txt": { + "type": "file", + "description": "Coverage statistics", + "pattern": "*.stats.txt", + "ontologies": [] + } + } + ] + ], + "hist": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.hist.txt": { + "type": "file", + "description": "Histogram of # occurrences of each depth level", + "pattern": "*.hist.txt", + "ontologies": [] + } + } + ] + ], + "versions_bbmap": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bbmap": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bbversion.sh | grep -v 'Duplicate cpuset'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_samtools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "samtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "samtools version | sed '1!d;s/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_pigz": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "pigz": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pigz --version 2>&1 | sed \"s/^.*pigz[[:space:]]*//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bbmap": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bbversion.sh | grep -v 'Duplicate cpuset'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "samtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "samtools version | sed '1!d;s/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "pigz": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pigz --version 2>&1 | sed \"s/^.*pigz[[:space:]]*//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@edmundmiller"], + "maintainers": ["@edmundmiller"] }, - { - "bam": { - "type": "file", - "description": "BAM file", - "pattern": "*.bam", - "ontologies": [] - } - } - ] - ], - "output": { - "stats": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.stats": { - "type": "file", - "description": "File containing alignment statistics", - "pattern": "*.stats", - "ontologies": [] - } - } - ] - ], - "versions_bamtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bamtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bamtools --version | sed '2!d;s/bamtools //g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@lescai" - ], - "maintainers": [ - "@lescai" - ], - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bamtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bamtools --version | sed '2!d;s/bamtools //g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "nascent", + "version": "2.3.0" + } ] - ] - } - }, - "pipelines": [ + }, { - "name": "hgtseq", - "version": "1.1.0" - } - ] - }, - { - "name": "bamutil_clipoverlap", - "path": "modules/nf-core/bamutil/clipoverlap/meta.yml", - "type": "module", - "meta": { - "name": "bamutil_clipoverlap", - "description": "clips overlapping read pairs. When two mates overlap, this tool will clip the record's whose clipped region would have the lowest average quality.", - "keywords": [ - "bam", - "clipping", - "clipOverlap", - "bamUtil" - ], - "tools": [ - { - "bamutil": { - "description": "Programs that perform operations on SAM/BAM files, all built into a single executable, bam.", - "homepage": "https://genome.sph.umich.edu/wiki/BamUtil", - "documentation": "https://genome.sph.umich.edu/wiki/BamUtil:_clipOverlap", - "tool_dev_url": "https://github.com/statgen/bamUtil", - "doi": "10.1101/gr.176552.114", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:bamutil" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } + "name": "bbmap_repair", + "path": "modules/nf-core/bbmap/repair/meta.yml", + "type": "module", + "meta": { + "name": "bbmap_repair", + "description": "Re-pairs reads that became disordered or had some mates eliminated.", + "keywords": ["paired reads re-pairing", "fastq", "preprocessing"], + "tools": [ + { + "repair": { + "description": "Repair.sh is a tool that re-pairs reads that became disordered or had some mates eliminated tools.", + "homepage": "https://jgi.doe.gov/data-and-tools/software-tools/bbtools/", + "documentation": "https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/", + "licence": ["UC-LBL license (see package)"], + "identifier": "biotools:bbmap" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input paired end fastq files\n", + "pattern": "*.{fastq,fq}.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ], + { + "interleave": { + "type": "boolean", + "description": "Indicates whether the input paired reads are interleaved or not\n" + } + } + ], + "output": { + "repaired": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*_repaired.fastq.gz": { + "type": "file", + "description": "re-paired reads", + "pattern": "*_repaired.fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "singleton": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}_singleton.fastq.gz": { + "type": "file", + "description": "singleton reads", + "pattern": "*singleton.fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "log": [ + { + "*.log": { + "type": "file", + "description": "log file containing stdout and stderr from repair.sh", + "pattern": "*.log", + "ontologies": [] + } + } + ], + "versions_bbmap": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bbmap": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bbversion.sh | grep -v \"Duplicate cpuset\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bbmap": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bbversion.sh | grep -v \"Duplicate cpuset\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@mazzalab"], + "maintainers": ["@mazzalab", "@tm4zza"] }, - { - "bam": { - "type": "file", - "description": "Coordinate/ReadName sorted BAM/SAM/uncompressedBAM file", - "pattern": "*.{bam,sam,ubam}", - "ontologies": [] - } - } - ] - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "Coordinate/ReadName sorted BAM/SAM/uncompressedBAM file", - "pattern": "*.{bam}", - "ontologies": [] - } - } - ] - ], - "stats_log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.log": { - "type": "file", - "description": "basic overlap statistics when unabled with --stats", - "pattern": "*.{log}", - "ontologies": [] - } - } - ] - ], - "versions_bamutil": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bamutil": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bam clipOverlap 2>&1 | grep '^Version:' | sed 's/^Version: //;s/;.*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bamutil": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bam clipOverlap 2>&1 | grep '^Version:' | sed 's/^Version: //;s/;.*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "fastqrepair", + "version": "1.0.0" + } ] - ] - }, - "authors": [ - "@Y-Pei" - ], - "maintainers": [ - "@Y-Pei" - ] - } - }, - { - "name": "bamutil_trimbam", - "path": "modules/nf-core/bamutil/trimbam/meta.yml", - "type": "module", - "meta": { - "name": "bamutil_trimbam", - "description": "trims the end of reads in a SAM/BAM file, changing read ends to ‘N’ and quality to ‘!’, or by soft clipping", - "keywords": [ - "bam", - "trim", - "clipping", - "bamUtil", - "trimBam" - ], - "tools": [ - { - "bamutil": { - "description": "Programs that perform operations on SAM/BAM files, all built into a single executable, bam.", - "homepage": "https://genome.sph.umich.edu/wiki/BamUtil", - "documentation": "https://genome.sph.umich.edu/wiki/BamUtil:_trimBam", - "tool_dev_url": "https://github.com/statgen/bamUtil", - "doi": "10.1101/gr.176552.114", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:bamutil" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file", - "pattern": "*.bam", - "ontologies": [] - } - }, - { - "trim_left": { - "type": "integer", - "description": "Number of bases to trim off the right-hand side of a read. Reverse strands are reversed before trimming." - } + }, + { + "name": "bbmap_sendsketch", + "path": "modules/nf-core/bbmap/sendsketch/meta.yml", + "type": "module", + "meta": { + "name": "bbmap_sendsketch", + "description": "Compares query sketches to reference sketches hosted on a remote server via the Internet.", + "keywords": ["taxonomy", "classification", "sketch", "query", "fastq", "fasta"], + "tools": [ + { + "bbmap": { + "description": "BBMap is a short read aligner, as well as various other bioinformatic tools.", + "homepage": "https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/", + "documentation": "https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/", + "licence": ["UC-LBL license (see package)"], + "identifier": "biotools:bbmap" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "file": { + "type": "file", + "description": "file with nucleotide sequences", + "pattern": "*.{fna, fa, fasta, fa.gz, fasta.gz, fna.gz, fastq.gz, fastq, fq.gz, fq}", + "ontologies": [] + } + } + ] + ], + "output": { + "hits": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": ".txt file containing hits from a query seuqnce to various reference sequences output", + "pattern": "*.{txt}", + "ontologies": [] + } + } + ] + ], + "versions_bbmap": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bbmap": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bbversion.sh | grep -v \"Duplicate cpuset\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bbmap": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bbversion.sh | grep -v \"Duplicate cpuset\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@phanhung2"], + "maintainers": ["@phanhung2"] }, - { - "trim_right": { - "type": "integer", - "description": "Number of bases to trim off the right-hand side of a read. Reverse strands are reversed before trimming." - } - } - ] - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "Trimmed but unsorted BAM file", - "pattern": "*.bam", - "ontologies": [] - } - } - ] - ], - "versions_bamutil": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bamutil": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bam trimBam 2>&1 | head -1 | sed 's/^Version: //;s/;.*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bamutil": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bam trimBam 2>&1 | head -1 | sed 's/^Version: //;s/;.*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "pathogensurveillance", + "version": "1.1.0" + } ] - ] - }, - "authors": [ - "@jfy133" - ], - "maintainers": [ - "@jfy133" - ] - } - }, - { - "name": "bandage_image", - "path": "modules/nf-core/bandage/image/meta.yml", - "type": "module", - "meta": { - "name": "bandage_image", - "description": "Render an assembly graph in GFA 1.0 format to PNG and SVG image formats", - "keywords": [ - "gfa", - "graph", - "assembly", - "visualisation" - ], - "tools": [ - { - "bandage": { - "description": "Bandage - a Bioinformatics Application for Navigating De novo Assembly Graphs Easily\n", - "homepage": "https://github.com/rrwick/Bandage", - "documentation": "https://github.com/rrwick/Bandage", - "licence": [ - "GPL-3.0-or-later" - ], - "identifier": "biotools:bandage" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + }, + { + "name": "bcftools_annotate", + "path": "modules/nf-core/bcftools/annotate/meta.yml", + "type": "module", + "meta": { + "name": "bcftools_annotate", + "description": "Add or remove annotations.", + "keywords": ["bcftools", "annotate", "vcf", "remove", "add"], + "tools": [ + { + "annotate": { + "description": "Add or remove annotations.", + "homepage": "http://samtools.github.io/bcftools/bcftools.html", + "documentation": "https://samtools.github.io/bcftools/bcftools.html#annotate", + "doi": "10.1093/bioinformatics/btp352", + "licence": ["MIT"], + "identifier": "biotools:bcftools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "Query VCF or BCF file, can be either uncompressed or compressed", + "ontologies": [] + } + }, + { + "index": { + "type": "file", + "description": "Index of the query VCF or BCF file", + "ontologies": [] + } + }, + { + "annotations": { + "type": "file", + "description": "Bgzip-compressed file with annotations", + "ontologies": [] + } + }, + { + "annotations_index": { + "type": "file", + "description": "Index of the annotations file", + "ontologies": [] + } + }, + { + "columns": { + "type": "file", + "description": "List of columns in the annotations file, one name per row", + "ontologies": [] + } + }, + { + "header_lines": { + "type": "file", + "description": "Contains lines to append to the output VCF header", + "ontologies": [] + } + }, + { + "rename_chrs": { + "type": "file", + "description": "Rename annotations according to this file containing \"old_name new_name\\n\" pairs separated by whitespaces, each on a separate line.", + "ontologies": [] + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.${extension}": { + "type": "file", + "description": "Compressed annotated VCF file", + "pattern": "*{vcf,vcf.gz,bcf,bcf.gz}", + "ontologies": [] + } + } + ] + ], + "tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.${extension}.tbi": { + "type": "file", + "description": "Alternative VCF file index", + "pattern": "*.tbi", + "ontologies": [] + } + } + ] + ], + "csi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.${extension}.csi": { + "type": "file", + "description": "Default VCF file index", + "pattern": "*.csi", + "ontologies": [] + } + } + ] + ], + "versions_bcftools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bcftools": { + "type": "string", + "description": "The tool name" + } + }, + { + "bcftools --version | sed '1!d; s/^.*bcftools //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bcftools": { + "type": "string", + "description": "The tool name" + } + }, + { + "bcftools --version | sed '1!d; s/^.*bcftools //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@projectoriented", "@ramprasadn"], + "maintainers": ["@projectoriented", "@ramprasadn"] }, - { - "gfa": { - "type": "file", - "description": "Assembly graph in GFA 1.0 format", - "pattern": "*.gfa", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3975" - } - ] - } - } - ] - ], - "output": { - "png": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.png": { - "type": "file", - "description": "Bandage image in PNG format", - "pattern": "*.png", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3603" - } - ] - } - } - ] - ], - "svg": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.svg": { - "type": "file", - "description": "Bandage image in SVG format", - "pattern": "*.svg", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3604" - } - ] - } - } - ] - ], - "versions_bandage": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bandage": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "export QT_QPA_PLATFORM=offscreen; Bandage --version 2>&1| grep Version | sed \"s/^Version: //\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bandage": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "export QT_QPA_PLATFORM=offscreen; Bandage --version 2>&1| grep Version | sed \"s/^Version: //\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "alleleexpression", + "version": "dev" + }, + { + "name": "phaseimpute", + "version": "1.1.0" + }, + { + "name": "raredisease", + "version": "3.0.0" + }, + { + "name": "rnavar", + "version": "1.2.3" + }, + { + "name": "sarek", + "version": "3.8.1" + }, + { + "name": "variantbenchmarking", + "version": "1.5.0" + }, + { + "name": "variantcatalogue", + "version": "dev" + } ] - ] - }, - "authors": [ - "@heuermh" - ], - "maintainers": [ - "@heuermh" - ] - }, - "pipelines": [ - { - "name": "viralrecon", - "version": "3.0.0" - } - ] - }, - { - "name": "barrnap", - "path": "modules/nf-core/barrnap/meta.yml", - "type": "module", - "meta": { - "name": "barrnap", - "description": "barrnap uses a hmmer profile to find rrnas in reads or contig fasta files", - "keywords": [ - "rrna", - "sequences", - "removal" - ], - "tools": [ - { - "barrnap": { - "description": "Barrnap predicts the location of ribosomal RNA genes in genomes (bacteria, archaea, metazoan mitochondria and eukaryotes).", - "homepage": "https://github.com/tseemann/barrnap", - "documentation": "https://github.com/tseemann/barrnap", - "tool_dev_url": "https://github.com/tseemann/barrnap", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:barrnap" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "fasta file", - "pattern": "*.fasta", - "ontologies": [] - } - }, - { - "dbname": { - "type": "string", - "description": "database to use(bacteria, archaea, eukaryota, metazoan mitochondria)" - } - } - ] - ], - "output": { - "gff": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*.gff": { - "type": "file", - "description": "gff file containing coordinates of genes", - "pattern": "*.gff", - "ontologies": [] - } - } - ] - ], - "versions_barrnap": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "barrnap": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "barrnap --version 2>&1 | sed \"s/barrnap //g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "barrnap": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "barrnap --version 2>&1 | sed \"s/barrnap //g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@danilodileo", - "@srisarya" - ], - "maintainers": [ - "@danilodileo" - ] - }, - "pipelines": [ - { - "name": "seqsubmit", - "version": "dev" - } - ] - }, - { - "name": "bases2fastq", - "path": "modules/nf-core/bases2fastq/meta.yml", - "type": "module", - "meta": { - "name": "bases2fastq", - "description": "Demultiplex Element Biosciences bases files", - "keywords": [ - "demultiplex", - "element", - "fastq" - ], - "tools": [ - { - "bases2fastq": { - "description": "Demultiplexes sequencing data and converts base calls into FASTQ files for secondary analysis", - "homepage": "https://go.elementbiosciences.com/bases2fastq-download", - "documentation": "https://www.elementbiosciences.com/resources/user-guides/workflow/bases2fastq", - "licence": [ - "http://go.elembio.link/eula" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "run_manifest": { - "type": "file", - "description": "RunManifest file", - "pattern": "*.{csv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - }, - { - "run_dir": { - "type": "directory", - "description": "Input run directory containing optionally containing a RunManifest.json if run_manifest is not supplied" - } - } - ] - ], - "output": { - "sample_fastq": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/Samples/**/*_R*.fastq.gz": { - "type": "file", - "description": "Demultiplexed sample FASTQ files", - "pattern": "${prefix}/Samples/*/*_R*.fastq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "sample_json": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/Samples/**/*_stats.json": { - "type": "file", - "description": "Demultiplexed sample stats", - "pattern": "${prefix}/Samples/*/*.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "qc_report": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/*_QC.html": { - "type": "file", - "description": "QC HTML report", - "pattern": "${prefix}//*_QC.html", - "ontologies": [] - } - } - ] - ], - "multiqc_report": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/multiqc_report.html": { - "type": "file", - "description": "Multiqc HTML report", - "pattern": "${prefix}/multiqc_report.html", - "ontologies": [] - } - } - ] - ], - "run_stats": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/RunStats.json": { - "type": "file", - "description": "QC HTML report", - "pattern": "${prefix}/*.html", - "ontologies": [] - } - } - ] - ], - "generated_run_manifest": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/RunManifest.json": { - "type": "file", - "description": "Updated Run Manifest JSON from the run_manifest csv", - "pattern": "${prefix}/RunManifest.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "metrics": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/Metrics.csv": { - "type": "file", - "description": "Sample metrics", - "pattern": "${prefix}/Metrics.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "unassigned": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/UnassignedSequences.csv": { - "type": "file", - "description": "Unassigned Sequences", - "pattern": "${prefix}/UnassignedSequences.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "versions_bases2fastq": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bases2fastq": { - "type": "string", - "description": "The tool name" - } - }, - { - "bases2fastq --version | sed \"s/.*version //;s/,.*//\"": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bases2fastq": { - "type": "string", - "description": "The tool name" - } - }, - { - "bases2fastq --version | sed \"s/.*version //;s/,.*//\"": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@edmundmiller" - ], - "maintainers": [ - "@edmundmiller" - ] - }, - "pipelines": [ - { - "name": "demultiplex", - "version": "1.7.1" - } - ] - }, - { - "name": "basicpy", - "path": "modules/nf-core/basicpy/meta.yml", - "type": "module", - "meta": { - "name": "basicpy", - "description": "BaSiCPy is a python package for background and shading correction of optical microscopy images. It is developed based on the Matlab version of BaSiC tool with major improvements in the algorithm.", - "keywords": [ - "illumiation_correction", - "background_correction", - "microscopy", - "imaging" - ], - "tools": [ - { - "basicpy": { - "description": "BaSiCPy is a python package for background and shading correction of optical microscopy images. It is developed based on the Matlab version of BaSiC tool with major improvements in the algorithm.", - "homepage": "https://github.com/peng-lab/BaSiCPy", - "documentation": "https://basicpy.readthedocs.io/en/latest/index.html", - "tool_dev_url": "https://github.com/peng-lab/BaSiCPy", - "doi": "10.1038/ncomms14836", - "license": [ - "MIT License" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "image": { - "type": "file", - "description": "BioFormats-compatible image file to be used for dark and flat field illumination correction", - "pattern": "*.{ome.tiff,ome.tif,rcpnl,btf,nd2,tiff,tif,czi}", - "ontologies": [] - } - } - ] - ], - "output": { - "profiles": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*-dfp.ome.tif": { - "type": "file", - "description": "OME-TIFF fields for dark field illumination correction", - "pattern": "*.{ome.tif}", - "ontologies": [] - } - }, - { - "*-ffp.ome.tif": { - "type": "file", - "description": "OME-TIFF fields for flat field illumination correction", - "pattern": "*.{ome.tif}", - "ontologies": [] - } - } - ] - ], - "versions_basicpy": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "basicpy": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "1.2.0": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "basicpy": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "1.2.0": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@FloWuenne" - ], - "maintainers": [ - "@FloWuenne" - ] - }, - "pipelines": [ - { - "name": "mcmicro", - "version": "dev" - } - ] - }, - { - "name": "bbmap_align", - "path": "modules/nf-core/bbmap/align/meta.yml", - "type": "module", - "meta": { - "name": "bbmap_align", - "description": "Align short or PacBio reads to a reference genome using BBMap", - "keywords": [ - "align", - "map", - "fasta", - "fastq", - "genome", - "reference" - ], - "tools": [ - { - "bbmap": { - "description": "BBMap is a short read aligner, as well as various other bioinformatic tools.", - "homepage": "https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/", - "documentation": "https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/", - "licence": [ - "UC-LBL license (see package)" - ], - "identifier": "biotools:bbmap" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fastq": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", - "ontologies": [] - } - } - ], - { - "ref": { - "type": "file", - "description": "Either \"ref\" a directory containing an index, the name of another directory\nwith a \"ref\" subdirectory containing an index or the name of a fasta formatted\nnucleotide file containing the reference to map to.\n", - "ontologies": [] - } - } - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "BAM file", - "pattern": "*.{bam}", - "ontologies": [] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.log": { - "type": "file", - "description": "Log file", - "pattern": "*.{log}", - "ontologies": [] - } - } - ] - ], - "versions_bbmap": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bbmap": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bbversion.sh | grep -v \"Duplicate cpuset\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bbmap": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bbversion.sh | grep -v \"Duplicate cpuset\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] }, - "authors": [ - "@erikrikarddaniel" - ], - "maintainers": [ - "@erikrikarddaniel" - ] - }, - "pipelines": [ { - "name": "magmap", - "version": "1.0.0" + "name": "bcftools_call", + "path": "modules/nf-core/bcftools/call/meta.yml", + "type": "module", + "meta": { + "name": "bcftools_call", + "description": "This command replaces the former bcftools view caller.\nSome of the original functionality has been temporarily lost in the process of transition under htslib, but will be added back on popular demand.\nThe original calling model can be invoked with the -c option.\n", + "keywords": ["variant calling", "view", "bcftools", "VCF"], + "tools": [ + { + "view": { + "description": "View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF\n", + "homepage": "http://samtools.github.io/bcftools/bcftools.html", + "documentation": "http://www.htslib.org/doc/bcftools.html", + "doi": "10.1093/bioinformatics/btp352", + "licence": ["MIT"], + "identifier": "biotools:bcftools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "The vcf file to be inspected.\ne.g. 'file.vcf'\n", + "ontologies": [] + } + }, + { + "index": { + "type": "file", + "description": "The tab index for the VCF file to be inspected.\ne.g. 'file.tbi'\n", + "ontologies": [] + } + } + ], + { + "regions": { + "type": "file", + "description": "Optionally, restrict the operation to regions listed in this file.\ne.g. 'file.vcf'\n", + "ontologies": [] + } + }, + { + "targets": { + "type": "file", + "description": "Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files)\ne.g. 'file.vcf'\n", + "ontologies": [] + } + }, + { + "samples": { + "type": "file", + "description": "Optional, file of sample names to be included or excluded.\ne.g. 'file.tsv'\n", + "ontologies": [] + } + } + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.gz": { + "type": "file", + "description": "VCF normalized output file", + "pattern": "*.{vcf.gz}", + "ontologies": [] + } + } + ] + ], + "tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tbi": { + "type": "file", + "description": "Alternative VCF file index", + "pattern": "*.tbi", + "ontologies": [] + } + } + ] + ], + "csi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.csi": { + "type": "file", + "description": "Default VCF file index", + "pattern": "*.csi", + "ontologies": [] + } + } + ] + ], + "versions_bcftools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bcftools": { + "type": "string", + "description": "The tool name" + } + }, + { + "bcftools --version | sed '1!d; s/^.*bcftools //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bcftools": { + "type": "string", + "description": "The tool name" + } + }, + { + "bcftools --version | sed '1!d; s/^.*bcftools //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@abhi18av", "@LouisLeNezet"], + "maintainers": ["@abhi18av", "@LouisLeNezet"] + } }, { - "name": "metatdenovo", - "version": "1.3.0" - } - ] - }, - { - "name": "bbmap_bbduk", - "path": "modules/nf-core/bbmap/bbduk/meta.yml", - "type": "module", - "meta": { - "name": "bbmap_bbduk", - "description": "Adapter and quality trimming of sequencing reads", - "keywords": [ - "trimming", - "adapter trimming", - "quality trimming", - "fastq" - ], - "tools": [ - { - "bbmap": { - "description": "BBMap is a short read aligner, as well as various other bioinformatic tools.", - "homepage": "https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/", - "documentation": "https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/", - "licence": [ - "UC-LBL license (see package)" - ], - "identifier": "biotools:bbmap" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + "name": "bcftools_concat", + "path": "modules/nf-core/bcftools/concat/meta.yml", + "type": "module", + "meta": { + "name": "bcftools_concat", + "description": "Concatenate VCF files", + "keywords": ["variant calling", "concat", "bcftools", "VCF"], + "tools": [ + { + "concat": { + "description": "Concatenate VCF files.\n", + "homepage": "http://samtools.github.io/bcftools/bcftools.html", + "documentation": "http://www.htslib.org/doc/bcftools.html", + "doi": "10.1093/bioinformatics/btp352", + "licence": ["MIT"], + "identifier": "biotools:bcftools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcfs": { + "type": "list", + "description": "List containing 2 or more vcf files\ne.g. [ 'file1.vcf', 'file2.vcf' ]\n" + } + }, + { + "tbi": { + "type": "list", + "description": "List containing 2 or more index files (optional)\ne.g. [ 'file1.tbi', 'file2.tbi' ]\n" + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.${extension}": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}" + } + } + ] + ], + "tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.${extension}.tbi": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*.tbi" + } + } + ] + ], + "csi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.${extension}.csi": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*.csi" + } + } + ] + ], + "versions_bcftools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bcftools": { + "type": "string", + "description": "The tool name" + } + }, + { + "bcftools --version | sed '1!d; s/^.*bcftools //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bcftools": { + "type": "string", + "description": "The tool name" + } + }, + { + "bcftools --version | sed '1!d; s/^.*bcftools //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@abhi18av", "@nvnieuwk"], + "maintainers": ["@abhi18av", "@nvnieuwk"] }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", - "ontologies": [] - } - } - ], - { - "contaminants": { - "type": "file", - "description": "Reference files containing adapter and/or contaminant sequences for sequence kmer matching\n", - "ontologies": [] - } - } - ], - "output": { - "reads": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.fastq.gz": { - "type": "file", - "description": "The trimmed/modified fastq reads", - "pattern": "*fastq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.log": { - "type": "file", - "description": "Bbduk log file", - "pattern": "*bbduk.log", - "ontologies": [] - } - } - ] - ], - "versions_bbmap": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bbmap": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bbversion.sh | grep -v \"Duplicate cpuset\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bbmap": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bbversion.sh | grep -v \"Duplicate cpuset\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "genomicrelatedness", + "version": "dev" + }, + { + "name": "pacsomatic", + "version": "dev" + }, + { + "name": "phaseimpute", + "version": "1.1.0" + }, + { + "name": "radseq", + "version": "dev" + }, + { + "name": "raredisease", + "version": "3.0.0" + }, + { + "name": "sarek", + "version": "3.8.1" + } ] - ] }, - "authors": [ - "@MGordon09" - ], - "maintainers": [ - "@MGordon09" - ] - }, - "pipelines": [ { - "name": "detaxizer", - "version": "1.3.0" + "name": "bcftools_consensus", + "path": "modules/nf-core/bcftools/consensus/meta.yml", + "type": "module", + "meta": { + "name": "bcftools_consensus", + "description": "Compresses VCF files", + "keywords": ["variant calling", "consensus", "VCF"], + "tools": [ + { + "consensus": { + "description": "Create consensus sequence by applying VCF variants to a reference fasta file.\n", + "homepage": "http://samtools.github.io/bcftools/bcftools.html", + "documentation": "http://www.htslib.org/doc/bcftools.html", + "doi": "10.1093/bioinformatics/btp352", + "licence": ["MIT"], + "identifier": "biotools:bcftools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF file", + "pattern": "*.{vcf}", + "ontologies": [] + } + }, + { + "tbi": { + "type": "file", + "description": "tabix index file", + "pattern": "*.{tbi}", + "ontologies": [] + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA reference file", + "pattern": "*.{fasta,fa}", + "ontologies": [] + } + }, + { + "mask": { + "type": "file", + "description": "BED file used for masking", + "pattern": "*.{bed}", + "ontologies": [] + } + } + ] + ], + "output": { + "fasta": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fa": { + "type": "file", + "description": "FASTA reference consensus file", + "pattern": "*.{fasta,fa}", + "ontologies": [] + } + } + ] + ], + "versions_bcftools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bcftools": { + "type": "string", + "description": "The tool name" + } + }, + { + "bcftools --version | sed '1!d; s/^.*bcftools //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bcftools": { + "type": "string", + "description": "The tool name" + } + }, + { + "bcftools --version | sed '1!d; s/^.*bcftools //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@joseespinosa", "@drpatelh"], + "maintainers": ["@joseespinosa", "@drpatelh"] + }, + "pipelines": [ + { + "name": "mag", + "version": "5.4.2" + }, + { + "name": "viralmetagenome", + "version": "1.1.1" + }, + { + "name": "viralrecon", + "version": "3.0.0" + } + ] }, { - "name": "magmap", - "version": "1.0.0" + "name": "bcftools_convert", + "path": "modules/nf-core/bcftools/convert/meta.yml", + "type": "module", + "meta": { + "name": "bcftools_convert", + "description": "Converts certain output formats to VCF", + "keywords": ["bcftools", "convert", "vcf", "gvcf"], + "tools": [ + { + "bcftools": { + "description": "BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations.", + "homepage": "https://samtools.github.io/bcftools/bcftools.html", + "documentation": "https://samtools.github.io/bcftools/bcftools.html#convert", + "tool_dev_url": "https://github.com/samtools/bcftools", + "doi": "10.1093/gigascience/giab008", + "licence": ["GPL"], + "identifier": "biotools:bcftools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "The input format. Each format needs a separate parameter to be specified in the `args`:\n- GEN/SAMPLE file: `--gensample2vcf`\n- gVCF file: `--gvcf2vcf`\n- HAP/SAMPLE file: `--hapsample2vcf`\n- HAP/LEGEND/SAMPLE file: `--haplegendsample2vcf`\n- TSV file: `--tsv2vcf`\n", + "pattern": "*.{gen,sample,g.vcf,hap,legend}{.gz,}", + "ontologies": [] + } + }, + { + "input_index": { + "type": "file", + "description": "(Optional) The index for the input files, if needed", + "pattern": "*.bed", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "(Optional) The reference fasta, only needed for gVCF conversion", + "pattern": "*.{fa,fasta}", + "ontologies": [] + } + } + ], + { + "bed": { + "type": "file", + "description": "(Optional) The BED file containing the regions for the VCF file", + "pattern": "*.bed", + "ontologies": [] + } + } + ], + "output": { + "vcf_gz": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "VCF merged output file (bgzipped) => when `--output-type z` is used", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf": { + "type": "file", + "description": "VCF merged output file => when `--output-type v` is used", + "pattern": "*.vcf", + "ontologies": [] + } + } + ] + ], + "bcf_gz": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bcf.gz": { + "type": "file", + "description": "BCF merged output file (bgzipped) => when `--output-type b` is used", + "pattern": "*.bcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "bcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bcf": { + "type": "file", + "description": "BCF merged output file => when `--output-type u` is used", + "pattern": "*.bcf", + "ontologies": [] + } + } + ] + ], + "hap": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.hap.gz": { + "type": "file", + "description": "hap format used by IMPUTE2 and SHAPEIT", + "pattern": "*.hap.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "legend": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.legend.gz": { + "type": "file", + "description": "legend format used by IMPUTE2 and SHAPEIT", + "pattern": "*.legend.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "samples": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.samples": { + "type": "file", + "description": "samples format used by IMPUTE2 and SHAPEIT", + "pattern": "*.samples", + "ontologies": [] + } + } + ] + ], + "tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tbi": { + "type": "file", + "description": "Alternative VCF file index", + "pattern": "*.tbi", + "ontologies": [] + } + } + ] + ], + "csi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.csi": { + "type": "file", + "description": "Default VCF file index", + "pattern": "*.csi", + "ontologies": [] + } + } + ] + ], + "versions_bcftools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bcftools": { + "type": "string", + "description": "The tool name" + } + }, + { + "bcftools --version | sed '1!d; s/^.*bcftools //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bcftools": { + "type": "string", + "description": "The tool name" + } + }, + { + "bcftools --version | sed '1!d; s/^.*bcftools //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@nvnieuwk", "@ramprasadn", "@atrigila"], + "maintainers": ["@nvnieuwk", "@ramprasadn", "@atrigila"] + }, + "pipelines": [ + { + "name": "phaseimpute", + "version": "1.1.0" + } + ] }, { - "name": "metatdenovo", - "version": "1.3.0" + "name": "bcftools_csq", + "path": "modules/nf-core/bcftools/csq/meta.yml", + "type": "module", + "meta": { + "name": "bcftools_csq", + "description": "bcftools Haplotype-aware consequence caller", + "keywords": ["annotation", "gff", "gff3", "protein", "functional", "vcf", "bcf", "bcftools"], + "tools": [ + { + "reheader": { + "description": "Haplotype-aware consequence caller\n", + "homepage": "http://samtools.github.io/bcftools/bcftools.html", + "documentation": "http://samtools.github.io/bcftools/bcftools.html#csq", + "doi": "10.1093/gigascience/giab008", + "licence": ["MIT"], + "identifier": "biotools:bcftools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF/BCF file", + "pattern": "*.{vcf.gz,vcf,bcf}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing fasta information\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Fasta reference", + "pattern": "*.{fasta,fa}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing fai information\n" + } + }, + { + "fai": { + "type": "file", + "description": "Fasta index", + "pattern": "*.{fai}", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing gff3 information\n" + } + }, + { + "gff3": { + "type": "file", + "description": "GFF3 file", + "pattern": "*.{gff,gff.gz,gff3,gff3.gz}", + "ontologies": [] + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.${extension}": { + "type": "file", + "description": "VCF with annotation, bgzipped per default", + "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}", + "ontologies": [] + } + } + ] + ], + "tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tbi": { + "type": "file", + "description": "Alternative VCF file index", + "pattern": "*.tbi", + "ontologies": [] + } + } + ] + ], + "csi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.csi": { + "type": "file", + "description": "Default VCF file index", + "pattern": "*.csi", + "ontologies": [] + } + } + ] + ], + "versions_bcftools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bcftools": { + "type": "string", + "description": "The tool name" + } + }, + { + "bcftools --version | sed '1!d; s/^.*bcftools //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bcftools": { + "type": "string", + "description": "The tool name" + } + }, + { + "bcftools --version | sed '1!d; s/^.*bcftools //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@lindenb"], + "maintainers": ["@lindenb"] + } }, { - "name": "taxprofiler", - "version": "2.0.0" + "name": "bcftools_filter", + "path": "modules/nf-core/bcftools/filter/meta.yml", + "type": "module", + "meta": { + "name": "bcftools_filter", + "description": "Filters VCF files", + "keywords": ["variant calling", "filtering", "VCF"], + "tools": [ + { + "filter": { + "description": "Apply fixed-threshold filters to VCF files.\n", + "homepage": "http://samtools.github.io/bcftools/bcftools.html", + "documentation": "http://www.htslib.org/doc/bcftools.html", + "doi": "10.1093/bioinformatics/btp352", + "licence": ["MIT"], + "identifier": "biotools:bcftools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF input file", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", + "ontologies": [] + } + }, + { + "tbi": { + "type": "file", + "description": "VCF index file", + "pattern": "*.tbi", + "ontologies": [] + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.${extension}": { + "type": "file", + "description": "VCF filtered output file", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", + "ontologies": [] + } + } + ] + ], + "tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tbi": { + "type": "file", + "description": "Alternative VCF file index", + "pattern": "*.tbi", + "ontologies": [] + } + } + ] + ], + "csi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.csi": { + "type": "file", + "description": "Default VCF file index", + "pattern": "*.csi", + "ontologies": [] + } + } + ] + ], + "versions_bcftools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bcftools": { + "type": "string", + "description": "The tool name" + } + }, + { + "bcftools --version | sed '1!d; s/^.*bcftools //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bcftools": { + "type": "string", + "description": "The tool name" + } + }, + { + "bcftools --version | sed '1!d; s/^.*bcftools //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@joseespinosa", "@drpatelh"], + "maintainers": ["@joseespinosa", "@drpatelh"] + }, + "pipelines": [ + { + "name": "raredisease", + "version": "3.0.0" + }, + { + "name": "variantbenchmarking", + "version": "1.5.0" + }, + { + "name": "variantprioritization", + "version": "1.0.0" + }, + { + "name": "viralmetagenome", + "version": "1.1.1" + }, + { + "name": "viralrecon", + "version": "3.0.0" + } + ] }, { - "name": "viralmetagenome", - "version": "1.1.1" - } - ] - }, - { - "name": "bbmap_bbmerge", - "path": "modules/nf-core/bbmap/bbmerge/meta.yml", - "type": "module", - "meta": { - "name": "bbmap_bbmerge", - "description": "Merging overlapping paired reads into a single read.", - "keywords": [ - "paired reads merging", - "fastq", - "overlap-based merging" - ], - "tools": [ - { - "bbmap": { - "description": "BBMap is a short read aligner, as well as various other bioinformatic tools.", - "homepage": "https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/", - "documentation": "https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/", - "licence": [ - "UC-LBL license (see package)" - ], - "identifier": "biotools:bbmap" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } + "name": "bcftools_index", + "path": "modules/nf-core/bcftools/index/meta.yml", + "type": "module", + "meta": { + "name": "bcftools_index", + "description": "Index VCF tools", + "keywords": ["vcf", "index", "bcftools", "csi", "tbi"], + "tools": [ + { + "bcftools": { + "description": "BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations.", + "homepage": "https://samtools.github.io/bcftools/", + "documentation": "https://samtools.github.io/bcftools/howtos/index.html", + "tool_dev_url": "https://github.com/samtools/bcftools", + "doi": "10.1093/gigascience/giab008", + "licence": ["MIT", "GPL-3.0-or-later"], + "identifier": "biotools:bcftools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF file (optionally GZIPPED)", + "pattern": "*.{vcf,vcf.gz}", + "ontologies": [] + } + } + ] + ], + "output": { + "csi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.csi": { + "type": "file", + "description": "Default VCF file index file", + "pattern": "*.csi", + "ontologies": [] + } + } + ] + ], + "tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tbi": { + "type": "file", + "description": "Alternative VCF file index file for larger files (activated with -t parameter)", + "pattern": "*.tbi", + "ontologies": [] + } + } + ] + ], + "versions_bcftools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bcftools": { + "type": "string", + "description": "The tool name" + } + }, + { + "bcftools --version | sed '1!d; s/^.*bcftools //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bcftools": { + "type": "string", + "description": "The tool name" + } + }, + { + "bcftools --version | sed '1!d; s/^.*bcftools //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@jfy133"], + "maintainers": ["@jfy133"] }, - { - "reads": { - "type": "file", - "description": "List of input paired end fastq files\n", - "pattern": "*.{fastq,fq}.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ], - { - "interleave": { - "type": "boolean", - "description": "Indicates whether the input paired reads are interleaved or not\n" - } - } - ], - "output": { - "merged": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*_merged.fastq.gz": { - "type": "file", - "description": "merged reads", - "pattern": "*_merged.fastq", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "unmerged": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*_unmerged.fastq.gz": { - "type": "file", - "description": "unmerged reads", - "pattern": "*_unmerged.fastq", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "ihist": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*_ihist.txt": { - "type": "file", - "description": "insert size histogram", - "pattern": "*_ihist.txt", - "ontologies": [] - } - } - ] - ], - "log": [ - { - "*.log": { - "type": "file", - "description": "log file containing stdout and stderr from bbmerge.sh", - "pattern": "*.log", - "ontologies": [] - } - } - ], - "versions_bbmap": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bbmap": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bbversion.sh | grep -v \"Duplicate cpuset\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bbmap": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bbversion.sh | grep -v \"Duplicate cpuset\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "alleleexpression", + "version": "dev" + }, + { + "name": "genomicrelatedness", + "version": "dev" + }, + { + "name": "mag", + "version": "5.4.2" + }, + { + "name": "pacsomatic", + "version": "dev" + }, + { + "name": "pacvar", + "version": "1.0.1" + }, + { + "name": "phaseimpute", + "version": "1.1.0" + } ] - ] - }, - "authors": [ - "@guille0387" - ], - "maintainers": [ - "@guille0387" - ] - } - }, - { - "name": "bbmap_bbnorm", - "path": "modules/nf-core/bbmap/bbnorm/meta.yml", - "type": "module", - "meta": { - "name": "bbmap_bbnorm", - "description": "BBNorm is designed to normalize coverage by down-sampling reads over high-depth areas of a genome, to result in a flat coverage distribution.", - "keywords": [ - "normalization", - "assembly", - "coverage" - ], - "tools": [ - { - "bbmap": { - "description": "BBMap is a short read aligner, as well as various other bioinformatic tools.", - "homepage": "https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/", - "documentation": "https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/", - "tool_dev_url": "https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbnorm-guide/", - "licence": [ - "BBMap - Bushnell B. - sourceforge.net/projects/bbmap/" - ], - "identifier": "biotools:bbmap" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + }, + { + "name": "bcftools_isec", + "path": "modules/nf-core/bcftools/isec/meta.yml", + "type": "module", + "meta": { + "name": "bcftools_isec", + "description": "Apply set operations to VCF files", + "keywords": ["variant calling", "intersect", "union", "complement", "VCF", "BCF"], + "tools": [ + { + "isec": { + "description": "Computes intersections, unions and complements of VCF files.\n", + "homepage": "http://samtools.github.io/bcftools/bcftools.html", + "documentation": "http://www.htslib.org/doc/bcftools.html", + "doi": "10.1093/bioinformatics/btp352", + "licence": ["MIT"], + "identifier": "biotools:bcftools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcfs": { + "type": "list", + "description": "List containing 2 or more vcf/bcf files. These must be compressed and have an associated index.\ne.g. [ 'file1.vcf.gz', 'file2.vcf' ]\n", + "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + }, + { + "edam": "http://edamontology.org/format_3570" + } + ] + } + }, + { + "tbis": { + "type": "list", + "description": "List containing the tbi index files corresponding to the vcf/bcf input files\n", + "pattern": "*.tbi", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, + { + "file_list": { + "type": "file", + "description": "Optional text file containing the list of VCF/BCF files to be processed by bcftools isec, one per line.\n", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + }, + { + "targets_file": { + "type": "file", + "description": "Optional file containing target regions to restrict the analysis to.\n", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3003" + }, + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, + { + "regions_file": { + "type": "file", + "description": "Optional file containing regions to restrict the analysis to.\n", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3003" + }, + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "output": { + "results": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}": { + "type": "directory", + "description": "Directory containing the output files from bcftools isec", + "pattern": "${prefix}/", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + }, + { + "edam": "http://edamontology.org/format_3570" + } + ] + } + } + ] + ], + "versions_bcftools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bcftools": { + "type": "string", + "description": "The tool name" + } + }, + { + "bcftools --version | sed '1!d; s/^.*bcftools //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bcftools": { + "type": "string", + "description": "The tool name" + } + }, + { + "bcftools --version | sed '1!d; s/^.*bcftools //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@joseespinosa", "@drpatelh"], + "maintainers": ["@joseespinosa", "@drpatelh"] }, - { - "fastq": { - "type": "file", - "description": "fastq file", - "pattern": "*.{fastq,fq}(.gz)?", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "output": { - "fastq": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.fastq.gz": { - "type": "file", - "description": "fastq file", - "pattern": "*.{fastq, fq}.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.log": { - "type": "file", - "description": "log file", - "pattern": "*.log", - "ontologies": [] - } - } - ] - ], - "versions_bbmap": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bbmap": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bbversion.sh | grep -v \"Duplicate cpuset\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bbmap": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bbversion.sh | grep -v \"Duplicate cpuset\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "genomicrelatedness", + "version": "dev" + }, + { + "name": "sarek", + "version": "3.8.1" + } ] - ] }, - "authors": [ - "@danilodileo" - ], - "maintainers": [ - "@danilodileo" - ] - }, - "pipelines": [ { - "name": "mag", - "version": "5.4.2" + "name": "bcftools_merge", + "path": "modules/nf-core/bcftools/merge/meta.yml", + "type": "module", + "meta": { + "name": "bcftools_merge", + "description": "Merge VCF files", + "keywords": ["variant calling", "merge", "VCF"], + "tools": [ + { + "merge": { + "description": "Merge VCF files.\n", + "homepage": "http://samtools.github.io/bcftools/bcftools.html", + "documentation": "http://www.htslib.org/doc/bcftools.html", + "doi": "10.1093/bioinformatics/btp352", + "licence": ["MIT"], + "identifier": "biotools:bcftools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcfs": { + "type": "file", + "description": "List containing 2 or more vcf files\ne.g. [ 'file1.vcf', 'file2.vcf' ]\n", + "ontologies": [] + } + }, + { + "tbis": { + "type": "file", + "description": "List containing the tbi index files corresponding to the vcfs input files\ne.g. [ 'file1.vcf.tbi', 'file2.vcf.tbi' ]\n", + "ontologies": [] + } + }, + { + "bed": { + "type": "file", + "description": "(Optional) The bed regions to merge on", + "pattern": "*.bed", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "(Optional) The fasta reference file (only necessary for the `--gvcf FILE` parameter)", + "pattern": "*.{fasta,fa}", + "ontologies": [] + } + }, + { + "fai": { + "type": "file", + "description": "(Optional) The fasta reference file index (only necessary for the `--gvcf FILE` parameter)", + "pattern": "*.fai", + "ontologies": [] + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{bcf,vcf}{,.gz}": { + "type": "file", + "description": "merged output file", + "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}", + "ontologies": [] + } + } + ] + ], + "index": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{csi,tbi}": { + "type": "file", + "description": "index of merged output", + "pattern": "*.{csi,tbi}", + "ontologies": [] + } + } + ] + ], + "versions_bcftools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bcftools": { + "type": "string", + "description": "The tool name" + } + }, + { + "bcftools --version | sed '1!d; s/^.*bcftools //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bcftools": { + "type": "string", + "description": "The tool name" + } + }, + { + "bcftools --version | sed '1!d; s/^.*bcftools //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@joseespinosa", "@drpatelh", "@nvnieuwk", "@ramprasadn"], + "maintainers": ["@joseespinosa", "@drpatelh", "@nvnieuwk", "@ramprasadn"] + }, + "pipelines": [ + { + "name": "phaseimpute", + "version": "1.1.0" + }, + { + "name": "raredisease", + "version": "3.0.0" + }, + { + "name": "sarek", + "version": "3.8.1" + }, + { + "name": "tbanalyzer", + "version": "dev" + }, + { + "name": "variantbenchmarking", + "version": "1.5.0" + } + ] }, { - "name": "metatdenovo", - "version": "1.3.0" - } - ] - }, - { - "name": "bbmap_bbsplit", - "path": "modules/nf-core/bbmap/bbsplit/meta.yml", - "type": "module", - "meta": { - "name": "bbmap_bbsplit", - "description": "Split sequencing reads by mapping them to multiple references simultaneously", - "keywords": [ - "align", - "map", - "fastq", - "genome", - "reference" - ], - "tools": [ - { - "bbmap": { - "description": "BBMap is a short read aligner, as well as various other bioinformatic tools.", - "homepage": "https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/", - "documentation": "https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/", - "licence": [ - "UC-LBL license (see package)" - ], - "identifier": "biotools:bbmap" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", - "ontologies": [] - } - } - ], - { - "index": { - "type": "directory", - "description": "Directory to place generated index", - "pattern": "*" - } - }, - { - "primary_ref": { - "type": "file", - "description": "Path to the primary reference", - "pattern": "*", - "ontologies": [] - } - }, - [ - { - "other_ref_names": { - "type": "list", - "description": "List of other reference ids apart from the primary" - } + "name": "bcftools_mpileup", + "path": "modules/nf-core/bcftools/mpileup/meta.yml", + "type": "module", + "meta": { + "name": "bcftools_mpileup", + "description": "Compresses VCF files", + "keywords": ["variant calling", "mpileup", "VCF"], + "tools": [ + { + "mpileup": { + "description": "Generates genotype likelihoods at each genomic position with coverage.\n", + "homepage": "http://samtools.github.io/bcftools/bcftools.html", + "documentation": "http://www.htslib.org/doc/bcftools.html", + "doi": "10.1093/bioinformatics/btp352", + "licence": ["MIT"], + "identifier": "biotools:bcftools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "Input BAM file", + "pattern": "*.{bam}", + "ontologies": [] + } + }, + { + "intervals_mpileup": { + "type": "file", + "description": "Input intervals file. A file (commonly '.bed') containing regions to subset used by mpileup", + "ontologies": [] + } + }, + { + "intervals_call": { + "type": "file", + "description": "Input intervals file. A file (commonly '.bed') containing regions to subset used by call but need a fourth column with REF,ALT", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA reference file", + "pattern": "*.{fasta,fa}", + "ontologies": [] + } + }, + { + "fai": { + "type": "file", + "description": "FASTA reference file index", + "pattern": "*.fai", + "ontologies": [] + } + } + ], + { + "save_mpileup": { + "type": "boolean", + "description": "Save mpileup file generated by bcftools mpileup" + } + } + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*vcf.gz": { + "type": "file", + "description": "VCF gzipped output file", + "pattern": "*.{vcf.gz}", + "ontologies": [] + } + } + ] + ], + "tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*vcf.gz.tbi": { + "type": "file", + "description": "tabix index file", + "pattern": "*.{vcf.gz.tbi}", + "ontologies": [] + } + } + ] + ], + "stats": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*stats.txt": { + "type": "file", + "description": "Text output file containing stats", + "pattern": "*{stats.txt}", + "ontologies": [] + } + } + ] + ], + "mpileup": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.mpileup.gz": { + "type": "file", + "description": "mpileup gzipped output for all positions", + "pattern": "{*.mpileup.gz}", + "ontologies": [] + } + } + ] + ], + "versions_bcftools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bcftools": { + "type": "string", + "description": "The tool name" + } + }, + { + "bcftools --version | sed '1!d; s/^.*bcftools //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bcftools": { + "type": "string", + "description": "The tool name" + } + }, + { + "bcftools --version | sed '1!d; s/^.*bcftools //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@joseespinosa"], + "maintainers": ["@joseespinosa"] }, - { - "other_ref_paths": { - "type": "list", - "description": "Path to other references paths corresponding to \"other_ref_names\"" - } - } - ], - { - "only_build_index": { - "type": "string", - "description": "true = only build index; false = mapping" - } - } - ], - "output": { - "index": [ - { - "bbsplit_index": { - "type": "directory", - "description": "Directory with index files", - "pattern": "bbsplit_index" - } - } - ], - "primary_fastq": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*primary*fastq.gz": { - "type": "file", - "description": "Output reads that map to the primary reference", - "pattern": "*primary*fastq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "all_fastq": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*fastq.gz": { - "type": "file", - "description": "All reads mapping to any of the references", - "pattern": "*fastq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "stats": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*txt": { - "type": "file", - "description": "Tab-delimited text file containing mapping statistics", - "pattern": "*.txt", - "ontologies": [] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.log": { - "type": "file", - "description": "Log file", - "pattern": "*.log", - "ontologies": [] - } - } - ] - ], - "versions_bbmap": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bbmap": { - "type": "string", - "description": "The tool name" - } - }, - { - "bbversion.sh | grep -v \"Duplicate cpuset\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bbmap": { - "type": "string", - "description": "The tool name" - } - }, - { - "bbversion.sh | grep -v \"Duplicate cpuset\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "phaseimpute", + "version": "1.1.0" + }, + { + "name": "sarek", + "version": "3.8.1" + }, + { + "name": "tumourevo", + "version": "dev" + }, + { + "name": "viralmetagenome", + "version": "1.1.1" + }, + { + "name": "viralrecon", + "version": "3.0.0" + } ] - ] }, - "authors": [ - "@joseespinosa", - "@drpatelh", - "@pinin4fjords" - ], - "maintainers": [ - "@joseespinosa", - "@drpatelh", - "@pinin4fjords" - ] - }, - "pipelines": [ { - "name": "lncpipe", - "version": "dev" + "name": "bcftools_norm", + "path": "modules/nf-core/bcftools/norm/meta.yml", + "type": "module", + "meta": { + "name": "bcftools_norm", + "description": "Normalize VCF file", + "keywords": ["normalize", "norm", "variant calling", "VCF"], + "tools": [ + { + "norm": { + "description": "Normalize VCF files.\n", + "homepage": "http://samtools.github.io/bcftools/bcftools.html", + "documentation": "http://www.htslib.org/doc/bcftools.html", + "doi": "10.1093/bioinformatics/btp352", + "licence": ["MIT"], + "identifier": "biotools:bcftools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "The vcf file to be normalized\ne.g. 'file1.vcf'\n", + "pattern": "*.{vcf,vcf.gz}", + "ontologies": [] + } + }, + { + "tbi": { + "type": "file", + "description": "An optional index of the VCF file (for when the VCF is compressed)\n", + "pattern": "*.vcf.gz.tbi", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA reference file", + "pattern": "*.{fasta,fa}", + "ontologies": [] + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{vcf,vcf.gz,bcf,bcf.gz}": { + "type": "file", + "description": "One of uncompressed VCF (.vcf), compressed VCF (.vcf.gz), compressed BCF (.bcf.gz) or uncompressed BCF (.bcf) normalized output file", + "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}", + "ontologies": [] + } + } + ] + ], + "tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tbi": { + "type": "file", + "description": "Alternative VCF file index", + "pattern": "*.tbi", + "ontologies": [] + } + } + ] + ], + "csi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.csi": { + "type": "file", + "description": "Default VCF file index", + "pattern": "*.csi", + "ontologies": [] + } + } + ] + ], + "versions_bcftools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bcftools": { + "type": "string", + "description": "The tool name" + } + }, + { + "bcftools --version | sed '1!d; s/^.*bcftools //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bcftools": { + "type": "string", + "description": "The tool name" + } + }, + { + "bcftools --version | sed '1!d; s/^.*bcftools //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@abhi18av", "@ramprasadn"], + "maintainers": ["@abhi18av", "@ramprasadn"] + }, + "pipelines": [ + { + "name": "pacsomatic", + "version": "dev" + }, + { + "name": "phaseimpute", + "version": "1.1.0" + }, + { + "name": "radseq", + "version": "dev" + }, + { + "name": "raredisease", + "version": "3.0.0" + }, + { + "name": "sarek", + "version": "3.8.1" + }, + { + "name": "variantbenchmarking", + "version": "1.5.0" + }, + { + "name": "variantcatalogue", + "version": "dev" + }, + { + "name": "variantprioritization", + "version": "1.0.0" + }, + { + "name": "viralmetagenome", + "version": "1.1.1" + }, + { + "name": "viralrecon", + "version": "3.0.0" + } + ] }, { - "name": "references", - "version": "0.1" + "name": "bcftools_plotvcfstats", + "path": "modules/nf-core/bcftools/plotvcfstats/meta.yml", + "type": "module", + "meta": { + "name": "bcftools_plotvcfstats", + "description": "Plots the output of bcftools stats", + "keywords": ["visualization", "stats", "VCF"], + "tools": [ + { + "plot": { + "description": "Script for processing output of bcftools stats, plots graphs and creates a PDF presentation.\n", + "homepage": "http://samtools.github.io/bcftools/bcftools.html", + "documentation": "http://www.htslib.org/doc/bcftools.html", + "doi": "10.1093/bioinformatics/btp352", + "licence": ["MIT"], + "identifier": "biotools:bcftools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample1' ]\n" + } + }, + { + "stats": { + "type": "file", + "description": "Text file from BCFtools stats output", + "pattern": "*_stats.txt", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + } + ] + ], + "output": { + "plot_dir": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample1' ]\n" + } + }, + { + "*plots*": { + "type": "directory", + "description": "Output directory containing plots, raw data, and log files", + "pattern": "*plots*", + "ontologies": [] + } + } + ] + ], + "plot_pdf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample1' ]\n" + } + }, + { + "*.pdf": { + "type": "file", + "description": "(Link to the original) summary output in PDF", + "pattern": "*.pdf", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3508" + } + ] + } + } + ] + ], + "versions_bcftools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bcftools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bcftools --version | sed '1!d; s/^.*bcftools //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bcftools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bcftools --version | sed '1!d; s/^.*bcftools //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@yz533cb"] + } }, { - "name": "riboseq", - "version": "1.2.0" + "name": "bcftools_pluginfilltags", + "path": "modules/nf-core/bcftools/pluginfilltags/meta.yml", + "type": "module", + "meta": { + "name": "bcftools_pluginfilltags", + "description": "Compute and fill various INFO tags", + "keywords": ["info", "bcftools", "tags", "vcf"], + "tools": [ + { + "bcftools": { + "description": "BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations.", + "homepage": "https://samtools.github.io/bcftools/howtos/index.html", + "documentation": "https://samtools.github.io/bcftools/bcftools.html", + "tool_dev_url": "https://github.com/samtools/bcftools", + "doi": "10.1093/bioinformatics/btp352", + "licence": ["MIT"], + "args_id": "$args", + "identifier": "biotools:bcftools" + } + }, + { + "bcftools plugin fill-tags": { + "description": "Bcftools plugins are tools that can be used with bcftools to manipulate variant calls in Variant Call Format (VCF) and BCF. The fill-tags plugin compute and fill various INFO tags", + "homepage": "https://samtools.github.io/bcftools/howtos/plugins.html", + "documentation": "https://samtools.github.io/bcftools/bcftools.html#plugin", + "tool_dev_url": "https://github.com/samtools/bcftools", + "doi": "10.1093/bioinformatics/btp352", + "licence": ["MIT"], + "args_id": "$args2", + "identifier": "biotools:bcftools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "The input file in variant calling format to be inspected.\ne.g. 'file.vcf.gz'\n", + "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}", + "ontologies": [] + } + }, + { + "index": { + "type": "file", + "description": "The tab index for the VCF file to be inspected.\ne.g. 'file.tbi'\n", + "ontologies": [] + } + } + ], + { + "regions": { + "type": "file", + "description": "Optionally, restrict the operation to regions listed in this file.\ne.g. 'file.vcf'\n", + "ontologies": [] + } + }, + { + "targets": { + "type": "file", + "description": "Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files)\ne.g. 'file.vcf'\n", + "ontologies": [] + } + }, + { + "samples": { + "type": "file", + "description": "Optionally, list of samples (first column) and tab-separated list of populations (second column)\ne.g. 'file.vcf'\n", + "ontologies": [] + } + } + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{vcf,vcf.gz,bcf,bcf.gz}": { + "type": "file", + "description": "VCF output file containing added INFO/INFO field", + "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}", + "ontologies": [] + } + } + ] + ], + "tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tbi": { + "type": "file", + "description": "Alternative VCF file tabix index", + "pattern": "*.tbi", + "ontologies": [] + } + } + ] + ], + "csi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.csi": { + "type": "file", + "description": "Default VCF file coordinate sorted index", + "pattern": "*.csi", + "ontologies": [] + } + } + ] + ], + "versions_bcftools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bcftools": { + "type": "string", + "description": "The tool name" + } + }, + { + "bcftools --version | sed '1!d; s/^.*bcftools //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bcftools": { + "type": "string", + "description": "The tool name" + } + }, + { + "bcftools --version | sed '1!d; s/^.*bcftools //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@LouisLeNezet"], + "maintainers": ["@LouisLeNezet"] + } }, { - "name": "rnaseq", - "version": "3.26.0" + "name": "bcftools_pluginfixploidy", + "path": "modules/nf-core/bcftools/pluginfixploidy/meta.yml", + "type": "module", + "meta": { + "name": "bcftools_pluginfixploidy", + "description": "The fixploidy plugin fixes ploidy in genotype fields according to specified ploidy rules, sample sex assignments, or a forced ploidy value. For example, haploid genotypes can be converted to diploid genotypes.", + "keywords": ["fixploidy", "bcftools", "ploidy", "vcf"], + "tools": [ + { + "bcftools": { + "description": "BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations.", + "homepage": "https://samtools.github.io/bcftools/howtos/index.html", + "documentation": "https://samtools.github.io/bcftools/bcftools.html", + "tool_dev_url": "https://github.com/samtools/bcftools", + "doi": "10.1093/bioinformatics/btp352", + "licence": ["MIT"], + "args_id": "$args", + "identifier": "biotools:bcftools" + } + }, + { + "bcftools plugin fixploidy": { + "description": "Bcftools plugins are tools that can be used with bcftools to manipulate variant calls in Variant Call Format (VCF) and BCF. The fixploidy plugin fixes ploidy in genotype fields according to specified ploidy rules, sample sex assignments, or a forced ploidy value. For example, haploid genotypes can be converted to diploid genotypes.", + "homepage": "https://samtools.github.io/bcftools/howtos/plugins.html", + "documentation": "https://samtools.github.io/bcftools/howtos/plugin.setGT.html", + "tool_dev_url": "https://github.com/samtools/bcftools", + "doi": "10.1093/bioinformatics/btp352", + "licence": ["MIT"], + "args_id": "$args2", + "identifier": "biotools:bcftools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "Input VCF/BCF file to fix ploidy in.\ne.g. 'sample.vcf.gz'\n", + "ontologies": [] + } + }, + { + "index": { + "type": "file", + "description": "Index file for the input VCF/BCF (e.g. .tbi or .csi).\ne.g. 'sample.vcf.gz.tbi'\n", + "ontologies": [] + } + } + ], + { + "ploidy": { + "type": "file", + "description": "Optional ploidy definition file for the fixploidy plugin (`-p`), with\nspace/tab-delimited columns: CHROM, FROM, TO, SEX, PLOIDY.\ne.g. 'ploidy.txt'\n", + "ontologies": [] + } + }, + { + "sex": { + "type": "file", + "description": "Optional sample sex assignment file for the fixploidy plugin (`-s`),\ncontaining lines of the form: NAME SEX.\nSamples not listed are treated as female by the plugin.\ne.g. 'samples_sex.txt'\n", + "ontologies": [] + } + }, + { + "regions": { + "type": "file", + "description": "Optionally restrict the operation to regions listed in this file\n(indexed input required; passed as a bcftools regions file argument).\ne.g. 'regions.bed'\n", + "ontologies": [] + } + }, + { + "targets": { + "type": "file", + "description": "Optionally restrict the operation to targets listed in this file\n(does not rely on index jumps in the same way as regions; passed as a\nbcftools targets file argument).\ne.g. 'targets.bed'\n", + "ontologies": [] + } + } + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{vcf,vcf.gz,bcf,bcf.gz}": { + "type": "file", + "description": "VCF output file containing GT fields with modified ploidy", + "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}", + "ontologies": [] + } + } + ] + ], + "tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tbi": { + "type": "file", + "description": "Alternative VCF file index", + "pattern": "*.tbi", + "ontologies": [] + } + } + ] + ], + "csi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.csi": { + "type": "file", + "description": "Default VCF file index", + "pattern": "*.csi", + "ontologies": [] + } + } + ] + ], + "versions_bcftools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bcftools": { + "type": "string", + "description": "The tool name" + } + }, + { + "bcftools --version | sed '1!d; s/^.*bcftools //'": { + "type": "eval", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bcftools": { + "type": "string", + "description": "The tool name" + } + }, + { + "bcftools --version | sed '1!d; s/^.*bcftools //'": { + "type": "eval", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@alkc"], + "maintainers": ["@alkc"] + } }, { - "name": "sarek", - "version": "3.8.1" - } - ] - }, - { - "name": "bbmap_clumpify", - "path": "modules/nf-core/bbmap/clumpify/meta.yml", - "type": "module", - "meta": { - "name": "bbmap_clumpify", - "description": "Create 30% Smaller, Faster Gzipped Fastq Files. And remove duplicates", - "keywords": [ - "clumping fastqs", - "smaller fastqs", - "deduping", - "fastq" - ], - "tools": [ - { - "bbmap": { - "description": "BBMap is a short read aligner, as well as various other bioinformatic tools.", - "homepage": "https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/clumpify-guide/", - "documentation": "https://www.biostars.org/p/225338/", - "licence": [ - "UC-LBL license (see package)" - ], - "identifier": "biotools:bbmap" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", - "ontologies": [] - } - } - ] - ], - "output": { - "reads": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.fastq.gz": { - "type": "file", - "description": "The reordered/clumped (and if necessary deduped) fastq reads", - "pattern": "*.clumped.fastq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.log": { - "type": "file", - "description": "Clumpify log file", - "pattern": "*clumpify.log", - "ontologies": [] - } - } - ] - ], - "versions_bbmap": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bbmap": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bbversion.sh | grep -v \"Duplicate cpuset\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bbmap": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bbversion.sh | grep -v \"Duplicate cpuset\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@tamuanand" - ], - "maintainers": [ - "@tamuanand" - ] - } - }, - { - "name": "bbmap_filterbyname", - "path": "modules/nf-core/bbmap/filterbyname/meta.yml", - "type": "module", - "meta": { - "name": "bbmap_filterbyname", - "description": "Filter out sequences by sequence header name(s)", - "keywords": [ - "fastq", - "fasta", - "filter" - ], - "tools": [ - { - "bbmap": { - "description": "BBMap is a short read aligner, as well as various other bioinformatic tools.", - "homepage": "https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/clumpify-guide/", - "documentation": "https://www.biostars.org/p/225338/", - "licence": [ - "UC-LBL license (see package)" - ], - "identifier": "biotools:bbmap" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and\npaired-end data, respectively.\n", - "ontologies": [] - } - } - ], - { - "names_to_filter": { - "type": "string", - "description": "String containing names of reads to filter out of the fastq files.\n" - } - }, - { - "output_format": { - "type": "string", - "description": "String with the format of the output file, e.g. fastq.gz, fasta, fasta.bz2\n" - } - }, - { - "interleaved_output": { - "type": "boolean", - "description": "Whether to produce an interleaved fastq output file\n" - } - } - ], - "output": { - "reads": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.${output_format}": { - "type": "file", - "description": "The trimmed/modified fastq reads", - "pattern": "*${output_format}", - "ontologies": [] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.log": { - "type": "file", - "description": "filterbyname.sh log file", - "pattern": "*.filterbyname.log", - "ontologies": [] - } - } - ] - ], - "versions_bbmap": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bbmap": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bbversion.sh | grep -v \"Duplicate cpuset\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bbmap": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bbversion.sh | grep -v \"Duplicate cpuset\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@tokarevvasily", - "@sppearce" - ], - "maintainers": [ - "@sppearce" - ] - }, - "pipelines": [ - { - "name": "detaxizer", - "version": "1.3.0" - } - ] - }, - { - "name": "bbmap_index", - "path": "modules/nf-core/bbmap/index/meta.yml", - "type": "module", - "meta": { - "name": "bbmap_index", - "description": "Creates an index from a fasta file, ready to be used by bbmap.sh in mapping mode.", - "keywords": [ - "map", - "index", - "fasta" - ], - "tools": [ - { - "bbmap": { - "description": "BBMap is a short read aligner, as well as various other bioinformatic tools.", - "homepage": "https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/", - "documentation": "https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/", - "licence": [ - "UC-LBL license (see package)" - ], - "identifier": "biotools:bbmap" - } - } - ], - "input": [ - { - "fasta": { - "type": "file", - "description": "fasta formatted file with nucleotide sequences", - "pattern": "*.{fna,fa,fasta}", - "ontologies": [] - } - } - ], - "output": { - "index": [ - { - "ref": { - "type": "directory", - "description": "Directory containing the index files" - } + "name": "bcftools_pluginimputeinfo", + "path": "modules/nf-core/bcftools/pluginimputeinfo/meta.yml", + "type": "module", + "meta": { + "name": "bcftools_pluginimputeinfo", + "description": "Adds imputation information metrics to the INFO field based on selected FORMAT tags. Only the IMPUTE2 INFO metric from FORMAT/GP tags is currently available.", + "keywords": ["impute-info", "bcftools", "imputation", "metrics", "tags", "vcf"], + "tools": [ + { + "bcftools": { + "description": "BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations.", + "homepage": "https://samtools.github.io/bcftools/howtos/index.html", + "documentation": "https://samtools.github.io/bcftools/bcftools.html", + "tool_dev_url": "https://github.com/samtools/bcftools", + "doi": "10.1093/bioinformatics/btp352", + "licence": ["MIT"], + "args_id": "$args", + "identifier": "biotools:bcftools" + } + }, + { + "bcftools plugin impute-info": { + "description": "Bcftools plugins are tools that can be used with bcftools to manipulate variant calls in Variant Call Format (VCF) and BCF. The impute-info plugin adds imputation information metrics to the INFO field based on selected FORMAT tags. Only the IMPUTE2 INFO metric from FORMAT/GP tags is currently available", + "homepage": "https://samtools.github.io/bcftools/howtos/plugins.html", + "documentation": "https://samtools.github.io/bcftools/bcftools.html#plugin", + "tool_dev_url": "https://github.com/samtools/bcftools", + "doi": "10.1093/bioinformatics/btp352", + "licence": ["MIT"], + "args_id": "$args2", + "identifier": "biotools:bcftools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "The vcf file to be inspected.\ne.g. 'file.vcf'\n", + "ontologies": [] + } + }, + { + "index": { + "type": "file", + "description": "The tab index for the VCF file to be inspected.\ne.g. 'file.tbi'\n", + "ontologies": [] + } + } + ], + { + "regions": { + "type": "file", + "description": "Optionally, restrict the operation to regions listed in this file.\ne.g. 'file.vcf'\n", + "ontologies": [] + } + }, + { + "targets": { + "type": "file", + "description": "Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files)\ne.g. 'file.vcf'\n", + "ontologies": [] + } + } + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{vcf,vcf.gz,bcf,bcf.gz}": { + "type": "file", + "description": "VCF output file containing added INFO/INFO field", + "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}", + "ontologies": [] + } + } + ] + ], + "tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tbi": { + "type": "file", + "description": "Alternative VCF file index", + "pattern": "*.tbi", + "ontologies": [] + } + } + ] + ], + "csi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.csi": { + "type": "file", + "description": "Default VCF file index", + "pattern": "*.csi", + "ontologies": [] + } + } + ] + ], + "versions_bcftools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bcftools": { + "type": "string", + "description": "The tool name" + } + }, + { + "bcftools --version | sed '1!d; s/^.*bcftools //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bcftools": { + "type": "string", + "description": "The tool name" + } + }, + { + "bcftools --version | sed '1!d; s/^.*bcftools //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@eweizy"], + "maintainers": ["@eweizy"] } - ], - "versions_bbmap": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bbmap": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bbversion.sh | grep -v \"Duplicate cpuset\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bbmap": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bbversion.sh | grep -v \"Duplicate cpuset\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] }, - "authors": [ - "@erikrikarddaniel" - ], - "maintainers": [ - "@erikrikarddaniel" - ] - }, - "pipelines": [ { - "name": "magmap", - "version": "1.0.0" + "name": "bcftools_pluginscatter", + "path": "modules/nf-core/bcftools/pluginscatter/meta.yml", + "type": "module", + "meta": { + "name": "bcftools_pluginscatter", + "description": "Split VCF by chunks or regions, creating multiple VCFs.", + "keywords": ["scatter", "vcf", "bcf", "genomics"], + "tools": [ + { + "pluginscatter": { + "description": "Split VCF by chunks or regions, creating multiple VCFs.\n", + "homepage": "http://samtools.github.io/bcftools/bcftools.html", + "documentation": "http://samtools.github.io/bcftools/bcftools.html#reheader", + "doi": "10.1093/gigascience/giab008", + "licence": ["MIT"], + "identifier": "biotools:bcftools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "The input VCF to scatter", + "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}", + "ontologies": [] + } + }, + { + "tbi": { + "type": "file", + "description": "Optional index of the input VCF", + "pattern": "*.tbi", + "ontologies": [] + } + } + ], + { + "sites_per_chunk": { + "type": "integer", + "description": "How many variants should be in each output file\nEither this or `scatter` or `scatter_file` have to be given\n" + } + }, + { + "scatter": { + "type": "string", + "description": "A comma delimited list of regions to scatter into\nEither this or `sites_per_chunk` or `scatter_file` have to be given\n" + } + }, + { + "scatter_file": { + "type": "file", + "description": "A file containing a region on each line with an optional second column containing the filename\nEither this or `sites_per_chunk` or `scatter` have to be given\n", + "ontologies": [] + } + }, + { + "regions": { + "type": "file", + "description": "Optional file containing the regions to work on", + "pattern": "*.bed", + "ontologies": [] + } + }, + { + "targets": { + "type": "file", + "description": "Optional file containing the regions to work on (but streams instead of index-jumping)", + "pattern": "*.bed", + "ontologies": [] + } + } + ], + "output": { + "scatter": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*{vcf,vcf.gz,bcf,bcf.gz}": { + "type": "file", + "description": "The resulting files of the scattering", + "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}", + "ontologies": [] + } + } + ] + ], + "tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tbi": { + "type": "file", + "description": "Alternative VCF file index", + "pattern": "*.tbi", + "ontologies": [] + } + } + ] + ], + "csi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.csi": { + "type": "file", + "description": "Default VCF file index", + "pattern": "*.csi", + "ontologies": [] + } + } + ] + ], + "versions_bcftools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bcftools": { + "type": "string", + "description": "The tool name" + } + }, + { + "bcftools --version | sed '1!d; s/^.*bcftools //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bcftools": { + "type": "string", + "description": "The tool name" + } + }, + { + "bcftools --version | sed '1!d; s/^.*bcftools //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@nvnieuwk"], + "maintainers": ["@nvnieuwk"] + } }, { - "name": "metatdenovo", - "version": "1.3.0" - } - ] - }, - { - "name": "bbmap_pileup", - "path": "modules/nf-core/bbmap/pileup/meta.yml", - "type": "module", - "meta": { - "name": "bbmap_pileup", - "description": "Calculates per-scaffold or per-base coverage information from an unsorted sam or bam file.", - "keywords": [ - "fasta", - "genome", - "coverage" - ], - "tools": [ - { - "bbmap": { - "description": "BBMap is a short read aligner, as well as various other bioinformatic tools.", - "homepage": "https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/", - "documentation": "https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/", - "tool_dev_url": "https://github.com/BioInfoTools/BBMap/blob/master/sh/pileup.sh", - "licence": [ - "UC-LBL license (see package)" - ], - "identifier": "biotools:bbmap" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } - } - ] - ], - "output": { - "covstats": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.stats.txt": { - "type": "file", - "description": "Coverage statistics", - "pattern": "*.stats.txt", - "ontologies": [] - } - } - ] - ], - "hist": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.hist.txt": { - "type": "file", - "description": "Histogram of # occurrences of each depth level", - "pattern": "*.hist.txt", - "ontologies": [] - } - } - ] - ], - "versions_bbmap": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bbmap": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bbversion.sh | grep -v 'Duplicate cpuset'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_samtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_pigz": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pigz": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pigz --version 2>&1 | sed \"s/^.*pigz[[:space:]]*//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bbmap": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bbversion.sh | grep -v 'Duplicate cpuset'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pigz": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pigz --version 2>&1 | sed \"s/^.*pigz[[:space:]]*//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@edmundmiller" - ], - "maintainers": [ - "@edmundmiller" - ] - }, - "pipelines": [ - { - "name": "nascent", - "version": "2.3.0" - } - ] - }, - { - "name": "bbmap_repair", - "path": "modules/nf-core/bbmap/repair/meta.yml", - "type": "module", - "meta": { - "name": "bbmap_repair", - "description": "Re-pairs reads that became disordered or had some mates eliminated.", - "keywords": [ - "paired reads re-pairing", - "fastq", - "preprocessing" - ], - "tools": [ - { - "repair": { - "description": "Repair.sh is a tool that re-pairs reads that became disordered or had some mates eliminated tools.", - "homepage": "https://jgi.doe.gov/data-and-tools/software-tools/bbtools/", - "documentation": "https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/", - "licence": [ - "UC-LBL license (see package)" - ], - "identifier": "biotools:bbmap" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } + "name": "bcftools_pluginsetgt", + "path": "modules/nf-core/bcftools/pluginsetgt/meta.yml", + "type": "module", + "meta": { + "name": "bcftools_pluginsetgt", + "description": "Sets genotypes according to the specified criteria and filtering expressions. For example, missing genotypes can be set to ref, but much more than that.", + "keywords": ["setgt", "bcftools", "genotype", "vcf"], + "tools": [ + { + "bcftools": { + "description": "BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations.", + "homepage": "https://samtools.github.io/bcftools/howtos/index.html", + "documentation": "https://samtools.github.io/bcftools/bcftools.html", + "tool_dev_url": "https://github.com/samtools/bcftools", + "doi": "10.1093/bioinformatics/btp352", + "licence": ["MIT"], + "args_id": "$args", + "identifier": "biotools:bcftools" + } + }, + { + "bcftools plugin setGT": { + "description": "Bcftools plugins are tools that can be used with bcftools to manipulate variant calls in Variant Call Format (VCF) and BCF. The setGT plugin sets genotypes according to the specified criteria and filtering expressions. For example, missing genotypes can be set to ref, but much more than that.", + "homepage": "https://samtools.github.io/bcftools/howtos/plugins.html", + "documentation": "https://samtools.github.io/bcftools/howtos/plugin.setGT.html", + "tool_dev_url": "https://github.com/samtools/bcftools", + "doi": "10.1093/bioinformatics/btp352", + "licence": ["MIT"], + "args_id": "$args2", + "identifier": "biotools:bcftools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "The vcf file to be inspected.\ne.g. 'file.vcf'\n", + "ontologies": [] + } + }, + { + "index": { + "type": "file", + "description": "The tab index for the VCF file to be inspected.\ne.g. 'file.tbi'\n", + "ontologies": [] + } + } + ], + { + "target_gt": { + "type": "string", + "description": "Genotypes to change\n" + } + }, + { + "new_gt": { + "type": "string", + "description": "Genotypes to set\n" + } + }, + { + "regions": { + "type": "file", + "description": "Optionally, restrict the operation to regions listed in this file.\ne.g. 'file.vcf'\n", + "ontologies": [] + } + }, + { + "targets": { + "type": "file", + "description": "Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files)\ne.g. 'file.vcf'\n", + "ontologies": [] + } + } + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{vcf,vcf.gz,bcf,bcf.gz}": { + "type": "file", + "description": "VCF output file containing set genotypes", + "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}", + "ontologies": [] + } + } + ] + ], + "tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tbi": { + "type": "file", + "description": "Alternative VCF file index", + "pattern": "*.tbi", + "ontologies": [] + } + } + ] + ], + "csi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.csi": { + "type": "file", + "description": "Default VCF file index", + "pattern": "*.csi", + "ontologies": [] + } + } + ] + ], + "versions_bcftools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bcftools": { + "type": "string", + "description": "The tool name" + } + }, + { + "bcftools --version | sed '1!d; s/^.*bcftools //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bcftools": { + "type": "string", + "description": "The tool name" + } + }, + { + "bcftools --version | sed '1!d; s/^.*bcftools //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@eweizy"], + "maintainers": ["@eweizy"] }, - { - "reads": { - "type": "file", - "description": "List of input paired end fastq files\n", - "pattern": "*.{fastq,fq}.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ], - { - "interleave": { - "type": "boolean", - "description": "Indicates whether the input paired reads are interleaved or not\n" - } - } - ], - "output": { - "repaired": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*_repaired.fastq.gz": { - "type": "file", - "description": "re-paired reads", - "pattern": "*_repaired.fastq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } + "pipelines": [ + { + "name": "raredisease", + "version": "3.0.0" + } ] - ], - "singleton": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "${prefix}_singleton.fastq.gz": { - "type": "file", - "description": "singleton reads", - "pattern": "*singleton.fastq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "log": [ - { - "*.log": { - "type": "file", - "description": "log file containing stdout and stderr from repair.sh", - "pattern": "*.log", - "ontologies": [] - } - } - ], - "versions_bbmap": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bbmap": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bbversion.sh | grep -v \"Duplicate cpuset\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bbmap": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bbversion.sh | grep -v \"Duplicate cpuset\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@mazzalab" - ], - "maintainers": [ - "@mazzalab", - "@tm4zza" - ] - }, - "pipelines": [ - { - "name": "fastqrepair", - "version": "1.0.0" - } - ] - }, - { - "name": "bbmap_sendsketch", - "path": "modules/nf-core/bbmap/sendsketch/meta.yml", - "type": "module", - "meta": { - "name": "bbmap_sendsketch", - "description": "Compares query sketches to reference sketches hosted on a remote server via the Internet.", - "keywords": [ - "taxonomy", - "classification", - "sketch", - "query", - "fastq", - "fasta" - ], - "tools": [ - { - "bbmap": { - "description": "BBMap is a short read aligner, as well as various other bioinformatic tools.", - "homepage": "https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/", - "documentation": "https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/", - "licence": [ - "UC-LBL license (see package)" - ], - "identifier": "biotools:bbmap" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "file": { - "type": "file", - "description": "file with nucleotide sequences", - "pattern": "*.{fna, fa, fasta, fa.gz, fasta.gz, fna.gz, fastq.gz, fastq, fq.gz, fq}", - "ontologies": [] - } - } - ] - ], - "output": { - "hits": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.txt": { - "type": "file", - "description": ".txt file containing hits from a query seuqnce to various reference sequences output", - "pattern": "*.{txt}", - "ontologies": [] - } - } - ] - ], - "versions_bbmap": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bbmap": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bbversion.sh | grep -v \"Duplicate cpuset\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bbmap": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bbversion.sh | grep -v \"Duplicate cpuset\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@phanhung2" - ], - "maintainers": [ - "@phanhung2" - ] - }, - "pipelines": [ - { - "name": "pathogensurveillance", - "version": "1.1.0" - } - ] - }, - { - "name": "bcftools_annotate", - "path": "modules/nf-core/bcftools/annotate/meta.yml", - "type": "module", - "meta": { - "name": "bcftools_annotate", - "description": "Add or remove annotations.", - "keywords": [ - "bcftools", - "annotate", - "vcf", - "remove", - "add" - ], - "tools": [ - { - "annotate": { - "description": "Add or remove annotations.", - "homepage": "http://samtools.github.io/bcftools/bcftools.html", - "documentation": "https://samtools.github.io/bcftools/bcftools.html#annotate", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "identifier": "biotools:bcftools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "Query VCF or BCF file, can be either uncompressed or compressed", - "ontologies": [] - } - }, - { - "index": { - "type": "file", - "description": "Index of the query VCF or BCF file", - "ontologies": [] - } - }, - { - "annotations": { - "type": "file", - "description": "Bgzip-compressed file with annotations", - "ontologies": [] - } - }, - { - "annotations_index": { - "type": "file", - "description": "Index of the annotations file", - "ontologies": [] - } - }, - { - "columns": { - "type": "file", - "description": "List of columns in the annotations file, one name per row", - "ontologies": [] - } - }, - { - "header_lines": { - "type": "file", - "description": "Contains lines to append to the output VCF header", - "ontologies": [] - } - }, - { - "rename_chrs": { - "type": "file", - "description": "Rename annotations according to this file containing \"old_name new_name\\n\" pairs separated by whitespaces, each on a separate line.", - "ontologies": [] - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.${extension}": { - "type": "file", - "description": "Compressed annotated VCF file", - "pattern": "*{vcf,vcf.gz,bcf,bcf.gz}", - "ontologies": [] - } - } - ] - ], - "tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.${extension}.tbi": { - "type": "file", - "description": "Alternative VCF file index", - "pattern": "*.tbi", - "ontologies": [] - } - } - ] - ], - "csi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.${extension}.csi": { - "type": "file", - "description": "Default VCF file index", - "pattern": "*.csi", - "ontologies": [] - } - } - ] - ], - "versions_bcftools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bcftools": { - "type": "string", - "description": "The tool name" - } - }, - { - "bcftools --version | sed '1!d; s/^.*bcftools //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bcftools": { - "type": "string", - "description": "The tool name" - } - }, - { - "bcftools --version | sed '1!d; s/^.*bcftools //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@projectoriented", - "@ramprasadn" - ], - "maintainers": [ - "@projectoriented", - "@ramprasadn" - ] - }, - "pipelines": [ - { - "name": "alleleexpression", - "version": "dev" - }, - { - "name": "phaseimpute", - "version": "1.1.0" - }, - { - "name": "raredisease", - "version": "3.0.0" }, { - "name": "rnavar", - "version": "1.2.3" - }, - { - "name": "sarek", - "version": "3.8.1" - }, - { - "name": "variantbenchmarking", - "version": "1.5.0" - }, - { - "name": "variantcatalogue", - "version": "dev" - } - ] - }, - { - "name": "bcftools_call", - "path": "modules/nf-core/bcftools/call/meta.yml", - "type": "module", - "meta": { - "name": "bcftools_call", - "description": "This command replaces the former bcftools view caller.\nSome of the original functionality has been temporarily lost in the process of transition under htslib, but will be added back on popular demand.\nThe original calling model can be invoked with the -c option.\n", - "keywords": [ - "variant calling", - "view", - "bcftools", - "VCF" - ], - "tools": [ - { - "view": { - "description": "View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF\n", - "homepage": "http://samtools.github.io/bcftools/bcftools.html", - "documentation": "http://www.htslib.org/doc/bcftools.html", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "identifier": "biotools:bcftools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "The vcf file to be inspected.\ne.g. 'file.vcf'\n", - "ontologies": [] - } - }, - { - "index": { - "type": "file", - "description": "The tab index for the VCF file to be inspected.\ne.g. 'file.tbi'\n", - "ontologies": [] - } - } - ], - { - "regions": { - "type": "file", - "description": "Optionally, restrict the operation to regions listed in this file.\ne.g. 'file.vcf'\n", - "ontologies": [] - } - }, - { - "targets": { - "type": "file", - "description": "Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files)\ne.g. 'file.vcf'\n", - "ontologies": [] - } - }, - { - "samples": { - "type": "file", - "description": "Optional, file of sample names to be included or excluded.\ne.g. 'file.tsv'\n", - "ontologies": [] - } - } - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.gz": { - "type": "file", - "description": "VCF normalized output file", - "pattern": "*.{vcf.gz}", - "ontologies": [] - } - } - ] - ], - "tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tbi": { - "type": "file", - "description": "Alternative VCF file index", - "pattern": "*.tbi", - "ontologies": [] - } - } - ] - ], - "csi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.csi": { - "type": "file", - "description": "Default VCF file index", - "pattern": "*.csi", - "ontologies": [] - } - } - ] - ], - "versions_bcftools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bcftools": { - "type": "string", - "description": "The tool name" - } - }, - { - "bcftools --version | sed '1!d; s/^.*bcftools //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bcftools": { - "type": "string", - "description": "The tool name" - } - }, - { - "bcftools --version | sed '1!d; s/^.*bcftools //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@abhi18av", - "@LouisLeNezet" - ], - "maintainers": [ - "@abhi18av", - "@LouisLeNezet" - ] - } - }, - { - "name": "bcftools_concat", - "path": "modules/nf-core/bcftools/concat/meta.yml", - "type": "module", - "meta": { - "name": "bcftools_concat", - "description": "Concatenate VCF files", - "keywords": [ - "variant calling", - "concat", - "bcftools", - "VCF" - ], - "tools": [ - { - "concat": { - "description": "Concatenate VCF files.\n", - "homepage": "http://samtools.github.io/bcftools/bcftools.html", - "documentation": "http://www.htslib.org/doc/bcftools.html", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "identifier": "biotools:bcftools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcfs": { - "type": "list", - "description": "List containing 2 or more vcf files\ne.g. [ 'file1.vcf', 'file2.vcf' ]\n" - } + "name": "bcftools_pluginsplit", + "path": "modules/nf-core/bcftools/pluginsplit/meta.yml", + "type": "module", + "meta": { + "name": "bcftools_pluginsplit", + "description": "Split VCF by sample, creating single- or multi-sample VCFs.", + "keywords": ["split", "vcf", "genomics"], + "tools": [ + { + "pluginsplit": { + "description": "Split VCF by sample, creating single- or multi-sample VCFs.\n", + "homepage": "http://samtools.github.io/bcftools/bcftools.html", + "documentation": "http://www.htslib.org/doc/bcftools.html", + "doi": "10.1093/bioinformatics/btp352", + "licence": ["MIT"], + "identifier": "biotools:bcftools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "The VCF file to split", + "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}", + "ontologies": [] + } + }, + { + "tbi": { + "type": "file", + "description": "OPTIONAL - The index of the input VCF/BCF", + "pattern": "*.tbi", + "ontologies": [] + } + }, + { + "samples": { + "type": "file", + "description": "A tab-separated file determining which samples should be in which output file\ncolumn 1: The sample name(s) in the input file\ncolumn 2: The sample name(s) to use in the output file (use `-` to keep the original name)\ncolumn 3: The name of the output file\nEither this or a groups file should be given\n", + "pattern": "*", + "ontologies": [] + } + }, + { + "groups": { + "type": "file", + "description": "A tab-separated file determining which samples should be in which output file(s)\ncolumn 1: The sample name(s) in the input file\ncolumn 2: The sample name(s) to use in the output file (use `-` to keep the original name)\ncolumn 3: The name of the output file(s)\nEither this or a samples file should be given\n", + "pattern": "*", + "ontologies": [] + } + }, + { + "regions": { + "type": "file", + "description": "A BED file containing regions to use", + "pattern": "*.bed", + "ontologies": [] + } + }, + { + "targets": { + "type": "file", + "description": "A BED file containing regions to use (but streams rather than index-jumps)", + "pattern": "*.bed", + "ontologies": [] + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{vcf,vcf.gz,bcf,bcf.gz}": { + "type": "file", + "description": "The resulting VCF files from the split", + "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}", + "ontologies": [] + } + } + ] + ], + "tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tbi": { + "type": "file", + "description": "TBI file", + "pattern": "*.tbi", + "ontologies": [] + } + } + ] + ], + "csi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.csi": { + "type": "file", + "description": "CSI file", + "pattern": "*.csi", + "ontologies": [] + } + } + ] + ], + "versions_bcftools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bcftools": { + "type": "string", + "description": "The tool name" + } + }, + { + "bcftools --version | sed '1!d; s/^.*bcftools //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bcftools": { + "type": "string", + "description": "The tool name" + } + }, + { + "bcftools --version | sed '1!d; s/^.*bcftools //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@nvnieuwk"], + "maintainers": ["@nvnieuwk"] }, - { - "tbi": { - "type": "list", - "description": "List containing 2 or more index files (optional)\ne.g. [ 'file1.tbi', 'file2.tbi' ]\n" - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.${extension}": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", - "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}" - } - } - ] - ], - "tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.${extension}.tbi": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", - "pattern": "*.tbi" - } - } - ] - ], - "csi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.${extension}.csi": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", - "pattern": "*.csi" - } - } - ] - ], - "versions_bcftools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bcftools": { - "type": "string", - "description": "The tool name" - } - }, - { - "bcftools --version | sed '1!d; s/^.*bcftools //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bcftools": { - "type": "string", - "description": "The tool name" - } - }, - { - "bcftools --version | sed '1!d; s/^.*bcftools //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } + "pipelines": [ + { + "name": "phaseimpute", + "version": "1.1.0" + } ] - ] - }, - "authors": [ - "@abhi18av", - "@nvnieuwk" - ], - "maintainers": [ - "@abhi18av", - "@nvnieuwk" - ] - }, - "pipelines": [ - { - "name": "genomicrelatedness", - "version": "dev" - }, - { - "name": "pacsomatic", - "version": "dev" - }, - { - "name": "phaseimpute", - "version": "1.1.0" }, { - "name": "radseq", - "version": "dev" + "name": "bcftools_plugintag2tag", + "path": "modules/nf-core/bcftools/plugintag2tag/meta.yml", + "type": "module", + "meta": { + "name": "bcftools_plugintag2tag", + "description": "Converts between similar tags, such as GL,PL,GP or QR,QA,QS or localized alleles, eg LPL,LAD.", + "keywords": ["tag2tag", "bcftools", "VCF"], + "tools": [ + { + "view": { + "description": "Converts between similar tags, such as GL,PL,GP or QR,QA,QS or localized alleles, eg LPL,LAD.\n", + "homepage": "http://samtools.github.io/bcftools/bcftools.html", + "documentation": "https://samtools.github.io/bcftools/howtos/plugin.tag2tag.html", + "doi": "10.1093/bioinformatics/btp352", + "licence": ["MIT"], + "identifier": "biotools:bcftools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "The vcf file to be inspected.\ne.g. 'file.vcf'\n", + "ontologies": [] + } + }, + { + "index": { + "type": "file", + "description": "The tab index for the VCF file to be inspected.\ne.g. 'file.tbi'\n", + "ontologies": [] + } + } + ], + { + "regions": { + "type": "file", + "description": "Optionally, restrict the operation to regions listed in this file.\ne.g. 'file.vcf'\n", + "ontologies": [] + } + }, + { + "targets": { + "type": "file", + "description": "Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files)\ne.g. 'file.vcf'\n", + "ontologies": [] + } + } + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{vcf,vcf.gz,bcf,bcf.gz}": { + "type": "file", + "description": "VCF normalized output file", + "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}", + "ontologies": [] + } + } + ] + ], + "tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tbi": { + "type": "file", + "description": "Alternative VCF file index", + "pattern": "*.tbi", + "ontologies": [] + } + } + ] + ], + "csi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.csi": { + "type": "file", + "description": "Default VCF file index", + "pattern": "*.csi", + "ontologies": [] + } + } + ] + ], + "versions_bcftools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bcftools": { + "type": "string", + "description": "The tool name" + } + }, + { + "bcftools --version | sed '1!d; s/^.*bcftools //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bcftools": { + "type": "string", + "description": "The tool name" + } + }, + { + "bcftools --version | sed '1!d; s/^.*bcftools //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@eweizy"], + "maintainers": ["@eweizy"] + } }, { - "name": "raredisease", - "version": "3.0.0" + "name": "bcftools_pluginvcf2table", + "path": "modules/nf-core/bcftools/pluginvcf2table/meta.yml", + "type": "module", + "meta": { + "name": "bcftools_pluginvcf2table", + "description": "Converts VCF/BCF files into a tab-delimited table using the bcftools +vcf2table plugin.\nEach variant is output as one row, with INFO and FORMAT fields as columns.\n", + "keywords": ["bcftools", "vcf", "table", "variant calling"], + "tools": [ + { + "bcftools": { + "description": "BCFtools is a set of utilities for variant calling and manipulating VCF/BCF files.\nThe +vcf2table plugin converts VCF records into a tab-delimited table format.\n", + "homepage": "http://samtools.github.io/bcftools/bcftools.html", + "documentation": "http://www.htslib.org/doc/bcftools.html", + "doi": "10.1093/gigascience/giab008", + "licence": ["MIT"], + "identifier": "biotools:bcftools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "ontologies": [] + } + }, + { + "vcf": { + "type": "file", + "description": "VCF/BCF file to be converted (optionally bgzipped).", + "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + } + ] + } + }, + { + "tbi": { + "type": "file", + "description": "Index of the VCF/BCF file (required when vcf is bgzipped).", + "pattern": "*.{tbi,csi}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing filter file information\ne.g. [ id:'test' ]\n" + } + }, + { + "regions": { + "type": "file", + "description": "Optional. Restrict the operation to regions listed in this BED or VCF file.\nRelies on a tabix index.\n", + "pattern": "*.{bed,vcf,vcf.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3003" + }, + { + "edam": "http://edamontology.org/format_3016" + } + ] + } + }, + { + "targets": { + "type": "file", + "description": "Optional. Restrict the operation to regions listed in this file\n(does not rely on index files).\n", + "pattern": "*.{bed,vcf,vcf.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3003" + }, + { + "edam": "http://edamontology.org/format_3016" + } + ] + } + }, + { + "samples": { + "type": "file", + "description": "Optional. File of sample names to include or exclude.\n", + "pattern": "*.txt", + "ontologies": [] + } + } + ] + ], + "output": { + "txt": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "ontologies": [] + } + }, + { + "*.txt": { + "type": "file", + "description": "Tab-delimited table output from bcftools +vcf2table.", + "pattern": "*.txt", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_bcftools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bcftools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bcftools --version | sed '1!d; s/^.*bcftools //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bcftools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bcftools --version | sed '1!d; s/^.*bcftools //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@emmcauley"], + "maintainers": ["@emmcauley"] + } }, { - "name": "sarek", - "version": "3.8.1" - } - ] - }, - { - "name": "bcftools_consensus", - "path": "modules/nf-core/bcftools/consensus/meta.yml", - "type": "module", - "meta": { - "name": "bcftools_consensus", - "description": "Compresses VCF files", - "keywords": [ - "variant calling", - "consensus", - "VCF" - ], - "tools": [ - { - "consensus": { - "description": "Create consensus sequence by applying VCF variants to a reference fasta file.\n", - "homepage": "http://samtools.github.io/bcftools/bcftools.html", - "documentation": "http://www.htslib.org/doc/bcftools.html", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "identifier": "biotools:bcftools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF file", - "pattern": "*.{vcf}", - "ontologies": [] - } - }, - { - "tbi": { - "type": "file", - "description": "tabix index file", - "pattern": "*.{tbi}", - "ontologies": [] - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA reference file", - "pattern": "*.{fasta,fa}", - "ontologies": [] - } + "name": "bcftools_query", + "path": "modules/nf-core/bcftools/query/meta.yml", + "type": "module", + "meta": { + "name": "bcftools_query", + "description": "Extracts fields from VCF or BCF files and outputs them in user-defined format.", + "keywords": ["query", "variant calling", "bcftools", "VCF"], + "tools": [ + { + "query": { + "description": "Extracts fields from VCF or BCF files and outputs them in user-defined format.\n", + "homepage": "http://samtools.github.io/bcftools/bcftools.html", + "documentation": "http://www.htslib.org/doc/bcftools.html", + "doi": "10.1093/bioinformatics/btp352", + "licence": ["MIT"], + "identifier": "biotools:bcftools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "The vcf file to be queried.\n", + "pattern": "*.{vcf.gz, vcf}", + "ontologies": [] + } + }, + { + "tbi": { + "type": "file", + "description": "The tab index for the VCF file to be inspected.\n", + "pattern": "*.tbi", + "ontologies": [] + } + } + ], + { + "regions": { + "type": "file", + "description": "Optionally, restrict the operation to regions listed in this file.\n", + "ontologies": [] + } + }, + { + "targets": { + "type": "file", + "description": "Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files)\n", + "ontologies": [] + } + }, + { + "samples": { + "type": "file", + "description": "Optional, file of sample names to be included or excluded.\ne.g. 'file.tsv'\n", + "ontologies": [] + } + } + ], + "output": { + "output": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.${suffix}": { + "type": "file", + "description": "BCFTools query output file", + "ontologies": [] + } + } + ] + ], + "versions_bcftools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bcftools": { + "type": "string", + "description": "The tool name" + } + }, + { + "bcftools --version | sed '1!d; s/^.*bcftools //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bcftools": { + "type": "string", + "description": "The tool name" + } + }, + { + "bcftools --version | sed '1!d; s/^.*bcftools //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@abhi18av", "@drpatelh"], + "maintainers": ["@abhi18av", "@drpatelh"] }, - { - "mask": { - "type": "file", - "description": "BED file used for masking", - "pattern": "*.{bed}", - "ontologies": [] - } - } - ] - ], - "output": { - "fasta": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.fa": { - "type": "file", - "description": "FASTA reference consensus file", - "pattern": "*.{fasta,fa}", - "ontologies": [] - } - } - ] - ], - "versions_bcftools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bcftools": { - "type": "string", - "description": "The tool name" - } - }, - { - "bcftools --version | sed '1!d; s/^.*bcftools //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bcftools": { - "type": "string", - "description": "The tool name" - } - }, - { - "bcftools --version | sed '1!d; s/^.*bcftools //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } + "pipelines": [ + { + "name": "genomicrelatedness", + "version": "dev" + }, + { + "name": "pacsomatic", + "version": "dev" + }, + { + "name": "phaseimpute", + "version": "1.1.0" + }, + { + "name": "viralrecon", + "version": "3.0.0" + } ] - ] }, - "authors": [ - "@joseespinosa", - "@drpatelh" - ], - "maintainers": [ - "@joseespinosa", - "@drpatelh" - ] - }, - "pipelines": [ { - "name": "mag", - "version": "5.4.2" - }, - { - "name": "viralmetagenome", - "version": "1.1.1" - }, - { - "name": "viralrecon", - "version": "3.0.0" - } - ] - }, - { - "name": "bcftools_convert", - "path": "modules/nf-core/bcftools/convert/meta.yml", - "type": "module", - "meta": { - "name": "bcftools_convert", - "description": "Converts certain output formats to VCF", - "keywords": [ - "bcftools", - "convert", - "vcf", - "gvcf" - ], - "tools": [ - { - "bcftools": { - "description": "BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations.", - "homepage": "https://samtools.github.io/bcftools/bcftools.html", - "documentation": "https://samtools.github.io/bcftools/bcftools.html#convert", - "tool_dev_url": "https://github.com/samtools/bcftools", - "doi": "10.1093/gigascience/giab008", - "licence": [ - "GPL" - ], - "identifier": "biotools:bcftools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "The input format. Each format needs a separate parameter to be specified in the `args`:\n- GEN/SAMPLE file: `--gensample2vcf`\n- gVCF file: `--gvcf2vcf`\n- HAP/SAMPLE file: `--hapsample2vcf`\n- HAP/LEGEND/SAMPLE file: `--haplegendsample2vcf`\n- TSV file: `--tsv2vcf`\n", - "pattern": "*.{gen,sample,g.vcf,hap,legend}{.gz,}", - "ontologies": [] - } - }, - { - "input_index": { - "type": "file", - "description": "(Optional) The index for the input files, if needed", - "pattern": "*.bed", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "(Optional) The reference fasta, only needed for gVCF conversion", - "pattern": "*.{fa,fasta}", - "ontologies": [] - } - } - ], - { - "bed": { - "type": "file", - "description": "(Optional) The BED file containing the regions for the VCF file", - "pattern": "*.bed", - "ontologies": [] - } - } - ], - "output": { - "vcf_gz": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.vcf.gz": { - "type": "file", - "description": "VCF merged output file (bgzipped) => when `--output-type z` is used", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.vcf": { - "type": "file", - "description": "VCF merged output file => when `--output-type v` is used", - "pattern": "*.vcf", - "ontologies": [] - } - } - ] - ], - "bcf_gz": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bcf.gz": { - "type": "file", - "description": "BCF merged output file (bgzipped) => when `--output-type b` is used", - "pattern": "*.bcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "bcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bcf": { - "type": "file", - "description": "BCF merged output file => when `--output-type u` is used", - "pattern": "*.bcf", - "ontologies": [] - } - } - ] - ], - "hap": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.hap.gz": { - "type": "file", - "description": "hap format used by IMPUTE2 and SHAPEIT", - "pattern": "*.hap.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "legend": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.legend.gz": { - "type": "file", - "description": "legend format used by IMPUTE2 and SHAPEIT", - "pattern": "*.legend.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "samples": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.samples": { - "type": "file", - "description": "samples format used by IMPUTE2 and SHAPEIT", - "pattern": "*.samples", - "ontologies": [] - } - } - ] - ], - "tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tbi": { - "type": "file", - "description": "Alternative VCF file index", - "pattern": "*.tbi", - "ontologies": [] - } - } - ] - ], - "csi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.csi": { - "type": "file", - "description": "Default VCF file index", - "pattern": "*.csi", - "ontologies": [] - } - } - ] - ], - "versions_bcftools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bcftools": { - "type": "string", - "description": "The tool name" - } - }, - { - "bcftools --version | sed '1!d; s/^.*bcftools //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bcftools": { - "type": "string", - "description": "The tool name" - } - }, - { - "bcftools --version | sed '1!d; s/^.*bcftools //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@nvnieuwk", - "@ramprasadn", - "@atrigila" - ], - "maintainers": [ - "@nvnieuwk", - "@ramprasadn", - "@atrigila" - ] - }, - "pipelines": [ - { - "name": "phaseimpute", - "version": "1.1.0" - } - ] - }, - { - "name": "bcftools_csq", - "path": "modules/nf-core/bcftools/csq/meta.yml", - "type": "module", - "meta": { - "name": "bcftools_csq", - "description": "bcftools Haplotype-aware consequence caller", - "keywords": [ - "annotation", - "gff", - "gff3", - "protein", - "functional", - "vcf", - "bcf", - "bcftools" - ], - "tools": [ - { - "reheader": { - "description": "Haplotype-aware consequence caller\n", - "homepage": "http://samtools.github.io/bcftools/bcftools.html", - "documentation": "http://samtools.github.io/bcftools/bcftools.html#csq", - "doi": "10.1093/gigascience/giab008", - "licence": [ - "MIT" - ], - "identifier": "biotools:bcftools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF/BCF file", - "pattern": "*.{vcf.gz,vcf,bcf}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing fasta information\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Fasta reference", - "pattern": "*.{fasta,fa}", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing fai information\n" - } - }, - { - "fai": { - "type": "file", - "description": "Fasta index", - "pattern": "*.{fai}", - "ontologies": [] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing gff3 information\n" - } - }, - { - "gff3": { - "type": "file", - "description": "GFF3 file", - "pattern": "*.{gff,gff.gz,gff3,gff3.gz}", - "ontologies": [] - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.${extension}": { - "type": "file", - "description": "VCF with annotation, bgzipped per default", - "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}", - "ontologies": [] - } - } - ] - ], - "tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tbi": { - "type": "file", - "description": "Alternative VCF file index", - "pattern": "*.tbi", - "ontologies": [] - } - } - ] - ], - "csi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.csi": { - "type": "file", - "description": "Default VCF file index", - "pattern": "*.csi", - "ontologies": [] - } - } - ] - ], - "versions_bcftools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bcftools": { - "type": "string", - "description": "The tool name" - } - }, - { - "bcftools --version | sed '1!d; s/^.*bcftools //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bcftools": { - "type": "string", - "description": "The tool name" - } - }, - { - "bcftools --version | sed '1!d; s/^.*bcftools //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@lindenb" - ], - "maintainers": [ - "@lindenb" - ] - } - }, - { - "name": "bcftools_filter", - "path": "modules/nf-core/bcftools/filter/meta.yml", - "type": "module", - "meta": { - "name": "bcftools_filter", - "description": "Filters VCF files", - "keywords": [ - "variant calling", - "filtering", - "VCF" - ], - "tools": [ - { - "filter": { - "description": "Apply fixed-threshold filters to VCF files.\n", - "homepage": "http://samtools.github.io/bcftools/bcftools.html", - "documentation": "http://www.htslib.org/doc/bcftools.html", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "identifier": "biotools:bcftools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF input file", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", - "ontologies": [] - } + "name": "bcftools_reheader", + "path": "modules/nf-core/bcftools/reheader/meta.yml", + "type": "module", + "meta": { + "name": "bcftools_reheader", + "description": "Reheader a VCF file", + "keywords": ["reheader", "vcf", "update header"], + "tools": [ + { + "reheader": { + "description": "Modify header of VCF/BCF files, change sample names.\n", + "homepage": "http://samtools.github.io/bcftools/bcftools.html", + "documentation": "http://samtools.github.io/bcftools/bcftools.html#reheader", + "doi": "10.1093/gigascience/giab008", + "licence": ["MIT"], + "identifier": "biotools:bcftools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF/BCF file", + "pattern": "*.{vcf.gz,vcf,bcf}", + "ontologies": [] + } + }, + { + "header": { + "type": "file", + "description": "New header to add to the VCF", + "pattern": "*.{header.txt}", + "ontologies": [] + } + }, + { + "samples": { + "type": "file", + "description": "File containing sample names to update (one sample per line)", + "pattern": "*.{samples.txt}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Fasta index to update header sequences with", + "pattern": "*.{fai}", + "ontologies": [] + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{vcf,vcf.gz,bcf,bcf.gz}": { + "type": "file", + "description": "VCF with updated header, bgzipped per default", + "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}", + "ontologies": [] + } + } + ] + ], + "index": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{csi,tbi}": { + "type": "file", + "description": "Index of VCF with updated header", + "pattern": "*.{csi,tbi}", + "ontologies": [] + } + } + ] + ], + "versions_bcftools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bcftools": { + "type": "string", + "description": "The tool name" + } + }, + { + "bcftools --version | sed '1!d; s/^.*bcftools //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bcftools": { + "type": "string", + "description": "The tool name" + } + }, + { + "bcftools --version | sed '1!d; s/^.*bcftools //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@bjohnnyd", "@jemten", "@ramprasadn"], + "maintainers": ["@bjohnnyd", "@jemten", "@ramprasadn"] }, - { - "tbi": { - "type": "file", - "description": "VCF index file", - "pattern": "*.tbi", - "ontologies": [] - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.${extension}": { - "type": "file", - "description": "VCF filtered output file", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", - "ontologies": [] - } - } - ] - ], - "tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tbi": { - "type": "file", - "description": "Alternative VCF file index", - "pattern": "*.tbi", - "ontologies": [] - } - } - ] - ], - "csi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.csi": { - "type": "file", - "description": "Default VCF file index", - "pattern": "*.csi", - "ontologies": [] - } - } - ] - ], - "versions_bcftools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bcftools": { - "type": "string", - "description": "The tool name" - } - }, - { - "bcftools --version | sed '1!d; s/^.*bcftools //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bcftools": { - "type": "string", - "description": "The tool name" - } - }, - { - "bcftools --version | sed '1!d; s/^.*bcftools //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } + "pipelines": [ + { + "name": "raredisease", + "version": "3.0.0" + }, + { + "name": "variantbenchmarking", + "version": "1.5.0" + } ] - ] - }, - "authors": [ - "@joseespinosa", - "@drpatelh" - ], - "maintainers": [ - "@joseespinosa", - "@drpatelh" - ] - }, - "pipelines": [ - { - "name": "raredisease", - "version": "3.0.0" - }, - { - "name": "variantbenchmarking", - "version": "1.5.0" - }, - { - "name": "variantprioritization", - "version": "1.0.0" - }, - { - "name": "viralmetagenome", - "version": "1.1.1" }, { - "name": "viralrecon", - "version": "3.0.0" - } - ] - }, - { - "name": "bcftools_index", - "path": "modules/nf-core/bcftools/index/meta.yml", - "type": "module", - "meta": { - "name": "bcftools_index", - "description": "Index VCF tools", - "keywords": [ - "vcf", - "index", - "bcftools", - "csi", - "tbi" - ], - "tools": [ - { - "bcftools": { - "description": "BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations.", - "homepage": "https://samtools.github.io/bcftools/", - "documentation": "https://samtools.github.io/bcftools/howtos/index.html", - "tool_dev_url": "https://github.com/samtools/bcftools", - "doi": "10.1093/gigascience/giab008", - "licence": [ - "MIT", - "GPL-3.0-or-later" - ], - "identifier": "biotools:bcftools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + "name": "bcftools_roh", + "path": "modules/nf-core/bcftools/roh/meta.yml", + "type": "module", + "meta": { + "name": "bcftools_roh", + "description": "A program for detecting runs of homo/autozygosity. Only bi-allelic sites are considered.", + "keywords": ["roh", "biallelic", "homozygosity", "autozygosity"], + "tools": [ + { + "roh": { + "description": "A program for detecting runs of homo/autozygosity. Only bi-allelic sites are considered.", + "homepage": "https://www.htslib.org/", + "documentation": "http://www.htslib.org/doc/bcftools.html", + "doi": "10.1093/bioinformatics/btp352", + "licence": ["MIT"], + "identifier": "biotools:bcftools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF file", + "pattern": "*.{vcf,.vcf.gz}", + "ontologies": [] + } + }, + { + "tbi": { + "type": "file", + "description": "TBI file", + "patthern": "*.tbi", + "ontologies": [] + } + } + ], + [ + { + "af_file": { + "type": "file", + "description": "Read allele frequencies from a tab-delimited file containing the columns: CHROM\tPOS\tREF,ALT\tAF.", + "ontologies": [] + } + }, + { + "af_file_tbi": { + "type": "file", + "description": "tbi index of af_file.", + "ontologies": [] + } + } + ], + { + "genetic_map": { + "type": "file", + "description": "Genetic map in the format required also by IMPUTE2.", + "ontologies": [] + } + }, + { + "regions_file": { + "type": "file", + "description": "Regions can be specified either on command line or in a VCF, BED, or tab-delimited file (the default).", + "ontologies": [] + } + }, + { + "samples_file": { + "type": "file", + "description": "File of sample names to include or exclude if prefixed with '^'.", + "ontologies": [] + } + }, + { + "targets_file": { + "type": "file", + "description": "Targets can be specified either on command line or in a VCF, BED, or tab-delimited file (the default).", + "ontologies": [] + } + } + ], + "output": { + "roh": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.roh": { + "type": "file", + "description": "Contains site-specific and/or per-region runs of homo/autozygosity calls.", + "pattern": "*.{roh}", + "ontologies": [] + } + } + ] + ], + "versions_bcftools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bcftools": { + "type": "string", + "description": "The tool name" + } + }, + { + "bcftools --version | sed '1!d; s/^.*bcftools //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bcftools": { + "type": "string", + "description": "The tool name" + } + }, + { + "bcftools --version | sed '1!d; s/^.*bcftools //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@ramprasadn"], + "maintainers": ["@ramprasadn"] }, - { - "vcf": { - "type": "file", - "description": "VCF file (optionally GZIPPED)", - "pattern": "*.{vcf,vcf.gz}", - "ontologies": [] - } - } - ] - ], - "output": { - "csi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.csi": { - "type": "file", - "description": "Default VCF file index file", - "pattern": "*.csi", - "ontologies": [] - } - } - ] - ], - "tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tbi": { - "type": "file", - "description": "Alternative VCF file index file for larger files (activated with -t parameter)", - "pattern": "*.tbi", - "ontologies": [] - } - } - ] - ], - "versions_bcftools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bcftools": { - "type": "string", - "description": "The tool name" - } - }, - { - "bcftools --version | sed '1!d; s/^.*bcftools //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bcftools": { - "type": "string", - "description": "The tool name" - } - }, - { - "bcftools --version | sed '1!d; s/^.*bcftools //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } + "pipelines": [ + { + "name": "raredisease", + "version": "3.0.0" + } ] - ] - }, - "authors": [ - "@jfy133" - ], - "maintainers": [ - "@jfy133" - ] - }, - "pipelines": [ - { - "name": "alleleexpression", - "version": "dev" }, { - "name": "genomicrelatedness", - "version": "dev" - }, - { - "name": "mag", - "version": "5.4.2" + "name": "bcftools_rohviz", + "path": "modules/nf-core/bcftools/rohviz/meta.yml", + "type": "module", + "meta": { + "name": "bcftools_rohviz", + "description": "Visualise the output of bcftools roh", + "keywords": ["visualisation", "RoH", "VCF"], + "tools": [ + { + "roh-viz": { + "description": "\"Visualise the output of bcftools roh. It creates an HTML/JavaScript document which can be interactively viewed in a web browser.\"\n", + "homepage": "http://samtools.github.io/bcftools/bcftools.html", + "documentation": "http://www.htslib.org/doc/bcftools.html", + "doi": "10.1093/bioinformatics/btp352", + "licence": ["MIT"], + "identifier": "biotools:bcftools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample1' ]\n" + } + }, + { + "roh": { + "type": "file", + "description": "Output of BCFtools_roh. Contains site-specific and/or per-region runs of homo/autozygosity calls.", + "pattern": "*.roh", + "ontologies": [] + } + } + ], + [ + { + "meta1": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample1' ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF file", + "pattern": "*.{vcf,.vcf.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + } + ] + } + } + ], + { + "regions_list": { + "type": "file", + "description": "Regions can be specified either on command line or in a VCF, BED, or tab-delimited file (the default).", + "ontologies": [] + } + }, + { + "samples_file": { + "type": "file", + "description": "File of sample names to include or exclude if prefixed with '^'.", + "ontologies": [] + } + } + ], + "output": { + "html": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample1' ]\n" + } + }, + { + "*.html": { + "type": "file", + "description": "RoH visual report file.", + "pattern": "*.html", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2331" + } + ] + } + } + ] + ], + "versions_bcftools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bcftools": { + "type": "string", + "description": "The tool name" + } + }, + { + "bcftools --version | sed '1!d; s/^.*bcftools //'": { + "type": "eval", + "description": "The command used to generate the version of the tool" + } + } + ] + ], + "versions_less": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "less": { + "type": "string", + "description": "The tool name" + } + }, + { + "less --version | head -n1 | sed 's/less //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bcftools": { + "type": "string", + "description": "The tool name" + } + }, + { + "bcftools --version | sed '1!d; s/^.*bcftools //'": { + "type": "eval", + "description": "The command used to generate the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "less": { + "type": "string", + "description": "The tool name" + } + }, + { + "less --version | head -n1 | sed 's/less //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@yz533cb"] + } }, { - "name": "pacsomatic", - "version": "dev" + "name": "bcftools_sort", + "path": "modules/nf-core/bcftools/sort/meta.yml", + "type": "module", + "meta": { + "name": "bcftools_sort", + "description": "Sorts VCF files", + "keywords": ["sorting", "VCF", "variant calling"], + "tools": [ + { + "sort": { + "description": "Sort VCF files by coordinates.", + "homepage": "http://samtools.github.io/bcftools/bcftools.html", + "documentation": "http://www.htslib.org/doc/bcftools.html", + "tool_dev_url": "https://github.com/samtools/bcftools", + "doi": "10.1093/bioinformatics/btp352", + "licence": ["MIT"], + "identifier": "biotools:bcftools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "The VCF/BCF file to be sorted", + "pattern": "*.{vcf.gz,vcf,bcf}", + "ontologies": [] + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{vcf,vcf.gz,bcf,bcf.gz}": { + "type": "file", + "description": "Sorted VCF file", + "pattern": "*.{vcf.gz}", + "ontologies": [] + } + } + ] + ], + "tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tbi": { + "type": "file", + "description": "Alternative VCF file index", + "pattern": "*.tbi", + "ontologies": [] + } + } + ] + ], + "csi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.csi": { + "type": "file", + "description": "Default VCF file index", + "pattern": "*.csi", + "ontologies": [] + } + } + ] + ], + "versions_bcftools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bcftools": { + "type": "string", + "description": "The tool name" + } + }, + { + "bcftools --version | sed '1!d; s/^.*bcftools //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bcftools": { + "type": "string", + "description": "The tool name" + } + }, + { + "bcftools --version | sed '1!d; s/^.*bcftools //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@Gwennid"], + "maintainers": ["@Gwennid"] + }, + "pipelines": [ + { + "name": "genomicrelatedness", + "version": "dev" + }, + { + "name": "nanoseq", + "version": "3.1.0" + }, + { + "name": "pacsomatic", + "version": "dev" + }, + { + "name": "pacvar", + "version": "1.0.1" + }, + { + "name": "radseq", + "version": "dev" + }, + { + "name": "raredisease", + "version": "3.0.0" + }, + { + "name": "rnadnavar", + "version": "dev" + }, + { + "name": "sarek", + "version": "3.8.1" + }, + { + "name": "variantbenchmarking", + "version": "1.5.0" + }, + { + "name": "viralmetagenome", + "version": "1.1.1" + }, + { + "name": "viralrecon", + "version": "3.0.0" + } + ] }, { - "name": "pacvar", - "version": "1.0.1" + "name": "bcftools_split", + "path": "modules/nf-core/bcftools/split/meta.yml", + "type": "module", + "meta": { + "name": "bcftools_split", + "description": "Split a vcf file into files per chromosome", + "keywords": ["vcf", "split", "genomics"], + "tools": [ + { + "bcftools": { + "description": "Sort VCF files by coordinates.", + "homepage": "http://samtools.github.io/bcftools/bcftools.html", + "documentation": "http://www.htslib.org/doc/bcftools.html", + "tool_dev_url": "https://github.com/samtools/bcftools", + "doi": "10.1093/bioinformatics/btp352", + "licence": ["MIT"], + "identifier": "biotools:bcftools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "Compressed vcf file", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + }, + { + "tbi": { + "type": "file", + "description": "Compressed vcf file index", + "pattern": "*.{tbi,csi}", + "ontologies": [] + } + } + ] + ], + "output": { + "split_vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "Compressed vcf files per chromosome", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "versions_bcftools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bcftools": { + "type": "string", + "description": "The tool name" + } + }, + { + "bcftools --version | sed '1!d; s/^.*bcftools //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bcftools": { + "type": "string", + "description": "The tool name" + } + }, + { + "bcftools --version | sed '1!d; s/^.*bcftools //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@matthdsm", "@atrigila"], + "maintainers": ["@matthdsm", "@atrigila"] + } }, { - "name": "phaseimpute", - "version": "1.1.0" - } - ] - }, - { - "name": "bcftools_isec", - "path": "modules/nf-core/bcftools/isec/meta.yml", - "type": "module", - "meta": { - "name": "bcftools_isec", - "description": "Apply set operations to VCF files", - "keywords": [ - "variant calling", - "intersect", - "union", - "complement", - "VCF", - "BCF" - ], - "tools": [ - { - "isec": { - "description": "Computes intersections, unions and complements of VCF files.\n", - "homepage": "http://samtools.github.io/bcftools/bcftools.html", - "documentation": "http://www.htslib.org/doc/bcftools.html", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "identifier": "biotools:bcftools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcfs": { - "type": "list", - "description": "List containing 2 or more vcf/bcf files. These must be compressed and have an associated index.\ne.g. [ 'file1.vcf.gz', 'file2.vcf' ]\n", - "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - }, - { - "edam": "http://edamontology.org/format_3570" - } - ] - } - }, - { - "tbis": { - "type": "list", - "description": "List containing the tbi index files corresponding to the vcf/bcf input files\n", - "pattern": "*.tbi", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - }, - { - "file_list": { - "type": "file", - "description": "Optional text file containing the list of VCF/BCF files to be processed by bcftools isec, one per line.\n", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2330" - } - ] - } - }, - { - "targets_file": { - "type": "file", - "description": "Optional file containing target regions to restrict the analysis to.\n", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3003" - }, - { - "edam": "http://edamontology.org/format_3475" - } - ] - } + "name": "bcftools_stats", + "path": "modules/nf-core/bcftools/stats/meta.yml", + "type": "module", + "meta": { + "name": "bcftools_stats", + "description": "Generates stats from VCF files", + "keywords": ["variant calling", "stats", "VCF"], + "tools": [ + { + "stats": { + "description": "Parses VCF or BCF and produces text file stats which is suitable for\nmachine processing and can be plotted using plot-vcfstats.\n", + "homepage": "http://samtools.github.io/bcftools/bcftools.html", + "documentation": "http://www.htslib.org/doc/bcftools.html", + "doi": "10.1093/bioinformatics/btp352", + "licence": ["MIT"], + "identifier": "biotools:bcftools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF input file", + "pattern": "*.{vcf}", + "ontologies": [] + } + }, + { + "tbi": { + "type": "file", + "description": "The tab index for the VCF file to be inspected. Optional: only required when parameter regions is chosen.\n", + "pattern": "*.tbi", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "regions": { + "type": "file", + "description": "Optionally, restrict the operation to regions listed in this file. (VCF, BED or tab-delimited)\n", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "targets": { + "type": "file", + "description": "Optionally, restrict the operation to regions listed in this file (doesn't rely upon tbi index files)\n", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "samples": { + "type": "file", + "description": "Optional, file of sample names to be included or excluded.\ne.g. 'file.tsv'\n", + "ontologies": [] + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "exons": { + "type": "file", + "description": "Tab-delimited file with exons for indel frameshifts (chr,beg,end; 1-based, inclusive, optionally bgzip compressed).\ne.g. 'exons.tsv.gz'\n", + "ontologies": [] + } + } + ], + [ + { + "meta6": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Faidx indexed reference sequence file to determine INDEL context.\ne.g. 'reference.fa'\n", + "ontologies": [] + } + } + ] + ], + "output": { + "stats": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*stats.txt": { + "type": "file", + "description": "Text output file containing stats", + "pattern": "*_{stats.txt}", + "ontologies": [] + } + } + ] + ], + "versions_bcftools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bcftools": { + "type": "string", + "description": "The tool name" + } + }, + { + "bcftools --version | sed '1!d; s/^.*bcftools //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bcftools": { + "type": "string", + "description": "The tool name" + } + }, + { + "bcftools --version | sed '1!d; s/^.*bcftools //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@joseespinosa", "@drpatelh", "@SusiJo", "@TCLamnidis"], + "maintainers": ["@joseespinosa", "@drpatelh", "@SusiJo", "@TCLamnidis"] }, - { - "regions_file": { - "type": "file", - "description": "Optional file containing regions to restrict the analysis to.\n", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3003" - }, - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "output": { - "results": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + "pipelines": [ + { + "name": "epitopeprediction", + "version": "3.1.0" + }, + { + "name": "genomicrelatedness", + "version": "dev" + }, + { + "name": "phaseimpute", + "version": "1.1.0" + }, + { + "name": "radseq", + "version": "dev" + }, + { + "name": "rnadnavar", + "version": "dev" + }, + { + "name": "sarek", + "version": "3.8.1" + }, + { + "name": "variantbenchmarking", + "version": "1.5.0" + }, + { + "name": "viralmetagenome", + "version": "1.1.1" + }, + { + "name": "viralrecon", + "version": "3.0.0" } - }, - { - "${prefix}": { - "type": "directory", - "description": "Directory containing the output files from bcftools isec", - "pattern": "${prefix}/", - "ontologies": [ + ] + }, + { + "name": "bcftools_view", + "path": "modules/nf-core/bcftools/view/meta.yml", + "type": "module", + "meta": { + "name": "bcftools_view", + "description": "View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF", + "keywords": ["variant calling", "view", "bcftools", "VCF"], + "tools": [ + { + "view": { + "description": "View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF\n", + "homepage": "http://samtools.github.io/bcftools/bcftools.html", + "documentation": "http://www.htslib.org/doc/bcftools.html", + "doi": "10.1093/bioinformatics/btp352", + "licence": ["MIT"], + "identifier": "biotools:bcftools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "The vcf file to be inspected.\ne.g. 'file.vcf'\n", + "ontologies": [] + } + }, + { + "index": { + "type": "file", + "description": "The tab index for the VCF file to be inspected.\ne.g. 'file.tbi'\n", + "ontologies": [] + } + } + ], + { + "regions": { + "type": "file", + "description": "Optionally, restrict the operation to regions listed in this file.\ne.g. 'file.vcf'\n", + "ontologies": [] + } + }, { - "edam": "http://edamontology.org/format_3016" + "targets": { + "type": "file", + "description": "Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files)\ne.g. 'file.vcf'\n", + "ontologies": [] + } }, { - "edam": "http://edamontology.org/format_3570" + "samples": { + "type": "file", + "description": "Optional, file of sample names to be included or excluded.\ne.g. 'file.tsv'\n", + "ontologies": [] + } } - ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{vcf,vcf.gz,bcf,bcf.gz}": { + "type": "file", + "description": "VCF normalized output file", + "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}", + "ontologies": [] + } + } + ] + ], + "tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tbi": { + "type": "file", + "description": "Alternative VCF file index", + "pattern": "*.tbi", + "ontologies": [] + } + } + ] + ], + "csi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.csi": { + "type": "file", + "description": "Default VCF file index", + "pattern": "*.csi", + "ontologies": [] + } + } + ] + ], + "versions_bcftools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bcftools": { + "type": "string", + "description": "The tool name" + } + }, + { + "bcftools --version | sed '1!d; s/^.*bcftools //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bcftools": { + "type": "string", + "description": "The tool name" + } + }, + { + "bcftools --version | sed '1!d; s/^.*bcftools //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@abhi18av"], + "maintainers": ["@abhi18av"] + }, + "pipelines": [ + { + "name": "alleleexpression", + "version": "dev" + }, + { + "name": "mag", + "version": "5.4.2" + }, + { + "name": "pacsomatic", + "version": "dev" + }, + { + "name": "phaseimpute", + "version": "1.1.0" + }, + { + "name": "radseq", + "version": "dev" + }, + { + "name": "raredisease", + "version": "3.0.0" + }, + { + "name": "sarek", + "version": "3.8.1" + }, + { + "name": "tbanalyzer", + "version": "dev" + }, + { + "name": "tumourevo", + "version": "dev" + }, + { + "name": "variantbenchmarking", + "version": "1.5.0" } - } - ] - ], - "versions_bcftools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bcftools": { - "type": "string", - "description": "The tool name" - } - }, - { - "bcftools --version | sed '1!d; s/^.*bcftools //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bcftools": { - "type": "string", - "description": "The tool name" - } - }, - { - "bcftools --version | sed '1!d; s/^.*bcftools //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } ] - ] }, - "authors": [ - "@joseespinosa", - "@drpatelh" - ], - "maintainers": [ - "@joseespinosa", - "@drpatelh" - ] - }, - "pipelines": [ { - "name": "genomicrelatedness", - "version": "dev" - }, - { - "name": "sarek", - "version": "3.8.1" - } - ] - }, - { - "name": "bcftools_merge", - "path": "modules/nf-core/bcftools/merge/meta.yml", - "type": "module", - "meta": { - "name": "bcftools_merge", - "description": "Merge VCF files", - "keywords": [ - "variant calling", - "merge", - "VCF" - ], - "tools": [ - { - "merge": { - "description": "Merge VCF files.\n", - "homepage": "http://samtools.github.io/bcftools/bcftools.html", - "documentation": "http://www.htslib.org/doc/bcftools.html", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "identifier": "biotools:bcftools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcfs": { - "type": "file", - "description": "List containing 2 or more vcf files\ne.g. [ 'file1.vcf', 'file2.vcf' ]\n", - "ontologies": [] - } - }, - { - "tbis": { - "type": "file", - "description": "List containing the tbi index files corresponding to the vcfs input files\ne.g. [ 'file1.vcf.tbi', 'file2.vcf.tbi' ]\n", - "ontologies": [] - } - }, - { - "bed": { - "type": "file", - "description": "(Optional) The bed regions to merge on", - "pattern": "*.bed", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "(Optional) The fasta reference file (only necessary for the `--gvcf FILE` parameter)", - "pattern": "*.{fasta,fa}", - "ontologies": [] - } + "name": "bcl2fastq", + "path": "modules/nf-core/bcl2fastq/meta.yml", + "type": "module", + "meta": { + "name": "bcl2fastq", + "description": "Demultiplex Illumina BCL files", + "keywords": ["demultiplex", "illumina", "fastq"], + "tools": [ + { + "bcl2fastq": { + "description": "Demultiplex Illumina BCL files", + "homepage": "https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software", + "documentation": "https://support.illumina.com/content/dam/illumina-support/documents/documentation/software_documentation/bcl2fastq/bcl2fastq2-v2-20-software-guide-15051736-03.pdf", + "licence": ["ILLUMINA"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "samplesheet": { + "type": "file", + "description": "Input samplesheet", + "pattern": "*.{csv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + }, + { + "run_dir": { + "type": "file", + "description": "Input run directory containing RunInfo.xml and BCL data\nCould be a directory or a tar of the directory\n", + "ontologies": [] + } + } + ] + ], + "output": { + "fastq": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "output/**_S[1-9]*_R?_00?.fastq.gz": { + "type": "file", + "description": "Demultiplexed sample FASTQ files", + "pattern": "**_S*_L00?_R?_00?.fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "fastq_idx": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "output/**_S[1-9]*_I?_00?.fastq.gz": { + "type": "file", + "description": "Optional demultiplexed index FASTQ files", + "pattern": "**_S*_L00?_I?_00?.fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "undetermined": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "output/**Undetermined_S0*_R?_00?.fastq.gz": { + "type": "file", + "description": "Optional undetermined sample FASTQ files", + "pattern": "Undetermined_S0_L00?_R?_00?.fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "undetermined_idx": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "output/**Undetermined_S0*_I?_00?.fastq.gz": { + "type": "file", + "description": "Optional undetermined index FASTQ files", + "pattern": "Undetermined_S0_L00?_I?_00?.fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "reports": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "output/Reports": { + "type": "file", + "description": "Demultiplexing Reports", + "pattern": "Reports", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2331" + } + ] + } + } + ] + ], + "stats": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "output/Stats": { + "type": "file", + "description": "Statistics files", + "pattern": "Stats", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + }, + { + "edam": "http://edamontology.org/format_2332" + }, + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "interop": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "InterOp/*.bin": { + "type": "file", + "description": "Interop files", + "pattern": "*.{bin}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2333" + } + ] + } + } + ] + ], + "xml": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "**/*.xml": { + "type": "file", + "description": "Output XML files, for example RunInfo.xml", + "pattern": "**/*.xml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2332" + } + ] + } + } + ] + ], + "versions_bcl2fastq": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bcl2fastq": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bcl2fastq -V 2>&1 | grep -m 1 bcl2fastq | sed 's/^.*bcl2fastq v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bcl2fastq": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bcl2fastq -V 2>&1 | grep -m 1 bcl2fastq | sed 's/^.*bcl2fastq v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@matthdsm"], + "maintainers": ["@matthdsm"] }, - { - "fai": { - "type": "file", - "description": "(Optional) The fasta reference file index (only necessary for the `--gvcf FILE` parameter)", - "pattern": "*.fai", - "ontologies": [] - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.{bcf,vcf}{,.gz}": { - "type": "file", - "description": "merged output file", - "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}", - "ontologies": [] - } - } - ] - ], - "index": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.{csi,tbi}": { - "type": "file", - "description": "index of merged output", - "pattern": "*.{csi,tbi}", - "ontologies": [] - } - } - ] - ], - "versions_bcftools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bcftools": { - "type": "string", - "description": "The tool name" - } - }, - { - "bcftools --version | sed '1!d; s/^.*bcftools //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bcftools": { - "type": "string", - "description": "The tool name" - } - }, - { - "bcftools --version | sed '1!d; s/^.*bcftools //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } + "pipelines": [ + { + "name": "demultiplex", + "version": "1.7.1" + } ] - ] - }, - "authors": [ - "@joseespinosa", - "@drpatelh", - "@nvnieuwk", - "@ramprasadn" - ], - "maintainers": [ - "@joseespinosa", - "@drpatelh", - "@nvnieuwk", - "@ramprasadn" - ] - }, - "pipelines": [ - { - "name": "phaseimpute", - "version": "1.1.0" - }, - { - "name": "raredisease", - "version": "3.0.0" - }, - { - "name": "sarek", - "version": "3.8.1" }, { - "name": "tbanalyzer", - "version": "dev" - }, - { - "name": "variantbenchmarking", - "version": "1.5.0" - } - ] - }, - { - "name": "bcftools_mpileup", - "path": "modules/nf-core/bcftools/mpileup/meta.yml", - "type": "module", - "meta": { - "name": "bcftools_mpileup", - "description": "Compresses VCF files", - "keywords": [ - "variant calling", - "mpileup", - "VCF" - ], - "tools": [ - { - "mpileup": { - "description": "Generates genotype likelihoods at each genomic position with coverage.\n", - "homepage": "http://samtools.github.io/bcftools/bcftools.html", - "documentation": "http://www.htslib.org/doc/bcftools.html", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "identifier": "biotools:bcftools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "Input BAM file", - "pattern": "*.{bam}", - "ontologies": [] - } - }, - { - "intervals_mpileup": { - "type": "file", - "description": "Input intervals file. A file (commonly '.bed') containing regions to subset used by mpileup", - "ontologies": [] - } - }, - { - "intervals_call": { - "type": "file", - "description": "Input intervals file. A file (commonly '.bed') containing regions to subset used by call but need a fourth column with REF,ALT", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA reference file", - "pattern": "*.{fasta,fa}", - "ontologies": [] - } + "name": "bclconvert", + "path": "modules/nf-core/bclconvert/meta.yml", + "type": "module", + "meta": { + "name": "bclconvert", + "description": "Demultiplex Illumina BCL files", + "keywords": ["demultiplex", "illumina", "fastq"], + "tools": [ + { + "bclconvert": { + "description": "Demultiplex Illumina BCL files", + "homepage": "https://support.illumina.com/sequencing/sequencing_software/bcl-convert.html", + "documentation": "https://support-docs.illumina.com/SW/BCL_Convert/Content/SW/FrontPages/BCL_Convert.htm", + "licence": ["ILLUMINA"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "samplesheet": { + "type": "file", + "description": "Input samplesheet", + "pattern": "*.{csv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + }, + { + "run_dir": { + "type": "file", + "description": "Input run directory containing RunInfo.xml and BCL data\nCould be a directory or a tar of the directory\n", + "ontologies": [] + } + } + ] + ], + "output": { + "fastq": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "output/**_S[1-9]*_R?_00?.fastq.gz": { + "type": "file", + "description": "Demultiplexed sample FASTQ files", + "pattern": "**_S*_L00?_R?_00?.fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ] + ], + "fastq_idx": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "output/**_S[1-9]*_I?_00?.fastq.gz": { + "type": "file", + "description": "Optional demultiplexed index FASTQ files", + "pattern": "**_S*_L00?_I?_00?.fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ] + ], + "undetermined": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "output/**Undetermined_S0*_R?_00?.fastq.gz": { + "type": "file", + "description": "Optional undetermined sample FASTQ files", + "pattern": "Undetermined_S0_L00?_R?_00?.fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ] + ], + "undetermined_idx": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "output/**Undetermined_S0*_I?_00?.fastq.gz": { + "type": "file", + "description": "Optional undetermined index FASTQ files", + "pattern": "Undetermined_S0_L00?_I?_00?.fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ] + ], + "reports": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "output/Reports": { + "type": "file", + "description": "Demultiplexing Reports", + "pattern": "Reports", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + }, + { + "edam": "http://edamontology.org/format_2332" + }, + { + "edam": "http://edamontology.org/format_2333" + } + ] + } + } + ] + ], + "logs": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "output/Logs": { + "type": "file", + "description": "Demultiplexing Logs", + "pattern": "Logs", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + } + ] + ], + "interop": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "output/InterOp/*.bin": { + "type": "file", + "description": "Interop files", + "pattern": "InterOp/*.bin", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2333" + } + ] + } + } + ] + ], + "versions_bclconvert": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bclconvert": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bcl-convert -V 2>&1 | head -n 1 | sed 's/^.*Version //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bclconvert": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bcl-convert -V 2>&1 | head -n 1 | sed 's/^.*Version //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@matthdsm"], + "maintainers": ["@matthdsm", "@maxulysse"] }, - { - "fai": { - "type": "file", - "description": "FASTA reference file index", - "pattern": "*.fai", - "ontologies": [] - } - } - ], - { - "save_mpileup": { - "type": "boolean", - "description": "Save mpileup file generated by bcftools mpileup" - } - } - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*vcf.gz": { - "type": "file", - "description": "VCF gzipped output file", - "pattern": "*.{vcf.gz}", - "ontologies": [] - } - } - ] - ], - "tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*vcf.gz.tbi": { - "type": "file", - "description": "tabix index file", - "pattern": "*.{vcf.gz.tbi}", - "ontologies": [] - } - } - ] - ], - "stats": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*stats.txt": { - "type": "file", - "description": "Text output file containing stats", - "pattern": "*{stats.txt}", - "ontologies": [] - } - } - ] - ], - "mpileup": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.mpileup.gz": { - "type": "file", - "description": "mpileup gzipped output for all positions", - "pattern": "{*.mpileup.gz}", - "ontologies": [] - } - } - ] - ], - "versions_bcftools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bcftools": { - "type": "string", - "description": "The tool name" - } - }, - { - "bcftools --version | sed '1!d; s/^.*bcftools //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bcftools": { - "type": "string", - "description": "The tool name" - } - }, - { - "bcftools --version | sed '1!d; s/^.*bcftools //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } + "pipelines": [ + { + "name": "demultiplex", + "version": "1.7.1" + } ] - ] - }, - "authors": [ - "@joseespinosa" - ], - "maintainers": [ - "@joseespinosa" - ] - }, - "pipelines": [ - { - "name": "phaseimpute", - "version": "1.1.0" - }, - { - "name": "sarek", - "version": "3.8.1" }, { - "name": "tumourevo", - "version": "dev" + "name": "beagle5_beagle", + "path": "modules/nf-core/beagle5/beagle/meta.yml", + "type": "module", + "meta": { + "name": "beagle5_beagle", + "description": "Beagle v5.5 is a software package for phasing genotypes and for imputing ungenotyped markers.", + "keywords": ["phasing", "imputation", "genotype"], + "tools": [ + { + "beagle5": { + "description": "Beagle is a software package for phasing genotypes and for imputing ungenotyped markers.", + "homepage": "https://faculty.washington.edu/browning/beagle/beagle.html", + "documentation": "https://faculty.washington.edu/browning/beagle/beagle_5.5_17Dec24.pdf", + "doi": "10.1016/j.ajhg.2021.08.005; doi:10.1016/j.ajhg.2018.07.015", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "target VCF input file to be imputed and or phased", + "pattern": "*.{vcf,vcf.gz}", + "ontologies": [] + } + }, + { + "vcf_index": { + "type": "file", + "description": "target VCF input file index", + "pattern": "*.{vcf,vcf.gz}.{tbi,csi}", + "ontologies": [] + } + }, + { + "refpanel": { + "type": "file", + "description": "target reference panel", + "ontologies": [], + "pattern": "*.{vcf,vcf.gz}" + } + }, + { + "refpanel_index": { + "type": "file", + "description": "target reference panel index", + "ontologies": [], + "pattern": "*.{vcf,vcf.gz}.{tbi,csi}" + } + }, + { + "genmap": { + "type": "file", + "description": "a PLINK format genetic map with cM units", + "pattern": "*.{map,map.gz,map.zip}", + "ontologies": [] + } + }, + { + "exclsamples": { + "type": "file", + "description": "text file containing samples one sample per line to be excluded from the analysis", + "pattern": "*.*", + "ontologies": [] + } + }, + { + "exclmarkers": { + "type": "file", + "description": "text file containing markers one marker per line to be excluded from the analysis", + "pattern": "*.*", + "ontologies": [] + } + }, + { + "region": { + "type": "string", + "description": "Region to perform imputation", + "pattern": "(chr)?\\d*:\\d*-\\d*" + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "bgzip compressed VCF file that contains phased non missing genotypes for all non reference samples", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "a summary of the analysis that includes the Beagle version, the command line arguments, and compute time.", + "pattern": "*.log", + "ontologies": [] + } + } + ] + ], + "versions_beagle": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "beagle": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "beagle 2>&1 | sed -n 's/.*version \\([^)]*\\).*/\\1/p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "beagle": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "beagle 2>&1 | sed -n 's/.*version \\([^)]*\\).*/\\1/p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@ashotmarg"], + "maintainers": ["@ashotmarg"] + }, + "pipelines": [ + { + "name": "alleleexpression", + "version": "dev" + }, + { + "name": "phaseimpute", + "version": "1.1.0" + } + ] }, { - "name": "viralmetagenome", - "version": "1.1.1" - }, - { - "name": "viralrecon", - "version": "3.0.0" - } - ] - }, - { - "name": "bcftools_norm", - "path": "modules/nf-core/bcftools/norm/meta.yml", - "type": "module", - "meta": { - "name": "bcftools_norm", - "description": "Normalize VCF file", - "keywords": [ - "normalize", - "norm", - "variant calling", - "VCF" - ], - "tools": [ - { - "norm": { - "description": "Normalize VCF files.\n", - "homepage": "http://samtools.github.io/bcftools/bcftools.html", - "documentation": "http://www.htslib.org/doc/bcftools.html", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "identifier": "biotools:bcftools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "The vcf file to be normalized\ne.g. 'file1.vcf'\n", - "pattern": "*.{vcf,vcf.gz}", - "ontologies": [] - } - }, - { - "tbi": { - "type": "file", - "description": "An optional index of the VCF file (for when the VCF is compressed)\n", - "pattern": "*.vcf.gz.tbi", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA reference file", - "pattern": "*.{fasta,fa}", - "ontologies": [] - } + "name": "bedgovcf", + "path": "modules/nf-core/bedgovcf/meta.yml", + "type": "module", + "meta": { + "name": "bedgovcf", + "description": "Convert a BED file to a VCF file according to a YAML config", + "keywords": ["bed", "vcf", "conversion", "variants"], + "tools": [ + { + "bedgovcf": { + "description": "A simple tool to convert BED files to VCF files", + "homepage": "https://github.com/nvnieuwk/bedgovcf", + "documentation": "https://github.com/nvnieuwk/bedgovcf", + "tool_dev_url": "https://github.com/nvnieuwk/bedgovcf", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "bed": { + "type": "file", + "description": "The BED file to convert to VCF", + "pattern": "*.bed", + "ontologies": [] + } + }, + { + "config": { + "type": "file", + "description": "The config file to use for the conversion", + "pattern": "*.{yml,yaml}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing fasta index information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "fai": { + "type": "file", + "description": "The fasta index file", + "pattern": "*.fai", + "ontologies": [] + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "The converted VCF file", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "versions_bedgovcf": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process name" + } + }, + { + "bedgovcf": { + "type": "string", + "description": "The tool name" + } + }, + { + "bedgovcf --version 2>&1 | sed 's/^bedgovcf version //'": { + "type": "eval", + "description": "The tool version" + } + } + ] + ], + "versions_bgzip": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process name" + } + }, + { + "bgzip": { + "type": "string", + "description": "The tool name" + } + }, + { + "bgzip --version | head -1 | sed \"s/bgzip (htslib) //\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process name" + } + }, + { + "bedgovcf": { + "type": "string", + "description": "The tool name" + } + }, + { + "bedgovcf --version 2>&1 | sed 's/^bedgovcf version //'": { + "type": "eval", + "description": "The tool version" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The process name" + } + }, + { + "bgzip": { + "type": "string", + "description": "The tool name" + } + }, + { + "bgzip --version | head -1 | sed \"s/bgzip (htslib) //\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@nvnieuwk"] } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.{vcf,vcf.gz,bcf,bcf.gz}": { - "type": "file", - "description": "One of uncompressed VCF (.vcf), compressed VCF (.vcf.gz), compressed BCF (.bcf.gz) or uncompressed BCF (.bcf) normalized output file", - "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}", - "ontologies": [] - } - } - ] - ], - "tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tbi": { - "type": "file", - "description": "Alternative VCF file index", - "pattern": "*.tbi", - "ontologies": [] - } - } - ] - ], - "csi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.csi": { - "type": "file", - "description": "Default VCF file index", - "pattern": "*.csi", - "ontologies": [] - } - } - ] - ], - "versions_bcftools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bcftools": { - "type": "string", - "description": "The tool name" - } - }, - { - "bcftools --version | sed '1!d; s/^.*bcftools //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bcftools": { - "type": "string", - "description": "The tool name" - } - }, - { - "bcftools --version | sed '1!d; s/^.*bcftools //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@abhi18av", - "@ramprasadn" - ], - "maintainers": [ - "@abhi18av", - "@ramprasadn" - ] - }, - "pipelines": [ - { - "name": "pacsomatic", - "version": "dev" - }, - { - "name": "phaseimpute", - "version": "1.1.0" - }, - { - "name": "radseq", - "version": "dev" - }, - { - "name": "raredisease", - "version": "3.0.0" - }, - { - "name": "sarek", - "version": "3.8.1" - }, - { - "name": "variantbenchmarking", - "version": "1.5.0" - }, - { - "name": "variantcatalogue", - "version": "dev" - }, - { - "name": "variantprioritization", - "version": "1.0.0" - }, - { - "name": "viralmetagenome", - "version": "1.1.1" }, { - "name": "viralrecon", - "version": "3.0.0" - } - ] - }, - { - "name": "bcftools_plotvcfstats", - "path": "modules/nf-core/bcftools/plotvcfstats/meta.yml", - "type": "module", - "meta": { - "name": "bcftools_plotvcfstats", - "description": "Plots the output of bcftools stats", - "keywords": [ - "visualization", - "stats", - "VCF" - ], - "tools": [ - { - "plot": { - "description": "Script for processing output of bcftools stats, plots graphs and creates a PDF presentation.\n", - "homepage": "http://samtools.github.io/bcftools/bcftools.html", - "documentation": "http://www.htslib.org/doc/bcftools.html", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "identifier": "biotools:bcftools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample1' ]\n" - } - }, - { - "stats": { - "type": "file", - "description": "Text file from BCFtools stats output", - "pattern": "*_stats.txt", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2330" - } - ] - } - } - ] - ], - "output": { - "plot_dir": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample1' ]\n" - } - }, - { - "*plots*": { - "type": "directory", - "description": "Output directory containing plots, raw data, and log files", - "pattern": "*plots*", - "ontologies": [] - } - } - ] - ], - "plot_pdf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample1' ]\n" - } - }, - { - "*.pdf": { - "type": "file", - "description": "(Link to the original) summary output in PDF", - "pattern": "*.pdf", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3508" - } - ] - } - } - ] - ], - "versions_bcftools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bcftools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bcftools --version | sed '1!d; s/^.*bcftools //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bcftools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bcftools --version | sed '1!d; s/^.*bcftools //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@yz533cb" - ] - } - }, - { - "name": "bcftools_pluginfilltags", - "path": "modules/nf-core/bcftools/pluginfilltags/meta.yml", - "type": "module", - "meta": { - "name": "bcftools_pluginfilltags", - "description": "Compute and fill various INFO tags", - "keywords": [ - "info", - "bcftools", - "tags", - "vcf" - ], - "tools": [ - { - "bcftools": { - "description": "BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations.", - "homepage": "https://samtools.github.io/bcftools/howtos/index.html", - "documentation": "https://samtools.github.io/bcftools/bcftools.html", - "tool_dev_url": "https://github.com/samtools/bcftools", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "args_id": "$args", - "identifier": "biotools:bcftools" - } - }, - { - "bcftools plugin fill-tags": { - "description": "Bcftools plugins are tools that can be used with bcftools to manipulate variant calls in Variant Call Format (VCF) and BCF. The fill-tags plugin compute and fill various INFO tags", - "homepage": "https://samtools.github.io/bcftools/howtos/plugins.html", - "documentation": "https://samtools.github.io/bcftools/bcftools.html#plugin", - "tool_dev_url": "https://github.com/samtools/bcftools", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "args_id": "$args2", - "identifier": "biotools:bcftools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "The input file in variant calling format to be inspected.\ne.g. 'file.vcf.gz'\n", - "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}", - "ontologies": [] - } - }, - { - "index": { - "type": "file", - "description": "The tab index for the VCF file to be inspected.\ne.g. 'file.tbi'\n", - "ontologies": [] - } - } - ], - { - "regions": { - "type": "file", - "description": "Optionally, restrict the operation to regions listed in this file.\ne.g. 'file.vcf'\n", - "ontologies": [] - } - }, - { - "targets": { - "type": "file", - "description": "Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files)\ne.g. 'file.vcf'\n", - "ontologies": [] - } - }, - { - "samples": { - "type": "file", - "description": "Optionally, list of samples (first column) and tab-separated list of populations (second column)\ne.g. 'file.vcf'\n", - "ontologies": [] - } - } - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.{vcf,vcf.gz,bcf,bcf.gz}": { - "type": "file", - "description": "VCF output file containing added INFO/INFO field", - "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}", - "ontologies": [] - } - } - ] - ], - "tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tbi": { - "type": "file", - "description": "Alternative VCF file tabix index", - "pattern": "*.tbi", - "ontologies": [] - } - } - ] - ], - "csi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.csi": { - "type": "file", - "description": "Default VCF file coordinate sorted index", - "pattern": "*.csi", - "ontologies": [] - } - } - ] - ], - "versions_bcftools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bcftools": { - "type": "string", - "description": "The tool name" - } - }, - { - "bcftools --version | sed '1!d; s/^.*bcftools //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bcftools": { - "type": "string", - "description": "The tool name" - } - }, - { - "bcftools --version | sed '1!d; s/^.*bcftools //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@LouisLeNezet" - ], - "maintainers": [ - "@LouisLeNezet" - ] - } - }, - { - "name": "bcftools_pluginfixploidy", - "path": "modules/nf-core/bcftools/pluginfixploidy/meta.yml", - "type": "module", - "meta": { - "name": "bcftools_pluginfixploidy", - "description": "The fixploidy plugin fixes ploidy in genotype fields according to specified ploidy rules, sample sex assignments, or a forced ploidy value. For example, haploid genotypes can be converted to diploid genotypes.", - "keywords": [ - "fixploidy", - "bcftools", - "ploidy", - "vcf" - ], - "tools": [ - { - "bcftools": { - "description": "BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations.", - "homepage": "https://samtools.github.io/bcftools/howtos/index.html", - "documentation": "https://samtools.github.io/bcftools/bcftools.html", - "tool_dev_url": "https://github.com/samtools/bcftools", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "args_id": "$args", - "identifier": "biotools:bcftools" - } - }, - { - "bcftools plugin fixploidy": { - "description": "Bcftools plugins are tools that can be used with bcftools to manipulate variant calls in Variant Call Format (VCF) and BCF. The fixploidy plugin fixes ploidy in genotype fields according to specified ploidy rules, sample sex assignments, or a forced ploidy value. For example, haploid genotypes can be converted to diploid genotypes.", - "homepage": "https://samtools.github.io/bcftools/howtos/plugins.html", - "documentation": "https://samtools.github.io/bcftools/howtos/plugin.setGT.html", - "tool_dev_url": "https://github.com/samtools/bcftools", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "args_id": "$args2", - "identifier": "biotools:bcftools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "Input VCF/BCF file to fix ploidy in.\ne.g. 'sample.vcf.gz'\n", - "ontologies": [] - } - }, - { - "index": { - "type": "file", - "description": "Index file for the input VCF/BCF (e.g. .tbi or .csi).\ne.g. 'sample.vcf.gz.tbi'\n", - "ontologies": [] - } - } - ], - { - "ploidy": { - "type": "file", - "description": "Optional ploidy definition file for the fixploidy plugin (`-p`), with\nspace/tab-delimited columns: CHROM, FROM, TO, SEX, PLOIDY.\ne.g. 'ploidy.txt'\n", - "ontologies": [] - } - }, - { - "sex": { - "type": "file", - "description": "Optional sample sex assignment file for the fixploidy plugin (`-s`),\ncontaining lines of the form: NAME SEX.\nSamples not listed are treated as female by the plugin.\ne.g. 'samples_sex.txt'\n", - "ontologies": [] - } - }, - { - "regions": { - "type": "file", - "description": "Optionally restrict the operation to regions listed in this file\n(indexed input required; passed as a bcftools regions file argument).\ne.g. 'regions.bed'\n", - "ontologies": [] - } - }, - { - "targets": { - "type": "file", - "description": "Optionally restrict the operation to targets listed in this file\n(does not rely on index jumps in the same way as regions; passed as a\nbcftools targets file argument).\ne.g. 'targets.bed'\n", - "ontologies": [] - } - } - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.{vcf,vcf.gz,bcf,bcf.gz}": { - "type": "file", - "description": "VCF output file containing GT fields with modified ploidy", - "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}", - "ontologies": [] - } - } - ] - ], - "tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tbi": { - "type": "file", - "description": "Alternative VCF file index", - "pattern": "*.tbi", - "ontologies": [] - } - } - ] - ], - "csi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.csi": { - "type": "file", - "description": "Default VCF file index", - "pattern": "*.csi", - "ontologies": [] - } - } - ] - ], - "versions_bcftools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bcftools": { - "type": "string", - "description": "The tool name" - } - }, - { - "bcftools --version | sed '1!d; s/^.*bcftools //'": { - "type": "eval", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bcftools": { - "type": "string", - "description": "The tool name" - } - }, - { - "bcftools --version | sed '1!d; s/^.*bcftools //'": { - "type": "eval", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@alkc" - ], - "maintainers": [ - "@alkc" - ] - } - }, - { - "name": "bcftools_pluginimputeinfo", - "path": "modules/nf-core/bcftools/pluginimputeinfo/meta.yml", - "type": "module", - "meta": { - "name": "bcftools_pluginimputeinfo", - "description": "Adds imputation information metrics to the INFO field based on selected FORMAT tags. Only the IMPUTE2 INFO metric from FORMAT/GP tags is currently available.", - "keywords": [ - "impute-info", - "bcftools", - "imputation", - "metrics", - "tags", - "vcf" - ], - "tools": [ - { - "bcftools": { - "description": "BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations.", - "homepage": "https://samtools.github.io/bcftools/howtos/index.html", - "documentation": "https://samtools.github.io/bcftools/bcftools.html", - "tool_dev_url": "https://github.com/samtools/bcftools", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "args_id": "$args", - "identifier": "biotools:bcftools" - } - }, - { - "bcftools plugin impute-info": { - "description": "Bcftools plugins are tools that can be used with bcftools to manipulate variant calls in Variant Call Format (VCF) and BCF. The impute-info plugin adds imputation information metrics to the INFO field based on selected FORMAT tags. Only the IMPUTE2 INFO metric from FORMAT/GP tags is currently available", - "homepage": "https://samtools.github.io/bcftools/howtos/plugins.html", - "documentation": "https://samtools.github.io/bcftools/bcftools.html#plugin", - "tool_dev_url": "https://github.com/samtools/bcftools", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "args_id": "$args2", - "identifier": "biotools:bcftools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "The vcf file to be inspected.\ne.g. 'file.vcf'\n", - "ontologies": [] - } - }, - { - "index": { - "type": "file", - "description": "The tab index for the VCF file to be inspected.\ne.g. 'file.tbi'\n", - "ontologies": [] - } - } - ], - { - "regions": { - "type": "file", - "description": "Optionally, restrict the operation to regions listed in this file.\ne.g. 'file.vcf'\n", - "ontologies": [] - } - }, - { - "targets": { - "type": "file", - "description": "Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files)\ne.g. 'file.vcf'\n", - "ontologies": [] - } - } - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.{vcf,vcf.gz,bcf,bcf.gz}": { - "type": "file", - "description": "VCF output file containing added INFO/INFO field", - "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}", - "ontologies": [] - } - } - ] - ], - "tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tbi": { - "type": "file", - "description": "Alternative VCF file index", - "pattern": "*.tbi", - "ontologies": [] - } - } - ] - ], - "csi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.csi": { - "type": "file", - "description": "Default VCF file index", - "pattern": "*.csi", - "ontologies": [] - } - } - ] - ], - "versions_bcftools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bcftools": { - "type": "string", - "description": "The tool name" - } - }, - { - "bcftools --version | sed '1!d; s/^.*bcftools //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bcftools": { - "type": "string", - "description": "The tool name" - } - }, - { - "bcftools --version | sed '1!d; s/^.*bcftools //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@eweizy" - ], - "maintainers": [ - "@eweizy" - ] - } - }, - { - "name": "bcftools_pluginscatter", - "path": "modules/nf-core/bcftools/pluginscatter/meta.yml", - "type": "module", - "meta": { - "name": "bcftools_pluginscatter", - "description": "Split VCF by chunks or regions, creating multiple VCFs.", - "keywords": [ - "scatter", - "vcf", - "bcf", - "genomics" - ], - "tools": [ - { - "pluginscatter": { - "description": "Split VCF by chunks or regions, creating multiple VCFs.\n", - "homepage": "http://samtools.github.io/bcftools/bcftools.html", - "documentation": "http://samtools.github.io/bcftools/bcftools.html#reheader", - "doi": "10.1093/gigascience/giab008", - "licence": [ - "MIT" - ], - "identifier": "biotools:bcftools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "The input VCF to scatter", - "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}", - "ontologies": [] - } - }, - { - "tbi": { - "type": "file", - "description": "Optional index of the input VCF", - "pattern": "*.tbi", - "ontologies": [] - } - } - ], - { - "sites_per_chunk": { - "type": "integer", - "description": "How many variants should be in each output file\nEither this or `scatter` or `scatter_file` have to be given\n" - } - }, - { - "scatter": { - "type": "string", - "description": "A comma delimited list of regions to scatter into\nEither this or `sites_per_chunk` or `scatter_file` have to be given\n" - } - }, - { - "scatter_file": { - "type": "file", - "description": "A file containing a region on each line with an optional second column containing the filename\nEither this or `sites_per_chunk` or `scatter` have to be given\n", - "ontologies": [] - } - }, - { - "regions": { - "type": "file", - "description": "Optional file containing the regions to work on", - "pattern": "*.bed", - "ontologies": [] - } - }, - { - "targets": { - "type": "file", - "description": "Optional file containing the regions to work on (but streams instead of index-jumping)", - "pattern": "*.bed", - "ontologies": [] - } - } - ], - "output": { - "scatter": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*{vcf,vcf.gz,bcf,bcf.gz}": { - "type": "file", - "description": "The resulting files of the scattering", - "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}", - "ontologies": [] - } - } - ] - ], - "tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tbi": { - "type": "file", - "description": "Alternative VCF file index", - "pattern": "*.tbi", - "ontologies": [] - } - } - ] - ], - "csi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.csi": { - "type": "file", - "description": "Default VCF file index", - "pattern": "*.csi", - "ontologies": [] - } - } - ] - ], - "versions_bcftools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bcftools": { - "type": "string", - "description": "The tool name" - } - }, - { - "bcftools --version | sed '1!d; s/^.*bcftools //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bcftools": { - "type": "string", - "description": "The tool name" - } - }, - { - "bcftools --version | sed '1!d; s/^.*bcftools //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@nvnieuwk" - ], - "maintainers": [ - "@nvnieuwk" - ] - } - }, - { - "name": "bcftools_pluginsetgt", - "path": "modules/nf-core/bcftools/pluginsetgt/meta.yml", - "type": "module", - "meta": { - "name": "bcftools_pluginsetgt", - "description": "Sets genotypes according to the specified criteria and filtering expressions. For example, missing genotypes can be set to ref, but much more than that.", - "keywords": [ - "setgt", - "bcftools", - "genotype", - "vcf" - ], - "tools": [ - { - "bcftools": { - "description": "BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations.", - "homepage": "https://samtools.github.io/bcftools/howtos/index.html", - "documentation": "https://samtools.github.io/bcftools/bcftools.html", - "tool_dev_url": "https://github.com/samtools/bcftools", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "args_id": "$args", - "identifier": "biotools:bcftools" - } - }, - { - "bcftools plugin setGT": { - "description": "Bcftools plugins are tools that can be used with bcftools to manipulate variant calls in Variant Call Format (VCF) and BCF. The setGT plugin sets genotypes according to the specified criteria and filtering expressions. For example, missing genotypes can be set to ref, but much more than that.", - "homepage": "https://samtools.github.io/bcftools/howtos/plugins.html", - "documentation": "https://samtools.github.io/bcftools/howtos/plugin.setGT.html", - "tool_dev_url": "https://github.com/samtools/bcftools", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "args_id": "$args2", - "identifier": "biotools:bcftools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "The vcf file to be inspected.\ne.g. 'file.vcf'\n", - "ontologies": [] - } - }, - { - "index": { - "type": "file", - "description": "The tab index for the VCF file to be inspected.\ne.g. 'file.tbi'\n", - "ontologies": [] - } - } - ], - { - "target_gt": { - "type": "string", - "description": "Genotypes to change\n" - } - }, - { - "new_gt": { - "type": "string", - "description": "Genotypes to set\n" - } - }, - { - "regions": { - "type": "file", - "description": "Optionally, restrict the operation to regions listed in this file.\ne.g. 'file.vcf'\n", - "ontologies": [] - } - }, - { - "targets": { - "type": "file", - "description": "Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files)\ne.g. 'file.vcf'\n", - "ontologies": [] - } - } - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.{vcf,vcf.gz,bcf,bcf.gz}": { - "type": "file", - "description": "VCF output file containing set genotypes", - "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}", - "ontologies": [] - } - } - ] - ], - "tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tbi": { - "type": "file", - "description": "Alternative VCF file index", - "pattern": "*.tbi", - "ontologies": [] - } - } - ] - ], - "csi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.csi": { - "type": "file", - "description": "Default VCF file index", - "pattern": "*.csi", - "ontologies": [] - } - } - ] - ], - "versions_bcftools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bcftools": { - "type": "string", - "description": "The tool name" - } - }, - { - "bcftools --version | sed '1!d; s/^.*bcftools //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bcftools": { - "type": "string", - "description": "The tool name" - } - }, - { - "bcftools --version | sed '1!d; s/^.*bcftools //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@eweizy" - ], - "maintainers": [ - "@eweizy" - ] - }, - "pipelines": [ - { - "name": "raredisease", - "version": "3.0.0" - } - ] - }, - { - "name": "bcftools_pluginsplit", - "path": "modules/nf-core/bcftools/pluginsplit/meta.yml", - "type": "module", - "meta": { - "name": "bcftools_pluginsplit", - "description": "Split VCF by sample, creating single- or multi-sample VCFs.", - "keywords": [ - "split", - "vcf", - "genomics" - ], - "tools": [ - { - "pluginsplit": { - "description": "Split VCF by sample, creating single- or multi-sample VCFs.\n", - "homepage": "http://samtools.github.io/bcftools/bcftools.html", - "documentation": "http://www.htslib.org/doc/bcftools.html", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "identifier": "biotools:bcftools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "The VCF file to split", - "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}", - "ontologies": [] - } - }, - { - "tbi": { - "type": "file", - "description": "OPTIONAL - The index of the input VCF/BCF", - "pattern": "*.tbi", - "ontologies": [] - } - }, - { - "samples": { - "type": "file", - "description": "A tab-separated file determining which samples should be in which output file\ncolumn 1: The sample name(s) in the input file\ncolumn 2: The sample name(s) to use in the output file (use `-` to keep the original name)\ncolumn 3: The name of the output file\nEither this or a groups file should be given\n", - "pattern": "*", - "ontologies": [] - } - }, - { - "groups": { - "type": "file", - "description": "A tab-separated file determining which samples should be in which output file(s)\ncolumn 1: The sample name(s) in the input file\ncolumn 2: The sample name(s) to use in the output file (use `-` to keep the original name)\ncolumn 3: The name of the output file(s)\nEither this or a samples file should be given\n", - "pattern": "*", - "ontologies": [] - } - }, - { - "regions": { - "type": "file", - "description": "A BED file containing regions to use", - "pattern": "*.bed", - "ontologies": [] - } - }, - { - "targets": { - "type": "file", - "description": "A BED file containing regions to use (but streams rather than index-jumps)", - "pattern": "*.bed", - "ontologies": [] - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.{vcf,vcf.gz,bcf,bcf.gz}": { - "type": "file", - "description": "The resulting VCF files from the split", - "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}", - "ontologies": [] - } - } - ] - ], - "tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tbi": { - "type": "file", - "description": "TBI file", - "pattern": "*.tbi", - "ontologies": [] - } - } - ] - ], - "csi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.csi": { - "type": "file", - "description": "CSI file", - "pattern": "*.csi", - "ontologies": [] - } - } - ] - ], - "versions_bcftools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bcftools": { - "type": "string", - "description": "The tool name" - } - }, - { - "bcftools --version | sed '1!d; s/^.*bcftools //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bcftools": { - "type": "string", - "description": "The tool name" - } - }, - { - "bcftools --version | sed '1!d; s/^.*bcftools //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@nvnieuwk" - ], - "maintainers": [ - "@nvnieuwk" - ] - }, - "pipelines": [ - { - "name": "phaseimpute", - "version": "1.1.0" - } - ] - }, - { - "name": "bcftools_plugintag2tag", - "path": "modules/nf-core/bcftools/plugintag2tag/meta.yml", - "type": "module", - "meta": { - "name": "bcftools_plugintag2tag", - "description": "Converts between similar tags, such as GL,PL,GP or QR,QA,QS or localized alleles, eg LPL,LAD.", - "keywords": [ - "tag2tag", - "bcftools", - "VCF" - ], - "tools": [ - { - "view": { - "description": "Converts between similar tags, such as GL,PL,GP or QR,QA,QS or localized alleles, eg LPL,LAD.\n", - "homepage": "http://samtools.github.io/bcftools/bcftools.html", - "documentation": "https://samtools.github.io/bcftools/howtos/plugin.tag2tag.html", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "identifier": "biotools:bcftools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "The vcf file to be inspected.\ne.g. 'file.vcf'\n", - "ontologies": [] - } - }, - { - "index": { - "type": "file", - "description": "The tab index for the VCF file to be inspected.\ne.g. 'file.tbi'\n", - "ontologies": [] - } - } - ], - { - "regions": { - "type": "file", - "description": "Optionally, restrict the operation to regions listed in this file.\ne.g. 'file.vcf'\n", - "ontologies": [] - } - }, - { - "targets": { - "type": "file", - "description": "Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files)\ne.g. 'file.vcf'\n", - "ontologies": [] - } - } - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.{vcf,vcf.gz,bcf,bcf.gz}": { - "type": "file", - "description": "VCF normalized output file", - "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}", - "ontologies": [] - } - } - ] - ], - "tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tbi": { - "type": "file", - "description": "Alternative VCF file index", - "pattern": "*.tbi", - "ontologies": [] - } - } - ] - ], - "csi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.csi": { - "type": "file", - "description": "Default VCF file index", - "pattern": "*.csi", - "ontologies": [] - } - } - ] - ], - "versions_bcftools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bcftools": { - "type": "string", - "description": "The tool name" - } - }, - { - "bcftools --version | sed '1!d; s/^.*bcftools //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bcftools": { - "type": "string", - "description": "The tool name" - } - }, - { - "bcftools --version | sed '1!d; s/^.*bcftools //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@eweizy" - ], - "maintainers": [ - "@eweizy" - ] - } - }, - { - "name": "bcftools_pluginvcf2table", - "path": "modules/nf-core/bcftools/pluginvcf2table/meta.yml", - "type": "module", - "meta": { - "name": "bcftools_pluginvcf2table", - "description": "Converts VCF/BCF files into a tab-delimited table using the bcftools +vcf2table plugin.\nEach variant is output as one row, with INFO and FORMAT fields as columns.\n", - "keywords": [ - "bcftools", - "vcf", - "table", - "variant calling" - ], - "tools": [ - { - "bcftools": { - "description": "BCFtools is a set of utilities for variant calling and manipulating VCF/BCF files.\nThe +vcf2table plugin converts VCF records into a tab-delimited table format.\n", - "homepage": "http://samtools.github.io/bcftools/bcftools.html", - "documentation": "http://www.htslib.org/doc/bcftools.html", - "doi": "10.1093/gigascience/giab008", - "licence": [ - "MIT" - ], - "identifier": "biotools:bcftools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", - "ontologies": [] - } - }, - { - "vcf": { - "type": "file", - "description": "VCF/BCF file to be converted (optionally bgzipped).", - "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - } - ] - } - }, - { - "tbi": { - "type": "file", - "description": "Index of the VCF/BCF file (required when vcf is bgzipped).", - "pattern": "*.{tbi,csi}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing filter file information\ne.g. [ id:'test' ]\n" - } - }, - { - "regions": { - "type": "file", - "description": "Optional. Restrict the operation to regions listed in this BED or VCF file.\nRelies on a tabix index.\n", - "pattern": "*.{bed,vcf,vcf.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3003" - }, - { - "edam": "http://edamontology.org/format_3016" - } - ] - } - }, - { - "targets": { - "type": "file", - "description": "Optional. Restrict the operation to regions listed in this file\n(does not rely on index files).\n", - "pattern": "*.{bed,vcf,vcf.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3003" - }, - { - "edam": "http://edamontology.org/format_3016" - } - ] - } - }, - { - "samples": { - "type": "file", - "description": "Optional. File of sample names to include or exclude.\n", - "pattern": "*.txt", - "ontologies": [] - } - } - ] - ], - "output": { - "txt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", - "ontologies": [] - } - }, - { - "*.txt": { - "type": "file", - "description": "Tab-delimited table output from bcftools +vcf2table.", - "pattern": "*.txt", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_bcftools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bcftools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bcftools --version | sed '1!d; s/^.*bcftools //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bcftools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bcftools --version | sed '1!d; s/^.*bcftools //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@emmcauley" - ], - "maintainers": [ - "@emmcauley" - ] - } - }, - { - "name": "bcftools_query", - "path": "modules/nf-core/bcftools/query/meta.yml", - "type": "module", - "meta": { - "name": "bcftools_query", - "description": "Extracts fields from VCF or BCF files and outputs them in user-defined format.", - "keywords": [ - "query", - "variant calling", - "bcftools", - "VCF" - ], - "tools": [ - { - "query": { - "description": "Extracts fields from VCF or BCF files and outputs them in user-defined format.\n", - "homepage": "http://samtools.github.io/bcftools/bcftools.html", - "documentation": "http://www.htslib.org/doc/bcftools.html", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "identifier": "biotools:bcftools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "The vcf file to be queried.\n", - "pattern": "*.{vcf.gz, vcf}", - "ontologies": [] - } + "name": "bedops_convert2bed", + "path": "modules/nf-core/bedops/convert2bed/meta.yml", + "type": "module", + "meta": { + "name": "bedops_convert2bed", + "description": "Convert BAM/GFF/GTF/GVF/PSL files to bed", + "keywords": ["convert", "bed", "genomics"], + "tools": [ + { + "bedops": { + "description": "High-performance genomic feature operations.", + "homepage": "https://bedops.readthedocs.io/en/latest/content/reference/file-management/conversion/convert2bed.html#convert2bed", + "documentation": "https://bedops.readthedocs.io/en/latest/", + "tool_dev_url": "https://github.com/bedops", + "doi": "10.1093/bioinformatics/bts277", + "licence": ["GNU v2"], + "identifier": "biotools:bedops" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "in_file": { + "type": "file", + "description": "Input file", + "ontologies": [] + } + } + ] + ], + "output": { + "bed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "Sorted BED file", + "pattern": "*.{bed}", + "ontologies": [] + } + } + ] + ], + "versions_bedops": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bedops": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "convert2bed --version | sed -n \"s/.*version: *\\([^ ]*\\).*/\\1/p\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bedops": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "convert2bed --version | sed -n \"s/.*version: *\\([^ ]*\\).*/\\1/p\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@rannick"], + "maintainers": ["@rannick"] }, - { - "tbi": { - "type": "file", - "description": "The tab index for the VCF file to be inspected.\n", - "pattern": "*.tbi", - "ontologies": [] - } - } - ], - { - "regions": { - "type": "file", - "description": "Optionally, restrict the operation to regions listed in this file.\n", - "ontologies": [] - } - }, - { - "targets": { - "type": "file", - "description": "Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files)\n", - "ontologies": [] - } - }, - { - "samples": { - "type": "file", - "description": "Optional, file of sample names to be included or excluded.\ne.g. 'file.tsv'\n", - "ontologies": [] - } - } - ], - "output": { - "output": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.${suffix}": { - "type": "file", - "description": "BCFTools query output file", - "ontologies": [] - } - } - ] - ], - "versions_bcftools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bcftools": { - "type": "string", - "description": "The tool name" - } - }, - { - "bcftools --version | sed '1!d; s/^.*bcftools //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bcftools": { - "type": "string", - "description": "The tool name" - } - }, - { - "bcftools --version | sed '1!d; s/^.*bcftools //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } + "pipelines": [ + { + "name": "variantbenchmarking", + "version": "1.5.0" + } ] - ] - }, - "authors": [ - "@abhi18av", - "@drpatelh" - ], - "maintainers": [ - "@abhi18av", - "@drpatelh" - ] - }, - "pipelines": [ - { - "name": "genomicrelatedness", - "version": "dev" - }, - { - "name": "pacsomatic", - "version": "dev" }, { - "name": "phaseimpute", - "version": "1.1.0" + "name": "bedops_gtf2bed", + "path": "modules/nf-core/bedops/gtf2bed/meta.yml", + "type": "module", + "meta": { + "name": "bedops_gtf2bed", + "description": "Convert gtf format to bed format", + "keywords": ["gtf", "bed", "conversion"], + "tools": [ + { + "gtf2bed": { + "description": "The gtf2bed script converts 1-based, closed [start, end] Gene Transfer Format v2.2 (GTF2.2) to sorted, 0-based, half-open [start-1, end) extended BED-formatted data.", + "homepage": "https://bedops.readthedocs.io/en/latest/content/reference/file-management/conversion/gtf2bed.html", + "documentation": "https://bedops.readthedocs.io/en/latest/content/reference/file-management/conversion/gtf2bed.html", + "tool_dev_url": "https://github.com/bedops/bedops", + "doi": "10.1093/bioinformatics/bts277", + "licence": ["GPL v2"], + "identifier": "biotools:bedops" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "gtf": { + "type": "file", + "description": "A reference file in GTF format", + "pattern": "*.{gtf,gtf.gz}", + "ontologies": [] + } + } + ] + ], + "output": { + "bed": [ + [ + { + "meta": { + "type": "file", + "description": "A reference file in BED format", + "pattern": "*.{bed}", + "ontologies": [] + } + }, + { + "*.bed": { + "type": "file", + "description": "A reference file in BED format", + "pattern": "*.{bed}", + "ontologies": [] + } + } + ] + ], + "versions_bedops": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bedops": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bedops --version | sed -n \"s/.*version: *\\([^ ]*\\).*/\\1/p\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bedops": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bedops --version | sed -n \"s/.*version: *\\([^ ]*\\).*/\\1/p\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@davidecarlson"] + } }, { - "name": "viralrecon", - "version": "3.0.0" - } - ] - }, - { - "name": "bcftools_reheader", - "path": "modules/nf-core/bcftools/reheader/meta.yml", - "type": "module", - "meta": { - "name": "bcftools_reheader", - "description": "Reheader a VCF file", - "keywords": [ - "reheader", - "vcf", - "update header" - ], - "tools": [ - { - "reheader": { - "description": "Modify header of VCF/BCF files, change sample names.\n", - "homepage": "http://samtools.github.io/bcftools/bcftools.html", - "documentation": "http://samtools.github.io/bcftools/bcftools.html#reheader", - "doi": "10.1093/gigascience/giab008", - "licence": [ - "MIT" - ], - "identifier": "biotools:bcftools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF/BCF file", - "pattern": "*.{vcf.gz,vcf,bcf}", - "ontologies": [] - } - }, - { - "header": { - "type": "file", - "description": "New header to add to the VCF", - "pattern": "*.{header.txt}", - "ontologies": [] - } - }, - { - "samples": { - "type": "file", - "description": "File containing sample names to update (one sample per line)", - "pattern": "*.{samples.txt}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fai": { - "type": "file", - "description": "Fasta index to update header sequences with", - "pattern": "*.{fai}", - "ontologies": [] - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.{vcf,vcf.gz,bcf,bcf.gz}": { - "type": "file", - "description": "VCF with updated header, bgzipped per default", - "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}", - "ontologies": [] - } - } - ] - ], - "index": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.{csi,tbi}": { - "type": "file", - "description": "Index of VCF with updated header", - "pattern": "*.{csi,tbi}", - "ontologies": [] - } - } - ] - ], - "versions_bcftools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bcftools": { - "type": "string", - "description": "The tool name" - } - }, - { - "bcftools --version | sed '1!d; s/^.*bcftools //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bcftools": { - "type": "string", - "description": "The tool name" - } - }, - { - "bcftools --version | sed '1!d; s/^.*bcftools //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@bjohnnyd", - "@jemten", - "@ramprasadn" - ], - "maintainers": [ - "@bjohnnyd", - "@jemten", - "@ramprasadn" - ] - }, - "pipelines": [ - { - "name": "raredisease", - "version": "3.0.0" - }, - { - "name": "variantbenchmarking", - "version": "1.5.0" - } - ] - }, - { - "name": "bcftools_roh", - "path": "modules/nf-core/bcftools/roh/meta.yml", - "type": "module", - "meta": { - "name": "bcftools_roh", - "description": "A program for detecting runs of homo/autozygosity. Only bi-allelic sites are considered.", - "keywords": [ - "roh", - "biallelic", - "homozygosity", - "autozygosity" - ], - "tools": [ - { - "roh": { - "description": "A program for detecting runs of homo/autozygosity. Only bi-allelic sites are considered.", - "homepage": "https://www.htslib.org/", - "documentation": "http://www.htslib.org/doc/bcftools.html", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "identifier": "biotools:bcftools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF file", - "pattern": "*.{vcf,.vcf.gz}", - "ontologies": [] - } - }, - { - "tbi": { - "type": "file", - "description": "TBI file", - "patthern": "*.tbi", - "ontologies": [] - } - } - ], - [ - { - "af_file": { - "type": "file", - "description": "Read allele frequencies from a tab-delimited file containing the columns: CHROM\tPOS\tREF,ALT\tAF.", - "ontologies": [] - } - }, - { - "af_file_tbi": { - "type": "file", - "description": "tbi index of af_file.", - "ontologies": [] - } - } - ], - { - "genetic_map": { - "type": "file", - "description": "Genetic map in the format required also by IMPUTE2.", - "ontologies": [] - } - }, - { - "regions_file": { - "type": "file", - "description": "Regions can be specified either on command line or in a VCF, BED, or tab-delimited file (the default).", - "ontologies": [] - } - }, - { - "samples_file": { - "type": "file", - "description": "File of sample names to include or exclude if prefixed with '^'.", - "ontologies": [] - } - }, - { - "targets_file": { - "type": "file", - "description": "Targets can be specified either on command line or in a VCF, BED, or tab-delimited file (the default).", - "ontologies": [] - } - } - ], - "output": { - "roh": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.roh": { - "type": "file", - "description": "Contains site-specific and/or per-region runs of homo/autozygosity calls.", - "pattern": "*.{roh}", - "ontologies": [] - } - } - ] - ], - "versions_bcftools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bcftools": { - "type": "string", - "description": "The tool name" - } - }, - { - "bcftools --version | sed '1!d; s/^.*bcftools //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bcftools": { - "type": "string", - "description": "The tool name" - } - }, - { - "bcftools --version | sed '1!d; s/^.*bcftools //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@ramprasadn" - ], - "maintainers": [ - "@ramprasadn" - ] - }, - "pipelines": [ - { - "name": "raredisease", - "version": "3.0.0" - } - ] - }, - { - "name": "bcftools_rohviz", - "path": "modules/nf-core/bcftools/rohviz/meta.yml", - "type": "module", - "meta": { - "name": "bcftools_rohviz", - "description": "Visualise the output of bcftools roh", - "keywords": [ - "visualisation", - "RoH", - "VCF" - ], - "tools": [ - { - "roh-viz": { - "description": "\"Visualise the output of bcftools roh. It creates an HTML/JavaScript document which can be interactively viewed in a web browser.\"\n", - "homepage": "http://samtools.github.io/bcftools/bcftools.html", - "documentation": "http://www.htslib.org/doc/bcftools.html", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "identifier": "biotools:bcftools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample1' ]\n" - } - }, - { - "roh": { - "type": "file", - "description": "Output of BCFtools_roh. Contains site-specific and/or per-region runs of homo/autozygosity calls.", - "pattern": "*.roh", - "ontologies": [] - } - } - ], - [ - { - "meta1": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample1' ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF file", - "pattern": "*.{vcf,.vcf.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - } - ] - } - } - ], - { - "regions_list": { - "type": "file", - "description": "Regions can be specified either on command line or in a VCF, BED, or tab-delimited file (the default).", - "ontologies": [] - } - }, - { - "samples_file": { - "type": "file", - "description": "File of sample names to include or exclude if prefixed with '^'.", - "ontologies": [] - } - } - ], - "output": { - "html": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample1' ]\n" - } - }, - { - "*.html": { - "type": "file", - "description": "RoH visual report file.", - "pattern": "*.html", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2331" - } - ] - } - } - ] - ], - "versions_bcftools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bcftools": { - "type": "string", - "description": "The tool name" - } - }, - { - "bcftools --version | sed '1!d; s/^.*bcftools //'": { - "type": "eval", - "description": "The command used to generate the version of the tool" - } - } - ] - ], - "versions_less": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "less": { - "type": "string", - "description": "The tool name" - } - }, - { - "less --version | head -n1 | sed 's/less //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bcftools": { - "type": "string", - "description": "The tool name" - } - }, - { - "bcftools --version | sed '1!d; s/^.*bcftools //'": { - "type": "eval", - "description": "The command used to generate the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "less": { - "type": "string", - "description": "The tool name" - } - }, - { - "less --version | head -n1 | sed 's/less //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@yz533cb" - ] - } - }, - { - "name": "bcftools_sort", - "path": "modules/nf-core/bcftools/sort/meta.yml", - "type": "module", - "meta": { - "name": "bcftools_sort", - "description": "Sorts VCF files", - "keywords": [ - "sorting", - "VCF", - "variant calling" - ], - "tools": [ - { - "sort": { - "description": "Sort VCF files by coordinates.", - "homepage": "http://samtools.github.io/bcftools/bcftools.html", - "documentation": "http://www.htslib.org/doc/bcftools.html", - "tool_dev_url": "https://github.com/samtools/bcftools", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "identifier": "biotools:bcftools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + "name": "bedtools_bamtobed", + "path": "modules/nf-core/bedtools/bamtobed/meta.yml", + "type": "module", + "meta": { + "name": "bedtools_bamtobed", + "description": "Converts a bam file to a bed12 file.", + "keywords": ["bam", "bed", "bedtools", "bamtobed", "converter"], + "tools": [ + { + "bedtools": { + "description": "A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.\n", + "documentation": "https://bedtools.readthedocs.io/en/latest/content/tools/complement.html", + "licence": ["MIT"], + "identifier": "biotools:bedtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "Input BAM file", + "pattern": "*.{bam}", + "ontologies": [] + } + } + ] + ], + "output": { + "bed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "Bed file containing genomic intervals.", + "pattern": "*.{bed}", + "ontologies": [] + } + } + ] + ], + "versions_bedtools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bedtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bedtools --version | sed -e 's/bedtools v//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bedtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bedtools --version | sed -e 's/bedtools v//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@yuukiiwa", "@drpatelh"], + "maintainers": ["@yuukiiwa", "@drpatelh"] }, - { - "vcf": { - "type": "file", - "description": "The VCF/BCF file to be sorted", - "pattern": "*.{vcf.gz,vcf,bcf}", - "ontologies": [] - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.{vcf,vcf.gz,bcf,bcf.gz}": { - "type": "file", - "description": "Sorted VCF file", - "pattern": "*.{vcf.gz}", - "ontologies": [] - } - } - ] - ], - "tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tbi": { - "type": "file", - "description": "Alternative VCF file index", - "pattern": "*.tbi", - "ontologies": [] - } - } - ] - ], - "csi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.csi": { - "type": "file", - "description": "Default VCF file index", - "pattern": "*.csi", - "ontologies": [] - } - } - ] - ], - "versions_bcftools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bcftools": { - "type": "string", - "description": "The tool name" - } - }, - { - "bcftools --version | sed '1!d; s/^.*bcftools //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bcftools": { - "type": "string", - "description": "The tool name" - } - }, - { - "bcftools --version | sed '1!d; s/^.*bcftools //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } + "pipelines": [ + { + "name": "cutandrun", + "version": "3.2.2" + }, + { + "name": "nascent", + "version": "2.3.0" + }, + { + "name": "radseq", + "version": "dev" + }, + { + "name": "ssds", + "version": "dev" + } ] - ] - }, - "authors": [ - "@Gwennid" - ], - "maintainers": [ - "@Gwennid" - ] - }, - "pipelines": [ - { - "name": "genomicrelatedness", - "version": "dev" - }, - { - "name": "nanoseq", - "version": "3.1.0" - }, - { - "name": "pacsomatic", - "version": "dev" - }, - { - "name": "pacvar", - "version": "1.0.1" - }, - { - "name": "radseq", - "version": "dev" - }, - { - "name": "raredisease", - "version": "3.0.0" - }, - { - "name": "rnadnavar", - "version": "dev" - }, - { - "name": "sarek", - "version": "3.8.1" - }, - { - "name": "variantbenchmarking", - "version": "1.5.0" }, { - "name": "viralmetagenome", - "version": "1.1.1" + "name": "bedtools_closest", + "path": "modules/nf-core/bedtools/closest/meta.yml", + "type": "module", + "meta": { + "name": "bedtools_closest", + "description": "For each feature in A, finds the closest feature (upstream or downstream) in B.", + "keywords": ["bedtools", "closest", "bed", "vcf", "gff"], + "tools": [ + { + "bedtools": { + "description": "A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.\n", + "documentation": "https://bedtools.readthedocs.io/en/latest/content/tools/closest.html", + "licence": ["MIT"], + "identifier": "biotools:bedtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input_1": { + "type": "file", + "description": "The file to find the closest features of", + "pattern": "*.{bed,vcf,gff}(.gz)?", + "ontologies": [] + } + }, + { + "input_2": { + "type": "list", + "description": "The input file(s) to find the closest features from", + "pattern": "*.{bed,vcf,gff}(.gz)?" + } + } + ], + { + "fasta_fai": { + "type": "file", + "description": "The index of the FASTA reference. Needed when the argument `--sorted` is used", + "pattern": "*.fai", + "ontologies": [] + } + } + ], + "output": { + "output": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.${extension}": { + "type": "file", + "description": "The resulting BED file containing the closest features", + "pattern": "*.{bed,vcf,gff}", + "ontologies": [] + } + } + ] + ], + "versions_bedtools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bedtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bedtools --version | sed -e 's/bedtools v//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bedtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bedtools --version | sed -e 's/bedtools v//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@nvnieuwk"], + "maintainers": ["@nvnieuwk"] + } }, { - "name": "viralrecon", - "version": "3.0.0" - } - ] - }, - { - "name": "bcftools_split", - "path": "modules/nf-core/bcftools/split/meta.yml", - "type": "module", - "meta": { - "name": "bcftools_split", - "description": "Split a vcf file into files per chromosome", - "keywords": [ - "vcf", - "split", - "genomics" - ], - "tools": [ - { - "bcftools": { - "description": "Sort VCF files by coordinates.", - "homepage": "http://samtools.github.io/bcftools/bcftools.html", - "documentation": "http://www.htslib.org/doc/bcftools.html", - "tool_dev_url": "https://github.com/samtools/bcftools", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "identifier": "biotools:bcftools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "Compressed vcf file", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - }, - { - "tbi": { - "type": "file", - "description": "Compressed vcf file index", - "pattern": "*.{tbi,csi}", - "ontologies": [] - } - } - ] - ], - "output": { - "split_vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.vcf.gz": { - "type": "file", - "description": "Compressed vcf files per chromosome", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "versions_bcftools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bcftools": { - "type": "string", - "description": "The tool name" - } - }, - { - "bcftools --version | sed '1!d; s/^.*bcftools //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bcftools": { - "type": "string", - "description": "The tool name" - } - }, - { - "bcftools --version | sed '1!d; s/^.*bcftools //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@matthdsm", - "@atrigila" - ], - "maintainers": [ - "@matthdsm", - "@atrigila" - ] - } - }, - { - "name": "bcftools_stats", - "path": "modules/nf-core/bcftools/stats/meta.yml", - "type": "module", - "meta": { - "name": "bcftools_stats", - "description": "Generates stats from VCF files", - "keywords": [ - "variant calling", - "stats", - "VCF" - ], - "tools": [ - { - "stats": { - "description": "Parses VCF or BCF and produces text file stats which is suitable for\nmachine processing and can be plotted using plot-vcfstats.\n", - "homepage": "http://samtools.github.io/bcftools/bcftools.html", - "documentation": "http://www.htslib.org/doc/bcftools.html", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "identifier": "biotools:bcftools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF input file", - "pattern": "*.{vcf}", - "ontologies": [] - } - }, - { - "tbi": { - "type": "file", - "description": "The tab index for the VCF file to be inspected. Optional: only required when parameter regions is chosen.\n", - "pattern": "*.tbi", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "regions": { - "type": "file", - "description": "Optionally, restrict the operation to regions listed in this file. (VCF, BED or tab-delimited)\n", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "targets": { - "type": "file", - "description": "Optionally, restrict the operation to regions listed in this file (doesn't rely upon tbi index files)\n", - "ontologies": [] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "samples": { - "type": "file", - "description": "Optional, file of sample names to be included or excluded.\ne.g. 'file.tsv'\n", - "ontologies": [] - } - } - ], - [ - { - "meta5": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "exons": { - "type": "file", - "description": "Tab-delimited file with exons for indel frameshifts (chr,beg,end; 1-based, inclusive, optionally bgzip compressed).\ne.g. 'exons.tsv.gz'\n", - "ontologies": [] - } - } - ], - [ - { - "meta6": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + "name": "bedtools_complement", + "path": "modules/nf-core/bedtools/complement/meta.yml", + "type": "module", + "meta": { + "name": "bedtools_complement", + "description": "Returns all intervals in a genome that are not covered by at least one interval in the input BED/GFF/VCF file.", + "keywords": ["bed", "gff", "vcf", "complement", "bedtools", "intervals"], + "tools": [ + { + "bedtools": { + "description": "A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.\n", + "documentation": "https://bedtools.readthedocs.io/en/latest/content/tools/complement.html", + "licence": ["MIT"], + "identifier": "biotools:bedtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bed": { + "type": "file", + "description": "Input BED file", + "pattern": "*.{bed}", + "ontologies": [] + } + } + ], + { + "sizes": { + "type": "file", + "description": "File which defines the chromosome lengths for a given genome", + "pattern": "*.{sizes}", + "ontologies": [] + } + } + ], + "output": { + "bed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "Bed file with all genomic intervals that are not covered by at least one record from the input file.", + "pattern": "*.{bed}", + "ontologies": [] + } + } + ] + ], + "versions_bedtools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bedtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bedtools --version | sed -e 's/bedtools v//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bedtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bedtools --version | sed -e 's/bedtools v//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@edmundmiller", "@sruthipsuresh", "@drpatelh"], + "maintainers": ["@edmundmiller", "@sruthipsuresh", "@drpatelh"] }, - { - "fasta": { - "type": "file", - "description": "Faidx indexed reference sequence file to determine INDEL context.\ne.g. 'reference.fa'\n", - "ontologies": [] - } - } - ] - ], - "output": { - "stats": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*stats.txt": { - "type": "file", - "description": "Text output file containing stats", - "pattern": "*_{stats.txt}", - "ontologies": [] - } - } - ] - ], - "versions_bcftools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bcftools": { - "type": "string", - "description": "The tool name" - } - }, - { - "bcftools --version | sed '1!d; s/^.*bcftools //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bcftools": { - "type": "string", - "description": "The tool name" - } - }, - { - "bcftools --version | sed '1!d; s/^.*bcftools //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } + "pipelines": [ + { + "name": "cutandrun", + "version": "3.2.2" + }, + { + "name": "tfactivity", + "version": "dev" + } ] - ] - }, - "authors": [ - "@joseespinosa", - "@drpatelh", - "@SusiJo", - "@TCLamnidis" - ], - "maintainers": [ - "@joseespinosa", - "@drpatelh", - "@SusiJo", - "@TCLamnidis" - ] - }, - "pipelines": [ - { - "name": "epitopeprediction", - "version": "3.1.0" - }, - { - "name": "genomicrelatedness", - "version": "dev" - }, - { - "name": "phaseimpute", - "version": "1.1.0" - }, - { - "name": "radseq", - "version": "dev" - }, - { - "name": "rnadnavar", - "version": "dev" - }, - { - "name": "sarek", - "version": "3.8.1" - }, - { - "name": "variantbenchmarking", - "version": "1.5.0" - }, - { - "name": "viralmetagenome", - "version": "1.1.1" }, { - "name": "viralrecon", - "version": "3.0.0" - } - ] - }, - { - "name": "bcftools_view", - "path": "modules/nf-core/bcftools/view/meta.yml", - "type": "module", - "meta": { - "name": "bcftools_view", - "description": "View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF", - "keywords": [ - "variant calling", - "view", - "bcftools", - "VCF" - ], - "tools": [ - { - "view": { - "description": "View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF\n", - "homepage": "http://samtools.github.io/bcftools/bcftools.html", - "documentation": "http://www.htslib.org/doc/bcftools.html", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "identifier": "biotools:bcftools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "The vcf file to be inspected.\ne.g. 'file.vcf'\n", - "ontologies": [] - } + "name": "bedtools_coverage", + "path": "modules/nf-core/bedtools/coverage/meta.yml", + "type": "module", + "meta": { + "name": "bedtools_coverage", + "description": "computes both the depth and breadth of coverage of features in file B on the features in file A", + "keywords": ["bedtools", "coverage", "bam", "bed", "gff", "vcf", "histogram"], + "tools": [ + { + "bedtools": { + "description": "A powerful toolset for genome arithmetic", + "homepage": "https://bedtools.readthedocs.io/en/latest/index.html", + "documentation": "https://bedtools.readthedocs.io/en/latest/content/bedtools-suite.html", + "tool_dev_url": "https://github.com/arq5x/bedtools2", + "doi": "10.1093/bioinformatics/btq033", + "licence": ["GPL v2", "MIT"], + "identifier": "biotools:bedtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input_A": { + "type": "file", + "description": "BAM/BED/GFF/VCF file", + "pattern": "*.{bam,bed,gff,vcf}", + "ontologies": [] + } + }, + { + "input_B": { + "type": "file", + "description": "One or more BAM/BED/GFF/VCF file", + "pattern": "*.{bam,bed,gff,vcf}", + "ontologies": [] + } + } + ], + { + "genome_file": { + "type": "file", + "description": "Optional reference genome 2 column file that defines the expected chromosome order\nin the input files for use with the -sorted option.\nWhen `genome_file` is provided, `-sorted` option is added to the command.\n", + "pattern": "*.{fai,txt,chromsizes}", + "ontologies": [] + } + } + ], + "output": { + "bed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "File containing coverage of sequence alignments", + "pattern": "*.bed", + "ontologies": [] + } + } + ] + ], + "versions_bedtools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bedtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bedtools --version | sed -e 's/bedtools v//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bedtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bedtools --version | sed -e 's/bedtools v//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@priyanka-surana"], + "maintainers": ["@priyanka-surana"] }, - { - "index": { - "type": "file", - "description": "The tab index for the VCF file to be inspected.\ne.g. 'file.tbi'\n", - "ontologies": [] - } - } - ], - { - "regions": { - "type": "file", - "description": "Optionally, restrict the operation to regions listed in this file.\ne.g. 'file.vcf'\n", - "ontologies": [] - } - }, - { - "targets": { - "type": "file", - "description": "Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files)\ne.g. 'file.vcf'\n", - "ontologies": [] - } - }, - { - "samples": { - "type": "file", - "description": "Optional, file of sample names to be included or excluded.\ne.g. 'file.tsv'\n", - "ontologies": [] - } - } - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.{vcf,vcf.gz,bcf,bcf.gz}": { - "type": "file", - "description": "VCF normalized output file", - "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}", - "ontologies": [] - } - } - ] - ], - "tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tbi": { - "type": "file", - "description": "Alternative VCF file index", - "pattern": "*.tbi", - "ontologies": [] - } - } - ] - ], - "csi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.csi": { - "type": "file", - "description": "Default VCF file index", - "pattern": "*.csi", - "ontologies": [] - } - } - ] - ], - "versions_bcftools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bcftools": { - "type": "string", - "description": "The tool name" - } - }, - { - "bcftools --version | sed '1!d; s/^.*bcftools //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bcftools": { - "type": "string", - "description": "The tool name" - } - }, - { - "bcftools --version | sed '1!d; s/^.*bcftools //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } + "pipelines": [ + { + "name": "radseq", + "version": "dev" + } ] - ] - }, - "authors": [ - "@abhi18av" - ], - "maintainers": [ - "@abhi18av" - ] - }, - "pipelines": [ - { - "name": "alleleexpression", - "version": "dev" - }, - { - "name": "mag", - "version": "5.4.2" - }, - { - "name": "pacsomatic", - "version": "dev" - }, - { - "name": "phaseimpute", - "version": "1.1.0" }, { - "name": "radseq", - "version": "dev" - }, - { - "name": "raredisease", - "version": "3.0.0" - }, - { - "name": "sarek", - "version": "3.8.1" - }, - { - "name": "tbanalyzer", - "version": "dev" - }, - { - "name": "tumourevo", - "version": "dev" + "name": "bedtools_flank", + "path": "modules/nf-core/bedtools/flank/meta.yml", + "type": "module", + "meta": { + "name": "bedtools_flank", + "description": "Creates two new flanking intervals for each interval in a BED/GFF/VCF file.", + "keywords": ["bed", "flankBed", "bedtools"], + "tools": [ + { + "bedtools": { + "description": "A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.\n", + "documentation": "https://bedtools.readthedocs.io/en/latest/content/tools/slop.html", + "licence": ["MIT"], + "identifier": "biotools:bedtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bed": { + "type": "file", + "description": "Input BED file", + "pattern": "*.{bed}", + "ontologies": [] + } + } + ], + { + "sizes": { + "type": "file", + "description": "Chromosome sizes file", + "ontologies": [] + } + } + ], + "output": { + "bed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "Flanked BED file", + "pattern": "*.{bed}", + "ontologies": [] + } + } + ] + ], + "versions_bedtools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bedtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bedtools --version | sed -e 's/bedtools v//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bedtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bedtools --version | sed -e 's/bedtools v//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@itrujnara"], + "maintainers": ["@itrujnara"] + } }, { - "name": "variantbenchmarking", - "version": "1.5.0" - } - ] - }, - { - "name": "bcl2fastq", - "path": "modules/nf-core/bcl2fastq/meta.yml", - "type": "module", - "meta": { - "name": "bcl2fastq", - "description": "Demultiplex Illumina BCL files", - "keywords": [ - "demultiplex", - "illumina", - "fastq" - ], - "tools": [ - { - "bcl2fastq": { - "description": "Demultiplex Illumina BCL files", - "homepage": "https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software", - "documentation": "https://support.illumina.com/content/dam/illumina-support/documents/documentation/software_documentation/bcl2fastq/bcl2fastq2-v2-20-software-guide-15051736-03.pdf", - "licence": [ - "ILLUMINA" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "samplesheet": { - "type": "file", - "description": "Input samplesheet", - "pattern": "*.{csv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - }, - { - "run_dir": { - "type": "file", - "description": "Input run directory containing RunInfo.xml and BCL data\nCould be a directory or a tar of the directory\n", - "ontologies": [] - } - } - ] - ], - "output": { - "fastq": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "output/**_S[1-9]*_R?_00?.fastq.gz": { - "type": "file", - "description": "Demultiplexed sample FASTQ files", - "pattern": "**_S*_L00?_R?_00?.fastq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - }, - { - "edam": "http://edamontology.org/format_3989" + "name": "bedtools_genomecov", + "path": "modules/nf-core/bedtools/genomecov/meta.yml", + "type": "module", + "meta": { + "name": "bedtools_genomecov", + "description": "Computes histograms (default), per-base reports (-d) and BEDGRAPH (-bg) summaries of feature coverage (e.g., aligned sequences) for a given genome.", + "keywords": ["bed", "bam", "genomecov", "bedtools", "histogram"], + "tools": [ + { + "bedtools": { + "description": "A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.\n", + "documentation": "https://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html", + "licence": ["MIT"], + "identifier": "biotools:bedtools" + } } - ] - } - } - ] - ], - "fastq_idx": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "output/**_S[1-9]*_I?_00?.fastq.gz": { - "type": "file", - "description": "Optional demultiplexed index FASTQ files", - "pattern": "**_S*_L00?_I?_00?.fastq.gz", - "ontologies": [ + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "intervals": { + "type": "file", + "description": "BAM/BED/GFF/VCF", + "pattern": "*.{bam|bed|gff|vcf}", + "ontologies": [] + } + }, + { + "scale": { + "type": "integer", + "description": "Number containing the scale factor for the output. Set to 1 to disable. Setting to a value other than 1 will also get the -bg bedgraph output format as this is required for this command switch" + } + } + ], { - "edam": "http://edamontology.org/format_1930" + "sizes": { + "type": "file", + "description": "Tab-delimited table of chromosome names in the first column and chromosome sizes in the second column", + "ontologies": [] + } }, { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "undetermined": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "output/**Undetermined_S0*_R?_00?.fastq.gz": { - "type": "file", - "description": "Optional undetermined sample FASTQ files", - "pattern": "Undetermined_S0_L00?_R?_00?.fastq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" + "extension": { + "type": "string", + "description": "Extension of the output file (e. g., \".bg\", \".bedgraph\", \".txt\", \".tab\", etc.) It is set arbitrarily by the user and corresponds to the file format which depends on arguments." + } }, { - "edam": "http://edamontology.org/format_3989" + "sort": { + "type": "boolean", + "description": "Sort the output" + } } - ] + ], + "output": { + "genomecov": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.${extension}": { + "type": "file", + "description": "Computed genome coverage file", + "pattern": "*.${extension}", + "ontologies": [] + } + } + ] + ], + "versions_bedtools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bedtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bedtools --version | sed -e 's/bedtools v//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bedtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bedtools --version | sed -e 's/bedtools v//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@edmundmiller", "@sruthipsuresh", "@drpatelh", "@sidorov-si", "@chris-cheshire"], + "maintainers": ["@edmundmiller", "@sruthipsuresh", "@drpatelh", "@sidorov-si", "@chris-cheshire"] + }, + "pipelines": [ + { + "name": "cutandrun", + "version": "3.2.2" + }, + { + "name": "hicar", + "version": "1.0.0" + }, + { + "name": "nascent", + "version": "2.3.0" + }, + { + "name": "raredisease", + "version": "3.0.0" + }, + { + "name": "rnaseq", + "version": "3.26.0" } - } ] - ], - "undetermined_idx": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "output/**Undetermined_S0*_I?_00?.fastq.gz": { - "type": "file", - "description": "Optional undetermined index FASTQ files", - "pattern": "Undetermined_S0_L00?_I?_00?.fastq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - }, + }, + { + "name": "bedtools_getfasta", + "path": "modules/nf-core/bedtools/getfasta/meta.yml", + "type": "module", + "meta": { + "name": "bedtools_getfasta", + "description": "extract sequences in a FASTA file based on intervals defined in a feature file.", + "keywords": ["bed", "fasta", "getfasta"], + "tools": [ + { + "bedtools": { + "description": "A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.\n", + "documentation": "https://bedtools.readthedocs.io/en/latest/content/tools/getfasta.html", + "licence": ["MIT"], + "identifier": "biotools:bedtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bed": { + "type": "file", + "description": "Bed feature file", + "pattern": "*.{bed}", + "ontologies": [] + } + } + ], { - "edam": "http://edamontology.org/format_3989" + "fasta": { + "type": "file", + "description": "Input fasta file", + "pattern": "*.{fa,fasta}", + "ontologies": [] + } } - ] + ], + "output": { + "fasta": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fa": { + "type": "file", + "description": "Output fasta file with extracted sequences", + "pattern": "*.{fa}", + "ontologies": [] + } + } + ] + ], + "versions_bedtools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bedtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bedtools --version | sed -e 's/bedtools v//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bedtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bedtools --version | sed -e 's/bedtools v//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@joseespinosa", "@drpatelh"], + "maintainers": ["@joseespinosa", "@drpatelh"] + }, + "pipelines": [ + { + "name": "circrna", + "version": "dev" + }, + { + "name": "deepmodeloptim", + "version": "dev" + }, + { + "name": "readsimulator", + "version": "1.0.1" + }, + { + "name": "tfactivity", + "version": "dev" + }, + { + "name": "viralrecon", + "version": "3.0.0" } - } - ] - ], - "reports": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "output/Reports": { - "type": "file", - "description": "Demultiplexing Reports", - "pattern": "Reports", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2331" - } - ] - } - } ] - ], - "stats": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "output/Stats": { - "type": "file", - "description": "Statistics files", - "pattern": "Stats", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2330" - }, - { - "edam": "http://edamontology.org/format_2332" - }, + }, + { + "name": "bedtools_groupby", + "path": "modules/nf-core/bedtools/groupby/meta.yml", + "type": "module", + "meta": { + "name": "bedtools_groupby", + "description": "Groups features in a BED file by given column(s) and computes summary statistics for each group to another column.", + "keywords": ["bed", "groupby", "bedtools"], + "tools": [ + { + "bedtools": { + "description": "A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.\n", + "documentation": "https://bedtools.readthedocs.io/en/latest/content/tools/groupby.html", + "homepage": "https://bedtools.readthedocs.io/en/latest/", + "doi": "10.1093/bioinformatics/btq033", + "licence": ["MIT"], + "identifier": "biotools:bedtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "bed": { + "type": "file", + "description": "Input BED file", + "pattern": "*.{bed}", + "ontologies": [] + } + } + ], { - "edam": "http://edamontology.org/format_3464" + "summary_col": { + "type": "string", + "description": "Column to summarize" + } } - ] - } - } - ] - ], - "interop": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "InterOp/*.bin": { - "type": "file", - "description": "Interop files", - "pattern": "*.{bin}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2333" - } - ] - } - } - ] - ], - "xml": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "**/*.xml": { - "type": "file", - "description": "Output XML files, for example RunInfo.xml", - "pattern": "**/*.xml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2332" - } - ] - } - } - ] - ], - "versions_bcl2fastq": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bcl2fastq": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bcl2fastq -V 2>&1 | grep -m 1 bcl2fastq | sed 's/^.*bcl2fastq v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bcl2fastq": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bcl2fastq -V 2>&1 | grep -m 1 bcl2fastq | sed 's/^.*bcl2fastq v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@matthdsm" - ], - "maintainers": [ - "@matthdsm" - ] - }, - "pipelines": [ - { - "name": "demultiplex", - "version": "1.7.1" - } - ] - }, - { - "name": "bclconvert", - "path": "modules/nf-core/bclconvert/meta.yml", - "type": "module", - "meta": { - "name": "bclconvert", - "description": "Demultiplex Illumina BCL files", - "keywords": [ - "demultiplex", - "illumina", - "fastq" - ], - "tools": [ - { - "bclconvert": { - "description": "Demultiplex Illumina BCL files", - "homepage": "https://support.illumina.com/sequencing/sequencing_software/bcl-convert.html", - "documentation": "https://support-docs.illumina.com/SW/BCL_Convert/Content/SW/FrontPages/BCL_Convert.htm", - "licence": [ - "ILLUMINA" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "samplesheet": { - "type": "file", - "description": "Input samplesheet", - "pattern": "*.{csv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } + ], + "output": { + "bed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "Grouped by bed file with combined features", + "pattern": "*.{bed}", + "ontologies": [] + } + } + ] + ], + "versions_bedtools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bedtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bedtools --version | sed -e 's/bedtools v//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bedtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bedtools --version | sed -e 's/bedtools v//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@mashehu"], + "maintainers": ["@mashehu"] }, - { - "run_dir": { - "type": "file", - "description": "Input run directory containing RunInfo.xml and BCL data\nCould be a directory or a tar of the directory\n", - "ontologies": [] - } - } - ] - ], - "output": { - "fastq": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "output/**_S[1-9]*_R?_00?.fastq.gz": { - "type": "file", - "description": "Demultiplexed sample FASTQ files", - "pattern": "**_S*_L00?_R?_00?.fastq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "fastq_idx": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "output/**_S[1-9]*_I?_00?.fastq.gz": { - "type": "file", - "description": "Optional demultiplexed index FASTQ files", - "pattern": "**_S*_L00?_I?_00?.fastq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "undetermined": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "output/**Undetermined_S0*_R?_00?.fastq.gz": { - "type": "file", - "description": "Optional undetermined sample FASTQ files", - "pattern": "Undetermined_S0_L00?_R?_00?.fastq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "undetermined_idx": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "output/**Undetermined_S0*_I?_00?.fastq.gz": { - "type": "file", - "description": "Optional undetermined index FASTQ files", - "pattern": "Undetermined_S0_L00?_I?_00?.fastq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "reports": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" + "pipelines": [ + { + "name": "circrna", + "version": "dev" } - }, - { - "output/Reports": { - "type": "file", - "description": "Demultiplexing Reports", - "pattern": "Reports", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - }, - { - "edam": "http://edamontology.org/format_2332" - }, - { - "edam": "http://edamontology.org/format_2333" - } - ] - } - } - ] - ], - "logs": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "output/Logs": { - "type": "file", - "description": "Demultiplexing Logs", - "pattern": "Logs", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2330" - } - ] - } - } ] - ], - "interop": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "output/InterOp/*.bin": { - "type": "file", - "description": "Interop files", - "pattern": "InterOp/*.bin", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2333" - } - ] - } - } - ] - ], - "versions_bclconvert": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bclconvert": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bcl-convert -V 2>&1 | head -n 1 | sed 's/^.*Version //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bclconvert": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bcl-convert -V 2>&1 | head -n 1 | sed 's/^.*Version //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@matthdsm" - ], - "maintainers": [ - "@matthdsm", - "@maxulysse" - ] - }, - "pipelines": [ - { - "name": "demultiplex", - "version": "1.7.1" - } - ] - }, - { - "name": "beagle5_beagle", - "path": "modules/nf-core/beagle5/beagle/meta.yml", - "type": "module", - "meta": { - "name": "beagle5_beagle", - "description": "Beagle v5.5 is a software package for phasing genotypes and for imputing ungenotyped markers.", - "keywords": [ - "phasing", - "imputation", - "genotype" - ], - "tools": [ - { - "beagle5": { - "description": "Beagle is a software package for phasing genotypes and for imputing ungenotyped markers.", - "homepage": "https://faculty.washington.edu/browning/beagle/beagle.html", - "documentation": "https://faculty.washington.edu/browning/beagle/beagle_5.5_17Dec24.pdf", - "doi": "10.1016/j.ajhg.2021.08.005; doi:10.1016/j.ajhg.2018.07.015", - "licence": [ - "GPL v3" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "target VCF input file to be imputed and or phased", - "pattern": "*.{vcf,vcf.gz}", - "ontologies": [] - } - }, - { - "vcf_index": { - "type": "file", - "description": "target VCF input file index", - "pattern": "*.{vcf,vcf.gz}.{tbi,csi}", - "ontologies": [] - } - }, - { - "refpanel": { - "type": "file", - 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"name": "ssds", - "version": "dev" - } - ] - }, - { - "name": "bedtools_closest", - "path": "modules/nf-core/bedtools/closest/meta.yml", - "type": "module", - "meta": { - "name": "bedtools_closest", - "description": "For each feature in A, finds the closest feature (upstream or downstream) in B.", - "keywords": [ - "bedtools", - "closest", - "bed", - "vcf", - "gff" - ], - "tools": [ - { - "bedtools": { - "description": "A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.\n", - "documentation": "https://bedtools.readthedocs.io/en/latest/content/tools/closest.html", - "licence": [ - "MIT" - ], - "identifier": "biotools:bedtools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input_1": { - "type": "file", - "description": "The file to find the closest features of", - "pattern": "*.{bed,vcf,gff}(.gz)?", - "ontologies": [] - } - }, - { - "input_2": { - "type": "list", - "description": "The input file(s) to find the closest features from", - "pattern": "*.{bed,vcf,gff}(.gz)?" - } - } - ], - { - "fasta_fai": { - "type": "file", - "description": "The index of the FASTA reference. Needed when the argument `--sorted` is used", - "pattern": "*.fai", - "ontologies": [] - } - } - ], - "output": { - "output": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.${extension}": { - "type": "file", - "description": "The resulting BED file containing the closest features", - "pattern": "*.{bed,vcf,gff}", - "ontologies": [] - } - } - ] - ], - "versions_bedtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bedtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bedtools --version | sed -e 's/bedtools v//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bedtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bedtools --version | sed -e 's/bedtools v//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@nvnieuwk" - ], - "maintainers": [ - "@nvnieuwk" - ] - } - }, - { - "name": "bedtools_complement", - "path": "modules/nf-core/bedtools/complement/meta.yml", - "type": "module", - "meta": { - "name": "bedtools_complement", - "description": "Returns all intervals in a genome that are not covered by at least one interval in the input BED/GFF/VCF file.", - "keywords": [ - "bed", - "gff", - "vcf", - "complement", - "bedtools", - "intervals" - ], - "tools": [ - { - "bedtools": { - "description": "A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.\n", - "documentation": "https://bedtools.readthedocs.io/en/latest/content/tools/complement.html", - "licence": [ - "MIT" - ], - "identifier": "biotools:bedtools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bed": { - "type": "file", - "description": "Input BED file", - "pattern": "*.{bed}", - "ontologies": [] - } - } - ], - { - "sizes": { - "type": "file", - "description": "File which defines the chromosome lengths for a given genome", - "pattern": "*.{sizes}", - "ontologies": [] - } - } - ], - "output": { - "bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bed": { - "type": "file", - "description": "Bed file with all genomic intervals that are not covered by at least one record from the input file.", - "pattern": "*.{bed}", - "ontologies": [] - } - } - ] - ], - "versions_bedtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bedtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bedtools --version | sed -e 's/bedtools v//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bedtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bedtools --version | sed -e 's/bedtools v//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@edmundmiller", - "@sruthipsuresh", - "@drpatelh" - ], - "maintainers": [ - "@edmundmiller", - "@sruthipsuresh", - "@drpatelh" - ] - }, - "pipelines": [ - { - "name": "cutandrun", - "version": "3.2.2" - }, - { - "name": "tfactivity", - "version": "dev" - } - ] - }, - { - "name": "bedtools_coverage", - "path": "modules/nf-core/bedtools/coverage/meta.yml", - "type": "module", - "meta": { - "name": "bedtools_coverage", - "description": "computes both the depth and breadth of coverage of features in file B on the features in file A", - "keywords": [ - "bedtools", - "coverage", - "bam", - "bed", - "gff", - "vcf", - "histogram" - ], - "tools": [ - { - "bedtools": { - "description": "A powerful toolset for genome arithmetic", - "homepage": "https://bedtools.readthedocs.io/en/latest/index.html", - "documentation": "https://bedtools.readthedocs.io/en/latest/content/bedtools-suite.html", - "tool_dev_url": "https://github.com/arq5x/bedtools2", - "doi": "10.1093/bioinformatics/btq033", - "licence": [ - "GPL v2", - "MIT" - ], - "identifier": "biotools:bedtools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input_A": { - "type": "file", - "description": "BAM/BED/GFF/VCF file", - "pattern": "*.{bam,bed,gff,vcf}", - "ontologies": [] - } - }, - { - "input_B": { - "type": "file", - "description": "One or more BAM/BED/GFF/VCF file", - "pattern": "*.{bam,bed,gff,vcf}", - "ontologies": [] - } - } - ], - { - "genome_file": { - "type": "file", - "description": "Optional reference genome 2 column file that defines the expected chromosome order\nin the input files for use with the -sorted option.\nWhen `genome_file` is provided, `-sorted` option is added to the command.\n", - "pattern": "*.{fai,txt,chromsizes}", - "ontologies": [] - } - } - ], - "output": { - "bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bed": { - "type": "file", - "description": "File containing coverage of sequence alignments", - "pattern": "*.bed", - "ontologies": [] - } - } - ] - ], - "versions_bedtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bedtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bedtools --version | sed -e 's/bedtools v//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bedtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bedtools --version | sed -e 's/bedtools v//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@priyanka-surana" - ], - "maintainers": [ - "@priyanka-surana" - ] - }, - "pipelines": [ - { - "name": "radseq", - "version": "dev" - } - ] - }, - { - "name": "bedtools_flank", - "path": "modules/nf-core/bedtools/flank/meta.yml", - "type": "module", - "meta": { - "name": "bedtools_flank", - "description": "Creates two new flanking intervals for each interval in a BED/GFF/VCF file.", - "keywords": [ - "bed", - "flankBed", - "bedtools" - ], - "tools": [ - { - "bedtools": { - "description": "A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.\n", - "documentation": "https://bedtools.readthedocs.io/en/latest/content/tools/slop.html", - "licence": [ - "MIT" - ], - "identifier": "biotools:bedtools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + "name": "bedtools_maskfasta", + "path": "modules/nf-core/bedtools/maskfasta/meta.yml", + "type": "module", + "meta": { + "name": "bedtools_maskfasta", + "description": "masks sequences in a FASTA file based on intervals defined in a feature file.", + "keywords": ["bed", "fasta", "maskfasta"], + "tools": [ + { + "bedtools": { + "description": "A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.\n", + "documentation": "https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html", + "licence": ["MIT"], + "identifier": "biotools:bedtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bed": { + "type": "file", + "description": "Bed feature file", + "pattern": "*.{bed}", + "ontologies": [] + } + } + ], + { + "fasta": { + "type": "file", + "description": "Input fasta file", + "pattern": "*.{fa,fasta}", + "ontologies": [] + } + } + ], + "output": { + "fasta": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fa": { + "type": "file", + "description": "Output masked fasta file", + "pattern": "*.{fa}", + "ontologies": [] + } + } + ] + ], + "versions_bedtools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bedtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bedtools --version | sed -e 's/bedtools v//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bedtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bedtools --version | sed -e 's/bedtools v//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@joseespinosa", "@drpatelh"], + "maintainers": ["@joseespinosa", "@drpatelh"] }, - { - "bed": { - "type": "file", - "description": "Input BED file", - "pattern": "*.{bed}", - "ontologies": [] - } - } - ], - { - "sizes": { - "type": "file", - "description": "Chromosome sizes file", - "ontologies": [] - } - } - ], - "output": { - "bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bed": { - "type": "file", - "description": "Flanked BED file", - "pattern": "*.{bed}", - "ontologies": [] - } - } - ] - ], - "versions_bedtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bedtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bedtools --version | sed -e 's/bedtools v//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bedtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bedtools --version | sed -e 's/bedtools v//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "callingcards", + "version": "1.0.0" + }, + { + "name": "viralmetagenome", + "version": "1.1.1" + }, + { + "name": "viralrecon", + "version": "3.0.0" + } ] - ] - }, - "authors": [ - "@itrujnara" - ], - "maintainers": [ - "@itrujnara" - ] - } - }, - { - "name": "bedtools_genomecov", - "path": "modules/nf-core/bedtools/genomecov/meta.yml", - "type": "module", - "meta": { - "name": "bedtools_genomecov", - "description": "Computes histograms (default), per-base reports (-d) and BEDGRAPH (-bg) summaries of feature coverage (e.g., aligned sequences) for a given genome.", - "keywords": [ - "bed", - "bam", - "genomecov", - "bedtools", - "histogram" - ], - "tools": [ - { - "bedtools": { - "description": "A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.\n", - "documentation": "https://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html", - "licence": [ - "MIT" - ], - "identifier": "biotools:bedtools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "intervals": { - "type": "file", - "description": "BAM/BED/GFF/VCF", - "pattern": "*.{bam|bed|gff|vcf}", - "ontologies": [] - } + }, + { + "name": "bedtools_merge", + "path": "modules/nf-core/bedtools/merge/meta.yml", + "type": "module", + "meta": { + "name": "bedtools_merge", + "description": "combines overlapping or “book-ended” features in an interval file into a single feature which spans all of the combined features.", + "keywords": ["bed", "merge", "bedtools", "overlapped bed"], + "tools": [ + { + "bedtools": { + "description": "A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.\n", + "documentation": "https://bedtools.readthedocs.io/en/latest/content/tools/merge.html", + "licence": ["MIT"], + "identifier": "biotools:bedtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bed": { + "type": "file", + "description": "Input BED file", + "pattern": "*.{bed}", + "ontologies": [] + } + } + ] + ], + "output": { + "bed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "Overlapped bed file with combined features", + "pattern": "*.{bed}", + "ontologies": [] + } + } + ] + ], + "versions_bedtools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bedtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bedtools --version | sed -e 's/bedtools v//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bedtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bedtools --version | sed -e 's/bedtools v//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@edmundmiller", "@sruthipsuresh", "@drpatelh"], + "maintainers": ["@edmundmiller", "@sruthipsuresh", "@drpatelh"] }, - { - "scale": { - "type": "integer", - "description": "Number containing the scale factor for the output. Set to 1 to disable. Setting to a value other than 1 will also get the -bg bedgraph output format as this is required for this command switch" - } - } - ], - { - "sizes": { - "type": "file", - "description": "Tab-delimited table of chromosome names in the first column and chromosome sizes in the second column", - "ontologies": [] - } - }, - { - "extension": { - "type": "string", - "description": "Extension of the output file (e. g., \".bg\", \".bedgraph\", \".txt\", \".tab\", etc.) It is set arbitrarily by the user and corresponds to the file format which depends on arguments." - } - }, - { - "sort": { - "type": "boolean", - "description": "Sort the output" - } - } - ], - "output": { - "genomecov": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.${extension}": { - "type": "file", - "description": "Computed genome coverage file", - "pattern": "*.${extension}", - "ontologies": [] - } - } - ] - ], - "versions_bedtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bedtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bedtools --version | sed -e 's/bedtools v//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bedtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bedtools --version | sed -e 's/bedtools v//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "cutandrun", + "version": "3.2.2" + }, + { + "name": "nascent", + "version": "2.3.0" + }, + { + "name": "radseq", + "version": "dev" + }, + { + "name": "rnavar", + "version": "1.2.3" + }, + { + "name": "tfactivity", + "version": "dev" + }, + { + "name": "variantbenchmarking", + "version": "1.5.0" + }, + { + "name": "viralmetagenome", + "version": "1.1.1" + }, + { + "name": "viralrecon", + "version": "3.0.0" + } ] - ] }, - "authors": [ - "@edmundmiller", - "@sruthipsuresh", - "@drpatelh", - "@sidorov-si", - "@chris-cheshire" - ], - "maintainers": [ - "@edmundmiller", - "@sruthipsuresh", - "@drpatelh", - "@sidorov-si", - "@chris-cheshire" - ] - }, - "pipelines": [ { - "name": "cutandrun", - "version": "3.2.2" + "name": "bedtools_multiinter", + "path": "modules/nf-core/bedtools/multiinter/meta.yml", + "type": "module", + "meta": { + "name": "bedtools_multiinter", + "description": "Identifies common intervals among multiple (and subsets thereof) sorted BED/GFF/VCF files.", + "keywords": ["bedtools", "multinterval", "bed", "vcf", "gff"], + "tools": [ + { + "bedtools": { + "description": "A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.\n", + "documentation": "https://bedtools.readthedocs.io/en/latest/content/tools/multiinter.html", + "licence": ["MIT"], + "identifier": "biotools:bedtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "beds": { + "type": "list", + "description": "List of files to be merged", + "pattern": "*.{bed,vcf,gff}" + } + } + ], + { + "chrom_sizes": { + "type": "file", + "description": "Chromosome sizes file", + "pattern": "*{.sizes,.txt}", + "ontologies": [] + } + } + ], + "output": { + "bed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "Common interval bed", + "pattern": "*.{bed}", + "ontologies": [] + } + } + ] + ], + "versions_bedtools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bedtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bedtools --version | sed -e 's/bedtools v//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bedtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bedtools --version | sed -e 's/bedtools v//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@matthdsm"], + "maintainers": ["@matthdsm"] + } }, { - "name": "hicar", - "version": "1.0.0" + "name": "bedtools_nuc", + "path": "modules/nf-core/bedtools/nuc/meta.yml", + "type": "module", + "meta": { + "name": "bedtools_nuc", + "description": "Profiles the nucleotide content of intervals in a fasta file.", + "keywords": [ + "bed", + "nucBed", + "bedtools", + "GC content", + "AT content", + "nucleotide content", + "intervals" + ], + "tools": [ + { + "bedtools": { + "description": "A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.", + "homepage": "https://bedtools.readthedocs.io", + "documentation": "https://bedtools.readthedocs.io/en/latest/content/tools/nuc.html", + "doi": "10.1093/bioinformatics/btq033", + "licence": ["MIT"], + "identifier": "biotools:bedtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Genome reference", + "pattern": "*.{fa,fasta}", + "ontologies": [] + } + }, + { + "intervals": { + "type": "file", + "description": "BED/GFF/VCF file of ranges to extract from -fi", + "pattern": "*.{bed,gff,vcf}", + "ontologies": [] + } + } + ] + ], + "output": { + "bed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "The following information will be reported after each BED entry: %AT content, %GC content, Number of As observed, Number of Cs observed, Number of Gs observed, Number of Ts observed, Number of Ns observed, Number of other bases observed, The length of the explored sequence/interval, The seq. extracted from the FASTA file. (opt., if -seq is used), The number of times a user's pattern was observed. (opt., if -pattern is used.)", + "pattern": "*.bed", + "ontologies": [] + } + } + ] + ], + "versions_bedtools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bedtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bedtools --version | sed -e 's/bedtools v//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bedtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bedtools --version | sed -e 's/bedtools v//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@lmfaber"], + "maintainers": ["@lmfaber"] + } }, { - "name": "nascent", - "version": "2.3.0" + "name": "bedtools_shift", + "path": "modules/nf-core/bedtools/shift/meta.yml", + "type": "module", + "meta": { + "name": "bedtools_shift", + "description": "Shifts each feature by specific number of bases", + "keywords": ["bed", "shiftBed", "region", "fai", "sizes", "genome", "bases"], + "tools": [ + { + "bedtools": { + "description": "A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.\n", + "documentation": "https://bedtools.readthedocs.io/en/latest/content/tools/slop.html", + "licence": ["MIT"], + "identifier": "biotools:bedtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bed": { + "type": "file", + "description": "Input BED file", + "pattern": "*.{bed}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "chrom_sizes": { + "type": "file", + "description": "Chromosome sizes file", + "pattern": "*{.sizes,.txt,.fai}", + "ontologies": [] + } + } + ] + ], + "output": { + "bed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "Shift BED file", + "pattern": "*.{bed}", + "ontologies": [] + } + } + ] + ], + "versions_bedtools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bedtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bedtools --version | sed -e 's/bedtools v//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bedtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bedtools --version | sed -e 's/bedtools v//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@ekushele"], + "maintainers": ["@ekushele"] + }, + "pipelines": [ + { + "name": "deepmodeloptim", + "version": "dev" + } + ] }, { - "name": "raredisease", - "version": "3.0.0" + "name": "bedtools_shuffle", + "path": "modules/nf-core/bedtools/shuffle/meta.yml", + "type": "module", + "meta": { + "name": "bedtools_shuffle", + "description": "bedtools shuffle will randomly permute the genomic locations of a feature file among a genome defined in a genome file", + "keywords": ["bed", "shuffleBed", "region", "fai", "sizes", "genome", "bases"], + "tools": [ + { + "bedtools": { + "description": "A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.\n", + "documentation": "https://bedtools.readthedocs.io/en/latest/content/tools/slop.html", + "licence": ["MIT"], + "identifier": "biotools:bedtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing interval information\ne.g. [ id:'test' ]\n" + } + }, + { + "intervals": { + "type": "file", + "description": "Input interval (BED/GFF/VCF) file", + "pattern": "*.{bed,gff,gff3,vcf}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3003" + }, + { + "edam": "http://edamontology.org/format_2305" + }, + { + "edam": "http://edamontology.org/format_3016" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing genome information\ne.g. [ id:'test' ]\n" + } + }, + { + "chrom_sizes": { + "type": "file", + "description": "Chromosome sizes file", + "pattern": "*{.genome,.sizes,.txt,.fai}", + "ontologies": [] + } + } + ], + { + "exclude_file": { + "type": "file", + "description": "BED file containing regions to exclude", + "pattern": "*.{bed}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3003" + } + ] + } + }, + { + "include_file": { + "type": "file", + "description": "BED file containing regions to include", + "pattern": "*.{bed}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3003" + } + ] + } + } + ], + "output": { + "bed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing interval information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "BED file with shuffled intervals", + "pattern": "*.{bed}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3003" + } + ] + } + } + ] + ], + "versions_bedtools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bedtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bedtools --version | sed -e 's/bedtools v//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bedtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bedtools --version | sed -e 's/bedtools v//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@itrujnara"], + "maintainers": ["@itrujnara"] + }, + "pipelines": [ + { + "name": "deepmodeloptim", + "version": "dev" + } + ] }, { - "name": "rnaseq", - "version": "3.26.0" - } - ] - }, - { - "name": "bedtools_getfasta", - "path": "modules/nf-core/bedtools/getfasta/meta.yml", - "type": "module", - "meta": { - "name": "bedtools_getfasta", - "description": "extract sequences in a FASTA file based on intervals defined in a feature file.", - "keywords": [ - "bed", - "fasta", - "getfasta" - ], - "tools": [ - { - "bedtools": { - "description": "A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.\n", - "documentation": "https://bedtools.readthedocs.io/en/latest/content/tools/getfasta.html", - "licence": [ - "MIT" - ], - "identifier": "biotools:bedtools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + "name": "bedtools_slop", + "path": "modules/nf-core/bedtools/slop/meta.yml", + "type": "module", + "meta": { + "name": "bedtools_slop", + "description": "Adds a specified number of bases in each direction (unique values may be specified for either -l or -r)", + "keywords": ["bed", "slopBed", "bedtools"], + "tools": [ + { + "bedtools": { + "description": "A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.\n", + "documentation": "https://bedtools.readthedocs.io/en/latest/content/tools/slop.html", + "licence": ["MIT"], + "identifier": "biotools:bedtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bed": { + "type": "file", + "description": "Input BED file", + "pattern": "*.{bed}", + "ontologies": [] + } + } + ], + { + "sizes": { + "type": "file", + "description": "Chromosome sizes file", + "ontologies": [] + } + } + ], + "output": { + "bed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "Slopped BED file", + "pattern": "*.{bed}", + "ontologies": [] + } + } + ] + ], + "versions_bedtools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bedtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bedtools --version | sed -e 's/bedtools v//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bedtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bedtools --version | sed -e 's/bedtools v//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@edmundmiller", "@sruthipsuresh", "@drpatelh"], + "maintainers": ["@edmundmiller", "@sruthipsuresh", "@drpatelh"] }, - { - "bed": { - "type": "file", - "description": "Bed feature file", - "pattern": "*.{bed}", - "ontologies": [] - } - } - ], - { - "fasta": { - "type": "file", - "description": "Input fasta file", - "pattern": "*.{fa,fasta}", - "ontologies": [] - } - } - ], - "output": { - "fasta": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.fa": { - "type": "file", - "description": "Output fasta file with extracted sequences", - "pattern": "*.{fa}", - "ontologies": [] - } - } - ] - ], - "versions_bedtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bedtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bedtools --version | sed -e 's/bedtools v//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bedtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bedtools --version | sed -e 's/bedtools v//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "deepmodeloptim", + "version": "dev" + }, + { + "name": "raredisease", + "version": "3.0.0" + }, + { + "name": "tfactivity", + "version": "dev" + } ] - ] }, - "authors": [ - "@joseespinosa", - "@drpatelh" - ], - "maintainers": [ - "@joseespinosa", - "@drpatelh" - ] - }, - "pipelines": [ { - "name": "circrna", - "version": "dev" + "name": "bedtools_sort", + "path": "modules/nf-core/bedtools/sort/meta.yml", + "type": "module", + "meta": { + "name": "bedtools_sort", + "description": "Sorts a feature file by chromosome and other criteria.", + "keywords": ["bed", "sort", "bedtools", "chromosome"], + "tools": [ + { + "bedtools": { + "description": "A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.\n", + "documentation": "https://bedtools.readthedocs.io/en/latest/content/tools/sort.html", + "licence": ["MIT"], + "identifier": "biotools:bedtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "intervals": { + "type": "file", + "description": "BED/BEDGRAPH", + "pattern": "*.{bed|bedGraph}", + "ontologies": [] + } + } + ], + { + "genome_file": { + "type": "file", + "description": "Optional reference genome 2 column file that defines the expected chromosome order.\n", + "pattern": "*.{fai,txt,chromsizes}", + "ontologies": [] + } + } + ], + "output": { + "sorted": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.${extension}": { + "type": "file", + "description": "Sorted output file", + "pattern": "*.${extension}", + "ontologies": [] + } + } + ] + ], + "versions_bedtools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bedtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bedtools --version | sed -e 's/bedtools v//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bedtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bedtools --version | sed -e 's/bedtools v//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@edmundmiller", "@sruthipsuresh", "@drpatelh", "@chris-cheshire", "@adamrtalbot"], + "maintainers": ["@edmundmiller", "@sruthipsuresh", "@drpatelh", "@chris-cheshire", "@adamrtalbot"] + }, + "pipelines": [ + { + "name": "circrna", + "version": "dev" + }, + { + "name": "hicar", + "version": "1.0.0" + }, + { + "name": "nascent", + "version": "2.3.0" + }, + { + "name": "radseq", + "version": "dev" + }, + { + "name": "rnavar", + "version": "1.2.3" + }, + { + "name": "ssds", + "version": "dev" + }, + { + "name": "tfactivity", + "version": "dev" + } + ] }, { - "name": "deepmodeloptim", - "version": "dev" + "name": "bedtools_split", + "path": "modules/nf-core/bedtools/split/meta.yml", + "type": "module", + "meta": { + "name": "bedtools_split", + "description": "Split BED files into several smaller BED files", + "keywords": ["bedtools", "split", "bed"], + "tools": [ + { + "bedtools": { + "description": "A powerful toolset for genome arithmetic", + "documentation": "https://bedtools.readthedocs.io/en/latest/content/tools/sort.html", + "licence": ["MIT", "GPL v2"], + "identifier": "biotools:bedtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bed": { + "type": "file", + "description": "BED file", + "pattern": "*.bed", + "ontologies": [] + } + }, + { + "count": { + "type": "integer", + "description": "Number of lines per split file" + } + } + ] + ], + "output": { + "beds": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed": { + "type": "list", + "description": "list of split BED files", + "pattern": "*.bed" + } + } + ] + ], + "versions_bedtools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bedtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bedtools --version | sed -e 's/bedtools v//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bedtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bedtools --version | sed -e 's/bedtools v//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@nvnieuwk"], + "maintainers": ["@nvnieuwk"] + } }, { - "name": "readsimulator", - "version": "1.0.1" + "name": "bedtools_subtract", + "path": "modules/nf-core/bedtools/subtract/meta.yml", + "type": "module", + "meta": { + "name": "bedtools_subtract", + "description": "Finds overlaps between two sets of regions (A and B), removes the overlaps from A and reports the remaining portion of A.", + "keywords": ["bed", "gff", "vcf", "subtract"], + "tools": [ + { + "bedtools": { + "description": "A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.\n", + "documentation": "https://bedtools.readthedocs.io/en/latest/content/tools/subtract.html", + "licence": ["MIT"], + "identifier": "biotools:bedtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "intervals1": { + "type": "file", + "description": "BED/GFF/VCF", + "pattern": "*.{bed|gff|vcf}", + "ontologies": [] + } + }, + { + "intervals2": { + "type": "file", + "description": "BED/GFF/VCF", + "pattern": "*.{bed|gff|vcf}", + "ontologies": [] + } + } + ] + ], + "output": { + "bed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "File containing the difference between the two sets of features", + "patters": "*.bed", + "ontologies": [] + } + } + ] + ], + "versions_bedtools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bedtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bedtools --version | sed -e 's/bedtools v//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bedtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bedtools --version | sed -e 's/bedtools v//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@sidorov-si"], + "maintainers": ["@sidorov-si"] + }, + "pipelines": [ + { + "name": "deepmodeloptim", + "version": "dev" + }, + { + "name": "tfactivity", + "version": "dev" + } + ] }, { - "name": "tfactivity", - "version": "dev" + "name": "bedtools_unionbedg", + "path": "modules/nf-core/bedtools/unionbedg/meta.yml", + "type": "module", + "meta": { + "name": "bedtools_unionbedg", + "description": "Combines multiple BedGraph files into a single file", + "keywords": ["bed", "unionBedGraphs", "bedGraph", "comparisons", "combine"], + "tools": [ + { + "bedtools": { + "description": "A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.\n", + "documentation": "https://bedtools.readthedocs.io/en/latest/content/tools/slop.html", + "licence": ["MIT"], + "identifier": "biotools:bedtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bedgraph": { + "type": "file", + "description": "Input BedGraph file: four column BED format, with 4th column with numerical values: integer or real, positive or negative\n", + "pattern": "*.{bedGraph,bedgraph}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing meta information for the reference chromosome sizes\ne.g. [ id:'test' ]\n" + } + }, + { + "chrom_sizes": { + "type": "file", + "description": "Chromosome sizes file", + "pattern": "*{.sizes,.txt}", + "ontologies": [] + } + } + ] + ], + "output": { + "bed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "Combined BED file with values from all bedGraph files", + "pattern": "*.{bed}", + "ontologies": [] + } + } + ] + ], + "versions_bedtools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bedtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bedtools --version | sed -e 's/bedtools v//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bedtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bedtools --version | sed -e 's/bedtools v//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@ekushele"], + "maintainers": ["@ekushele"] + } }, { - "name": "viralrecon", - "version": "3.0.0" - } - ] - }, - { - "name": "bedtools_groupby", - "path": "modules/nf-core/bedtools/groupby/meta.yml", - "type": "module", - "meta": { - "name": "bedtools_groupby", - "description": "Groups features in a BED file by given column(s) and computes summary statistics for each group to another column.", - "keywords": [ - "bed", - "groupby", - "bedtools" - ], - "tools": [ - { - "bedtools": { - "description": "A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.\n", - "documentation": "https://bedtools.readthedocs.io/en/latest/content/tools/groupby.html", - "homepage": "https://bedtools.readthedocs.io/en/latest/", - "doi": "10.1093/bioinformatics/btq033", - "licence": [ - "MIT" - ], - "identifier": "biotools:bedtools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "bed": { - "type": "file", - "description": "Input BED file", - "pattern": "*.{bed}", - "ontologies": [] - } - } - ], - { - "summary_col": { - "type": "string", - "description": "Column to summarize" - } - } - ], - "output": { - "bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*.bed": { - "type": "file", - "description": "Grouped by bed file with combined features", - "pattern": "*.{bed}", - "ontologies": [] - } - } - ] - ], - "versions_bedtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bedtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bedtools --version | sed -e 's/bedtools v//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bedtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bedtools --version | sed -e 's/bedtools v//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@mashehu" - ], - "maintainers": [ - "@mashehu" - ] - }, - "pipelines": [ - { - "name": "circrna", - "version": "dev" - } - ] - }, - { - "name": "bedtools_intersect", - "path": "modules/nf-core/bedtools/intersect/meta.yml", - "type": "module", - "meta": { - "name": "bedtools_intersect", - "description": "Allows one to screen for overlaps between two sets of genomic features.", - "keywords": [ - "bed", - "intersect", - "overlap" - ], - "tools": [ - { - "bedtools": { - "description": "A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.\n", - "documentation": "https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html", - "licence": [ - "MIT" - ], - "identifier": "biotools:bedtools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "intervals1": { - "type": "file", - "description": "BAM/BED/GFF/VCF", - "pattern": "*.{bam|bed|gff|vcf}", - "ontologies": [] - } - }, - { - "intervals2": { - "type": "file", - "description": "BAM/BED/GFF/VCF", - "pattern": "*.{bam|bed|gff|vcf}", - "ontologies": [] - } + "name": "bff", + "path": "modules/nf-core/bff/meta.yml", + "type": "module", + "meta": { + "name": "bff", + "description": "Generating cell hashing calls from a matrix of count data.", + "keywords": ["demultiplexing", "hashing-based deconvolution", "single-cell"], + "tools": [ + { + "bff": { + "description": "A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) , Macosko E, Basu A, Satija R, et al (2015) , and Butler A and Satija R (2017) for more details.", + "homepage": "https://rdrr.io/github/BimberLab/cellhashR/man/GenerateCellHashingCalls.html", + "documentation": "https://rdrr.io/github/BimberLab/cellhashR/man/GenerateCellHashingCalls.html", + "tool_dev_url": "https://github.com/BimberLab/cellhashR", + "doi": "10.5281/zenodo.6402477", + "licence": ["GPL-3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "hto_matrix": { + "type": "file", + "description": "Directory that contains the HTO matrix in a 10X format.\n", + "ontologies": [ + { + "edam": "http://edamontology.org/data_3917" + } + ] + } + }, + { + "methods": { + "type": "string", + "description": "Decides whether 'RAW', 'CLUSTER' OR 'COMBINED' should be selected as the call method.\n" + } + }, + { + "preprocessing": { + "type": "string", + "description": "Decides whether the HTO matrix should undergo a preprocessing step ('TRUE') or not ('FALSE').\n" + } + } + ] + ], + "output": { + "assignment": [ + [ + { + "meta": { + "type": "file", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n", + "ontologies": [] + } + }, + { + "*_assignment_bff.csv": { + "type": "file", + "description": "Contains the assignment results of demultiplexing.", + "pattern": "assignment_bff.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "metrics": [ + [ + { + "meta": { + "type": "file", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n", + "ontologies": [] + } + }, + { + "*_metrics_bff.csv": { + "type": "file", + "description": "Summary metrics will be written to this file.", + "pattern": "_metrics_bff.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "params": [ + [ + { + "meta": { + "type": "file", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n", + "ontologies": [] + } + }, + { + "*_params_bff.csv": { + "type": "file", + "description": "The used parameters to call HTODemux in the R-Script.", + "pattern": "params_htodemux.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "versions_bff": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions.", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "topics": { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions.", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@LuisHeinzlmeier"], + "maintainers": ["@LuisHeinzlmeier"] } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference chromosome sizes\ne.g. [ id:'test' ]\n" - } + }, + { + "name": "bftools_showinf", + "path": "modules/nf-core/bftools/showinf/meta.yml", + "type": "module", + "meta": { + "name": "bftools_showinf", + "description": "Extract OME xml data from OME-tif", + "keywords": ["metadata", "ome-tif", "ome-tiff", "imaging", "bioinformatics tools"], + "tools": [ + { + "bftools": { + "description": "Suite of tools to handle several imaging protocols.", + "homepage": "https://www.openmicroscopy.org/bio-formats", + "documentation": "https://bio-formats.readthedocs.io/en/stable/users/index.html", + "tool_dev_url": "https://github.com/ome/bioformats", + "doi": "10.1083/jcb.201004104", + "licence": ["GNU General Public License v2.0"], + "identifier": "biotools:bio-formats" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "image": { + "type": "file", + "description": "Path to image file containing OME metadata", + "ontologies": [] + } + } + ] + ], + "output": { + "xml": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.xml.gz": { + "type": "file", + "description": "Compressed XML with OME tag metadata", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2332" + } + ] + } + } + ] + ], + "versions_bftools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bftools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "showinf -version | sed -n '1s/[^ ]* //p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bftools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "showinf -version | sed -n '1s/[^ ]* //p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@AlexBarbera"], + "maintainers": ["@AlexBarbera"] }, - { - "chrom_sizes": { - "type": "file", - "description": "Chromosome sizes file", - "pattern": "*{.sizes,.txt}", - "ontologies": [] - } - } - ] - ], - "output": { - "intersect": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.${extension}": { - "type": "file", - "description": "File containing the description of overlaps found between the two features", - "pattern": "*.${extension}", - "ontologies": [] - } - } - ] - ], - "versions_bedtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bedtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bedtools --version | sed -e 's/bedtools v//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bedtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bedtools --version | sed -e 's/bedtools v//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "mcmicro", + "version": "dev" + } ] - ] }, - "authors": [ - "@edmundmiller", - "@sruthipsuresh", - "@drpatelh", - "@sidorov-si" - ], - "maintainers": [ - "@edmundmiller", - "@sruthipsuresh", - "@drpatelh", - "@sidorov-si" - ] - }, - "pipelines": [ { - "name": "circrna", - "version": "dev" + "name": "bigslice", + "path": "modules/nf-core/bigslice/meta.yml", + "type": "module", + "meta": { + "name": "bigslice", + "description": "A scalable tool for large-scale analysis of Biosynthetic Gene Clusters (BGCs).\nIt takes genome regions in GenBank format along with an HMM database and produces a SQLite database and FASTA outputs of predicted features.\n", + "keywords": ["biosynthetic gene clusters", "genomics", "analysis"], + "tools": [ + { + "bigslice": { + "description": "A highly scalable, user-interactive tool for the large scale analysis of Biosynthetic Gene Clusters data", + "homepage": "https://github.com/medema-group/bigslice", + "documentation": "https://github.com/medema-group/bigslice", + "tool_dev_url": "https://github.com/medema-group/bigslice", + "doi": "10.1093/gigascience/giaa154", + "licence": ["AGPL v3-or-later"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "bgc": { + "type": "file", + "description": "List of GenBank (.gbk) files containing genomic region annotations for BiG-SLiCE input.\nEach file represents a BGC region. The module internally organises them into the required\nBiG-SLiCE input folder structure (datasets.tsv and taxonomy TSV).\n", + "pattern": "*.gbk", + "ontologies": [] + } + } + ], + { + "hmmdb": { + "type": "directory", + "description": "Path to the BiG-SLiCE HMM database folder containing biosynthetic and sub Pfams for annotation, in the required BiG-SLiCE format.\nAn example directory in compressed archive format can be found here: https://github.com/medema-group/bigslice/releases/download/v2.0.0rc/bigslice-models.2022-11-30.tar.gz\n" + } + }, + { + "export_tsv": { + "type": "boolean", + "description": "If true, runs a second BiG-SLiCE invocation to export all results from the SQLite database\nto TSV files under `tsv_export/`. Additional arguments for this step can be passed via `task.ext.args2`.\n" + } + } + ], + "output": { + "output": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample/dataset information" + } + }, + { + "${prefix}/result": { + "type": "directory", + "description": "BiG-SLiCE result directory containing the SQLite database (`data.db`),\npredicted feature FASTA files (`tmp/**/*.fa`), and optionally TSV exports\n(`tsv_export/`) when `export_tsv` is `true`.\n", + "pattern": "result" + } + } + ] + ], + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample/dataset information" + } + }, + { + "${prefix}/result/tsv_export": { + "type": "directory", + "description": "Directory containing TSV exports of all parsed BGC metadata, vectorized\nfeatures and clustering results. Only present when `export_tsv` input is\nset to `true`.\n", + "pattern": "tsv_export" + } + } + ] + ], + "versions_bigslice": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bigslice": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "2.0.2": { + "type": "string", + "description": "The version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bigslice": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "2.0.2": { + "type": "string", + "description": "The version of the tool" + } + } + ] + ] + }, + "authors": ["@vagkaratzas", "@SkyLex"], + "maintainers": ["@vagkaratzas", "@SkyLex"] + } }, { - "name": "cutandrun", - "version": "3.2.2" + "name": "bigslice_bigslice", + "path": "modules/nf-core/bigslice/bigslice/meta.yml", + "type": "module", + "meta": { + "name": "bigslice_bigslice", + "description": "A scalable tool for large-scale analysis of Biosynthetic Gene Clusters (BGCs).\nIt takes genome regions in GenBank format along with an HMM database and produces a SQLite database and FASTA outputs of predicted features.\n", + "keywords": ["biosynthetic gene clusters", "genomics", "analysis"], + "tools": [ + { + "bigslice": { + "description": "A highly scalable, user-interactive tool for the large scale analysis of Biosynthetic Gene Clusters data", + "homepage": "https://github.com/medema-group/bigslice", + "documentation": "https://github.com/medema-group/bigslice", + "tool_dev_url": "https://github.com/medema-group/bigslice", + "doi": "10.1093/gigascience/giaa154", + "licence": ["AGPL v3-or-later"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "bgc": { + "type": "file", + "description": "List of GenBank (.gbk) files containing genomic region annotations for BiG-SLiCE input.\nEach file represents a BGC region. The module internally organises them into the required\nBiG-SLiCE input folder structure (datasets.tsv and taxonomy TSV).\n", + "pattern": "*.gbk", + "ontologies": [] + } + } + ], + { + "hmmdb": { + "type": "directory", + "description": "Path to the BiG-SLiCE HMM database folder containing biosynthetic and sub Pfams for annotation, in the required BiG-SLiCE format.\nAn example directory in compressed archive format can be found here: https://github.com/medema-group/bigslice/releases/download/v2.0.0rc/bigslice-models.2022-11-30.tar.gz\n" + } + }, + { + "export_tsv": { + "type": "boolean", + "description": "If true, runs a second BiG-SLiCE invocation to export all results from the SQLite database\nto TSV files under `tsv_export/`. Additional arguments for this step can be passed via `task.ext.args2`.\n" + } + } + ], + "output": { + "output": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample/dataset information" + } + }, + { + "${prefix}/result": { + "type": "directory", + "description": "BiG-SLiCE result directory containing the SQLite database (`data.db`),\npredicted feature FASTA files (`tmp/**/*.fa`), and optionally TSV exports\n(`tsv_export/`) when `export_tsv` is `true`.\n", + "pattern": "result" + } + } + ] + ], + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample/dataset information" + } + }, + { + "${prefix}/result/tsv_export": { + "type": "directory", + "description": "Directory containing TSV exports of all parsed BGC metadata, vectorized\nfeatures and clustering results. Only present when `export_tsv` input is\nset to `true`.\n", + "pattern": "tsv_export" + } + } + ] + ], + "versions_bigslice": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bigslice": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "2.0.2": { + "type": "string", + "description": "The version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bigslice": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "2.0.2": { + "type": "string", + "description": "The version of the tool" + } + } + ] + ] + }, + "authors": ["@vagkaratzas", "@SkyLex"], + "maintainers": ["@vagkaratzas", "@SkyLex"] + } }, { - "name": "methylseq", - "version": "4.2.0" + "name": "bigslice_downloaddb", + "path": "modules/nf-core/bigslice/downloaddb/meta.yml", + "type": "module", + "meta": { + "name": "bigslice_downloaddb", + "description": "Downloads and extracts the BiG-SLiCE HMM database (biosynthetic and sub Pfams)\nusing the bundled `download_bigslice_hmmdb` script shipped with BiG-SLiCE.\nThe resulting directory can be passed directly as the `hmmdb` input to the\n`BIGSLICE` module.\n", + "keywords": ["biosynthetic gene clusters", "genomics", "database", "download"], + "tools": [ + { + "bigslice": { + "description": "A highly scalable, user-interactive tool for the large scale analysis of Biosynthetic Gene Clusters data", + "homepage": "https://github.com/medema-group/bigslice", + "documentation": "https://github.com/medema-group/bigslice", + "tool_dev_url": "https://github.com/medema-group/bigslice", + "doi": "10.1093/gigascience/giaa154", + "licence": ["AGPL v3-or-later"], + "identifier": "" + } + } + ], + "input": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. `[ id:'test' ]`" + } + } + ], + "output": { + "db": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. `[ id:'test' ]`" + } + }, + { + "bigslice-models": { + "type": "directory", + "description": "Downloaded and extracted BiG-SLiCE HMM database directory containing biosynthetic Pfam HMMs and sub-Pfam profiles. Pass this directly as `hmmdb` to the `BIGSLICE` module.", + "pattern": "bigslice-models" + } + } + ] + ], + "versions_bigslice": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bigslice": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "2.0.2": { + "type": "string", + "description": "The version of the tool" + } + } + ] + ], + "versions_python": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "python": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python --version | sed 's/Python //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bigslice": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "2.0.2": { + "type": "string", + "description": "The version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "python": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python --version | sed 's/Python //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@vagkaratzas", "@SkyLex"], + "maintainers": ["@vagkaratzas", "@SkyLex"] + } }, { - "name": "nascent", - "version": "2.3.0" + "name": "bio2zarr_vcf2zarrconvert", + "path": "modules/nf-core/bio2zarr/vcf2zarrconvert/meta.yml", + "type": "module", + "meta": { + "name": "bio2zarr_vcf2zarrconvert", + "description": "Convert VCF data to the VCF Zarr specification reliably, in parallel or distributed over a cluster.", + "keywords": ["vcf", "zarr", "convert", "genomics"], + "tools": [ + { + "vcf2zarr": { + "description": "Convert bioinformatics data to Zarr", + "homepage": "https://sgkit-dev.github.io/bio2zarr/vcf2zarr/overview.html", + "documentation": "https://sgkit-dev.github.io/bio2zarr/", + "tool_dev_url": "https://github.com/sgkit-dev/bio2zarr", + "doi": "10.1101/2024.06.11.598241", + "licence": ["Apache-2.0"], + "identifier": "biotools:bio2zarr" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "vcf": { + "type": "file", + "description": "Input VCF/BCF file to convert", + "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + }, + { + "edam": "http://edamontology.org/format_3020" + } + ] + } + } + ] + ], + "output": { + "vcz": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.vcz": { + "type": "directory", + "description": "Output VCF Zarr store directory", + "pattern": "*.vcz", + "ontologies": [] + } + } + ] + ], + "versions_vcf2zarr": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "vcf2zarr": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "vcf2zarr --version |& sed -n \"s/.* //p\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "vcf2zarr": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "vcf2zarr --version |& sed -n \"s/.* //p\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@camlloyd"], + "maintainers": ["@camlloyd"] + } }, { - "name": "radseq", - "version": "dev" + "name": "bio2zarr_vcf2zarrexplode", + "path": "modules/nf-core/bio2zarr/vcf2zarrexplode/meta.yml", + "type": "module", + "meta": { + "name": "bio2zarr_vcf2zarrexplode", + "description": "Convert VCF(s) to intermediate columnar format (ICF)", + "keywords": ["vcf", "icf", "zarr", "convert", "genomics"], + "tools": [ + { + "vcf2zarr": { + "description": "Convert bioinformatics data to Zarr", + "homepage": "https://sgkit-dev.github.io/bio2zarr/vcf2zarr/overview.html", + "documentation": "https://sgkit-dev.github.io/bio2zarr/", + "tool_dev_url": "https://github.com/sgkit-dev/bio2zarr", + "doi": "10.1101/2024.06.11.598241", + "licence": ["Apache-2.0"], + "identifier": "biotools:bio2zarr" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "vcf": { + "type": "file", + "description": "Input VCF/BCF file(s)", + "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + } + ] + } + } + ] + ], + "output": { + "icf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.icf": { + "type": "directory", + "description": "Intermediate columnar format (ICF) directory produced by vcf2zarr explode", + "pattern": "*.icf", + "ontologies": [] + } + } + ] + ], + "versions_vcf2zarr": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "vcf2zarr": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "vcf2zarr --version |& sed -n \"s/.* //p\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "vcf2zarr": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "vcf2zarr --version |& sed -n \"s/.* //p\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@camlloyd"], + "maintainers": ["@camlloyd"] + } }, { - "name": "sammyseq", - "version": "dev" + "name": "bio2zarr_vcfpartition", + "path": "modules/nf-core/bio2zarr/vcfpartition/meta.yml", + "type": "module", + "meta": { + "name": "bio2zarr_vcfpartition", + "description": "Outputs a set of region strings that partition indexed VCF/BCF files for parallel processing.", + "keywords": ["vcf", "bcf", "partition", "regions", "parallel", "genomics"], + "tools": [ + { + "bio2zarr": { + "description": "Convert bioinformatics data to Zarr", + "homepage": "https://sgkit-dev.github.io/bio2zarr/", + "documentation": "https://sgkit-dev.github.io/bio2zarr", + "tool_dev_url": "https://github.com/sgkit-dev/bio2zarr", + "doi": "10.1101/2024.06.11.598241", + "licence": ["Apache-2.0"], + "identifier": "biotools:bio2zarr" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "vcf": { + "type": "file", + "description": "Indexed VCF/BCF file to partition", + "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + }, + { + "edam": "http://edamontology.org/format_3020" + } + ] + } + }, + { + "index": { + "type": "file", + "description": "Index for the VCF/BCF file", + "pattern": "*.{tbi,csi}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3700" + } + ] + } + } + ] + ], + "output": { + "partitions": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "The output tab-delimited region strings and the file path", + "pattern": "*.{tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_vcfpartition": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "vcfpartition": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "vcfpartition --version | sed 's/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "vcfpartition": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "vcfpartition --version | sed 's/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@camlloyd"], + "maintainers": ["@camlloyd"] + } }, { - "name": "tfactivity", - "version": "dev" - } - ] - }, - { - "name": "bedtools_jaccard", - "path": "modules/nf-core/bedtools/jaccard/meta.yml", - "type": "module", - "meta": { - "name": "bedtools_jaccard", - "description": "Calculate Jaccard statistic b/w two feature files.", - "keywords": [ - "vcf", - "gff", - "bed", - "jaccard", - "intersection", - "union", - "statistics" - ], - "tools": [ - { - "bedtools": { - "description": "A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.\n", - "documentation": "https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html", - "licence": [ - "MIT" - ], - "identifier": "biotools:bedtools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input_a": { - "type": "file", - "description": "VCF,GFF or BED file to use with the `-a` option", - "pattern": "*.{vcf,vcf.gz,bed,bed.gz,gff}", - "ontologies": [] - } - }, - { - "input_b": { - "type": "file", - "description": "VCF,GFF or BED file to use with the `-b` option", - "pattern": "*.{vcf,vcf.gz,bed,bed.gz,gff}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing genome file information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "genome_file": { - "type": "file", - "description": "A file containing all the contigs of the genome used to create the input files", - "pattern": "*.{txt,sizes,fai}", - "ontologies": [] - } - } - ] - ], - "output": { - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "TSV file containing the results", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_bedtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bedtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bedtools --version | sed -e 's/bedtools v//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bedtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bedtools --version | sed -e 's/bedtools v//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@nvnieuwk" - ], - "maintainers": [ - "@nvnieuwk" - ] - } - }, - { - "name": "bedtools_makewindows", - "path": "modules/nf-core/bedtools/makewindows/meta.yml", - "type": "module", - "meta": { - "name": "bedtools_makewindows", - "description": "Makes adjacent or sliding windows across a genome or BED file.", - "keywords": [ - "bed", - "windows", - "fai", - "chunking" - ], - "tools": [ - { - "bedtools": { - "description": "A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.", - "homepage": "https://bedtools.readthedocs.io", - "documentation": "https://bedtools.readthedocs.io/en/latest/content/tools/makewindows.html", - "doi": "10.1093/bioinformatics/btq033", - "licence": [ - "MIT" - ], - "identifier": "biotools:bedtools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + "name": "bioawk", + "path": "modules/nf-core/bioawk/meta.yml", + "type": "module", + "meta": { + "name": "bioawk", + "description": "Bioawk is an extension to Brian Kernighan's awk, adding the support of several common biological data formats.", + "keywords": ["bioawk", "fastq", "fasta", "sam", "file manipulation", "awk"], + "tools": [ + { + "bioawk": { + "description": "BWK awk modified for biological data", + "homepage": "https://github.com/lh3/bioawk", + "documentation": "https://github.com/lh3/bioawk", + "tool_dev_url": "https://github.com/lh3/bioawk", + "licence": [ + "Free software license (https://github.com/lh3/bioawk/blob/master/README.awk#L1)" + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "Input biological sequence file (optionally gzipped) to be manipulated via the program specified in `$args`.\n", + "pattern": "*.{bed,gff,sam,vcf,fastq,fasta,tab,bed.gz,gff.gz,sam.gz,vcf.gz,fastq.gz,fasta.gz,tab.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3003" + }, + { + "edam": "http://edamontology.org/format_3016" + }, + { + "edam": "http://edamontology.org/format_3989" + }, + { + "edam": "http://edamontology.org/format_1975" + }, + { + "edam": "http://edamontology.org/format_1929" + }, + { + "edam": "http://edamontology.org/format_1930" + }, + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + { + "program_file": { + "type": "file", + "description": "Optional file containing logic for awk to execute. If you don't wish to use a file, you can use `ext.args2` to specify the logic.", + "pattern": "*", + "ontologies": [ + { + "edam": "http://edamontology.org/data_3671" + } + ] + } + }, + { + "disable_redirect_output": { + "type": "boolean", + "description": "Disable the redirection of awk output to a given file. This is\nuseful if you want to use awk's built-in redirect to write files instead\nof the shell's redirect.\n" + } + }, + { + "output_file_extension": { + "type": "string", + "description": "The suffix to add to the output file name." + } + } + ], + "output": { + "output": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.${output_file_extension}": { + "type": "file", + "description": "Manipulated version of the input sequence file.", + "ontologies": [] + } + } + ] + ], + "versions_bioawk": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bioawk": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "1.0": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bioawk": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "1.0": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@jfy133"], + "maintainers": ["@jfy133"], + "schema_version": "1.1.0" }, - { - "regions": { - "type": "file", - "description": "BED file OR Genome details file ()", - "pattern": "*.{bed,tab,fai}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "output": { - "bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bed": { - "type": "file", - "description": "BED file containing the windows", - "pattern": "*.bed", - "ontologies": [] - } - } - ] - ], - "versions_bedtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bedtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bedtools --version | sed -e 's/bedtools v//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bedtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bedtools --version | sed -e 's/bedtools v//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "circrna", + "version": "dev" + }, + { + "name": "rnafusion", + "version": "4.1.2" + }, + { + "name": "smrnaseq", + "version": "2.4.1" + } ] - ] }, - "authors": [ - "@kevbrick", - "@nvnieuwk" - ], - "maintainers": [ - "@kevbrick", - "@nvnieuwk" - ] - }, - "pipelines": [ { - "name": "phaseimpute", - "version": "1.1.0" + "name": "biobambam_bammarkduplicates2", + "path": "modules/nf-core/biobambam/bammarkduplicates2/meta.yml", + "type": "module", + "meta": { + "name": "biobambam_bammarkduplicates2", + "description": "Locate and tag duplicate reads in a BAM file", + "keywords": ["markduplicates", "bam", "cram"], + "tools": [ + { + "biobambam": { + "description": "biobambam is a set of tools for early stage alignment file processing.\n", + "homepage": "https://gitlab.com/german.tischler/biobambam2", + "documentation": "https://gitlab.com/german.tischler/biobambam2/-/blob/master/README.md", + "doi": "10.1186/1751-0473-9-13", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM file", + "pattern": "*.{bam,cram}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + }, + { + "edam": "http://edamontology.org/format_2573" + } + ] + } + } + ] + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "BAM file with duplicate reads marked/removed", + "pattern": "*.{bam}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + } + ] + ], + "metrics": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.metrics.txt": { + "type": "file", + "description": "Duplicate metrics file generated by biobambam", + "pattern": "*.{metrics.txt}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3673" + } + ] + } + } + ] + ], + "versions_biobambam": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "biobambam": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bammarkduplicates2 --version |& sed '1!d; s/.*version //; s/.\\$//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "biobambam": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bammarkduplicates2 --version |& sed '1!d; s/.*version //; s/.\\$//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@muffato"], + "maintainers": ["@muffato"] + } }, { - "name": "radseq", - "version": "dev" + "name": "biobambam_bammerge", + "path": "modules/nf-core/biobambam/bammerge/meta.yml", + "type": "module", + "meta": { + "name": "biobambam_bammerge", + "description": "Merge a list of sorted bam files", + "keywords": ["merge", "bam", "sorted"], + "tools": [ + { + "biobambam": { + "description": "biobambam is a set of tools for early stage alignment file processing.\n", + "homepage": "https://gitlab.com/german.tischler/biobambam2", + "documentation": "https://gitlab.com/german.tischler/biobambam2/-/blob/master/README.md", + "doi": "10.1186/1751-0473-9-13", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "List containing 1 or more bam files", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + } + ] + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.bam": { + "type": "file", + "description": "Merged BAM file", + "pattern": "*.bam", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + } + ] + ], + "bam_index": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bai": { + "type": "file", + "description": "BAM index file", + "pattern": "*.bai", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2573" + } + ] + } + } + ] + ], + "checksum": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.md5": { + "type": "file", + "description": "Checksum file", + "pattern": "*.md5", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + } + ] + ], + "versions_biobambam": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "biobambam": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bammerge --version |& sed '1!d; s/.*version //; s/.\\$//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "biobambam": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bammerge --version |& sed '1!d; s/.*version //; s/.\\$//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@matthdsm"], + "maintainers": ["@matthdsm"] + } }, { - "name": "sammyseq", - "version": "dev" + "name": "biobambam_bamsormadup", + "path": "modules/nf-core/biobambam/bamsormadup/meta.yml", + "type": "module", + "meta": { + "name": "biobambam_bamsormadup", + "description": "Parallel sorting and duplicate marking", + "keywords": ["markduplicates", "sort", "bam", "cram"], + "tools": [ + { + "biobambam": { + "description": "biobambam is a set of tools for early stage alignment file processing.\n", + "homepage": "https://gitlab.com/german.tischler/biobambam2", + "documentation": "https://gitlab.com/german.tischler/biobambam2/-/blob/master/README.md", + "doi": "10.1186/1751-0473-9-13", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bams": { + "type": "file", + "description": "List containing 1 or more bam files", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing genome information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference genome in FASTA format (optional)", + "pattern": "*.{fa,fasta,fna}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + }, + { + "fai": { + "type": "file", + "description": "Reference genome in FASTA index format (optional)", + "pattern": "*.{fai}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3673" + } + ] + } + } + ] + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "BAM file with duplicate reads marked/removed", + "pattern": "*.bam", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + } + ] + ], + "bam_index": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam.bai": { + "type": "file", + "description": "BAM index file", + "pattern": "*.bai", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3692" + } + ] + } + } + ] + ], + "cram": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.cram": { + "type": "file", + "description": "CRAM file with duplicate reads marked/removed", + "pattern": "*.cram", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3674" + } + ] + } + } + ] + ], + "metrics": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.metrics.txt": { + "type": "file", + "description": "Duplicate metrics file generated by biobambam", + "pattern": "*.{metrics.txt}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3675" + } + ] + } + } + ] + ], + "versions_biobambam": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "biobambam": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bamsormadup --version |& sed '1!d; s/.*version //; s/.\\$//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "biobambam": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bamsormadup --version |& sed '1!d; s/.*version //; s/.\\$//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@matthdsm"], + "maintainers": ["@matthdsm"] + } }, { - "name": "ssds", - "version": "dev" - } - ] - }, - { - "name": "bedtools_map", - "path": "modules/nf-core/bedtools/map/meta.yml", - "type": "module", - "meta": { - "name": "bedtools_map", - "description": "Allows one to screen for overlaps between two sets of genomic features.", - "keywords": [ - "bed", - "vcf", - "gff", - "map", - "bedtools" - ], - "tools": [ - { - "bedtools": { - "description": "A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.\n", - "documentation": "https://bedtools.readthedocs.io/en/latest/content/tools/map.html", - "licence": [ - "MIT" - ], - "identifier": "biotools:bedtools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "intervals1": { - "type": "file", - "description": "BAM/BED/GFF/VCF", - "pattern": "*.{bed|gff|vcf}", - "ontologies": [] - } - }, - { - "intervals2": { - "type": "file", - "description": "BAM/BED/GFF/VCF", - "pattern": "*.{bed|gff|vcf}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference chromosome sizes\ne.g. [ id:'test' ]\n" - } - }, - { - "chrom_sizes": { - "type": "file", - "description": "Chromosome sizes file", - "pattern": "*{.sizes,.txt}", - "ontologies": [] - } - } - ] - ], - "output": { - "mapped": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.${extension}": { - "type": "file", - "description": "File containing the description of overlaps found between the features in A and the features in B, with statistics", - "pattern": "*.${extension}", - "ontologies": [] - } - } - ] - ], - "versions_bedtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bedtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bedtools --version | sed -e 's/bedtools v//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bedtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bedtools --version | sed -e 's/bedtools v//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@ekushele" - ], - "maintainers": [ - "@ekushele" - ] - } - }, - { - "name": "bedtools_maskfasta", - "path": "modules/nf-core/bedtools/maskfasta/meta.yml", - "type": "module", - "meta": { - "name": "bedtools_maskfasta", - "description": "masks sequences in a FASTA file based on intervals defined in a feature file.", - "keywords": [ - "bed", - "fasta", - "maskfasta" - ], - "tools": [ - { - "bedtools": { - "description": "A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.\n", - "documentation": "https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html", - "licence": [ - "MIT" - ], - "identifier": "biotools:bedtools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bed": { - "type": "file", - "description": "Bed feature file", - "pattern": "*.{bed}", - "ontologies": [] - } - } - ], - { - "fasta": { - "type": "file", - "description": "Input fasta file", - "pattern": "*.{fa,fasta}", - "ontologies": [] + "name": "bioformats2raw", + "path": "modules/nf-core/bioformats2raw/meta.yml", + "type": "module", + "meta": { + "name": "bioformats2raw", + "description": "Java application to convert image file formats, including .mrxs, to an intermediate Zarr structure compatible with the OME-NGFF specification.", + "keywords": ["zarr", "ome-ngff", "imaging"], + "tools": [ + { + "bioformats2raw": { + "description": "Java application to convert image file formats, including .mrxs, to an intermediate Zarr structure compatible with the OME-NGFF specification.", + "homepage": "https://github.com/glencoesoftware/bioformats2raw", + "documentation": "https://github.com/glencoesoftware/bioformats2raw", + "tool_dev_url": "https://github.com/glencoesoftware/bioformats2raw", + "licence": ["GPL-2.0"], + "identifier": "biotools:bioformats2raw" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "image": { + "type": "file", + "description": "bioformats supported image file format", + "pattern": "*.{tif,tiff,svs,mrxs}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3727" + }, + { + "edam": "http://edamontology.org/format_3591" + } + ] + } + } + ] + ], + "output": { + "omezarr": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "*ome.zarr": { + "type": "directory", + "description": "OME-Zarr fileset for image data storage. Specification can be found at https://ngff.openmicroscopy.org/latest/#storage-format", + "pattern": "*{ome.zarr}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3915" + } + ] + } + } + ] + ], + "versions_bioformats2raw": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bioformats2raw": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bioformats2raw --version |& sed -n \"1s/Version = //p\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_bioformats": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bio-formats": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bioformats2raw --version |& sed -n \"2s/Bio-Formats version = //p\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_ngff": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "ngff": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bioformats2raw --version |& sed -n \"3s/NGFF specification version = //p\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bioformats2raw": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bioformats2raw --version |& sed -n \"1s/Version = //p\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bio-formats": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bioformats2raw --version |& sed -n \"2s/Bio-Formats version = //p\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "ngff": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bioformats2raw --version |& sed -n \"3s/NGFF specification version = //p\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@CaroAMN"], + "maintainers": ["@CaroAMN"] } - } - ], - "output": { - "fasta": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.fa": { - "type": "file", - "description": "Output masked fasta file", - "pattern": "*.{fa}", - "ontologies": [] - } - } - ] - ], - "versions_bedtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bedtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bedtools --version | sed -e 's/bedtools v//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bedtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bedtools --version | sed -e 's/bedtools v//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] }, - "authors": [ - "@joseespinosa", - "@drpatelh" - ], - "maintainers": [ - "@joseespinosa", - "@drpatelh" - ] - }, - "pipelines": [ { - "name": "callingcards", - "version": "1.0.0" + "name": "biohansel", + "path": "modules/nf-core/biohansel/meta.yml", + "type": "module", + "meta": { + "name": "biohansel", + "description": "Use k-mers to rapidly subtype S. enterica genomes", + "keywords": ["Salmonella enterica", "subtyping", "prokaryote"], + "tools": [ + { + "biohansel": { + "description": "Subtype Salmonella enterica genomes using 33bp k-mer typing schemes.", + "homepage": "https://github.com/phac-nml/biohansel", + "documentation": "https://github.com/phac-nml/biohansel", + "tool_dev_url": "https://github.com/phac-nml/biohansel", + "doi": "10.1101/2020.01.10.902056", + "licence": ["Apache-2.0 license"], + "identifier": "biotools:biohansel" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "seqs": { + "type": "file", + "description": "FASTA or FASTQ", + "pattern": "*.{fasta.gz,fa.gz,fna.gz,fastq.gz,fq.gz}", + "ontologies": [] + } + } + ], + { + "scheme_metadata": { + "type": "file", + "description": "Scheme subtype metadata table", + "pattern": "*.{tab,tsv,txt}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + "output": { + "summary": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}-summary.txt": { + "type": "file", + "description": "Tab-delimited subtyping summary output", + "pattern": "*summary.txt", + "ontologies": [] + } + } + ] + ], + "kmer_results": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}-kmer-results.txt": { + "type": "file", + "description": "Tab-delimited subtyping kmer matching output", + "pattern": "*kmer-results.txt", + "ontologies": [] + } + } + ] + ], + "simple_summary": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}-simple-summary.txt": { + "type": "file", + "description": "A simple version of summary output", + "pattern": "*simple-summary.txt", + "ontologies": [] + } + } + ] + ], + "versions_biohansel": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "biohansel": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "hansel --version 2>&1 | sed 's/^.*hansel //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "biohansel": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "hansel --version 2>&1 | sed 's/^.*hansel //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@rpetit3"], + "maintainers": ["@rpetit3"] + } }, { - "name": "viralmetagenome", - "version": "1.1.1" + "name": "biomformat_convert", + "path": "modules/nf-core/biomformat/convert/meta.yml", + "type": "module", + "meta": { + "name": "biomformat_convert", + "description": "Convert biom table to different format.\nConversion between text tab-delimited, BIOM-v1 (JSON), and BIOM-v2 (HDF5) formats are supported\n", + "keywords": [ + "biom", + "feature table", + "formatting", + "conversion", + "amplicon sequences", + "metagenomics", + "metatranscriptomics" + ], + "tools": [ + { + "biomformat": { + "description": "Biological Observation Matrix (BIOM) format.\nThis package includes basic tools for converting, summarizing, and adding metadata to biom-format files.\n", + "homepage": "http://biom-format.org/index.html", + "documentation": "http://biom-format.org/documentation/index.html", + "tool_dev_url": "https://github.com/biocore/biom-format", + "doi": "10.1186/2047-217X-1-7", + "licence": ["BSD License"], + "identifier": "biotools:biomformat" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "biom": { + "type": "file", + "description": "Biom formatted feature table file", + "pattern": "*.{biom,txt,tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3746" + }, + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "output": { + "biom": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.biom": { + "type": "file", + "description": "Converted biom file", + "pattern": "*.biom", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3746" + } + ] + } + } + ] + ], + "txt": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "Converted txt file", + "pattern": "*.txt", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_biomformat": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "biom-format": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "biom --version | sed 's/biom, version //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "biom-format": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "biom --version | sed 's/biom, version //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@jcbioinformatics"], + "maintainers": ["@jcbioinformatics"] + } }, { - "name": "viralrecon", - "version": "3.0.0" - } - ] - }, - { - "name": "bedtools_merge", - "path": "modules/nf-core/bedtools/merge/meta.yml", - "type": "module", - "meta": { - "name": "bedtools_merge", - "description": "combines overlapping or “book-ended” features in an interval file into a single feature which spans all of the combined features.", - "keywords": [ - "bed", - "merge", - "bedtools", - "overlapped bed" - ], - "tools": [ - { - "bedtools": { - "description": "A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.\n", - "documentation": "https://bedtools.readthedocs.io/en/latest/content/tools/merge.html", - "licence": [ - "MIT" - ], - "identifier": "biotools:bedtools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bed": { - "type": "file", - "description": "Input BED file", - "pattern": "*.{bed}", - "ontologies": [] - } + "name": "biscuit_align", + "path": "modules/nf-core/biscuit/align/meta.yml", + "type": "module", + "meta": { + "name": "biscuit_align", + "description": "Aligns single- or paired-end reads from bisulfite-converted libraries to a reference genome using Biscuit.", + "keywords": ["biscuit", "DNA methylation", "WGBS", "scWGBS", "bisulfite sequencing", "aligner", "bam"], + "tools": [ + { + "biscuit": { + "description": "A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data", + "homepage": "https://huishenlab.github.io/biscuit/", + "documentation": "https://huishenlab.github.io/biscuit/docs/alignment", + "tool_dev_url": "https://github.com/huishenlab/biscuit", + "licence": ["MIT"], + "identifier": "biotools:biscuit" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input genome fasta file", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "index": { + "type": "directory", + "description": "Directory containing biscuit genome index" + } + } + ] + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Output BAM file containing read alignments", + "pattern": "*.{bam}", + "ontologies": [] + } + } + ] + ], + "bai": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bai": { + "type": "file", + "description": "Output BAM index", + "pattern": "*.{bai}", + "ontologies": [] + } + } + ] + ], + "versions_biscuit": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "biscuit": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "biscuit version |& sed '1!d; s/^.*BISCUIT Version: //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_samtools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "samtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "samtools --version |& sed '1!d; s/^.*samtools //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "biscuit": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "biscuit version |& sed '1!d; s/^.*BISCUIT Version: //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "samtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "samtools --version |& sed '1!d; s/^.*samtools //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@njspix"], + "maintainers": ["@njspix", "@sateeshperi"] } - ] - ], - "output": { - "bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bed": { - "type": "file", - "description": "Overlapped bed file with combined features", - "pattern": "*.{bed}", - "ontologies": [] - } - } - ] - ], - "versions_bedtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bedtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bedtools --version | sed -e 's/bedtools v//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bedtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bedtools --version | sed -e 's/bedtools v//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] }, - "authors": [ - "@edmundmiller", - "@sruthipsuresh", - "@drpatelh" - ], - "maintainers": [ - "@edmundmiller", - "@sruthipsuresh", - "@drpatelh" - ] - }, - "pipelines": [ { - "name": "cutandrun", - "version": "3.2.2" + "name": "biscuit_biscuitblaster", + "path": "modules/nf-core/biscuit/biscuitblaster/meta.yml", + "type": "module", + "meta": { + "name": "biscuit_blaster", + "description": "A fast, compact one-liner to produce duplicate-marked, sorted, and indexed BAM files using Biscuit", + "keywords": ["biscuit", "DNA methylation", "WGBS", "scWGBS", "bisulfite sequencing", "aligner", "bam"], + "tools": [ + { + "biscuit": { + "description": "A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data", + "homepage": "https://huishenlab.github.io/biscuit/", + "documentation": "https://huishenlab.github.io/biscuit/biscuitblaster/", + "tool_dev_url": "https://github.com/huishenlab/biscuit", + "licence": ["MIT"], + "identifier": "biotools:biscuit" + } + }, + { + "samblaster": { + "description": "samblaster is a fast and flexible program for marking duplicates in read-id grouped paired-end SAM files.\nIt can also optionally output discordant read pairs and/or split read mappings to separate SAM files,\nand/or unmapped/clipped reads to a separate FASTQ file.\nBy default, samblaster reads SAM input from stdin and writes SAM to stdout.\n", + "documentation": "https://github.com/GregoryFaust/samblaster", + "tool_dev_url": "https://github.com/GregoryFaust/samblaster", + "doi": "10.1093/bioinformatics/btu314", + "licence": ["MIT"], + "identifier": "biotools:biscuit" + } + }, + { + "samtools": { + "description": "SAMtools is a set of utilities for interacting with and post-processing\nshort DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.\nThese files are generated as output by short read aligners like BWA.\n", + "homepage": "http://www.htslib.org/", + "documentation": "http://www.htslib.org/doc/samtools.html", + "doi": "10.1093/bioinformatics/btp352", + "licence": ["MIT"], + "identifier": "biotools:biscuit" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input genome fasta file", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "index": { + "type": "directory", + "description": "Directory containing biscuit genome index" + } + } + ] + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Output BAM file containing read alignments", + "pattern": "*.{bam}", + "ontologies": [] + } + } + ] + ], + "bai": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bai": { + "type": "file", + "description": "Output BAM index", + "pattern": "*.{bai}", + "ontologies": [] + } + } + ] + ], + "versions_biscuit": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "biscuit": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "biscuit version |& sed '1!d; s/^.*BISCUIT Version: //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_samtools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "samtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "samtools --version |& sed '1!d; s/^.*samtools //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_samblaster": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "samblaster": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "samblaster --version |& sed 's/^.*samblaster: Version //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "biscuit": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "biscuit version |& sed '1!d; s/^.*BISCUIT Version: //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "samtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "samtools --version |& sed '1!d; s/^.*samtools //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "samblaster": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "samblaster --version |& sed 's/^.*samblaster: Version //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@njspix"], + "maintainers": ["@njspix", "@sateeshperi"] + } }, { - "name": "nascent", - "version": "2.3.0" + "name": "biscuit_bsconv", + "path": "modules/nf-core/biscuit/bsconv/meta.yml", + "type": "module", + "meta": { + "name": "biscuit_bsconv", + "description": "Summarize and/or filter reads based on bisulfite conversion rate", + "keywords": [ + "biscuit", + "DNA methylation", + "WGBS", + "scWGBS", + "bisulfite sequencing", + "aligner", + "bam", + "filter" + ], + "tools": [ + { + "biscuit": { + "description": "A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data", + "homepage": "https://huishenlab.github.io/biscuit/", + "documentation": "https://huishenlab.github.io/biscuit/docs/subcommand_help.html#biscuit-bsconv", + "tool_dev_url": "https://github.com/huishenlab/biscuit", + "licence": ["MIT"], + "identifier": "biotools:biscuit" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file contained mapped reads", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bai": { + "type": "file", + "description": "BAM file index", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input genome fasta file", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "index": { + "type": "directory", + "description": "Directory containing biscuit genome index" + } + } + ] + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Output BAM file containing filtered read alignments", + "pattern": "*.{bam}", + "ontologies": [] + } + } + ] + ], + "versions_biscuit": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "biscuit": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "biscuit version |& sed '1!d; s/^.*BISCUIT Version: //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "biscuit": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "biscuit version |& sed '1!d; s/^.*BISCUIT Version: //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@njspix"], + "maintainers": ["@njspix", "@sateeshperi"] + } }, { - "name": "radseq", - "version": "dev" + "name": "biscuit_epiread", + "path": "modules/nf-core/biscuit/epiread/meta.yml", + "type": "module", + "meta": { + "name": "biscuit_epiread", + "description": "Summarizes read-level methylation (and optionally SNV) information from a\nBiscuit BAM file in a standard-compliant BED format.\n", + "keywords": ["biscuit", "DNA methylation", "WGBS", "scWGBS", "bisulfite sequencing", "aligner", "bam"], + "tools": [ + { + "biscuit": { + "description": "A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data", + "homepage": "https://huishenlab.github.io/biscuit/", + "documentation": "https://huishenlab.github.io/biscuit/epiread_format/", + "tool_dev_url": "https://github.com/huishenlab/biscuit", + "licence": ["MIT"], + "identifier": "biotools:biscuit" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file contained mapped reads", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bai": { + "type": "file", + "description": "BAM file index", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "snp_bed": { + "type": "file", + "description": "BED file containing SNP information (optional)", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input genome fasta file", + "ontologies": [] + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "index": { + "type": "directory", + "description": "Directory containing biscuit genome index" + } + } + ] + ], + "output": { + "bed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed.gz": { + "type": "file", + "description": "Gzipped BED file with methylation (and optionally SNV) information", + "pattern": "*.{epiread.bed.gz}", + "ontologies": [] + } + } + ] + ], + "versions_biscuit": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "biscuit": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "biscuit version |& sed '1!d; s/^.*BISCUIT Version: //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_samtools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "samtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "samtools --version |& sed '1!d; s/^.*samtools //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "biscuit": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "biscuit version |& sed '1!d; s/^.*BISCUIT Version: //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "samtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "samtools --version |& sed '1!d; s/^.*samtools //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@njspix"], + "maintainers": ["@njspix", "@sateeshperi"] + } }, { - "name": "rnavar", - "version": "1.2.3" + "name": "biscuit_index", + "path": "modules/nf-core/biscuit/index/meta.yml", + "type": "module", + "meta": { + "name": "biscuit_index", + "description": "Indexes a reference genome for use with Biscuit", + "keywords": [ + "biscuit", + "DNA methylation", + "WGBS", + "scWGBS", + "bisulfite sequencing", + "index", + "reference", + "fasta" + ], + "tools": [ + { + "biscuit": { + "description": "A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data", + "homepage": "https://huishenlab.github.io/biscuit/", + "documentation": "https://huishenlab.github.io/biscuit/docs/alignment", + "tool_dev_url": "https://github.com/huishenlab/biscuit", + "licence": ["MIT"], + "identifier": "biotools:biscuit" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input genome fasta file", + "ontologies": [] + } + } + ] + ], + "output": { + "index": [ + [ + { + "meta": { + "type": "directory", + "description": "Directory containing biscuit genome index", + "pattern": "index" + } + }, + { + "BiscuitIndex": { + "type": "directory", + "description": "Directory containing biscuit genome index", + "pattern": "index" + } + } + ] + ], + "versions_biscuit": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "biscuit": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "biscuit version |& sed '1!d; s/^.*BISCUIT Version: //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "biscuit": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "biscuit version |& sed '1!d; s/^.*BISCUIT Version: //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@njspix"], + "maintainers": ["@njspix", "@sateeshperi"] + } }, { - "name": "tfactivity", - "version": "dev" + "name": "biscuit_mergecg", + "path": "modules/nf-core/biscuit/mergecg/meta.yml", + "type": "module", + "meta": { + "name": "biscuit_mergecg", + "description": "Merges methylation information for opposite-strand C's in a CpG context", + "keywords": ["biscuit", "DNA methylation", "WGBS", "scWGBS", "bisulfite sequencing", "aligner", "bed"], + "tools": [ + { + "biscuit": { + "description": "A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data", + "homepage": "https://huishenlab.github.io/biscuit/", + "documentation": "https://huishenlab.github.io/biscuit/docs/methylextraction.html", + "tool_dev_url": "https://github.com/huishenlab/biscuit", + "licence": ["MIT"], + "identifier": "biotools:biscuit" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bed": { + "type": "file", + "description": "Biscuit BED file (output of biscuit vcf2bed)\n", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input genome fasta file", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "index": { + "type": "directory", + "description": "Directory containing biscuit genome index" + } + } + ] + ], + "output": { + "bed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed.gz": { + "type": "file", + "description": "Gzipped BED file with merged methylation information", + "pattern": "*.bed.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "versions_biscuit": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "biscuit": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "biscuit version |& sed '1!d; s/^.*BISCUIT Version: //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_samtools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "samtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "samtools --version |& sed '1!d; s/^.*samtools //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "biscuit": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "biscuit version |& sed '1!d; s/^.*BISCUIT Version: //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "samtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "samtools --version |& sed '1!d; s/^.*samtools //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@njspix"], + "maintainers": ["@njspix", "@sateeshperi"] + } }, { - "name": "variantbenchmarking", - "version": "1.5.0" + "name": "biscuit_pileup", + "path": "modules/nf-core/biscuit/pileup/meta.yml", + "type": "module", + "meta": { + "name": "biscuit_pileup", + "description": "Computes cytosine methylation and callable SNV mutations, optionally in reference to a germline BAM to call somatic variants", + "keywords": [ + "bisulfite", + "DNA methylation", + "pileup", + "variant calling", + "WGBS", + "scWGBS", + "bam", + "vcf" + ], + "tools": [ + { + "biscuit": { + "description": "A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data", + "homepage": "https://huishenlab.github.io/biscuit/", + "documentation": "https://huishenlab.github.io/biscuit/docs/pileup.html", + "tool_dev_url": "https://github.com/huishenlab/biscuit", + "licence": ["MIT"], + "identifier": "biotools:biscuit" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "normal_bams": { + "type": "file", + "description": "BAM files to be analyzed. If no tumor_bam file is provided, any number of \"normal\" BAMs may be provided\n(\"normal\" here is just a semantic issue, these BAMs could be from tumor or any other kind of tissue). If a\ntumor BAM file is provided, exactly one normal (germline) BAM must be provided.\n", + "pattern": "*.{bam}", + "ontologies": [] + } + }, + { + "normal_bais": { + "type": "file", + "description": "BAM index file or files corresponding to the provided normal_bams", + "pattern": "*.{bai}", + "ontologies": [] + } + }, + { + "tumor_bam": { + "type": "file", + "description": "Optional. If a tumor BAM file is provided, pileup will run in \"somatic\" mode and will annotate variants with\ntheir somatic state (present in tumor only, present in normal only, present in both, etc). Note that if a\ntumor BAM file is provided, exactly one normal BAM must be provided.\n", + "pattern": "*.{bam}", + "ontologies": [] + } + }, + { + "tumor_bai": { + "type": "file", + "description": "Optional. BAM index file corresponding to provided tumor_bam", + "pattern": "*.{bai}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input genome fasta file", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "index": { + "type": "directory", + "description": "Directory containing biscuit genome index" + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "vcf file with methylation information", + "pattern": "*.{vcf.gz}", + "ontologies": [] + } + } + ] + ], + "versions_biscuit": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "biscuit": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "biscuit version |& sed '1!d; s/^.*BISCUIT Version: //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_bgzip": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bgzip": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bgzip --version | head -1 | sed \"s/bgzip (htslib) //\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "biscuit": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "biscuit version |& sed '1!d; s/^.*BISCUIT Version: //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bgzip": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bgzip --version | head -1 | sed \"s/bgzip (htslib) //\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@njspix"], + "maintainers": ["@njspix", "@sateeshperi"] + } }, { - "name": "viralmetagenome", - "version": "1.1.1" + "name": "biscuit_qc", + "path": "modules/nf-core/biscuit/qc/meta.yml", + "type": "module", + "meta": { + "name": "biscuit_qc", + "description": "Perform basic quality control on a BAM file generated with Biscuit", + "keywords": [ + "biscuit", + "DNA methylation", + "WGBS", + "scWGBS", + "bisulfite sequencing", + "index", + "BAM", + "quality control" + ], + "tools": [ + { + "biscuit": { + "description": "A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data", + "homepage": "https://huishenlab.github.io/biscuit/", + "documentation": "https://huishenlab.github.io/biscuit/docs/subcommand_help.html#biscuit-qc", + "tool_dev_url": "https://github.com/huishenlab/biscuit", + "licence": ["MIT"], + "identifier": "biotools:biscuit" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file produced using Biscuit", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input genome fasta file", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "index": { + "type": "directory", + "description": "Directory containing biscuit genome index" + } + } + ] + ], + "output": { + "reports": [ + [ + { + "meta": { + "type": "file", + "description": "Summary files containing the following information:\n - CpG retention by position in read\n - CpH retention by position in read\n - Read duplication statistics\n - Insert size distribution\n - Distribution of mapping qualities\n - Proportion of reads mapping to each strand\n - Read-averaged cytosine conversion rate for CpA, CpC, CpG, and CpT\n", + "pattern": "*.txt", + "ontologies": [] + } + }, + { + "*.txt": { + "type": "file", + "description": "Summary files containing the following information:\n - CpG retention by position in read\n - CpH retention by position in read\n - Read duplication statistics\n - Insert size distribution\n - Distribution of mapping qualities\n - Proportion of reads mapping to each strand\n - Read-averaged cytosine conversion rate for CpA, CpC, CpG, and CpT\n", + "pattern": "*.txt", + "ontologies": [] + } + } + ] + ], + "versions_biscuit": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "biscuit": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "biscuit version |& sed '1!d; s/^.*BISCUIT Version: //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "biscuit": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "biscuit version |& sed '1!d; s/^.*BISCUIT Version: //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@njspix"], + "maintainers": ["@njspix", "@sateeshperi"] + } }, { - "name": "viralrecon", - "version": "3.0.0" - } - ] - }, - { - "name": "bedtools_multiinter", - "path": "modules/nf-core/bedtools/multiinter/meta.yml", - "type": "module", - "meta": { - "name": "bedtools_multiinter", - "description": "Identifies common intervals among multiple (and subsets thereof) sorted BED/GFF/VCF files.", - "keywords": [ - "bedtools", - "multinterval", - "bed", - "vcf", - "gff" - ], - "tools": [ - { - "bedtools": { - "description": "A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.\n", - "documentation": "https://bedtools.readthedocs.io/en/latest/content/tools/multiinter.html", - "licence": [ - "MIT" - ], - "identifier": "biotools:bedtools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "beds": { - "type": "list", - "description": "List of files to be merged", - "pattern": "*.{bed,vcf,gff}" - } - } - ], - { - "chrom_sizes": { - "type": "file", - "description": "Chromosome sizes file", - "pattern": "*{.sizes,.txt}", - "ontologies": [] - } - } - ], - "output": { - "bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bed": { - "type": "file", - "description": "Common interval bed", - "pattern": "*.{bed}", - "ontologies": [] - } - } - ] - ], - "versions_bedtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bedtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bedtools --version | sed -e 's/bedtools v//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bedtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bedtools --version | sed -e 's/bedtools v//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@matthdsm" - ], - "maintainers": [ - "@matthdsm" - ] - } - }, - { - "name": "bedtools_nuc", - "path": "modules/nf-core/bedtools/nuc/meta.yml", - "type": "module", - "meta": { - "name": "bedtools_nuc", - "description": "Profiles the nucleotide content of intervals in a fasta file.", - "keywords": [ - "bed", - "nucBed", - "bedtools", - "GC content", - "AT content", - "nucleotide content", - "intervals" - ], - "tools": [ - { - "bedtools": { - "description": "A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.", - "homepage": "https://bedtools.readthedocs.io", - "documentation": "https://bedtools.readthedocs.io/en/latest/content/tools/nuc.html", - "doi": "10.1093/bioinformatics/btq033", - "licence": [ - "MIT" - ], - "identifier": "biotools:bedtools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Genome reference", - "pattern": "*.{fa,fasta}", - "ontologies": [] - } - }, - { - "intervals": { - "type": "file", - "description": "BED/GFF/VCF file of ranges to extract from -fi", - "pattern": "*.{bed,gff,vcf}", - "ontologies": [] - } - } - ] - ], - "output": { - "bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bed": { - "type": "file", - "description": "The following information will be reported after each BED entry: %AT content, %GC content, Number of As observed, Number of Cs observed, Number of Gs observed, Number of Ts observed, Number of Ns observed, Number of other bases observed, The length of the explored sequence/interval, The seq. extracted from the FASTA file. 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"type": "module", - "meta": { - "name": "bedtools_shift", - "description": "Shifts each feature by specific number of bases", - "keywords": [ - "bed", - "shiftBed", - "region", - "fai", - "sizes", - "genome", - "bases" - ], - "tools": [ - { - "bedtools": { - "description": "A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.\n", - "documentation": "https://bedtools.readthedocs.io/en/latest/content/tools/slop.html", - "licence": [ - "MIT" - ], - "identifier": "biotools:bedtools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bed": { - "type": "file", - "description": "Input BED file", - "pattern": "*.{bed}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "chrom_sizes": { - "type": "file", - "description": "Chromosome sizes file", - "pattern": "*{.sizes,.txt,.fai}", - "ontologies": [] - } - } - ] - ], - "output": { - "bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bed": { - "type": "file", - "description": "Shift BED file", - "pattern": "*.{bed}", - "ontologies": [] - } - } - ] - ], - "versions_bedtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bedtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bedtools --version | sed -e 's/bedtools v//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bedtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bedtools --version | sed -e 's/bedtools v//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@ekushele" - ], - "maintainers": [ - "@ekushele" - ] - }, - "pipelines": [ - { - "name": "deepmodeloptim", - "version": "dev" - } - ] - }, - { - "name": "bedtools_shuffle", - "path": "modules/nf-core/bedtools/shuffle/meta.yml", - "type": "module", - "meta": { - "name": "bedtools_shuffle", - "description": "bedtools shuffle will randomly permute the genomic locations of a feature file among a genome defined in a genome file", - "keywords": [ - "bed", - "shuffleBed", - "region", - "fai", - "sizes", - "genome", - "bases" - ], - "tools": [ - { - "bedtools": { - "description": "A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.\n", - "documentation": "https://bedtools.readthedocs.io/en/latest/content/tools/slop.html", - "licence": [ - "MIT" - ], - "identifier": "biotools:bedtools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing interval information\ne.g. [ id:'test' ]\n" - } - }, - { - "intervals": { - "type": "file", - "description": "Input interval (BED/GFF/VCF) file", - "pattern": "*.{bed,gff,gff3,vcf}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3003" - }, - { - "edam": "http://edamontology.org/format_2305" - }, - { - "edam": "http://edamontology.org/format_3016" - } - ] - } + "name": "biscuit_vcf2bed", + "path": "modules/nf-core/biscuit/vcf2bed/meta.yml", + "type": "module", + "meta": { + "name": "biscuit_vcf2bed", + "description": "Summarizes methylation or SNV information from a Biscuit VCF in a\nstandard-compliant BED file.\n", + "keywords": ["biscuit", "DNA methylation", "WGBS", "scWGBS", "bisulfite sequencing", "aligner", "vcf"], + "tools": [ + { + "biscuit": { + "description": "A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data", + "homepage": "https://huishenlab.github.io/biscuit/", + "documentation": "https://huishenlab.github.io/biscuit/docs/methylextraction.html", + "tool_dev_url": "https://github.com/huishenlab/biscuit", + "licence": ["MIT"], + "identifier": "biotools:biscuit" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "Biscuit vcf file (output of biscuit pileup)", + "ontologies": [] + } + } + ] + ], + "output": { + "bed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed.gz": { + "type": "file", + "description": "Gzipped BED file with methylation or SNV information", + "pattern": "*.{bed.gz}", + "ontologies": [] + } + } + ] + ], + "versions_biscuit": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "biscuit": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "biscuit version |& sed '1!d; s/^.*BISCUIT Version: //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_samtools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "samtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "samtools --version |& sed '1!d; s/^.*samtools //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "biscuit": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "biscuit version |& sed '1!d; s/^.*BISCUIT Version: //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "samtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "samtools --version |& sed '1!d; s/^.*samtools //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@njspix"], + "maintainers": ["@njspix", "@sateeshperi"] } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing genome information\ne.g. [ id:'test' ]\n" - } + }, + { + "name": "bismark_align", + "path": "modules/nf-core/bismark/align/meta.yml", + "type": "module", + "meta": { + "name": "bismark_align", + "description": "Performs alignment of BS-Seq reads using bismark", + "keywords": [ + "bismark", + "3-letter genome", + "map", + "methylation", + "5mC", + "methylseq", + "bisulphite", + "bisulfite", + "bam" + ], + "tools": [ + { + "bismark": { + "description": "Bismark is a tool to map bisulfite treated sequencing reads\nand perform methylation calling in a quick and easy-to-use fashion.\n", + "homepage": "https://github.com/FelixKrueger/Bismark", + "documentation": "https://github.com/FelixKrueger/Bismark/tree/master/Docs", + "doi": "10.1093/bioinformatics/btr167", + "licence": ["GPL-3.0-or-later"], + "identifier": "biotools:bismark" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference genome FASTA file\n", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "index": { + "type": "directory", + "description": "Bismark genome index directory", + "pattern": "BismarkIndex" + } + } + ] + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*bam": { + "type": "file", + "description": "Output BAM file containing read alignments", + "pattern": "*.{bam}", + "ontologies": [] + } + } + ] + ], + "report": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*report.txt": { + "type": "file", + "description": "Bismark alignment reports", + "pattern": "*{report.txt}", + "ontologies": [] + } + } + ] + ], + "unmapped": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*fq.gz": { + "type": "file", + "description": "Output FastQ file(s) containing unmapped reads", + "pattern": "*.{fq.gz}", + "ontologies": [] + } + } + ] + ], + "versions_bismark": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bismark": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bismark -v 2>&1 | sed -n 's/^.*Bismark Version: v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bismark": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bismark -v 2>&1 | sed -n 's/^.*Bismark Version: v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@phue"], + "maintainers": ["@phue", "@sateeshperi"] }, - 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s/ .*\\$//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "blastdbcmd": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "blastdbcmd -version 2>&1 | head -n1 | sed 's/^.*blastdbcmd: //; s/ .*\\$//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@toniher"], + "maintainers": ["@toniher"] + } }, { - "name": "tfactivity", - "version": "dev" - } - ] - }, - { - "name": "bedtools_unionbedg", - "path": "modules/nf-core/bedtools/unionbedg/meta.yml", - "type": "module", - "meta": { - "name": "bedtools_unionbedg", - "description": "Combines multiple BedGraph files into a single file", - "keywords": [ - "bed", - "unionBedGraphs", - "bedGraph", - "comparisons", - "combine" - ], - "tools": [ - { - "bedtools": { - "description": "A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.\n", - "documentation": "https://bedtools.readthedocs.io/en/latest/content/tools/slop.html", - "licence": [ - "MIT" - ], - "identifier": "biotools:bedtools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bedgraph": { - "type": "file", - "description": "Input BedGraph file: four column BED format, with 4th column with numerical values: integer or real, positive or negative\n", - "pattern": "*.{bedGraph,bedgraph}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing meta information for the reference chromosome sizes\ne.g. [ id:'test' ]\n" - } - }, - { - "chrom_sizes": { - "type": "file", - "description": "Chromosome sizes file", - "pattern": "*{.sizes,.txt}", - "ontologies": [] - } - } - ] - ], - "output": { - "bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bed": { - "type": "file", - "description": "Combined BED file with values from all bedGraph files", - "pattern": "*.{bed}", - "ontologies": [] - } - } - ] - ], - "versions_bedtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bedtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bedtools --version | sed -e 's/bedtools v//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bedtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bedtools --version | sed -e 's/bedtools v//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@ekushele" - ], - "maintainers": [ - "@ekushele" - ] - } - }, - { - "name": "bff", - "path": "modules/nf-core/bff/meta.yml", - "type": "module", - "meta": { - "name": "bff", - "description": "Generating cell hashing calls from a matrix of count data.", - "keywords": [ - "demultiplexing", - "hashing-based deconvolution", - "single-cell" - ], - "tools": [ - { - "bff": { - "description": "A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) , Macosko E, Basu A, Satija R, et al (2015) , and Butler A and Satija R (2017) for more details.", - "homepage": "https://rdrr.io/github/BimberLab/cellhashR/man/GenerateCellHashingCalls.html", - "documentation": "https://rdrr.io/github/BimberLab/cellhashR/man/GenerateCellHashingCalls.html", - "tool_dev_url": "https://github.com/BimberLab/cellhashR", - "doi": "10.5281/zenodo.6402477", - "licence": [ - "GPL-3" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "hto_matrix": { - "type": "file", - "description": "Directory that contains the HTO matrix in a 10X format.\n", - "ontologies": [ - { - "edam": "http://edamontology.org/data_3917" - } - ] - } - }, - { - "methods": { - "type": "string", - "description": "Decides whether 'RAW', 'CLUSTER' OR 'COMBINED' should be selected as the call method.\n" - } - }, - { - "preprocessing": { - "type": "string", - "description": "Decides whether the HTO matrix should undergo a preprocessing step ('TRUE') or not ('FALSE').\n" - } - } - ] - ], - "output": { - "assignment": [ - [ - { - "meta": { - "type": "file", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n", - "ontologies": [] - } - }, - { - "*_assignment_bff.csv": { - "type": "file", - "description": "Contains the assignment results of demultiplexing.", - "pattern": "assignment_bff.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "metrics": [ - [ - { - "meta": { - "type": "file", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n", - "ontologies": [] - } - }, - { - "*_metrics_bff.csv": { - "type": "file", - "description": "Summary metrics will be written to this file.", - "pattern": "_metrics_bff.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "params": [ - [ - { - "meta": { - "type": "file", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n", - "ontologies": [] - } - }, - { - "*_params_bff.csv": { - "type": "file", - "description": "The used parameters to call HTODemux in the R-Script.", - "pattern": "params_htodemux.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "versions_bff": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions.", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "topics": { - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions.", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@LuisHeinzlmeier" - ], - "maintainers": [ - "@LuisHeinzlmeier" - ] - } - }, - { - "name": "bftools_showinf", - "path": "modules/nf-core/bftools/showinf/meta.yml", - "type": "module", - "meta": { - "name": "bftools_showinf", - "description": "Extract OME xml data from OME-tif", - "keywords": [ - "metadata", - "ome-tif", - "ome-tiff", - "imaging", - "bioinformatics tools" - ], - "tools": [ - { - "bftools": { - "description": "Suite of tools to handle several imaging protocols.", - "homepage": "https://www.openmicroscopy.org/bio-formats", - "documentation": "https://bio-formats.readthedocs.io/en/stable/users/index.html", - "tool_dev_url": "https://github.com/ome/bioformats", - "doi": "10.1083/jcb.201004104", - "licence": [ - "GNU General Public License v2.0" - ], - "identifier": "biotools:bio-formats" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "image": { - "type": "file", - "description": "Path to image file containing OME metadata", - "ontologies": [] - } - } - ] - ], - "output": { - "xml": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.xml.gz": { - "type": "file", - "description": "Compressed XML with OME tag metadata", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2332" - } - ] - } - } - ] - ], - "versions_bftools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bftools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "showinf -version | sed -n '1s/[^ ]* //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bftools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "showinf -version | sed -n '1s/[^ ]* //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@AlexBarbera" - ], - "maintainers": [ - "@AlexBarbera" - ] - }, - "pipelines": [ - { - "name": "mcmicro", - "version": "dev" - } - ] - }, - { - "name": "bigslice", - "path": "modules/nf-core/bigslice/meta.yml", - "type": "module", - "meta": { - "name": "bigslice", - "description": "A scalable tool for large-scale analysis of Biosynthetic Gene Clusters (BGCs).\nIt takes genome regions in GenBank format along with an HMM database and produces a SQLite database and FASTA outputs of predicted features.\n", - "keywords": [ - "biosynthetic gene clusters", - "genomics", - "analysis" - ], - "tools": [ - { - "bigslice": { - "description": "A highly scalable, user-interactive tool for the large scale analysis of Biosynthetic Gene Clusters data", - "homepage": "https://github.com/medema-group/bigslice", - "documentation": "https://github.com/medema-group/bigslice", - "tool_dev_url": "https://github.com/medema-group/bigslice", - "doi": "10.1093/gigascience/giaa154", - "licence": [ - "AGPL v3-or-later" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "bgc": { - "type": "file", - "description": "List of GenBank (.gbk) files containing genomic region annotations for BiG-SLiCE input.\nEach file represents a BGC region. The module internally organises them into the required\nBiG-SLiCE input folder structure (datasets.tsv and taxonomy TSV).\n", - "pattern": "*.gbk", - "ontologies": [] - } - } - ], - { - "hmmdb": { - "type": "directory", - "description": "Path to the BiG-SLiCE HMM database folder containing biosynthetic and sub Pfams for annotation, in the required BiG-SLiCE format.\nAn example directory in compressed archive format can be found here: https://github.com/medema-group/bigslice/releases/download/v2.0.0rc/bigslice-models.2022-11-30.tar.gz\n" - } - }, - { - "export_tsv": { - "type": "boolean", - "description": "If true, runs a second BiG-SLiCE invocation to export all results from the SQLite database\nto TSV files under `tsv_export/`. Additional arguments for this step can be passed via `task.ext.args2`.\n" - } - } - ], - "output": { - "output": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample/dataset information" - } - }, - { - "${prefix}/result": { - "type": "directory", - "description": "BiG-SLiCE result directory containing the SQLite database (`data.db`),\npredicted feature FASTA files (`tmp/**/*.fa`), and optionally TSV exports\n(`tsv_export/`) when `export_tsv` is `true`.\n", - "pattern": "result" - } - } - ] - ], - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample/dataset information" - } - }, - { - "${prefix}/result/tsv_export": { - "type": "directory", - "description": "Directory containing TSV exports of all parsed BGC metadata, vectorized\nfeatures and clustering results. Only present when `export_tsv` input is\nset to `true`.\n", - "pattern": "tsv_export" - } - } - ] - ], - "versions_bigslice": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bigslice": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "2.0.2": { - "type": "string", - "description": "The version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bigslice": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "2.0.2": { - "type": "string", - "description": "The version of the tool" - } - } - ] - ] - }, - "authors": [ - "@vagkaratzas", - "@SkyLex" - ], - "maintainers": [ - "@vagkaratzas", - "@SkyLex" - ] - } - }, - { - "name": "bigslice_bigslice", - "path": "modules/nf-core/bigslice/bigslice/meta.yml", - "type": "module", - "meta": { - "name": "bigslice_bigslice", - "description": "A scalable tool for large-scale analysis of Biosynthetic Gene Clusters (BGCs).\nIt takes genome regions in GenBank format along with an HMM database and produces a SQLite database and FASTA outputs of predicted features.\n", - "keywords": [ - "biosynthetic gene clusters", - "genomics", - "analysis" - ], - "tools": [ - { - "bigslice": { - "description": "A highly scalable, user-interactive tool for the large scale analysis of Biosynthetic Gene Clusters data", - "homepage": "https://github.com/medema-group/bigslice", - "documentation": "https://github.com/medema-group/bigslice", - "tool_dev_url": "https://github.com/medema-group/bigslice", - "doi": "10.1093/gigascience/giaa154", - "licence": [ - "AGPL v3-or-later" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "bgc": { - "type": "file", - "description": "List of GenBank (.gbk) files containing genomic region annotations for BiG-SLiCE input.\nEach file represents a BGC region. The module internally organises them into the required\nBiG-SLiCE input folder structure (datasets.tsv and taxonomy TSV).\n", - "pattern": "*.gbk", - "ontologies": [] - } - } - ], - { - "hmmdb": { - "type": "directory", - "description": "Path to the BiG-SLiCE HMM database folder containing biosynthetic and sub Pfams for annotation, in the required BiG-SLiCE format.\nAn example directory in compressed archive format can be found here: https://github.com/medema-group/bigslice/releases/download/v2.0.0rc/bigslice-models.2022-11-30.tar.gz\n" - } - }, - { - "export_tsv": { - "type": "boolean", - "description": "If true, runs a second BiG-SLiCE invocation to export all results from the SQLite database\nto TSV files under `tsv_export/`. Additional arguments for this step can be passed via `task.ext.args2`.\n" - } - } - ], - "output": { - "output": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample/dataset information" - } - }, - { - "${prefix}/result": { - "type": "directory", - "description": "BiG-SLiCE result directory containing the SQLite database (`data.db`),\npredicted feature FASTA files (`tmp/**/*.fa`), and optionally TSV exports\n(`tsv_export/`) when `export_tsv` is `true`.\n", - "pattern": "result" - } - } - ] - ], - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample/dataset information" - } - }, - { - "${prefix}/result/tsv_export": { - "type": "directory", - "description": "Directory containing TSV exports of all parsed BGC metadata, vectorized\nfeatures and clustering results. Only present when `export_tsv` input is\nset to `true`.\n", - "pattern": "tsv_export" - } - } - ] - ], - "versions_bigslice": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bigslice": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "2.0.2": { - "type": "string", - "description": "The version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bigslice": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "2.0.2": { - "type": "string", - "description": "The version of the tool" - } - } - ] - ] - }, - "authors": [ - "@vagkaratzas", - "@SkyLex" - ], - "maintainers": [ - "@vagkaratzas", - "@SkyLex" - ] - } - }, - { - "name": "bigslice_downloaddb", - "path": "modules/nf-core/bigslice/downloaddb/meta.yml", - "type": "module", - "meta": { - "name": "bigslice_downloaddb", - "description": "Downloads and extracts the BiG-SLiCE HMM database (biosynthetic and sub Pfams)\nusing the bundled `download_bigslice_hmmdb` script shipped with BiG-SLiCE.\nThe resulting directory can be passed directly as the `hmmdb` input to the\n`BIGSLICE` module.\n", - "keywords": [ - "biosynthetic gene clusters", - "genomics", - "database", - "download" - ], - "tools": [ - { - "bigslice": { - "description": "A highly scalable, user-interactive tool for the large scale analysis of Biosynthetic Gene Clusters data", - "homepage": "https://github.com/medema-group/bigslice", - "documentation": "https://github.com/medema-group/bigslice", - "tool_dev_url": "https://github.com/medema-group/bigslice", - "doi": "10.1093/gigascience/giaa154", - "licence": [ - "AGPL v3-or-later" - ], - "identifier": "" - } - } - ], - "input": [ - { + "name": "blast_blastn", + "path": "modules/nf-core/blast/blastn/meta.yml", + "type": "module", "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. `[ id:'test' ]`" - } - } - ], - "output": { - "db": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. `[ id:'test' ]`" - } - }, - { - "bigslice-models": { - "type": "directory", - "description": "Downloaded and extracted BiG-SLiCE HMM database directory containing biosynthetic Pfam HMMs and sub-Pfam profiles. Pass this directly as `hmmdb` to the `BIGSLICE` module.", - "pattern": "bigslice-models" - } - } - ] - ], - "versions_bigslice": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bigslice": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "2.0.2": { - "type": "string", - "description": "The version of the tool" - } - } - ] - ], - "versions_python": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "python": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python --version | sed 's/Python //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bigslice": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "2.0.2": { - "type": "string", - "description": "The version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "python": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python --version | sed 's/Python //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@vagkaratzas", - "@SkyLex" - ], - "maintainers": [ - "@vagkaratzas", - "@SkyLex" - ] - } - }, - { - "name": "bio2zarr_vcf2zarrconvert", - "path": "modules/nf-core/bio2zarr/vcf2zarrconvert/meta.yml", - "type": "module", - "meta": { - "name": "bio2zarr_vcf2zarrconvert", - "description": "Convert VCF data to the VCF Zarr specification reliably, in parallel or distributed over a cluster.", - "keywords": [ - "vcf", - "zarr", - "convert", - "genomics" - ], - "tools": [ - { - "vcf2zarr": { - "description": "Convert bioinformatics data to Zarr", - "homepage": "https://sgkit-dev.github.io/bio2zarr/vcf2zarr/overview.html", - "documentation": "https://sgkit-dev.github.io/bio2zarr/", - "tool_dev_url": "https://github.com/sgkit-dev/bio2zarr", - "doi": "10.1101/2024.06.11.598241", - "licence": [ - "Apache-2.0" - ], - "identifier": "biotools:bio2zarr" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } + "name": "blast_blastn", + "description": "Queries a BLAST DNA database", + "keywords": ["fasta", "blast", "blastn", "DNA sequence", "taxids"], + "tools": [ + { + "blast": { + "description": "BLAST finds regions of similarity between biological sequences.\n", + "homepage": "https://blast.ncbi.nlm.nih.gov/Blast.cgi", + "documentation": "https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs", + "doi": "10.1016/S0022-2836(05)80360-2", + "licence": ["US-Government-Work"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input fasta file containing queries sequences", + "pattern": "*.{fa,fasta,fa.gz,fasta.gz}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing db information\ne.g. [ id:'test2', single_end:false ]\n" + } + }, + { + "db": { + "type": "directory", + "description": "Directory containing the blast database", + "pattern": "*" + } + } + ], + { + "taxidlist": { + "type": "file", + "description": "File containing NCBI taxon ids, one per line, for filtering the database.", + "pattern": "*.{txt}", + "ontologies": [] + } + }, + { + "taxids": { + "type": "string", + "description": "Comma-delimited list of NCBI taxon ids for filtering the database.", + "pattern": "^[0-9]+(,[0-9]+)*$" + } + }, + { + "negative_tax": { + "type": "boolean", + "description": "Use negative filtering (true) to exclude taxon ids or normal filtering (false).", + "pattern": "true or false" + } + } + ], + "output": { + "txt": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "File containing blastn hits", + "pattern": "*.txt", + "ontologies": [] + } + } + ] + ], + "versions_blastn": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "blastn": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "blastn -version 2>&1 | sed 's/^.*blastn: //; s/ .*\\$//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "blastn": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "blastn -version 2>&1 | sed 's/^.*blastn: //; s/ .*\\$//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@joseespinosa", "@drpatelh"], + "maintainers": ["@joseespinosa", "@drpatelh", "@vagkaratzas"] }, - { - "vcf": { - "type": "file", - "description": "Input VCF/BCF file to convert", - "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - }, - { - "edam": "http://edamontology.org/format_3020" - } - ] - } - } - ] - ], - "output": { - "vcz": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.vcz": { - "type": "directory", - "description": "Output VCF Zarr store directory", - "pattern": "*.vcz", - "ontologies": [] - } - } - ] - ], - "versions_vcf2zarr": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "vcf2zarr": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "vcf2zarr --version |& sed -n \"s/.* //p\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "vcf2zarr": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "vcf2zarr --version |& sed -n \"s/.* //p\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "detaxizer", + "version": "1.3.0" + }, + { + "name": "phageannotator", + "version": "dev" + }, + { + "name": "viralmetagenome", + "version": "1.1.1" + }, + { + "name": "viralrecon", + "version": "3.0.0" + } ] - ] - }, - "authors": [ - "@camlloyd" - ], - "maintainers": [ - "@camlloyd" - ] - } - }, - { - "name": "bio2zarr_vcf2zarrexplode", - "path": "modules/nf-core/bio2zarr/vcf2zarrexplode/meta.yml", - "type": "module", - "meta": { - "name": "bio2zarr_vcf2zarrexplode", - "description": "Convert VCF(s) to intermediate columnar format (ICF)", - "keywords": [ - "vcf", - "icf", - "zarr", - "convert", - "genomics" - ], - "tools": [ - { - "vcf2zarr": { - "description": "Convert bioinformatics data to Zarr", - "homepage": "https://sgkit-dev.github.io/bio2zarr/vcf2zarr/overview.html", - "documentation": "https://sgkit-dev.github.io/bio2zarr/", - "tool_dev_url": "https://github.com/sgkit-dev/bio2zarr", - "doi": "10.1101/2024.06.11.598241", - "licence": [ - "Apache-2.0" - ], - "identifier": "biotools:bio2zarr" + }, + { + "name": "blast_blastp", + "path": "modules/nf-core/blast/blastp/meta.yml", + "type": "module", + "meta": { + "name": "blast_blastp", + "description": "BLASTP (Basic Local Alignment Search Tool- Protein) compares an amino acid (protein) query sequence against a protein database", + "keywords": ["fasta", "blast", "blastp", "protein"], + "tools": [ + { + "blast": { + "description": "BLAST+ is a new suite of BLAST tools that utilizes the NCBI C++ Toolkit.\n", + "homepage": "https://blast.ncbi.nlm.nih.gov/Blast.cgi", + "documentation": "https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs", + "doi": "10.1016/S0022-2836(05)80360-2", + "licence": ["US-Government-Work"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input fasta file containing queries sequences", + "pattern": "*.{fa,fasta,fa.gz,fasta.gz}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing db information\ne.g. [ id:'test2', single_end:false ]\n" + } + }, + { + "db": { + "type": "directory", + "description": "Directory containing the blast database", + "pattern": "*" + } + } + ], + { + "out_ext": { + "type": "string", + "description": "Specify the type of output file to be generated. `xml` corresponds to BLAST xml format.\n`tsv` corresponds to BLAST tabular format. `csv` corresponds to BLAST comma separated format.\n", + "pattern": "xml|tsv|csv" + } + } + ], + "output": { + "xml": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.xml*": { + "type": "file", + "description": "File containing blastp hits in XML format", + "pattern": "*.{xml}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2332" + } + ] + } + } + ] + ], + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.tsv*": { + "type": "file", + "description": "File containing blastp hits in tabular format", + "pattern": "*.{tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "csv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.csv*": { + "type": "file", + "description": "File containing blastp hits in comma separated format", + "pattern": "*.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "versions_blastp": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "blastp": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "blastp -version 2>&1 | sed 's/^.*blastp: //; s/ .*\\$//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "blastp": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "blastp -version 2>&1 | sed 's/^.*blastp: //; s/ .*\\$//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@vagkaratzas"], + "maintainers": ["@vagkaratzas"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } + }, + { + "name": "blast_makeblastdb", + "path": "modules/nf-core/blast/makeblastdb/meta.yml", + "type": "module", + "meta": { + "name": "blast_makeblastdb", + "description": "Builds a BLAST database", + "keywords": ["fasta", "blast", "database"], + "tools": [ + { + "blast": { + "description": "BLAST finds regions of similarity between biological sequences.\n", + "homepage": "https://blast.ncbi.nlm.nih.gov/Blast.cgi", + "documentation": "https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs", + "doi": "10.1016/S0022-2836(05)80360-2", + "licence": ["US-Government-Work"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input fasta file", + "pattern": "*.{fa,fasta,fa.gz,fasta.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + { + "taxid_map": { + "type": "file", + "description": "taxID mapping files are tab-delimited text files used to map custom sequence IDs to NCBI taxonomic identifiers (taxIDs) during the creation of a BLAST database", + "pattern": "*.txt", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + } + ], + "output": { + "db": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}": { + "type": "directory", + "description": "Output directory containing blast database files", + "pattern": "*" + } + } + ] + ], + "versions_makeblastdb": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "makeblastdb": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "makeblastdb -version 2>&1 | sed 's/^.*makeblastdb: //; s/ .*\\$//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "makeblastdb": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "makeblastdb -version 2>&1 | sed 's/^.*makeblastdb: //; s/ .*\\$//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@joseespinosa", "@drpatelh"], + "maintainers": ["@joseespinosa", "@drpatelh", "@vagkaratzas", "@DLBPointon"] }, - { - "vcf": { - "type": "file", - "description": "Input VCF/BCF file(s)", - "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - } - ] - } - } - ] - ], - "output": { - "icf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.icf": { - "type": "directory", - "description": "Intermediate columnar format (ICF) directory produced by vcf2zarr explode", - "pattern": "*.icf", - "ontologies": [] - } - } - ] - ], - "versions_vcf2zarr": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "vcf2zarr": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "vcf2zarr --version |& sed -n \"s/.* //p\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "vcf2zarr": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "vcf2zarr --version |& sed -n \"s/.* //p\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "detaxizer", + "version": "1.3.0" + }, + { + "name": "phageannotator", + "version": "dev" + }, + { + "name": "viralmetagenome", + "version": "1.1.1" + }, + { + "name": "viralrecon", + "version": "3.0.0" + } ] - ] - }, - "authors": [ - "@camlloyd" - ], - "maintainers": [ - "@camlloyd" - ] - } - }, - { - "name": "bio2zarr_vcfpartition", - "path": "modules/nf-core/bio2zarr/vcfpartition/meta.yml", - "type": "module", - "meta": { - "name": "bio2zarr_vcfpartition", - "description": "Outputs a set of region strings that partition indexed VCF/BCF files for parallel processing.", - "keywords": [ - "vcf", - "bcf", - "partition", - "regions", - "parallel", - "genomics" - ], - "tools": [ - { - "bio2zarr": { - "description": "Convert bioinformatics data to Zarr", - "homepage": "https://sgkit-dev.github.io/bio2zarr/", - "documentation": "https://sgkit-dev.github.io/bio2zarr", - "tool_dev_url": "https://github.com/sgkit-dev/bio2zarr", - "doi": "10.1101/2024.06.11.598241", - "licence": [ - "Apache-2.0" - ], - "identifier": "biotools:bio2zarr" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "vcf": { - "type": "file", - "description": "Indexed VCF/BCF file to partition", - "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - }, - { - "edam": "http://edamontology.org/format_3020" - } - ] - } - }, - { - "index": { - "type": "file", - "description": "Index for the VCF/BCF file", - "pattern": "*.{tbi,csi}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3700" - } - ] - } + }, + { + "name": "blast_tblastn", + "path": "modules/nf-core/blast/tblastn/meta.yml", + "type": "module", + "meta": { + "name": "blast_tblastn", + "description": "Queries a BLAST DNA database", + "keywords": ["fasta", "blast", "tblastn", "DNA sequence"], + "tools": [ + { + "blast": { + "description": "Protein to Translated Nucleotide BLAST.\n", + "homepage": "https://blast.ncbi.nlm.nih.gov/Blast.cgi", + "documentation": "https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs", + "doi": "10.1016/S0022-2836(05)80360-2", + "licence": ["US-Government-Work"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input fasta file containing queries sequences", + "pattern": "*.{fa,fasta,fa.gz,fasta.gz}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing db information\ne.g. [ id:'test2', single_end:false ]\n" + } + }, + { + "db": { + "type": "directory", + "description": "Directory containing the blast database", + "pattern": "*" + } + } + ] + ], + "output": { + "txt": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "File containing blastn hits", + "pattern": "*.txt", + "ontologies": [] + } + } + ] + ], + "versions_tblastn": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "tblastn": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "tblastn -version 2>&1 | sed 's/^.*tblastn: //; s/ .*\\$//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "tblastn": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "tblastn -version 2>&1 | sed 's/^.*tblastn: //; s/ .*\\$//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@yumisims", "@gq2"], + "maintainers": ["@yumisims", "@gq2", "@vagkaratzas"] } - ] - ], - "output": { - "partitions": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "The output tab-delimited region strings and the file path", - "pattern": "*.{tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_vcfpartition": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "vcfpartition": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "vcfpartition --version | sed 's/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "vcfpartition": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "vcfpartition --version | sed 's/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@camlloyd" - ], - "maintainers": [ - "@camlloyd" - ] - } - }, - { - "name": "bioawk", - "path": "modules/nf-core/bioawk/meta.yml", - "type": "module", - "meta": { - "name": "bioawk", - "description": "Bioawk is an extension to Brian Kernighan's awk, adding the support of several common biological data formats.", - "keywords": [ - "bioawk", - "fastq", - "fasta", - "sam", - "file manipulation", - "awk" - ], - "tools": [ - { - "bioawk": { - "description": "BWK awk modified for biological data", - "homepage": "https://github.com/lh3/bioawk", - "documentation": "https://github.com/lh3/bioawk", - "tool_dev_url": "https://github.com/lh3/bioawk", - "licence": [ - "Free software license (https://github.com/lh3/bioawk/blob/master/README.awk#L1)" - ], - "identifier": "" + }, + { + "name": "blast_updateblastdb", + "path": "modules/nf-core/blast/updateblastdb/meta.yml", + "type": "module", + "meta": { + "name": "blast_updateblastdb", + "description": "Downloads a BLAST database from NCBI", + "keywords": ["fasta", "blast", "download", "database"], + "tools": [ + { + "blast": { + "description": "BLAST finds regions of similarity between biological sequences.\n", + "homepage": "https://blast.ncbi.nlm.nih.gov/Blast.cgi", + "documentation": "https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs", + "doi": "10.1016/S0022-2836(05)80360-2", + "licence": ["US-Government-Work"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'mito', single_end:false ]\n" + } + }, + { + "name": { + "type": "string", + "description": "Name of the NCBI BLAST database to be downloaded" + } + } + ] + ], + "output": { + "db": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'mito', single_end:false ]\n" + } + }, + { + "prefix": { + "type": "directory", + "description": "Output directory containing blast database files", + "pattern": "*" + } + } + ] + ], + "versions_updateblastdb": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "updateblastdb": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "update_blastdb.pl -version 2>&1 | tail -n1 | rev | cut -f1 -d ' ' | rev": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "updateblastdb": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "update_blastdb.pl -version 2>&1 | tail -n1 | rev | cut -f1 -d ' ' | rev": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@toniher"], + "maintainers": ["@toniher"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + }, + { + "name": "blat", + "path": "modules/nf-core/blat/meta.yml", + "type": "module", + "meta": { + "name": "blat", + "description": "Queries a sequence subject", + "keywords": ["blat", "sequence", "search"], + "tools": [ + { + "blat": { + "description": "BLAT is a bioinformatics software tool which performs rapid mRNA/DNA and cross-species protein alignments.", + "homepage": "https://kentinformatics.com/", + "documentation": "https://kentinformatics.com/documentation", + "doi": "10.1101/gr.229202", + "licence": ["Free for academic, nonprofit and personal use"], + "identifier": "biotools:blat" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "query": { + "type": "file", + "description": "Sequence file", + "pattern": "*.{fasta,fasta.gz,fa,fa.gz,nib,2bit}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing subject information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "subject": { + "type": "file", + "description": "Sequence file", + "pattern": "*.{fa,nib,2bit}", + "ontologies": [] + } + } + ] + ], + "output": { + "psl": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.psl": { + "type": "file", + "description": "Search results", + "pattern": "*.{psl}", + "ontologies": [] + } + } + ] + ], + "versions_blat": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "blat": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "blat 2>&1 | sed '1!d;s/^.*BLAT v. //;s/ fast.*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "blat": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "blat 2>&1 | sed '1!d;s/^.*BLAT v. //;s/ fast.*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@d-jch"], + "maintainers": ["@d-jch"] }, - { - "input": { - "type": "file", - "description": "Input biological sequence file (optionally gzipped) to be manipulated via the program specified in `$args`.\n", - "pattern": "*.{bed,gff,sam,vcf,fastq,fasta,tab,bed.gz,gff.gz,sam.gz,vcf.gz,fastq.gz,fasta.gz,tab.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3003" - }, - { - "edam": "http://edamontology.org/format_3016" - }, - { - "edam": "http://edamontology.org/format_3989" - }, - { - "edam": "http://edamontology.org/format_1975" - }, - { - "edam": "http://edamontology.org/format_1929" - }, - { - "edam": "http://edamontology.org/format_1930" - }, - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - { - "program_file": { - "type": "file", - "description": "Optional file containing logic for awk to execute. If you don't wish to use a file, you can use `ext.args2` to specify the logic.", - "pattern": "*", - "ontologies": [ + "pipelines": [ { - "edam": "http://edamontology.org/data_3671" + "name": "smrnaseq", + "version": "2.4.1" } - ] - } - }, - { - "disable_redirect_output": { - "type": "boolean", - "description": "Disable the redirection of awk output to a given file. This is\nuseful if you want to use awk's built-in redirect to write files instead\nof the shell's redirect.\n" - } - }, - { - "output_file_extension": { - "type": "string", - "description": "The suffix to add to the output file name." - } - } - ], - "output": { - "output": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.${output_file_extension}": { - "type": "file", - "description": "Manipulated version of the input sequence file.", - "ontologies": [] - } - } - ] - ], - "versions_bioawk": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bioawk": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "1.0": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bioawk": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "1.0": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } ] - ] }, - "authors": [ - "@jfy133" - ], - "maintainers": [ - "@jfy133" - ], - "schema_version": "1.1.0" - }, - "pipelines": [ { - "name": "circrna", - "version": "dev" + "name": "blobtk_create", + "path": "modules/nf-core/blobtk/create/meta.yml", + "type": "module", + "meta": { + "name": "blobtk_create", + "description": "Creates a minimal blobdir.\n", + "keywords": ["blobdir", "btk", "blobtoolkit", "metadata"], + "tools": [ + { + "btk": { + "description": "BlobTk contains a set of core functions used by BlobToolKit tools.\nImplemented in Rust, these functions are intended to be accessible\nfrom the command line, as python modules and will include web assembly\ncode for use in javascript.\n", + "homepage": "https://github.com/genomehubs/blobtk/", + "documentation": "https://github.com/genomehubs/blobtk/wiki/", + "licence": ["MIT"], + "identifier": "biotools:btk" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information and blobtk arguments\ne.g. `[ id:'sample1']`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input assembly FASTA.\n", + "pattern": "*.fasta", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + }, + { + "full_table": { + "type": "file", + "description": "Full table TSV from busco.\n", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1915" + } + ] + } + } + ] + ], + "output": { + "blobdir": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}/": { + "type": "directory", + "description": "A minimal blobdir directory\n", + "ontologies": [] + } + } + ] + ], + "versions_blobtk": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "blobtk": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "blobtk --version | cut -d' ' -f2": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "blobtk": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "blobtk --version | cut -d' ' -f2": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@DLBPointon"], + "maintainers": ["@DLBPointon"] + } }, { - "name": "rnafusion", - "version": "4.1.2" + "name": "blobtk_depth", + "path": "modules/nf-core/blobtk/depth/meta.yml", + "type": "module", + "meta": { + "name": "blobtk_depth", + "description": "Creates a bed file containing the depth of data at intervals of an aligned bam.\n", + "keywords": ["bam", "gzipped", "blobtoolkit", "depth"], + "tools": [ + { + "blobtk": { + "description": "BlobTk contains a set of core functions used by BlobToolKit tools.\nImplemented in Rust, these functions are intended to be accessible\nfrom the command line, as python modules and will include web assembly\ncode for use in javascript.\n", + "homepage": "https://github.com/genomehubs/blobtk/", + "documentation": "https://github.com/genomehubs/blobtk/wiki/", + "licence": ["MIT"], + "identifier": "biotools:blobtk" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "bam": { + "type": "file", + "description": "Algined BAM file.\n", + "pattern": "*.bam", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + }, + { + "index": { + "type": "file", + "description": "Algined BAM index file.\n", + "pattern": "*.bai|*.csi", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3327" + } + ] + } + } + ] + ], + "output": { + "bed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.regions.bed.gz": { + "type": "file", + "description": "Bed file describing the depth of regions across the genome.\n" + } + } + ] + ], + "versions_blobtk": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "blobtk": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "blobtk --version | cut -d' ' -f2": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "blobtk": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "blobtk --version | cut -d' ' -f2": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@DLBPointon"], + "maintainers": ["@DLBPointon"] + } }, { - "name": "smrnaseq", - "version": "2.4.1" - } - ] - }, - { - "name": "biobambam_bammarkduplicates2", - "path": "modules/nf-core/biobambam/bammarkduplicates2/meta.yml", - "type": "module", - "meta": { - "name": "biobambam_bammarkduplicates2", - "description": "Locate and tag duplicate reads in a BAM file", - "keywords": [ - "markduplicates", - "bam", - "cram" - ], - "tools": [ - { - "biobambam": { - "description": "biobambam is a set of tools for early stage alignment file processing.\n", - "homepage": "https://gitlab.com/german.tischler/biobambam2", - "documentation": "https://gitlab.com/german.tischler/biobambam2/-/blob/master/README.md", - "doi": "10.1186/1751-0473-9-13", - "licence": [ - "GPL v3" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM file", - "pattern": "*.{bam,cram}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - }, - { - "edam": "http://edamontology.org/format_2573" - } - ] - } + "name": "blobtk_plot", + "path": "modules/nf-core/blobtk/plot/meta.yml", + "type": "module", + "meta": { + "name": "blobtk_plot", + "description": "Creates differing styles of blobplots depending on provided arguments.\n", + "keywords": ["png", "svg", "btk", "blobtoolkit", "plot"], + "tools": [ + { + "blobtk": { + "description": "BlobTk contains a set of core functions used by BlobToolKit tools.\nImplemented in Rust, these functions are intended to be accessible\nfrom the command line, as python modules and will include web assembly\ncode for use in javascript.\n", + "homepage": "https://github.com/genomehubs/blobtk/", + "documentation": "https://github.com/genomehubs/blobtk/wiki/", + "licence": ["MIT"], + "identifier": "biotools:blobtk" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information and blobtk arguments\ne.g. `[ id:'sample1']`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input assembly FASTA.\n", + "pattern": "*.fasta", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + { + "local_path": { + "type": "directory", + "description": "A path to a Blob Dir generated as part of a greater pipeline.\n", + "pattern": "*/" + } + }, + { + "online_path": { + "type": "string", + "description": "A webaddress to a Blob Dir e.g. hosted on a BlobToolKit Viewer.\n", + "pattern": "*/" + } + }, + { + "extra_args": { + "type": "map", + "description": "Groovy Map containing sample information and blobtk arguments\ne.g. `[name: 'VIEW', args: \"-v\"]`\n" + } + }, + { + "format": { + "type": "string", + "description": "Value indicating the output format.\ne.g. `\"png\" or \"svg\"`\n" + } + } + ], + "output": { + "png": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.png": { + "type": "file", + "description": "Blobplot PNG results of input arguments.\n", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3603" + } + ] + } + } + ] + ], + "svg": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.svg": { + "type": "file", + "description": "Blobplot SVG results of input arguments.\n", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3604" + } + ] + } + } + ] + ], + "versions_blobtk": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "blobtk": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "blobtk --version | cut -d' ' -f2": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "blobtk": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "blobtk --version | cut -d' ' -f2": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@DLBPointon"], + "maintainers": ["@DLBPointon"] } - ] - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "BAM file with duplicate reads marked/removed", - "pattern": "*.{bam}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - } - ] - ], - "metrics": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.metrics.txt": { - "type": "file", - "description": "Duplicate metrics file generated by biobambam", - "pattern": "*.{metrics.txt}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3673" - } - ] - } - } - ] - ], - "versions_biobambam": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "biobambam": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bammarkduplicates2 --version |& sed '1!d; s/.*version //; s/.\\$//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "biobambam": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bammarkduplicates2 --version |& sed '1!d; s/.*version //; s/.\\$//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@muffato" - ], - "maintainers": [ - "@muffato" - ] - } - }, - { - "name": "biobambam_bammerge", - "path": "modules/nf-core/biobambam/bammerge/meta.yml", - "type": "module", - "meta": { - "name": "biobambam_bammerge", - "description": "Merge a list of sorted bam files", - "keywords": [ - "merge", - "bam", - "sorted" - ], - "tools": [ - { - "biobambam": { - "description": "biobambam is a set of tools for early stage alignment file processing.\n", - "homepage": "https://gitlab.com/german.tischler/biobambam2", - "documentation": "https://gitlab.com/german.tischler/biobambam2/-/blob/master/README.md", - "doi": "10.1186/1751-0473-9-13", - "licence": [ - "GPL v3" - ], - "identifier": "" + }, + { + "name": "blobtk_snail", + "path": "modules/nf-core/blobtk/snail/meta.yml", + "type": "module", + "meta": { + "name": "blobtk_snail", + "description": "Creates blobtk snail plots.\n", + "keywords": ["svg", "btk", "blobtoolkit", "snailplot"], + "tools": [ + { + "btk": { + "description": "BlobTk contains a set of core functions used by BlobToolKit tools.\nImplemented in Rust, these functions are intended to be accessible\nfrom the command line, as python modules and will include web assembly\ncode for use in javascript.\n", + "homepage": "https://github.com/genomehubs/blobtk/", + "documentation": "https://github.com/genomehubs/blobtk/wiki/", + "licence": ["MIT"], + "identifier": "biotools:btk" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information and blobtk arguments\ne.g. `[ id:'sample1']`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input assembly FASTA.\n", + "pattern": "*.fasta", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + }, + { + "full_table": { + "type": "file", + "description": "Full table TSV from busco.\n", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1915" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information and blobtk arguments\ne.g. `[ id:'sample1']`\n" + } + }, + { + "blob_dir": { + "type": "directory", + "description": "A local path to a BlobDir.\n", + "pattern": "*/" + } + } + ], + { + "format": { + "type": "string", + "description": "Output format for the snail plot.\n", + "pattern": "{png,svg,json,yaml}" + } + } + ], + "output": { + "images": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.{svg,png}": { + "type": "file", + "description": "BlobTK image results of input arguments.\n", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3604" + }, + { + "edam": "http://edamontology.org/format_3603" + } + ] + } + } + ] + ], + "descriptions": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.{json,yaml}": { + "type": "file", + "description": "BlobTK files describing the snail plot.\n", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + }, + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + ], + "versions_blobtk": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "blobtk": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "blobtk --version | cut -d' ' -f2": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "blobtk": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "blobtk --version | cut -d' ' -f2": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@DLBPointon"], + "maintainers": ["@DLBPointon"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + }, + { + "name": "bowtie2_align", + "path": "modules/nf-core/bowtie2/align/meta.yml", + "type": "module", + "meta": { + "name": "bowtie2_align", + "description": "Align reads to a reference genome using bowtie2", + "keywords": ["align", "map", "fasta", "fastq", "genome", "reference"], + "tools": [ + { + "bowtie2": { + "description": "Bowtie 2 is an ultrafast and memory-efficient tool for aligning\nsequencing reads to long reference sequences.\n", + "homepage": "http://bowtie-bio.sourceforge.net/bowtie2/index.shtml", + "documentation": "http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml", + "doi": "10.1186/gb-2009-10-3-r25", + "licence": ["GPL-3.0-or-later"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "index": { + "type": "file", + "description": "Bowtie2 genome index files", + "pattern": "*.ebwt", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference genome FASTA file", + "pattern": "*.{fa,fasta,fna}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + { + "save_unaligned": { + "type": "boolean", + "description": "Save reads that do not map to the reference (true) or discard them (false)\n(default: false)\n" + } + }, + { + "sort_bam": { + "type": "boolean", + "description": "use samtools sort (true) or samtools view (false)", + "pattern": "true or false" + } + } + ], + "output": { + "sam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.sam": { + "type": "file", + "description": "Output SAM file containing read alignments", + "pattern": "*.sam", + "ontologies": [] + } + } + ] + ], + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.bam": { + "type": "file", + "description": "Output BAM file containing read alignments", + "pattern": "*.bam", + "ontologies": [] + } + } + ] + ], + "cram": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.cram": { + "type": "file", + "description": "Output CRAM file containing read alignments", + "pattern": "*.cram", + "ontologies": [] + } + } + ] + ], + "csi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.csi": { + "type": "file", + "description": "Output SAM/BAM index for large inputs", + "pattern": "*.csi", + "ontologies": [] + } + } + ] + ], + "crai": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.crai": { + "type": "file", + "description": "Output CRAM index", + "pattern": "*.crai", + "ontologies": [] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.log": { + "type": "file", + "description": "Alignment log", + "pattern": "*.log", + "ontologies": [] + } + } + ] + ], + "fastq": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*fastq.gz": { + "type": "file", + "description": "Unaligned FastQ files", + "pattern": "*.fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "versions_bowtie2": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bowtie2": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bowtie2 --version 2>&1 | sed -n 's/.*bowtie2-align-s version //p'": { + "type": "eval", + "description": "The expression to obtain the version of bowtie2" + } + } + ] + ], + "versions_samtools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "samtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "samtools version | sed '1!d;s/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of samtools" + } + } + ] + ], + "versions_pigz": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "pigz": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pigz --version 2>&1 | sed 's/pigz //'": { + "type": "eval", + "description": "The expression to obtain the version of pigz" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bowtie2": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bowtie2 --version 2>&1 | sed -n 's/.*bowtie2-align-s version //p'": { + "type": "eval", + "description": "The expression to obtain the version of bowtie2" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "samtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "samtools version | sed '1!d;s/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of samtools" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "pigz": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pigz --version 2>&1 | sed 's/pigz //'": { + "type": "eval", + "description": "The expression to obtain the version of pigz" + } + } + ] + ] + }, + "authors": ["@joseespinosa", "@drpatelh"], + "maintainers": ["@joseespinosa", "@drpatelh"] }, - { - "bam": { - "type": "file", - "description": "List containing 1 or more bam files", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - } - ] - ], - "output": { - 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"http://edamontology.org/format_2330" - } - ] - } - } - ] - ], - "versions_biobambam": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "biobambam": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bammerge --version |& sed '1!d; s/.*version //; s/.\\$//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "biobambam": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bammerge --version |& sed '1!d; s/.*version //; s/.\\$//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "atacseq", + "version": "2.1.2" + }, + { + "name": "callingcards", + "version": "1.0.0" + }, + { + "name": "chipseq", + 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"map", - "description": "Groovy Map containing genome information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome in FASTA format (optional)", - "pattern": "*.{fa,fasta,fna}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } + }, + { + "name": "bowtie2_build", + "path": "modules/nf-core/bowtie2/build/meta.yml", + "type": "module", + "meta": { + "name": "bowtie2_build", + "description": "Builds bowtie index for reference genome", + "keywords": ["build", "index", "fasta", "genome", "reference"], + "tools": [ + { + "bowtie2": { + "description": "Bowtie 2 is an ultrafast and memory-efficient tool for aligning\nsequencing reads to long reference sequences.\n", + "homepage": "http://bowtie-bio.sourceforge.net/bowtie2/index.shtml", + "documentation": "http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml", + "doi": "10.1038/nmeth.1923", + "licence": ["GPL-3.0-or-later"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference genome FASTA file", + "pattern": "*.{fa,fasta,fna}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ] + ], + "output": { + "index": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bowtie2": { + "type": "directory", + "description": "Bowtie2 genome index files", + "pattern": "*.bt2", + "ontologies": [] + } + } + ] + ], + "versions_bowtie2": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bowtie2": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bowtie2 --version 2>&1 | sed -n 's/.*bowtie2-align-s version //p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bowtie2": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bowtie2 --version 2>&1 | sed -n 's/.*bowtie2-align-s version //p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@joseespinosa", "@drpatelh"], + "maintainers": ["@joseespinosa", "@drpatelh"] }, - { - "fai": { - "type": "file", - "description": "Reference genome in FASTA index format (optional)", - "pattern": "*.{fai}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3673" - } - ] - } - } - ] - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - 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"description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.metrics.txt": { - "type": "file", - "description": "Duplicate metrics file generated by biobambam", - "pattern": "*.{metrics.txt}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3675" - } - ] - } - } - ] - ], - "versions_biobambam": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "biobambam": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bamsormadup --version |& sed '1!d; s/.*version //; s/.\\$//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "biobambam": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bamsormadup --version |& sed '1!d; s/.*version //; s/.\\$//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "atacseq", + "version": "2.1.2" + }, + { + "name": "callingcards", + "version": "1.0.0" + }, + { + "name": "chipseq", + "version": "2.1.0" + }, + { + "name": "circrna", + "version": "dev" + }, + { + "name": "coproid", + "version": "2.0.1" + }, + { + "name": "crisprseq", + "version": "2.3.0" + }, + { + "name": "cutandrun", + "version": "3.2.2" + }, + { + "name": "hic", + "version": "2.1.0" + }, + { + "name": "marsseq", + "version": "1.0.3" + }, + { + "name": "nascent", + "version": "2.3.0" + }, + { + "name": "phageannotator", + "version": "dev" + }, + { + "name": "readsimulator", + "version": "1.0.1" + }, + { + "name": "references", + "version": "0.1" + }, + { + "name": "rnaseq", + "version": "3.26.0" + }, + { + "name": "sammyseq", + "version": "dev" + }, + { + "name": "smrnaseq", + "version": "2.4.1" + }, + { + "name": "taxprofiler", + "version": "2.0.0" + }, + { + "name": "viralmetagenome", + "version": "1.1.1" + }, + { + "name": "viralrecon", + "version": "3.0.0" + } ] - ] - }, - "authors": [ - "@matthdsm" - ], - "maintainers": [ - "@matthdsm" - ] - } - }, - { - "name": "bioformats2raw", - "path": "modules/nf-core/bioformats2raw/meta.yml", - "type": "module", - "meta": { - "name": "bioformats2raw", - "description": "Java application to convert image file formats, including .mrxs, to an intermediate Zarr structure compatible with the OME-NGFF specification.", - "keywords": [ - "zarr", - "ome-ngff", - "imaging" - ], - "tools": [ - { - "bioformats2raw": { - "description": "Java application to convert image file formats, including .mrxs, to an intermediate Zarr structure compatible with the OME-NGFF specification.", - "homepage": "https://github.com/glencoesoftware/bioformats2raw", - "documentation": "https://github.com/glencoesoftware/bioformats2raw", - "tool_dev_url": "https://github.com/glencoesoftware/bioformats2raw", - "licence": [ - "GPL-2.0" - ], - "identifier": "biotools:bioformats2raw" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } + }, + { + "name": "bowtie_align", + "path": "modules/nf-core/bowtie/align/meta.yml", + "type": "module", + "meta": { + "name": "bowtie_align", + "description": "Align reads to a reference genome using bowtie", + "keywords": ["align", "map", "fastq", "fasta", "genome", "reference"], + "tools": [ + { + "bowtie": { + "description": "bowtie is a software package for mapping DNA sequences against\na large reference genome, such as the human genome.\n", + "homepage": "http://bowtie-bio.sourceforge.net/index.shtml", + "documentation": "http://bowtie-bio.sourceforge.net/manual.shtml", + "arxiv": "arXiv:1303.3997", + "licence": ["Artistic-2.0"], + "identifier": "biotools:bowtie" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing genome information\ne.g. [ id:'sarscov2' ]\n" + } + }, + { + "index": { + "type": "file", + "description": "Bowtie genome index files", + "pattern": "*.ebwt", + "ontologies": [] + } + } + ], + { + "save_unaligned": { + "type": "boolean", + "description": "Whether to save fastq files containing the reads which did not align." + } + } + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.bam": { + "type": "file", + "description": "Output BAM file containing read alignments", + "pattern": "*.{bam}", + "ontologies": [] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.out": { + "type": "file", + "description": "Log file", + "pattern": "*.log", + "ontologies": [] + } + } + ] + ], + "fastq": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*fastq.gz": { + "type": "file", + "description": "Unaligned FastQ files", + "pattern": "*.fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "versions_bowtie": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bowtie": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bowtie --version 2>&1 | sed -n 's/.*bowtie-align-s version //p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_samtools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "samtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "samtools version | sed '1!d;s/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_gzip": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gzip": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gzip --version 2>&1 | sed '1!d;s/gzip //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bowtie": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bowtie --version 2>&1 | sed -n 's/.*bowtie-align-s version //p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "samtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "samtools version | sed '1!d;s/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gzip": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gzip --version 2>&1 | sed '1!d;s/gzip //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@kevinmenden"], + "maintainers": ["@kevinmenden"] }, - { - "image": { - "type": "file", - "description": "bioformats supported image file format", - "pattern": "*.{tif,tiff,svs,mrxs}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3727" - }, - { - "edam": "http://edamontology.org/format_3591" - } - ] - } - } - ] - ], - "output": { - "omezarr": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } - }, - { - "*ome.zarr": { - "type": "directory", - "description": "OME-Zarr fileset for image data storage. Specification can be found at https://ngff.openmicroscopy.org/latest/#storage-format", - "pattern": "*{ome.zarr}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3915" - } - ] - } - } - ] - ], - "versions_bioformats2raw": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bioformats2raw": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bioformats2raw --version |& sed -n \"1s/Version = //p\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_bioformats": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bio-formats": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bioformats2raw --version |& sed -n \"2s/Bio-Formats version = //p\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_ngff": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "ngff": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bioformats2raw --version |& sed -n \"3s/NGFF specification version = //p\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bioformats2raw": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bioformats2raw --version |& sed -n \"1s/Version = //p\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bio-formats": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bioformats2raw --version |& sed -n \"2s/Bio-Formats version = //p\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "ngff": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bioformats2raw --version |& sed -n \"3s/NGFF specification version = //p\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "callingcards", + "version": "1.0.0" + }, + { + "name": "circrna", + "version": "dev" + }, + { + "name": "smrnaseq", + "version": "2.4.1" + } ] - ] - }, - "authors": [ - "@CaroAMN" - ], - "maintainers": [ - "@CaroAMN" - ] - } - }, - { - "name": "biohansel", - "path": "modules/nf-core/biohansel/meta.yml", - "type": "module", - "meta": { - "name": "biohansel", - "description": "Use k-mers to rapidly subtype S. enterica genomes", - "keywords": [ - "Salmonella enterica", - "subtyping", - "prokaryote" - ], - "tools": [ - { - "biohansel": { - "description": "Subtype Salmonella enterica genomes using 33bp k-mer typing schemes.", - "homepage": "https://github.com/phac-nml/biohansel", - "documentation": "https://github.com/phac-nml/biohansel", - "tool_dev_url": "https://github.com/phac-nml/biohansel", - "doi": "10.1101/2020.01.10.902056", - "licence": [ - "Apache-2.0 license" - ], - "identifier": "biotools:biohansel" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + }, + { + "name": "bowtie_build", + "path": "modules/nf-core/bowtie/build/meta.yml", + "type": "module", + "meta": { + "name": "bowtie_build", + "description": "Create bowtie index for reference genome", + "keywords": ["index", "fasta", "genome", "reference"], + "tools": [ + { + "bowtie": { + "description": "bowtie is a software package for mapping DNA sequences against\na large reference genome, such as the human genome.\n", + "homepage": "http://bowtie-bio.sourceforge.net/index.shtml", + "documentation": "http://bowtie-bio.sourceforge.net/manual.shtml", + "arxiv": "arXiv:1303.3997", + "licence": ["Artistic-2.0"], + "identifier": "biotools:bowtie" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information about the genome fasta\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input genome fasta file", + "ontologies": [] + } + } + ] + ], + "output": { + "index": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information about the genome fasta\ne.g. [ id:'test' ]\n" + } + }, + { + "bowtie": { + "type": "string", + "description": "Folder containing bowtie genome index files", + "pattern": "*.ebwt", + "ontologies": [] + } + } + ] + ], + "versions_bowtie": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bowtie": { + "type": "string", + "description": "Folder containing bowtie genome index files", + "pattern": "*.ebwt", + "ontologies": [] + } + }, + { + "bowtie --version 2>&1 | sed -n 's/.*bowtie-align-s version //p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bowtie": { + "type": "string", + "description": "Folder containing bowtie genome index files", + "pattern": "*.ebwt", + "ontologies": [] + } + }, + { + "bowtie --version 2>&1 | sed -n 's/.*bowtie-align-s version //p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@kevinmenden", "@drpatelh"], + "maintainers": ["@kevinmenden", "@drpatelh"] }, - { - "seqs": { - "type": "file", - "description": "FASTA or FASTQ", - "pattern": "*.{fasta.gz,fa.gz,fna.gz,fastq.gz,fq.gz}", - "ontologies": [] - } - } - ], - { - "scheme_metadata": { - "type": "file", - "description": "Scheme subtype metadata table", - "pattern": "*.{tab,tsv,txt}", - "ontologies": [ + "pipelines": [ + { + "name": "callingcards", + "version": "1.0.0" + }, + { + "name": "circrna", + "version": "dev" + }, + { + "name": "references", + "version": "0.1" + }, { - "edam": "http://edamontology.org/format_3475" + "name": "smrnaseq", + "version": "2.4.1" } - ] - } - } - ], - "output": { - "summary": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}-summary.txt": { - "type": "file", - "description": "Tab-delimited subtyping summary output", - "pattern": "*summary.txt", - "ontologies": [] - } - } - ] - ], - "kmer_results": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}-kmer-results.txt": { - "type": "file", - "description": "Tab-delimited subtyping kmer matching output", - "pattern": "*kmer-results.txt", - "ontologies": [] - } - } - ] - ], - "simple_summary": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}-simple-summary.txt": { - "type": "file", - "description": "A simple version of summary output", - "pattern": "*simple-summary.txt", - "ontologies": [] - } - } ] - ], - "versions_biohansel": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "biohansel": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "hansel --version 2>&1 | sed 's/^.*hansel //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "biohansel": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "hansel --version 2>&1 | sed 's/^.*hansel //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@rpetit3" - ], - "maintainers": [ - "@rpetit3" - ] - } - }, - { - "name": "biomformat_convert", - "path": "modules/nf-core/biomformat/convert/meta.yml", - "type": "module", - "meta": { - "name": "biomformat_convert", - "description": "Convert biom table to different format.\nConversion between text tab-delimited, BIOM-v1 (JSON), and BIOM-v2 (HDF5) formats are supported\n", - "keywords": [ - "biom", - "feature table", - "formatting", - "conversion", - "amplicon sequences", - "metagenomics", - "metatranscriptomics" - ], - "tools": [ - { - "biomformat": { - "description": "Biological Observation Matrix (BIOM) format.\nThis package includes basic tools for converting, summarizing, and adding metadata to biom-format files.\n", - "homepage": "http://biom-format.org/index.html", - "documentation": "http://biom-format.org/documentation/index.html", - "tool_dev_url": "https://github.com/biocore/biom-format", - "doi": "10.1186/2047-217X-1-7", - "licence": [ - "BSD License" - ], - "identifier": "biotools:biomformat" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } + }, + { + "name": "bracken_bracken", + "path": "modules/nf-core/bracken/bracken/meta.yml", + "type": "module", + "meta": { + "name": "bracken_bracken", + "description": "Re-estimate taxonomic abundance of metagenomic samples analyzed by kraken.", + "keywords": ["bracken", "metagenomics", "abundance", "kraken2"], + "tools": [ + { + "bracken": { + "description": "Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.", + "homepage": "https://ccb.jhu.edu/software/bracken/", + "documentation": "https://ccb.jhu.edu/software/bracken/index.shtml?t=manual", + "tool_dev_url": "https://github.com/jenniferlu717/Bracken", + "doi": "10.7717/peerj-cs.104", + "licence": ["GPL v3"], + "identifier": "biotools:bracken" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "kraken_report": { + "type": "file", + "description": "TSV file with six columns coming from kraken2 output", + "pattern": "*.{tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + { + "database": { + "type": "file", + "description": "Directory containing the kraken2/Bracken files for analysis", + "pattern": "*", + "ontologies": [] + } + } + ], + "output": { + "reports": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*.{tsv}" + } + }, + { + "bracken_report": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*.{tsv}" + } + } + ] + ], + "txt": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*.{tsv}" + } + }, + { + "bracken_kraken_style_report": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*.txt" + } + } + ] + ], + "versions_bracken": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bracken": { + "type": "string", + "description": "The tool name" + } + }, + { + "bracken -v | cut -f2 -d\"v\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bracken": { + "type": "string", + "description": "The tool name" + } + }, + { + "bracken -v | cut -f2 -d\"v\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@Midnighter"], + "maintainers": ["@Midnighter"] }, - { - "biom": { - "type": "file", - "description": "Biom formatted feature table file", - "pattern": "*.{biom,txt,tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3746" - }, - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "output": { - "biom": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.biom": { - "type": "file", - "description": "Converted biom file", - "pattern": "*.biom", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3746" - } - ] - } - } - ] - ], - "txt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.txt": { - "type": "file", - "description": "Converted txt file", - "pattern": "*.txt", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_biomformat": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "biom-format": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "biom --version | sed 's/biom, version //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "biom-format": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "biom --version | sed 's/biom, version //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "rnaseq", + "version": "3.26.0" + }, + { + "name": "taxprofiler", + "version": "2.0.0" + }, + { + "name": "viralmetagenome", + "version": "1.1.1" + } ] - ] - }, - "authors": [ - "@jcbioinformatics" - ], - "maintainers": [ - "@jcbioinformatics" - ] - } - }, - { - "name": "biscuit_align", - "path": "modules/nf-core/biscuit/align/meta.yml", - "type": "module", - "meta": { - "name": "biscuit_align", - "description": "Aligns single- or paired-end reads from bisulfite-converted libraries to a reference genome using Biscuit.", - "keywords": [ - "biscuit", - "DNA methylation", - "WGBS", - "scWGBS", - "bisulfite sequencing", - "aligner", - "bam" - ], - "tools": [ - { - "biscuit": { - "description": "A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data", - "homepage": "https://huishenlab.github.io/biscuit/", - "documentation": "https://huishenlab.github.io/biscuit/docs/alignment", - "tool_dev_url": "https://github.com/huishenlab/biscuit", - "licence": [ - "MIT" - ], - "identifier": "biotools:biscuit" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input genome fasta file", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + }, + { + "name": "bracken_build", + "path": "modules/nf-core/bracken/build/meta.yml", + "type": "module", + "meta": { + "name": "bracken_build", + "description": "Extends a Kraken2 database to be compatible with Bracken", + "keywords": ["kraken2", "bracken", "database", "build"], + "tools": [ + { + "bracken": { + "description": "Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.", + "homepage": "https://ccb.jhu.edu/software/bracken/", + "documentation": "https://ccb.jhu.edu/software/bracken/", + "tool_dev_url": "https://github.com/jenniferlu717/Bracken/", + "doi": "10.7717/peerj-cs.104 ", + "licence": ["GPL v3"], + "identifier": "biotools:bracken" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "k2d": { + "type": "file", + "description": "Kraken2 k2d binary database files", + "pattern": "*.k2d", + "ontologies": [] + } + }, + { + "map": { + "type": "file", + "description": "Kraken2 k2d binary database taxonomy to sequencing mapping file", + "pattern": "*.map", + "ontologies": [] + } + }, + { + "library": { + "type": "file", + "description": "Kraken2 masked FASTA files used to build the database", + "pattern": "*.fasta", + "ontologies": [] + } + }, + { + "taxonomy": { + "type": "file", + "description": "Kraken2 nodes.dmp, names.dmp, and .accession2taxid taxonomy files", + "pattern": "*.{dmp,accession2taxid}", + "ontologies": [] + } + } + ] + ], + "output": { + "db": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "bracken-database/": { + "type": "directory", + "description": "Directory contains the database that can be used to perform taxonomic classification\n\nIMPORTANT: this output directory will be hardcoded as 'bracken-database/' inside the module\nto prevent issues of containers following symlinks in symlinks.\n\nTo give a user the option to provide custom name for the database directory within a pipeline, you should\ncustomise this name using during pipeline output publication via the pipeline's publishDir or workflow output customisation options.\n", + "pattern": "bracken-database/", + "ontologies": [ + { + "edam": "http://edamontology.org/data_1049" + } + ] + } + } + ] + ], + "db_separated": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "bracken-database/database*": { + "type": "file", + "description": "Bracken kmer distribution files", + "pattern": "database*", + "ontologies": [] + } + }, + { + "bracken-database/*k2d": { + "type": "file", + "description": "Kraken2 k2d binary database files", + "pattern": "*.k2d", + "ontologies": [] + } + }, + { + "bracken-database/*map": { + "type": "file", + "description": "Kraken2 k2d binary database taxonomy to sequencing mapping file", + "pattern": "*.map", + "ontologies": [] + } + }, + { + "bracken-database/library/added/*": { + "type": "file", + "description": "Kraken2 masked FASTA files used to build the database", + "pattern": "*.fasta", + "ontologies": [] + } + }, + { + "bracken-database/taxonomy/*": { + "type": "file", + "description": "Kraken2 nodes.dmp, names.dmp, and .accession2taxid taxonomy files", + "pattern": "*.{dmp,accession2taxid}", + "ontologies": [] + } + } + ] + ], + "versions_bracken": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bracken": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bracken -v | cut -f2 -d'v'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bracken": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bracken -v | cut -f2 -d'v'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@jfy133"], + "maintainers": ["@jfy133"] }, - { - "index": { - "type": "directory", - "description": "Directory containing biscuit genome index" - } - } - ] - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "Output BAM file containing read alignments", - "pattern": "*.{bam}", - "ontologies": [] - } - } - ] - ], - "bai": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bai": { - "type": "file", - "description": "Output BAM index", - "pattern": "*.{bai}", - "ontologies": [] - } - } - ] - ], - "versions_biscuit": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "biscuit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "biscuit version |& sed '1!d; s/^.*BISCUIT Version: //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_samtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools --version |& sed '1!d; s/^.*samtools //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "biscuit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "biscuit version |& sed '1!d; s/^.*BISCUIT Version: //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools --version |& sed '1!d; s/^.*samtools //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "createtaxdb", + "version": "3.0.0" + } ] - ] - }, - "authors": [ - "@njspix" - ], - "maintainers": [ - "@njspix", - "@sateeshperi" - ] - } - }, - { - "name": "biscuit_biscuitblaster", - "path": "modules/nf-core/biscuit/biscuitblaster/meta.yml", - "type": "module", - "meta": { - "name": "biscuit_blaster", - "description": "A fast, compact one-liner to produce duplicate-marked, sorted, and indexed BAM files using Biscuit", - "keywords": [ - "biscuit", - "DNA methylation", - "WGBS", - "scWGBS", - "bisulfite sequencing", - "aligner", - "bam" - ], - "tools": [ - { - "biscuit": { - "description": "A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data", - "homepage": "https://huishenlab.github.io/biscuit/", - "documentation": "https://huishenlab.github.io/biscuit/biscuitblaster/", - "tool_dev_url": "https://github.com/huishenlab/biscuit", - "licence": [ - "MIT" - ], - "identifier": "biotools:biscuit" - } - }, - { - "samblaster": { - "description": "samblaster is a fast and flexible program for marking duplicates in read-id grouped paired-end SAM files.\nIt can also optionally output discordant read pairs and/or split read mappings to separate SAM files,\nand/or unmapped/clipped reads to a separate FASTQ file.\nBy default, samblaster reads SAM input from stdin and writes SAM to stdout.\n", - "documentation": "https://github.com/GregoryFaust/samblaster", - "tool_dev_url": "https://github.com/GregoryFaust/samblaster", - "doi": "10.1093/bioinformatics/btu314", - "licence": [ - "MIT" - ], - "identifier": "biotools:biscuit" - } - }, - { - "samtools": { - "description": "SAMtools is a set of utilities for interacting with and post-processing\nshort DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.\nThese files are generated as output by short read aligners like BWA.\n", - "homepage": "http://www.htslib.org/", - "documentation": "http://www.htslib.org/doc/samtools.html", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "identifier": "biotools:biscuit" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input genome fasta file", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + }, + { + "name": "bracken_combinebrackenoutputs", + "path": "modules/nf-core/bracken/combinebrackenoutputs/meta.yml", + "type": "module", + "meta": { + "name": "bracken_combinebrackenoutputs", + "description": "Combine output of metagenomic samples analyzed by bracken.", + "keywords": ["bracken", "metagenomics", "postprocessing", "reporting"], + "tools": [ + { + "bracken": { + "description": "Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.", + "homepage": "https://ccb.jhu.edu/software/bracken/", + "documentation": "https://ccb.jhu.edu/software/bracken/index.shtml?t=manual", + "tool_dev_url": "https://github.com/jenniferlu717/Bracken", + "doi": "10.7717/peerj-cs.104", + "licence": ["GPL v3"], + "identifier": "biotools:bracken" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "List of output files from bracken", + "pattern": "*", + "ontologies": [] + } + } + ] + ], + "output": { + "txt": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "Combined output in table format", + "pattern": "*.txt", + "ontologies": [] + } + } + ] + ], + "versions_combine_bracken_outputs": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "combine_bracken_outputs": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bracken -v | cut -f2 -d\"v\"": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "combine_bracken_outputs": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bracken -v | cut -f2 -d\"v\"": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@jfy133"], + "maintainers": ["@jfy133"] }, - { - "index": { - "type": "directory", - "description": "Directory containing biscuit genome index" - } - } - ] - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "Output BAM file containing read alignments", - "pattern": "*.{bam}", - "ontologies": [] - } - } - ] - ], - "bai": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bai": { - "type": "file", - "description": "Output BAM index", - "pattern": "*.{bai}", - "ontologies": [] - } - } - ] - ], - "versions_biscuit": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "biscuit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "biscuit version |& sed '1!d; s/^.*BISCUIT Version: //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_samtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools --version |& sed '1!d; s/^.*samtools //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_samblaster": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samblaster": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samblaster --version |& sed 's/^.*samblaster: Version //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "biscuit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "biscuit version |& sed '1!d; s/^.*BISCUIT Version: //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools --version |& sed '1!d; s/^.*samtools //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samblaster": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samblaster --version |& sed 's/^.*samblaster: Version //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@njspix" - ], - "maintainers": [ - "@njspix", - "@sateeshperi" - ] - } - }, - { - "name": "biscuit_bsconv", - "path": "modules/nf-core/biscuit/bsconv/meta.yml", - "type": "module", - "meta": { - "name": "biscuit_bsconv", - "description": "Summarize and/or filter reads based on bisulfite conversion rate", - "keywords": [ - "biscuit", - "DNA methylation", - "WGBS", - "scWGBS", - "bisulfite sequencing", - "aligner", - "bam", - "filter" - ], - "tools": [ - { - "biscuit": { - "description": "A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data", - "homepage": "https://huishenlab.github.io/biscuit/", - "documentation": "https://huishenlab.github.io/biscuit/docs/subcommand_help.html#biscuit-bsconv", - "tool_dev_url": "https://github.com/huishenlab/biscuit", - "licence": [ - "MIT" - ], - "identifier": "biotools:biscuit" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file contained mapped reads", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bai": { - "type": "file", - "description": "BAM file index", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input genome fasta file", - "ontologies": [] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "index": { - "type": "directory", - "description": "Directory containing biscuit genome index" - } - } - ] - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "Output BAM file containing filtered read alignments", - "pattern": "*.{bam}", - "ontologies": [] - } - } - ] - ], - "versions_biscuit": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "biscuit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "biscuit version |& sed '1!d; s/^.*BISCUIT Version: //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "biscuit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "biscuit version |& sed '1!d; s/^.*BISCUIT Version: //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@njspix" - ], - "maintainers": [ - "@njspix", - "@sateeshperi" - ] - } - }, - { - "name": "biscuit_epiread", - "path": "modules/nf-core/biscuit/epiread/meta.yml", - "type": "module", - "meta": { - "name": "biscuit_epiread", - "description": "Summarizes read-level methylation (and optionally SNV) information from a\nBiscuit BAM file in a standard-compliant BED format.\n", - "keywords": [ - "biscuit", - "DNA methylation", - "WGBS", - "scWGBS", - "bisulfite sequencing", - "aligner", - "bam" - ], - "tools": [ - { - "biscuit": { - "description": "A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data", - "homepage": "https://huishenlab.github.io/biscuit/", - "documentation": "https://huishenlab.github.io/biscuit/epiread_format/", - "tool_dev_url": "https://github.com/huishenlab/biscuit", - "licence": [ - "MIT" - ], - "identifier": "biotools:biscuit" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file contained mapped reads", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bai": { - "type": "file", - "description": "BAM file index", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "snp_bed": { - "type": "file", - "description": "BED file containing SNP information (optional)", - "ontologies": [] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input genome fasta file", - "ontologies": [] - } - } - ], - [ - { - "meta5": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "index": { - "type": "directory", - "description": "Directory containing biscuit genome index" - } - } - ] - ], - "output": { - "bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bed.gz": { - "type": "file", - "description": "Gzipped BED file with methylation (and optionally SNV) information", - "pattern": "*.{epiread.bed.gz}", - "ontologies": [] - } - } - ] - ], - "versions_biscuit": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "biscuit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "biscuit version |& sed '1!d; s/^.*BISCUIT Version: //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_samtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools --version |& sed '1!d; s/^.*samtools //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "biscuit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "biscuit version |& sed '1!d; s/^.*BISCUIT Version: //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools --version |& sed '1!d; s/^.*samtools //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@njspix" - ], - "maintainers": [ - "@njspix", - "@sateeshperi" - ] - } - }, - { - "name": "biscuit_index", - "path": "modules/nf-core/biscuit/index/meta.yml", - "type": "module", - "meta": { - "name": "biscuit_index", - "description": "Indexes a reference genome for use with Biscuit", - "keywords": [ - "biscuit", - "DNA methylation", - "WGBS", - "scWGBS", - "bisulfite sequencing", - "index", - "reference", - "fasta" - ], - "tools": [ - { - "biscuit": { - "description": "A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data", - "homepage": "https://huishenlab.github.io/biscuit/", - "documentation": "https://huishenlab.github.io/biscuit/docs/alignment", - "tool_dev_url": "https://github.com/huishenlab/biscuit", - "licence": [ - "MIT" - ], - "identifier": "biotools:biscuit" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input genome fasta file", - "ontologies": [] - } - } - ] - ], - "output": { - "index": [ - [ - { - "meta": { - "type": "directory", - "description": "Directory containing biscuit genome index", - "pattern": "index" - } - }, - { - "BiscuitIndex": { - "type": "directory", - "description": "Directory containing biscuit genome index", - "pattern": "index" - } - } - ] - ], - "versions_biscuit": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "biscuit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "biscuit version |& sed '1!d; s/^.*BISCUIT Version: //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "biscuit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "biscuit version |& sed '1!d; s/^.*BISCUIT Version: //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@njspix" - ], - "maintainers": [ - "@njspix", - "@sateeshperi" - ] - } - }, - { - "name": "biscuit_mergecg", - "path": "modules/nf-core/biscuit/mergecg/meta.yml", - "type": "module", - "meta": { - "name": "biscuit_mergecg", - "description": "Merges methylation information for opposite-strand C's in a CpG context", - "keywords": [ - "biscuit", - "DNA methylation", - "WGBS", - "scWGBS", - "bisulfite sequencing", - "aligner", - "bed" - ], - "tools": [ - { - "biscuit": { - "description": "A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data", - "homepage": "https://huishenlab.github.io/biscuit/", - "documentation": "https://huishenlab.github.io/biscuit/docs/methylextraction.html", - "tool_dev_url": "https://github.com/huishenlab/biscuit", - "licence": [ - "MIT" - ], - "identifier": "biotools:biscuit" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bed": { - "type": "file", - "description": "Biscuit BED file (output of biscuit vcf2bed)\n", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input genome fasta file", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "index": { - "type": "directory", - "description": "Directory containing biscuit genome index" - } - } - ] - ], - "output": { - "bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bed.gz": { - "type": "file", - "description": "Gzipped BED file with merged methylation information", - "pattern": "*.bed.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "versions_biscuit": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "biscuit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "biscuit version |& sed '1!d; s/^.*BISCUIT Version: //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_samtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools --version |& sed '1!d; s/^.*samtools //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "biscuit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "biscuit version |& sed '1!d; s/^.*BISCUIT Version: //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools --version |& sed '1!d; s/^.*samtools //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@njspix" - ], - "maintainers": [ - "@njspix", - "@sateeshperi" - ] - } - }, - { - "name": "biscuit_pileup", - "path": "modules/nf-core/biscuit/pileup/meta.yml", - "type": "module", - "meta": { - "name": "biscuit_pileup", - "description": "Computes cytosine methylation and callable SNV mutations, optionally in reference to a germline BAM to call somatic variants", - "keywords": [ - "bisulfite", - "DNA methylation", - "pileup", - "variant calling", - "WGBS", - "scWGBS", - "bam", - "vcf" - ], - "tools": [ - { - "biscuit": { - "description": "A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data", - "homepage": "https://huishenlab.github.io/biscuit/", - "documentation": "https://huishenlab.github.io/biscuit/docs/pileup.html", - "tool_dev_url": "https://github.com/huishenlab/biscuit", - "licence": [ - "MIT" - ], - "identifier": "biotools:biscuit" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "normal_bams": { - "type": "file", - "description": "BAM files to be analyzed. If no tumor_bam file is provided, any number of \"normal\" BAMs may be provided\n(\"normal\" here is just a semantic issue, these BAMs could be from tumor or any other kind of tissue). If a\ntumor BAM file is provided, exactly one normal (germline) BAM must be provided.\n", - "pattern": "*.{bam}", - "ontologies": [] - } - }, - { - "normal_bais": { - "type": "file", - "description": "BAM index file or files corresponding to the provided normal_bams", - "pattern": "*.{bai}", - "ontologies": [] - } - }, - { - "tumor_bam": { - "type": "file", - "description": "Optional. If a tumor BAM file is provided, pileup will run in \"somatic\" mode and will annotate variants with\ntheir somatic state (present in tumor only, present in normal only, present in both, etc). Note that if a\ntumor BAM file is provided, exactly one normal BAM must be provided.\n", - "pattern": "*.{bam}", - "ontologies": [] - } - }, - { - "tumor_bai": { - "type": "file", - "description": "Optional. BAM index file corresponding to provided tumor_bam", - "pattern": "*.{bai}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input genome fasta file", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "index": { - "type": "directory", - "description": "Directory containing biscuit genome index" - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.vcf.gz": { - "type": "file", - "description": "vcf file with methylation information", - "pattern": "*.{vcf.gz}", - "ontologies": [] - } - } - ] - ], - "versions_biscuit": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "biscuit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "biscuit version |& sed '1!d; s/^.*BISCUIT Version: //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_bgzip": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bgzip": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bgzip --version | head -1 | sed \"s/bgzip (htslib) //\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "biscuit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "biscuit version |& sed '1!d; s/^.*BISCUIT Version: //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bgzip": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bgzip --version | head -1 | sed \"s/bgzip (htslib) //\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@njspix" - ], - "maintainers": [ - "@njspix", - "@sateeshperi" - ] - } - }, - { - "name": "biscuit_qc", - "path": "modules/nf-core/biscuit/qc/meta.yml", - "type": "module", - "meta": { - "name": "biscuit_qc", - "description": "Perform basic quality control on a BAM file generated with Biscuit", - "keywords": [ - "biscuit", - "DNA methylation", - "WGBS", - "scWGBS", - "bisulfite sequencing", - "index", - "BAM", - "quality control" - ], - "tools": [ - { - "biscuit": { - "description": "A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data", - "homepage": "https://huishenlab.github.io/biscuit/", - "documentation": "https://huishenlab.github.io/biscuit/docs/subcommand_help.html#biscuit-qc", - "tool_dev_url": "https://github.com/huishenlab/biscuit", - "licence": [ - "MIT" - ], - "identifier": "biotools:biscuit" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file produced using Biscuit", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input genome fasta file", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "index": { - "type": "directory", - "description": "Directory containing biscuit genome index" - } - } - ] - ], - "output": { - "reports": [ - [ - { - "meta": { - "type": "file", - "description": "Summary files containing the following information:\n - CpG retention by position in read\n - CpH retention by position in read\n - Read duplication statistics\n - Insert size distribution\n - Distribution of mapping qualities\n - Proportion of reads mapping to each strand\n - Read-averaged cytosine conversion rate for CpA, CpC, CpG, and CpT\n", - "pattern": "*.txt", - "ontologies": [] - } - }, - { - "*.txt": { - "type": "file", - "description": "Summary files containing the following information:\n - CpG retention by position in read\n - CpH retention by position in read\n - Read duplication statistics\n - Insert size distribution\n - Distribution of mapping qualities\n - Proportion of reads mapping to each strand\n - Read-averaged cytosine conversion rate for CpA, CpC, CpG, and CpT\n", - "pattern": "*.txt", - "ontologies": [] - } - } - ] - ], - "versions_biscuit": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "biscuit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "biscuit version |& sed '1!d; s/^.*BISCUIT Version: //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "biscuit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "biscuit version |& sed '1!d; s/^.*BISCUIT Version: //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@njspix" - ], - "maintainers": [ - "@njspix", - "@sateeshperi" - ] - } - }, - { - "name": "biscuit_vcf2bed", - "path": "modules/nf-core/biscuit/vcf2bed/meta.yml", - "type": "module", - "meta": { - "name": "biscuit_vcf2bed", - "description": "Summarizes methylation or SNV information from a Biscuit VCF in a\nstandard-compliant BED file.\n", - "keywords": [ - "biscuit", - "DNA methylation", - "WGBS", - "scWGBS", - "bisulfite sequencing", - "aligner", - "vcf" - ], - "tools": [ - { - "biscuit": { - "description": "A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data", - "homepage": "https://huishenlab.github.io/biscuit/", - "documentation": "https://huishenlab.github.io/biscuit/docs/methylextraction.html", - "tool_dev_url": "https://github.com/huishenlab/biscuit", - "licence": [ - "MIT" - ], - "identifier": "biotools:biscuit" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "Biscuit vcf file (output of biscuit pileup)", - "ontologies": [] - } - } - ] - ], - "output": { - "bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bed.gz": { - "type": "file", - "description": "Gzipped BED file with methylation or SNV information", - "pattern": "*.{bed.gz}", - "ontologies": [] - } - } - ] - ], - "versions_biscuit": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "biscuit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "biscuit version |& sed '1!d; s/^.*BISCUIT Version: //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_samtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools --version |& sed '1!d; s/^.*samtools //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "biscuit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "biscuit version |& sed '1!d; s/^.*BISCUIT Version: //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools --version |& sed '1!d; s/^.*samtools //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@njspix" - ], - "maintainers": [ - "@njspix", - "@sateeshperi" - ] - } - }, - { - "name": "bismark_align", - "path": "modules/nf-core/bismark/align/meta.yml", - "type": "module", - "meta": { - "name": "bismark_align", - "description": "Performs alignment of BS-Seq reads using bismark", - "keywords": [ - "bismark", - "3-letter genome", - "map", - "methylation", - "5mC", - "methylseq", - "bisulphite", - "bisulfite", - "bam" - ], - "tools": [ - { - "bismark": { - "description": "Bismark is a tool to map bisulfite treated sequencing reads\nand perform methylation calling in a quick and easy-to-use fashion.\n", - "homepage": "https://github.com/FelixKrueger/Bismark", - "documentation": "https://github.com/FelixKrueger/Bismark/tree/master/Docs", - "doi": "10.1093/bioinformatics/btr167", - "licence": [ - "GPL-3.0-or-later" - ], - "identifier": "biotools:bismark" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome FASTA file\n", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "index": { - "type": "directory", - "description": "Bismark genome index directory", - "pattern": "BismarkIndex" - } - } - ] - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*bam": { - "type": "file", - "description": "Output BAM file containing read alignments", - "pattern": "*.{bam}", - "ontologies": [] - } - } - ] - ], - "report": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*report.txt": { - "type": "file", - "description": "Bismark alignment reports", - "pattern": "*{report.txt}", - "ontologies": [] - } - } - ] - ], - "unmapped": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*fq.gz": { - "type": "file", - "description": "Output FastQ file(s) containing unmapped reads", - "pattern": "*.{fq.gz}", - "ontologies": [] - } - } - ] - ], - "versions_bismark": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bismark": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bismark -v 2>&1 | sed -n 's/^.*Bismark Version: v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bismark": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bismark -v 2>&1 | sed -n 's/^.*Bismark Version: v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@phue" - ], - "maintainers": [ - "@phue", - "@sateeshperi" - ] - }, - "pipelines": [ - { - "name": "methylseq", - "version": "4.2.0" - } - ] - }, - { - "name": "bismark_coverage2cytosine", - "path": "modules/nf-core/bismark/coverage2cytosine/meta.yml", - "type": "module", - "meta": { - "name": "bismark_coverage2cytosine", - "description": "Relates methylation calls back to genomic cytosine contexts.", - "keywords": [ - "bismark", - "consensus", - "map", - "methylation", - "5mC", - "methylseq", - "bisulphite", - "bisulfite", - "bam", - "bedGraph" - ], - "tools": [ - { - "bismark": { - "description": "Bismark is a tool to map bisulfite treated sequencing reads\nand perform methylation calling in a quick and easy-to-use fashion.\n", - "homepage": "https://github.com/FelixKrueger/Bismark", - "documentation": "https://github.com/FelixKrueger/Bismark/tree/master/Docs", - "doi": "10.1093/bioinformatics/btr167", - "licence": [ - "GPL-3.0-or-later" - ], - "identifier": "biotools:bismark" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "coverage_file": { - "type": "file", - "description": "A file containing methylation calls per position, in the format produced by bismark_methylation_extractor.\n", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome FASTA file\n", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "index": { - "type": "directory", - "description": "Bismark genome index directory", - "pattern": "BismarkIndex" - } - } - ] - ], - "output": { - "coverage": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.cov.gz": { - "type": "file", - "description": "A file containing methylation calls per position.", - "pattern": "*.cov.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "report": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*report.txt.gz": { - "type": "file", - "description": "Genomic cytosine context results.", - "pattern": "*report.txt.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "summary": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*cytosine_context_summary.txt": { - "type": "file", - "description": "Cyotosine context summary report.", - "pattern": "*cytosine_context_summary.txt", - "ontologies": [] - } - } - ] - ], - "versions_bismark": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bismark": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bismark -v 2>&1 | sed -n 's/^.*Bismark Version: v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bismark": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bismark -v 2>&1 | sed -n 's/^.*Bismark Version: v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@ewels" - ], - "maintainers": [ - "@ewels", - "@sateeshperi" - ] - }, - "pipelines": [ - { - "name": "methylseq", - "version": "4.2.0" - } - ] - }, - { - "name": "bismark_deduplicate", - "path": "modules/nf-core/bismark/deduplicate/meta.yml", - "type": "module", - "meta": { - "name": "bismark_deduplicate", - "description": "Removes alignments to the same position in the genome\nfrom the Bismark mapping output.\n", - "keywords": [ - "bismark", - "3-letter genome", - "map", - "methylation", - "5mC", - "methylseq", - "bisulphite", - "bisulfite", - "bam" - ], - "tools": [ - { - "bismark": { - "description": "Bismark is a tool to map bisulfite treated sequencing reads\nand perform methylation calling in a quick and easy-to-use fashion.\n", - "homepage": "https://github.com/FelixKrueger/Bismark", - "documentation": "https://github.com/FelixKrueger/Bismark/tree/master/Docs", - "doi": "10.1093/bioinformatics/btr167", - "licence": [ - "GPL-3.0-or-later" - ], - "identifier": "biotools:bismark" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file containing read alignments", - "pattern": "*.{bam}", - "ontologies": [] - } - } - ] - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.deduplicated.bam": { - "type": "file", - "description": "Deduplicated output BAM file containing read alignments", - "pattern": "*.{deduplicated.bam}", - "ontologies": [] - } - } - ] - ], - "report": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.deduplication_report.txt": { - "type": "file", - "description": "Bismark deduplication reports", - "pattern": "*.{deduplication_report.txt}", - "ontologies": [] - } - } - ] - ], - "versions_bismark": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bismark": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bismark -v 2>&1 | sed -n 's/^.*Bismark Version: v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bismark": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bismark -v 2>&1 | sed -n 's/^.*Bismark Version: v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@phue" - ], - "maintainers": [ - "@phue", - "@sateeshperi" - ] - }, - "pipelines": [ - { - "name": "methylseq", - "version": "4.2.0" - } - ] - }, - { - "name": "bismark_genomepreparation", - "path": "modules/nf-core/bismark/genomepreparation/meta.yml", - "type": "module", - "meta": { - "name": "bismark_genomepreparation", - "description": "Converts a specified reference genome into two different bisulfite\nconverted versions and indexes them for alignments.\n", - "keywords": [ - "bismark", - "3-letter genome", - "index", - "methylation", - "5mC", - "methylseq", - "bisulphite", - "bisulfite", - "fasta" - ], - "tools": [ - { - "bismark": { - "description": "Bismark is a tool to map bisulfite treated sequencing reads\nand perform methylation calling in a quick and easy-to-use fashion.\n", - "homepage": "https://github.com/FelixKrueger/Bismark", - "documentation": "https://github.com/FelixKrueger/Bismark/tree/master/Docs", - "doi": "10.1093/bioinformatics/btr167", - "licence": [ - "GPL-3.0-or-later" - ], - "identifier": "biotools:bismark" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input genome fasta file", - "ontologies": [] - } - } - ] - ], - "output": { - "index": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "BismarkIndex": { - "type": "directory", - "description": "Bismark genome index directory", - "pattern": "BismarkIndex" - } - } - ] - ], - "versions_bismark": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bismark": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bismark -v 2>&1 | sed -n 's/^.*Bismark Version: v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bismark": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bismark -v 2>&1 | sed -n 's/^.*Bismark Version: v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@phue" - ], - "maintainers": [ - "@phue", - "@sateeshperi" - ] - }, - "pipelines": [ - { - "name": "methylseq", - "version": "4.2.0" - } - ] - }, - { - "name": "bismark_methylationextractor", - "path": "modules/nf-core/bismark/methylationextractor/meta.yml", - "type": "module", - "meta": { - "name": "bismark_methylationextractor", - "description": "Extracts methylation information for individual cytosines from alignments.", - "keywords": [ - "bismark", - "consensus", - "map", - "methylation", - "5mC", - "methylseq", - "bisulphite", - "bisulfite", - "bam", - "bedGraph" - ], - "tools": [ - { - "bismark": { - "description": "Bismark is a tool to map bisulfite treated sequencing reads\nand perform methylation calling in a quick and easy-to-use fashion.\n", - "homepage": "https://github.com/FelixKrueger/Bismark", - "documentation": "https://github.com/FelixKrueger/Bismark/tree/master/Docs", - "doi": "10.1093/bioinformatics/btr167", - "licence": [ - "GPL-3.0-or-later" - ], - "identifier": "biotools:bismark" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file containing read alignments", - "pattern": "*.{bam}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "index": { - "type": "directory", - "description": "Bismark genome index directory", - "pattern": "BismarkIndex" - } - } - ] - ], - "output": { - "bedgraph": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bedGraph.gz": { - "type": "file", - "description": "Bismark output file containing coverage and methylation metrics", - "pattern": "*.{bedGraph.gz}", - "ontologies": [] - } - } - ] - ], - "methylation_calls": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.txt.gz": { - "type": "file", - "description": "Bismark output file containing strand-specific methylation calls", - "pattern": "*.{txt.gz}", - "ontologies": [] - } - } - ] - ], - "coverage": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.cov.gz": { - "type": "file", - "description": "Bismark output file containing coverage metrics", - "pattern": "*.{cov.gz}", - "ontologies": [] - } - } - ] - ], - "report": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_splitting_report.txt": { - "type": "file", - "description": "Bismark splitting reports", - "pattern": "*_{splitting_report.txt}", - "ontologies": [] - } - } - ] - ], - "mbias": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.M-bias.txt": { - "type": "file", - "description": "Text file containing methylation bias information", - "pattern": "*.{M-bias.txt}", - "ontologies": [] - } - } - ] - ], - "versions_bismark": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bismark": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bismark -v 2>&1 | sed -n 's/^.*Bismark Version: v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bismark": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bismark -v 2>&1 | sed -n 's/^.*Bismark Version: v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@phue" - ], - "maintainers": [ - "@phue", - "@sateeshperi" - ] - }, - "pipelines": [ - { - "name": "methylseq", - "version": "4.2.0" - } - ] - }, - { - "name": "bismark_report", - "path": "modules/nf-core/bismark/report/meta.yml", - "type": "module", - "meta": { - "name": "bismark_report", - "description": "Collects bismark alignment reports", - "keywords": [ - "bismark", - "qc", - "methylation", - "5mC", - "methylseq", - "bisulphite", - "bisulfite", - "report" - ], - "tools": [ - { - "bismark": { - "description": "Bismark is a tool to map bisulfite treated sequencing reads\nand perform methylation calling in a quick and easy-to-use fashion.\n", - "homepage": "https://github.com/FelixKrueger/Bismark", - "documentation": "https://github.com/FelixKrueger/Bismark/tree/master/Docs", - "doi": "10.1093/bioinformatics/btr167", - "licence": [ - "GPL-3.0-or-later" - ], - "identifier": "biotools:bismark" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "align_report": { - "type": "file", - "description": "Bismark alignment reports", - "pattern": "*{report.txt}", - "ontologies": [] - } - }, - { - "dedup_report": { - "type": "file", - "description": "Bismark deduplication reports", - "pattern": "*.{deduplication_report.txt}", - "ontologies": [] - } - }, - { - "splitting_report": { - "type": "file", - "description": "Bismark splitting reports", - "pattern": "*{splitting_report.txt}", - "ontologies": [] - } - }, - { - "mbias": { - "type": "file", - "description": "Text file containing methylation bias information", - "pattern": "*.{txt}", - "ontologies": [] - } - } - ] - ], - "output": { - "report": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*report.{html,txt}": { - "type": "file", - "description": "Bismark reports", - "pattern": "*.{html,txt}", - "ontologies": [] - } - } - ] - ], - "versions_bismark": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bismark": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bismark -v 2>&1 | sed -n 's/^.*Bismark Version: v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bismark": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bismark -v 2>&1 | sed -n 's/^.*Bismark Version: v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@phue" - ], - "maintainers": [ - "@phue", - "@sateeshperi" - ] - }, - "pipelines": [ - { - "name": "methylseq", - "version": "4.2.0" - } - ] - }, - { - "name": "bismark_summary", - "path": "modules/nf-core/bismark/summary/meta.yml", - "type": "module", - "meta": { - "name": "bismark_summary", - "description": "Uses Bismark report files of several samples in a run folder to generate a graphical summary HTML report.", - "keywords": [ - "bismark", - "qc", - "methylation", - "5mC", - "methylseq", - "bisulphite", - "bisulfite", - "report", - "summary" - ], - "tools": [ - { - "bismark": { - "description": "Bismark is a tool to map bisulfite treated sequencing reads\nand perform methylation calling in a quick and easy-to-use fashion.\n", - "homepage": "https://github.com/FelixKrueger/Bismark", - "documentation": "https://github.com/FelixKrueger/Bismark/tree/master/Docs", - "doi": "10.1093/bioinformatics/btr167", - "licence": [ - "GPL-3.0-or-later" - ], - "identifier": "biotools:bismark" - } - } - ], - "input": [ - { - "bam": { - "type": "list", - "description": "List of Bismark alignment BAM filenames", - "pattern": "*.bam" - } - }, - { - "align_report": { - "type": "file", - "description": "Bismark alignment reports", - "pattern": "*report.txt", - "ontologies": [] - } - }, - { - "dedup_report": { - "type": "file", - "description": "Bismark deduplication reports", - "pattern": "*.deduplication_report.txt", - "ontologies": [] - } - }, - { - "splitting_report": { - "type": "file", - "description": "Bismark splitting reports", - "pattern": "*splitting_report.txt", - "ontologies": [] - } - }, - { - "mbias": { - "type": "file", - "description": "Text file containing methylation bias information", - "pattern": "*.txt", - "ontologies": [] - } - } - ], - "output": { - "summary": [ - { - "*report.{html,txt}": { - "type": "file", - "description": "Bismark summary", - "pattern": "*.{html,txt}", - "ontologies": [] - } - } - ], - "versions_bismark": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bismark": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bismark -v 2>&1 | sed -n 's/^.*Bismark Version: v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bismark": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bismark -v 2>&1 | sed -n 's/^.*Bismark Version: v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@phue" - ], - "maintainers": [ - "@phue", - "@sateeshperi" - ] - }, - "pipelines": [ - { - "name": "methylseq", - "version": "4.2.0" - } - ] - }, - { - "name": "blast_blastdbcmd", - "path": "modules/nf-core/blast/blastdbcmd/meta.yml", - "type": "module", - "meta": { - "name": "blast_blastdbcmd", - "description": "Retrieve entries from a BLAST database", - "keywords": [ - "fasta", - "blast", - "database", - "retrieval", - "identifier" - ], - "tools": [ - { - "blast": { - "description": "BLAST finds regions of similarity between biological sequences.\n", - "homepage": "https://blast.ncbi.nlm.nih.gov/Blast.cgi", - "documentation": "https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs", - "doi": "10.1016/S0022-2836(05)80360-2", - "licence": [ - "US-Government-Work" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "entry": { - "type": "string", - "description": "Entry identifier of sequence in database. It cannot be used along with entry_batch" - } - }, - { - "entry_batch": { - "type": "file", - "description": "File with a list of entry identifiers of sequences in database (one identifier per line). It cannot be used along with entry\n", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing db information\ne.g. [ id:'test2', single_end:false ]\n" - } - }, - { - "db": { - "type": "file", - "description": "Input BLAST-indexed database", - "pattern": "*.{fa.*,fasta.*}", - "ontologies": [] - } - } - ] - ], - "output": { - "fasta": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.fasta": { - "type": "file", - "description": "Output fasta file (default format)", - "pattern": "*.{fasta}", - "ontologies": [] - } - } - ] - ], - "text": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.txt": { - "type": "file", - "description": "Output text file (generic format if fasta not used, i.e. `--outfmt` is supplied to `ext.args`)\n", - "pattern": "*.{txt}", - "ontologies": [] - } - } - ] - ], - "versions_blastdbcmd": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "blastdbcmd": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "blastdbcmd -version 2>&1 | head -n1 | sed 's/^.*blastdbcmd: //; s/ .*\\$//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "blastdbcmd": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "blastdbcmd -version 2>&1 | head -n1 | sed 's/^.*blastdbcmd: //; s/ .*\\$//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@toniher" - ], - "maintainers": [ - "@toniher" - ] - } - }, - { - "name": "blast_blastn", - "path": "modules/nf-core/blast/blastn/meta.yml", - "type": "module", - "meta": { - "name": "blast_blastn", - "description": "Queries a BLAST DNA database", - "keywords": [ - "fasta", - "blast", - "blastn", - "DNA sequence", - "taxids" - ], - "tools": [ - { - "blast": { - "description": "BLAST finds regions of similarity between biological sequences.\n", - "homepage": "https://blast.ncbi.nlm.nih.gov/Blast.cgi", - "documentation": "https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs", - "doi": "10.1016/S0022-2836(05)80360-2", - "licence": [ - "US-Government-Work" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input fasta file containing queries sequences", - "pattern": "*.{fa,fasta,fa.gz,fasta.gz}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing db information\ne.g. [ id:'test2', single_end:false ]\n" - } - }, - { - "db": { - "type": "directory", - "description": "Directory containing the blast database", - "pattern": "*" - } - } - ], - { - "taxidlist": { - "type": "file", - "description": "File containing NCBI taxon ids, one per line, for filtering the database.", - "pattern": "*.{txt}", - "ontologies": [] - } - }, - { - "taxids": { - "type": "string", - "description": "Comma-delimited list of NCBI taxon ids for filtering the database.", - "pattern": "^[0-9]+(,[0-9]+)*$" - } - }, - { - "negative_tax": { - "type": "boolean", - "description": "Use negative filtering (true) to exclude taxon ids or normal filtering (false).", - "pattern": "true or false" - } - } - ], - "output": { - "txt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.txt": { - "type": "file", - "description": "File containing blastn hits", - "pattern": "*.txt", - "ontologies": [] - } - } - ] - ], - "versions_blastn": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "blastn": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "blastn -version 2>&1 | sed 's/^.*blastn: //; s/ .*\\$//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "blastn": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "blastn -version 2>&1 | sed 's/^.*blastn: //; s/ .*\\$//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@joseespinosa", - "@drpatelh" - ], - "maintainers": [ - "@joseespinosa", - "@drpatelh", - "@vagkaratzas" - ] - }, - "pipelines": [ - { - "name": "detaxizer", - "version": "1.3.0" - }, - { - "name": "phageannotator", - "version": "dev" - }, - { - "name": "viralmetagenome", - "version": "1.1.1" - }, - { - "name": "viralrecon", - "version": "3.0.0" - } - ] - }, - { - "name": "blast_blastp", - "path": "modules/nf-core/blast/blastp/meta.yml", - "type": "module", - "meta": { - "name": "blast_blastp", - "description": "BLASTP (Basic Local Alignment Search Tool- Protein) compares an amino acid (protein) query sequence against a protein database", - "keywords": [ - "fasta", - "blast", - "blastp", - "protein" - ], - "tools": [ - { - "blast": { - "description": "BLAST+ is a new suite of BLAST tools that utilizes the NCBI C++ Toolkit.\n", - "homepage": "https://blast.ncbi.nlm.nih.gov/Blast.cgi", - "documentation": "https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs", - "doi": "10.1016/S0022-2836(05)80360-2", - "licence": [ - "US-Government-Work" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input fasta file containing queries sequences", - "pattern": "*.{fa,fasta,fa.gz,fasta.gz}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing db information\ne.g. [ id:'test2', single_end:false ]\n" - } - }, - { - "db": { - "type": "directory", - "description": "Directory containing the blast database", - "pattern": "*" - } - } - ], - { - "out_ext": { - "type": "string", - "description": "Specify the type of output file to be generated. `xml` corresponds to BLAST xml format.\n`tsv` corresponds to BLAST tabular format. `csv` corresponds to BLAST comma separated format.\n", - "pattern": "xml|tsv|csv" - } - } - ], - "output": { - "xml": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*.xml*": { - "type": "file", - "description": "File containing blastp hits in XML format", - "pattern": "*.{xml}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2332" - } - ] - } - } - ] - ], - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*.tsv*": { - "type": "file", - "description": "File containing blastp hits in tabular format", - "pattern": "*.{tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "csv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*.csv*": { - "type": "file", - "description": "File containing blastp hits in comma separated format", - "pattern": "*.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "versions_blastp": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "blastp": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "blastp -version 2>&1 | sed 's/^.*blastp: //; s/ .*\\$//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "blastp": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "blastp -version 2>&1 | sed 's/^.*blastp: //; s/ .*\\$//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@vagkaratzas" - ], - "maintainers": [ - "@vagkaratzas" - ] - } - }, - { - "name": "blast_makeblastdb", - "path": "modules/nf-core/blast/makeblastdb/meta.yml", - "type": "module", - "meta": { - "name": "blast_makeblastdb", - "description": "Builds a BLAST database", - "keywords": [ - "fasta", - "blast", - "database" - ], - "tools": [ - { - "blast": { - "description": "BLAST finds regions of similarity between biological sequences.\n", - "homepage": "https://blast.ncbi.nlm.nih.gov/Blast.cgi", - "documentation": "https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs", - "doi": "10.1016/S0022-2836(05)80360-2", - "licence": [ - "US-Government-Work" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input fasta file", - "pattern": "*.{fa,fasta,fa.gz,fasta.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - { - "taxid_map": { - "type": "file", - "description": "taxID mapping files are tab-delimited text files used to map custom sequence IDs to NCBI taxonomic identifiers (taxIDs) during the creation of a BLAST database", - "pattern": "*.txt", - "ontologies": [ + "pipelines": [ { - "edam": "http://edamontology.org/format_2330" + "name": "taxprofiler", + "version": "2.0.0" } - ] - } - } - ], - "output": { - "db": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}": { - "type": "directory", - "description": "Output directory containing blast database files", - "pattern": "*" - } - } - ] - ], - "versions_makeblastdb": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "makeblastdb": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "makeblastdb -version 2>&1 | sed 's/^.*makeblastdb: //; s/ .*\\$//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "makeblastdb": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "makeblastdb -version 2>&1 | sed 's/^.*makeblastdb: //; s/ .*\\$//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@joseespinosa", - "@drpatelh" - ], - "maintainers": [ - "@joseespinosa", - "@drpatelh", - "@vagkaratzas", - "@DLBPointon" - ] - }, - "pipelines": [ - { - "name": "detaxizer", - "version": "1.3.0" - }, - { - "name": "phageannotator", - "version": "dev" - }, - { - "name": "viralmetagenome", - "version": "1.1.1" }, { - "name": "viralrecon", - "version": "3.0.0" - } - ] - }, - { - "name": "blast_tblastn", - "path": "modules/nf-core/blast/tblastn/meta.yml", - "type": "module", - "meta": { - "name": "blast_tblastn", - "description": "Queries a BLAST DNA database", - "keywords": [ - "fasta", - "blast", - "tblastn", - "DNA sequence" - ], - "tools": [ - { - "blast": { - "description": "Protein to Translated Nucleotide BLAST.\n", - "homepage": "https://blast.ncbi.nlm.nih.gov/Blast.cgi", - "documentation": "https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs", - "doi": "10.1016/S0022-2836(05)80360-2", - "licence": [ - "US-Government-Work" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input fasta file containing queries sequences", - "pattern": "*.{fa,fasta,fa.gz,fasta.gz}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing db information\ne.g. [ id:'test2', single_end:false ]\n" - } - }, - { - "db": { - "type": "directory", - "description": "Directory containing the blast database", - "pattern": "*" - } - } - ] - ], - "output": { - "txt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.txt": { - "type": "file", - "description": "File containing blastn hits", - "pattern": "*.txt", - "ontologies": [] - } - } - ] - ], - "versions_tblastn": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "tblastn": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "tblastn -version 2>&1 | sed 's/^.*tblastn: //; s/ .*\\$//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "tblastn": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "tblastn -version 2>&1 | sed 's/^.*tblastn: //; s/ .*\\$//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@yumisims", - "@gq2" - ], - "maintainers": [ - "@yumisims", - "@gq2", - "@vagkaratzas" - ] - } - }, - { - "name": "blast_updateblastdb", - "path": "modules/nf-core/blast/updateblastdb/meta.yml", - "type": "module", - "meta": { - "name": "blast_updateblastdb", - "description": "Downloads a BLAST database from NCBI", - "keywords": [ - "fasta", - "blast", - "download", - "database" - ], - "tools": [ - { - "blast": { - "description": "BLAST finds regions of similarity between biological sequences.\n", - "homepage": "https://blast.ncbi.nlm.nih.gov/Blast.cgi", - "documentation": "https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs", - "doi": "10.1016/S0022-2836(05)80360-2", - "licence": [ - "US-Government-Work" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'mito', single_end:false ]\n" - } - }, - { - "name": { - "type": "string", - "description": "Name of the NCBI BLAST database to be downloaded" - } - } - ] - ], - "output": { - "db": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'mito', single_end:false ]\n" - } - }, - { - "prefix": { - "type": "directory", - "description": "Output directory containing blast database files", - "pattern": "*" - } - } - ] - ], - "versions_updateblastdb": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "updateblastdb": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "update_blastdb.pl -version 2>&1 | tail -n1 | rev | cut -f1 -d ' ' | rev": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "updateblastdb": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "update_blastdb.pl -version 2>&1 | tail -n1 | rev | cut -f1 -d ' ' | rev": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@toniher" - ], - "maintainers": [ - "@toniher" - ] - } - }, - { - "name": "blat", - "path": "modules/nf-core/blat/meta.yml", - "type": "module", - "meta": { - "name": "blat", - "description": "Queries a sequence subject", - "keywords": [ - "blat", - "sequence", - "search" - ], - "tools": [ - { - "blat": { - "description": "BLAT is a bioinformatics software tool which performs rapid mRNA/DNA and cross-species protein alignments.", - "homepage": "https://kentinformatics.com/", - "documentation": "https://kentinformatics.com/documentation", - "doi": "10.1101/gr.229202", - "licence": [ - "Free for academic, nonprofit and personal use" - ], - "identifier": "biotools:blat" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "query": { - "type": "file", - "description": "Sequence file", - "pattern": "*.{fasta,fasta.gz,fa,fa.gz,nib,2bit}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing subject information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "subject": { - "type": "file", - "description": "Sequence file", - "pattern": "*.{fa,nib,2bit}", - "ontologies": [] - } - } - ] - ], - "output": { - "psl": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*.psl": { - "type": "file", - "description": "Search results", - "pattern": "*.{psl}", - "ontologies": [] - } - } - ] - ], - "versions_blat": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "blat": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "blat 2>&1 | sed '1!d;s/^.*BLAT v. //;s/ fast.*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "blat": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "blat 2>&1 | sed '1!d;s/^.*BLAT v. //;s/ fast.*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@d-jch" - ], - "maintainers": [ - "@d-jch" - ] - }, - "pipelines": [ - { - "name": "smrnaseq", - "version": "2.4.1" - } - ] - }, - { - "name": "blobtk_create", - "path": "modules/nf-core/blobtk/create/meta.yml", - "type": "module", - "meta": { - "name": "blobtk_create", - "description": "Creates a minimal blobdir.\n", - "keywords": [ - "blobdir", - "btk", - "blobtoolkit", - "metadata" - ], - "tools": [ - { - "btk": { - "description": "BlobTk contains a set of core functions used by BlobToolKit tools.\nImplemented in Rust, these functions are intended to be accessible\nfrom the command line, as python modules and will include web assembly\ncode for use in javascript.\n", - "homepage": "https://github.com/genomehubs/blobtk/", - "documentation": "https://github.com/genomehubs/blobtk/wiki/", - "licence": [ - "MIT" - ], - "identifier": "biotools:btk" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information and blobtk arguments\ne.g. `[ id:'sample1']`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input assembly FASTA.\n", - "pattern": "*.fasta", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - }, - { - "full_table": { - "type": "file", - "description": "Full table TSV from busco.\n", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1915" - } - ] - } - } - ] - ], - "output": { - "blobdir": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}/": { - "type": "directory", - "description": "A minimal blobdir directory\n", - "ontologies": [] - } - } - ] - ], - "versions_blobtk": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "blobtk": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "blobtk --version | cut -d' ' -f2": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "blobtk": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "blobtk --version | cut -d' ' -f2": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@DLBPointon" - ], - "maintainers": [ - "@DLBPointon" - ] - } - }, - { - "name": "blobtk_depth", - "path": "modules/nf-core/blobtk/depth/meta.yml", - "type": "module", - "meta": { - "name": "blobtk_depth", - "description": "Creates a bed file containing the depth of data at intervals of an aligned bam.\n", - "keywords": [ - "bam", - "gzipped", - "blobtoolkit", - "depth" - ], - "tools": [ - { - "blobtk": { - "description": "BlobTk contains a set of core functions used by BlobToolKit tools.\nImplemented in Rust, these functions are intended to be accessible\nfrom the command line, as python modules and will include web assembly\ncode for use in javascript.\n", - "homepage": "https://github.com/genomehubs/blobtk/", - "documentation": "https://github.com/genomehubs/blobtk/wiki/", - "licence": [ - "MIT" - ], - "identifier": "biotools:blobtk" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "Algined BAM file.\n", - "pattern": "*.bam", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - }, - { - "index": { - "type": "file", - "description": "Algined BAM index file.\n", - "pattern": "*.bai|*.csi", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3327" - } - ] - } - } - ] - ], - "output": { - "bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.regions.bed.gz": { - "type": "file", - "description": "Bed file describing the depth of regions across the genome.\n" - } - } - ] - ], - "versions_blobtk": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "blobtk": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "blobtk --version | cut -d' ' -f2": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "blobtk": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "blobtk --version | cut -d' ' -f2": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@DLBPointon" - ], - "maintainers": [ - "@DLBPointon" - ] - } - }, - { - "name": "blobtk_plot", - "path": "modules/nf-core/blobtk/plot/meta.yml", - "type": "module", - "meta": { - "name": "blobtk_plot", - "description": "Creates differing styles of blobplots depending on provided arguments.\n", - "keywords": [ - "png", - "svg", - "btk", - "blobtoolkit", - "plot" - ], - "tools": [ - { - "blobtk": { - "description": "BlobTk contains a set of core functions used by BlobToolKit tools.\nImplemented in Rust, these functions are intended to be accessible\nfrom the command line, as python modules and will include web assembly\ncode for use in javascript.\n", - "homepage": "https://github.com/genomehubs/blobtk/", - "documentation": "https://github.com/genomehubs/blobtk/wiki/", - "licence": [ - "MIT" - ], - "identifier": "biotools:blobtk" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information and blobtk arguments\ne.g. `[ id:'sample1']`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input assembly FASTA.\n", - "pattern": "*.fasta", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - { - "local_path": { - "type": "directory", - "description": "A path to a Blob Dir generated as part of a greater pipeline.\n", - "pattern": "*/" - } - }, - { - "online_path": { - "type": "string", - "description": "A webaddress to a Blob Dir e.g. hosted on a BlobToolKit Viewer.\n", - "pattern": "*/" - } - }, - { - "extra_args": { - "type": "map", - "description": "Groovy Map containing sample information and blobtk arguments\ne.g. `[name: 'VIEW', args: \"-v\"]`\n" - } - }, - { - "format": { - "type": "string", - "description": "Value indicating the output format.\ne.g. `\"png\" or \"svg\"`\n" - } - } - ], - "output": { - "png": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.png": { - "type": "file", - "description": "Blobplot PNG results of input arguments.\n", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3603" - } - ] - } - } - ] - ], - "svg": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.svg": { - "type": "file", - "description": "Blobplot SVG results of input arguments.\n", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3604" - } - ] - } - } - ] - ], - "versions_blobtk": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "blobtk": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "blobtk --version | cut -d' ' -f2": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "blobtk": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "blobtk --version | cut -d' ' -f2": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@DLBPointon" - ], - "maintainers": [ - "@DLBPointon" - ] - } - }, - { - "name": "blobtk_snail", - "path": "modules/nf-core/blobtk/snail/meta.yml", - "type": "module", - "meta": { - "name": "blobtk_snail", - "description": "Creates blobtk snail plots.\n", - "keywords": [ - "svg", - "btk", - "blobtoolkit", - "snailplot" - ], - "tools": [ - { - "btk": { - "description": "BlobTk contains a set of core functions used by BlobToolKit tools.\nImplemented in Rust, these functions are intended to be accessible\nfrom the command line, as python modules and will include web assembly\ncode for use in javascript.\n", - "homepage": "https://github.com/genomehubs/blobtk/", - "documentation": "https://github.com/genomehubs/blobtk/wiki/", - "licence": [ - "MIT" - ], - "identifier": "biotools:btk" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information and blobtk arguments\ne.g. `[ id:'sample1']`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input assembly FASTA.\n", - "pattern": "*.fasta", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - }, - { - "full_table": { - "type": "file", - "description": "Full table TSV from busco.\n", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1915" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information and blobtk arguments\ne.g. `[ id:'sample1']`\n" - } - }, - { - "blob_dir": { - "type": "directory", - "description": "A local path to a BlobDir.\n", - "pattern": "*/" - } - } - ], - { - "format": { - "type": "string", - "description": "Output format for the snail plot.\n", - "pattern": "{png,svg,json,yaml}" - } - } - ], - "output": { - "images": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.{svg,png}": { - "type": "file", - "description": "BlobTK image results of input arguments.\n", - "ontologies": [ + "name": "braker3", + "path": "modules/nf-core/braker3/meta.yml", + "type": "module", + "meta": { + "name": "braker3", + "description": "Gene prediction in novel genomes using RNA-seq and protein homology information\n", + "keywords": ["genome", "annotation", "braker", "gff", "gtf"], + "tools": [ + { + "braker3": { + "description": "BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures using protein and RNA-seq and protein homology information", + "homepage": "https://github.com/Gaius-Augustus/BRAKER", + "documentation": "https://github.com/Gaius-Augustus/BRAKER", + "tool_dev_url": "https://github.com/Gaius-Augustus/BRAKER", + "doi": "10.13140/RG.2.2.20047.36004", + "licence": ["Artistic-1.0"], + "identifier": "biotools:braker3" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Genome assembly fasta", + "pattern": "*.{fasta,fa,fas,faa,fna}", + "ontologies": [] + } + } + ], { - "edam": "http://edamontology.org/format_3604" + "bam": { + "type": "file", + "description": "BAM file of RNA-seq data to be passed to --bam", + "pattern": "*.bam", + "ontologies": [] + } }, { - "edam": "http://edamontology.org/format_3603" - } - ] - } - } - ] - ], - "descriptions": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.{json,yaml}": { - "type": "file", - "description": "BlobTK files describing the snail plot.\n", - "ontologies": [ + "rnaseq_sets_dirs": { + "type": "file", + "description": "Directories of RNA-seq data sets to be passed to --rnaseq_sets_dirs", + "ontologies": [] + } + }, + { + "rnaseq_sets_ids": { + "type": "file", + "description": "IDs of RNA-seq data sets to be passed to --rnaseq_sets_ids", + "ontologies": [] + } + }, { - "edam": "http://edamontology.org/format_3464" + "proteins": { + "type": "file", + "description": "Protein evidence to be passed to --proteins", + "pattern": "*.{fasta,fa,fas,faa}", + "ontologies": [] + } }, { - "edam": "http://edamontology.org/format_3750" + "hintsfile": { + "type": "file", + "description": "Hintsfile to be passed to --hintsfile", + "pattern": "*.{gff, gtf, gff3}", + "ontologies": [] + } } - ] - } - } - ] - ], - "versions_blobtk": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "blobtk": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "blobtk --version | cut -d' ' -f2": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "blobtk": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "blobtk --version | cut -d' ' -f2": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@DLBPointon" - ], - "maintainers": [ - "@DLBPointon" - ] - } - }, - { - "name": "bowtie2_align", - "path": "modules/nf-core/bowtie2/align/meta.yml", - "type": "module", - "meta": { - "name": "bowtie2_align", - "description": "Align reads to a reference genome using bowtie2", - "keywords": [ - "align", - "map", - "fasta", - "fastq", - "genome", - "reference" - ], - "tools": [ - { - "bowtie2": { - "description": "Bowtie 2 is an ultrafast and memory-efficient tool for aligning\nsequencing reads to long reference sequences.\n", - "homepage": "http://bowtie-bio.sourceforge.net/bowtie2/index.shtml", - "documentation": "http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml", - "doi": "10.1186/gb-2009-10-3-r25", - "licence": [ - "GPL-3.0-or-later" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "index": { - "type": "file", - "description": "Bowtie2 genome index files", - "pattern": "*.ebwt", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome FASTA file", - "pattern": "*.{fa,fasta,fna}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - { - "save_unaligned": { - "type": "boolean", - "description": "Save reads that do not map to the reference (true) or discard them (false)\n(default: false)\n" - } - }, - { - "sort_bam": { - "type": "boolean", - "description": "use samtools sort (true) or samtools view (false)", - "pattern": "true or false" + ], + "output": { + "gtf": [ + [ + { + "meta": { + "type": "file", + "description": "Gene transfer format file as output by BRAKER3", + "pattern": "*.{gtf}", + "ontologies": [] + } + }, + { + "$prefix/braker.gtf": { + "type": "file", + "description": "Gene transfer format file as output by BRAKER3", + "pattern": "*.{gtf}", + "ontologies": [] + } + } + ] + ], + "cds": [ + [ + { + "meta": { + "type": "file", + "description": "Gene transfer format file as output by BRAKER3", + "pattern": "*.{gtf}", + "ontologies": [] + } + }, + { + "$prefix/braker.codingseq": { + "type": "file", + "description": "Coding sequence file as output by BRAKER3", + "pattern": "*.{codingseq}", + "ontologies": [] + } + } + ] + ], + "aa": [ + [ + { + "meta": { + "type": "file", + "description": "Gene transfer format file as output by BRAKER3", + "pattern": "*.{gtf}", + "ontologies": [] + } + }, + { + "$prefix/braker.aa": { + "type": "file", + "description": "Protein sequence file as output by BRAKER3", + "pattern": "*.{aa}", + "ontologies": [] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "file", + "description": "Gene transfer format file as output by BRAKER3", + "pattern": "*.{gtf}", + "ontologies": [] + } + }, + { + "$prefix/braker.log": { + "type": "file", + "description": "BRAKER3 log file", + "pattern": "*.log", + "ontologies": [] + } + } + ] + ], + "hintsfile": [ + [ + { + "meta": { + "type": "file", + "description": "Gene transfer format file as output by BRAKER3", + "pattern": "*.{gtf}", + "ontologies": [] + } + }, + { + "$prefix/hintsfile.gff": { + "type": "file", + "description": "Hints file as output by BRAKER3", + "pattern": "*hintsfile.{gff}", + "ontologies": [] + } + } + ] + ], + "gff3": [ + [ + { + "meta": { + "type": "file", + "description": "Gene transfer format file as output by BRAKER3", + "pattern": "*.{gtf}", + "ontologies": [] + } + }, + { + "$prefix/braker.gff3": { + "type": "file", + "description": "GFF3 file as output by BRAKER3", + "pattern": "*.{gff3}", + "ontologies": [] + } + } + ] + ], + "citations": [ + [ + { + "meta": { + "type": "file", + "description": "Gene transfer format file as output by BRAKER3", + "pattern": "*.{gtf}", + "ontologies": [] + } + }, + { + "$prefix/what-to-cite.txt": { + "type": "file", + "description": "BRAKER3 citations", + "pattern": "what-to-cite.txt", + "ontologies": [] + } + } + ] + ], + "versions_braker3": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "braker3": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "braker.pl --version 2>/dev/null | sed 's/braker.pl version //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_augustus": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "augustus": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "augustus --version |& sed -n 's/AUGUSTUS (\\(.*\\)) is a gene .*/\\1/p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_genemarketp": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "genemark-etp": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gmetp.pl |& sed -n 's/ETP version \\(.*\\)/\\1/p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_prothint": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "prothint": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "prothint.py --version |& sed 's/prothint.py //1'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "braker3": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "braker.pl --version 2>/dev/null | sed 's/braker.pl version //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "augustus": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "augustus --version |& sed -n 's/AUGUSTUS (\\(.*\\)) is a gene .*/\\1/p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "genemark-etp": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gmetp.pl |& sed -n 's/ETP version \\(.*\\)/\\1/p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "prothint": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "prothint.py --version |& sed 's/prothint.py //1'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@kherronism", "@GallVp"], + "maintainers": ["@GallVp"] } - } - ], - "output": { - "sam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*.sam": { - "type": "file", - "description": "Output SAM file containing read alignments", - "pattern": "*.sam", - "ontologies": [] - } - } - ] - ], - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*.bam": { - "type": "file", - "description": "Output BAM file containing read alignments", - "pattern": "*.bam", - "ontologies": [] - } - } - ] - ], - "cram": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*.cram": { - "type": "file", - "description": "Output CRAM file containing read alignments", - "pattern": "*.cram", - "ontologies": [] - } - } - ] - ], - "csi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*.csi": { - "type": "file", - "description": "Output SAM/BAM index for large inputs", - "pattern": "*.csi", - "ontologies": [] - } - } - ] - ], - "crai": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*.crai": { - "type": "file", - "description": "Output CRAM index", - "pattern": "*.crai", - "ontologies": [] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*.log": { - "type": "file", - "description": "Alignment log", - "pattern": "*.log", - "ontologies": [] - } - } - ] - ], - "fastq": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*fastq.gz": { - "type": "file", - "description": "Unaligned FastQ files", - "pattern": "*.fastq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "versions_bowtie2": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bowtie2": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bowtie2 --version 2>&1 | sed -n 's/.*bowtie2-align-s version //p'": { - "type": "eval", - "description": "The expression to obtain the version of bowtie2" - } - } - ] - ], - "versions_samtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of samtools" - } - } - ] - ], - "versions_pigz": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pigz": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pigz --version 2>&1 | sed 's/pigz //'": { - "type": "eval", - "description": "The expression to obtain the version of pigz" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - 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{ + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Nucleic or amino acid sequence file in FASTA format.", + "pattern": "*.{fasta,fna,fa,fasta.gz,fna.gz,fa.gz}", + "ontologies": [] + } + } + ], + { + "mode": { + "type": "string", + "description": "The mode to run Busco in. 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"batch_summary_failed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*-busco.batch_summary.failed.txt": { + "type": "file", + "description": "Batch summary lines indicating BUSCO run failures", + "pattern": "*-busco.batch_summary.failed.txt", + "ontologies": [] + } + } + ] + ], + "short_summaries_txt": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "short_summary.*.txt": { + "type": "file", + "description": "Short Busco summary in plain text format", + "pattern": "short_summary.*.txt", + "ontologies": [] + } + } + ] + ], + "short_summaries_json": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "short_summary.*.json": { + "type": "file", + "description": "Short Busco summary in JSON format", + "pattern": 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"description": "List of missing BUSCOs", + "pattern": "missing_busco_list.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "single_copy_proteins": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*-busco/*/run_*/single_copy_proteins.faa": { + "type": "file", + "description": "Fasta file of single copy proteins (transcriptome mode)", + "pattern": "single_copy_proteins.faa", + "ontologies": [] + } + } + ] + ], + "seq_dir": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*-busco/*/run_*/busco_sequences": { + "type": "directory", + "description": "BUSCO sequence directory", + "pattern": "busco_sequences" + } + } + ] + ], + "translated_dir": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*-busco/*/translated_proteins": { + "type": "directory", + "description": "Six frame translations of each transcript made by the transcriptome mode", + "pattern": "translated_dir" + } + } + ] + ], + "busco_dir": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*-busco": { + "type": "directory", + "description": "BUSCO lineage specific output", + "pattern": "*-busco" + } + } + ] + ], + "downloaded_lineages": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "busco_downloads/lineages/*": { + "type": "directory", + "description": "Lineages downloaded by BUSCO when running the analysis, for example bacteria_odb12", + "pattern": "busco_downloads/lineages/*" + } + } + ] + ], + "single_copy_faa": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*-busco/*/run_*/busco_sequences/single_copy_busco_sequences/*.faa": { + "type": "file", + "description": "Single copy .faa sequence files", + "pattern": "*-busco/*/run_*/busco_sequences/single_copy_busco_sequences/*.faa", + "ontologies": [] + } + } + ] + ], + "single_copy_fna": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*-busco/*/run_*/busco_sequences/single_copy_busco_sequences/*.fna": { + "type": "file", + "description": "Single copy .fna sequence files", + "pattern": "*-busco/*/run_*/busco_sequences/single_copy_busco_sequences/*.fna", + "ontologies": [] + } + } + ] + ], + "versions_busco": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "busco": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "busco --version 2> /dev/null | sed 's/BUSCO //g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "busco": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "busco --version 2> /dev/null | sed 's/BUSCO //g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": [ + "@priyanka-surana", + "@charles-plessy", + "@mahesh-panchal", + "@muffato", + "@jvhagey", + "@gallvp" + ], + "maintainers": [ + "@priyanka-surana", + "@charles-plessy", + "@mahesh-panchal", + "@muffato", + "@jvhagey", + "@gallvp" ] - } - } - ] - ], - "output": { - "index": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bowtie2": { - "type": "directory", - "description": "Bowtie2 genome index files", - 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"genomeassembler", + "version": "1.1.0" + }, + { + "name": "genomeqc", + "version": "dev" + }, + { + "name": "mag", + "version": "5.4.2" + }, + { + "name": "pathogensurveillance", + "version": "1.1.0" + } ] - ] - }, - "authors": [ - "@joseespinosa", - "@drpatelh" - ], - "maintainers": [ - "@joseespinosa", - "@drpatelh" - ] - }, - "pipelines": [ - { - "name": "atacseq", - "version": "2.1.2" - }, - { - "name": "callingcards", - "version": "1.0.0" - }, - { - "name": "chipseq", - "version": "2.1.0" - }, - { - "name": "circrna", - "version": "dev" - }, - { - "name": "coproid", - "version": "2.0.1" - }, - { - "name": "crisprseq", - "version": "2.3.0" - }, - { - "name": "cutandrun", - "version": "3.2.2" - }, - { - "name": "hic", - "version": "2.1.0" - }, - { - "name": "marsseq", - "version": "1.0.3" }, { - "name": "nascent", - "version": "2.3.0" - }, - { - "name": "phageannotator", - "version": "dev" - }, - { - "name": "readsimulator", - "version": "1.0.1" - }, - { - "name": "references", - 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expectations of gene content from near-universal single-copy orthologs selected from OrthoDB.", + "homepage": "https://busco.ezlab.org/", + "documentation": "https://busco.ezlab.org/busco_userguide.html", + "tool_dev_url": "https://gitlab.com/ezlab/busco", + "doi": "10.1007/978-1-4939-9173-0_14", + "licence": ["MIT"], + "identifier": "biotools:busco" + } + } + ], + "input": [ + { + "lineage": { + "type": "string", + "description": "The BUSCO lineage to use, or \"auto\", \"auto_prok\" or \"auto_euk\" to automatically select lineage" + } + } + ], + "output": { + "download_dir": [ + { + "busco_downloads": { + "type": "file", + "description": "Directory with busco database", + "pattern": "busco_downloads", + "ontologies": [] + } + } + ], + "versions_busco": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "busco": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "busco --version 2> /dev/null | sed 's/BUSCO //g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "busco": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "busco --version 2> /dev/null | sed 's/BUSCO //g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@zachary-foster"], + "maintainers": ["@zachary-foster"] }, - { - "index": { - "type": "file", - "description": "Bowtie genome index files", - "pattern": "*.ebwt", - "ontologies": [] - } - } - ], - { - "save_unaligned": { - "type": "boolean", - "description": "Whether to save fastq files containing the reads which did not align." - } - } - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, 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//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_samtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_gzip": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gzip": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gzip --version 2>&1 | sed '1!d;s/gzip //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bowtie": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bowtie --version 2>&1 | sed -n 's/.*bowtie-align-s version //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gzip": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gzip --version 2>&1 | sed '1!d;s/gzip //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "pathogensurveillance", + "version": "1.1.0" + } ] - ] }, - "authors": [ - "@kevinmenden" - ], - "maintainers": [ - "@kevinmenden" - ] - }, - "pipelines": [ { - "name": "callingcards", - "version": "1.0.0" + "name": "busco_generateplot", + "path": "modules/nf-core/busco/generateplot/meta.yml", + "type": "module", + "meta": { + "name": "busco_generateplot", + "description": "BUSCO plot generation tool", + "keywords": ["genome", "fasta", "annotation", "busco", "transcriptome", "quality control"], + "tools": [ + { + "busco": { + "description": "BUSCO provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs selected from OrthoDB.", + "homepage": "https://busco.ezlab.org/", + "documentation": "https://busco.ezlab.org/busco_userguide.html", + "tool_dev_url": "https://gitlab.com/ezlab/busco", + "doi": "10.1007/978-1-4939-9173-0_14", + "licence": ["MIT"], + "identifier": "biotools:busco" + } + } + ], + "input": [ + { + "short_summary_txt": { + "type": "file", + "description": "One or more short summary txt files from BUSCO", + "pattern": "short_summary.*.txt", + "ontologies": [] + } + } + ], + "output": { + "png": [ + { + "*.png": { + "type": "file", + "description": "A summary plot in png format", + "pattern": "*.png", + "ontologies": [] + } + } + ], + "versions_busco": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "busco": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "busco --version 2> /dev/null | sed 's/BUSCO //g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "busco": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "busco --version 2> /dev/null | sed 's/BUSCO //g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@GallVp"], + "maintainers": ["@GallVp"] + } }, { - "name": "circrna", - "version": "dev" + "name": "busco_phylogenomics", + "path": "modules/nf-core/busco/phylogenomics/meta.yml", + "type": "module", + "meta": { + "name": "busco_phylogenomics", + "description": "Construct species phylogenies using BUSCO proteins", + "keywords": ["phylogenies", "orthologs", "alignment"], + "tools": [ + { + "busco": { + "description": "Construct species phylogenies using BUSCO proteins", + "homepage": "https://github.com/jamiemcg/BUSCO_phylogenomics", + "documentation": "https://github.com/jamiemcg/BUSCO_phylogenomics", + "tool_dev_url": "https://github.com/jamiemcg/BUSCO_phylogenomics", + "doi": "10.1371/journal.pgen.1011512", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "busco": { + "type": "directory", + "description": "BUSCO lineage specific output", + "pattern": "*" + } + } + ] + ], + "output": { + "gene_trees": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}/gene_trees_single_copy/": { + "type": "directory", + "description": "Gene trees of BUSCO families", + "pattern": "${prefix}/gene_trees_single_copy" + } + } + ] + ], + "supermatrix": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}/supermatrix/": { + "type": "directory", + "description": "Concatenated supermatrix alignments of BUSCO families", + "pattern": "${prefix}/supermatrix" + } + } + ] + ], + "versions_buscophylogenomics": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "busco_phylogenomics": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "echo 20240919": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "busco_phylogenomics": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "echo 20240919": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@vagkaratzas"], + "maintainers": ["@vagkaratzas"] + } }, { - "name": "smrnaseq", - "version": "2.4.1" - } - ] - }, - { - "name": "bowtie_build", - "path": "modules/nf-core/bowtie/build/meta.yml", - "type": "module", - "meta": { - "name": "bowtie_build", - "description": "Create bowtie index for reference genome", - "keywords": [ - "index", - "fasta", - "genome", - "reference" - ], - "tools": [ - { - "bowtie": { - "description": "bowtie is a software package for mapping DNA sequences against\na large reference genome, such as the human genome.\n", - "homepage": "http://bowtie-bio.sourceforge.net/index.shtml", - "documentation": "http://bowtie-bio.sourceforge.net/manual.shtml", - "arxiv": "arXiv:1303.3997", - "licence": [ - "Artistic-2.0" - ], - "identifier": "biotools:bowtie" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing information about the genome fasta\ne.g. [ id:'test' ]\n" - } + "name": "bwa_aln", + "path": "modules/nf-core/bwa/aln/meta.yml", + "type": "module", + "meta": { + "name": "bwa_aln", + "description": "Find SA coordinates of the input reads for bwa short-read mapping", + "keywords": ["bwa", "aln", "short-read", "align", "reference", "fasta", "map", "fastq"], + "tools": [ + { + "bwa": { + "description": "BWA is a software package for mapping DNA sequences against\na large reference genome, such as the human genome.\n", + "homepage": "http://bio-bwa.sourceforge.net/", + "documentation": "https://bio-bwa.sourceforge.net/bwa.shtml", + "doi": "10.1093/bioinformatics/btp324", + "licence": ["GPL-3.0-or-later"], + "identifier": "biotools:bwa" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", + "ontologies": [ + { + "edam": "http://edamontology.org/data_2044" + }, + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "index": { + "type": "file", + "description": "BWA genome index files", + "pattern": "Directory containing BWA index *.{amb,ann,bwt,pac,sa}", + "ontologies": [ + { + "edam": "http://edamontology.org/data_3210" + } + ] + } + } + ] + ], + "output": { + "sai": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.sai": { + "type": "file", + "description": "Single or paired SA coordinate files", + "pattern": "*.sai", + "ontologies": [] + } + } + ] + ], + "versions_bwa": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bwa": { + "type": "string", + "description": "The tool name" + } + }, + { + "bwa 2>&1 | sed -n \"s/^Version: //p\"": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bwa": { + "type": "string", + "description": "The tool name" + } + }, + { + "bwa 2>&1 | sed -n \"s/^Version: //p\"": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@jfy133"], + "maintainers": ["@jfy133", "@gallvp"] }, - { - "fasta": { - "type": "file", - "description": "Input genome fasta file", - "ontologies": [] - } - } - ] - ], - "output": { - "index": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing information about the genome fasta\ne.g. [ id:'test' ]\n" - } - }, - { - "bowtie": { - "type": "string", - "description": "Folder containing bowtie genome index files", - "pattern": "*.ebwt", - "ontologies": [] - } - } - ] - ], - "versions_bowtie": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bowtie": { - "type": "string", - "description": "Folder containing bowtie genome index files", - "pattern": "*.ebwt", - "ontologies": [] - } - }, - { - "bowtie --version 2>&1 | sed -n 's/.*bowtie-align-s version //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bowtie": { - "type": "string", - "description": "Folder containing bowtie genome index files", - "pattern": "*.ebwt", - "ontologies": [] - } - }, - { - "bowtie --version 2>&1 | sed -n 's/.*bowtie-align-s version //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "callingcards", + "version": "1.0.0" + }, + { + "name": "sammyseq", + "version": "dev" + } ] - ] - }, - "authors": [ - "@kevinmenden", - "@drpatelh" - ], - "maintainers": [ - "@kevinmenden", - "@drpatelh" - ] - }, - "pipelines": [ - { - "name": "callingcards", - "version": "1.0.0" - }, - { - "name": "circrna", - "version": "dev" - }, - { - "name": "references", - "version": "0.1" }, { - "name": "smrnaseq", - "version": "2.4.1" - } - ] - }, - { - "name": "bracken_bracken", - "path": "modules/nf-core/bracken/bracken/meta.yml", - "type": "module", - "meta": { - "name": "bracken_bracken", - "description": "Re-estimate taxonomic abundance of metagenomic samples analyzed by kraken.", - "keywords": [ - "bracken", - "metagenomics", - "abundance", - "kraken2" - ], - "tools": [ - { - "bracken": { - "description": "Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.", - "homepage": "https://ccb.jhu.edu/software/bracken/", - "documentation": "https://ccb.jhu.edu/software/bracken/index.shtml?t=manual", - "tool_dev_url": "https://github.com/jenniferlu717/Bracken", - "doi": "10.7717/peerj-cs.104", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:bracken" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + "name": "bwa_index", + "path": "modules/nf-core/bwa/index/meta.yml", + "type": "module", + "meta": { + "name": "bwa_index", + "description": "Create BWA index for reference genome", + "keywords": ["index", "fasta", "genome", "reference"], + "tools": [ + { + "bwa": { + "description": "BWA is a software package for mapping DNA sequences against\na large reference genome, such as the human genome.\n", + "homepage": "http://bio-bwa.sourceforge.net/", + "documentation": "https://bio-bwa.sourceforge.net/bwa.shtml", + "arxiv": "arXiv:1303.3997", + "licence": ["GPL-3.0-or-later"], + "identifier": "biotools:bwa" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input genome fasta file", + "ontologies": [ + { + "edam": "http://edamontology.org/data_2044" + }, + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ] + ], + "output": { + "index": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bwa": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*.{amb,ann,bwt,pac,sa}", + "ontologies": [ + { + "edam": "http://edamontology.org/data_3210" + } + ] + } + } + ] + ], + "versions_bwa": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bwa": { + "type": "string", + "description": "The tool name" + } + }, + { + "bwa 2>&1 | sed -n \"s/^Version: //p\"": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bwa": { + "type": "string", + "description": "The tool name" + } + }, + { + "bwa 2>&1 | sed -n \"s/^Version: //p\"": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@drpatelh", "@maxulysse"], + "maintainers": ["@maxulysse", "@gallvp"] }, - { - "kraken_report": { - "type": "file", - "description": "TSV file with six columns coming from kraken2 output", - "pattern": "*.{tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - { - "database": { - "type": "file", - "description": "Directory containing the kraken2/Bracken files for analysis", - "pattern": "*", - "ontologies": [] - } - } - ], - "output": { - "reports": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", - "pattern": "*.{tsv}" - } - }, - { - "bracken_report": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", - "pattern": "*.{tsv}" - } - } - ] - ], - "txt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", - "pattern": "*.{tsv}" - } - }, - { - "bracken_kraken_style_report": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", - "pattern": "*.txt" - } - } - ] - ], - "versions_bracken": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bracken": { - "type": "string", - "description": "The tool name" - } - }, - { - "bracken -v | cut -f2 -d\"v\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bracken": { - "type": "string", - "description": "The tool name" - } - }, - { - "bracken -v | cut -f2 -d\"v\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "atacseq", + "version": "2.1.2" + }, + { + "name": "callingcards", + "version": "1.0.0" + }, + { + "name": "chipseq", + "version": "2.1.0" + }, + { + "name": "circdna", + "version": "1.1.0" + }, + { + "name": "circrna", + "version": "dev" + }, + { + "name": "crisprseq", + "version": "2.3.0" + }, + { + "name": "deepmutscan", + "version": "dev" + }, + { + "name": "fastquorum", + "version": "1.2.0" + }, + { + "name": "hgtseq", + "version": "1.1.0" + }, + { + "name": "hicar", + "version": "1.0.0" + }, + { + "name": "methylseq", + "version": "4.2.0" + }, + { + "name": "nascent", + "version": "2.3.0" + }, + { + "name": "oncoanalyser", + "version": "2.3.0" + }, + { + "name": "pathogensurveillance", + "version": "1.1.0" + }, + { + "name": "radseq", + "version": "dev" + }, + { + "name": "raredisease", + "version": "3.0.0" + }, + { + "name": "references", + "version": "0.1" + }, + { + "name": "rnadnavar", + "version": "dev" + }, + { + "name": "sammyseq", + "version": "dev" + }, + { + "name": "sarek", + "version": "3.8.1" + }, + { + "name": "ssds", + "version": "dev" + }, + { + "name": "variantcatalogue", + "version": "dev" + } ] - ] - }, - "authors": [ - "@Midnighter" - ], - "maintainers": [ - "@Midnighter" - ] - }, - "pipelines": [ - { - "name": "rnaseq", - "version": "3.26.0" }, { - "name": "taxprofiler", - "version": "2.0.0" - }, - { - "name": "viralmetagenome", - "version": "1.1.1" - } - ] - }, - { - "name": "bracken_build", - "path": "modules/nf-core/bracken/build/meta.yml", - "type": "module", - "meta": { - "name": "bracken_build", - "description": "Extends a Kraken2 database to be compatible with Bracken", - "keywords": [ - "kraken2", - "bracken", - "database", - "build" - ], - "tools": [ - { - "bracken": { - "description": "Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.", - "homepage": "https://ccb.jhu.edu/software/bracken/", - "documentation": "https://ccb.jhu.edu/software/bracken/", - "tool_dev_url": "https://github.com/jenniferlu717/Bracken/", - "doi": "10.7717/peerj-cs.104 ", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:bracken" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "k2d": { - "type": "file", - "description": "Kraken2 k2d binary database files", - "pattern": "*.k2d", - "ontologies": [] - } - }, - { - "map": { - "type": "file", - "description": "Kraken2 k2d binary database taxonomy to sequencing mapping file", - "pattern": "*.map", - "ontologies": [] - } - }, - { - "library": { - "type": "file", - "description": "Kraken2 masked FASTA files used to build the database", - "pattern": "*.fasta", - "ontologies": [] - } - }, - { - "taxonomy": { - "type": "file", - "description": "Kraken2 nodes.dmp, names.dmp, and .accession2taxid taxonomy files", - "pattern": "*.{dmp,accession2taxid}", - "ontologies": [] - } - } - ] - ], - "output": { - "db": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "bracken-database/": { - "type": "directory", - "description": "Directory contains the database that can be used to perform taxonomic classification\n\nIMPORTANT: this output directory will be hardcoded as 'bracken-database/' inside the module\nto prevent issues of containers following symlinks in symlinks.\n\nTo give a user the option to provide custom name for the database directory within a pipeline, you should\ncustomise this name using during pipeline output publication via the pipeline's publishDir or workflow output customisation options.\n", - "pattern": "bracken-database/", - "ontologies": [ - { - "edam": "http://edamontology.org/data_1049" - } - ] - } - } - ] - ], - "db_separated": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "bracken-database/database*": { - "type": "file", - "description": "Bracken kmer distribution files", - "pattern": "database*", - "ontologies": [] - } - }, - { - "bracken-database/*k2d": { - "type": "file", - "description": "Kraken2 k2d binary database files", - "pattern": "*.k2d", - "ontologies": [] - } - }, - { - "bracken-database/*map": { - "type": "file", - "description": "Kraken2 k2d binary database taxonomy to sequencing mapping file", - "pattern": "*.map", - "ontologies": [] - } - }, - { - "bracken-database/library/added/*": { - "type": "file", - "description": "Kraken2 masked FASTA files used to build the database", - "pattern": "*.fasta", - "ontologies": [] - } - }, - { - "bracken-database/taxonomy/*": { - "type": "file", - "description": "Kraken2 nodes.dmp, names.dmp, and .accession2taxid taxonomy files", - "pattern": "*.{dmp,accession2taxid}", - "ontologies": [] - } - } - ] - ], - "versions_bracken": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bracken": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bracken -v | cut -f2 -d'v'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bracken": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bracken -v | cut -f2 -d'v'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@jfy133" - ], - "maintainers": [ - "@jfy133" - ] - }, - "pipelines": [ - { - "name": "createtaxdb", - "version": "3.0.0" - } - ] - }, - { - "name": "bracken_combinebrackenoutputs", - "path": "modules/nf-core/bracken/combinebrackenoutputs/meta.yml", - "type": "module", - "meta": { - "name": "bracken_combinebrackenoutputs", - "description": "Combine output of metagenomic samples analyzed by bracken.", - "keywords": [ - "bracken", - "metagenomics", - "postprocessing", - "reporting" - ], - "tools": [ - { - "bracken": { - "description": "Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.", - "homepage": "https://ccb.jhu.edu/software/bracken/", - "documentation": "https://ccb.jhu.edu/software/bracken/index.shtml?t=manual", - "tool_dev_url": "https://github.com/jenniferlu717/Bracken", - "doi": "10.7717/peerj-cs.104", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:bracken" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "List of output files from bracken", - "pattern": "*", - "ontologies": [] - } - } - ] - ], - "output": { - "txt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.txt": { - "type": "file", - "description": "Combined output in table format", - "pattern": "*.txt", - "ontologies": [] - } - } - ] - ], - "versions_combine_bracken_outputs": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "combine_bracken_outputs": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bracken -v | cut -f2 -d\"v\"": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "combine_bracken_outputs": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bracken -v | cut -f2 -d\"v\"": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@jfy133" - ], - "maintainers": [ - "@jfy133" - ] - }, - "pipelines": [ - { - "name": "taxprofiler", - "version": "2.0.0" - } - ] - }, - { - "name": "braker3", - "path": "modules/nf-core/braker3/meta.yml", - "type": "module", - "meta": { - "name": "braker3", - "description": "Gene prediction in novel genomes using RNA-seq and protein homology information\n", - "keywords": [ - "genome", - "annotation", - "braker", - "gff", - "gtf" - ], - "tools": [ - { - "braker3": { - "description": "BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures using protein and RNA-seq and protein homology information", - "homepage": "https://github.com/Gaius-Augustus/BRAKER", - "documentation": "https://github.com/Gaius-Augustus/BRAKER", - "tool_dev_url": "https://github.com/Gaius-Augustus/BRAKER", - "doi": "10.13140/RG.2.2.20047.36004", - "licence": [ - "Artistic-1.0" - ], - "identifier": "biotools:braker3" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Genome assembly fasta", - "pattern": "*.{fasta,fa,fas,faa,fna}", - "ontologies": [] - } - } - ], - { - "bam": { - "type": "file", - "description": "BAM file of RNA-seq data to be passed to --bam", - "pattern": "*.bam", - "ontologies": [] - } - }, - { - "rnaseq_sets_dirs": { - "type": "file", - "description": "Directories of RNA-seq data sets to be passed to --rnaseq_sets_dirs", - "ontologies": [] - } - }, - { - "rnaseq_sets_ids": { - "type": "file", - "description": "IDs of RNA-seq data sets to be passed to --rnaseq_sets_ids", - "ontologies": [] - } - }, - { - "proteins": { - "type": "file", - "description": "Protein evidence to be passed to --proteins", - "pattern": "*.{fasta,fa,fas,faa}", - "ontologies": [] - } - }, - { - "hintsfile": { - "type": "file", - "description": "Hintsfile to be passed to --hintsfile", - "pattern": "*.{gff, gtf, gff3}", - "ontologies": [] - } - } - ], - "output": { - "gtf": [ - [ - { - "meta": { - "type": "file", - "description": "Gene transfer format file as output by BRAKER3", - "pattern": "*.{gtf}", - "ontologies": [] - } - }, - { - "$prefix/braker.gtf": { - "type": "file", - "description": "Gene transfer format file as output by BRAKER3", - "pattern": "*.{gtf}", - "ontologies": [] - } - } - ] - ], - "cds": [ - [ - { - "meta": { - "type": "file", - "description": "Gene transfer format file as output by BRAKER3", - "pattern": "*.{gtf}", - "ontologies": [] - } - }, - { - "$prefix/braker.codingseq": { - "type": "file", - "description": "Coding sequence file as output by BRAKER3", - "pattern": "*.{codingseq}", - "ontologies": [] - } - } - ] - ], - "aa": [ - [ - { - "meta": { - "type": "file", - "description": "Gene transfer format file as output by BRAKER3", - "pattern": "*.{gtf}", - "ontologies": [] - } - }, - { - "$prefix/braker.aa": { - "type": "file", - "description": "Protein sequence file as output by BRAKER3", - "pattern": "*.{aa}", - "ontologies": [] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "file", - "description": "Gene transfer format file as output by BRAKER3", - "pattern": "*.{gtf}", - "ontologies": [] - } - }, - { - "$prefix/braker.log": { - "type": "file", - "description": "BRAKER3 log file", - "pattern": "*.log", - "ontologies": [] - } - } - ] - ], - "hintsfile": [ - [ - { - "meta": { - "type": "file", - "description": "Gene transfer format file as output by BRAKER3", - "pattern": "*.{gtf}", - "ontologies": [] - } - }, - { - "$prefix/hintsfile.gff": { - "type": "file", - "description": "Hints file as output by BRAKER3", - "pattern": "*hintsfile.{gff}", - "ontologies": [] - } - } - ] - ], - "gff3": [ - [ - { - "meta": { - "type": "file", - "description": "Gene transfer format file as output by BRAKER3", - "pattern": "*.{gtf}", - "ontologies": [] - } - }, - { - "$prefix/braker.gff3": { - "type": "file", - "description": "GFF3 file as output by BRAKER3", - "pattern": "*.{gff3}", - "ontologies": [] - } - } - ] - ], - "citations": [ - [ - { - "meta": { - "type": "file", - "description": "Gene transfer format file as output by BRAKER3", - "pattern": "*.{gtf}", - "ontologies": [] - } - }, - { - "$prefix/what-to-cite.txt": { - "type": "file", - "description": "BRAKER3 citations", - "pattern": "what-to-cite.txt", - "ontologies": [] - } - } - ] - ], - "versions_braker3": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "braker3": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "braker.pl --version 2>/dev/null | sed 's/braker.pl version //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_augustus": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "augustus": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "augustus --version |& sed -n 's/AUGUSTUS (\\(.*\\)) is a gene .*/\\1/p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_genemarketp": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "genemark-etp": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gmetp.pl |& sed -n 's/ETP version \\(.*\\)/\\1/p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_prothint": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "prothint": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "prothint.py --version |& sed 's/prothint.py //1'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "braker3": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "braker.pl --version 2>/dev/null | sed 's/braker.pl version //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "augustus": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "augustus --version |& sed -n 's/AUGUSTUS (\\(.*\\)) is a gene .*/\\1/p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "genemark-etp": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gmetp.pl |& sed -n 's/ETP version \\(.*\\)/\\1/p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "prothint": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "prothint.py --version |& sed 's/prothint.py //1'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@kherronism", - "@GallVp" - ], - "maintainers": [ - "@GallVp" - ] - } - }, - { - "name": "busco_busco", - "path": "modules/nf-core/busco/busco/meta.yml", - "type": "module", - "meta": { - "name": "busco_busco", - "description": "Benchmarking Universal Single Copy Orthologs", - "keywords": [ - "quality control", - "genome", - "transcriptome", - "proteome" - ], - "tools": [ - { - "busco": { - "description": "BUSCO provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs selected from OrthoDB.", - "homepage": "https://busco.ezlab.org/", - "documentation": "https://busco.ezlab.org/busco_userguide.html", - "tool_dev_url": "https://gitlab.com/ezlab/busco", - "doi": "10.1007/978-1-4939-9173-0_14", - "licence": [ - "MIT" - ], - "identifier": "biotools:busco" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + "name": "bwa_mem", + "path": "modules/nf-core/bwa/mem/meta.yml", + "type": "module", + "meta": { + "name": "bwa_mem", + "description": "Performs fastq alignment to a fasta reference using BWA", + "keywords": ["mem", "bwa", "alignment", "map", "fastq", "bam", "sam"], + "tools": [ + { + "bwa": { + "description": "BWA is a software package for mapping DNA sequences against\na large reference genome, such as the human genome.\n", + "homepage": "http://bio-bwa.sourceforge.net/", + "documentation": "https://bio-bwa.sourceforge.net/bwa.shtml", + "arxiv": "arXiv:1303.3997", + "licence": ["GPL-3.0-or-later"], + "identifier": "biotools:bwa" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", + "ontologies": [ + { + "edam": "http://edamontology.org/data_2044" + }, + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "index": { + "type": "file", + "description": "BWA genome index files", + "pattern": "Directory containing BWA index *.{amb,ann,bwt,pac,sa}", + "ontologies": [ + { + "edam": "http://edamontology.org/data_3210" + } + ] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference genome in FASTA format", + "pattern": "*.{fasta,fa}", + "ontologies": [ + { + "edam": "http://edamontology.org/data_2044" + }, + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + { + "sort_bam": { + "type": "boolean", + "description": "use samtools sort (true) or samtools view (false)", + "pattern": "true or false" + } + } + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.bam": { + "type": "file", + "description": "Output BAM file containing read alignments", + "pattern": "*.{bam}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + } + ] + ], + "cram": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.cram": { + "type": "file", + "description": "Output CRAM file containing read alignments", + "pattern": "*.{cram}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3462" + } + ] + } + } + ] + ], + "sam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.sam": { + "type": "file", + "description": "Output SAM file containing read alignments", + "pattern": "*.{sam}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2573" + } + ] + } + } + ] + ], + "csi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.csi": { + "type": "file", + "description": "Optional index file for BAM file", + "pattern": "*.{csi}", + "ontologies": [] + } + } + ] + ], + "crai": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.crai": { + "type": "file", + "description": "Optional index file for CRAM file", + "pattern": "*.{crai}", + "ontologies": [] + } + } + ] + ], + "versions_bwa": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bwa": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bwa 2>&1 | sed -n \"s/^Version: //p\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_samtools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "samtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "samtools version | sed '1!d;s/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bwa": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bwa 2>&1 | sed -n \"s/^Version: //p\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "samtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "samtools version | sed '1!d;s/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@drpatelh", "@jeremy1805", "@matthdsm"], + "maintainers": ["@drpatelh", "@jeremy1805", "@matthdsm"] }, - { - "fasta": { - "type": "file", - "description": "Nucleic or amino acid sequence file in FASTA format.", - "pattern": "*.{fasta,fna,fa,fasta.gz,fna.gz,fa.gz}", - "ontologies": [] - } - } - ], - { - "mode": { - "type": "string", - "description": "The mode to run Busco in. One of genome, proteins, or transcriptome", - "pattern": "{genome,proteins,transcriptome}" - } - }, - { - "lineage": { - "type": "string", - "description": "The BUSCO lineage to use, or \"auto\", \"auto_prok\" or \"auto_euk\" to automatically select lineage" - } - }, - { - "busco_lineages_path": { - "type": "directory", - "description": "Path to local BUSCO lineages directory." - } - }, - { - "config_file": { - "type": "file", - "description": "Path to BUSCO config file.", - "ontologies": [] - } - }, - { - "clean_intermediates": { - "type": "boolean", - "description": "Flag to remove intermediate files." - } - } - ], - "output": { - "batch_summary": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*-busco.batch_summary.txt": { - "type": "file", - "description": "Summary of all sequence files analyzed", - "pattern": "*-busco.batch_summary.txt", - "ontologies": [] - } - } - ] - ], - "batch_summary_failed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*-busco.batch_summary.failed.txt": { - "type": "file", - "description": "Batch summary lines indicating BUSCO run failures", - "pattern": "*-busco.batch_summary.failed.txt", - "ontologies": [] - } - } - ] - ], - "short_summaries_txt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "short_summary.*.txt": { - "type": "file", - "description": "Short Busco summary in plain text format", - "pattern": "short_summary.*.txt", - "ontologies": [] - } - } - ] - ], - "short_summaries_json": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "short_summary.*.json": { - "type": "file", - "description": "Short Busco summary in JSON format", - "pattern": "short_summary.*.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*-busco.log": { - "type": "file", - "description": "BUSCO main log", - "pattern": "*-busco.log", - "ontologies": [] - } - } - ] - ], - "full_table": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*-busco/*/run_*/full_table.tsv": { - "type": "file", - "description": "Full BUSCO results table", - "pattern": "full_table.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "missing_busco_list": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*-busco/*/run_*/missing_busco_list.tsv": { - "type": "file", - "description": "List of missing BUSCOs", - "pattern": "missing_busco_list.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "single_copy_proteins": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*-busco/*/run_*/single_copy_proteins.faa": { - "type": "file", - "description": "Fasta file of single copy proteins (transcriptome mode)", - "pattern": "single_copy_proteins.faa", - "ontologies": [] - } - } - ] - ], - "seq_dir": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*-busco/*/run_*/busco_sequences": { - "type": "directory", - "description": "BUSCO sequence directory", - "pattern": "busco_sequences" - } - } - ] - ], - "translated_dir": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*-busco/*/translated_proteins": { - "type": "directory", - "description": "Six frame translations of each transcript made by the transcriptome mode", - "pattern": "translated_dir" - } - } - ] - ], - "busco_dir": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*-busco": { - "type": "directory", - "description": "BUSCO lineage specific output", - "pattern": "*-busco" - } - } - ] - ], - "downloaded_lineages": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "busco_downloads/lineages/*": { - "type": "directory", - "description": "Lineages downloaded by BUSCO when running the analysis, for example bacteria_odb12", - "pattern": "busco_downloads/lineages/*" - } - } - ] - ], - "single_copy_faa": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' 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"The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "busco": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "busco --version 2> /dev/null | sed 's/BUSCO //g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "atacseq", + "version": "2.1.2" + }, + { + "name": "chipseq", + "version": "2.1.0" + }, + { + "name": "circrna", + "version": "dev" + }, + { + "name": "crisprseq", + "version": "2.3.0" + }, + { + "name": "deepmutscan", + "version": "dev" + }, + { + "name": "hgtseq", + "version": "1.1.0" + }, + { + "name": "hicar", + "version": "1.0.0" + }, + { + "name": "methylseq", + "version": "4.2.0" + }, + { + "name": "nascent", + "version": "2.3.0" + }, + { + "name": "pathogensurveillance", + "version": "1.1.0" + }, + { + "name": "radseq", + "version": "dev" + }, + { + "name": "raredisease", + "version": "3.0.0" + }, + { + "name": "rnadnavar", + "version": "dev" + }, + { + "name": "sammyseq", + "version": "dev" + }, + { + "name": "sarek", + "version": "3.8.1" + }, + { + "name": "ssds", + "version": "dev" + }, + { + "name": "variantcatalogue", + "version": "dev" + } ] - ] }, - "authors": [ - "@priyanka-surana", - "@charles-plessy", - "@mahesh-panchal", - "@muffato", - "@jvhagey", - "@gallvp" - ], - "maintainers": [ - "@priyanka-surana", - "@charles-plessy", - "@mahesh-panchal", - "@muffato", - "@jvhagey", - "@gallvp" - ] - }, - "pipelines": [ { - "name": "bacass", - "version": "2.6.0" - }, - { - "name": "denovotranscript", - "version": "1.2.1" + "name": "bwa_sampe", + "path": "modules/nf-core/bwa/sampe/meta.yml", + "type": "module", + "meta": { + "name": "bwa_sampe", + "description": "Convert paired-end bwa SA coordinate files to SAM format", + "keywords": ["bwa", "aln", "short-read", "align", "reference", "fasta", "map", "sam", "bam"], + "tools": [ + { + "bwa": { + "description": "BWA is a software package for mapping DNA sequences against\na large reference genome, such as the human genome.\n", + "homepage": "http://bio-bwa.sourceforge.net/", + "documentation": "https://bio-bwa.sourceforge.net/bwa.shtml", + "doi": "10.1093/bioinformatics/btp324", + "licence": ["GPL-3.0-or-later"], + "identifier": "biotools:bwa" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "FASTQ files specified alongside meta in input channel.", + "pattern": "*.{fastq,fq}.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/data_2044" + }, + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + }, + { + "sai": { + "type": "file", + "description": "SAI file specified alongside meta and reads in input channel.", + "pattern": "*.sai", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "index": { + "type": "directory", + "description": "Directory containing BWA index files (amb,ann,bwt,pac,sa) from BWA_INDEX", + "pattern": "bwa/", + "ontologies": [ + { + "edam": "http://edamontology.org/data_3210" + } + ] + } + } + ] + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "BAM file", + "pattern": "*.bam", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + } + ] + ], + "versions_bwa": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bwa": { + "type": "string", + "description": "The tool name" + } + }, + { + "bwa 2>&1 | sed -n \"s/^Version: //p\"": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ], + "versions_samtools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "samtools": { + "type": "string", + "description": "The tool name" + } + }, + { + "samtools version | sed '1!d;s/.* //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bwa": { + "type": "string", + "description": "The tool name" + } + }, + { + "bwa 2>&1 | sed -n \"s/^Version: //p\"": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", 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genome.\n", + "homepage": "http://bio-bwa.sourceforge.net/", + "documentation": "https://bio-bwa.sourceforge.net/bwa.shtml", + "doi": "10.1093/bioinformatics/btp324", + "licence": ["GPL-3.0-or-later"], + "identifier": "biotools:bwa" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "FASTQ files specified alongside meta in input channel.", + "pattern": "*.{fastq,fq}.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/data_2044" + }, + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + }, + { + "sai": { + "type": "file", + "description": "SAI file specified alongside meta and reads in input channel.", + "pattern": "*.sai", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "index": { + "type": "directory", + "description": "Directory containing BWA index files (amb,ann,bwt,pac,sa) from BWA_INDEX", + "pattern": "bwa/", + "ontologies": [ + { + "edam": "http://edamontology.org/data_3210" + } + ] + } + } + ] + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "BAM file", + "pattern": "*.bam", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + } + ] + ], + "versions_bwa": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bwa": { + "type": "string", + "description": "The tool name" + } + }, + { + "bwa 2>&1 | sed -n \"s/^Version: //p\"": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ], + "versions_samtools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "samtools": { + "type": "string", + "description": "The tool name" + } + }, + { + "samtools version | sed '1!d;s/.* //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bwa": { + "type": "string", + "description": "The tool name" + } + }, + { + "bwa 2>&1 | sed -n \"s/^Version: //p\"": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "samtools": { + "type": "string", + "description": "The tool name" + } + }, + { + "samtools version | sed '1!d;s/.* //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@jfy133"], + "maintainers": ["@jfy133"] + }, + "pipelines": [ + { + "name": "callingcards", + "version": "1.0.0" + }, + { + "name": "sammyseq", + "version": "dev" + } + ] }, { - "name": "genomeqc", - "version": "dev" + "name": "bwamem2_index", + "path": "modules/nf-core/bwamem2/index/meta.yml", + "type": "module", + "meta": { + "name": "bwamem2_index", + "description": "Create BWA-mem2 index for reference genome", + "keywords": ["index", "fasta", "genome", "reference"], + "tools": [ + { + "bwamem2": { + "description": "BWA-mem2 is a software package for mapping DNA sequences against\na large reference genome, such as the human genome.\n", + "homepage": "https://github.com/bwa-mem2/bwa-mem2", + "documentation": "https://github.com/bwa-mem2/bwa-mem2#usage", + "licence": ["MIT"], + "identifier": "biotools:bwa-mem2" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input genome fasta file", + "ontologies": [ + { + "edam": "http://edamontology.org/data_2044" + }, + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ] + ], + "output": { + "index": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bwamem2": { + "type": "string", + "description": "BWA genome index files", + "pattern": "*.{0123,amb,ann,bwt.2bit.64,pac}", + "ontologies": [ + { + "edam": "http://edamontology.org/data_3210" + } + ] + } + } + ] + ], + "versions_bwamem2": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bwamem2": { + "type": "string", + "description": "BWA genome index files", + "pattern": "*.{0123,amb,ann,bwt.2bit.64,pac}", + "ontologies": [ + { + "edam": "http://edamontology.org/data_3210" + } + ] + } + }, + { + "bwa-mem2 version | grep -o -E \"[0-9]+(\\.[0-9]+)+\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bwamem2": { + "type": "string", + "description": "BWA genome index files", + "pattern": "*.{0123,amb,ann,bwt.2bit.64,pac}", + "ontologies": [ + { + "edam": "http://edamontology.org/data_3210" + } + ] + } + }, + { + "bwa-mem2 version | grep -o -E \"[0-9]+(\\.[0-9]+)+\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@maxulysse"], + "maintainers": ["@maxulysse"] + }, + "pipelines": [ + { + "name": "callingcards", + "version": "1.0.0" + }, + { + "name": "genomicrelatedness", + "version": "dev" + }, + { + "name": "hgtseq", + "version": "1.1.0" + }, + { + "name": "nascent", + "version": "2.3.0" + }, + { + "name": "oncoanalyser", + "version": "2.3.0" + }, + { + "name": "radseq", + "version": "dev" + }, + { + "name": "raredisease", + "version": "3.0.0" + }, + { + "name": "references", + "version": "0.1" + }, + { + "name": "rnadnavar", + "version": "dev" + }, + { + "name": "sarek", + "version": "3.8.1" + }, + { + "name": "seqinspector", + "version": "1.0.1" + }, + { + "name": "tbanalyzer", + "version": "dev" + }, + { + "name": "viralmetagenome", + "version": "1.1.1" + } + ] }, { - "name": "mag", - "version": "5.4.2" + "name": "bwamem2_mem", + "path": "modules/nf-core/bwamem2/mem/meta.yml", + "type": "module", + "meta": { + "name": "bwamem2_mem", + "description": "Performs fastq alignment to a fasta reference using BWA", + "keywords": ["mem", "bwa", "alignment", "map", "fastq", "bam", "sam"], + "tools": [ + { + "bwa": { + "description": "BWA-mem2 is a software package for mapping DNA sequences against\na large reference genome, such as the human genome.\n", + "homepage": "https://github.com/bwa-mem2/bwa-mem2", + "documentation": "http://www.htslib.org/doc/samtools.html", + "arxiv": "arXiv:1303.3997", + "licence": ["MIT"], + "identifier": "biotools:bwa-mem2" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", + "ontologies": [ + { + "edam": "http://edamontology.org/data_2044" + }, + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference/index information\ne.g. [ id:'test' ]\n" + } + }, + { + "index": { + "type": "file", + "description": "BWA genome index files", + "pattern": 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"*.{sam}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2573" + } + ] + } + } + ] + ], + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Output BAM file containing read alignments", + "pattern": "*.{bam}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + } + ] + ], + "cram": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.cram": { + "type": "file", + "description": "Output CRAM file containing read alignments", + "pattern": "*.{cram}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3462" + } + ] + } + } + ] + ], + "crai": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', 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single_end:false ]\n" + } + }, + { + "index": { + "type": "directory", + "description": "Directory containing bwameth genome index" + } + } + ] + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Output BAM file containing read alignments", + "pattern": "*.{bam}", + "ontologies": [] + } + } + ] + ], + "versions_bwameth": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bwameth": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bwameth.py --version | cut -f2 -d ' '": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_samtools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "samtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "samtools version | sed '1!d;s/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of samtools" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bwameth": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bwameth.py --version | cut -f2 -d ' '": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "samtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "samtools version | sed '1!d;s/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of samtools" + } + } + ] + ] + }, + "authors": ["@phue"], + "maintainers": ["@phue"] + }, + "pipelines": [ + { + "name": "methylseq", + "version": "4.2.0" + } + ] }, { - "name": "sammyseq", - "version": "dev" - } - ] - }, - { - "name": "bwa_index", - "path": "modules/nf-core/bwa/index/meta.yml", - "type": "module", - "meta": { - "name": "bwa_index", - "description": "Create BWA index for reference genome", - "keywords": [ - "index", - "fasta", - "genome", - "reference" - ], - "tools": [ - { - "bwa": { - "description": "BWA is a software package for mapping DNA sequences against\na large reference genome, such as the human genome.\n", - "homepage": "http://bio-bwa.sourceforge.net/", - "documentation": "https://bio-bwa.sourceforge.net/bwa.shtml", - "arxiv": "arXiv:1303.3997", - "licence": [ - "GPL-3.0-or-later" - ], - "identifier": "biotools:bwa" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } + "name": "bwameth_index", + "path": "modules/nf-core/bwameth/index/meta.yml", + "type": "module", + "meta": { + "name": "bwameth_index", + "description": "Performs indexing of c2t converted reference genome", + "keywords": ["bwameth", "3-letter genome", "index", "methylseq", "bisulphite", "bisulfite", "fasta"], + "tools": [ + { + "bwameth": { + "description": "Fast and accurate alignment of BS-Seq reads\nusing bwa-mem and a 3-letter genome.\n", + "homepage": "https://github.com/brentp/bwa-meth", + "documentation": "https://github.com/brentp/bwa-meth", + "arxiv": "arXiv:1401.1129", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input genome fasta file", + "ontologies": [] + } + } + ], + { + "use_mem2": { + "type": "boolean", + "description": "If true, use bwameth index-mem2 for indexing. If false, use bwameth index (default: false)\n" + } + } + ], + "output": { + "index": [ + [ + { + "meta": { + "type": "directory", + "description": "Directory containing bwameth genome index", + "pattern": "index" + } + }, + { + "BwamethIndex": { + "type": "directory", + "description": "Directory containing bwameth genome index", + "pattern": "index" + } + } + ] + ], + "versions_bwameth_index": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bwameth": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bwameth.py --version | cut -f2 -d' '": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bwameth": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bwameth.py --version | cut -f2 -d' '": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@phue"], + "maintainers": ["@phue", "@sateeshperi"] }, - { - "fasta": { - "type": "file", - "description": "Input genome fasta file", - "ontologies": [ - { - "edam": "http://edamontology.org/data_2044" - }, - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ], - "output": { - "index": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bwa": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n", - "pattern": "*.{amb,ann,bwt,pac,sa}", - "ontologies": [ - { - "edam": "http://edamontology.org/data_3210" - } - ] - } - } - ] - ], - "versions_bwa": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bwa": { - "type": "string", - "description": "The tool name" - } - }, - { - "bwa 2>&1 | sed -n \"s/^Version: //p\"": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bwa": { - "type": "string", - "description": "The tool name" - } - }, - { - "bwa 2>&1 | sed -n \"s/^Version: //p\"": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } + "pipelines": [ + { + "name": "methylseq", + "version": "4.2.0" + } ] - ] }, - "authors": [ - "@drpatelh", - "@maxulysse" - ], - "maintainers": [ - "@maxulysse", - "@gallvp" - ] - }, - "pipelines": [ { - "name": "atacseq", - "version": "2.1.2" + "name": "caalm_caalm", + "path": "modules/nf-core/caalm/caalm/meta.yml", + "type": "module", + "meta": { + "name": "caalm_caalm", + "description": "Annotates carbohydrate-active enzyme (CAZyme) families from protein sequences\nusing protein language model (ESM) embeddings and FAISS-based nearest-neighbour\nsearch. Performs three-level hierarchical classification: binary CAZyme detection\n(Level 0), CAZy class assignment (Level 1), and CAZy family assignment (Level 2).\n", + "keywords": ["cazyme", "annotation", "protein", "language model", "deep learning", "classification"], + "tools": [ + { + "caalm": { + "description": "CAALM (Carbohydrate Activity Annotation with protein Language Models) predicts\nCAZyme class and family membership from protein FASTA sequences using ESM-based\nembeddings and FAISS nearest-neighbour retrieval.\n", + "homepage": "https://github.com/lczong/CAALM", + "documentation": "https://github.com/lczong/CAALM", + "tool_dev_url": "https://github.com/lczong/CAALM", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Protein sequences in FASTA format.", + "pattern": "*.{fa,fasta,faa}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + [ + { + "level0": { + "type": "directory", + "description": "Directory containing the Level 0 (binary CAZyme detection) model files,\nas produced by CAALM_DOWNLOADMODELS.\n", + "pattern": "models/level0", + "ontologies": [] + } + }, + { + "level1": { + "type": "directory", + "description": "Directory containing the Level 1 (CAZy class assignment) model files,\nas produced by CAALM_DOWNLOADMODELS.\n", + "pattern": "models/level1", + "ontologies": [] + } + }, + { + "level2": { + "type": "directory", + "description": "Directory containing the Level 2 (CAZy family assignment) model files,\nas produced by CAALM_DOWNLOADMODELS.\n", + "pattern": "models/level2", + "ontologies": [] + } + } + ] + ], + "output": { + "predictions": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}_predictions.tsv": { + "type": "file", + "description": "Tab-separated file with per-sequence CAZy class and family predictions\nacross all three classification levels.\n", + "pattern": "*_predictions.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "probabilities": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}_probabilities.jsonl": { + "type": "file", + "description": "JSON Lines file with per-sequence probability scores at all three\nclassification levels.\n", + "pattern": "*_probabilities.jsonl", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "statistics": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}_statistics.tsv": { + "type": "file", + "description": "Tab-separated summary file with counts and percentages of predicted\nCAZyme classes and families across the input sequences.\n", + "pattern": "*_statistics.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "embeddings_level0": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}_level0_embeddings.npy": { + "type": "file", + "description": "NumPy array file containing Level 0 ESM embeddings for each input\nsequence. Optional; produced when `--save-level0-embeddings` is passed.\n", + "pattern": "*_level0_embeddings.npy", + "ontologies": [] + } + } + ] + ], + "embeddings_level1": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}_level1_embeddings.npy": { + "type": "file", + "description": "NumPy array file containing Level 1 projected embeddings for each input\nsequence. Optional; produced when `--save-level1-embeddings` is passed.\n", + "pattern": "*_level1_embeddings.npy", + "ontologies": [] + } + } + ] + ], + "embeddings_level2": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}_level2_embeddings.npy": { + "type": "file", + "description": "NumPy array file containing Level 2 projected embeddings for each input\nsequence. Optional; produced when `--save-level2-embeddings` is passed.\n", + "pattern": "*_level2_embeddings.npy", + "ontologies": [] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}.log": { + "type": "file", + "description": "Log file containing the stdout and stderr output of the caalm run.", + "pattern": "*.log", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + } + ] + ], + "versions_caalm": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "caalm": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "caalm --version 2>&1 | head -1": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_python": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "python": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python --version | sed 's/Python //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_torch": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "torch": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python -c 'import torch; print(torch.__version__)'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_faiss": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "faiss": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python -c 'import faiss; print(faiss.__version__)'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "caalm": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "caalm --version 2>&1 | head -1": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "python": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python --version | sed 's/Python //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "torch": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python -c 'import torch; print(torch.__version__)'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "faiss": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python -c 'import faiss; print(faiss.__version__)'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@vagkaratzas"], + "maintainers": ["@vagkaratzas"] + } }, { - "name": "callingcards", - "version": "1.0.0" + "name": "caalm_downloadmodels", + "path": "modules/nf-core/caalm/downloadmodels/meta.yml", + "type": "module", + "meta": { + "name": "caalm_downloadmodels", + "description": "Downloads the CAALM model weights from HuggingFace Hub (lczong/CAALM) into a\nlocal models/ directory. The downloaded directory is used as input to the\nCAALM_CAALM annotation module for CAZyme prediction.\n", + "keywords": ["cazyme", "model", "download", "huggingface", "deep learning"], + "tools": [ + { + "huggingface_hub": { + "description": "huggingface_hub is a Python library for interacting with the Hugging Face Hub,\nproviding utilities for downloading and uploading models, datasets, and spaces.\n", + "homepage": "https://github.com/huggingface/huggingface_hub", + "documentation": "https://huggingface.co/docs/huggingface_hub", + "tool_dev_url": "https://github.com/huggingface/huggingface_hub", + "licence": ["Apache-2.0"], + "identifier": "" + } + } + ], + "input": [], + "output": { + "models": [ + [ + { + "models/level0": { + "type": "directory", + "description": "Directory containing the Level 0 (binary CAZyme detection) model files\ndownloaded from HuggingFace Hub (lczong/CAALM).\n", + "pattern": "models/level0", + "ontologies": [] + } + }, + { + "models/level1": { + "type": "directory", + "description": "Directory containing the Level 1 (CAZy class assignment) model files\ndownloaded from HuggingFace Hub (lczong/CAALM).\n", + "pattern": "models/level1", + "ontologies": [] + } + }, + { + "models/level2": { + "type": "directory", + "description": "Directory containing the Level 2 (CAZy family assignment) model files\ndownloaded from HuggingFace Hub (lczong/CAALM), including the FAISS index,\nreference database, and model weights.\n", + "pattern": "models/level2", + "ontologies": [] + } + } + ] + ], + "versions_huggingface_hub": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "huggingface_hub": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python -c 'import huggingface_hub; print(huggingface_hub.__version__)'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_python": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "python": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python --version | sed 's/Python //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "huggingface_hub": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python -c 'import huggingface_hub; print(huggingface_hub.__version__)'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "python": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python --version | sed 's/Python //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@vagkaratzas"], + "maintainers": ["@vagkaratzas"] + } }, { - "name": "chipseq", - "version": "2.1.0" + "name": "cadd", + "path": "modules/nf-core/cadd/meta.yml", + "type": "module", + "meta": { + "name": "cadd", + "description": "CADD is a tool for scoring the deleteriousness of single nucleotide variants as well as insertion/deletions variants in the human genome.", + "keywords": ["cadd", "annotate", "variants"], + "tools": [ + { + "cadd": { + "description": "CADD scripts release for offline scoring", + "homepage": "https://cadd.gs.washington.edu/", + "documentation": "https://github.com/kircherlab/CADD-scripts/blob/master/README.md", + "tool_dev_url": "https://github.com/kircherlab/CADD-scripts/", + "doi": "10.1093/nar/gky1016", + "licence": ["Restricted. Free for non-commercial users."], + "identifier": "biotools:cadd_phred" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "Input file for annotation in vcf or vcf.gz format", + "pattern": "*.{vcf,vcf.gz}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "annotation_dir": { + "type": "directory", + "description": "Path to folder containing the vcf files with precomputed CADD scores.\nThis folder contains the uncompressed files that would otherwise be in data/annotation folder as described in https://github.com/kircherlab/CADD-scripts/#manual-installation.\n" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "prescored_dir": { + "type": "directory", + "description": "Path to folder containing prescored CADD score files.\nExpected structure mirrors data/prescored/ from the CADD-scripts installation:\n /\n GRCh38_v1.7/\n incl_anno/ # *.tsv.gz + *.tsv.gz.tbi (scores with annotations)\n no_anno/ # *.tsv.gz + *.tsv.gz.tbi (scores only)\n GRCh37_v1.7/\n incl_anno/\n no_anno/\nSee https://github.com/kircherlab/CADD-scripts/#manual-installation for details.\n" + } + } + ] + ], + "output": { + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.tsv.gz": { + "type": "file", + "description": "Annotated tsv file", + "pattern": "*.{tsv,tsv.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_cadd": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cadd": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "1.7.3": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cadd": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "1.7.3": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@ramprasadn"], + "maintainers": ["@ramprasadn"] + }, + "pipelines": [ + { + "name": "raredisease", + "version": "3.0.0" + } + ] }, { - "name": "circdna", - "version": "1.1.0" + "name": "cafe", + "path": "modules/nf-core/cafe/meta.yml", + "type": "module", + "meta": { + "name": "cafe", + "description": "Analysis of gene family evolution", + "keywords": ["gene", "phylogeny", "genomics"], + "tools": [ + { + "cafe": { + "description": "Computational Analysis of gene Family Evolution (CAFE)", + "homepage": "https://github.com/hahnlab/CAFE5", + "documentation": "https://github.com/hahnlab/CAFE5", + "tool_dev_url": "https://github.com/hahnlab/CAFE5", + "doi": "10.1093/bioinformatics/btaa1027", + "licence": [ + "IU OPEN SOURCE LICENSE (see https://github.com/hahnlab/CAFE5/blob/master/LICENSE)" + ], + "identifier": "biotools:CaFE_Calculation_of_Free_Energy" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "infile": { + "type": "file", + "description": "Gene counts table (from OrthoMCL, SwiftOrtho, FastOrtho, OrthAgogue or OrthoFinder)", + "pattern": "*.{txt,tsv,tab}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + { + "tree": { + "type": "file", + "description": "Newick formatted tree", + "pattern": "*.{txt}", + "ontologies": [] + } + } + ], + "output": { + "cafe": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "${prefix}": { + "type": "directory", + "description": "A folder with all the cafe output" + } + } + ] + ], + "cafe_base_count": [ + { + "$prefix/*_count.tab": { + "type": "file", + "description": "File containing counts of genes per orthogroup", + "pattern": "*_count.tab", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + "cafe_significant_trees": [ + { + "$prefix/*.tre": { + "type": "file", + "description": "File containing significant trees (newick format)", + "pattern": "*.tre", + "ontologies": [] + } + } + ], + "cafe_report": [ + { + "$prefix/*_report.cafe": { + "type": "file", + "description": "File containing the final report from cafe", + "pattern": "*_report.cafe", + "ontologies": [] + } + } + ], + "cafe_results": [ + { + "$prefix/*results.txt": { + "type": "file", + "description": "File containing the main result files from cafe", + "pattern": "*results.txt", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + } + ], + "versions_cafe": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cafe": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "echo 5.1.0": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cafe": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "echo 5.1.0": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@chriswyatt1"], + "maintainers": ["@chriswyatt1"] + } }, { - "name": "circrna", - "version": "dev" + "name": "calder2", + "path": "modules/nf-core/calder2/meta.yml", + "type": "module", + "meta": { + "name": "calder2", + "description": "Hierarchical Hi-C compartment computation", + "keywords": ["calder2", "genome", "topology", "compartments", "domains", "hi-c"], + "tools": [ + { + "calder2": { + "description": "Hierarchical Hi-C compartment computation", + "homepage": "https://github.com/CSOgroup/CALDER2", + "documentation": "https://github.com/CSOgroup/CALDER2", + "tool_dev_url": "https://github.com/CSOgroup/CALDER2", + "doi": "10.1038/s41467-021-22666-3", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information. E.g. [ id:'test', single_end:false ]" + } + }, + { + "cool": { + "type": "file", + "description": "Path to COOL file", + "pattern": "*.{cool.mcool}", + "ontologies": [] + } + } + ], + { + "resolution": { + "type": "integer", + "description": "In case a .mcool file is provided, which resolution level to use for the analysis" + } + } + ], + "output": { + "output_folder": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information. E.g. [ id:'test', single_end:false ]" + } + }, + { + "${prefix}/": { + "type": "directory", + "description": "Output folder containing sub-compartment (.tsv/.bed) and domain boundaries calls (.bed)" + } + } + ] + ], + "intermediate_data_folder": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information. E.g. [ id:'test', single_end:false ]" + } + }, + { + "${prefix}/intermediate_data/": { + "type": "directory", + "description": "Output folder containing intermediate data produced during the computation" + } + } + ] + ], + "versions_calder": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "calder": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "0.7": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "calder": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "0.7": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@lucananni93"], + "maintainers": ["@lucananni93"] + } }, { - "name": "crisprseq", - "version": "2.3.0" + "name": "canu", + "path": "modules/nf-core/canu/meta.yml", + "type": "module", + "meta": { + "name": "canu", + "description": "Accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads.", + "keywords": ["Assembly", "pacbio", "hifi", "nanopore"], + "tools": [ + { + "canu": { + "description": "Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing.", + "homepage": "https://canu.readthedocs.io/en/latest/index.html#", + "documentation": "https://canu.readthedocs.io/en/latest/tutorial.html", + "tool_dev_url": "https://github.com/marbl/canu", + "doi": "10.1101/gr.215087.116", + "licence": ["GPL v2 and others"], + "identifier": "biotools:canu" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:true ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "fasta/fastq file", + "pattern": "*.{fasta,fastq}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ], + { + "mode": { + "type": "string", + "description": "Canu mode depending on the input data (source and error rate)", + "pattern": "-pacbio|-nanopore|-pacbio-hifi" + } + }, + { + "genomesize": { + "type": "string", + "description": "An estimate of the size of the genome. Common suffices are allowed, for example, 3.7m or 2.8g", + "pattern": "[g|m|k]" + } + } + ], + "output": { + "report": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.report": { + "type": "file", + "description": "Most of the analysis reported during assembly", + "pattern": "*.report", + "ontologies": [] + } + } + ] + ], + "assembly": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.contigs.fasta.gz": { + "type": "file", + "description": "Everything which could be assembled and is the full assembly, including both unique, repetitive, and bubble elements.", + "pattern": "*.contigs.fasta", + "ontologies": [] + } + } + ] + ], + "contigs": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.unassembled.fasta.gz": { + "type": "file", + "description": "Reads and low-coverage contigs which could not be incorporated into the primary assembly.", + "pattern": "*.unassembled.fasta", + "ontologies": [] + } + } + ] + ], + "corrected_reads": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.correctedReads.fasta.gz": { + "type": "file", + "description": "The reads after correction.", + "pattern": "*.correctedReads.fasta.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "corrected_trimmed_reads": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.trimmedReads.fasta.gz": { + "type": "file", + "description": "The corrected reads after overlap based trimming", + "pattern": "*.trimmedReads.fasta.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "metadata": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.contigs.layout": { + "type": "file", + "description": "(undocumented)", + "pattern": "*.contigs.layout", + "ontologies": [] + } + } + ] + ], + "contig_position": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.contigs.layout.readToTig": { + "type": "file", + "description": "The position of each read in a contig", + "pattern": "*.contigs.layout.readToTig", + "ontologies": [] + } + } + ] + ], + "contig_info": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.contigs.layout.tigInfo": { + "type": "file", + "description": "A list of the contigs, lengths, coverage, number of reads and other metadata. Essentially the same information provided in the FASTA header line.", + "pattern": "*.contigs.layout.tigInfo", + "ontologies": [] + } + } + ] + ], + "versions_canu": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "canu": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "2.3": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_minimap2": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "minimap2": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "minimap2 --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_samtools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "samtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "samtools version | sed '1!d;s/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "canu": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "2.3": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "minimap2": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "minimap2 --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "samtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "samtools version | sed '1!d;s/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@scorreard"], + "maintainers": ["@scorreard"] + }, + "pipelines": [ + { + "name": "bacass", + "version": "2.6.0" + } + ] }, { - "name": "deepmutscan", - "version": "dev" - }, - { - "name": "fastquorum", - "version": "1.2.0" - }, - { - "name": "hgtseq", - "version": "1.1.0" - }, - { - "name": "hicar", - "version": "1.0.0" - }, - { - "name": "methylseq", - "version": "4.2.0" - }, - { - "name": "nascent", - "version": "2.3.0" - }, - { - "name": "oncoanalyser", - "version": "2.3.0" - }, - { - "name": "pathogensurveillance", - "version": "1.1.0" - }, - { - "name": "radseq", - "version": "dev" - }, - { - "name": "raredisease", - "version": "3.0.0" - }, - { - "name": "references", - "version": "0.1" - }, - { - "name": "rnadnavar", - "version": "dev" - }, - { - "name": "sammyseq", - "version": "dev" - }, - { - "name": "sarek", - "version": "3.8.1" + "name": "canvas_germline", + "path": "modules/nf-core/canvas/germline/meta.yml", + "type": "module", + "meta": { + "name": "canvas_germline", + "description": "Calls germline copy number variants (CNVs) from whole genome sequencing data using\nIllumina Canvas in SmallPedigree-WGS mode. Although named SmallPedigree-WGS, this\nmode is recommended for single germline samples as well as small pedigrees.\nThe module accepts aligned reads (BAM), germline SNV calls, and sex-specific ploidy\ninformation, and outputs a VCF with copy number status across the genome together\nwith a coverage-and-variant-frequency file used for downstream segmentation.\n", + "keywords": ["CNV", "copy number variants", "germline", "WGS", "canvas"], + "tools": [ + { + "canvas": { + "description": "Canvas is a tool for calling copy number variants (CNVs) from human DNA sequencing data.\n", + "homepage": "https://github.com/Illumina/canvas", + "documentation": "https://github.com/Illumina/canvas/wiki", + "tool_dev_url": "https://github.com/Illumina/canvas", + "licence": ["GPL-3.0"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information.\ne.g. `[ id:'sample1' ]`\n", + "ontologies": [] + } + }, + { + "bam": { + "type": "file", + "description": "Sorted BAM file of aligned WGS reads.", + "pattern": "*.bam", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + }, + { + "bai": { + "type": "file", + "description": "BAM index file.", + "pattern": "*.bai", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3327" + } + ] + } + } + ], + { + "germline_snv_vcf": { + "type": "file", + "description": "VCF (or gzipped VCF) containing germline SNV b-allele sites (PASS filter only).\nTypically produced by a variant caller such as DNAscope or DeepVariant.\n", + "pattern": "*.{vcf,vcf.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + } + ] + } + }, + [ + { + "sex": { + "type": "string", + "description": "Sample sex. Must be either \"male\" or \"female\". Used to select the\nappropriate ploidy VCF for sex chromosomes.\n" + } + }, + { + "male_ploidy_vcf": { + "type": "file", + "description": "VCF defining expected ploidy for sex chromosomes in male samples.\nBoth ploidy VCFs (male and female) must always be provided. The module\nautomatically selects the correct one based on the sex value.\nThe sample name in the VCF header is automatically updated to match the SM tag in the BAM header.\nExpected format (hg38 example):\n\n```\n##fileformat=VCFv4.1\n##INFO=\n##FORMAT=\n#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE\nchrX 0 . N . PASS END=10001 CN 1\nchrX 2781479 . N . PASS END=155701383 CN 1\nchrX 156030895 . N . PASS END=156040895 CN 1\nchrY 0 . N . PASS END=57227415 CN 1\n```\n", + "pattern": "*.vcf", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + } + ] + } + }, + { + "female_ploidy_vcf": { + "type": "file", + "description": "VCF defining expected ploidy for sex chromosomes in female samples.\nBoth ploidy VCFs (male and female) must always be provided. The module\nautomatically selects the correct one based on the sex value.\nThe sample name in the VCF header is automatically updated to match the SM tag in the BAM header.\nExpected format (hg38 example):\n\n```\n##fileformat=VCFv4.1\n##INFO=\n##FORMAT=\n#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE\nchrY 0 . N . PASS END=57227415 CN 0\n```\n", + "pattern": "*.vcf", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + } + ] + } + } + ], + { + "genomedir": { + "type": "directory", + "description": "Canvas genome reference directory containing genome.fa and GenomeSize.xml.\nAvailable for GRCh37/hg19/GRCh38 from s3://canvas-cnv-public.\n" + } + }, + { + "reference": { + "type": "file", + "description": "Canvas-ready kmer reference file (kmer.fa).\nAvailable from s3://canvas-cnv-public.\n", + "pattern": "*.fa", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + }, + { + "filter13": { + "type": "file", + "description": "BED file of regions to exclude from CNV calling (e.g. centromeres, telomeres).\nNamed filter13 following Canvas reference package conventions.\nAvailable from s3://canvas-cnv-public.\n", + "pattern": "*.bed", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3003" + } + ] + } + } + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information.\ne.g. `[ id:'sample1' ]`\n", + "ontologies": [] + } + }, + { + "${prefix}.vcf.gz": { + "type": "file", + "description": "Bgzipped VCF file containing germline CNV calls. Canvas:REF entries (non-variant regions)\nare excluded. Requires further annotation for standard SV ALT notation.\n", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + } + ] + } + } + ] + ], + "covandvarfreq": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information.\ne.g. `[ id:'sample1' ]`\n", + "ontologies": [] + } + }, + { + "${prefix}.CoverageAndVariantFrequency.txt": { + "type": "file", + "description": "Tab-separated file with per-bin coverage and variant allele frequency values.\nUsed as input for CANVAS_CREATESEG to generate segmentation files.\n", + "pattern": "*.CoverageAndVariantFrequency.txt", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_canvas": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "canvas": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "1.40.0": { + "type": "string", + "description": "The version of the tool (hardcoded as Canvas is an archived tool)" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "canvas": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "1.40.0": { + "type": "string", + "description": "The version of the tool (hardcoded as Canvas is an archived tool)" + } + } + ] + ] + }, + "authors": ["@ktruve"], + "maintainers": ["@ktruve"] + } }, { - "name": "ssds", - "version": "dev" + "name": "carveme_carve", + "path": "modules/nf-core/carveme/carve/meta.yml", + "type": "module", + "meta": { + "name": "carveme_carve", + "description": "Reconstruct genome-scale metabolic models from protein FASTA files using CarveMe", + "keywords": [ + "metabolic model", + "genome-scale", + "sbml", + "flux balance analysis", + "metabolic reconstruction" + ], + "tools": [ + { + "carveme": { + "description": "CarveMe is a python-based tool for genome-scale metabolic model reconstruction.", + "homepage": "https://carveme.readthedocs.io", + "documentation": "https://carveme.readthedocs.io", + "tool_dev_url": "https://github.com/cdanielmachado/carveme", + "doi": "10.1093/nar/gky537", + "licence": ["Apache-2.0"], + "identifier": "biotools:carveme" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Protein FASTA file\nor DNA fasta file if the --dna flag is provided\n", + "pattern": "*.{fa,faa,fasta,fna}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + }, + { + "universe_file": { + "type": "file", + "description": "Optional. Reaction universe file in SBML format, passed to --universe-file.", + "pattern": "*.xml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2332" + } + ] + } + }, + { + "mediadb": { + "type": "file", + "description": "Optional. Media database file, passed to --mediadb.\n--gapfill X,Y,Z with medium names from the database must also be provided\n", + "pattern": "*.{tsv,csv,txt}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + }, + { + "edam": "http://edamontology.org/format_3752" + }, + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + }, + { + "soft": { + "type": "file", + "description": "Optional. Soft constraints file, passed to --soft.", + "pattern": "*.{tsv,csv,txt}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + }, + { + "edam": "http://edamontology.org/format_3752" + }, + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + }, + { + "hard": { + "type": "file", + "description": "Optional. Hard constraints file, passed to --hard.", + "pattern": "*.{tsv,csv,txt}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + }, + { + "edam": "http://edamontology.org/format_3752" + }, + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + }, + { + "reference": { + "type": "file", + "description": "Optional. Manually curated model of a close reference species, passed to --reference.", + "pattern": "*.xml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2332" + } + ] + } + } + ] + ], + "output": { + "model": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}.xml": { + "type": "file", + "description": "SBML genome-scale metabolic model file", + "pattern": "*.xml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2332" + } + ] + } + } + ] + ], + "gene_scores": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}_gene_scores.tsv": { + "type": "file", + "description": "Optional. Tab-separated file produced when --debug is passed. Maps each query gene to its\ncorresponding BiGG gene identifier, protein group, reaction, source model, and BLAST\nbit-score used during model reconstruction.\n", + "pattern": "*_gene_scores.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "milp_problem": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}_milp_problem.lp": { + "type": "file", + "description": "Optional. Linear programming problem file in LP format produced when --debug is passed.\nContains the MILP formulation (variables, constraints, and objective function) passed to\nthe SCIP solver during gap-filling or reaction selection.\n", + "pattern": "*_milp_problem.lp", + "ontologies": [] + } + } + ] + ], + "milp_solution": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}_milp_solution.tsv": { + "type": "file", + "description": "Optional. Tab-separated file produced when --debug is passed. Contains the MILP solver\nsolution, listing each reaction identifier and its corresponding flux value selected\nduring model gap-filling.\n", + "pattern": "*_milp_solution.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "protein_scores": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}_protein_scores.tsv": { + "type": "file", + "description": "Optional. Tab-separated file produced when --debug is passed. Lists the BLAST alignment\nscores for each query protein against the template model database, including the matched\nprotein group, reaction, source model, and GPR rule used for scoring.\n", + "pattern": "*_protein_scores.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "reaction_scores": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}_reaction_scores.tsv": { + "type": "file", + "description": "Optional. Tab-separated file produced when --debug is passed. Lists each candidate\nreaction with its GPR rule, raw BLAST bit-score, and normalised score used to weight\nthe MILP objective during model reconstruction.\n", + "pattern": "*_reaction_scores.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_carveme": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "carveme": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pip show carveme | sed -n 's/^Version: //p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "carveme": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pip show carveme | sed -n 's/^Version: //p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@vagkaratzas"], + "maintainers": ["@vagkaratzas"] + } }, { - "name": "variantcatalogue", - "version": "dev" - } - ] - }, - { - "name": "bwa_mem", - "path": "modules/nf-core/bwa/mem/meta.yml", - "type": "module", - "meta": { - "name": "bwa_mem", - "description": "Performs fastq alignment to a fasta reference using BWA", - "keywords": [ - "mem", - "bwa", - "alignment", - "map", - "fastq", - "bam", - "sam" - ], - "tools": [ - { - "bwa": { - "description": "BWA is a software package for mapping DNA sequences against\na large reference genome, such as the human genome.\n", - "homepage": "http://bio-bwa.sourceforge.net/", - "documentation": "https://bio-bwa.sourceforge.net/bwa.shtml", - "arxiv": "arXiv:1303.3997", - "licence": [ - "GPL-3.0-or-later" - ], - "identifier": "biotools:bwa" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", - "ontologies": [ - { - "edam": "http://edamontology.org/data_2044" - }, - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "index": { - "type": "file", - "description": "BWA genome index files", - "pattern": "Directory containing BWA index *.{amb,ann,bwt,pac,sa}", - "ontologies": [ - { - "edam": "http://edamontology.org/data_3210" - } - ] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + "name": "cat_cat", + "path": "modules/nf-core/cat/cat/meta.yml", + "type": "module", + "meta": { + "name": "cat_cat", + "description": "A module for concatenation of gzipped or uncompressed files", + "deprecated": true, + "keywords": ["concatenate", "gzip", "cat"], + "tools": [ + { + "cat": { + "description": "Just concatenation", + "documentation": "https://man7.org/linux/man-pages/man1/cat.1.html", + "licence": ["GPL-3.0-or-later"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "files_in": { + "type": "file", + "description": "List of compressed / uncompressed files", + "pattern": "*", + "ontologies": [] + } + } + ] + ], + "output": { + "file_out": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "${prefix}": { + "type": "file", + "description": "Concatenated file. Will be gzipped if file_out ends with \".gz\"", + "pattern": "${file_out}", + "ontologies": [] + } + } + ] + ], + "versions_cat": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "pigz": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pigz --version 2>&1 | sed 's/pigz //g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "pigz": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pigz --version 2>&1 | sed 's/pigz //g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@erikrikarddaniel", "@FriederikeHanssen"], + "maintainers": ["@erikrikarddaniel", "@FriederikeHanssen"] }, - { - "fasta": { - "type": "file", - "description": "Reference genome in FASTA format", - "pattern": "*.{fasta,fa}", - "ontologies": [ - { - "edam": "http://edamontology.org/data_2044" - }, - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - { - "sort_bam": { - "type": "boolean", - "description": "use samtools sort (true) or samtools view (false)", - "pattern": "true or false" - } - } - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*.bam": { - "type": "file", - "description": "Output BAM file containing read alignments", - "pattern": "*.{bam}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - } - ] - ], - "cram": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*.cram": { - "type": "file", - "description": "Output CRAM file containing read alignments", - "pattern": "*.{cram}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3462" - } - ] - } - } - ] - ], - "sam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*.sam": { - "type": "file", - "description": "Output SAM file containing read alignments", - "pattern": "*.{sam}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2573" - } - ] - } - } - ] - ], - "csi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*.csi": { - "type": "file", - "description": "Optional index file for BAM file", - "pattern": "*.{csi}", - "ontologies": [] - } - } - ] - ], - "crai": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*.crai": { - "type": "file", - "description": "Optional index file for CRAM file", - "pattern": "*.{crai}", - "ontologies": [] - } - } - ] - ], - "versions_bwa": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bwa": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bwa 2>&1 | sed -n \"s/^Version: //p\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_samtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bwa": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bwa 2>&1 | sed -n \"s/^Version: //p\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "circrna", + "version": "dev" + }, + { + "name": "denovotranscript", + "version": "1.2.1" + }, + { + "name": "epitopeprediction", + "version": "3.1.0" + }, + { + "name": "magmap", + "version": "1.0.0" + }, + { + "name": "marsseq", + "version": "1.0.3" + }, + { + "name": "metatdenovo", + "version": "1.3.0" + }, + { + "name": "nascent", + "version": "2.3.0" + }, + { + "name": "phageannotator", + "version": "dev" + }, + { + "name": "raredisease", + "version": "3.0.0" + }, + { + "name": "reportho", + "version": "1.1.0" + }, + { + "name": "rnadnavar", + "version": "dev" + }, + { + "name": "rnafusion", + "version": "4.1.2" + }, + { + "name": "sarek", + "version": "3.8.1" + }, + { + "name": "scnanoseq", + "version": "1.2.2" + }, + { + "name": "tfactivity", + "version": "dev" + }, + { + "name": "variantbenchmarking", + "version": "1.5.0" + }, + { + "name": "viralmetagenome", + "version": "1.1.1" + } ] - ] - }, - "authors": [ - "@drpatelh", - "@jeremy1805", - "@matthdsm" - ], - "maintainers": [ - "@drpatelh", - "@jeremy1805", - "@matthdsm" - ] - }, - "pipelines": [ - { - "name": "atacseq", - "version": "2.1.2" - }, - { - "name": "chipseq", - "version": "2.1.0" - }, - { - "name": "circrna", - "version": "dev" - }, - { - "name": "crisprseq", - "version": "2.3.0" - }, - { - "name": "deepmutscan", - "version": "dev" - }, - { - "name": "hgtseq", - "version": "1.1.0" - }, - { - "name": "hicar", - "version": "1.0.0" - }, - { - "name": "methylseq", - "version": "4.2.0" - }, - { - "name": "nascent", - "version": "2.3.0" - }, - { - "name": "pathogensurveillance", - "version": "1.1.0" - }, - { - "name": "radseq", - "version": "dev" - }, - { - "name": "raredisease", - "version": "3.0.0" - }, - { - "name": "rnadnavar", - "version": "dev" }, { - "name": "sammyseq", - "version": "dev" + "name": "cat_fastq", + "path": "modules/nf-core/cat/fastq/meta.yml", + "type": "module", + "meta": { + "name": "cat_fastq", + "description": "Concatenates fastq files. Supports both compressed (.gz) and uncompressed inputs; uncompressed files are automatically gzip-compressed during concatenation.", + "keywords": ["cat", "fastq", "concatenate", "compress"], + "tools": [ + { + "cat": { + "description": "The cat utility reads files sequentially, writing them to the standard output.\n", + "documentation": "https://www.gnu.org/software/coreutils/manual/html_node/cat-invocation.html", + "licence": ["GPL-3.0-or-later"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files to be concatenated.\nAccepts both gzip-compressed (.fastq.gz) and uncompressed (.fastq) files.\n", + "ontologies": [] + } + } + ] + ], + "output": { + "reads": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.merged.fastq.gz": { + "type": "file", + "description": "Merged fastq file", + "pattern": "*.{merged.fastq.gz}", + "ontologies": [] + } + } + ] + ], + "versions_cat": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "cat": { + "type": "string", + "description": "The tool name" + } + }, + { + "cat --version 2>&1 | head -n 1 | sed 's/^.*coreutils) //; s/ .*\\$//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "cat": { + "type": "string", + "description": "The tool name" + } + }, + { + "cat --version 2>&1 | head -n 1 | sed 's/^.*coreutils) //; s/ .*\\$//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@joseespinosa", "@drpatelh"], + "maintainers": ["@joseespinosa", "@drpatelh"] + }, + "pipelines": [ + { + "name": "airrflow", + "version": "5.0.0" + }, + { + "name": "bacass", + "version": "2.6.0" + }, + { + "name": "bamtofastq", + "version": "2.2.1" + }, + { + "name": "circdna", + "version": "1.1.0" + }, + { + "name": "circrna", + "version": "dev" + }, + { + "name": "crisprseq", + "version": "2.3.0" + }, + { + "name": "cutandrun", + "version": "3.2.2" + }, + { + "name": "denovotranscript", + "version": "1.2.1" + }, + { + "name": "funcprofiler", + "version": "dev" + }, + { + "name": "genomeannotator", + "version": "dev" + }, + { + "name": "hlatyping", + "version": "2.2.0" + }, + { + "name": "lncpipe", + "version": "dev" + }, + { + "name": "mag", + "version": "5.4.2" + }, + { + "name": "magmap", + "version": "1.0.0" + }, + { + "name": "metatdenovo", + "version": "1.3.0" + }, + { + "name": "methylseq", + "version": "4.2.0" + }, + { + "name": "nascent", + 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"catpack_addnames", + "description": "Taxonomic classification of long DNA sequences and metagenome assembled genomes (e.g. MAGs / bins).", + "keywords": ["taxonomic classification", "classification", "long reads", "mags", "assembly"], + "tools": [ + { + "catpack": { + "description": "CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)", + "homepage": "https://github.com/MGXlab/CAT_pack", + "documentation": "https://github.com/MGXlab/CAT_pack", + "tool_dev_url": "https://github.com/MGXlab/CAT_pack", + "doi": "10.1186/s13059-019-1817-x", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "input": { + "type": "file", + "description": "Classification or ORF2LCA output file from CAT/BAT/RAT", + "pattern": "*.txt", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "taxonomy": { + "type": "directory", + "description": "Directory containing taxonomy files: names.dmp, nodes.dmp, acc2taxid.txt", + "pattern": "*/", + "ontologies": [ + { + "edam": "http://edamontology.org/data_1049" + } + ] + } + } + ] + ], + "output": { + "txt": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}.txt": { + "type": "map", + "description": "CAT/BAT/RAT classification file with added taxonomic names\n", + "pattern": "*.{bam,cram,sam}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_catpack": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "catpack": { + "type": "string", + "description": "The tool name" + } + }, + { + "CAT_pack --version | sed 's/CAT_pack pack v//g;s/ .*//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "catpack": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "CAT_pack --version | sed 's/CAT_pack pack v//g;s/ .*//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@jfy133"], + "maintainers": ["@jfy133"] + }, + "pipelines": [ + { + "name": "mag", + "version": "5.4.2" + }, + { + "name": "seqsubmit", + "version": "dev" + } + ] }, { - "name": "ssds", - "version": "dev" + "name": "catpack_bins", + "path": "modules/nf-core/catpack/bins/meta.yml", + "type": "module", + "meta": { + "name": "catpack_bins", + "description": "Taxonomic classification of long DNA sequences and metagenome assembled genomes (e.g. MAGs / bins).", + "keywords": ["taxonomic classification", "classification", "long reads", "mags", "assembly"], + "tools": [ + { + "catpack": { + "description": "CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)", + "homepage": "https://github.com/MGXlab/CAT_pack", + "documentation": "https://github.com/MGXlab/CAT_pack", + "tool_dev_url": "https://github.com/MGXlab/CAT_pack", + "doi": "10.1186/s13059-019-1817-x", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "bins": { + "type": "file", + "description": "One or more nucleotide FASTA file containing binned long DNA sequences.", + "pattern": "*.{fasta,fna,fa,fas}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "database": { + "type": "directory", + "description": "Directory containing CAT_pack database files (e.g. output from CAT_pack prepare)", + "pattern": "*/", + "ontologies": [ + { + "edam": "http://edamontology.org/data_1049" + } + ] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "taxonomy": { + "type": "directory", + "description": "Directory containing CAT_pack taxonomy files (e.g. output from CAT_pack prepare)", + "pattern": "*/", + "ontologies": [ + { + "edam": "http://edamontology.org/data_1049" + } + ] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "proteins": { + "type": "directory", + "description": "Optional pre predicted-made proteins FASTA", + "pattern": "*.{fasta,faa,fa,fas}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "diamond_table": { + "type": "directory", + "description": "Optional pre-made DIAMOND alignment table", + "pattern": "*", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3751" + } + ] + } + } + ], + { + "bin_suffix": { + "type": "string", + "description": "Suffix to search for in the input files when `bins` is a directory." + } + } + ], + "output": { + "orf2lca": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.ORF2LCA.txt": { + "type": "file", + "description": "A TSV file with per-ORF hit stats and identified lineage", + "pattern": "*.ORF2LCA.txt", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "bin2classification": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.bin2classification.txt": { + "type": "file", + "description": "A TSV file with per-bin hit stats and assignment justification information", + "pattern": "*.bin2classification.txt", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.log": { + "type": "file", + "description": "Log file with run messages and basic statistics", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + } + ] + ], + "diamond": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.diamond": { + "type": "file", + "description": "Intermediate DIAMOND TSV summary output file with alignment results", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "faa": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.predicted_proteins.faa": { + "type": "file", + "description": "FAA file of DIAMOND predicted proteins hits", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "gff": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.gff": { + "type": "file", + "description": "GFF file of DIAMOND predicted proteins hits", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2305" + } + ] + } + } + ] + ], + "versions_catpack": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "catpack": { + "type": "string", + "description": "The tool name" + } + }, + { + "CAT_pack --version | sed 's/CAT_pack pack v//g;s/ .*//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "catpack": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "CAT_pack --version | sed 's/CAT_pack pack v//g;s/ .*//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@jfy133"], + "maintainers": ["@jfy133"] + }, + "pipelines": [ + { + "name": "mag", + "version": "5.4.2" + }, + { + "name": "seqsubmit", + "version": "dev" + } + ] }, { - "name": "variantcatalogue", - "version": "dev" - } - ] - }, - { - "name": "bwa_sampe", - "path": "modules/nf-core/bwa/sampe/meta.yml", - "type": "module", - "meta": { - "name": "bwa_sampe", - "description": "Convert paired-end bwa SA coordinate files to SAM format", - "keywords": [ - "bwa", - "aln", - "short-read", - "align", - "reference", - "fasta", - "map", - "sam", - "bam" - ], - "tools": [ - { - "bwa": { - "description": "BWA is a software package for mapping DNA sequences against\na large reference genome, such as the human genome.\n", - "homepage": "http://bio-bwa.sourceforge.net/", - "documentation": "https://bio-bwa.sourceforge.net/bwa.shtml", - "doi": "10.1093/bioinformatics/btp324", - "licence": [ - "GPL-3.0-or-later" - ], - "identifier": "biotools:bwa" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "FASTQ files specified alongside meta in input channel.", - "pattern": "*.{fastq,fq}.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/data_2044" - }, - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - }, - { - "sai": { - "type": "file", - "description": "SAI file specified alongside meta and reads in input channel.", - "pattern": "*.sai", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } + "name": "catpack_contigs", + "path": "modules/nf-core/catpack/contigs/meta.yml", + "type": "module", + "meta": { + "name": "catpack_contigs", + "description": "Taxonomic classification of long DNA sequences and metagenome assembled genomes (e.g. contigs, MAGs / bins).", + "keywords": ["taxonomic classification", "classification", "long reads", "mags", "assembly"], + "tools": [ + { + "catpack": { + "description": "CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)", + "homepage": "https://github.com/MGXlab/CAT_pack", + "documentation": "https://github.com/MGXlab/CAT_pack", + "tool_dev_url": "https://github.com/MGXlab/CAT_pack", + "doi": "10.1186/s13059-019-1817-x", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "contigs": { + "type": "file", + "description": "A nucleotide FASTA file containing long DNA sequences such as contigs.", + "pattern": "*.{fasta,fna,fa,fas}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "database": { + "type": "directory", + "description": "Directory containing CAT_pack database files (e.g. output from CAT_pack prepare)", + "pattern": "*/", + "ontologies": [ + { + "edam": "http://edamontology.org/data_1049" + } + ] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "taxonomy": { + "type": "directory", + "description": "Directory containing CAT_pack taxonomy files (e.g. output from CAT_pack prepare)", + "pattern": "*/", + "ontologies": [ + { + "edam": "http://edamontology.org/data_1049" + } + ] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "proteins": { + "type": "directory", + "description": "Optional pre predicted-made proteins FASTA", + "pattern": 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"Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.contig2classification.txt": { + "type": "file", + "description": "A TSV file with per-contig hit stats and assignment justification information", + "pattern": "*.contig2classification.txt", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.log": { + "type": "file", + "description": "Log file with run messages and basic statistics", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + } + ] + ], + "diamond": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.diamond": { + "type": "file", + "description": "Intermediate DIAMOND TSV summary output file with alignment results", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "faa": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.predicted_proteins.faa": { + "type": "file", + "description": "FAA file of DIAMOND predicted proteins hits", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "gff": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.gff": { + "type": "file", + "description": "GFF file of DIAMOND predicted proteins hits", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2305" + } + ] + } + } + ] + ], + "versions_catpack": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "catpack": { + "type": "string", + "description": "The tool name" + } + }, + { + "CAT_pack --version | sed 's/CAT_pack pack v//g;s/ .*//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "catpack": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "CAT_pack --version | sed 's/CAT_pack pack v//g;s/ .*//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@jfy133"], + "maintainers": ["@jfy133"] }, - { - "index": { - "type": "directory", - "description": "Directory containing BWA index files (amb,ann,bwt,pac,sa) from BWA_INDEX", - "pattern": "bwa/", - "ontologies": [ - { - "edam": "http://edamontology.org/data_3210" - } - ] - } - } - ] - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "BAM file", - "pattern": "*.bam", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - } - ] - ], - "versions_bwa": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bwa": { - "type": "string", - "description": "The tool name" - } - }, - { - "bwa 2>&1 | sed -n \"s/^Version: //p\"": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ], - "versions_samtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "samtools": { - "type": "string", - "description": "The tool name" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bwa": { - "type": "string", - "description": "The tool name" - } - }, - { - "bwa 2>&1 | sed -n \"s/^Version: //p\"": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "samtools": { - "type": "string", - "description": "The tool name" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } + "pipelines": [ + { + "name": "mag", + "version": "5.4.2" + }, + { + "name": "seqsubmit", + "version": "dev" + } ] - ] }, - "authors": [ - "@jfy133" - ], - "maintainers": [ - "@jfy133" - ] - }, - "pipelines": [ { - "name": "callingcards", - "version": "1.0.0" + "name": "catpack_download", + "path": "modules/nf-core/catpack/download/meta.yml", + "type": "module", + "meta": { + "name": "catpack_download", + "description": "Downloads the required files for either Nr or GTDB for building into a CAT database", + "keywords": ["taxonomic classification", "classification", "database", "download"], + "tools": [ + { + "catpack": { + "description": "CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)", + "homepage": "https://github.com/MGXlab/CAT_pack", + "documentation": "https://github.com/MGXlab/CAT_pack", + "tool_dev_url": "https://github.com/MGXlab/CAT_pack", + "doi": "10.1186/s13059-019-1817-x", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "db": { + "type": "string", + "description": "Which database to download", + "pattern": "nr|GTDB" + } + } + ] + ], + "output": { + "fasta": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}/*.${db}.gz": { + "type": "file", + "description": "FASTA file containing all the NCBI NR or GTDB sequences", + "pattern": "*.${db}.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ] + ], + "names": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}/*.names.dmp": { + "type": "file", + "description": "NCBI taxonomy-style names.dmp text file", + "pattern": "*.names.dmp", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1964" + } + ] + } + } + ] + ], + "nodes": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}/*.nodes.dmp": { + "type": "file", + "description": "NCBI taxonomy-style nodes.dmp text file", + "pattern": "*.nodes.dmp", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1964" + } + ] + } + } + ] + ], + "acc2tax": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}/*accession2taxid*.gz": { + "type": "file", + "description": "NCBI taxonomy names accession to taxonomy file", + "pattern": "*accession2taxid*", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1964" + } + ] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}/*.log": { + "type": "file", + "description": "Log file of the download process", + "pattern": "*.log", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1964" + } + ] + } + } + ] + ], + "versions_catpack": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "catpack": { + "type": "string", + "description": "The tool name" + } + }, + { + "CAT_pack --version | sed 's/CAT_pack pack v//g;s/ .*//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "catpack": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "CAT_pack --version | sed 's/CAT_pack pack v//g;s/ .*//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@jfy133"], + "maintainers": ["@jfy133"] + }, + "pipelines": [ + { + "name": "mag", + "version": "5.4.2" + }, + { + "name": "seqsubmit", + "version": "dev" + } + ] }, { - "name": "sammyseq", - "version": "dev" - } - ] - }, - { - "name": "bwa_samse", - "path": "modules/nf-core/bwa/samse/meta.yml", - "type": "module", - "meta": { - "name": "bwa_samse", - "description": "Convert bwa SA coordinate file to SAM format", - "keywords": [ - "bwa", - "aln", - "short-read", - "align", - "reference", - "fasta", - "map", - "sam", - "bam" - ], - "tools": [ - { - "bwa": { - "description": "BWA is a software package for mapping DNA sequences against\na large reference genome, such as the human genome.\n", - "homepage": "http://bio-bwa.sourceforge.net/", - "documentation": "https://bio-bwa.sourceforge.net/bwa.shtml", - "doi": "10.1093/bioinformatics/btp324", - "licence": [ - "GPL-3.0-or-later" - ], - "identifier": "biotools:bwa" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "FASTQ files specified alongside meta in input channel.", - "pattern": "*.{fastq,fq}.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/data_2044" - }, - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - }, - { - "sai": { - "type": "file", - "description": "SAI file specified alongside meta and reads in input channel.", - "pattern": "*.sai", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } + "name": "catpack_prepare", + "path": "modules/nf-core/catpack/prepare/meta.yml", + "type": "module", + "meta": { + "name": "catpack_prepare", + "description": "Creates a CAT_pack database based on input FASTAs", + "keywords": ["catpack", "cat", "prepare", "database", "profiling", "build"], + "tools": [ + { + "catpack": { + "description": "CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)", + "homepage": "https://github.com/MGXlab/CAT_pack", + "documentation": "https://github.com/MGXlab/CAT_pack", + "tool_dev_url": "https://github.com/MGXlab/CAT_pack", + "doi": "10.1186/s13059-019-1817-x", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "db_fasta": { + "type": "file", + "description": "A FASTA file containing all sequences to be included in the database", + "pattern": "*.{fasta,fa,fna}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + { + "names": { + "type": "file", + "description": "An NCBI taxonomy-style names text file", + "pattern": "*", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1964" + } + ] + } + }, + { + "nodes": { + "type": "file", + "description": "An NCBI taxonomy-style nodes text file", + "pattern": "*", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1964" + } + ] + } + }, + { + "acc2tax": { + "type": "file", + "description": "An NCBI taxonomy names accession to taxonomy file", + "pattern": "*", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1964" + } + ] + } + } + ], + "output": { + "db": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}/db/": { + "type": "directory", + "description": "Directory containing CAT database files", + "pattern": "${db}/", + "ontologies": [ + { + "edam": "http://edamontology.org/data_1049" + } + ] + } + } + ] + ], + "taxonomy": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}/tax/": { + "type": "directory", + "description": "Directory containing CAT prepared taxonomy database files", + "pattern": "${db}/", + "ontologies": [ + { + "edam": "http://edamontology.org/data_1049" + } + ] + } + } + ] + ], + "versions_catpack": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "catpack": { + "type": "string", + "description": "The tool name" + } + }, + { + "CAT_pack --version | sed 's/CAT_pack pack v//g;s/ .*//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "catpack": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "CAT_pack --version | sed 's/CAT_pack pack v//g;s/ .*//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@jfy133"], + "maintainers": ["@jfy133"] }, - { - "index": { - "type": "directory", - "description": "Directory containing BWA index files (amb,ann,bwt,pac,sa) from BWA_INDEX", - "pattern": "bwa/", - "ontologies": [ - { - "edam": "http://edamontology.org/data_3210" - } - ] - } - } - ] - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "BAM file", - "pattern": "*.bam", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - } - ] - ], - "versions_bwa": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bwa": { - "type": "string", - "description": "The tool name" - } - }, - { - "bwa 2>&1 | sed -n \"s/^Version: //p\"": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ], - "versions_samtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "samtools": { - "type": "string", - "description": "The tool name" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bwa": { - "type": "string", - "description": "The tool name" - } - }, - { - "bwa 2>&1 | sed -n \"s/^Version: //p\"": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "samtools": { - "type": "string", - "description": "The tool name" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } + "pipelines": [ + { + "name": "mag", + "version": "5.4.2" + }, + { + "name": "seqsubmit", + "version": "dev" + } ] - ] }, - "authors": [ - "@jfy133" - ], - "maintainers": [ - "@jfy133" - ] - }, - "pipelines": [ { - "name": "callingcards", - "version": "1.0.0" + "name": "catpack_reads", + "path": "modules/nf-core/catpack/reads/meta.yml", + "type": "module", + "meta": { + "name": "catpack_reads", + "description": "Taxonomic classification plus read-based abundance estimation from long DNA sequences and metagenome assembled genomes (e.g. contigs, MAGs / bins).", + "keywords": [ + "taxonomic classification", + "classification", + "long reads", + "mags", + "assembly", + "abundance", + "taxonomic composition" + ], + "tools": [ + { + "catpack": { + "description": "CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)", + "homepage": "https://github.com/MGXlab/CAT_pack", + "documentation": "https://github.com/MGXlab/CAT_pack", + "tool_dev_url": "https://github.com/MGXlab/CAT_pack", + "doi": "10.1186/s13059-019-1817-x", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "reads": { + "type": "file", + "description": "One or a pair of nucleotide FASTQ files (R1, R2) containing reads for mapping. Interleaved not supported.", + "pattern": "*.{fastq,fq,fastq.gz,fq.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2182" + }, + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "contigs": { + "type": "file", + "description": "A nucleotide FASTA file containing long DNA sequences such as contigs. Optional if `bins` supplied.", + "pattern": "*.{fasta,fna,fa,fas}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "database": { + "type": "directory", + "description": "Directory containing CAT_pack database files (e.g. output from CAT_pack prepare)", + "pattern": "*/", + "ontologies": [ + { + "edam": "http://edamontology.org/data_1049" + } + ] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "taxonomy": { + "type": "directory", + "description": "Directory containing CAT_pack taxonomy files (e.g. output from CAT_pack prepare)", + "pattern": "*/", + "ontologies": [ + { + "edam": "http://edamontology.org/data_1049" + } + ] + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "bins": { + "type": "file", + "description": "One or more nucleotide FASTA file containing binned long DNA sequences.\nOptional if `contigs` supplied.\nNote: if you supply bins, you must also give the `-s `\ncorresponding to the file extension of the bins via `ext.args`\n", + "pattern": "*.{fasta,fna,fa,fas}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + { + "mode": { + "type": "string", + "description": "Mode of operation of CAT_pack reads, \"mcr\": integrate annotations from MAGs (bins), contigs, and\nreads; \"cr\": integrate annotations from contigs and reads; \"mr\": integrate\nannotations from MAGs (bins) and reads.\n", + "pattern": "mcr|cr|mr" + } + }, + [ + { + "meta6": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "bam_aligned": { + "type": "file", + "description": "Optional pre-aligned and sorted reads mapped against contigs/bins.", + "pattern": "*.bam", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + } + ], + [ + { + "meta7": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "bam_unaligned": { + "type": "file", + "description": "Optional sorted unaligned reads from mapping against contigs/bins.", + "pattern": "*.bam", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + } + ], + [ + { + "meta8": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "contig2classification": { + "type": "file", + "description": "Optional TSV file with per-contig hit stats and assignment justification information", + "pattern": "*.contig2classification.txt", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + [ + { + "meta9": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "bin2classification": { + "type": "file", + "description": "Optional TSV file with per-bin hit stats and assignment justification information", + "pattern": "*.bin2classification.txt", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + [ + { + "meta10": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "unclassified2classification": { + "type": "file", + "description": "Optional TSV file with pre-made CAT_pack reads unmapped2classification.txt file information", + "pattern": "*.txt", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + [ + { + "meta11": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "proteins": { + "type": "directory", + "description": "Optional pre predicted-made proteins FASTA", + "pattern": "*.{fasta,faa,fa,fas}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + [ + { + "meta12": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "diamond_alignment": { + "type": "directory", + "description": "Optional pre-made DIAMOND alignment table", + "pattern": "*", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3751" + } + ] + } + } + ] + ], + "output": { + "rat_log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}.log": { + "type": "map", + "description": "Log file from RAT run\n", + "pattern": "*.log", + "ontologies": [ + { + "edam": "http://edamontology.org/data_3106" + } + ] + } + } + ] + ], + "complete_abundance": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.complete.abundance.txt": { + "type": "file", + "description": "TSV file containing complete abundance information\n", + "pattern": "*.contig.abundance.txt", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3751" + } + ] + } + } + ] + ], + "contig_abundance": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.contig.abundance.txt": { + "type": "file", + "description": "TSV file containing contig abundance information\n", + "pattern": "*.contig.abundance.txt", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3751" + } + ] + } + } + ] + ], + "read2classification": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.read2classification.txt": { + "type": "file", + "description": "A TSV file with per-read hit stats and assignment justification information", + "pattern": "*.read2classification.txt", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "alignment_diamond": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.alignment.diamond": { + "type": "file", + "description": "Intermediate DIAMOND TSV summary output file with alignment results", + "pattern": "*.alignment.diamond", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "contig2classification": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample 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+ { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "filtered": { + "type": "file", + "description": "AnnData file containing filtered data (without empty droplets)", + "pattern": "*.h5ad", + "ontologies": [] + } + }, + { + "unfiltered": { + "type": "file", + "description": "AnnData file containing unfiltered data (with empty droplets)", + "pattern": "*.h5ad", + "ontologies": [] + } + }, + { + "cellbender_h5": { + "type": "file", + "description": "CellBender h5 file containing ambient RNA estimates", + "pattern": "*.h5", + "ontologies": [] + } + } + ], + { + "output_layer_name": { + "type": "string", + "description": "The name of the layer to store counts" + } + } + ], + "output": { + "h5ad": [ + [ + { + "meta": { + "type": "file", + "description": "AnnData file containing decontaminated counts as `adata.X`", + "pattern": "*.h5ad", + "ontologies": [] + } + }, + { + "${prefix}.h5ad": { + "type": "file", + "description": "AnnData file containing decontaminated counts as `adata.X`", + "pattern": "*.h5ad", + "ontologies": [] + } + } + ] + ], + "versions_cellbender": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software version", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "topics": { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software version", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@nictru"], + "maintainers": ["@nictru"] + }, + "pipelines": [ + { + "name": "scdownstream", + "version": "dev" + } + ] }, { - "name": "oncoanalyser", - "version": "2.3.0" - }, - { - "name": "radseq", - "version": "dev" + "name": "cellbender_removebackground", + "path": "modules/nf-core/cellbender/removebackground/meta.yml", + "type": "module", + "meta": { + "name": "cellbender_removebackground", + "description": "Module to use CellBender to estimate ambient RNA from single-cell RNA-seq data", + "keywords": ["single-cell", "scRNA-seq", "ambient RNA removal"], + "tools": [ + { + "cellbender": { + "description": "CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.", + "documentation": "https://cellbender.readthedocs.io/en/latest/", + "tool_dev_url": "https://github.com/broadinstitute/CellBender", + "licence": ["BSD-3-Clause"], + "identifier": "biotools:CellBender" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "h5ad": { + "type": "file", + "description": "AnnData file containing unfiltered data (with empty droplets)", + "pattern": "*.h5ad", + "ontologies": [] + } + } + ] + ], + "output": { + "h5": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "${prefix}.h5": { + "type": "file", + "description": "Full count matrix as an h5 file, with background RNA removed. This file contains all the original droplet barcodes.", + "pattern": "*.h5", + "ontologies": [] + } + } + ] + ], + "filtered_h5": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "${prefix}_filtered.h5": { + "type": "file", + "description": "Full count matrix as an h5 file, with background RNA removed. This file contains only the droplet barcodes which were determined to have a > 50% posterior probability of containing cells.\n", + "pattern": "*.h5", + "ontologies": [] + } + } + ] + ], + "posterior_h5": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "${prefix}_posterior.h5": { + "type": "file", + "description": "The full posterior probability of noise counts. This is not normally used downstream.\n", + "pattern": "*.h5", + "ontologies": [] + } + } + ] + ], + "barcodes": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "${prefix}_cell_barcodes.csv": { + "type": "file", + "description": "CSV file containing all the droplet barcodes which were determined to have a > 50% posterior probability of containing cells. |\nBarcodes are written in plain text. This information is also contained in each of the above outputs, |\nbut is included as a separate output for convenient use in certain downstream applications.\n", + "pattern": "*.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "metrics": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "${prefix}_metrics.csv": { + "type": "file", + "description": "Metrics describing the run, potentially to be used to flag problematic runs |\nwhen using CellBender as part of a large-scale automated pipeline.\n", + "pattern": "*.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "report": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "${prefix}_report.html": { + "type": "file", + "description": "HTML report including plots and commentary, along with any warnings or suggestions for improved parameter settings.\n", + "pattern": "*.html", + "ontologies": [] + } + } + ] + ], + "pdf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "${prefix}.pdf": { + "type": "file", + "description": "PDF file that provides a standard graphical summary of the inference procedure.", + "pattern": "*.pdf", + "ontologies": [] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "${prefix}.log": { + "type": "file", + "description": "Log file produced by the cellbender remove-background run.", + "pattern": "*.log", + "ontologies": [] + } + } + ] + ], + "checkpoint": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "ckpt.tar.gz": { + "type": "file", + "description": "Checkpoint file which contains the trained model and the full posterior.", + "pattern": "*.ckpt", + "ontologies": [] + } + } + ] + ], + "versions_cellbender": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cellbender": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cellbender --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cellbender": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cellbender --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@nictru"], + "maintainers": ["@nictru"] + }, + "pipelines": [ + { + "name": "scdownstream", + "version": "dev" + }, + { + "name": "scrnaseq", + "version": "4.1.0" + } + ] }, { - "name": "raredisease", - "version": "3.0.0" + "name": "cellpose", + "path": "modules/nf-core/cellpose/meta.yml", + "type": "module", + "meta": { + "name": "cellpose", + "description": "cellpose segments cells in images using GPU-accelerated deep learning", + "keywords": ["segmentation", "image", "cellpose", "gpu", "spatial-transcriptomics"], + "tools": [ + { + "cellpose": { + "description": "cellpose is an anatomical segmentation algorithm written in Python 3 by Carsen Stringer and Marius Pachitariu", + "homepage": "https://github.com/MouseLand/cellpose", + "documentation": "https://cellpose.readthedocs.io/en/latest/command.html", + "tool_dev_url": "https://github.com/MouseLand/cellpose", + "doi": "10.1038/s41592-022-01663-4", + "licence": ["BSD 3-Clause"], + "identifier": "biotools:cellpose" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\n(sample id)\n" + } + }, + { + "image": { + "type": "file", + "description": "tif file ready for segmentation", + "pattern": "*.{tif,tiff}", + "ontologies": [] + } + } + ], + { + "model": { + "type": "file", + "description": "Optional custom cellpose model file. When provided, passed as\n--pretrained_model to cellpose. Pass [] (empty list) to use the\ndefault model (cpsam in cellpose 4).\n", + "pattern": "*", + "ontologies": [] + } + } + ], + "output": { + "mask": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\n[sample id]\n" + } + }, + { + "${prefix}/*masks.tif": { + "type": "file", + "description": "labelled mask output from cellpose in tif format", + "pattern": "${prefix}/*masks.tif", + "ontologies": [] + } + } + ] + ], + "flows": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\n[sample id]\n" + } + }, + { + "${prefix}/*flows.tif": { + "type": "file", + "description": "cell flow output from cellpose", + "pattern": "${prefix}/*flows.tif", + "ontologies": [] + } + } + ] + ], + "cells": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\n[sample id]\n" + } + }, + { + "${prefix}/*seg.npy": { + "type": "file", + "description": "numpy array with cell segmentation data", + "pattern": "${prefix}/*seg.npy", + "ontologies": [] + } + } + ] + ], + "versions_cellpose": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cellpose": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cellpose --version | sed -n 's/cellpose version:[[:space:]]*//p' | tr -d '[:space:]'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_python": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "python": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cellpose --version | sed -n 's/python version:[[:space:]]*//p' | tr -d '[:space:]'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_torch": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "torch": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cellpose --version | sed -n 's/torch version:[[:space:]]*//p' | tr -d '[:space:]'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cellpose": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cellpose --version | sed -n 's/cellpose version:[[:space:]]*//p' | tr -d '[:space:]'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "python": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cellpose --version | sed -n 's/python version:[[:space:]]*//p' | tr -d '[:space:]'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "torch": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cellpose --version | sed -n 's/torch version:[[:space:]]*//p' | tr -d '[:space:]'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "notes": "When `accelerator` is set (e.g. `accelerator = 1`), the module\nautomatically passes `--use_gpu` to cellpose. The container (built via Seqera\nContainers) includes PyTorch 2.10.0 with CUDA 12.8 and falls back to CPU\nautomatically when no GPU is available. Use the `process_gpu` label to request\nGPU resources from your executor. When running with conda/mamba, GPU support\ndepends on having a CUDA-enabled PyTorch installation in your environment.\n\nModel selection via the model input channel:\n - Custom model file: file(\"/path/to/model\")\n - Default (cpsam): []\n\nAdditional cellpose CLI arguments can be passed via `task.ext.args`:\n ext.args = '--diameter 30 --flow_threshold 0.4 --cellprob_threshold 0'\n\nDeprecated in cellpose 4.0.1+: `--chan`, `--chan2`, `--invert`, `--all_channels`,\n`--diam_mean`, `--pretrained_model_ortho`. Do not pass these via ext.args.\n\nModel weights are not bundled in the container. Cellpose downloads them on first\nuse to `$CELLPOSE_LOCAL_MODELS_PATH` (set to the work directory).\n", + "authors": ["@josenimo", "@FloWuenne", "@dongzehe"], + "maintainers": ["@josenimo", "@FloWuenne", "@kbestak"] + }, + "pipelines": [ + { + "name": "mcmicro", + "version": "dev" + }, + { + "name": "molkart", + "version": "1.2.0" + }, + { + "name": "spatialxe", + "version": "dev" + } + ] }, { - "name": "references", - "version": "0.1" + "name": "cellranger_count", + "path": "modules/nf-core/cellranger/count/meta.yml", + "type": "module", + "meta": { + "name": "cellranger_count", + "description": "Module to use Cell Ranger's pipelines analyze sequencing data produced from Chromium Single Cell Gene Expression.", + "keywords": ["align", "count", "reference"], + "tools": [ + { + "cellranger": { + "description": "Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.", + "homepage": "https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger", + "documentation": "https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov", + "tool_dev_url": "https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov", + "licence": ["10x Genomics EULA"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files. The order of the input files MUST be [\"sample1 R1\", \"sample1 R2\", \"sample2, R1\",\n\"sample2, R2\", ...]. This can usually be achieved by sorting the input files by file name.\n\nBackground: 10x data is always paired-end with R1 containing cell barcode and UMI\nand R2 containing the actual read sequence. Cell Ranger requires files to adhere to the following file-name\nconvention: `${Sample_Name}_S1_L00${Lane_Number}_${R1,R2}_001.fastq.gz`. This module automatically\nrenames files to match this convention based on the order of input files to avoid various\nissues (see https://github.com/nf-core/scrnaseq/issues/241). To avoid mistakes, the module\nthrows an error if a pair of R1 and R2 fastq files does not have the same filename except for the \"_R1\"/\"_R2\" part.\nRenaming the files does not affect the results (see README.md for detailed tests).\n", + "pattern": "*{R1,R2}*.fastq.gz", + "ontologies": [] + } + } + ], + { + "reference": { + "type": "directory", + "description": "Folder containing all the reference indices needed by Cell Ranger" + } + } + ], + "output": { + "outs": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "**/outs/**": { + "type": "file", + "description": "Files containing the outputs of Cell Ranger, see official 10X Genomics documentation for a complete list", + "pattern": "${meta.id}/outs/*", + "ontologies": [] + } + } + ] + ], + "versions_cellranger": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software version", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "topics": { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software version", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@ggabernet", "@edmundmiller"], + "maintainers": ["@ggabernet", "@edmundmiller"], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "YAML file containing versions of tools used in the module" + } + } + ] + }, + "pipelines": [ + { + "name": "scrnaseq", + "version": "4.1.0" + } + ] }, { - "name": "rnadnavar", - "version": "dev" + "name": "cellranger_mkfastq", + "path": "modules/nf-core/cellranger/mkfastq/meta.yml", + "type": "module", + "meta": { + "name": "cellranger_mkfastq", + "description": "Module to create FASTQs needed by the 10x Genomics Cell Ranger tool. Uses the cellranger mkfastq command.", + "keywords": ["reference", "mkfastq", "fastq", "illumina", "bcl2fastq"], + "tools": [ + { + "cellranger": { + "description": "Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.", + "homepage": "https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger", + "documentation": "https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov", + "tool_dev_url": "https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov", + "licence": ["10X Genomics EULA"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "csv": { + "type": "file", + "description": "Sample sheet", + "pattern": "*.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + }, + { + "bcl": { + "type": "file", + "description": "Base call files", + "pattern": "*.bcl.bgzf", + "ontologies": [] + } + } + ] + ], + "output": { + "fastq": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*_outs/outs/fastq_path/**/**_S[0-9]*_R?_00?.fastq.gz": { + "type": "file", + "description": "Read FastQ files", + "pattern": "*_S[0-9]*_R?_00?.fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "fastq_idx": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*_outs/outs/fastq_path/**/**_S[0-9]*_I?_00?.fastq.gz": { + "type": "file", + "description": "Index FastQ files", + "pattern": "*_S[0-9]*_I?_00?.fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "undetermined_fastq": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*_outs/outs/fastq_path/Undetermined*.fastq.gz": { + "type": "file", + "description": "Undetermined FastQ files", + "pattern": "Undetermined*.fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "reports": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*_outs/outs/fastq_path/Reports": { + "type": "directory", + "description": "Reports", + "pattern": "Reports" + } + } + ] + ], + "stats": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*_outs/outs/fastq_path/Stats": { + "type": "directory", + "description": "Stats", + "pattern": "Stats" + } + } + ] + ], + "interop": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*_outs/outs/interop_path/*.bin": { + "type": "file", + "description": "InterOp files", + "pattern": "*.bin", + "ontologies": [] + } + } + ] + ], + "versions_cellranger": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cellranger": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cellranger --version | sed \"s/.*-//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cellranger": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cellranger --version | sed \"s/.*-//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@ggabernet", "@edmundmiller", "@RHReynolds"], + "maintainers": ["@ggabernet", "@edmundmiller", "@RHReynolds"] + }, + "pipelines": [ + { + "name": "demultiplex", + "version": "1.7.1" + } + ] }, { - "name": "sarek", - "version": "3.8.1" + "name": "cellranger_mkgtf", + "path": "modules/nf-core/cellranger/mkgtf/meta.yml", + "type": "module", + "meta": { + "name": "cellranger_mkgtf", + "description": "Module to build a filtered GTF needed by the 10x Genomics Cell Ranger tool. Uses the cellranger mkgtf command.", + "keywords": ["reference", "mkref", "index"], + "tools": [ + { + "cellranger": { + "description": "Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.", + "homepage": "https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger", + "documentation": "https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov", + "tool_dev_url": "https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov", + "licence": ["10X Genomics EULA"], + "identifier": "" + } + } + ], + "input": [ + { + "gtf": { + "type": "file", + "description": "The reference GTF transcriptome file", + "pattern": "*.gtf", + "ontologies": [] + } + } + ], + "output": { + "gtf": [ + { + "*.gtf": { + "type": "directory", + "description": "The filtered GTF transcriptome file", + "pattern": "*.filtered.gtf" + } + } + ], + "versions_cellranger": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cellranger": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cellranger --version | sed \"s/.*-//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cellranger": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cellranger --version | sed \"s/.*-//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@ggabernet", "@edmundmiller"], + "maintainers": ["@ggabernet", "@edmundmiller"] + }, + "pipelines": [ + { + "name": "scrnaseq", + "version": "4.1.0" + } + ] }, { - "name": "seqinspector", - "version": "1.0.1" + "name": "cellranger_mkref", + "path": "modules/nf-core/cellranger/mkref/meta.yml", + "type": "module", + "meta": { + "name": "cellranger_mkref", + "description": "Module to build the reference needed by the 10x Genomics Cell Ranger tool. Uses the cellranger mkref command.", + "keywords": ["reference", "mkref", "index"], + "tools": [ + { + "cellranger": { + "description": "Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.", + "homepage": "https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger", + "documentation": "https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov", + "tool_dev_url": "https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov", + "licence": ["10X Genomics EULA"], + "identifier": "" + } + } + ], + "input": [ + { + "fasta": { + "type": "file", + "description": "Reference genome FASTA file", + "pattern": "*.{fasta,fa}", + "ontologies": [] + } + }, + { + "gtf": { + "type": "file", + "description": "Reference transcriptome GTF file", + "pattern": "*.gtf", + "ontologies": [] + } + }, + { + "reference_name": { + "type": "string", + "description": "The name to give the new reference folder", + "pattern": "str" + } + } + ], + "output": { + "reference": [ + { + "${reference_name}": { + "type": "directory", + "description": "Folder containing all the reference indices needed by Cell Ranger" + } + } + ], + "versions_cellranger": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cellranger": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cellranger --version | sed \"s/.*-//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cellranger": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cellranger --version | sed \"s/.*-//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@ggabernet"], + "maintainers": ["@ggabernet"] + }, + "pipelines": [ + { + "name": "scrnaseq", + "version": "4.1.0" + } + ] }, { - "name": "tbanalyzer", - "version": "dev" + "name": "cellranger_mkvdjref", + "path": "modules/nf-core/cellranger/mkvdjref/meta.yml", + "type": "module", + "meta": { + "name": "cellranger_mkvdjref", + "description": "Module to build the VDJ reference needed by the 10x Genomics Cell Ranger tool. Uses the cellranger mkvdjref command.", + "keywords": ["reference", "mkvdjref", "index", "immunoprofiling", "single-cell", "cellranger"], + "tools": [ + { + "cellranger": { + "description": "Cell Ranger processes data from 10X Genomics Chromium kits. `cellranger vdj` takes FASTQ files from `cellranger mkfastq` or `bcl2fastq` for V(D)J libraries and performs sequence assembly and paired clonotype calling. It uses the Chromium cellular barcodes and UMIs to assemble V(D)J transcripts per cell. Clonotypes and CDR3 sequences are output as a `.vloupe` file which can be loaded into Loupe V(D)J Browser.", + "homepage": "https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/what-is-cell-ranger", + "documentation": "https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/advanced/references", + "tool_dev_url": "https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/advanced/references", + "licence": ["10x Genomics EULA"], + "identifier": "" + } + } + ], + "input": [ + { + "fasta": { + "type": "file", + "description": "Reference genome FASTA file (optional)", + "pattern": "*.{fasta,fa}", + "ontologies": [] + } + }, + { + "gtf": { + "type": "file", + "description": "Reference genome GTF file (optional)", + "pattern": "*.gtf", + "ontologies": [] + } + }, + { + "seqs": { + "type": "file", + "description": "Reference genome FASTA file from the 10X Genomics fetch-imgt workflow (optional)", + "pattern": "*.{fasta,fa}", + "ontologies": [] + } + }, + { + "reference_name": { + "type": "string", + "description": "The name to give the new reference folder, e.g. `my_vdj_ref`. This flag is required", + "pattern": "str" + } + } + ], + "output": { + "reference": [ + { + "${reference_name}": { + "type": "directory", + "description": "Folder containing all the reference indices needed by Cell Ranger" + } + } + ], + "versions_cellranger": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cellranger": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cellranger --version | sed \"s/.*-//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cellranger": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cellranger --version | sed \"s/.*-//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@ggabernet", "@klkeys"], + "maintainers": ["@ggabernet", "@klkeys"] + }, + "pipelines": [ + { + "name": "airrflow", + "version": "5.0.0" + }, + { + "name": "scrnaseq", + "version": "4.1.0" + } + ] }, { - "name": "viralmetagenome", - "version": "1.1.1" - } - ] - }, - { - "name": "bwamem2_mem", - "path": "modules/nf-core/bwamem2/mem/meta.yml", - "type": "module", - "meta": { - "name": "bwamem2_mem", - "description": "Performs fastq alignment to a fasta reference using BWA", - "keywords": [ - "mem", - "bwa", - "alignment", - "map", - "fastq", - "bam", - "sam" - ], - "tools": [ - { - "bwa": { - "description": "BWA-mem2 is a software package for mapping DNA sequences against\na large reference genome, such as the human genome.\n", - "homepage": "https://github.com/bwa-mem2/bwa-mem2", - "documentation": "http://www.htslib.org/doc/samtools.html", - "arxiv": "arXiv:1303.3997", - "licence": [ - "MIT" - ], - "identifier": "biotools:bwa-mem2" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", - "ontologies": [ - { - "edam": "http://edamontology.org/data_2044" - }, - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference/index information\ne.g. [ id:'test' ]\n" - } - }, - { - "index": { - "type": "file", - "description": "BWA genome index files", - "pattern": "Directory containing BWA index *.{0132,amb,ann,bwt.2bit.64,pac}", - "ontologies": [ - { - "edam": "http://edamontology.org/data_3210" - } - ] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } + "name": "cellranger_multi", + "path": "modules/nf-core/cellranger/multi/meta.yml", + "type": "module", + "meta": { + "name": "cellranger_multi", + "description": "Module to use Cell Ranger's pipelines to analyze sequencing data produced from various Chromium technologies, including Single Cell Gene Expression, Single Cell Immune Profiling, Feature Barcoding, and Cell Multiplexing.", + "keywords": [ + "align", + "reference", + "cellranger", + "multiomics", + "gene expression", + "vdj", + "antigen capture", + "antibody capture", + "crispr" + ], + "tools": [ + { + "cellranger": { + "description": "Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.", + "homepage": "https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger", + "documentation": "https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_cp", + "tool_dev_url": "https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_cp", + "licence": ["10X Genomics EULA"], + "identifier": "" + } + } + ], + "input": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + [ + { + "meta_gex": { + "type": "map", + "description": "Groovy Map containing sample information\n" + } + }, + { + "gex_fastqs": { + "type": "file", + "description": "FASTQ files", + "pattern": "*.fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ], + [ + { + "meta_vdj": { + "type": "map", + "description": "Groovy Map containing sample information\n" + } + }, + { + "vdj_fastqs": { + "type": "file", + "description": "FASTQ files", + "pattern": "*.fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ], + [ + { + "meta_ab": { + "type": "map", + "description": "Groovy Map containing sample information\n" + } + }, + { + "ab_fastqs": { + "type": "file", + "description": "FASTQ files", + "pattern": "*.fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ], + [ + { + "meta_beam": { + "type": "map", + "description": "Groovy Map containing sample information\n" + } + }, + { + "beam_fastqs": { + "type": "file", + "description": "FASTQ files", + "pattern": "*.fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ], + [ + { + "meta_cmo": { + "type": "map", + "description": "Groovy Map containing sample information\n" + } + }, + { + "cmo_fastqs": { + "type": "file", + "description": "FASTQ files", + "pattern": "*.fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ], + [ + { + "meta_crispr": { + "type": "map", + "description": "Groovy Map containing sample information\n" + } + }, + { + "crispr_fastqs": { + "type": "file", + "description": "FASTQ files", + "pattern": "*.fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ], + { + "gex_reference": { + "type": "directory", + "description": "Folder containing Cellranger gene expression reference. Can also be a gzipped tarball", + "pattern": "*.tar.gz" + } + }, + { + "gex_frna_probeset": { + "type": "file", + "description": "Fixed RNA profiling information containing custom probes in CSV format", + "pattern": "*.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + }, + { + "gex_targetpanel": { + "type": "file", + "description": "Declaration of the target panel for Targeted Gene Expression analysis", + "pattern": "*.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + }, + { + "vdj_reference": { + "type": "directory", + "description": "Folder containing Cellranger V(D)J reference. Can also be a gzipped tarball", + "pattern": "*.tar.gz" + } + }, + { + "vdj_primer_index": { + "type": "file", + "description": "List of custom V(D)J inner enrichment primers", + "pattern": "*.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + }, + { + "fb_reference": { + "type": "file", + "description": "The Feature Barcodes used for reference in Feature Barcoding Analysis", + "pattern": "*.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + }, + { + "beam_antigen_panel": { + "type": "file", + "description": "The BEAM manifest in Feature Barcode CSV format", + "pattern": "*.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + }, + { + "beam_control_panel": { + "type": "file", + "description": "The BEAM antigens set to control status, with corresponding MHC alleles, in Feature Barcode CSV format", + "pattern": "*.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + }, + { + "cmo_reference": { + "type": "file", + "description": "Path to a custom Cell Multiplexing CSV reference IDs, or the `cmo-set` option in Cellranger", + "pattern": "*.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + }, + { + "cmo_barcodes": { + "type": "file", + "description": "A CSV file appended to the Cellranger multi config linking samples to CMO IDs", + "pattern": "*.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + }, + { + "cmo_barcode_assignment": { + "type": "file", + "description": "A CSV file that specifies the barcode-sample assignment in Cell Multiplexing analysis", + "pattern": "*.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + }, + { + "frna_sampleinfo": { + "type": "file", + "description": "Sample information for fixed RNA analysis", + "pattern": "*.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + }, + { + "ocm_barcodes": { + "type": "file", + "description": "A CSV file appended to the Cellranger multi config linking samples to OCM IDs", + "pattern": "*.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + }, + { + "skip_renaming": { + "type": "boolean", + "description": "Skip renaming" + } + } + ], + "output": { + "config": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "cellranger_multi_config.csv": { + "type": "file", + "description": "The resolved Cellranger multi config used for analysis", + "pattern": "cellranger_multi_config.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "outs": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "**/outs/**": { + "type": "file", + "description": "Files containing the outputs of Cell Ranger", + "pattern": "${meta.id}/outs/*", + "ontologies": [] + } + } + ] + ], + "versions_cellranger": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "topics": { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@klkeys"], + "maintainers": ["@klkeys"] }, - { - "fasta": { - "type": "file", - "description": "Reference genome in FASTA format", - "pattern": "*.{fa,fasta,fna}", - "ontologies": [ - { - "edam": "http://edamontology.org/data_2044" - }, - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - { - "sort_bam": { - "type": "boolean", - "description": "use samtools sort (true) or samtools view (false)", - "pattern": "true or false" - } - } - ], - "output": { - "sam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.sam": { - "type": "file", - "description": "Output SAM file containing read alignments", - "pattern": "*.{sam}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2573" - } - ] - } - } - ] - ], - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "Output BAM file containing read alignments", - "pattern": "*.{bam}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - } - ] - ], - "cram": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.cram": { - "type": "file", - "description": "Output CRAM file containing read alignments", - "pattern": "*.{cram}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3462" - } - ] - } - } - ] - ], - "crai": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.crai": { - "type": "file", - "description": "Index file for CRAM file", - "pattern": "*.{crai}", - "ontologies": [] - } - } - ] - ], - "csi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - 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It uses the Chromium cellular barcodes and UMIs to assemble V(D)J transcripts per cell. Clonotypes and CDR3 sequences are output as a `.vloupe` file which can be loaded into Loupe V(D)J Browser.", + "homepage": "https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/what-is-cell-ranger", + "documentation": "https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/tutorial/tutorial-vdj", + "tool_dev_url": "https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/tutorial/tutorial-vdj", + "licence": ["10X Genomics EULA"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", + "pattern": "${Sample_Name}_S1_L00${Lane_Number}_${I1,I2,R1,R2}_001.fastq.gz", + "ontologies": [] + } + } + ], + { + "reference": { + "type": "directory", + "description": "Folder containing all the reference indices needed by Cell Ranger" + } + } + ], + "output": { + "outs": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "**/outs/**": { + "type": "file", + "description": "Files containing the outputs of Cell Ranger, see official 10X Genomics documentation for a complete list", + "pattern": "${meta.id}/outs/*", + "ontologies": [] + } + } + ] + ], + "versions_cellranger": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cellranger": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cellranger --version | sed \"s/.*-//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cellranger": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cellranger --version | sed \"s/.*-//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@ggabernet", "@edmundmiller", "@klkeys"], + "maintainers": ["@ggabernet", "@edmundmiller", "@klkeys"] + }, + "pipelines": [ + { + "name": "airrflow", + "version": "5.0.0" + } + ] }, { - "name": "genomicrelatedness", - "version": "dev" + "name": "cellrangerarc_count", + "path": "modules/nf-core/cellrangerarc/count/meta.yml", + "type": "module", + "meta": { + "name": "cellrangerarc_count", + "description": "Module to use Cell Ranger's ARC pipelines analyze sequencing data produced from Chromium Single Cell ARC. Uses the cellranger-arc count command.", + "keywords": ["align", "count", "reference"], + "tools": [ + { + "cellrangerarc": { + "description": "Cell Ranger ARC is a set of analysis pipelines that process Chromium Single Cell ARC data.", + "homepage": "https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc", + "documentation": "https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc", + "tool_dev_url": "https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc", + "licence": ["10x Genomics EULA"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "sample_type": { + "type": "string", + "description": "The type of sample" + } + }, + { + "sub_sample": { + "type": "string", + "description": "The name of sub sample" + } + }, + { + "reads": { + "type": "file", + "description": "FASTQ files produced using Cell Ranger ARC", + "pattern": "*.fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reference": { + "type": "directory", + "description": "Directory containing all the reference indices needed by Cell Ranger ARC" + } + } + ] + ], + "output": { + "outs": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "${prefix}/outs/**": { + "type": "file", + "description": "Files containing the outputs of Cell Ranger ARC", + "pattern": "${prefix}/outs/*", + "ontologies": [] + } + } + ] + ], + "lib": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "${prefix}_lib.csv": { + "type": "file", + "description": "Library", + "pattern": "${prefix}_lib.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "versions_cellrangerarc": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cellrangerarc": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cellranger-arc --version 2>&1 | sed 's/cellranger-arc cellranger-arc-//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cellrangerarc": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cellranger-arc --version 2>&1 | sed 's/cellranger-arc cellranger-arc-//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@ggabernet", "@edmundmiller", "@heylf"] + }, + "pipelines": [ + { + "name": "scrnaseq", + "version": "4.1.0" + } + ] }, { - "name": "hgtseq", - "version": "1.1.0" + "name": "cellrangerarc_mkfastq", + "path": "modules/nf-core/cellrangerarc/mkfastq/meta.yml", + "type": "module", + "meta": { + "name": "cellrangerarc_mkfastq", + "description": "Module to create fastqs needed by the 10x Genomics Cell Ranger Arc tool. 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Uses the cellranger-arc mkgtf command.", + "keywords": ["reference", "mkref", "index"], + "tools": [ + { + "cellrangerarc": { + "description": "Cell Ranger Arc by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.", + "homepage": "https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc", + "documentation": "https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc", + "tool_dev_url": "https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc", + "licence": ["10x Genomics EULA"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "gtf": { + "type": "file", + "description": "The reference GTF transcriptome file", + "pattern": "*.gtf", + "ontologies": [] + } + } + ] + ], + "output": { + "gtf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.gtf": { + "type": "directory", + "description": "The filtered GTF transcriptome file", + "pattern": "${prefix}.gtf" + } + } + ] + ], + "versions_cellrangerarc": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cellrangerarc": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cellranger-arc --version 2>&1 | sed 's/cellranger-arc cellranger-arc-//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cellrangerarc": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cellranger-arc --version 2>&1 | sed 's/cellranger-arc cellranger-arc-//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@ggabernet", "@edmundmiller", "@heylf"] + }, + "pipelines": [ + { + "name": "scrnaseq", + "version": "4.1.0" + } + ] }, { - "name": "radseq", - "version": "dev" + "name": "cellrangerarc_mkref", + "path": "modules/nf-core/cellrangerarc/mkref/meta.yml", + "type": "module", + "meta": { + "name": "cellrangerarc_mkref", + "description": "Module to build the reference needed by the 10x Genomics Cell Ranger Arc tool. Uses the cellranger-arc mkref command.", + "keywords": ["reference", "mkref", "index"], + "tools": [ + { + "cellrangerarc": { + "description": "Cell Ranger Arc is a set of analysis pipelines that process Chromium Single Cell Arc data.", + "homepage": "https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc", + "documentation": "https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc", + "tool_dev_url": "https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc", + "licence": ["10x Genomics EULA"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing genome information\ne.g. `[ id:'genome' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference genome FASTA file", + "pattern": "*.{fasta,fa}", + "ontologies": [] + } + }, + { + "gtf": { + "type": "file", + "description": "Reference transcriptome GTF file", + "pattern": "*.gtf", + "ontologies": [] + } + }, + { + "motifs": { + "type": "file", + "description": "Sequence motif file (e.g., from transcription factors)", + "pattern": "*.txt", + "ontologies": [] + } + }, + { + "reference_config": { + "type": "file", + "description": "JSON-like file holding organism, genome, reference fasta path, reference annotation gtf path, contigs that should be excluded and sequence format motif file path", + "pattern": "config", + "ontologies": [] + } + } + ] + ], + "output": { + "reference": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing genome information\ne.g. `[ id:'genome' ]`\n" + } + }, + { + "${prefix}": { + "type": "directory", + "description": "Folder called like the reference_name containing all the reference indices needed by Cell Ranger Arc" + } + } + ] + ], + "config": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing genome information\ne.g. `[ id:'genome' ]`\n" + } + }, + { + "config": { + "type": "file", + "description": "Configuration file", + "ontologies": [] + } + } + ] + ], + "versions_cellrangerarc": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cellrangerarc": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cellranger-arc --version 2>&1 | sed 's/cellranger-arc cellranger-arc-//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cellrangerarc": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cellranger-arc --version 2>&1 | sed 's/cellranger-arc cellranger-arc-//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@ggabernet", "@heylf"] + }, + "pipelines": [ + { + "name": "scrnaseq", + "version": "4.1.0" + } + ] }, { - "name": "raredisease", - "version": "3.0.0" + "name": "cellrangeratac_count", + "path": "modules/nf-core/cellrangeratac/count/meta.yml", + "type": "module", + "meta": { + "name": "cellrangeratac_count", + "description": "Module to use Cell Ranger's ATAC pipelines analyze sequencing data produced from Chromium Single Cell ATAC.", + "keywords": ["align", "count", "reference"], + "tools": [ + { + "cellranger-atac": { + "description": "Cell Ranger ATAC is a set of analysis pipelines that process Chromium Single Cell ATAC data.", + "homepage": "https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac", + "documentation": "https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac", + "tool_dev_url": "https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac", + "licence": ["10x Genomics EULA"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively, plus an additional FastQ for the barcodes\n", + "ontologies": [] + } + } + ], + { + "reference": { + "type": "directory", + "description": "Directory containing all the reference indices needed by Cell Ranger ATAC" + } + } + ], + "output": { + "outs": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "${meta.id}/outs/*": { + "type": "file", + "description": "Files containing the outputs of Cell Ranger ATAC", + "pattern": "sample-${meta.gem}/outs/*", + "ontologies": [] + } + } + ] + ], + "versions_cellrangeratac": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cellrangeratac": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cellranger-atac --version | sed 's/.*cellranger-atac-//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cellrangeratac": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cellranger-atac --version | sed 's/.*cellranger-atac-//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@ggabernet", "@edmundmiller", "@heylf"], + "maintainers": ["@ggabernet", "@edmundmiller", "@heylf"] + } }, { - "name": "rnadnavar", - "version": "dev" + "name": "cellrangeratac_mkfastq", + "path": "modules/nf-core/cellrangeratac/mkfastq/meta.yml", + "type": "module", + "meta": { + "name": "cellrangeratac_mkfastq", + "description": "Module to create fastqs needed by the 10x Genomics Cell Ranger ATAC tool. Uses the cellranger-atac mkfastq command.", + "keywords": ["reference", "mkfastq", "fastq", "illumina", "bcl2fastq"], + "tools": [ + { + "cellranger-atac": { + "description": "Cell Ranger ATAC by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.", + "homepage": "https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac", + "documentation": "https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac", + "tool_dev_url": "https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac", + "licence": ["10x Genomics EULA"], + "identifier": "" + } + } + ], + "input": [ + { + "bcl": { + "type": "file", + "description": "Base call files", + "pattern": "*.bcl.bgzf", + "ontologies": [] + } + }, + { + "csv": { + "type": "file", + "description": "Sample sheet", + "pattern": "*.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ], + "output": { + "fastq": [ + { + "${bcl.getSimpleName()}/outs/fastq_path/*.fastq.gz": { + "type": "file", + "description": "Unaligned FastQ files", + "pattern": "*.fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ], + "versions_cellrangeratac": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cellrangeratac": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cellranger-atac --version | sed 's/.*cellranger-atac-//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cellrangeratac": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cellranger-atac --version | sed 's/.*cellranger-atac-//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@ggabernet", "@edmundmiller", "@RHReynolds", "@heylf"], + "maintainers": ["@ggabernet", "@edmundmiller", "@RHReynolds", "@heylf"] + } }, { - "name": "sammyseq", - "version": "dev" + "name": "cellrangeratac_mkref", + "path": "modules/nf-core/cellrangeratac/mkref/meta.yml", + "type": "module", + "meta": { + "name": "cellrangeratac_mkref", + "description": "Module to build the reference needed by the 10x Genomics Cell Ranger ATAC tool. Uses the cellranger-atac mkref command.", + "keywords": ["reference", "mkref", "index"], + "tools": [ + { + "cellranger-atac": { + "description": "Cell Ranger ATAC is a set of analysis pipelines that process Chromium Single Cell ATAC data.", + "homepage": "https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac", + "documentation": "https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac", + "tool_dev_url": "https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac", + "licence": ["10x Genomics EULA"], + "identifier": "" + } + } + ], + "input": [ + { + "fasta": { + "type": "file", + "description": "Reference genome FASTA file", + "pattern": "*.{fasta,fa}", + "ontologies": [] + } + }, + { + "gtf": { + "type": "file", + "description": "Reference transcriptome GTF file", + "pattern": "*.gtf", + "ontologies": [] + } + }, + { + "motifs": { + "type": "file", + "description": "Sequence motif file (e.g., of transcription factors)", + "pattern": "*.txt", + "ontologies": [] + } + }, + { + "reference_config": { + "type": "file", + "description": "JSON-like config file holding organism, genome, reference fasta path, reference annotation gtf path, contigs that should be excluded and sequence format motif file path", + "pattern": "config", + "ontologies": [] + } + }, + { + "reference_name": { + "type": "string", + "description": "The name to give the new reference folder", + "pattern": "str" + } + } + ], + "output": { + "reference": [ + { + "${reference_name}": { + "type": "directory", + "description": "Folder called regarding reference_name containing all the reference indices needed by Cell Ranger ATAC" + } + } + ], + "versions_cellrangeratac": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cellrangeratac": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cellranger-atac --version 2>&1 | sed 's/.*cellranger-atac-//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cellrangeratac": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cellranger-atac --version 2>&1 | sed 's/.*cellranger-atac-//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@ggabernet", "@heylf"], + "maintainers": ["@ggabernet", "@heylf"] + } }, { - "name": "sarek", - "version": "3.8.1" + "name": "cellsnp_modea", + "path": "modules/nf-core/cellsnp/modea/meta.yml", + "type": "module", + "meta": { + "name": "cellsnp_modea", + "description": "Cellsnp-lite is a C/C++ tool for efficient genotyping bi-allelic SNPs on single cells. You can use the mode A of cellsnp-lite after read alignment to obtain the snp x cell pileup UMI or read count matrices for each alleles of given or detected SNPs for droplet based single cell data.", + "keywords": ["genotyping", "single cell", "SNP", "droplet based single cells"], + "tools": [ + { + "cellsnp": { + "description": "Efficient genotyping bi-allelic SNPs on single cells", + "homepage": "https://github.com/single-cell-genetics/cellsnp-lite", + "documentation": "https://cellsnp-lite.readthedocs.io", + "tool_dev_url": "https://github.com/single-cell-genetics/cellsnp-lite", + "doi": "10.1093/bioinformatics/btab358", + "licence": ["Apache-2.0"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "bam": { + "type": "file", + "description": "A single BAM/SAM/CRAM file, e.g., from CellRanger.", + "pattern": "*.{bam,cram,sam}", + "ontologies": [] + } + }, + { + "bai": { + "type": "file", + "description": "The index of the BAM/CRAM file.", + "pattern": "*.{bai,crai}", + "ontologies": [] + } + }, + { + "region_vcf": { + "type": "file", + "description": "A optional vcf file listing all candidate SNPs for genotyping.", + "pattern": "*.{vcf, vcf.gz}", + "ontologies": [] + } + }, + { + "barcode": { + "type": "file", + "description": "A plain file listing all effective cell barcodes.", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "output": { + "base": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.base.vcf.gz": { + "type": "file", + "description": "A VCF file listing genotyped SNPs and aggregated AD & DP information (without GT).", + "pattern": "*.base.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "cell": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.cells.vcf.gz": { + "type": "file", + "description": "A VCF file listing genotyped SNPs and aggregated AD & DP information & genotype (GT) information for each cell or sample.", + "pattern": "*.cells.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "sample": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.samples.tsv": { + "type": "file", + "description": "A TSV file listing cell barcodes or sample IDs.", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "allele_depth": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.tag.AD.mtx": { + "type": "file", + "description": "A file in “Matrix Market exchange formats”, containing the allele depths of the alternative (ALT) alleles.", + "pattern": "*.tag.AD.mtx", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3916" + } + ] + } + } + ] + ], + "depth_coverage": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.tag.DP.mtx": { + "type": "file", + "description": "A file in “Matrix Market exchange formats”, containing the sum of allele depths of the reference and alternative alleles (REF + ALT).", + "pattern": "*.tag.DP.mtx", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3916" + } + ] + } + } + ] + ], + "depth_other": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.tag.OTH.mtx": { + "type": "file", + "description": "A file in “Matrix Market exchange formats”, containing the sum of allele depths of all the alleles other than REF and ALT.", + "pattern": "*.tag.OTH.mtx", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3916" + } + ] + } + } + ] + ], + "versions_cellsnp": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cellsnp": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cellsnp-lite --v | cut -f2 -d ' '": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cellsnp": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cellsnp-lite --v | cut -f2 -d ' '": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@wxicu"], + "maintainers": ["@wxicu"] + } }, { - "name": "seqinspector", - "version": "1.0.1" + "name": "centrifuge_build", + "path": "modules/nf-core/centrifuge/build/meta.yml", + "type": "module", + "meta": { + "name": "centrifuge_build", + "description": "Build centrifuge database for taxonomic profiling", + "keywords": ["database", "metagenomics", "build", "db", "fasta"], + "tools": [ + { + "centrifuge": { + "description": "Classifier for metagenomic sequences", + "homepage": "https://ccb.jhu.edu/software/centrifuge/", + "documentation": "https://ccb.jhu.edu/software/centrifuge/manual.shtml", + "doi": "10.1101/gr.210641.116", + "licence": ["GPL v3"], + "identifier": "biotools:centrifuge" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Fasta file containing sequences to be used in centrifuge database.", + "pattern": "*.{fasta,fna}", + "ontologies": [] + } + } + ], + { + "conversion_table": { + "type": "file", + "description": "A tab-separated file with sequence ID to taxonomy ID mapping", + "pattern": "*.{map}", + "ontologies": [] + } + }, + { + "taxonomy_tree": { + "type": "file", + "description": "A \\t|\\t-separated file mapping taxonomy. Typically nodes.dmp from the NCBI taxonomy dump. Links taxonomy IDs to their parents", + "pattern": "*.{dmp}", + "ontologies": [] + } + }, + { + "name_table": { + "type": "file", + "description": "A '|'-separated file mapping taxonomy IDs to a name. Typically names.dmp from the NCBI taxonomy dump. Links taxonomy IDs to their scientific name", + "pattern": "*.{dmp}", + "ontologies": [] + } + }, + { + "size_table": { + "type": "file", + "description": "Optional list of taxonomic IDs and lengths of the sequences belonging to the same taxonomic IDs.", + "pattern": "*", + "ontologies": [] + } + } + ], + "output": { + "cf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "${prefix}/" + } + }, + { + "${prefix}/": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "${prefix}/" + } + } + ] + ], + "versions_centrifuge": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "centrifuge": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "centrifuge --version 2>&1 | sed '1!d;s/.* version //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "centrifuge": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "centrifuge --version 2>&1 | sed '1!d;s/.* version //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@sarah-buddle", "@jfy133"] + }, + "pipelines": [ + { + "name": "createtaxdb", + "version": "3.0.0" + } + ] }, { - "name": "tbanalyzer", - "version": "dev" + "name": "centrifuge_centrifuge", + "path": "modules/nf-core/centrifuge/centrifuge/meta.yml", + "type": "module", + "meta": { + "name": "centrifuge_centrifuge", + "description": "Classifies metagenomic sequence data", + "keywords": ["classify", "metagenomics", "fastq", "db"], + "tools": [ + { + "centrifuge": { + "description": "Centrifuge is a classifier for metagenomic sequences.", + "homepage": "https://ccb.jhu.edu/software/centrifuge/", + "documentation": "https://ccb.jhu.edu/software/centrifuge/manual.shtml", + "doi": "10.1101/gr.210641.116", + "licence": ["GPL v3"], + "identifier": "biotools:centrifuge" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", + "ontologies": [] + } + } + ], + { + "db": { + "type": "directory", + "description": "Path to directory containing centrifuge database files" + } + }, + { + "save_unaligned": { + "type": "boolean", + "description": "If true unmapped fastq files are saved" + } + }, + { + "save_aligned": { + "type": "boolean", + "description": "If true mapped fastq files are saved" + } + } + ], + "output": { + "report": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*report.txt": { + "type": "file", + "description": "File containing a classification summary\n", + "pattern": "*.{report.txt}", + "ontologies": [] + } + } + ] + ], + "results": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*results.txt": { + "type": "file", + "description": "File containing classification results\n", + "pattern": "*.{results.txt}", + "ontologies": [] + } + } + ] + ], + "sam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{sam,tab}": { + "type": "file", + "description": "Optional output file containing read alignments (SAM format )or a table of per-read hit information (TAB)s\n", + "pattern": "*.{sam,tab}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "fastq_mapped": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.mapped.fastq{,.1,.2}.gz": { + "type": "file", + "description": "Mapped fastq files", + "pattern": "*.mapped.fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "fastq_unmapped": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.unmapped.fastq{,.1,.2}.gz": { + "type": "file", + "description": "Unmapped fastq files", + "pattern": "*.unmapped.fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "versions_centrifuge": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "centrifuge": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "centrifuge --version 2>&1 | sed '1!d;s/.* version //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "centrifuge": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "centrifuge --version 2>&1 | sed '1!d;s/.* version //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@sofstam", "@jfy133", "@sateeshperi"], + "maintainers": ["@sofstam", "@jfy133", "@sateeshperi"] + }, + "pipelines": [ + { + "name": "taxprofiler", + "version": "2.0.0" + } + ] }, { - "name": "viralmetagenome", - "version": "1.1.1" - } - ] - }, - { - "name": "bwameme_index", - "path": "modules/nf-core/bwameme/index/meta.yml", - "type": "module", - "meta": { - "name": "bwameme_index", - "description": "Create BWA-MEME index for reference genome", - "keywords": [ - "index", - "fasta", - "genome", - "reference" - ], - "tools": [ - { - "bwameme": { - "description": "Faster BWA-MEM2 using learned-index", - "homepage": "https://github.com/kaist-ina/BWA-MEME", - "documentation": "https://github.com/kaist-ina/BWA-MEME#getting-started", - "doi": "10.1093/bioinformatics/btac137", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } + "name": "centrifuge_kreport", + "path": "modules/nf-core/centrifuge/kreport/meta.yml", + "type": "module", + "meta": { + "name": "centrifuge_kreport", + "description": "Creates Kraken-style reports from centrifuge out files", + "keywords": ["classify", "metagenomics", "fastq", "db", "report", "kraken"], + "tools": [ + { + "centrifuge": { + "description": "Centrifuge is a classifier for metagenomic sequences.", + "homepage": "https://ccb.jhu.edu/software/centrifuge/", + "documentation": "https://ccb.jhu.edu/software/centrifuge/manual.shtml", + "doi": "10.1101/gr.210641.116", + "licence": ["GPL v3"], + "identifier": "biotools:centrifuge" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "report": { + "type": "file", + "description": "File containing the centrifuge classification report", + "pattern": "*.{txt}", + "ontologies": [] + } + } + ], + { + "db": { + "type": "directory", + "description": "Path to directory containing centrifuge database files" + } + } + ], + "output": { + "kreport": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "File containing kraken-style report from centrifuge\nout files.\n", + "pattern": "*.{txt}", + "ontologies": [] + } + } + ] + ], + "versions_centrifuge": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "centrifuge": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "centrifuge --version 2>&1 | sed '1!d;s/.* version //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "centrifuge": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "centrifuge --version 2>&1 | sed '1!d;s/.* version //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@sofstam", "@jfy133"], + "maintainers": ["@sofstam", "@jfy133"] }, - { - "fasta": { - "type": "file", - "description": "Input genome fasta file", - "ontologies": [] - } - } - ] - ], - "output": { - "index": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "bwameme": { - "type": "file", - "description": "BWA-MEME genome index files", - "pattern": "*.{0123,amb,ann,pac,pos_packed,suffixarray_uint64,suffixarray_uint64_L0_PARAMETERS,suffixarray_uint64_L1_PARAMETERS,suffixarray_uint64_L2_PARAMETERS}", - "ontologies": [] - } - } - ] - ], - "versions_bwameme": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bwameme": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "1.0.6": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bwameme": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "1.0.6": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "taxprofiler", + "version": "2.0.0" + } ] - ] - }, - "authors": [ - "@ramprasadn" - ], - "maintainers": [ - "@ramprasadn" - ] - }, - "pipelines": [ - { - "name": "raredisease", - "version": "3.0.0" - } - ] - }, - { - "name": "bwameme_mem", - "path": "modules/nf-core/bwameme/mem/meta.yml", - "type": "module", - "meta": { - "name": "bwameme_mem", - "description": "Performs fastq alignment to a fasta reference using BWA-MEME", - "keywords": [ - "mem", - "bwa", - "bwamem2", - "bwameme", - "alignment", - "map", - "fastq", - "bam", - "sam", - "cram" - ], - "tools": [ - { - "bwameme": { - "description": "Faster BWA-MEM2 using learned-index", - "homepage": "https://github.com/kaist-ina/BWA-MEME", - "documentation": "https://github.com/kaist-ina/BWA-MEME#getting-started", - "doi": "10.1093/bioinformatics/btac137", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference/index information\ne.g. [ id:'test' ]\n" - } - }, - { - "index": { - "type": "file", - "description": "BWA genome index files", - "pattern": "Directory containing BWA index *.{0132,amb,ann,bwt.2bit.64,pac}", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome in FASTA format", - "pattern": "*.{fa,fasta,fna}", - "ontologies": [] - } - } - ], - { - "sort_bam": { - "type": "boolean", - "description": "use samtools sort (true) or samtools view (false)", - "pattern": "true or false" - } - }, - { - "mbuffer": { - "type": "integer", - "description": "memory for mbuffer in megabytes (default 3072)" + }, + { + "name": "centrifuger_build", + "path": "modules/nf-core/centrifuger/build/meta.yml", + "type": "module", + "meta": { + "name": "centrifuger_build", + "description": "Build centrifuger database for taxonomic profiling", + "keywords": ["metagenomics", "taxonomic-classification", "database-build", "centrifuger", "centrifuge"], + "tools": [ + { + "centrifuger": { + "description": "Lossless compression of microbial genomes for efficient and accurate metagenomic sequence classification.", + "homepage": "https://github.com/mourisl/centrifuger", + "documentation": "https://github.com/mourisl/centrifuger", + "tool_dev_url": "https://github.com/mourisl/centrifuger", + "doi": "10.1186/s13059-024-03244-4", + "licence": ["MIT"], + "identifier": "biotools:centrifuger" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information. e.g. `[id:'test',\nsingle_end:false ]`\n" + } + }, + { + "references": { + "type": "file", + "description": "One or more reference genome sequence files in FASTA format.\nThese are staged into the work directory and used to generate.a renference list file (used with -l option).\n", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + { + "taxonomy_nodes": { + "type": "file", + "description": "File describing parent-child relationships of a taxonomic tree in NCBI nodes.dmp format", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1964" + } + ] + } + }, + { + "taxonomy_names": { + "type": "file", + "description": "File describing individual members of a taxonomic tree in NCBI names.dmp format", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1964" + } + ] + } + }, + { + "conversion_table": { + "type": "file", + "description": "Required: a tab-seperated file, mapping sequence IDs to taxonomy IDs.\n", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + "output": { + "db": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}": { + "type": "directory", + "description": "Centrifuger database index files", + "pattern": "${prefix}", + "ontologies": [] + } + } + ] + ], + "versions_centrifuger": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "centrifuger": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "centrifuger -v 2>&1 | sed 's/Centrifuger v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "centrifuger": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "centrifuger -v 2>&1 | sed 's/Centrifuger v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@haris18s"], + "maintainers": ["@haris18s"] } - }, - { - "samtools_threads": { - "type": "integer", - "description": "number of threads for samtools (default 2)" + }, + { + "name": "centrifuger_centrifuger", + "path": "modules/nf-core/centrifuger/centrifuger/meta.yml", + "type": "module", + "meta": { + "name": "centrifuger_centrifuger", + "description": "Classification of sequencing reads using the Centrifuger tool.", + "keywords": ["metagenomics", "classification", "centrifuger"], + "tools": [ + { + "centrifuger": { + "description": "Lossless compression of microbial genomes for efficient and accurate metagenomic sequence classification.", + "homepage": "https://github.com/mourisl/centrifuger", + "documentation": "https://github.com/mourisl/centrifuger", + "tool_dev_url": "https://github.com/mourisl/centrifuger", + "doi": "10.1186/s13059-024-03244-4", + "licence": ["MIT"], + "identifier": "biotools:centrifuger" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information. e.g. `[ id:'sample1', single_end:false ]`" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end, respectively.\n", + "pattern": "*.{fastq,fq,fastq.gz,fq.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information. e.g. `[ id:'sample1', single_end:false ]`" + } + }, + { + "db": { + "type": "directory", + "description": "Path to directory containing Centrifuger database files (that end in `.cfr`)." + } + } + ], + { + "save_unclassified": { + "type": "boolean", + "description": "Optional - if true, output unclassified reads.\n" + } + }, + { + "save_classified": { + "type": "boolean", + "description": "Optional - if true, output classified reads.\n" + } + }, + { + "barcode": { + "type": "file", + "description": "Optional barcode file.\n" + } + }, + { + "umi": { + "type": "file", + "description": "Optional UMI file.\n" + } + } + ], + "output": { + "classification_file": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information. e.g. `[ id:'sample1', single_end:false ]`" + } + }, + { + "*.tsv": { + "type": "file", + "description": "File containing classification results\n", + "pattern": "${prefix}.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "fastq_classified": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.classified*.fq.gz": { + "type": "file", + "description": "FASTQ file(s) containing classified reads", + "pattern": "*.{fastq,fq,fastq.gz,fq.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ] + ], + "fastq_unclassified": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.unclassified*.fq.gz": { + "type": "file", + "description": "FASTQ file(s) containing unclassified reads", + "pattern": "*.{fastq,fq,fastq.gz,fq.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ] + ], + "versions_centrifuger": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "centrifuger": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "centrifuger -v 2>&1 | sed 's/Centrifuger v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "centrifuger": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "centrifuger -v 2>&1 | sed 's/Centrifuger v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@haris18s"], + "maintainers": ["@haris18s", "@sofstam", "@jfy133"] } - } - ], - "output": { - "sam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.sam": { - "type": "file", - "description": "Output SAM file containing read alignments", - "pattern": "*.{sam}", - "ontologies": [] - } - } - ] - ], - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "Output BAM file containing read alignments", - "pattern": "*.{bam}", - "ontologies": [] - } - } - ] - ], - "cram": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.cram": { - "type": "file", - "description": "Output CRAM file containing read alignments", - "pattern": "*.{cram}", - "ontologies": [] - } - } - ] - ], - "crai": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.crai": { - "type": "file", - "description": "Index file for CRAM file", - "pattern": "*.{crai}", - "ontologies": [] - } - } - ] - ], - "csi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.csi": { - "type": "file", - "description": "Index file for BAM file", - "pattern": "*.{csi}", - "ontologies": [] - } - } - ] - ], - "versions_bwameme": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bwameme": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "1.0.6": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_samtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "Name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "Name of the tool" - } - }, - { - "samtools version | sed \"1!d;s/.* //\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bwameme": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "1.0.6": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "Name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "Name of the tool" - } - }, - { - "samtools version | sed \"1!d;s/.* //\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@ramprasadn" - ], - "maintainers": [ - "@ramprasadn" - ] - }, - "pipelines": [ - { - "name": "raredisease", - "version": "3.0.0" - } - ] - }, - { - "name": "bwameth_align", - "path": "modules/nf-core/bwameth/align/meta.yml", - "type": "module", - "meta": { - "name": "bwameth_align", - "description": "Performs alignment of BS-Seq reads using bwameth", - "keywords": [ - "bwameth", - "alignment", - "3-letter genome", - "map", - "methylation", - "5mC", - "methylseq", - "bisulphite", - "bisulfite", - "fastq", - "bam" - ], - "tools": [ - { - "bwameth": { - "description": "Fast and accurate alignment of BS-Seq reads\nusing bwa-mem and a 3-letter genome.\n", - "homepage": "https://github.com/brentp/bwa-meth", - "documentation": "https://github.com/brentp/bwa-meth", - "arxiv": "arXiv:1401.1129", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input genome fasta file", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "index": { - "type": "directory", - "description": "Directory containing bwameth genome index" - } - } - ] - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "Output BAM file containing read alignments", - "pattern": "*.{bam}", - "ontologies": [] - } - } - ] - ], - "versions_bwameth": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bwameth": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bwameth.py --version | cut -f2 -d ' '": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_samtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of samtools" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bwameth": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bwameth.py --version | cut -f2 -d ' '": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of samtools" - } - } - ] - ] - }, - "authors": [ - "@phue" - ], - "maintainers": [ - "@phue" - ] - }, - "pipelines": [ - { - "name": "methylseq", - "version": "4.2.0" - } - ] - }, - { - "name": "bwameth_index", - "path": "modules/nf-core/bwameth/index/meta.yml", - "type": "module", - "meta": { - "name": "bwameth_index", - "description": "Performs indexing of c2t converted reference genome", - "keywords": [ - "bwameth", - "3-letter genome", - "index", - "methylseq", - "bisulphite", - "bisulfite", - "fasta" - ], - "tools": [ - { - "bwameth": { - "description": "Fast and accurate alignment of BS-Seq reads\nusing bwa-mem and a 3-letter genome.\n", - "homepage": "https://github.com/brentp/bwa-meth", - "documentation": "https://github.com/brentp/bwa-meth", - "arxiv": "arXiv:1401.1129", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input genome fasta file", - "ontologies": [] - } - } - ], - { - "use_mem2": { - "type": "boolean", - "description": "If true, use bwameth index-mem2 for indexing. If false, use bwameth index (default: false)\n" - } - } - ], - "output": { - "index": [ - [ - { - "meta": { - "type": "directory", - "description": "Directory containing bwameth genome index", - "pattern": "index" - } - }, - { - "BwamethIndex": { - "type": "directory", - "description": "Directory containing bwameth genome index", - "pattern": "index" - } - } - ] - ], - "versions_bwameth_index": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bwameth": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bwameth.py --version | cut -f2 -d' '": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bwameth": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bwameth.py --version | cut -f2 -d' '": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@phue" - ], - "maintainers": [ - "@phue", - "@sateeshperi" - ] - }, - "pipelines": [ - { - "name": "methylseq", - "version": "4.2.0" - } - ] - }, - { - "name": "caalm_caalm", - "path": "modules/nf-core/caalm/caalm/meta.yml", - "type": "module", - "meta": { - "name": "caalm_caalm", - "description": "Annotates carbohydrate-active enzyme (CAZyme) families from protein sequences\nusing protein language model (ESM) embeddings and FAISS-based nearest-neighbour\nsearch. Performs three-level hierarchical classification: binary CAZyme detection\n(Level 0), CAZy class assignment (Level 1), and CAZy family assignment (Level 2).\n", - "keywords": [ - "cazyme", - "annotation", - "protein", - "language model", - "deep learning", - "classification" - ], - "tools": [ - { - "caalm": { - "description": "CAALM (Carbohydrate Activity Annotation with protein Language Models) predicts\nCAZyme class and family membership from protein FASTA sequences using ESM-based\nembeddings and FAISS nearest-neighbour retrieval.\n", - "homepage": "https://github.com/lczong/CAALM", - "documentation": "https://github.com/lczong/CAALM", - "tool_dev_url": "https://github.com/lczong/CAALM", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Protein sequences in FASTA format.", - "pattern": "*.{fa,fasta,faa}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - [ - { - "level0": { - "type": "directory", - "description": "Directory containing the Level 0 (binary CAZyme detection) model files,\nas produced by CAALM_DOWNLOADMODELS.\n", - "pattern": "models/level0", - "ontologies": [] - } - }, - { - "level1": { - "type": "directory", - "description": "Directory containing the Level 1 (CAZy class assignment) model files,\nas produced by CAALM_DOWNLOADMODELS.\n", - "pattern": "models/level1", - "ontologies": [] - } - }, - { - "level2": { - "type": "directory", - "description": "Directory containing the Level 2 (CAZy family assignment) model files,\nas produced by CAALM_DOWNLOADMODELS.\n", - "pattern": "models/level2", - "ontologies": [] - } - } - ] - ], - "output": { - "predictions": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}_predictions.tsv": { - "type": "file", - "description": "Tab-separated file with per-sequence CAZy class and family predictions\nacross all three classification levels.\n", - "pattern": "*_predictions.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "probabilities": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}_probabilities.jsonl": { - "type": "file", - "description": "JSON Lines file with per-sequence probability scores at all three\nclassification levels.\n", - "pattern": "*_probabilities.jsonl", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "statistics": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}_statistics.tsv": { - "type": "file", - "description": "Tab-separated summary file with counts and percentages of predicted\nCAZyme classes and families across the input sequences.\n", - "pattern": "*_statistics.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "embeddings_level0": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}_level0_embeddings.npy": { - "type": "file", - "description": "NumPy array file containing Level 0 ESM embeddings for each input\nsequence. Optional; produced when `--save-level0-embeddings` is passed.\n", - "pattern": "*_level0_embeddings.npy", - "ontologies": [] - } - } - ] - ], - "embeddings_level1": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}_level1_embeddings.npy": { - "type": "file", - "description": "NumPy array file containing Level 1 projected embeddings for each input\nsequence. Optional; produced when `--save-level1-embeddings` is passed.\n", - "pattern": "*_level1_embeddings.npy", - "ontologies": [] - } - } - ] - ], - "embeddings_level2": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}_level2_embeddings.npy": { - "type": "file", - "description": "NumPy array file containing Level 2 projected embeddings for each input\nsequence. Optional; produced when `--save-level2-embeddings` is passed.\n", - "pattern": "*_level2_embeddings.npy", - "ontologies": [] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}.log": { - "type": "file", - "description": "Log file containing the stdout and stderr output of the caalm run.", - "pattern": "*.log", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2330" - } - ] - } - } - ] - ], - "versions_caalm": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "caalm": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "caalm --version 2>&1 | head -1": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_python": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "python": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python --version | sed 's/Python //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_torch": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "torch": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python -c 'import torch; print(torch.__version__)'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_faiss": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "faiss": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python -c 'import faiss; print(faiss.__version__)'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "caalm": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "caalm --version 2>&1 | head -1": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "python": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python --version | sed 's/Python //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "torch": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python -c 'import torch; print(torch.__version__)'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "faiss": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python -c 'import faiss; print(faiss.__version__)'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@vagkaratzas" - ], - "maintainers": [ - "@vagkaratzas" - ] - } - }, - { - "name": "caalm_downloadmodels", - "path": "modules/nf-core/caalm/downloadmodels/meta.yml", - "type": "module", - "meta": { - "name": "caalm_downloadmodels", - "description": "Downloads the CAALM model weights from HuggingFace Hub (lczong/CAALM) into a\nlocal models/ directory. The downloaded directory is used as input to the\nCAALM_CAALM annotation module for CAZyme prediction.\n", - "keywords": [ - "cazyme", - "model", - "download", - "huggingface", - "deep learning" - ], - "tools": [ - { - "huggingface_hub": { - "description": "huggingface_hub is a Python library for interacting with the Hugging Face Hub,\nproviding utilities for downloading and uploading models, datasets, and spaces.\n", - "homepage": "https://github.com/huggingface/huggingface_hub", - "documentation": "https://huggingface.co/docs/huggingface_hub", - "tool_dev_url": "https://github.com/huggingface/huggingface_hub", - "licence": [ - "Apache-2.0" - ], - "identifier": "" - } - } - ], - "input": [], - "output": { - "models": [ - [ - { - "models/level0": { - "type": "directory", - "description": "Directory containing the Level 0 (binary CAZyme detection) model files\ndownloaded from HuggingFace Hub (lczong/CAALM).\n", - "pattern": "models/level0", - "ontologies": [] - } - }, - { - "models/level1": { - "type": "directory", - "description": "Directory containing the Level 1 (CAZy class assignment) model files\ndownloaded from HuggingFace Hub (lczong/CAALM).\n", - "pattern": "models/level1", - "ontologies": [] - } - }, - { - "models/level2": { - "type": "directory", - "description": "Directory containing the Level 2 (CAZy family assignment) model files\ndownloaded from HuggingFace Hub (lczong/CAALM), including the FAISS index,\nreference database, and model weights.\n", - "pattern": "models/level2", - "ontologies": [] - } - } - ] - ], - "versions_huggingface_hub": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "huggingface_hub": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python -c 'import huggingface_hub; print(huggingface_hub.__version__)'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_python": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "python": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python --version | sed 's/Python //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "huggingface_hub": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python -c 'import huggingface_hub; print(huggingface_hub.__version__)'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "python": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python --version | sed 's/Python //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@vagkaratzas" - ], - "maintainers": [ - "@vagkaratzas" - ] - } - }, - { - "name": "cadd", - "path": "modules/nf-core/cadd/meta.yml", - "type": "module", - "meta": { - "name": "cadd", - "description": "CADD is a tool for scoring the deleteriousness of single nucleotide variants as well as insertion/deletions variants in the human genome.", - "keywords": [ - "cadd", - "annotate", - "variants" - ], - "tools": [ - { - "cadd": { - "description": "CADD scripts release for offline scoring", - "homepage": "https://cadd.gs.washington.edu/", - "documentation": "https://github.com/kircherlab/CADD-scripts/blob/master/README.md", - "tool_dev_url": "https://github.com/kircherlab/CADD-scripts/", - "doi": "10.1093/nar/gky1016", - "licence": [ - "Restricted. Free for non-commercial users." - ], - "identifier": "biotools:cadd_phred" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "Input file for annotation in vcf or vcf.gz format", - "pattern": "*.{vcf,vcf.gz}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "annotation_dir": { - "type": "directory", - "description": "Path to folder containing the vcf files with precomputed CADD scores.\nThis folder contains the uncompressed files that would otherwise be in data/annotation folder as described in https://github.com/kircherlab/CADD-scripts/#manual-installation.\n" - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "prescored_dir": { - "type": "directory", - "description": "Path to folder containing prescored CADD score files.\nExpected structure mirrors data/prescored/ from the CADD-scripts installation:\n /\n GRCh38_v1.7/\n incl_anno/ # *.tsv.gz + *.tsv.gz.tbi (scores with annotations)\n no_anno/ # *.tsv.gz + *.tsv.gz.tbi (scores only)\n GRCh37_v1.7/\n incl_anno/\n no_anno/\nSee https://github.com/kircherlab/CADD-scripts/#manual-installation for details.\n" - } - } - ] - ], - "output": { - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.tsv.gz": { - "type": "file", - "description": "Annotated tsv file", - "pattern": "*.{tsv,tsv.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_cadd": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cadd": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "1.7.3": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cadd": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "1.7.3": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@ramprasadn" - ], - "maintainers": [ - "@ramprasadn" - ] - }, - "pipelines": [ - { - "name": "raredisease", - "version": "3.0.0" - } - ] - }, - { - "name": "cafe", - "path": "modules/nf-core/cafe/meta.yml", - "type": "module", - "meta": { - "name": "cafe", - "description": "Analysis of gene family evolution", - "keywords": [ - "gene", - "phylogeny", - "genomics" - ], - "tools": [ - { - "cafe": { - "description": "Computational Analysis of gene Family Evolution (CAFE)", - "homepage": "https://github.com/hahnlab/CAFE5", - "documentation": "https://github.com/hahnlab/CAFE5", - "tool_dev_url": "https://github.com/hahnlab/CAFE5", - "doi": "10.1093/bioinformatics/btaa1027", - "licence": [ - "IU OPEN SOURCE LICENSE (see https://github.com/hahnlab/CAFE5/blob/master/LICENSE)" - ], - "identifier": "biotools:CaFE_Calculation_of_Free_Energy" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "infile": { - "type": "file", - "description": "Gene counts table (from OrthoMCL, SwiftOrtho, FastOrtho, OrthAgogue or OrthoFinder)", - "pattern": "*.{txt,tsv,tab}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - { - "tree": { - "type": "file", - "description": "Newick formatted tree", - "pattern": "*.{txt}", - "ontologies": [] - } - } - ], - "output": { - "cafe": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "${prefix}": { - "type": "directory", - "description": "A folder with all the cafe output" - } - } - ] - ], - "cafe_base_count": [ - { - "$prefix/*_count.tab": { - "type": "file", - "description": "File containing counts of genes per orthogroup", - "pattern": "*_count.tab", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - "cafe_significant_trees": [ - { - "$prefix/*.tre": { - "type": "file", - "description": "File containing significant trees (newick format)", - "pattern": "*.tre", - "ontologies": [] - } - } - ], - "cafe_report": [ - { - "$prefix/*_report.cafe": { - "type": "file", - "description": "File containing the final report from cafe", - "pattern": "*_report.cafe", - "ontologies": [] - } - } - ], - "cafe_results": [ - { - "$prefix/*results.txt": { - "type": "file", - "description": "File containing the main result files from cafe", - "pattern": "*results.txt", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2330" - } - ] - } - } - ], - "versions_cafe": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cafe": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "echo 5.1.0": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cafe": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "echo 5.1.0": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@chriswyatt1" - ], - "maintainers": [ - "@chriswyatt1" - ] - } - }, - { - "name": "calder2", - "path": "modules/nf-core/calder2/meta.yml", - "type": "module", - "meta": { - "name": "calder2", - "description": "Hierarchical Hi-C compartment computation", - "keywords": [ - "calder2", - "genome", - "topology", - "compartments", - "domains", - "hi-c" - ], - "tools": [ - { - "calder2": { - "description": "Hierarchical Hi-C compartment computation", - "homepage": "https://github.com/CSOgroup/CALDER2", - "documentation": "https://github.com/CSOgroup/CALDER2", - "tool_dev_url": "https://github.com/CSOgroup/CALDER2", - "doi": "10.1038/s41467-021-22666-3", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information. E.g. [ id:'test', single_end:false ]" - } - }, - { - "cool": { - "type": "file", - "description": "Path to COOL file", - "pattern": "*.{cool.mcool}", - "ontologies": [] - } - } - ], - { - "resolution": { - "type": "integer", - "description": "In case a .mcool file is provided, which resolution level to use for the analysis" - } - } - ], - "output": { - "output_folder": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information. E.g. [ id:'test', single_end:false ]" - } - }, - { - "${prefix}/": { - "type": "directory", - "description": "Output folder containing sub-compartment (.tsv/.bed) and domain boundaries calls (.bed)" - } - } - ] - ], - "intermediate_data_folder": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information. E.g. [ id:'test', single_end:false ]" - } - }, - { - "${prefix}/intermediate_data/": { - "type": "directory", - "description": "Output folder containing intermediate data produced during the computation" - } - } - ] - ], - "versions_calder": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "calder": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "0.7": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "calder": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "0.7": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@lucananni93" - ], - "maintainers": [ - "@lucananni93" - ] - } - }, - { - "name": "canu", - "path": "modules/nf-core/canu/meta.yml", - "type": "module", - "meta": { - "name": "canu", - "description": "Accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads.", - "keywords": [ - "Assembly", - "pacbio", - "hifi", - "nanopore" - ], - "tools": [ - { - "canu": { - "description": "Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing.", - "homepage": "https://canu.readthedocs.io/en/latest/index.html#", - "documentation": "https://canu.readthedocs.io/en/latest/tutorial.html", - "tool_dev_url": "https://github.com/marbl/canu", - "doi": "10.1101/gr.215087.116", - "licence": [ - "GPL v2 and others" - ], - "identifier": "biotools:canu" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:true ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "fasta/fastq file", - "pattern": "*.{fasta,fastq}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ], - { - "mode": { - "type": "string", - "description": "Canu mode depending on the input data (source and error rate)", - "pattern": "-pacbio|-nanopore|-pacbio-hifi" - } - }, - { - "genomesize": { - "type": "string", - "description": "An estimate of the size of the genome. Common suffices are allowed, for example, 3.7m or 2.8g", - "pattern": "[g|m|k]" - } - } - ], - "output": { - "report": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.report": { - "type": "file", - "description": "Most of the analysis reported during assembly", - "pattern": "*.report", - "ontologies": [] - } - } - ] - ], - "assembly": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.contigs.fasta.gz": { - "type": "file", - "description": "Everything which could be assembled and is the full assembly, including both unique, repetitive, and bubble elements.", - "pattern": "*.contigs.fasta", - "ontologies": [] - } - } - ] - ], - "contigs": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.unassembled.fasta.gz": { - "type": "file", - "description": "Reads and low-coverage contigs which could not be incorporated into the primary assembly.", - "pattern": "*.unassembled.fasta", - "ontologies": [] - } - } - ] - ], - "corrected_reads": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.correctedReads.fasta.gz": { - "type": "file", - "description": "The reads after correction.", - "pattern": "*.correctedReads.fasta.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "corrected_trimmed_reads": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.trimmedReads.fasta.gz": { - "type": "file", - "description": "The corrected reads after overlap based trimming", - "pattern": "*.trimmedReads.fasta.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "metadata": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.contigs.layout": { - "type": "file", - "description": "(undocumented)", - "pattern": "*.contigs.layout", - "ontologies": [] - } - } - ] - ], - "contig_position": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.contigs.layout.readToTig": { - "type": "file", - "description": "The position of each read in a contig", - "pattern": "*.contigs.layout.readToTig", - "ontologies": [] - } - } - ] - ], - "contig_info": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.contigs.layout.tigInfo": { - "type": "file", - "description": "A list of the contigs, lengths, coverage, number of reads and other metadata. Essentially the same information provided in the FASTA header line.", - "pattern": "*.contigs.layout.tigInfo", - "ontologies": [] - } - } - ] - ], - "versions_canu": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "canu": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "2.3": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_minimap2": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "minimap2": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "minimap2 --version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_samtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "canu": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "2.3": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "minimap2": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "minimap2 --version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@scorreard" - ], - "maintainers": [ - "@scorreard" - ] - }, - "pipelines": [ - { - "name": "bacass", - "version": "2.6.0" - } - ] - }, - { - "name": "canvas_germline", - "path": "modules/nf-core/canvas/germline/meta.yml", - "type": "module", - "meta": { - "name": "canvas_germline", - "description": "Calls germline copy number variants (CNVs) from whole genome sequencing data using\nIllumina Canvas in SmallPedigree-WGS mode. Although named SmallPedigree-WGS, this\nmode is recommended for single germline samples as well as small pedigrees.\nThe module accepts aligned reads (BAM), germline SNV calls, and sex-specific ploidy\ninformation, and outputs a VCF with copy number status across the genome together\nwith a coverage-and-variant-frequency file used for downstream segmentation.\n", - "keywords": [ - "CNV", - "copy number variants", - "germline", - "WGS", - "canvas" - ], - "tools": [ - { - "canvas": { - "description": "Canvas is a tool for calling copy number variants (CNVs) from human DNA sequencing data.\n", - "homepage": "https://github.com/Illumina/canvas", - "documentation": "https://github.com/Illumina/canvas/wiki", - "tool_dev_url": "https://github.com/Illumina/canvas", - "licence": [ - "GPL-3.0" - ], - "identifier": "" + }, + { + "name": "centrifuger_quantification", + "path": "modules/nf-core/centrifuger/quantification/meta.yml", + "type": "module", + "meta": { + "name": "centrifuger_quantification", + "description": "Quantification (taxonomic profiling) of Centrifuger model", + "keywords": ["metagenomics", "quantification", "Centrifuger"], + "tools": [ + { + "centrifuger": { + "description": "Centrifuger is an efficient taxonomic classification method that compares sequencing reads against a microbial genome database.", + "homepage": "https://github.com/mourisl/centrifuger", + "documentation": "https://github.com/mourisl/centrifuger", + "tool_dev_url": "https://github.com/mourisl/centrifuger", + "doi": "10.1186/s13059-024-03244-4", + "licence": ["MIT"], + "identifier": "biotools:centrifuger" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' single_end:false ]`" + } + }, + { + "classification_file": { + "type": "file", + "description": "Path to file containing classification results" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information. e.g. `[ id:'sample1', single_end:false ]`" + } + }, + { + "db": { + "type": "directory", + "description": "Path to directory containing Centrifuger database files (that end in `.cfr`)." + } + } + ], + { + "taxonomy_nodes": { + "type": "file", + "description": "File describing parent-child relationships of a taxonomic tree in NCBI nodes.dmp format", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1964" + } + ] + } + }, + { + "taxonomy_names": { + "type": "file", + "description": "File describing individual members of a taxonomic tree in NCBI names.dmp format", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1964" + } + ] + } + }, + { + "size_table": { + "type": "file", + "description": "Optional - Table of contig (or genome) sizes." + } + } + ], + "output": { + "report_file": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" + } + }, + { + "${meta.id}.tsv": { + "type": "file", + "description": "File containing taxonomic profiling results\n", + "pattern": "${prefix}.tsv" + } + } + ] + ], + "versions_centrifuger": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "centrifuger": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "centrifuger -v 2>&1 | sed 's/Centrifuger v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "centrifuger": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "centrifuger -v 2>&1 | sed 's/Centrifuger v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@haris18s"], + "maintainers": ["@haris18s", "@sofstam", "@jfy133"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information.\ne.g. `[ id:'sample1' ]`\n", - "ontologies": [] - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM file of aligned WGS reads.", - "pattern": "*.bam", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } + }, + { + "name": "checkm2_databasedownload", + "path": "modules/nf-core/checkm2/databasedownload/meta.yml", + "type": "module", + "meta": { + "name": "checkm2_databasedownload", + "description": "CheckM2 database download", + "keywords": ["checkm", "mag", "metagenome", "quality", "completeness", "contamination", "bins"], + "tools": [ + { + "checkm2": { + "description": "CheckM2 - Rapid assessment of genome bin quality using machine learning", + "homepage": "https://github.com/chklovski/CheckM2", + "doi": "10.1038/s41592-023-01940-w", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + { + "db_zenodo_id": { + "type": "integer", + "description": "Zenodo ID of the CheckM2 database to download" + } + } + ], + "output": { + "database": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing database information\ne.g. `[ id:'test', version:1 ]`\n" + } + }, + { + "checkm2_db_v${db_version}.dmnd": { + "type": "file", + "description": "CheckM2 database file", + "pattern": "checkm2_db_v*.dmnd", + "ontologies": [] + } + } + ] + ], + "versions_checkm2_databasedownload": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "aria2": { + "type": "string", + "description": "The tool name" + } + }, + { + "aria2c --version 2>&1 | sed '1s/[^ ]* [^ ]* //; q'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "aria2": { + "type": "string", + "description": "The tool name" + } + }, + { + "aria2c --version 2>&1 | sed '1s/[^ ]* [^ ]* //; q'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@dialvarezs", "@eit-maxlcummins"] }, - { - "bai": { - "type": "file", - "description": "BAM index file.", - "pattern": "*.bai", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3327" - } - ] - } - } - ], - { - "germline_snv_vcf": { - "type": "file", - "description": "VCF (or gzipped VCF) containing germline SNV b-allele sites (PASS filter only).\nTypically produced by a variant caller such as DNAscope or DeepVariant.\n", - "pattern": "*.{vcf,vcf.gz}", - "ontologies": [ + "pipelines": [ { - "edam": "http://edamontology.org/format_3016" + "name": "mag", + "version": "5.4.2" + }, + { + "name": "seqsubmit", + "version": "dev" } - ] - } - }, - [ - { - "sex": { - "type": "string", - "description": "Sample sex. Must be either \"male\" or \"female\". Used to select the\nappropriate ploidy VCF for sex chromosomes.\n" - } - }, - { - "male_ploidy_vcf": { - "type": "file", - "description": "VCF defining expected ploidy for sex chromosomes in male samples.\nBoth ploidy VCFs (male and female) must always be provided. The module\nautomatically selects the correct one based on the sex value.\nThe sample name in the VCF header is automatically updated to match the SM tag in the BAM header.\nExpected format (hg38 example):\n\n```\n##fileformat=VCFv4.1\n##INFO=\n##FORMAT=\n#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE\nchrX 0 . N . PASS END=10001 CN 1\nchrX 2781479 . N . PASS END=155701383 CN 1\nchrX 156030895 . N . PASS END=156040895 CN 1\nchrY 0 . N . PASS END=57227415 CN 1\n```\n", - "pattern": "*.vcf", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - } - ] - } + ] + }, + { + "name": "checkm2_predict", + "path": "modules/nf-core/checkm2/predict/meta.yml", + "type": "module", + "meta": { + "name": "checkm2_predict", + "description": "CheckM2 bin quality prediction", + "keywords": ["checkm", "mag", "metagenome", "quality", "completeness", "contamination", "bins"], + "tools": [ + { + "checkm2": { + "description": "CheckM2 - Rapid assessment of genome bin quality using machine learning", + "homepage": "https://github.com/chklovski/CheckM2", + "doi": "10.1038/s41592-023-01940-w", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "One or multiple FASTA files of each bin", + "pattern": "*.{fasta,fna,fa}", + "ontologies": [] + } + } + ], + [ + { + "dbmeta": { + "type": "map", + "description": "Groovy Map containing database information\ne.g. `[ id:'test', version:1 ]`\n" + } + }, + { + "db": { + "type": "file", + "description": "CheckM2 database", + "ontologies": [] + } + } + ] + ], + "output": { + "checkm2_output": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "${prefix}": { + "type": "directory", + "description": "CheckM2 output directory", + "pattern": "${prefix}/" + } + } + ] + ], + "checkm2_tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "${prefix}_checkm2_report.tsv": { + "type": "file", + "description": "CheckM2 summary completeness statistics table", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_checkm2_predict": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "checkm2": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "checkm2 --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "checkm2": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "checkm2 --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@dialvarezs", "@eit-maxlcummins"] }, - { - "female_ploidy_vcf": { - "type": "file", - "description": "VCF defining expected ploidy for sex chromosomes in female samples.\nBoth ploidy VCFs (male and female) must always be provided. The module\nautomatically selects the correct one based on the sex value.\nThe sample name in the VCF header is automatically updated to match the SM tag in the BAM header.\nExpected format (hg38 example):\n\n```\n##fileformat=VCFv4.1\n##INFO=\n##FORMAT=\n#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE\nchrY 0 . N . PASS END=57227415 CN 0\n```\n", - "pattern": "*.vcf", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - } - ] - } - } - ], - { - "genomedir": { - "type": "directory", - "description": "Canvas genome reference directory containing genome.fa and GenomeSize.xml.\nAvailable for GRCh37/hg19/GRCh38 from s3://canvas-cnv-public.\n" - } - }, - { - "reference": { - "type": "file", - "description": "Canvas-ready kmer reference file (kmer.fa).\nAvailable from s3://canvas-cnv-public.\n", - "pattern": "*.fa", - "ontologies": [ + "pipelines": [ { - "edam": "http://edamontology.org/format_1929" - } - ] - } - }, - { - "filter13": { - "type": "file", - "description": "BED file of regions to exclude from CNV calling (e.g. centromeres, telomeres).\nNamed filter13 following Canvas reference package conventions.\nAvailable from s3://canvas-cnv-public.\n", - "pattern": "*.bed", - "ontologies": [ + "name": "mag", + "version": "5.4.2" + }, { - "edam": "http://edamontology.org/format_3003" + "name": "seqsubmit", + "version": "dev" } - ] - } - } - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information.\ne.g. `[ id:'sample1' ]`\n", - "ontologies": [] - } - }, - { - "${prefix}.vcf.gz": { - "type": "file", - "description": "Bgzipped VCF file containing germline CNV calls. Canvas:REF entries (non-variant regions)\nare excluded. Requires further annotation for standard SV ALT notation.\n", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - } - ] - } - } - ] - ], - "covandvarfreq": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information.\ne.g. `[ id:'sample1' ]`\n", - "ontologies": [] - } - }, - { - "${prefix}.CoverageAndVariantFrequency.txt": { - "type": "file", - "description": "Tab-separated file with per-bin coverage and variant allele frequency values.\nUsed as input for CANVAS_CREATESEG to generate segmentation files.\n", - "pattern": "*.CoverageAndVariantFrequency.txt", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_canvas": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "canvas": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "1.40.0": { - "type": "string", - "description": "The version of the tool (hardcoded as Canvas is an archived tool)" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "canvas": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "1.40.0": { - "type": "string", - "description": "The version of the tool (hardcoded as Canvas is an archived tool)" - } - } - ] - ] - }, - "authors": [ - "@ktruve" - ], - "maintainers": [ - "@ktruve" - ] - } - }, - { - "name": "carveme_carve", - "path": "modules/nf-core/carveme/carve/meta.yml", - "type": "module", - "meta": { - "name": "carveme_carve", - "description": "Reconstruct genome-scale metabolic models from protein FASTA files using CarveMe", - "keywords": [ - "metabolic model", - "genome-scale", - "sbml", - "flux balance analysis", - "metabolic reconstruction" - ], - "tools": [ - { - "carveme": { - "description": "CarveMe is a python-based tool for genome-scale metabolic model reconstruction.", - "homepage": "https://carveme.readthedocs.io", - "documentation": "https://carveme.readthedocs.io", - "tool_dev_url": "https://github.com/cdanielmachado/carveme", - "doi": "10.1093/nar/gky537", - "licence": [ - "Apache-2.0" - ], - "identifier": "biotools:carveme" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Protein FASTA file\nor DNA fasta file if the --dna flag is provided\n", - "pattern": "*.{fa,faa,fasta,fna}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - }, - { - "universe_file": { - "type": "file", - "description": "Optional. Reaction universe file in SBML format, passed to --universe-file.", - "pattern": "*.xml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2332" - } - ] - } - }, - { - "mediadb": { - "type": "file", - "description": "Optional. Media database file, passed to --mediadb.\n--gapfill X,Y,Z with medium names from the database must also be provided\n", - "pattern": "*.{tsv,csv,txt}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - }, - { - "edam": "http://edamontology.org/format_3752" - }, - { - "edam": "http://edamontology.org/format_2330" - } - ] - } - }, - { - "soft": { - "type": "file", - "description": "Optional. Soft constraints file, passed to --soft.", - "pattern": "*.{tsv,csv,txt}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - }, - { - "edam": "http://edamontology.org/format_3752" - }, - { - "edam": "http://edamontology.org/format_2330" - } - ] - } - }, - { - "hard": { - "type": "file", - "description": "Optional. Hard constraints file, passed to --hard.", - "pattern": "*.{tsv,csv,txt}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - }, - { - "edam": "http://edamontology.org/format_3752" - }, - { - "edam": "http://edamontology.org/format_2330" - } - ] - } - }, - { - "reference": { - "type": "file", - "description": "Optional. Manually curated model of a close reference species, passed to --reference.", - "pattern": "*.xml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2332" - } - ] - } - } - ] - ], - "output": { - "model": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}.xml": { - "type": "file", - "description": "SBML genome-scale metabolic model file", - "pattern": "*.xml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2332" - } - ] - } - } - ] - ], - "gene_scores": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}_gene_scores.tsv": { - "type": "file", - "description": "Optional. Tab-separated file produced when --debug is passed. Maps each query gene to its\ncorresponding BiGG gene identifier, protein group, reaction, source model, and BLAST\nbit-score used during model reconstruction.\n", - "pattern": "*_gene_scores.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "milp_problem": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}_milp_problem.lp": { - "type": "file", - "description": "Optional. Linear programming problem file in LP format produced when --debug is passed.\nContains the MILP formulation (variables, constraints, and objective function) passed to\nthe SCIP solver during gap-filling or reaction selection.\n", - "pattern": "*_milp_problem.lp", - "ontologies": [] - } - } ] - ], - "milp_solution": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}_milp_solution.tsv": { - "type": "file", - "description": "Optional. Tab-separated file produced when --debug is passed. Contains the MILP solver\nsolution, listing each reaction identifier and its corresponding flux value selected\nduring model gap-filling.\n", - "pattern": "*_milp_solution.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "protein_scores": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}_protein_scores.tsv": { - "type": "file", - "description": "Optional. Tab-separated file produced when --debug is passed. Lists the BLAST alignment\nscores for each query protein against the template model database, including the matched\nprotein group, reaction, source model, and GPR rule used for scoring.\n", - "pattern": "*_protein_scores.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "reaction_scores": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}_reaction_scores.tsv": { - "type": "file", - "description": "Optional. Tab-separated file produced when --debug is passed. Lists each candidate\nreaction with its GPR rule, raw BLAST bit-score, and normalised score used to weight\nthe MILP objective during model reconstruction.\n", - "pattern": "*_reaction_scores.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_carveme": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "carveme": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pip show carveme | sed -n 's/^Version: //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "carveme": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pip show carveme | sed -n 's/^Version: //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@vagkaratzas" - ], - "maintainers": [ - "@vagkaratzas" - ] - } - }, - { - "name": "cat_cat", - "path": "modules/nf-core/cat/cat/meta.yml", - "type": "module", - "meta": { - "name": "cat_cat", - "description": "A module for concatenation of gzipped or uncompressed files", - "deprecated": true, - "keywords": [ - "concatenate", - "gzip", - "cat" - ], - "tools": [ - { - "cat": { - "description": "Just concatenation", - "documentation": "https://man7.org/linux/man-pages/man1/cat.1.html", - "licence": [ - "GPL-3.0-or-later" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "files_in": { - "type": "file", - "description": "List of compressed / uncompressed files", - "pattern": "*", - "ontologies": [] - } - } - ] - ], - "output": { - "file_out": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "${prefix}": { - "type": "file", - "description": "Concatenated file. Will be gzipped if file_out ends with \".gz\"", - "pattern": "${file_out}", - "ontologies": [] - } - } - ] - ], - "versions_cat": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pigz": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pigz --version 2>&1 | sed 's/pigz //g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pigz": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pigz --version 2>&1 | sed 's/pigz //g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@erikrikarddaniel", - "@FriederikeHanssen" - ], - "maintainers": [ - "@erikrikarddaniel", - "@FriederikeHanssen" - ] - }, - "pipelines": [ - { - "name": "circrna", - "version": "dev" - }, - { - "name": "denovotranscript", - "version": "1.2.1" - }, - { - "name": "epitopeprediction", - "version": "3.1.0" - }, - { - "name": "magmap", - "version": "1.0.0" - }, - { - "name": "marsseq", - "version": "1.0.3" - }, - { - "name": "metatdenovo", - "version": "1.3.0" - }, - { - "name": "nascent", - "version": "2.3.0" - }, - { - "name": "phageannotator", - "version": "dev" }, { - "name": "raredisease", - "version": "3.0.0" + "name": "checkm_lineagewf", + "path": "modules/nf-core/checkm/lineagewf/meta.yml", + "type": "module", + "meta": { + "name": "checkm_lineagewf", + "description": "CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.", + "keywords": [ + "checkm", + "mag", + "metagenome", + "quality", + "isolates", + "microbes", + "single cells", + "completeness", + "contamination", + "bins", + "genome bins" + ], + "tools": [ + { + "checkm": { + "description": "Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes.", + "homepage": "https://ecogenomics.github.io/CheckM/", + "documentation": "https://github.com/Ecogenomics/CheckM/wiki", + "tool_dev_url": "https://github.com/Ecogenomics/CheckM", + "doi": "10.1101/gr.186072.114", + "licence": ["GPL v3"], + "identifier": "biotools:checkm" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "One or a list of multiple FASTA files of each bin, with extension defined with the fasta_ext value", + "pattern": "*.{$fasta_ext}", + "ontologies": [] + } + } + ], + { + "fasta_ext": { + "type": "string", + "description": "The file-type extension suffix of the input FASTA files (e.g., fasta, fna, fa, fas)" + } + }, + { + "db": { + "type": "directory", + "description": "Optional directory pointing to checkM database to prevent re-downloading" + } + } + ], + "output": { + "checkm_output": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample', bin:'1' ]\n" + } + }, + { + "${prefix}": { + "type": "directory", + "description": "CheckM output directory", + "pattern": "*/" + } + } + ] + ], + "marker_file": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample', bin:'1' ]\n" + } + }, + { + "${prefix}/lineage.ms": { + "type": "file", + "description": "Lineage file", + "pattern": "*.ms", + "ontologies": [] + } + } + ] + ], + "checkm_tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample', bin:'1' ]\n" + } + }, + { + "${prefix}.tsv": { + "type": "file", + "description": "CheckM summary completeness statistics table", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_checkm": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "checkm": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "checkm 2>&1 | grep '...:::' | sed 's/.*CheckM v//;s/ .*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "checkm": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "checkm 2>&1 | grep '...:::' | sed 's/.*CheckM v//;s/ .*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@jfy133"], + "maintainers": ["@jfy133"] + }, + "pipelines": [ + { + "name": "mag", + "version": "5.4.2" + } + ] }, { - "name": "reportho", - "version": "1.1.0" + "name": "checkm_qa", + "path": "modules/nf-core/checkm/qa/meta.yml", + "type": "module", + "meta": { + "name": "checkm_qa", + "description": "CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.", + "keywords": [ + "checkm", + "mag", + "metagenome", + "quality", + "isolates", + "microbes", + "single cells", + "completeness", + "contamination", + "bins", + "genome bins", + "qa", + "quality assurnce" + ], + "tools": [ + { + "checkm": { + "description": "Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes.", + "homepage": "https://ecogenomics.github.io/CheckM/", + "documentation": "https://github.com/Ecogenomics/CheckM/wiki", + "tool_dev_url": "https://github.com/Ecogenomics/CheckM", + "doi": "10.1101/gr.186072.114", + "licence": ["GPL v3"], + "identifier": "biotools:checkm" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "analysis_dir": { + "type": "file", + "description": "Directory containing output of checkm/analyze or checkm/lineage_wf etc.", + "pattern": "*", + "ontologies": [] + } + }, + { + "marker_file": { + "type": "file", + "description": "Marker file specified during checkm/analyze or produced by checkm/{lineage,taxonomy}_wf", + "pattern": "*.ms", + "ontologies": [] + } + }, + { + "coverage_file": { + "type": "file", + "description": "File containing coverage of each sequence (generated by checkm coverage)", + "ontologies": [] + } + } + ], + { + "exclude_marker_file": { + "type": "file", + "description": "File specifying markers to exclude from marker sets", + "ontologies": [] + } + }, + { + "db": { + "type": "directory", + "description": "CheckM database directory", + "ontologies": [] + } + } + ], + "output": { + "output": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.txt": { + "type": "file", + "description": "Default completeness statistics in various formats, as specified with --out_format (excluding option: 9)", + "pattern": "*.txt", + "ontologies": [] + } + } + ] + ], + "fasta": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.fasta": { + "type": "file", + "description": "Output in fasta format (only if --out_format 9)", + "pattern": "*.fasta", + "ontologies": [] + } + } + ] + ], + "versions_checkm": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "checkm": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "checkm 2>&1 | grep '...:::' | sed 's/.*CheckM v//;s/ .*//'": { + "type": "eval", + "description": "The expression to obtain the 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"http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "*_logging_info.txt": { + "type": "file", + "description": "File contains the log information", + "pattern": "*_logging_info.txt", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + } + ] + ], + "paralogous_counts": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "*_paralogous_counts.tsv": { + "type": "file", + "description": "File contains the list of paralogous loci and the number of times those loci matched a CDS that was also similar to other loci in the schema", + "pattern": "*_paralogous_counts.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "paralogous_loci": [ + [ + { + "meta": { + "type": "map", 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] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "chewbbaca": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "chewie --version 2>&1 | sed 's/chewBBACA version: //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@anwarMZ"] + } }, { - "name": "variantbenchmarking", - "version": "1.5.0" + "name": "chewbbaca_createschema", + "path": "modules/nf-core/chewbbaca/createschema/meta.yml", + "type": "module", + "meta": { + "name": "chewbbaca_createschema", + "description": "Create a schema to determine the allelic profiles of a genome", + "keywords": ["cgMLST", "WGS", "genomics"], + "tools": [ + { + "chewbbaca": { + "description": "A complete suite for gene-by-gene schema creation and strain identification.", + "homepage": "https://chewbbaca.readthedocs.io/en/latest/index.html", + "documentation": "https://chewbbaca.readthedocs.io/en/latest/index.html", + "tool_dev_url": "https://github.com/B-UMMI/chewBBACA", + "doi": "10.1099/mgen.0.000166", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "fasta": { + "type": "directory", + "description": "One or multiple FASTA files to create schema from", + "pattern": "*.{fasta,fa,fas,fna,fasta.gz,fa.gz,fas.gz,fna.gz}" + } + } + ], + { + "prodigal_tf": { + "type": "file", + "description": "File containing the prodigal training file", + "pattern": "*.ptf", + "ontologies": [] + } + }, + { + "cds": { + "type": "file", + "description": "File containing the prodigal cds file", + "pattern": "*.cds", + "ontologies": [] + } + } + ], + "output": { + "schema": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "results/$meta.id": { + "type": "directory", + "description": "Schema directory", + "pattern": "*/" + } + } + ] + ], + "cds_coordinates": [ + { + "results/cds_coordinates.tsv": { + "type": "file", + "description": "File containing the coordinates of the CDS in the input sample", + "pattern": "*_cds_coordinates.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + "invalid_cds": [ + { + "results/invalid_cds.txt": { + "type": "file", + "description": "File containing the list of alleles predicted by Prodigal that were excluded", + "pattern": "*_invalid_cds.txt", + "ontologies": [] + } + } + ], + "versions_chewbbaca": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "chewbbaca": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "chewie --version 2>&1 | sed 's/chewBBACA version: //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "chewbbaca": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "chewie --version 2>&1 | sed 's/chewBBACA version: //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@anwarMZ"] + } }, { - "name": "viralmetagenome", - "version": "1.1.1" - } - ] - }, - { - "name": "cat_fastq", - "path": "modules/nf-core/cat/fastq/meta.yml", - "type": "module", - "meta": { - "name": "cat_fastq", - "description": "Concatenates fastq files. Supports both compressed (.gz) and uncompressed inputs; uncompressed files are automatically gzip-compressed during concatenation.", - "keywords": [ - "cat", - "fastq", - "concatenate", - "compress" - ], - "tools": [ - { - "cat": { - "description": "The cat utility reads files sequentially, writing them to the standard output.\n", - "documentation": "https://www.gnu.org/software/coreutils/manual/html_node/cat-invocation.html", - "licence": [ - "GPL-3.0-or-later" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + "name": "chopper", + "path": "modules/nf-core/chopper/meta.yml", + "type": "module", + "meta": { + "name": "chopper", + "description": "Filter and trim long read data.", + "keywords": ["filter", "trimming", "fastq", "nanopore", "qc"], + "tools": [ + { + "zcat": { + "description": "zcat uncompresses either a list of files on the command line or its standard input and writes the uncompressed data on standard output.", + "documentation": "https://linux.die.net/man/1/zcat", + "args_id": "$args", + "identifier": "" + } + }, + { + "chopper": { + "description": "A rust command line for filtering and trimming long reads.", + "homepage": "https://github.com/wdecoster/chopper", + "documentation": "https://github.com/wdecoster/chopper", + "tool_dev_url": "https://github.com/wdecoster/chopper", + "doi": "10.1093/bioinformatics/bty149", + "licence": ["MIT"], + "args_id": "$args2", + "identifier": "" + } + }, + { + "gzip": { + "description": "Gzip reduces the size of the named files using Lempel-Ziv coding (LZ77).", + "documentation": "https://linux.die.net/man/1/gzip", + "args_id": "$args3", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fastq": { + "type": "file", + "description": "FastQ with reads from long read sequencing e.g. PacBio or ONT", + "pattern": "*.{fastq.gz}", + "ontologies": [] + } + } + ], + { + "fasta": { + "type": "file", + "description": "An optional reference fasta file against which to remove reads that align to it.", + "pattern": "*.fasta", + "ontologies": [] + } + } + ], + "output": { + "fastq": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fastq.gz": { + "type": "file", + "description": "Filtered and trimmed FastQ file", + "pattern": "*.{fastq.gz}", + "ontologies": [] + } + } + ] + ], + "versions_chopper": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "chopper": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "chopper --version 2>&1 | cut -d ' ' -f 2": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "chopper": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "chopper --version 2>&1 | cut -d ' ' -f 2": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@FynnFreyer"], + "maintainers": ["@FynnFreyer"] }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files to be concatenated.\nAccepts both gzip-compressed (.fastq.gz) and uncompressed (.fastq) files.\n", - "ontologies": [] - } - } - ] - ], - "output": { - "reads": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.merged.fastq.gz": { - "type": "file", - "description": "Merged fastq file", - "pattern": "*.{merged.fastq.gz}", - "ontologies": [] - } - } - ] - ], - "versions_cat": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "cat": { - "type": "string", - "description": "The tool name" - } - }, - { - "cat --version 2>&1 | head -n 1 | sed 's/^.*coreutils) //; s/ .*\\$//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "cat": { - "type": "string", - "description": "The tool name" - } - }, - { - "cat --version 2>&1 | head -n 1 | sed 's/^.*coreutils) //; s/ .*\\$//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "mag", + "version": "5.4.2" + } ] - ] - }, - "authors": [ - "@joseespinosa", - "@drpatelh" - ], - "maintainers": [ - "@joseespinosa", - "@drpatelh" - ] - }, - "pipelines": [ - { - "name": "airrflow", - "version": "5.0.0" }, { - "name": "bacass", - "version": "2.6.0" - }, - { - "name": "bamtofastq", - "version": "2.2.1" + "name": "chromap_chromap", + "path": "modules/nf-core/chromap/chromap/meta.yml", + "type": "module", + "meta": { + "name": "chromap_chromap", + "description": "Performs preprocessing and alignment of chromatin fastq files to fasta reference files using chromap.\n", + "keywords": [ + "chromap", + "alignment", + "map", + "fastq", + "bam", + "sam", + "hi-c", + "atac-seq", + "chip-seq", + "trimming", + "duplicate removal" + ], + "tools": [ + { + "chromap": { + "description": "Fast alignment and preprocessing of chromatin profiles\n", + "homepage": "https://github.com/haowenz/chromap", + "documentation": "https://github.com/haowenz/chromap", + "tool_dev_url": "https://github.com/haowenz/chromap", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing information for the fasta\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference genome FASTA file", + "pattern": "*.{fa,fasta,fna}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing information for the index\ne.g. [ id:'test' ]\n" + } + }, + { + "index": { + "type": "file", + "description": "Chromap genome index files (*.index)\n", + "ontologies": [] + } + } + ], + { + "barcodes": { + "type": "file", + "description": "Cell barcode files\n", + "ontologies": [] + } + }, + { + "whitelist": { + "type": "file", + "description": "Cell barcode whitelist file\n", + "ontologies": [] + } + }, + { + "chr_order": { + "type": "file", + "description": "Custom chromosome order\n", + "ontologies": [] + } + }, + { + "pairs_chr_order": { + "type": "file", + "description": "Natural chromosome order for pairs flipping\n", + "ontologies": [] + } + } + ], + "output": { + "bed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed.gz": { + "type": "file", + "description": "BED file", + "pattern": "*.bed.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "BAM file", + "pattern": "*.bam", + "ontologies": [] + } + } + ] + ], + "tagAlign": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tagAlign.gz": { + "type": "file", + "description": "tagAlign file", + "pattern": "*.tagAlign.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "pairs": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.pairs.gz": { + "type": "file", + "description": "pairs file", + "pattern": "*.pairs.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "versions_chromap": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "chromap": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "chromap --version 2>&1": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_samtools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "samtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "samtools version | sed '1!d;s/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "chromap": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "chromap --version 2>&1": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "samtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "samtools version | sed '1!d;s/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@mahesh-panchal", "@joseespinosa"], + "maintainers": ["@mahesh-panchal", "@joseespinosa"] + }, + "pipelines": [ + { + "name": "atacseq", + "version": "2.1.2" + }, + { + "name": "chipseq", + "version": "2.1.0" + } + ] }, { - "name": "circdna", - "version": "1.1.0" + "name": "chromap_index", + "path": "modules/nf-core/chromap/index/meta.yml", + "type": "module", + "meta": { + "name": "chromap_index", + "description": "Indexes a fasta reference genome ready for chromatin profiling.", + "keywords": ["index", "fasta", "genome", "reference"], + "tools": [ + { + "chromap": { + "description": "Fast alignment and preprocessing of chromatin profiles", + "homepage": "https://github.com/haowenz/chromap", + "documentation": "https://github.com/haowenz/chromap", + "tool_dev_url": "https://github.com/haowenz/chromap", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference genome FASTA file", + "pattern": "*.{fa,fasta,fna}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ] + ], + "output": { + "index": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.index": { + "type": "file", + "description": "Index file of the reference genome", + "pattern": "*.{index}", + "ontologies": [] + } + } + ] + ], + "versions_chromap": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "chromap": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "chromap --version 2>&1": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "chromap": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "chromap --version 2>&1": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@mahesh-panchal", "@joseespinosa"], + "maintainers": ["@mahesh-panchal", "@joseespinosa"] + }, + "pipelines": [ + { + "name": "atacseq", + "version": "2.1.2" + }, + { + "name": "chipseq", + "version": "2.1.0" + } + ] }, { - "name": "circrna", - "version": "dev" + "name": "chromograph", + "path": "modules/nf-core/chromograph/meta.yml", + "type": "module", + "meta": { + "name": "chromograph", + "description": "Chromograph is a python package to create PNG images from genetics data such as BED and WIG files.", + "keywords": ["chromosome_visualization", "bed", "wig", "png"], + "tools": [ + { + "chromograph": { + "description": "Chromograph is a python package to create PNG images from genetics data such as BED and WIG files.", + "homepage": "https://github.com/Clinical-Genomics/chromograph", + "documentation": "https://github.com/Clinical-Genomics/chromograph/blob/master/README.md", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "autozyg": { + "type": "file", + "description": "Bed file containing the regions of autozygosity", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "coverage": { + "type": "file", + "description": "Wig file containing the coverage information", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "exome": { + "type": "file", + "description": "Bed file containing the coverage for exome.", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fracsnp": { + "type": "file", + "description": "Wig file containing the fraction of homozygous SNPs", + "ontologies": [] + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "ideogram": { + "type": "file", + "description": "Bed file containing information necessary for ideogram plots.\nFormat ['chrom', 'start', 'end', 'name', 'gStain']\n", + "ontologies": [] + } + } + ], + [ + { + "meta6": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "regions": { + "type": "file", + "description": "Bed file containing UPD regions", + "ontologies": [] + } + } + ], + [ + { + "meta7": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "sites": { + "type": "file", + "description": "Bed file containing UPD sites", + "ontologies": [] + } + } + ] + ], + "output": { + "plots": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.png": { + "type": "file", + "description": "Plot(s) in PNG format", + "ontologies": [] + } + } + ] + ], + "versions_chromograph": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "chromograph": { + "type": "string", + "description": "The tool name" + } + }, + { + "chromograph --version | sed 's/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "chromograph": { + "type": "string", + "description": "The tool name" + } + }, + { + "chromograph --version | sed 's/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@ramprasadn"], + "maintainers": ["@ramprasadn"] + }, + "pipelines": [ + { + "name": "raredisease", + "version": "3.0.0" + } + ] }, { - "name": "crisprseq", - "version": "2.3.0" + "name": "circexplorer2_annotate", + "path": "modules/nf-core/circexplorer2/annotate/meta.yml", + "type": "module", + "meta": { + "name": "circexplorer2_annotate", + "description": "Annotate circRNAs detected in the output from CIRCexplorer2 parse", + "keywords": ["rna", "circrna", "annotate"], + "tools": [ + { + "circexplorer2": { + "description": "Circular RNA analysis toolkits", + "homepage": "https://github.com/YangLab/CIRCexplorer2/", + "documentation": "https://circexplorer2.readthedocs.io/en/latest/", + "doi": "10.1101/gr.202895.115", + "licence": ["MIT License"], + "identifier": "biotools:CIRCexplorer2" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "junctions": { + "type": "file", + "description": "Reformatted junctions file", + "pattern": "*.{junction}", + "ontologies": [] + } + } + ], + { + "fasta": { + "type": "file", + "description": "Genome FASTA file", + "pattern": "*.{fa,fasta}", + "ontologies": [] + } + }, + { + "gene_annotation": { + "type": "file", + "description": "Reformatted GTF file for CIRCexplorer2", + "pattern": "*.{txt}", + "ontologies": [] + } + } + ], + "output": { + "txt": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "Annotated circRNA TXT file", + "pattern": "*.{txt}", + "ontologies": [] + } + } + ] + ], + "versions_circexplorer2": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "circexplorer2": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "CIRCexplorer2 --version 2>&1; true": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "circexplorer2": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "CIRCexplorer2 --version 2>&1; true": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@BarryDigby"], + "maintainers": ["@BarryDigby"] + }, + "pipelines": [ + { + "name": "circrna", + "version": "dev" + } + ] }, { - "name": "cutandrun", - "version": "3.2.2" + "name": "circexplorer2_parse", + "path": "modules/nf-core/circexplorer2/parse/meta.yml", + "type": "module", + "meta": { + "name": "circexplorer2_parse", + "description": "CIRCexplorer2 parses fusion junction files from multiple aligners to prepare them for CIRCexplorer2 annotate.", + "keywords": ["parse", "circrna", "splice"], + "tools": [ + { + "circexplorer2": { + "description": "Circular RNA analysis toolkit", + "homepage": "https://github.com/YangLab/CIRCexplorer2/", + "documentation": "https://circexplorer2.readthedocs.io/en/latest/", + "doi": "10.1101/gr.202895.115", + "licence": ["MIT License"], + "identifier": "biotools:CIRCexplorer2" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fusions": { + "type": "file", + "description": "BAM (BWA), BED (Segemehl), TXT (MapSplice), or Junction (STAR) file. Aligner will be autodetected based on file suffix.", + "pattern": "*.{bam,junction,bed,txt}", + "ontologies": [] + } + } + ] + ], + "output": { + "junction": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "BED file", + "pattern": "*.bed", + "ontologies": [] + } + } + ] + ], + "versions_circexplorer2": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "circexplorer2": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "CIRCexplorer2 --version 2>&1; true": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "circexplorer2": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "CIRCexplorer2 --version 2>&1; true": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@BarryDigby"], + "maintainers": ["@BarryDigby"] + }, + "pipelines": [ + { + "name": "circrna", + "version": "dev" + } + ] }, { - 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"name": "rnafusion", - "version": "4.1.2" + "name": "circularmapper_realignsamfile", + "path": "modules/nf-core/circularmapper/realignsamfile/meta.yml", + "type": "module", + "meta": { + "name": "circularmapper_realignsamfile", + "description": "Realign reads mapped with BWA to elongated reference genome", + "keywords": ["realign", "circular", "map", "reference", "fasta", "bam", "short-read", "bwa"], + "tools": [ + { + "circularmapper": { + "description": "A method to improve mappings on circular genomes such as Mitochondria.", + "homepage": "https://circularmapper.readthedocs.io/en/latest/index.html", + "documentation": "https://circularmapper.readthedocs.io/en/latest/index.html", + "tool_dev_url": "https://github.com/apeltzer/CircularMapper/", + "doi": "10.1186/s13059-016-0918-z", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/SAM file", + "pattern": "*.{bam,sam}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input elongated genome fasta", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "elongation_factor": { + "type": "integer", + "description": "The elongation factor used when running circulargenerator, i.e. the number of bases that the ends of the target chromosome in the reference genome was elongated by" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "elongated_chr_list": { + "type": "file", + "description": "File listing the chromosomes that were elongated", + "pattern": "*_elongated", + "ontologies": [] + } + } + ] + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*_realigned.bam": { + "type": "file", + "description": "Realigned BAM file", + "pattern": "*.bam", + "ontologies": [] + } + } + ] + ], + "versions_circularmapper": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "circularmapper": { + "type": "string", + "description": "The tool name" + } + }, + { + "1.93.5": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "circularmapper": { + "type": "string", + "description": "The tool name" + } + }, + { + "1.93.5": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@shyama-mama", "@jbv2", "@TCLamnidis"] + } }, { - "name": "rnaseq", - "version": "3.26.0" + "name": "civicpy_annotate", + "path": "modules/nf-core/civicpy/annotate/meta.yml", + "type": "module", + "meta": { + "name": "civicpy_annotate", + "description": "A python client and analysis toolkit to annotate variants with information from the Clinical Interpretations of Variants in Cancer (CIViC) knowledgebase", + "keywords": ["clinical interpretation", "variant annotation", "genetic variation analysis", "genomics"], + "tools": [ + { + "civicpy": { + "description": "CIViC variant knowledgebase analysis toolkit.", + "homepage": "https://docs.civicpy.org/en/latest/", + "documentation": "https://docs.civicpy.org/en/latest/", + "tool_dev_url": "https://github.com/griffithlab/civicpy", + "doi": "10.1200/CCI.19.00127", + "licence": ["MIT"], + "identifier": "biotools:CIViCpy" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "vcf": { + "type": "file", + "description": "Sorted and indexed VCF file", + "pattern": "*.{vcf}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + } + ] + } + }, + { + "tbi": { + "type": "file", + "description": "Tabix index for the input VCF", + "pattern": "*.tbi", + "ontologies": [] + } + } + ], + { + "annotation_genome_version": { + "type": "string", + "description": "Reference genome version passed to civicpy (e.g. GRCh38)" + } + }, + { + "cache": { + "type": "file", + "description": "Optional civicpy cache file (*.pkl). If not provided, civicpy will download and cache data locally.", + "pattern": "*.pkl", + "ontologies": [] + } + } + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "Annotated bgzipped VCF file", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "versions_civicpy": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "civicpy": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "civicpy --version | sed 's/.*version //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_htslib": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "htslib": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bgzip --version 2>&1 | head -1 | sed 's/bgzip (htslib) //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "civicpy": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "civicpy --version | sed 's/.*version //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "htslib": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bgzip --version 2>&1 | head -1 | sed 's/bgzip (htslib) //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@emmcauley"], + "maintainers": ["@emmcauley"] + } }, { - "name": "rnasplice", - "version": "1.0.4" + "name": "clair3", + "path": "modules/nf-core/clair3/meta.yml", + "type": "module", + "meta": { + "name": "clair3", + "description": "Clair3 is a germline small variant caller for long-reads", + "keywords": ["germline", "variant", "Indel", "SNV"], + "tools": [ + { + "clair3": { + "description": "Clair3 is a small variant caller for long-reads. Compare to PEPPER (r0.4), Clair3 (v0.1) shows a better SNP F1-score with ≤30-fold of ONT data (precisionFDA Truth Challenge V2), and a better Indel F1-score, while runs generally four times faster. Clair3 makes the best of both worlds of using pileup or full-alignment as input for deep-learning based long-read small variant calling. Clair3 is simple and modular for easy deployment and integration.", + "homepage": "https://github.com/HKU-BAL/Clair3", + "documentation": "https://github.com/HKU-BAL/Clair3", + "tool_dev_url": "https://github.com/HKU-BAL/Clair3", + "doi": "10.1038/s43588-022-00387-x", + "licence": ["BSD-3-clause"], + "identifier": "biotools:clair3" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "bam": { + "type": "file", + "description": "Sorted BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_25722" + }, + { + "edam": "http://edamontology.org/format_2573" + }, + { + "edam": "http://edamontology.org/format_3462" + } + ] + } + }, + { + "bai": { + "type": "file", + "description": "BAM index file", + "pattern": "*.bai", + "ontologies": [] + } + }, + { + "packaged_model": { + "type": "string", + "description": "string containing the name of a prepackaged Clair3 model full list of models and their descriptions is provided at https://github.com/HKU-BAL/Clair3?tab=readme-ov-file#pre-trained-models" + } + }, + { + "user_model": { + "type": "directory", + "description": "directory containing Clair3 model files" + } + }, + { + "platform": { + "type": "string", + "description": "val in ['hifi','ont', 'ilmn'] to indicate pacbio, ONT, or illumina respectively" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "reference": { + "type": "file", + "description": "reference fasta file", + "pattern": "*.fasta", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "index": { + "type": "file", + "description": "reference index file", + "pattern": "*.fai", + "ontologies": [] + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n", + "pattern": "*.{vcf,vcf.gz}" + } + }, + { + "${prefix}merge_output.vcf.gz": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n", + "pattern": "*.{vcf,vcf.gz}" + } + } + ] + ], + "tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n", + "pattern": "*.{vcf,vcf.gz}" + } + }, + { + "${prefix}merge_output.vcf.gz.tbi": { + "type": "file", + "description": "index for vcf files", + "pattern": "*.{vcf.tbi,vcf.tbi.gz}", + "ontologies": [] + } + } + ] + ], + "phased_vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n", + "pattern": "*.{vcf,vcf.gz}" + } + }, + { + "${prefix}phased_merge_output.vcf.gz": { + "type": "file", + "description": "phased vcf", + "pattern": "*.{vcf,vcf.gz}", + "ontologies": [] + } + } + ] + ], + "phased_tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n", + "pattern": "*.{vcf,vcf.gz}" + } + }, + { + "${prefix}phased_merge_output.vcf.gz.tbi": { + "type": "file", + "description": "index for vcf files", + "pattern": "*.{vcf.tbi,vcf.tbi.gz}", + "ontologies": [] + } + } + ] + ], + "gvcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n", + "pattern": "*.{vcf,vcf.gz}" + } + }, + { + "${prefix}merge_output.gvcf.gz": { + "type": "file", + "description": "gvcf file", + "pattern": "*.{gvcf,gvcf.gz}", + "ontologies": [] + } + } + ] + ], + "gtbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n", + "pattern": "*.{vcf,vcf.gz}" + } + }, + { + "${prefix}merge_output.gvcf.gz.tbi": { + "type": "file", + "description": "index for gvcf file", + "pattern": "*.{vcf.tbi,vcf.tbi.gz}", + "ontologies": [] + } + } + ] + ], + "versions_clair3": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "clair3": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "run_clair3.sh --version | sed \"s/^Clair3 v//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "clair3": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "run_clair3.sh --version | sed \"s/^Clair3 v//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@robert-a-forsyth"], + "maintainers": ["@robert-a-forsyth"] + }, + "pipelines": [ + { + "name": "methylong", + "version": "2.0.0" + }, + { + "name": "pacsomatic", + "version": "dev" + } + ] }, { - "name": "rnavar", - "version": "1.2.3" + "name": "clame", + "path": "modules/nf-core/clame/meta.yml", + "type": "module", + "meta": { + "name": "clame", + "description": "binning of metagenomic sequences", + "keywords": ["sort", "genomics", "binning", "metagenomics"], + "tools": [ + { + "clame": { + "description": "CLAME is a binning software for metagenomic reads. It immplements a fm-index search algorithm for nucleotide sequence alignment. Then it uses strongly connected component strategy to bin sequences with similar DNA composition.", + "homepage": "https://github.com/andvides/CLAME", + "documentation": "https://github.com/andvides/CLAME", + "tool_dev_url": "https://github.com/andvides/CLAME", + "doi": "10.1186/s12864-018-5191-y", + "licence": ["GPLv3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Nucleotide sequences in FASTA format", + "pattern": "*.{fasta,fa,fna,faa}", + "ontologies": [] + } + } + ] + ], + "output": { + "fasta": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.fasta": { + "type": "file", + "description": "Output fasta file for all the bins reported, optional since it will be created when bins can be found", + "pattern": "*.{fasta}", + "ontologies": [] + } + } + ] + ], + "bins": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.binning": { + "type": "file", + "description": "All bins reported", + "pattern": "*.{binning}", + "ontologies": [] + } + } + ] + ], + "fm": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.fm9": { + "type": "file", + "description": "FM-index output", + "pattern": "*.{fm9}", + "ontologies": [] + } + } + ] + ], + "index": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.index": { + "type": "file", + "description": "1st column contains the original name for each read, 2nd column the index used by CLAME", + "pattern": "*.{index}", + "ontologies": [] + } + } + ] + ], + "links": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.links": { + "type": "file", + "description": "Histogram links by number of reads", + "pattern": "*.{links}", + "ontologies": [] + } + } + ] + ], + "result": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.result": { + "type": "file", + "description": "Adjacency list for the overlap detected by each read", + "pattern": "*.{result}", + "ontologies": [] + } + } + ] + ], + "versions_clame": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "clame": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "clame -h 2>&1 | sed '2!d;s/version //;s/ .*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "clame": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "clame -h 2>&1 | sed '2!d;s/version //;s/ .*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@alxndrdiaz"] + } }, { - "name": "sammyseq", - "version": "dev" + "name": "clipkit", + "path": "modules/nf-core/clipkit/meta.yml", + "type": "module", + "meta": { + "name": "clipkit", + "description": "A multiple sequence alignment-trimming algorithm for accurate phylogenomic inference.", + "keywords": ["alignment", "trimming", "phylogeny"], + "tools": [ + { + "clipkit": { + "description": "ClipKIT is a fast and flexible alignment trimming tool that keeps\nphylogenetically informative sites and removes those with poor phylogenetic signal.\n", + "homepage": "https://jlsteenwyk.com/ClipKIT/", + "documentation": "https://jlsteenwyk.com/ClipKIT/", + "tool_dev_url": "https://github.com/JLSteenwyk/ClipKIT", + "doi": "10.1371/journal.pbio.3001007", + "licence": ["MIT"], + "identifier": "biotools:clipkit" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "aln": { + "type": "file", + "description": "Multiple sequence alignment file in various supported formats.", + "pattern": "*.{fa,fasta,fna,faa,alnfaa,aln,sto,stk,mauve,alignment,clustal}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1921" + }, + { + "edam": "http://edamontology.org/format_1984" + }, + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + { + "out_format": { + "type": "string", + "description": "Output format (aln,msa,fas,etc.), default is clipkit.", + "pattern": "*" + } + }, + { + "auxiliary_file": { + "type": "file", + "description": "Optional tab-delimited auxiliary file specifying which sites to keep or\ntrim. Used in conjunction with the custom site trimming (cst) mode.\n", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + "output": { + "clipkit": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}.${out_extension}": { + "type": "file", + "description": "Trimmed multiple sequence alignment file.", + "pattern": "*.*", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1921" + }, + { + "edam": "http://edamontology.org/format_1984" + } + ] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}.${out_extension}.log": { + "type": "file", + "description": "Log file with per-site trimming statistics from ClipKIT execution.", + "pattern": "*.log", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + } + ] + ], + "metadata": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}.${out_extension}.txt": { + "type": "file", + "description": "Tab-delimited text file with per-site statistics including site position,\nparsimony-informativeness status, and whether the site was kept or trimmed.\n", + "pattern": "*.txt", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + } + ] + ], + "complementary": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}.${out_extension}.complement": { + "type": "file", + "description": "File containing the trimmed/removed sites from the alignment, i.e. the\ncomplement of the clipkit output. Optional; only produced when the\ncomplementary input is true (passes `-c` to clipkit).\n", + "pattern": "*.complement", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1921" + } + ] + } + } + ] + ], + "json": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}.${out_extension}.report.json": { + "type": "file", + "description": "JSON report file with summary statistics of the trimming run.\nOptional; only produced when ClipKIT is run with the appropriate reporting flag.\n", + "pattern": "*.report.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "versions_clipkit": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "clipkit": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "clipkit --version 2>&1 | sed 's/clipkit //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "clipkit": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "clipkit --version 2>&1 | sed 's/clipkit //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@vagkaratzas"], + "maintainers": ["@vagkaratzas"] + }, + "pipelines": [ + { + "name": "proteinfamilies", + "version": "2.3.0" + } + ] }, { - 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"name": "smrnaseq", - "version": "2.4.1" + "name": "clustalo_align", + "path": "modules/nf-core/clustalo/align/meta.yml", + "type": "module", + "meta": { + "name": "clustalo_align", + "description": "Align sequences using Clustal Omega", + "keywords": ["alignment", "MSA", "genomics"], + "tools": [ + { + "clustalo": { + "description": "Latest version of Clustal: a multiple sequence alignment program for DNA or proteins", + "homepage": "http://www.clustal.org/omega/", + "documentation": "http://www.clustal.org/omega/", + "tool_dev_url": "http://www.clustal.org/omega/", + "doi": "10.1038/msb.2011.75", + "licence": ["GPL v2"], + "identifier": "" + } + }, + { + "pigz": { + "description": "Parallel implementation of the gzip algorithm.", + "homepage": "https://zlib.net/pigz/", + "documentation": "https://zlib.net/pigz/pigz.pdf", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input sequences in FASTA format", + "pattern": "*.{fa,fasta,faa,fna}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1919" + }, + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing tree information\ne.g. `[ id:'test_tree']`\n" + } + }, + { + "tree": { + "type": "file", + "description": "Input guide tree in Newick format", + "pattern": "*.{dnd}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2006" + } + ] + } + } + ], + { + "hmm_in": { + "type": "file", + "description": "HMM file for profile alignment", + "pattern": "*.hmm", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1391" + } + ] + } + }, + { + "hmm_batch": { + "type": "file", + "description": "specify HMMs for individual sequences", + "pattern": "*.hmm", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1391" + } + ] + } + }, + { + "profile1": { + "type": "file", + "description": "Pre-aligned multiple sequence file 1", + "pattern": "*.{alnfaa,faa,fa,fasta}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + }, + { + "edam": "http://edamontology.org/format_2554" + }, + { + "edam": "http://edamontology.org/format_1921" + }, + { + "edam": "http://edamontology.org/format_1984" + } + ] + } + }, + { + "profile2": { + "type": "file", + "description": "Pre-aligned multiple sequence file 2", + "pattern": "*.{alnfaa,faa,fa,fasta}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + }, + { + "edam": "http://edamontology.org/format_2554" + }, + { + "edam": "http://edamontology.org/format_1921" + }, + { + "edam": "http://edamontology.org/format_1984" + } + ] + } + }, + { + "compress": { + "type": "boolean", + "description": "Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded." + } + } + ], + "output": { + "alignment": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" + } + }, + { + "*.aln{.gz,}": { + "type": "file", + "description": "Alignment file, in gzipped fasta format", + "pattern": "*.aln{.gz,}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2554" + }, + { + "edam": "http://edamontology.org/format_1921" + }, + { + "edam": "http://edamontology.org/format_1984" + } + ] + } + } + ] + ], + "versions_clustalo": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "clustalo": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "clustalo --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_pigz": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "pigz": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pigz --version 2>&1 | sed \"s/^.*pigz[[:space:]]*//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "clustalo": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "clustalo --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "pigz": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pigz --version 2>&1 | sed \"s/^.*pigz[[:space:]]*//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@luisas", "@joseespinosa"], + "maintainers": ["@luisas", "@joseespinosa", "@lrauschning"] + }, + "pipelines": [ + { + "name": "ampliseq", + "version": "2.17.0" + }, + { + "name": "multiplesequencealign", + "version": "1.1.1" + }, + { + "name": "phyloplace", + "version": "2.0.0" + } + ] }, { - "name": "taxprofiler", - "version": "2.0.0" + "name": "clustalo_guidetree", + "path": "modules/nf-core/clustalo/guidetree/meta.yml", + "type": "module", + "meta": { + "name": "clustalo_guidetree", + "description": "Renders a guidetree in clustalo", + "keywords": ["guide tree", "msa", "newick"], + "tools": [ + { + "clustalo": { + "description": "Latest version of Clustal: a multiple sequence alignment program for DNA or proteins", + "homepage": "http://www.clustal.org/omega/", + "documentation": "http://www.clustal.org/omega/", + "tool_dev_url": "http://www.clustal.org/omega/", + "doi": "10.1038/msb.2011.75", + "licence": ["GPL v2"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input sequences in FASTA format", + "pattern": "*.{fa,fasta}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1919" + }, + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ] + ], + "output": { + "tree": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" + } + }, + { + "*.dnd": { + "type": "file", + "description": "Guide tree file in Newick format", + "pattern": "*.{dnd}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2006" + } + ] + } + } + ] + ], + "versions_clustalo": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "clustalo": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "clustalo --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "clustalo": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "clustalo --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@luisas", "@JoseEspinosa"], + "maintainers": ["@luisas", "@JoseEspinosa"] + }, + "pipelines": [ + { + "name": "multiplesequencealign", + "version": "1.1.1" + } + ] }, { - "name": "viralmetagenome", - "version": "1.1.1" + "name": "clusty", + "path": "modules/nf-core/clusty/meta.yml", + "type": "module", + "meta": { + "name": "clusty", + "description": "Clusty is a tool for large-scale clustering using sparse distance matrices, suitable for datasets with millions of objects.", + "keywords": ["cluster", "network", "contig", "scaffold", "alignment", "protein"], + "tools": [ + { + "clusty": { + "description": "Clusty is a tool for large-scale data clustering.", + "homepage": "https://github.com/refresh-bio/clusty", + "documentation": "https://github.com/refresh-bio/clusty", + "tool_dev_url": "https://github.com/refresh-bio/clusty", + "doi": "10.1038/s41592-025-02701-7", + "licence": ["GPL v3-or-later"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "distances": { + "type": "file", + "description": "pairwise distances file (e.g., TSV format)", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "objects": { + "type": "file", + "description": "Optional TSV file containing object identifiers", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "output": { + "assignments": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "TSV file with cluster assignments", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_clusty": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "clusty": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "echo $(clusty --version 2>&1": { + "type": "string", + "description": "The version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "clusty": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "echo $(clusty --version 2>&1": { + "type": "string", + "description": "The version of the tool" + } + } + ] + ] + }, + "authors": ["@Joon-Klaps"], + "maintainers": ["@Joon-Klaps"] + }, + "pipelines": [ + { + "name": "viralmetagenome", + "version": "1.1.1" + } + ] }, { - "name": "viralrecon", - "version": "3.0.0" - } - ] - }, - { - "name": "catpack_addnames", - "path": "modules/nf-core/catpack/addnames/meta.yml", - "type": "module", - "meta": { - "name": "catpack_addnames", - "description": "Taxonomic classification of long DNA sequences and metagenome assembled genomes (e.g. MAGs / bins).", - "keywords": [ - "taxonomic classification", - "classification", - "long reads", - "mags", - "assembly" - ], - "tools": [ - { - "catpack": { - "description": "CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)", - "homepage": "https://github.com/MGXlab/CAT_pack", - "documentation": "https://github.com/MGXlab/CAT_pack", - "tool_dev_url": "https://github.com/MGXlab/CAT_pack", - "doi": "10.1186/s13059-019-1817-x", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "input": { - "type": "file", - "description": "Classification or ORF2LCA output file from CAT/BAT/RAT", - "pattern": "*.txt", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } + "name": "cmaple", + "path": "modules/nf-core/cmaple/meta.yml", + "type": "module", + "meta": { + "name": "cmaple", + "description": "Efficient phylogenetic tree reconstruction for sequences using the CMAPLE algorithm", + "keywords": [ + "phylogeny", + "phylogenetic tree", + "maximum likelihood", + "dna", + "amino acid", + "alignment", + "tree reconstruction", + "cmaple", + "iqtree" + ], + "tools": [ + { + "cmaple": { + "description": "CMAPLE (Comprehensive Maximum-likelihood Analysis for Phylogenetic Likelihood Estimation)\nis an efficient implementation of the MAPLE algorithm for phylogenetic tree reconstruction,\nparticularly optimized for pathogen sequences with low divergence such as SARS-CoV-2.\nIt is integrated within IQ-TREE.\n", + "homepage": "https://github.com/iqtree/cmaple", + "documentation": "https://github.com/iqtree/cmaple/wiki/User-Manual", + "tool_dev_url": "https://github.com/iqtree/cmaple", + "doi": "10.1093/molbev/msae134", + "licence": ["GPL-2.0"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "aln": { + "type": "file", + "description": "Multiple sequence alignment file in FASTA, PHYLIP, or MAPLE format.\nCan be gzipped on uncompressed.\n", + "pattern": "*.{fa,fasta,faa,fna,fas,aln,afa,phy,phylip,maple}{.gz,}", + "ontologies": [ + { + "edam": "http://edamontology.org/data_0863" + }, + { + "edam": "http://edamontology.org/format_1929" + }, + { + "edam": "http://edamontology.org/format_1997" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + }, + { + "newick": { + "type": "file", + "description": "A Newick formatted tree based on multiple sequence alignment", + "pattern": "*.{newick,nwk,treefile}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1910" + } + ] + } + } + ] + ], + "output": { + "treefile": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.treefile": { + "type": "file", + "description": "Maximum likelihood phylogenetic tree in Newick format", + "pattern": "*.treefile", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1910" + } + ] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.log": { + "type": "file", + "description": "Log file containing detailed information about the tree reconstruction process", + "pattern": "*.log", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + } + ] + ], + "versions_cmaple": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cmaple": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cmaple --help | grep -m1 -oE \"[0-9]+(\\.[0-9]+)+\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cmaple": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cmaple --help | grep -m1 -oE \"[0-9]+(\\.[0-9]+)+\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@vagkaratzas"], + "maintainers": ["@vagkaratzas"] }, - { - "taxonomy": { - "type": "directory", - "description": "Directory containing taxonomy files: names.dmp, nodes.dmp, acc2taxid.txt", - "pattern": "*/", - "ontologies": [ - { - "edam": "http://edamontology.org/data_1049" - } - ] - } - } - ] - ], - "output": { - "txt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "${prefix}.txt": { - "type": "map", - "description": "CAT/BAT/RAT classification file with added taxonomic names\n", - "pattern": "*.{bam,cram,sam}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_catpack": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "catpack": { - "type": "string", - "description": "The tool name" - } - }, - { - "CAT_pack --version | sed 's/CAT_pack pack v//g;s/ .*//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "catpack": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "CAT_pack --version | sed 's/CAT_pack pack v//g;s/ .*//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "proteinfamilies", + "version": "2.3.0" + } ] - ] }, - "authors": [ - "@jfy133" - ], - "maintainers": [ - "@jfy133" - ] - }, - "pipelines": [ { - "name": "mag", - "version": "5.4.2" + "name": "cmseq_polymut", + "path": "modules/nf-core/cmseq/polymut/meta.yml", + "type": "module", + "meta": { + "name": "cmseq_polymut", + "description": "Calculates polymorphic site rates over protein coding genes", + "keywords": [ + "polymut", + "polymorphic", + "mags", + "assembly", + "polymorphic sites", + "estimation", + "protein coding genes", + "cmseq", + "bam", + "coverage" + ], + "tools": [ + { + "cmseq": { + "description": "Set of utilities on sequences and BAM files", + "homepage": "https://github.com/SegataLab/cmseq", + "documentation": "https://github.com/SegataLab/cmseq", + "tool_dev_url": "https://github.com/SegataLab/cmseq", + "licence": ["MIT License"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file", + "pattern": "*.bam", + "ontologies": [] + } + }, + { + "bai": { + "type": "file", + "description": "BAM index file", + "pattern": "*.bai", + "ontologies": [] + } + }, + { + "gff": { + "type": "file", + "description": "GFF file used to extract protein-coding genes", + "pattern": "*.gff", + "ontologies": [] + } + }, + { + "fasta": { + "type": "file", + "description": "Optional fasta file to run on a subset of references in the BAM file.", + "pattern": ".{fa,fasta,fas,fna}", + "ontologies": [] + } + } + ] + ], + "output": { + "polymut": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "Polymut report in `.txt` format.", + "pattern": "*.txt", + "ontologies": [] + } + } + ] + ], + "versions_cmseq": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "cmseq": { + "type": "string", + "description": "The tool name" + } + }, + { + "VERSION": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "cmseq": { + "type": "string", + "description": "The tool name" + } + }, + { + "VERSION": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@maxibor"], + "maintainers": ["@maxibor"] + } }, { - "name": "seqsubmit", - "version": "dev" - } - ] - }, - { - "name": "catpack_bins", - "path": "modules/nf-core/catpack/bins/meta.yml", - "type": "module", - "meta": { - "name": "catpack_bins", - "description": "Taxonomic classification of long DNA sequences and metagenome assembled genomes (e.g. MAGs / bins).", - "keywords": [ - "taxonomic classification", - "classification", - "long reads", - "mags", - "assembly" - ], - "tools": [ - { - "catpack": { - "description": "CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)", - "homepage": "https://github.com/MGXlab/CAT_pack", - "documentation": "https://github.com/MGXlab/CAT_pack", - "tool_dev_url": "https://github.com/MGXlab/CAT_pack", - "doi": "10.1186/s13059-019-1817-x", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "bins": { - "type": "file", - "description": "One or more nucleotide FASTA file containing binned long DNA sequences.", - "pattern": "*.{fasta,fna,fa,fas}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "database": { - "type": "directory", - "description": "Directory containing CAT_pack database files (e.g. output from CAT_pack prepare)", - "pattern": "*/", - "ontologies": [ - { - "edam": "http://edamontology.org/data_1049" - } - ] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "taxonomy": { - "type": "directory", - "description": "Directory containing CAT_pack taxonomy files (e.g. output from CAT_pack prepare)", - "pattern": "*/", - "ontologies": [ - { - "edam": "http://edamontology.org/data_1049" - } - ] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "proteins": { - "type": "directory", - "description": "Optional pre predicted-made proteins FASTA", - "pattern": "*.{fasta,faa,fa,fas}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - [ - { - "meta5": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } + "name": "cnaqc", + "path": "modules/nf-core/cnaqc/meta.yml", + "type": "module", + "meta": { + "name": "cnaqc", + "description": "Quality control of copy number data from bulk WGS assays", + "keywords": ["WGS", "copy number", "quality control"], + "tools": [ + { + "cnaqc": { + "description": "Copy number quality control", + "homepage": "https://caravagnalab.github.io/CNAqc/", + "documentation": "https://caravagnalab.github.io/CNAqc/", + "tool_dev_url": "https://github.com/caravagnalab/CNAqc", + "licence": ["GPL v3-or-later"], + "identifier": "biotools:cnaqc" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "snv_rds": { + "type": "file", + "description": "R object with mutation data", + "pattern": "*.rds", + "ontologies": [] + } + }, + { + "cna_rds": { + "type": "file", + "description": "R object with copy number data", + "pattern": "*.rds", + "ontologies": [] + } + }, + { + "tumour_sample": { + "type": "string", + "description": "string containing sample name", + "ontologies": [] + } + } + ] + ], + "output": { + "qc_rds": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', tumour_sample:'tumour_sample1_name' ]`\n" + } + }, + { + "*_qc.rds": { + "type": "file", + "description": "R object containing quality control results for the sample", + "pattern": "*{_qc.rds}", + "ontologies": [] + } + } + ] + ], + "data_plot_rds": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', tumour_sample:'tumour_sample1_name' ]`\n" + } + }, + { + "*_data_plot.rds": { + "type": "file", + "description": "R object containing plots of the CNA statistics for the sample", + "pattern": "*{_data_plot.rds}", + "ontologies": [] + } + }, + { + "*_qc_plot.rds": { + "type": "file", + "description": "R object containing plots of the quality control results for the sample", + "pattern": "*{_qc_plot.rds}", + "ontologies": [] + } + } + ] + ], + "qc_plot_rds": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', tumour_sample:'tumour_sample1_name' ]`\n" + } + }, + { + "*_qc_plot.rds": { + "type": "file", + "description": "R object containing plots of the quality control results for the sample", + "pattern": "*{_qc_plot.rds}", + "ontologies": [] + } + } + ] + ], + "plot_pdf_data": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', tumour_sample:'tumour_sample1_name' ]`\n" + } + }, + { + "*_data.pdf": { + "type": "file", + "description": "plots of the CNA statistics for the sample", + "pattern": "*{_data.pdf}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3508" + } + ] + } + } + ] + ], + "plot_pdf_qc": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', tumour_sample:'tumour_sample1_name' ]`\n" + } + }, + { + "*_qc.pdf": { + "type": "file", + "description": "plots of the quality control results for the sample", + "pattern": "*{_qc.pdf}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3508" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "YAML file containing versions of tools used in the module", + "ontologies": [] + } + } + ] + }, + "topics": { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "YAML file containing versions of tools used in the module", + "ontologies": [] + } + } + ] + }, + "authors": ["@vvvirgy"], + "maintainers": ["@vvvirgy"] }, - { - "diamond_table": { - "type": "directory", - "description": "Optional pre-made DIAMOND alignment table", - "pattern": "*", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3751" - } - ] - } - } - ], - { - "bin_suffix": { - "type": "string", - "description": "Suffix to search for in the input files when `bins` is a directory." - } - } - ], - "output": { - "orf2lca": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.ORF2LCA.txt": { - "type": "file", - "description": "A TSV file with per-ORF hit stats and identified lineage", - "pattern": "*.ORF2LCA.txt", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "bin2classification": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.bin2classification.txt": { - "type": "file", - "description": "A TSV file with per-bin hit stats and assignment justification information", - "pattern": "*.bin2classification.txt", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.log": { - "type": "file", - "description": "Log file with run messages and basic statistics", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2330" - } - ] - } - } - ] - ], - "diamond": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.diamond": { - "type": "file", - "description": "Intermediate DIAMOND TSV summary output file with alignment results", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "faa": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.predicted_proteins.faa": { - "type": "file", - "description": "FAA file of DIAMOND predicted proteins hits", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "gff": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.gff": { - "type": "file", - "description": "GFF file of DIAMOND predicted proteins hits", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2305" - } - ] - } - } - ] - ], - "versions_catpack": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "catpack": { - "type": "string", - "description": "The tool name" - } - }, - { - "CAT_pack --version | sed 's/CAT_pack pack v//g;s/ .*//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "catpack": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "CAT_pack --version | sed 's/CAT_pack pack v//g;s/ .*//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "tumourevo", + "version": "dev" + } ] - ] }, - "authors": [ - "@jfy133" - ], - "maintainers": [ - "@jfy133" - ] - }, - "pipelines": [ { - "name": "mag", - "version": "5.4.2" + "name": "cnvkit_access", + "path": "modules/nf-core/cnvkit/access/meta.yml", + "type": "module", + "meta": { + "name": "cnvkit_access", + "description": "Calculate the sequence-accessible coordinates in chromosomes from the given reference genome, output as a BED file.", + "keywords": ["cvnkit", "access", "fasta", "copy number"], + "tools": [ + { + "cnvkit": { + "description": "CNVkit is a Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data.\nIt is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent.\n", + "homepage": "https://cnvkit.readthedocs.io/en/stable/index.html", + "documentation": "https://cnvkit.readthedocs.io/en/stable/index.html", + "tool_dev_url": "https://github.com/etal/cnvkit", + "doi": "10.1371/journal.pcbi.1004873", + "licence": ["Apache-2.0"], + "identifier": "biotools:cnvkit" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Genome FASTA.", + "pattern": "*.fasta", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "exclude_bed": { + "type": "file", + "description": "Additional regions to exclude, in BED format. Can be used multiple times.", + "ontologies": [] + } + } + ] + ], + "output": { + "bed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "File containing accessible regions.", + "pattern": "*.{bed}", + "ontologies": [] + } + } + ] + ], + "versions_cnvkit": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "cnvkit": { + "type": "string", + "description": "The tool name" + } + }, + { + "cnvkit.py version | sed -e \"s/cnvkit v//g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "cnvkit": { + "type": "string", + "description": "The tool name" + } + }, + { + "cnvkit.py version | sed -e \"s/cnvkit v//g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@adamrtalbot", "@priesgo"], + "maintainers": ["@adamrtalbot", "@priesgo"] + } }, { - "name": "seqsubmit", - "version": "dev" - } - ] - }, - { - "name": "catpack_contigs", - "path": "modules/nf-core/catpack/contigs/meta.yml", - "type": "module", - "meta": { - "name": "catpack_contigs", - "description": "Taxonomic classification of long DNA sequences and metagenome assembled genomes (e.g. contigs, MAGs / bins).", - "keywords": [ - "taxonomic classification", - "classification", - "long reads", - "mags", - "assembly" - ], - "tools": [ - { - "catpack": { - "description": "CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)", - "homepage": "https://github.com/MGXlab/CAT_pack", - "documentation": "https://github.com/MGXlab/CAT_pack", - "tool_dev_url": "https://github.com/MGXlab/CAT_pack", - "doi": "10.1186/s13059-019-1817-x", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "contigs": { - "type": "file", - "description": "A nucleotide FASTA file containing long DNA sequences such as contigs.", - "pattern": "*.{fasta,fna,fa,fas}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "database": { - "type": "directory", - "description": "Directory containing CAT_pack database files (e.g. output from CAT_pack prepare)", - "pattern": "*/", - "ontologies": [ - { - "edam": "http://edamontology.org/data_1049" - } - ] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "taxonomy": { - "type": "directory", - "description": "Directory containing CAT_pack taxonomy files (e.g. output from CAT_pack prepare)", - "pattern": "*/", - "ontologies": [ - { - "edam": "http://edamontology.org/data_1049" - } - ] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "proteins": { - "type": "directory", - "description": "Optional pre predicted-made proteins FASTA", - "pattern": "*.{fasta,faa,fa,fas}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - [ - { - "meta5": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } + "name": "cnvkit_antitarget", + "path": "modules/nf-core/cnvkit/antitarget/meta.yml", + "type": "module", + "meta": { + "name": "cnvkit_antitarget", + "description": "Derive off-target (“antitarget”) bins from target regions.", + "keywords": ["cvnkit", "antitarget", "cnv", "copy number"], + "tools": [ + { + "cnvkit": { + "description": "CNVkit is a Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data.\nIt is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent.\n", + "homepage": "https://cnvkit.readthedocs.io/en/stable/index.html", + "documentation": "https://cnvkit.readthedocs.io/en/stable/index.html", + "tool_dev_url": "https://github.com/etal/cnvkit", + "doi": "10.1371/journal.pcbi.1004873", + "licence": ["Apache-2.0"], + "identifier": "biotools:cnvkit" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "targets": { + "type": "file", + "description": "File containing genomic regions", + "pattern": "*.{bed}", + "ontologies": [] + } + } + ] + ], + "output": { + "bed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "File containing off-target regions", + "pattern": "*.{bed}", + "ontologies": [] + } + } + ] + ], + "versions_cnvkit": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cnvkit": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cnvkit.py version | sed -e \"s/cnvkit v//g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cnvkit": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cnvkit.py version | sed -e \"s/cnvkit v//g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@adamrtalbot", "@priesgo", "@SusiJo"], + "maintainers": ["@adamrtalbot", "@priesgo", "@SusiJo"] }, - { - "diamond_table": { - "type": "directory", - "description": "Optional pre-made DIAMOND alignment table", - "pattern": "*", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3751" - } - ] - } - } - ] - ], - "output": { - "orf2lca": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.ORF2LCA.txt": { - "type": "file", - "description": "A TSV file with per-ORF hit stats and identified lineage", - "pattern": "*.ORF2LCA.txt", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "contig2classification": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.contig2classification.txt": { - "type": "file", - "description": "A TSV file with per-contig hit stats and assignment justification information", - "pattern": "*.contig2classification.txt", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.log": { - "type": "file", - "description": "Log file with run messages and basic statistics", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2330" - } - ] - } - } - ] - ], - "diamond": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.diamond": { - "type": "file", - "description": "Intermediate DIAMOND TSV summary output file with alignment results", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "faa": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.predicted_proteins.faa": { - "type": "file", - "description": "FAA file of DIAMOND predicted proteins hits", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "gff": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.gff": { - "type": "file", - "description": "GFF file of DIAMOND predicted proteins hits", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2305" - } - ] - } - } - ] - ], - "versions_catpack": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "catpack": { - "type": "string", - "description": "The tool name" - } - }, - { - "CAT_pack --version | sed 's/CAT_pack pack v//g;s/ .*//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "catpack": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "CAT_pack --version | sed 's/CAT_pack pack v//g;s/ .*//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "sarek", + "version": "3.8.1" + } ] - ] }, - "authors": [ - "@jfy133" - ], - "maintainers": [ - "@jfy133" - ] - }, - "pipelines": [ { - "name": "mag", - "version": "5.4.2" + "name": "cnvkit_batch", + "path": "modules/nf-core/cnvkit/batch/meta.yml", + "type": "module", + "meta": { + "name": "cnvkit_batch", + "description": "Copy number variant detection from high-throughput sequencing data", + "keywords": ["cnvkit", "bam", "fasta", "copy number"], + "tools": [ + { + "cnvkit": { + "description": "CNVkit is a Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent.\n", + "homepage": "https://cnvkit.readthedocs.io/en/stable/index.html", + "documentation": "https://cnvkit.readthedocs.io/en/stable/index.html", + "licence": ["Apache-2.0"], + "identifier": "biotools:cnvkit" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "tumor": { + "type": "file", + "description": "Input tumour sample bam file (or cram)\n", + "pattern": "*.{bam,cram}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + }, + { + "edam": "http://edamontology.org/format_3462" + } + ] + } + }, + { + "tumor_index": { + "type": "file", + "description": "Input tumour sample bam/cram index file (only needed for bam input)\n", + "pattern": "*.{bai,crai}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3327" + } + ] + } + }, + { + "normal": { + "type": "file", + "description": "Input normal sample bam file (or cram)\n", + "pattern": "*.{bam,cram}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + }, + { + "edam": "http://edamontology.org/format_3462" + } + ] + } + }, + { + "normal_index": { + "type": "file", + "description": "Input normal sample bam/cram index file (only needed for bam input)\n", + "pattern": "*.{bai,crai}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3327" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input reference genome fasta file (only needed for cram_input and/or when normal_samples are provided)\n", + "pattern": "*.{fa,fasta}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + }, + { + "fasta_fai": { + "type": "file", + "description": "Input reference genome fasta index (optional, but recommended for cram_input)\n", + "pattern": "*.{fai}", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing information about target file\ne.g. [ id:'test' ]\n" + } + }, + { + "targets": { + "type": "file", + "description": "Input target bed file\n", + "pattern": "*.{bed}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3003" + } + ] + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing information about reference file\ne.g. [ id:'test' ]\n" + } + }, + { + "reference": { + "type": "file", + "description": "Input reference cnn-file (only for germline and tumor-only running)\n", + "pattern": "*.{cnn}", + "ontologies": [] + } + } + ], + { + "panel_of_normals": { + "type": "file", + "description": "Input panel of normals file\n", + "pattern": "*.{cnn}", + "ontologies": [] + } + } + ], + "output": { + "bed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "File containing genomic regions", + "pattern": "*.{bed}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3003" + } + ] + } + } + ] + ], + "cnn": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.cnn": { + "type": "file", + "description": "File containing coverage information", + "pattern": "*.{cnn}", + "ontologies": [] + } + } + ] + ], + "cnr": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.cnr": { + "type": "file", + "description": "File containing copy number ratio information", + "pattern": "*.{cnr}", + "ontologies": [] + } + } + ] + ], + "cns": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.cns": { + "type": "file", + "description": "File containing copy number segment information", + "pattern": "*.{cns}", + "ontologies": [] + } + } + ] + ], + "pdf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.pdf": { + "type": "file", + "description": "File with plot of copy numbers or segments on chromosomes", + "pattern": "*.{pdf}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3508" + } + ] + } + } + ] + ], + "png": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.png": { + "type": "file", + "description": "File with plot of bin-level log2 coverages and segmentation calls", + "pattern": "*.{png}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3603" + } + ] + } + } + ] + ], + "versions_cnvkit": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cnvkit": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cnvkit.py version | sed -e \"s/cnvkit v//g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_samtools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "samtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "samtools version | sed '1!d;s/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cnvkit": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cnvkit.py version | sed -e \"s/cnvkit v//g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "samtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "samtools version | sed '1!d;s/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": [ + "@adamrtalbot", + "@drpatelh", + "@fbdtemme", + "@kaurravneet4123", + "@KevinMenden", + "@lassefolkersen", + "@MaxUlysse", + "@priesgo", + "@SusiJo" + ], + "maintainers": [ + "@adamrtalbot", + "@drpatelh", + "@fbdtemme", + "@kaurravneet4123", + "@KevinMenden", + "@lassefolkersen", + "@MaxUlysse", + "@priesgo", + "@SusiJo" + ] + }, + "pipelines": [ + { + "name": "createpanelrefs", + "version": "dev" + }, + { + "name": "pacsomatic", + "version": "dev" + }, + { + "name": "sarek", + "version": "3.8.1" + } + ] }, { - "name": "seqsubmit", - "version": "dev" - } - ] - }, - { - "name": "catpack_download", - "path": "modules/nf-core/catpack/download/meta.yml", - "type": "module", - "meta": { - "name": "catpack_download", - "description": "Downloads the required files for either Nr or GTDB for building into a CAT database", - "keywords": [ - "taxonomic classification", - "classification", - "database", - "download" - ], - "tools": [ - { - "catpack": { - "description": "CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)", - "homepage": "https://github.com/MGXlab/CAT_pack", - "documentation": "https://github.com/MGXlab/CAT_pack", - "tool_dev_url": "https://github.com/MGXlab/CAT_pack", - "doi": "10.1186/s13059-019-1817-x", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } + "name": "cnvkit_call", + "path": "modules/nf-core/cnvkit/call/meta.yml", + "type": "module", + "meta": { + "name": "cnvkit_call", + "description": "Given segmented log2 ratio estimates (.cns), derive each segment’s absolute integer copy number", + "keywords": ["cnvkit", "bam", "fasta", "copy number"], + "tools": [ + { + "cnvkit": { + "description": "CNVkit is a Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent.\n", + "homepage": "https://cnvkit.readthedocs.io/en/stable/index.html", + "documentation": "https://cnvkit.readthedocs.io/en/stable/index.html", + "licence": ["Apache-2.0"], + "identifier": "biotools:cnvkit" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "cns": { + "type": "file", + "description": "CNVKit CNS file.", + "pattern": "*.cns", + "ontologies": [] + } + }, + { + "vcf": { + "type": "file", + "description": "Germline VCF file for BAF.", + "pattern": "*.vcf{,.gz}", + "ontologies": [] + } + } + ] + ], + "output": { + "cns": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.cns": { + "type": "file", + "description": "CNS file.", + "pattern": "*.cns", + "ontologies": [] + } + } + ] + ], + "versions_cnvkit": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cnvkit": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cnvkit.py version | sed -e \"s/cnvkit v//g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cnvkit": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cnvkit.py version | sed -e \"s/cnvkit v//g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@adamrtalbot", "@priesgo"], + "maintainers": ["@adamrtalbot", "@priesgo"] }, - { - "db": { - "type": "string", - "description": "Which database to download", - "pattern": "nr|GTDB" - } - } - ] - ], - "output": { - "fasta": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "${prefix}/*.${db}.gz": { - "type": "file", - "description": "FASTA file containing all the NCBI NR or GTDB sequences", - "pattern": "*.${db}.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ], - "names": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "${prefix}/*.names.dmp": { - "type": "file", - "description": "NCBI taxonomy-style names.dmp text file", - "pattern": "*.names.dmp", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1964" - } - ] - } - } - ] - ], - "nodes": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "${prefix}/*.nodes.dmp": { - "type": "file", - "description": "NCBI taxonomy-style nodes.dmp text file", - "pattern": "*.nodes.dmp", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1964" - } - ] - } - } - ] - ], - "acc2tax": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "${prefix}/*accession2taxid*.gz": { - "type": "file", - "description": "NCBI taxonomy names accession to taxonomy file", - "pattern": "*accession2taxid*", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1964" - } - ] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "${prefix}/*.log": { - "type": "file", - "description": "Log file of the download process", - "pattern": "*.log", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1964" - } - ] - } - } - ] - ], - "versions_catpack": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "catpack": { - "type": "string", - "description": "The tool name" - } - }, - { - "CAT_pack --version | sed 's/CAT_pack pack v//g;s/ .*//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "catpack": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "CAT_pack --version | sed 's/CAT_pack pack v//g;s/ .*//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "pacsomatic", + "version": "dev" + }, + { + "name": "sarek", + "version": "3.8.1" + } ] - ] }, - "authors": [ - "@jfy133" - ], - "maintainers": [ - "@jfy133" - ] - }, - "pipelines": [ { - "name": "mag", - "version": "5.4.2" + "name": "cnvkit_coverage", + "path": "modules/nf-core/cnvkit/coverage/meta.yml", + "type": "module", + "meta": { + "name": "cnvkit_coverage", + "description": "Calculate coverage in the given regions from BAM/CRAM or bedGraph files read depths.", + "keywords": ["cnvkit", "coverage", "BAM", "CRAM", "bedGraph", "read depth", "genomics"], + "tools": [ + { + "cnvkit": { + "description": "Copy number variant detection from high-throughput sequencing.", + "homepage": "https://cnvkit.readthedocs.io/en/stable", + "documentation": "https://cnvkit.readthedocs.io/en/stable", + "tool_dev_url": "https://github.com/etal/cnvkit", + "doi": "10.1371/journal.pcbi.1004873", + "licence": ["Apache-2.0"], + "identifier": "biotools:cnvkit" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "alignment_file": { + "type": "file", + "description": "Sorted BAM/CRAM, or bedGraph file containing read alignements.", + "pattern": "*.{bam,cram,bed.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + }, + { + "edam": "http://edamontology.org/format_2573" + }, + { + "edam": "http://edamontology.org/format_3583" + } + ] + } + }, + { + "interval": { + "type": "file", + "description": "bed file containing the target or antitarget regions.", + "pattern": "*.{target,antitarget}.bed", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3003" + } + ] + } + } + ] + ], + "output": { + "coverage": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.cnn": { + "type": "file", + "description": "Coverage bedfile with .cnn extension.", + "pattern": "*.{targetcoverage,antitargetcoverage}.cnn", + "ontologies": [] + } + } + ] + ], + "versions_cnvkit": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cnvkit": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cnvkit.py version | sed -e \"s/cnvkit v//g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cnvkit": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cnvkit.py version | sed -e \"s/cnvkit v//g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@aadecock"], + "maintainers": ["@aadecock"] + } }, { - "name": "seqsubmit", - "version": "dev" - } - ] - }, - { - "name": "catpack_prepare", - "path": "modules/nf-core/catpack/prepare/meta.yml", - "type": "module", - "meta": { - "name": "catpack_prepare", - "description": "Creates a CAT_pack database based on input FASTAs", - "keywords": [ - "catpack", - "cat", - "prepare", - "database", - "profiling", - "build" - ], - "tools": [ - { - "catpack": { - "description": "CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)", - "homepage": "https://github.com/MGXlab/CAT_pack", - "documentation": "https://github.com/MGXlab/CAT_pack", - "tool_dev_url": "https://github.com/MGXlab/CAT_pack", - "doi": "10.1186/s13059-019-1817-x", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } + "name": "cnvkit_export", + "path": "modules/nf-core/cnvkit/export/meta.yml", + "type": "module", + "meta": { + "name": "cnvkit_export", + "description": "Convert copy number ratio tables (.cnr files) or segments (.cns) to another format.", + "keywords": ["cnvkit", "copy number", "export"], + "tools": [ + { + "cnvkit": { + "description": "CNVkit is a Python library and command-line software toolkit to infer and\nvisualize copy number from high-throughput DNA sequencing data.\nIt is designed for use with hybrid capture, including both whole-exome and custom\ntarget panels, and short-read sequencing platforms such as Illumina and Ion Torrent.\n", + "homepage": "https://cnvkit.readthedocs.io/en/stable/index.html", + "documentation": "https://cnvkit.readthedocs.io/en/stable/index.html", + "licence": ["Apache-2.0"], + "identifier": "biotools:cnvkit" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "cns": { + "type": "file", + "description": "CNVKit CNS file.", + "pattern": "*.cns", + "ontologies": [] + } + } + ] + ], + "output": { + "output": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.${suffix}": { + "type": "file", + "description": "Output file", + "ontologies": [] + } + } + ] + ], + "versions_cnvkit": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cnvkit": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cnvkit.py version | sed -e \"s/cnvkit v//g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cnvkit": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cnvkit.py version | sed -e \"s/cnvkit v//g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@adamrtalbot", "@priesgo"], + "maintainers": ["@adamrtalbot", "@priesgo"] }, - { - "db_fasta": { - "type": "file", - "description": "A FASTA file containing all sequences to be included in the database", - "pattern": "*.{fasta,fa,fna}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - { - "names": { - "type": "file", - "description": "An NCBI taxonomy-style names text file", - "pattern": "*", - "ontologies": [ + "pipelines": [ { - "edam": "http://edamontology.org/format_1964" + "name": "sarek", + "version": "3.8.1" } - ] - } - }, - { - "nodes": { - "type": "file", - "description": "An NCBI taxonomy-style nodes text file", - "pattern": "*", - "ontologies": [ + ] + }, + { + "name": "cnvkit_genemetrics", + "path": "modules/nf-core/cnvkit/genemetrics/meta.yml", + "type": "module", + "meta": { + "name": "cnvkit_genemetrics", + "description": "Copy number variant detection from high-throughput sequencing data", + "keywords": ["cnvkit", "bam", "fasta", "copy number"], + "tools": [ + { + "cnvkit": { + "description": "CNVkit is a Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent.\n", + "homepage": "https://cnvkit.readthedocs.io/en/stable/index.html", + "documentation": "https://cnvkit.readthedocs.io/en/stable/index.html", + "licence": ["Apache-2.0"], + "identifier": "biotools:cnvkit" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "cnr": { + "type": "file", + "description": "CNR file", + "pattern": "*.cnr", + "ontologies": [] + } + }, + { + "cns": { + "type": "file", + "description": "CNS file [Optional]", + "pattern": "*.cns", + "ontologies": [] + } + } + ] + ], + "output": { + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "TSV file", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_cnvkit": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cnvkit": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cnvkit.py version | sed -e \"s/cnvkit v//g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cnvkit": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cnvkit.py version | sed -e \"s/cnvkit v//g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@adamrtalbot", "@marrip", "@priesgo"], + "maintainers": ["@adamrtalbot", "@marrip", "@priesgo"] + }, + "pipelines": [ { - "edam": "http://edamontology.org/format_1964" + "name": "sarek", + "version": "3.8.1" } - ] - } - }, - { - "acc2tax": { - "type": "file", - "description": "An NCBI taxonomy names accession to taxonomy file", - "pattern": "*", - "ontologies": [ + ] + }, + { + "name": "cnvkit_reference", + "path": "modules/nf-core/cnvkit/reference/meta.yml", + "type": "module", + "meta": { + "name": "cnvkit_reference", + "description": "Compile a coverage reference from the given files (normal samples).", + "keywords": ["cnvkit", "reference", "cnv", "copy number"], + "tools": [ + { + "cnvkit": { + "description": "CNVkit is a Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data.\nIt is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent.\n", + "homepage": "https://cnvkit.readthedocs.io/en/stable/index.html", + "documentation": "https://cnvkit.readthedocs.io/en/stable/index.html", + "tool_dev_url": "https://github.com/etal/cnvkit", + "doi": "10.1371/journal.pcbi.1004873", + "licence": ["Apache-2.0"], + "identifier": "biotools:cnvkit" + } + } + ], + "input": [ + { + "fasta": { + "type": "file", + "description": "File containing reference genome", + "pattern": "*.{fasta}", + "ontologies": [] + } + }, + { + "targets": { + "type": "file", + "description": "File containing genomic regions", + "pattern": "*.{bed}", + "ontologies": [] + } + }, + { + "antitargets": { + "type": "file", + "description": "File containing off-target genomic regions", + "pattern": "*.{bed}", + "ontologies": [] + } + } + ], + "output": { + "cnn": [ + { + "*.cnn": { + "type": "file", + "description": "File containing a copy-number reference (required for CNV calling in tumor_only mode)", + "pattern": "*.{cnn}", + "ontologies": [] + } + } + ], + "versions_cnvkit": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cnvkit": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cnvkit.py version | sed -e \"s/cnvkit v//g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cnvkit": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cnvkit.py version | sed -e \"s/cnvkit v//g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@adamrtalbot", "@priesgo", "@SusiJo"], + "maintainers": ["@adamrtalbot", "@priesgo", "@SusiJo"] + }, + "pipelines": [ { - "edam": "http://edamontology.org/format_1964" + "name": "sarek", + "version": "3.8.1" } - ] - } - } - ], - "output": { - "db": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "${prefix}/db/": { - "type": "directory", - "description": "Directory containing CAT database files", - "pattern": "${db}/", - "ontologies": [ - { - "edam": "http://edamontology.org/data_1049" - } - ] - } - } ] - ], - "taxonomy": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "${prefix}/tax/": { - "type": "directory", - "description": "Directory containing CAT prepared taxonomy database files", - "pattern": "${db}/", - "ontologies": [ - { - "edam": "http://edamontology.org/data_1049" - } - ] - } - } - ] - ], - "versions_catpack": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "catpack": { - "type": "string", - "description": "The tool name" - } - }, - { - "CAT_pack --version | sed 's/CAT_pack pack v//g;s/ .*//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "catpack": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "CAT_pack --version | sed 's/CAT_pack pack v//g;s/ .*//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] }, - "authors": [ - "@jfy133" - ], - "maintainers": [ - "@jfy133" - ] - }, - "pipelines": [ { - "name": "mag", - "version": "5.4.2" + "name": "cnvkit_target", + "path": "modules/nf-core/cnvkit/target/meta.yml", + "type": "module", + "meta": { + "name": "cnvkit_target", + "description": "Transform bait intervals into targets more suitable for CNVkit.", + "keywords": ["cnvkit", "target", "cnv", "copy number"], + "tools": [ + { + "cnvkit": { + "description": "CNVkit is a Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data.\nIt is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent.\n", + "homepage": "https://cnvkit.readthedocs.io/en/stable/index.html", + "documentation": "https://cnvkit.readthedocs.io/en/stable/index.html", + "tool_dev_url": "https://github.com/etal/cnvkit", + "doi": "10.1371/journal.pcbi.1004873", + "licence": ["Apache-2.0"], + "identifier": "biotools:cnvkit" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "baits": { + "type": "file", + "description": "BED or interval file listing the targeted regions.", + "pattern": "*.{bed}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "annotation": { + "type": "file", + "description": "Use gene models from this file to assign names to the target regions.", + "pattern": "*.{txt,bed,gff3,pil}", + "ontologies": [] + } + } + ] + ], + "output": { + "bed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "File containing target regions", + "pattern": "*.{bed}", + "ontologies": [] + } + } + ] + ], + "versions_cnvkit": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cnvkit": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cnvkit.py version | sed -e \"s/cnvkit v//g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cnvkit": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cnvkit.py version | sed -e \"s/cnvkit v//g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@adamrtalbot", "@priesgo"], + "maintainers": ["@adamrtalbot", "@priesgo"] + } }, { - "name": "seqsubmit", - "version": "dev" - } - ] - }, - { - "name": "catpack_reads", - "path": "modules/nf-core/catpack/reads/meta.yml", - "type": "module", - "meta": { - "name": "catpack_reads", - "description": "Taxonomic classification plus read-based abundance estimation from long DNA sequences and metagenome assembled genomes (e.g. contigs, MAGs / bins).", - "keywords": [ - "taxonomic classification", - "classification", - "long reads", - "mags", - "assembly", - "abundance", - "taxonomic composition" - ], - "tools": [ - { - "catpack": { - "description": "CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)", - "homepage": "https://github.com/MGXlab/CAT_pack", - "documentation": "https://github.com/MGXlab/CAT_pack", - "tool_dev_url": "https://github.com/MGXlab/CAT_pack", - "doi": "10.1186/s13059-019-1817-x", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "reads": { - "type": "file", - "description": "One or a pair of nucleotide FASTQ files (R1, R2) containing reads for mapping. Interleaved not supported.", - "pattern": "*.{fastq,fq,fastq.gz,fq.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2182" - }, - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "contigs": { - "type": "file", - "description": "A nucleotide FASTA file containing long DNA sequences such as contigs. Optional if `bins` supplied.", - "pattern": "*.{fasta,fna,fa,fas}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "database": { - "type": "directory", - "description": "Directory containing CAT_pack database files (e.g. output from CAT_pack prepare)", - "pattern": "*/", - "ontologies": [ - { - "edam": "http://edamontology.org/data_1049" - } - ] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "taxonomy": { - "type": "directory", - "description": "Directory containing CAT_pack taxonomy files (e.g. output from CAT_pack prepare)", - "pattern": "*/", - "ontologies": [ - { - "edam": "http://edamontology.org/data_1049" - } - ] - } - } - ], - [ - { - "meta5": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "bins": { - "type": "file", - "description": "One or more nucleotide FASTA file containing binned long DNA sequences.\nOptional if `contigs` supplied.\nNote: if you supply bins, you must also give the `-s `\ncorresponding to the file extension of the bins via `ext.args`\n", - "pattern": "*.{fasta,fna,fa,fas}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - { - "mode": { - "type": "string", - "description": "Mode of operation of CAT_pack reads, \"mcr\": integrate annotations from MAGs (bins), contigs, and\nreads; \"cr\": integrate annotations from contigs and reads; \"mr\": integrate\nannotations from MAGs (bins) and reads.\n", - "pattern": "mcr|cr|mr" - } - }, - [ - { - "meta6": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "bam_aligned": { - "type": "file", - "description": "Optional pre-aligned and sorted reads mapped against contigs/bins.", - "pattern": "*.bam", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - } - ], - [ - { - "meta7": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "bam_unaligned": { - "type": "file", - "description": "Optional sorted unaligned reads from mapping against contigs/bins.", - "pattern": "*.bam", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - } - ], - [ - { - "meta8": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "contig2classification": { - "type": "file", - "description": "Optional TSV file with per-contig hit stats and assignment justification information", - "pattern": "*.contig2classification.txt", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - [ - { - "meta9": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "bin2classification": { - "type": "file", - "description": "Optional TSV file with per-bin hit stats and assignment justification information", - "pattern": "*.bin2classification.txt", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - [ - { - "meta10": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "unclassified2classification": { - "type": "file", - "description": "Optional TSV file with pre-made CAT_pack reads unmapped2classification.txt file information", - "pattern": "*.txt", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - [ - { - "meta11": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "proteins": { - "type": "directory", - "description": "Optional pre predicted-made proteins FASTA", - "pattern": "*.{fasta,faa,fa,fas}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - [ - { - "meta12": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "diamond_alignment": { - "type": "directory", - "description": "Optional pre-made DIAMOND alignment table", - "pattern": "*", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3751" - } - ] - } - } - ] - ], - "output": { - "rat_log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "${prefix}.log": { - "type": "map", - "description": "Log file from RAT run\n", - "pattern": "*.log", - "ontologies": [ - { - "edam": "http://edamontology.org/data_3106" - } - ] - } - } - ] - ], - "complete_abundance": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.complete.abundance.txt": { - "type": "file", - "description": "TSV file containing complete abundance information\n", - "pattern": "*.contig.abundance.txt", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3751" - } - ] - } - } - ] - ], - "contig_abundance": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.contig.abundance.txt": { - "type": "file", - "description": "TSV file containing contig abundance information\n", - "pattern": "*.contig.abundance.txt", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3751" - } - ] - } - } - ] - ], - "read2classification": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.read2classification.txt": { - "type": "file", - "description": "A TSV file with per-read hit stats and assignment justification information", - "pattern": "*.read2classification.txt", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "alignment_diamond": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.alignment.diamond": { - "type": "file", - "description": "Intermediate DIAMOND TSV summary output file with alignment results", - "pattern": "*.alignment.diamond", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "contig2classification": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.contig2classification.txt": { - "type": "file", - "description": "A TSV file with per-contig hit stats and assignment justification information", - "pattern": "*.contig2classification.txt", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "cat_log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.CAT.log": { - "type": "file", - "description": "CAT log file with run messages and basic statistics", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2330" - } - ] - } - } - ] - ], - "orf2lca": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.ORF2LCA.txt": { - "type": "file", - "description": "A TSV file with per-ORF hit stats and identified lineage", - "pattern": "*.ORF2LCA.txt", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "faa": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.predicted_proteins.faa": { - "type": "file", - "description": "FAA file of DIAMOND predicted proteins hits", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "gff": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.predicted_proteins.gff": { - "type": "file", - "description": "GFF file of DIAMOND predicted proteins hits", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2305" - } - ] - } - } - ] - ], - "unmapped_diamond": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*_unmapped.alignment.diamond": { - "type": "file", - "description": "Intermediate DIAMOND TSV summary output file list of unassigned hits", - "pattern": "*.alignment.diamond", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "unmapped_fasta": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*_unmapped.fasta": { - "type": "file", - "description": "Nucleotide FASTA file of contigs with no hits", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ], - "unmapped2classification": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.unmapped2classification.txt": { - "type": "file", - "description": "A TSV file with per-contig unmapped assignment justification information", - "pattern": "*.contig2classification.txt", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_catpack": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "catpack": { - "type": "string", - "description": "The tool name" - } - }, - { - "CAT_pack --version | sed 's/CAT_pack pack v//g;s/ .*//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "catpack": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "CAT_pack --version | sed 's/CAT_pack pack v//g;s/ .*//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@jfy133" - ], - "maintainers": [ - "@jfy133" - ] - } - }, - { - "name": "catpack_summarise", - "path": "modules/nf-core/catpack/summarise/meta.yml", - "type": "module", - "meta": { - "name": "catpack_summarise", - "description": "Summarises results from CAT/BAT/RAT classification steps", - "keywords": [ - "taxonomic classification", - "classification", - "long reads", - "mags", - "assembly" - ], - "tools": [ - { - "catpack": { - "description": "CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)", - "homepage": "https://github.com/MGXlab/CAT_pack", - "documentation": "https://github.com/MGXlab/CAT_pack", - "tool_dev_url": "https://github.com/MGXlab/CAT_pack", - "doi": "10.1186/s13059-019-1817-x", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "classification": { - "type": "file", - "description": "CAT/BAT/RAT classification table annotated with official names (from CAT_pack addnames)", - "pattern": "*.txt", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } + "name": "cnvnator_cnvnator", + "path": "modules/nf-core/cnvnator/cnvnator/meta.yml", + "type": "module", + "meta": { + "name": "cnvnator_cnvnator", + "description": "CNVnator is a command line tool for CNV/CNA analysis from depth-of-coverage by mapped reads.", + "keywords": ["cnvnator", "cnv", "cna"], + "tools": [ + { + "cnvnator": { + "description": "Tool for calling copy number variations.", + "homepage": "https://github.com/abyzovlab/CNVnator", + "documentation": "https://github.com/abyzovlab/CNVnator/blob/master/README.md", + "tool_dev_url": "https://github.com/abyzovlab/CNVnator", + "licence": ["MIT"], + "identifier": "biotools:cnvnator" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "bam": { + "type": "file", + "description": "Sorted BAM/CRAM/SAM file", + "pattern": "*.bam", + "ontologies": [] + } + }, + { + "bai": { + "type": "file", + "description": "Sorted BAM/CRAM/SAM file", + "pattern": "*.bam", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "root": { + "type": "file", + "description": "ROOT file", + "pattern": "*.root", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Path to a directory containing fasta files or a fasta file", + "pattern": "*.fa", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "fai": { + "type": "file", + "description": "Path to a fasta file index", + "pattern": "*.fai", + "ontologies": [] + } + } + ], + { + "step": { + "type": "string", + "description": "One of \"his\", \"rd\", \"call\", \"stat\", and \"partition\"" + } + } + ], + "output": { + "root": [ + [ + { + "output_meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "${prefix}.root": { + "type": "file", + "description": "A ROOT file", + "pattern": "*.root", + "ontologies": [] + } + } + ] + ], + "tab": [ + [ + { + "output_meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "${prefix}.tab": { + "type": "file", + "description": "A tab file containing cnvnator calls", + "pattern": "*.tab", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_cnvnator": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cnvnator": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cnvnator 2>&1 | sed -n '3s/CNVnator v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cnvnator": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cnvnator 2>&1 | sed -n '3s/CNVnator v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@ramprasadn"], + "maintainers": ["@ramprasadn"] }, - { - "contigs": { - "type": "file", - "description": "Optional nucleotide FASTA file containing long DNA sequences such as contigs that were classified (only if classification table is from CAT_pack contigs)", - "pattern": "*.{fasta,fna,fa,fas}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ], - "output": { - "txt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.txt": { - "type": "file", - "description": "Summary statistics table of CAT/BAT/RAT results\n", - "pattern": "*.txt", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_catpack": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "catpack": { - "type": "string", - "description": "The tool name" - } - }, - { - "CAT_pack --version | sed 's/CAT_pack pack v//g;s/ .*//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "catpack": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "CAT_pack --version | sed 's/CAT_pack pack v//g;s/ .*//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "raredisease", + "version": "3.0.0" + } ] - ] }, - "authors": [ - "@jfy133" - ], - "maintainers": [ - "@jfy133" - ] - }, - "pipelines": [ { - "name": "mag", - "version": "5.4.2" - }, - { - "name": "seqsubmit", - "version": "dev" - } - ] - }, - { - "name": "cdhit_cdhit", - "path": "modules/nf-core/cdhit/cdhit/meta.yml", - "type": "module", - "meta": { - "name": "cdhit_cdhit", - "description": "Cluster protein sequences using sequence similarity", - "keywords": [ - "cluster", - "protein", - "alignment", - "fasta" - ], - "tools": [ - { - "cdhit": { - "description": "Clusters and compares protein or nucleotide sequences", - "homepage": "https://sites.google.com/view/cd-hit/home", - "documentation": "https://github.com/weizhongli/cdhit/wiki", - "tool_dev_url": "https://github.com/weizhongli/cdhit", - "doi": "10.1093/bioinformatics/btl158", - "licence": [ - "GPL v2" - ], - "identifier": "biotools:cd-hit" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "sequences": { - "type": "file", - "description": "fasta file of sequences to be clustered", - "pattern": "*.{fa,fasta}", - "ontologies": [] - } - } - ] - ], - "output": { - "fasta": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.fasta": { - "type": "file", - "description": "fasta file of the representative sequences for each cluster", - "pattern": "*.{fasta}", - "ontologies": [] - } - } - ] - ], - "clusters": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.clstr": { - "type": "file", - "description": "List of clusters", - "pattern": "*.{clstr}", - "ontologies": [] - } - } - ] - ], - "versions_cdhit": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cdhit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cd-hit -h | sed -n '1s/.*version \\([0-9.]*\\).*/\\1/p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cdhit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cd-hit -h | sed -n '1s/.*version \\([0-9.]*\\).*/\\1/p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@timslittle", - "@Puumanamana" - ], - "maintainers": [ - "@timslittle", - "@Puumanamana" - ] - }, - "pipelines": [ - { - "name": "radseq", - "version": "dev" - } - ] - }, - { - "name": "cdhit_cdhitest", - "path": "modules/nf-core/cdhit/cdhitest/meta.yml", - "type": "module", - "meta": { - "name": "cdhit_cdhitest", - "description": "Cluster nucleotide sequences using sequence similarity", - "keywords": [ - "cluster", - "nucleotide", - "alignment", - "fasta" - ], - "tools": [ - { - "cdhit": { - "description": "Clusters and compares protein or nucleotide sequences", - "homepage": "https://sites.google.com/view/cd-hit/home", - "documentation": "https://github.com/weizhongli/cdhit/wiki", - "tool_dev_url": "https://github.com/weizhongli/cdhit", - "doi": "10.1093/bioinformatics/btl158", - "licence": [ - "GPL v2" - ], - "identifier": "biotools:cd-hit" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "sequences": { - "type": "file", - "description": "fasta or fastq file of sequences to be clustered", - "pattern": "*.{fasta,fastq}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "output": { - "fasta": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.{fa,fq}": { - "type": "file", - "description": "fasta or fastq file of the representative sequences for each cluster", - "pattern": "*.{fasta,fastq}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "clusters": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.clstr": { - "type": "file", - "description": "List of clusters", - "pattern": "*.{clstr}", - "ontologies": [] - } - } - ] - ], - "versions_cdhitest": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cdhit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cd-hit-est -h | sed -n '1s/.*version \\([0-9.]*\\).*/\\1/p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cdhit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cd-hit-est -h | sed -n '1s/.*version \\([0-9.]*\\).*/\\1/p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@Joon-Klaps" - ], - "maintainers": [ - "@Joon-Klaps" - ] - }, - "pipelines": [ - { - "name": "viralmetagenome", - "version": "1.1.1" - } - ] - }, - { - "name": "celesta", - "path": "modules/nf-core/celesta/meta.yml", - "type": "module", - "meta": { - "name": "celesta", - "description": "Unsupervised machine learning for cell type identification in multiplexed imaging using protein expression and cell neighborhood information without ground truth", - "keywords": [ - "highly_multiplexed_imaging", - "cell_type_identification", - "cell_phenotyping", - "image_analysis", - "mcmicro", - "machine_learning" - ], - "tools": [ - { - "celesta": { - "description": "Automate unsupervised machine learning cell type identification using both protein expressions and cell spatial neighborhood information", - "homepage": "https://github.com/SchapiroLabor/mcmicro-celesta", - "documentation": "https://github.com/SchapiroLabor/mcmicro-celesta/blob/main/README.md", - "tool_dev_url": "https://github.com/plevritis-lab/CELESTA", - "doi": "10.1038/s41592-022-01498-z", - "licence": [ - "Apache-2.0" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" - } + "name": "cnvnator_convert2vcf", + "path": "modules/nf-core/cnvnator/convert2vcf/meta.yml", + "type": "module", + "meta": { + "name": "cnvnator_convert2vcf", + "description": "convert2vcf.pl is command line tool to convert CNVnator calls to vcf format.", + "keywords": ["cnvnator", "cnv", "cna"], + "tools": [ + { + "cnvnator": { + "description": "Tool for calling copy number variations.", + "homepage": "https://github.com/abyzovlab/CNVnator", + "documentation": "https://github.com/abyzovlab/CNVnator/blob/master/README.md", + "tool_dev_url": "https://github.com/abyzovlab/CNVnator", + "licence": ["MIT"], + "identifier": "biotools:cnvnator" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "calls": { + "type": "file", + "description": "A tab file containing CNVnator calls", + "pattern": "*.tab", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.vcf": { + "type": "file", + "description": "CNVnator calls in vcf format", + "pattern": "*.vcf", + "ontologies": [] + } + } + ] + ], + "versions_cnvnator": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cnvnator": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cnvnator 2>&1 | sed -n '3s/CNVnator v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cnvnator": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cnvnator 2>&1 | sed -n '3s/CNVnator v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@ramprasadn"], + "maintainers": ["@ramprasadn"] }, - { - "img_data": { - "type": "file", - "description": "Quantification table with single cells as rows, markers (e.g. CD3 or CD8 but names do not have to match exactly) and X/Y coordinates as columns", - "pattern": "*.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ], - { - "signature": { - "type": "file", - "description": "Signature Matrix containing the definition of cell types according to markers", - "pattern": "*.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - }, - { - "high_thresholds": { - "type": "file", - "description": "csv file with user-defined probability high thresholds for anchor cell (row 1) and index cell (row 2) definition", - "pattern": "*.csv", - "ontologies": [ + "pipelines": [ { - "edam": "http://edamontology.org/format_3752" + "name": "raredisease", + "version": "3.0.0" } - ] - } - }, - { - "low_thresholds": { - "type": "file", - "description": "optional csv file with user-defined probability low thresholds for anchor cell (row 1) and index cell (row 2) definition", - "pattern": "*.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ], - "output": { - "celltypes": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*results.csv": { - "type": "file", - "description": "File with final celltype annotations concatenated to the original input quantification, due to the mechanism its non-deterministic", - "pattern": "*.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "quality": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*quality.csv": { - "type": "file", - "description": "File with final calculated marker probabilities for inspection, non-deterministic", - "pattern": "*.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "versions_celesta": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "celesta": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "1.0.0": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "celesta": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "1.0.0": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@LukasHats", - "@ArozHada" - ], - "maintainers": [ - "@LukasHats", - "@ArozHada" - ] - } - }, - { - "name": "cellbender_merge", - "path": "modules/nf-core/cellbender/merge/meta.yml", - "type": "module", - "meta": { - "name": "cellbender_merge", - "description": "Module to use CellBender to remove ambient RNA from single-cell RNA-seq data", - "keywords": [ - "single-cell", - "scRNA-seq", - "ambient RNA removal" - ], - "tools": [ - { - "cellbender": { - "description": "CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.", - "documentation": "https://cellbender.readthedocs.io/en/latest/", - "tool_dev_url": "https://github.com/broadinstitute/CellBender", - "licence": [ - "BSD-3-Clause" - ], - "identifier": "biotools:CellBender" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "filtered": { - "type": "file", - "description": "AnnData file containing filtered data (without empty droplets)", - "pattern": "*.h5ad", - "ontologies": [] - } - }, - { - "unfiltered": { - "type": "file", - "description": "AnnData file containing unfiltered data (with empty droplets)", - "pattern": "*.h5ad", - "ontologies": [] - } - }, - { - "cellbender_h5": { - "type": "file", - "description": "CellBender h5 file containing ambient RNA estimates", - "pattern": "*.h5", - "ontologies": [] - } - } - ], - { - "output_layer_name": { - "type": "string", - "description": "The name of the layer to store counts" - } - } - ], - "output": { - "h5ad": [ - [ - { - "meta": { - "type": "file", - "description": "AnnData file containing decontaminated counts as `adata.X`", - "pattern": "*.h5ad", - "ontologies": [] - } - }, - { - "${prefix}.h5ad": { - "type": "file", - "description": "AnnData file containing decontaminated counts as `adata.X`", - "pattern": "*.h5ad", - "ontologies": [] - } - } - ] - ], - "versions_cellbender": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software version", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "topics": { - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software version", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@nictru" - ], - "maintainers": [ - "@nictru" - ] - }, - "pipelines": [ - { - "name": "scdownstream", - "version": "dev" - } - ] - }, - { - "name": "cellbender_removebackground", - "path": "modules/nf-core/cellbender/removebackground/meta.yml", - "type": "module", - "meta": { - "name": "cellbender_removebackground", - "description": "Module to use CellBender to estimate ambient RNA from single-cell RNA-seq data", - "keywords": [ - "single-cell", - "scRNA-seq", - "ambient RNA removal" - ], - "tools": [ - { - "cellbender": { - "description": "CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.", - "documentation": "https://cellbender.readthedocs.io/en/latest/", - "tool_dev_url": "https://github.com/broadinstitute/CellBender", - "licence": [ - "BSD-3-Clause" - ], - "identifier": "biotools:CellBender" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "h5ad": { - "type": "file", - "description": "AnnData file containing unfiltered data (with empty droplets)", - "pattern": "*.h5ad", - "ontologies": [] - } - } - ] - ], - "output": { - "h5": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "${prefix}.h5": { - "type": "file", - "description": "Full count matrix as an h5 file, with background RNA removed. This file contains all the original droplet barcodes.", - "pattern": "*.h5", - "ontologies": [] - } - } - ] - ], - "filtered_h5": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "${prefix}_filtered.h5": { - "type": "file", - "description": "Full count matrix as an h5 file, with background RNA removed. This file contains only the droplet barcodes which were determined to have a > 50% posterior probability of containing cells.\n", - "pattern": "*.h5", - "ontologies": [] - } - } - ] - ], - "posterior_h5": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "${prefix}_posterior.h5": { - "type": "file", - "description": "The full posterior probability of noise counts. This is not normally used downstream.\n", - "pattern": "*.h5", - "ontologies": [] - } - } - ] - ], - "barcodes": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "${prefix}_cell_barcodes.csv": { - "type": "file", - "description": "CSV file containing all the droplet barcodes which were determined to have a > 50% posterior probability of containing cells. |\nBarcodes are written in plain text. This information is also contained in each of the above outputs, |\nbut is included as a separate output for convenient use in certain downstream applications.\n", - "pattern": "*.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "metrics": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "${prefix}_metrics.csv": { - "type": "file", - "description": "Metrics describing the run, potentially to be used to flag problematic runs |\nwhen using CellBender as part of a large-scale automated pipeline.\n", - "pattern": "*.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "report": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "${prefix}_report.html": { - "type": "file", - "description": "HTML report including plots and commentary, along with any warnings or suggestions for improved parameter settings.\n", - "pattern": "*.html", - "ontologies": [] - } - } ] - ], - "pdf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "${prefix}.pdf": { - "type": "file", - "description": "PDF file that provides a standard graphical summary of the inference procedure.", - "pattern": "*.pdf", - "ontologies": [] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "${prefix}.log": { - "type": "file", - "description": "Log file produced by the cellbender remove-background run.", - "pattern": "*.log", - "ontologies": [] - } - } - ] - ], - "checkpoint": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "ckpt.tar.gz": { - "type": "file", - "description": "Checkpoint file which contains the trained model and the full posterior.", - "pattern": "*.ckpt", - "ontologies": [] - } - } - ] - ], - "versions_cellbender": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cellbender": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cellbender --version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cellbender": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cellbender --version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] }, - "authors": [ - "@nictru" - ], - "maintainers": [ - "@nictru" - ] - }, - "pipelines": [ { - "name": "scdownstream", - "version": "dev" + "name": "cnvpytor_callcnvs", + "path": "modules/nf-core/cnvpytor/callcnvs/meta.yml", + "type": "module", + "meta": { + "name": "cnvpytor_callcnvs", + "description": "Command line tool for calling CNVs in whole genome sequencing data", + "keywords": ["CNV", "call", "wgs"], + "tools": [ + { + "cnvpytor": { + "description": "calling CNVs using read depth", + "homepage": "https://github.com/abyzovlab/CNVpytor", + "documentation": "https://github.com/abyzovlab/CNVpytor", + "tool_dev_url": "https://github.com/abyzovlab/CNVpytor", + "doi": "10.1101/2021.01.27.428472v1", + "licence": ["MIT"], + "identifier": "biotools:cnvpytor" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "pytor": { + "type": "file", + "description": "pytor file containing partitions of read depth histograms using mean-shift method", + "pattern": "*.{pytor}", + "ontologies": [] + } + } + ], + { + "bin_sizes": { + "type": "string", + "description": "list of binsizes separated by space e.g. \"1000 10000\" and \"1000\"" + } + } + ], + "output": { + "pytor": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "${pytor.baseName}.pytor": { + "type": "file", + "description": "pytor files containing cnv calls", + "pattern": "*.{pytor}", + "ontologies": [] + } + } + ] + ], + "versions_cnvpytor": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cnvpytor": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cnvpytor --version | sed -n 's/.*CNVpytor \\(.*\\)/\\1/p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cnvpytor": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cnvpytor --version | sed -n 's/.*CNVpytor \\(.*\\)/\\1/p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@sima-r"], + "maintainers": ["@sima-r"] + } }, { - "name": "scrnaseq", - "version": "4.1.0" - } - ] - }, - { - "name": "cellpose", - "path": "modules/nf-core/cellpose/meta.yml", - "type": "module", - "meta": { - "name": "cellpose", - "description": "cellpose segments cells in images using GPU-accelerated deep learning", - "keywords": [ - "segmentation", - "image", - "cellpose", - "gpu", - "spatial-transcriptomics" - ], - "tools": [ - { - "cellpose": { - "description": "cellpose is an anatomical segmentation algorithm written in Python 3 by Carsen Stringer and Marius Pachitariu", - "homepage": "https://github.com/MouseLand/cellpose", - "documentation": "https://cellpose.readthedocs.io/en/latest/command.html", - "tool_dev_url": "https://github.com/MouseLand/cellpose", - "doi": "10.1038/s41592-022-01663-4", - "licence": [ - "BSD 3-Clause" - ], - "identifier": "biotools:cellpose" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\n(sample id)\n" - } - }, - { - "image": { - "type": "file", - "description": "tif file ready for segmentation", - "pattern": "*.{tif,tiff}", - "ontologies": [] - } - } - ], - { - "model": { - "type": "file", - "description": "Optional custom cellpose model file. When provided, passed as\n--pretrained_model to cellpose. Pass [] (empty list) to use the\ndefault model (cpsam in cellpose 4).\n", - "pattern": "*", - "ontologies": [] + "name": "cnvpytor_histogram", + "path": "modules/nf-core/cnvpytor/histogram/meta.yml", + "type": "module", + "meta": { + "name": "cnvpytor_histogram", + "description": "calculates read depth histograms", + "keywords": ["cnv calling", "histogram", "read depth"], + "tools": [ + { + "cnvpytor": { + "description": "calling CNVs using read depth", + "homepage": "https://github.com/abyzovlab/CNVpytor", + "documentation": "https://github.com/abyzovlab/CNVpytor", + "tool_dev_url": "https://github.com/abyzovlab/CNVpytor", + "doi": "10.1101/2021.01.27.428472v1", + "licence": ["MIT"], + "identifier": "biotools:cnvpytor" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "pytor": { + "type": "file", + "description": "pytor file containing read depth data", + "pattern": "*.{pytor}", + "ontologies": [] + } + } + ], + { + "bin_sizes": { + "type": "string", + "description": "list of binsizes separated by space e.g. \"1000 10000\" and \"1000\"" + } + } + ], + "output": { + "pytor": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "${pytor.baseName}.pytor": { + "type": "file", + "description": "pytor file containing read depth histograms binned based on given bin size(s)", + "pattern": "*.{pytor}", + "ontologies": [] + } + } + ] + ], + "versions_cnvpytor": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cnvpytor": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "1.3.2": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cnvpytor": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "1.3.2": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@sima-r", "@ramprasadn"], + "maintainers": ["@sima-r", "@ramprasadn"] } - } - ], - "output": { - "mask": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\n[sample id]\n" - } - }, - { - "${prefix}/*masks.tif": { - "type": "file", - "description": "labelled mask output from cellpose in tif format", - "pattern": "${prefix}/*masks.tif", - "ontologies": [] - } - } - ] - ], - "flows": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\n[sample id]\n" - } - }, - { - "${prefix}/*flows.tif": { - "type": "file", - "description": "cell flow output from cellpose", - "pattern": "${prefix}/*flows.tif", - "ontologies": [] - } - } - ] - ], - "cells": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\n[sample id]\n" - } - }, - { - "${prefix}/*seg.npy": { - "type": "file", - "description": "numpy array with cell segmentation data", - "pattern": "${prefix}/*seg.npy", - "ontologies": [] - } - } - ] - ], - "versions_cellpose": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cellpose": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cellpose --version | sed -n 's/cellpose version:[[:space:]]*//p' | tr -d '[:space:]'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_python": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "python": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cellpose --version | sed -n 's/python version:[[:space:]]*//p' | tr -d '[:space:]'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_torch": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "torch": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cellpose --version | sed -n 's/torch version:[[:space:]]*//p' | tr -d '[:space:]'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cellpose": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cellpose --version | sed -n 's/cellpose version:[[:space:]]*//p' | tr -d '[:space:]'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "python": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cellpose --version | sed -n 's/python version:[[:space:]]*//p' | tr -d '[:space:]'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "torch": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cellpose --version | sed -n 's/torch version:[[:space:]]*//p' | tr -d '[:space:]'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] }, - "notes": "When `accelerator` is set (e.g. `accelerator = 1`), the module\nautomatically passes `--use_gpu` to cellpose. The container (built via Seqera\nContainers) includes PyTorch 2.10.0 with CUDA 12.8 and falls back to CPU\nautomatically when no GPU is available. Use the `process_gpu` label to request\nGPU resources from your executor. When running with conda/mamba, GPU support\ndepends on having a CUDA-enabled PyTorch installation in your environment.\n\nModel selection via the model input channel:\n - Custom model file: file(\"/path/to/model\")\n - Default (cpsam): []\n\nAdditional cellpose CLI arguments can be passed via `task.ext.args`:\n ext.args = '--diameter 30 --flow_threshold 0.4 --cellprob_threshold 0'\n\nDeprecated in cellpose 4.0.1+: `--chan`, `--chan2`, `--invert`, `--all_channels`,\n`--diam_mean`, `--pretrained_model_ortho`. Do not pass these via ext.args.\n\nModel weights are not bundled in the container. Cellpose downloads them on first\nuse to `$CELLPOSE_LOCAL_MODELS_PATH` (set to the work directory).\n", - "authors": [ - "@josenimo", - "@FloWuenne", - "@dongzehe" - ], - "maintainers": [ - "@josenimo", - "@FloWuenne", - "@kbestak" - ] - }, - "pipelines": [ { - "name": "mcmicro", - "version": "dev" + "name": "cnvpytor_importreaddepth", + "path": "modules/nf-core/cnvpytor/importreaddepth/meta.yml", + "type": "module", + "meta": { + "name": "cnvpytor_importreaddepth", + "description": "command line tool for CNV/CNA analysis. This step imports the read depth data into a root pytor file.", + "keywords": ["read depth", "cnv", "cna", "call"], + "tools": [ + { + "cnvpytor -rd": { + "description": "calling CNVs using read depth", + "homepage": "https://github.com/abyzovlab/CNVpytor", + "documentation": "https://github.com/abyzovlab/CNVpytor", + "tool_dev_url": "https://github.com/abyzovlab/CNVpytor", + "doi": "10.1101/2021.01.27.428472v1", + "licence": ["MIT"], + "identifier": "biotools:cnvpytor" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "input_file": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram}", + "ontologies": [] + } + }, + { + "index": { + "type": "file", + "description": "bam file index", + "pattern": "*.{bai,crai}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing genome information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "specifies reference genome file (only for cram file without reference genome)", + "pattern": "*.{fasta,fasta.gz,fa,fa.gz}", + "ontologies": [] + } + }, + { + "fai": { + "type": "file", + "description": "Index of reference fasta file", + "pattern": "*.fai", + "ontologies": [] + } + } + ] + ], + "output": { + "pytor": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.pytor": { + "type": "file", + "description": "read depth root file in which read depth data binned to 100 base pair bins will be stored.", + "pattern": "*.{pytor}", + "ontologies": [] + } + } + ] + ], + "versions_cnvpytor": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cnvpytor": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cnvpytor --version 2>&1 | sed -n 's/.*CNVpytor //p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cnvpytor": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cnvpytor --version 2>&1 | sed -n 's/.*CNVpytor //p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@sima-r", "@ramprasadn"], + "maintainers": ["@sima-r", "@ramprasadn"] + } }, { - "name": "molkart", - "version": "1.2.0" + "name": "cnvpytor_partition", + "path": "modules/nf-core/cnvpytor/partition/meta.yml", + "type": "module", + "meta": { + "name": "cnvpytor_partition", + "description": "Calculate segmentation for specified bin size (multiple bin sizes separate by space)", + "keywords": ["cnv", "call", "partition", "histogram"], + "tools": [ + { + "cnvpytor": { + "description": "Calling CNVs using read depth", + "homepage": "https://github.com/abyzovlab/CNVpytor", + "documentation": "https://github.com/abyzovlab/CNVpytor", + "tool_dev_url": "https://github.com/abyzovlab/CNVpytor", + "doi": "10.1101/2021.01.27.428472v1", + "licence": ["MIT"], + "identifier": "biotools:cnvpytor" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "pytor": { + "type": "file", + "description": "pytor file containing read depth data", + "pattern": "*.{pytor}", + "ontologies": [] + } + } + ], + { + "bin_sizes": { + "type": "string", + "description": "list of binsizes separated by space e.g. \"1000 10000\" default is \"1000\"" + } + } + ], + "output": { + "pytor": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "${prefix}.pytor": { + "type": "file", + "description": "pytor file", + "pattern": "*.pytor", + "ontologies": [] + } + } + ] + ], + "versions_cnvpytor": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "cnvpytor": { + "type": "string", + "description": "The tool name" + } + }, + { + "cnvpytor --version 2>&1 | sed -n 's/.*CNVpytor //p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "cnvpytor": { + "type": "string", + "description": "The tool name" + } + }, + { + "cnvpytor --version 2>&1 | sed -n 's/.*CNVpytor //p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@sima-r", "@ramprasadn"], + "maintainers": ["@sima-r", "@ramprasadn"] + } }, { - "name": "spatialxe", - "version": "dev" - } - ] - }, - { - "name": "cellranger_count", - "path": "modules/nf-core/cellranger/count/meta.yml", - "type": "module", - "meta": { - "name": "cellranger_count", - "description": "Module to use Cell Ranger's pipelines analyze sequencing data produced from Chromium Single Cell Gene Expression.", - "keywords": [ - "align", - "count", - "reference" - ], - "tools": [ - { - "cellranger": { - "description": "Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.", - "homepage": "https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger", - "documentation": "https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov", - "tool_dev_url": "https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov", - "licence": [ - "10x Genomics EULA" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files. The order of the input files MUST be [\"sample1 R1\", \"sample1 R2\", \"sample2, R1\",\n\"sample2, R2\", ...]. This can usually be achieved by sorting the input files by file name.\n\nBackground: 10x data is always paired-end with R1 containing cell barcode and UMI\nand R2 containing the actual read sequence. Cell Ranger requires files to adhere to the following file-name\nconvention: `${Sample_Name}_S1_L00${Lane_Number}_${R1,R2}_001.fastq.gz`. This module automatically\nrenames files to match this convention based on the order of input files to avoid various\nissues (see https://github.com/nf-core/scrnaseq/issues/241). To avoid mistakes, the module\nthrows an error if a pair of R1 and R2 fastq files does not have the same filename except for the \"_R1\"/\"_R2\" part.\nRenaming the files does not affect the results (see README.md for detailed tests).\n", - "pattern": "*{R1,R2}*.fastq.gz", - "ontologies": [] - } - } - ], - { - "reference": { - "type": "directory", - "description": "Folder containing all the reference indices needed by Cell Ranger" - } - } - ], - "output": { - "outs": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "**/outs/**": { - "type": "file", - "description": "Files containing the outputs of Cell Ranger, see official 10X Genomics documentation for a complete list", - "pattern": "${meta.id}/outs/*", - "ontologies": [] - } - } - ] - ], - "versions_cellranger": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software version", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "topics": { - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software version", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@ggabernet", - "@edmundmiller" - ], - "maintainers": [ - "@ggabernet", - "@edmundmiller" - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "YAML file containing versions of tools used in the module" + "name": "cnvpytor_view", + "path": "modules/nf-core/cnvpytor/view/meta.yml", + "type": "module", + "meta": { + "name": "cnvpytor_view", + "description": "view function to generate vcfs", + "keywords": ["cnv", "calling", "vcf"], + "tools": [ + { + "cnvpytor": { + "description": "calling CNVs using read depth", + "homepage": "https://github.com/abyzovlab/CNVpytor", + "documentation": "https://github.com/abyzovlab/CNVpytor", + "tool_dev_url": "https://github.com/abyzovlab/CNVpytor", + "doi": "10.1101/2021.01.27.428472v1", + "licence": ["MIT"], + "identifier": "biotools:cnvpytor" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "pytor_files": { + "type": "file", + "description": "pytor file containing cnv calls. To merge calls from multiple samples use a list of files.", + "pattern": "*.{pytor}", + "ontologies": [] + } + } + ], + { + "bin_sizes": { + "type": "string", + "description": "list of binsizes separated by space e.g. \"1000 10000\" and \"1000\"" + } + }, + { + "output_format": { + "type": "string", + "description": "output format of the cnv calls. Valid entries are \"tsv\", \"vcf\", and \"xls\"" + } + } + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.vcf": { + "type": "file", + "description": "vcf file containing cnv calls", + "pattern": "*.{vcf}", + "ontologies": [] + } + } + ] + ], + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "tsv file containing cnv calls", + "pattern": "*.{tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "xls": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.xls": { + "type": "file", + "description": "xls file containing cnv calls", + "pattern": "*.{xls}", + "ontologies": [] + } + } + ] + ], + "versions_cnvpytor": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cnvpytor": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "1.3.2": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cnvpytor": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "1.3.2": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@sima-r", "@ramprasadn"], + "maintainers": ["@sima-r", "@ramprasadn"] } - } - ] - }, - "pipelines": [ + }, { - "name": "scrnaseq", - "version": "4.1.0" - } - ] - }, - { - "name": "cellranger_mkfastq", - "path": "modules/nf-core/cellranger/mkfastq/meta.yml", - "type": "module", - "meta": { - "name": "cellranger_mkfastq", - "description": "Module to create FASTQs needed by the 10x Genomics Cell Ranger tool. Uses the cellranger mkfastq command.", - "keywords": [ - "reference", - "mkfastq", - "fastq", - "illumina", - "bcl2fastq" - ], - "tools": [ - { - "cellranger": { - "description": "Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.", - "homepage": "https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger", - "documentation": "https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov", - "tool_dev_url": "https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov", - "licence": [ - "10X Genomics EULA" - ], - "identifier": "" + "name": "cobiontid_kmercounter", + "path": "modules/nf-core/cobiontid/kmercounter/meta.yml", + "type": "module", + "meta": { + "name": "cobiontid_kmercounter", + "description": "A rust based tool based on Needletail's FASTA parser tallies k-mer counts\nfor large sequencing rounds. Written with downstream processing with Tensorflow\nor numpy in mind.\n", + "keywords": ["cobiontid", "kmer", "counts", "npy", "fasta"], + "tools": [ + { + "kmer-counter": { + "description": "A rust based tool based on Needletail's FASTA parser tallies k-mer counts\nfor large sequencing rounds. Written with downstream processing with Tensorflow\nor numpy in mind.\n", + "homepage": "https://github.com/CobiontID/kmer-counter", + "documentation": "https://github.com/CobiontID/kmer-counter", + "license": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input fasta assembly file\n", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + { + "kmer_size": { + "type": "integer", + "description": "Size of kmer to scan the genome for.\n" + } + } + ], + "output": { + "npy": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.npy": { + "type": "file", + "description": "A Numpy file containing the kmer counts.\n", + "ontologies": [ + { + "edam": "http://edamontology.org/format_4003" + } + ] + } + } + ] + ], + "versions_kmercounter": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "kmer-counter": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "kmer-counter --version | sed -e \"s/K-mer counter //g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "kmer-counter": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "kmer-counter --version | sed -e \"s/K-mer counter //g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@DLBPointon"], + "maintainers": ["@DLBPointon"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "csv": { - "type": "file", - "description": "Sample sheet", - "pattern": "*.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } + }, + { + "name": "cobrameta", + "path": "modules/nf-core/cobrameta/meta.yml", + "type": "module", + "meta": { + "name": "cobrameta", + "description": "A tool to raise the quality of viral genomes assembled from short-read metagenomes via resolving and joining of contigs fragmented during de novo assembly.", + "keywords": ["cobra", "contig", "scaffold", "assembly", "extension", "virus", "phage"], + "tools": [ + { + "cobra-meta": { + "description": "COBRA is a tool to get higher quality viral genomes assembled from metagenomes.", + "homepage": "https://github.com/linxingchen/cobra", + "documentation": "https://github.com/linxingchen/cobra", + "tool_dev_url": "https://github.com/linxingchen/cobra", + "doi": "10.1038/s41564-023-01598-2", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Assembly file (contigs/scaffolds) in FASTA format\n", + "pattern": "*.{fa,fasta,fna,fa.gz,fasta.gz,fna.gz}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "coverage": { + "type": "file", + "description": "TSV file with 2 columns containing 1) the contig/scaffold id and\n2) the coverage depth of the sequence specified in column 1\n", + "pattern": "*.{tsv,txt}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "query": { + "type": "file", + "description": "File containing the query contigs that the user wants COBRA to extend. This\ncan be provided in one-column TXT or FASTA format. (The IDs must match the IDs\nin the `--fasta` file exactly)\n", + "pattern": "*.{txt,fasta}", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "Sorted BAM/CRAM/SAM file resulting from mapping reads used in assembly\nto the resulting assembly FASTA\n", + "pattern": "*.{bam,cram,sam}", + "ontologies": [] + } + } + ], + { + "assembler": { + "type": "string", + "description": "The name of the tool used to assemble contigs", + "pattern": "{metaspades,megahit,idba}" + } + }, + { + "mink": { + "type": "integer", + "description": "The minimum kmer size used to assemble contigs", + "pattern": "[0-9]+" + } + }, + { + "maxk": { + "type": "integer", + "description": "The maximum kmer size used to assemble contigs", + "pattern": "[0-9]+" + } + } + ], + "output": { + "self_circular": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}/COBRA_category_i_self_circular.fasta.gz": { + "type": "file", + "description": "fasta file", + "pattern": "*/COBRA_category_i_self_circular.fasta.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "extended_circular": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}/COBRA_category_ii-a_extended_circular_unique.fasta.gz": { + "type": "file", + "description": "Gzipped FASTA file containing query contigs that were joined and extended\ninto a circular genome\n", + "pattern": "${prefix}/COBRA_category_ii-a_extended_circular_unique.fasta.gz", + "ontologies": [] + } + } + ] + ], + "extended_partial": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}/COBRA_category_ii-b_extended_partial_unique.fasta.gz": { + "type": "file", + "description": "Gzipped FASTA file containing query contigs were joined and extended, but\nnot into circular sequences\n", + "pattern": "${prefix}/COBRA_category_ii-b_extended_partial_unique.fasta.gz", + "ontologies": [] + } + } + ] + ], + "extended_failed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}/COBRA_category_ii-c_extended_failed.fasta.gz": { + "type": "file", + "description": "Gzipped FASTA file containing query contigs that could not be extended due\nto COBRA rules\n", + "pattern": "${prefix}/COBRA_category_ii-c_extended_failed.fasta.gz", + "ontologies": [] + } + } + ] + ], + "orphan_end": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}/COBRA_category_iii_orphan_end.fasta.gz": { + "type": "file", + "description": "Gzipped FASTA file containing query contigs that do not shared the\n\"expected overlap length\" with other contigs\n", + "pattern": "${prefix}/COBRA_category_iii_orphan_end.fasta.gz", + "ontologies": [] + } + } + ] + ], + "all_cobra_assemblies": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}/COBRA_all_assemblies.fasta.gz": { + "type": "file", + "description": "Gzipped FASTA file containing all the assemblies generated by COBRA", + "pattern": "*/COBRA_all_assemblies.fasta.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "joining_summary": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}/COBRA_joining_summary.txt": { + "type": "file", + "description": "TSV file containing information regarding COBRA's extension results\n", + "pattern": "${prefix}/COBRA_joining_summary.txt", + "ontologies": [] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}/log": { + "type": "file", + "description": "Log file containing the contents of each processing\n", + "pattern": "${prefix}/log", + "ontologies": [] + } + } + ] + ], + "versions_cobra": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cobra": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cobra-meta --version 2>&1 | sed 's/^.*cobra v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cobra": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cobra-meta --version 2>&1 | sed 's/^.*cobra v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@CarsonJM"], + "maintainers": ["@CarsonJM"] }, - { - "bcl": { - "type": "file", - "description": "Base call files", - "pattern": "*.bcl.bgzf", - "ontologies": [] - } - } - ] - ], - "output": { - "fastq": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*_outs/outs/fastq_path/**/**_S[0-9]*_R?_00?.fastq.gz": { - "type": "file", - "description": "Read FastQ files", - "pattern": "*_S[0-9]*_R?_00?.fastq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "fastq_idx": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*_outs/outs/fastq_path/**/**_S[0-9]*_I?_00?.fastq.gz": { - "type": "file", - "description": "Index FastQ files", - "pattern": "*_S[0-9]*_I?_00?.fastq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "undetermined_fastq": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*_outs/outs/fastq_path/Undetermined*.fastq.gz": { - "type": "file", - "description": "Undetermined FastQ files", - "pattern": "Undetermined*.fastq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "reports": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*_outs/outs/fastq_path/Reports": { - "type": "directory", - "description": "Reports", - "pattern": "Reports" - } - } - ] - ], - "stats": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*_outs/outs/fastq_path/Stats": { - "type": "directory", - "description": "Stats", - "pattern": "Stats" - } - } - ] - ], - "interop": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*_outs/outs/interop_path/*.bin": { - "type": "file", - "description": "InterOp files", - "pattern": "*.bin", - "ontologies": [] - } - } - ] - ], - "versions_cellranger": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cellranger": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cellranger --version | sed \"s/.*-//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cellranger": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cellranger --version | sed \"s/.*-//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@ggabernet", - "@edmundmiller", - "@RHReynolds" - ], - "maintainers": [ - "@ggabernet", - "@edmundmiller", - "@RHReynolds" - ] - }, - "pipelines": [ - { - "name": "demultiplex", - "version": "1.7.1" - } - ] - }, - { - "name": "cellranger_mkgtf", - "path": "modules/nf-core/cellranger/mkgtf/meta.yml", - "type": "module", - "meta": { - "name": "cellranger_mkgtf", - "description": "Module to build a filtered GTF needed by the 10x Genomics Cell Ranger tool. Uses the cellranger mkgtf command.", - "keywords": [ - "reference", - "mkref", - "index" - ], - "tools": [ - { - "cellranger": { - "description": "Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.", - "homepage": "https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger", - "documentation": "https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov", - "tool_dev_url": "https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov", - "licence": [ - "10X Genomics EULA" - ], - "identifier": "" - } - } - ], - "input": [ - { - "gtf": { - "type": "file", - "description": "The reference GTF transcriptome file", - "pattern": "*.gtf", - "ontologies": [] - } - } - ], - "output": { - "gtf": [ - { - "*.gtf": { - "type": "directory", - "description": "The filtered GTF transcriptome file", - "pattern": "*.filtered.gtf" - } - } - ], - "versions_cellranger": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cellranger": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cellranger --version | sed \"s/.*-//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cellranger": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cellranger --version | sed \"s/.*-//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@ggabernet", - "@edmundmiller" - ], - "maintainers": [ - "@ggabernet", - "@edmundmiller" - ] - }, - "pipelines": [ - { - "name": "scrnaseq", - "version": "4.1.0" - } - ] - }, - { - "name": "cellranger_mkref", - "path": "modules/nf-core/cellranger/mkref/meta.yml", - "type": "module", - "meta": { - "name": "cellranger_mkref", - "description": "Module to build the reference needed by the 10x Genomics Cell Ranger tool. Uses the cellranger mkref command.", - "keywords": [ - "reference", - "mkref", - "index" - ], - "tools": [ - { - "cellranger": { - "description": "Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.", - "homepage": "https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger", - "documentation": "https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov", - "tool_dev_url": "https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov", - "licence": [ - "10X Genomics EULA" - ], - "identifier": "" - } - } - ], - "input": [ - { - "fasta": { - "type": "file", - "description": "Reference genome FASTA file", - "pattern": "*.{fasta,fa}", - "ontologies": [] - } - }, - { - "gtf": { - "type": "file", - "description": "Reference transcriptome GTF file", - "pattern": "*.gtf", - "ontologies": [] - } - }, - { - "reference_name": { - "type": "string", - "description": "The name to give the new reference folder", - "pattern": "str" - } - } - ], - "output": { - "reference": [ - { - "${reference_name}": { - "type": "directory", - "description": "Folder containing all the reference indices needed by Cell Ranger" - } - } - ], - "versions_cellranger": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cellranger": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cellranger --version | sed \"s/.*-//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cellranger": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cellranger --version | sed \"s/.*-//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@ggabernet" - ], - "maintainers": [ - "@ggabernet" - ] - }, - "pipelines": [ - { - "name": "scrnaseq", - "version": "4.1.0" - } - ] - }, - { - "name": "cellranger_mkvdjref", - "path": "modules/nf-core/cellranger/mkvdjref/meta.yml", - "type": "module", - "meta": { - "name": "cellranger_mkvdjref", - "description": "Module to build the VDJ reference needed by the 10x Genomics Cell Ranger tool. Uses the cellranger mkvdjref command.", - "keywords": [ - "reference", - "mkvdjref", - "index", - "immunoprofiling", - "single-cell", - "cellranger" - ], - "tools": [ - { - "cellranger": { - "description": "Cell Ranger processes data from 10X Genomics Chromium kits. `cellranger vdj` takes FASTQ files from `cellranger mkfastq` or `bcl2fastq` for V(D)J libraries and performs sequence assembly and paired clonotype calling. It uses the Chromium cellular barcodes and UMIs to assemble V(D)J transcripts per cell. Clonotypes and CDR3 sequences are output as a `.vloupe` file which can be loaded into Loupe V(D)J Browser.", - "homepage": "https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/what-is-cell-ranger", - "documentation": "https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/advanced/references", - "tool_dev_url": "https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/advanced/references", - "licence": [ - "10x Genomics EULA" - ], - "identifier": "" - } - } - ], - "input": [ - { - "fasta": { - "type": "file", - "description": "Reference genome FASTA file (optional)", - "pattern": "*.{fasta,fa}", - "ontologies": [] - } - }, - { - "gtf": { - "type": "file", - "description": "Reference genome GTF file (optional)", - "pattern": "*.gtf", - "ontologies": [] - } - }, - { - "seqs": { - "type": "file", - "description": "Reference genome FASTA file from the 10X Genomics fetch-imgt workflow (optional)", - "pattern": "*.{fasta,fa}", - "ontologies": [] - } - }, - { - "reference_name": { - "type": "string", - "description": "The name to give the new reference folder, e.g. `my_vdj_ref`. This flag is required", - "pattern": "str" - } - } - ], - "output": { - "reference": [ - { - "${reference_name}": { - "type": "directory", - "description": "Folder containing all the reference indices needed by Cell Ranger" - } - } - ], - "versions_cellranger": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cellranger": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cellranger --version | sed \"s/.*-//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cellranger": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cellranger --version | sed \"s/.*-//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "phageannotator", + "version": "dev" + } ] - ] }, - "authors": [ - "@ggabernet", - "@klkeys" - ], - "maintainers": [ - "@ggabernet", - "@klkeys" - ] - }, - "pipelines": [ { - "name": "airrflow", - "version": "5.0.0" + "name": "cobs_classicconstruct", + "path": "modules/nf-core/cobs/classicconstruct/meta.yml", + "type": "module", + "meta": { + "name": "cobs_classicconstruct", + "description": "Builds a classic bloom filter COBS index", + "keywords": ["COBS", "index", "k-mer index", "bloom filter"], + "tools": [ + { + "cobs": { + "description": "Compact Bit-Sliced Signature Index (for Genomic k-Mer Data or q-Grams)", + "homepage": "https://panthema.net/cobs", + "documentation": "https://github.com/iqbal-lab-org/cobs", + "tool_dev_url": "https://github.com/iqbal-lab-org/cobs", + "doi": "10.1007/978-3-030-32686-9_21", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "input": { + "type": "file", + "description": "The file or directory to be indexed.\nCOBS can read:\n 1. FASTA files (*.fa, *.fasta, *.fna, *.ffn, *.faa, *.frn, *.fa.gz, *.fasta.gz, *.fna.gz, *.ffn.gz, *.faa.gz, *.frn.gz),\n 2. FASTQ files (*.fq, *.fastq, *.fq.gz., *.fastq.gz),\n 3. \"Multi-FASTA\" and \"Multi-FASTQ\" files (*.mfasta, *.mfastq),\n 4. McCortex files (*.ctx),\n 5. or text files (*.txt).\nYou can either recursively scan a directory for all files matching any of these files,\nor pass a *.list file which lists all paths COBS should index.\n", + "pattern": "*.*", + "ontologies": [] + } + } + ] + ], + "output": { + "index": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.index.cobs_classic": { + "type": "file", + "description": "The COBS classic index", + "pattern": "*.index.cobs_classic", + "ontologies": [] + } + } + ] + ], + "versions_cobs": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cobs": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cobs version 2>&1 | grep -Eo '[0-9]+\\.[0-9]+\\.[0-9]+'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cobs": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cobs version 2>&1 | grep -Eo '[0-9]+\\.[0-9]+\\.[0-9]+'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@leoisl"], + "maintainers": ["@leoisl"] + } }, { - "name": "scrnaseq", - "version": "4.1.0" - } - ] - }, - { - "name": "cellranger_multi", - "path": "modules/nf-core/cellranger/multi/meta.yml", - "type": "module", - "meta": { - "name": "cellranger_multi", - "description": "Module to use Cell Ranger's pipelines to analyze sequencing data produced from various Chromium technologies, including Single Cell Gene Expression, Single Cell Immune Profiling, Feature Barcoding, and Cell Multiplexing.", - "keywords": [ - "align", - "reference", - "cellranger", - "multiomics", - "gene expression", - "vdj", - "antigen capture", - "antibody capture", - "crispr" - ], - "tools": [ - { - "cellranger": { - "description": "Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.", - "homepage": "https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger", - "documentation": "https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_cp", - "tool_dev_url": "https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_cp", - "licence": [ - "10X Genomics EULA" - ], - "identifier": "" - } - } - ], - "input": [ - { + "name": "cobs_compactconstruct", + "path": "modules/nf-core/cobs/compactconstruct/meta.yml", + "type": "module", "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - [ - { - "meta_gex": { - "type": "map", - "description": "Groovy Map containing sample information\n" - } - }, - { - "gex_fastqs": { - "type": "file", - "description": "FASTQ files", - "pattern": "*.fastq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ], - [ - { - "meta_vdj": { - "type": "map", - "description": "Groovy Map containing sample information\n" - } - }, - { - "vdj_fastqs": { - "type": "file", - "description": "FASTQ files", - "pattern": "*.fastq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ], - [ - { - "meta_ab": { - "type": "map", - "description": "Groovy Map containing sample information\n" - } - }, - { - "ab_fastqs": { - "type": "file", - "description": "FASTQ files", - "pattern": "*.fastq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ], - [ - { - "meta_beam": { - "type": "map", - "description": "Groovy Map containing sample information\n" - } - }, - { - "beam_fastqs": { - "type": "file", - "description": "FASTQ files", - "pattern": "*.fastq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ], - [ - { - "meta_cmo": { - "type": "map", - "description": "Groovy Map containing sample information\n" - } - }, - { - "cmo_fastqs": { - "type": "file", - "description": "FASTQ files", - "pattern": "*.fastq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } + "name": "cobs_compactconstruct", + "description": "Builds a compact bloom filter COBS index", + "keywords": ["COBS", "index", "k-mer index", "bloom filter"], + "tools": [ + { + "cobs": { + "description": "Compact Bit-Sliced Signature Index (for Genomic k-Mer Data or q-Grams)", + "homepage": "https://panthema.net/cobs", + "documentation": "https://github.com/iqbal-lab-org/cobs", + "doi": "10.1007/978-3-030-32686-9_21", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "input": { + "type": "file", + "description": "The file or directory to be indexed.\nCOBS can read:\n 1. FASTA files (`*.fa`, `*.fasta`, `*.fna`, `*.ffn`, `*.faa`, `*.frn`, `*.fa.gz`, `*.fasta.gz`, `*.fna.gz`, `*.ffn.gz`, `*.faa.gz`, `*.frn.gz`),\n 2. FASTQ files (`*.fq`, `*.fastq`, `*.fq.gz.`, `*.fastq.gz`),\n 3. \"Multi-FASTA\" and \"Multi-FASTQ\" files (`*.mfasta`, `*.mfastq`),\n 4. McCortex files (`*.ctx`),\n 5. or text files (`*.txt`).\nYou can either recursively scan a directory for all files matching any of these files,\nor pass a `*.list` file which lists all paths COBS should index.\n", + "pattern": "*.*", + "ontologies": [] + } + } + ] + ], + "output": { + "index": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.index.cobs_compact": { + "type": "file", + "description": "The COBS compact index", + "pattern": "*.index.cobs_compact", + "ontologies": [] + } + } + ] + ], + "versions_cobs": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cobs": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cobs version 2>&1 | grep -Eo '[0-9]+\\.[0-9]+\\.[0-9]+'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cobs": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cobs version 2>&1 | grep -Eo '[0-9]+\\.[0-9]+\\.[0-9]+'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@leoisl"], + "maintainers": ["@leoisl"] } - ], - [ - { - "meta_crispr": { - "type": "map", - "description": "Groovy Map containing sample information\n" - } + }, + { + "name": "comebin_runcomebin", + "path": "modules/nf-core/comebin/runcomebin/meta.yml", + "type": "module", + "meta": { + "name": "comebin_runcomebin", + "description": "Effective binning of metagenomic contigs using COntrastive Multi-viEw representation learning", + "keywords": ["metagenomics", "binning", "clustering"], + "tools": [ + { + "comebin": { + "description": "COMEBin allows effective binning of metagenomic contigs using COntrastive Multi-viEw representation learning", + "homepage": "https://github.com/ziyewang/COMEBin", + "documentation": "https://github.com/ziyewang/COMEBin", + "tool_dev_url": "https://github.com/ziyewang/COMEBin", + "doi": "10.1038/s41467-023-44290-z", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "assembly": { + "type": "file", + "description": "FASTA file of contigs for binning", + "pattern": "*.{fa,fas,fasta,fna,fa.gz,fas.gz,fasta.gz,fna.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + }, + { + "bam": { + "type": "file", + "description": "List of sorted bam files of reads mapped to the reference assembly. Not compatible with TSV input.\n", + "pattern": "*.bam", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + } + ] + ], + "output": { + "bins": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" + } + }, + { + "${prefix}/comebin_res_bins/*.fa.gz": { + "type": "file", + "description": "List of FASTA files of binned contigs", + "pattern": "*.fna.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" + } + }, + { + "${prefix}/comebin_res.tsv": { + "type": "file", + "description": "TSV mapping the output clusters to contigs\n", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" + } + }, + { + "${prefix}/comebin.log": { + "type": "file", + "description": "COMEBin log file\n", + "pattern": "*.log", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3671" + } + ] + } + } + ] + ], + "embeddings": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" + } + }, + { + "${prefix}/embeddings.tsv": { + "type": "file", + "description": "TSV describing the embeddings of the contigs\n", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "covembeddings": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" + } + }, + { + "${prefix}/covembeddings.tsv": { + "type": "file", + "description": "TSV describing the embeddings of the contigs\n", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_comebin": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "comebin": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "run_comebin.sh | sed '2!d;s/COMEBin version: //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "comebin": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "run_comebin.sh | sed '2!d;s/COMEBin version: //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@prototaxites"], + "maintainers": ["@prototaxites"] }, - { - "crispr_fastqs": { - "type": "file", - "description": "FASTQ files", - "pattern": "*.fastq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ], - { - "gex_reference": { - "type": "directory", - "description": "Folder containing Cellranger gene expression reference. Can also be a gzipped tarball", - "pattern": "*.tar.gz" - } - }, - { - "gex_frna_probeset": { - "type": "file", - "description": "Fixed RNA profiling information containing custom probes in CSV format", - "pattern": "*.csv", - "ontologies": [ + "pipelines": [ { - "edam": "http://edamontology.org/format_3752" + "name": "mag", + "version": "5.4.2" } - ] - } - }, - { - "gex_targetpanel": { - "type": "file", - "description": "Declaration of the target panel for Targeted Gene Expression analysis", - "pattern": "*.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - }, - { - "vdj_reference": { - "type": "directory", - "description": "Folder containing Cellranger V(D)J reference. 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Uses the cellranger-arc count command.", - "keywords": [ - "align", - "count", - "reference" - ], - "tools": [ - { - "cellrangerarc": { - "description": "Cell Ranger ARC is a set of analysis pipelines that process Chromium Single Cell ARC data.", - "homepage": "https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc", - "documentation": "https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc", - "tool_dev_url": "https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc", - "licence": [ - "10x Genomics EULA" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "sample_type": { - "type": "string", - "description": "The type of sample" - } - }, - { - "sub_sample": { - "type": "string", - "description": "The name of sub sample" - } - }, - { - "reads": { - "type": "file", - "description": "FASTQ files produced using Cell Ranger ARC", - "pattern": "*.fastq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reference": { - "type": "directory", - "description": "Directory containing all the reference indices needed by Cell Ranger ARC" - } - } - ] - ], - "output": { - "outs": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "${prefix}/outs/**": { - "type": "file", - "description": "Files containing the outputs of Cell Ranger ARC", - "pattern": "${prefix}/outs/*", - "ontologies": [] - } - } - ] - ], - "lib": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "${prefix}_lib.csv": { - "type": "file", - "description": "Library", - "pattern": "${prefix}_lib.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "versions_cellrangerarc": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cellrangerarc": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cellranger-arc --version 2>&1 | sed 's/cellranger-arc cellranger-arc-//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cellrangerarc": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cellranger-arc --version 2>&1 | sed 's/cellranger-arc cellranger-arc-//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } ] - ] - }, - "authors": [ - "@ggabernet", - "@edmundmiller", - "@heylf" - ] - }, - "pipelines": [ - { - "name": "scrnaseq", - "version": "4.1.0" - } - ] - }, - { - "name": "cellrangerarc_mkfastq", - "path": "modules/nf-core/cellrangerarc/mkfastq/meta.yml", - "type": "module", - "meta": { - "name": "cellrangerarc_mkfastq", - "description": "Module to create fastqs needed by the 10x Genomics Cell Ranger Arc tool. 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id:'sample1' ]`\n" - } + }, + { + "name": "controlfreec_freec", + "path": "modules/nf-core/controlfreec/freec/meta.yml", + "type": "module", + "meta": { + "name": "controlfreec_freec", + "description": "Copy number and genotype annotation from whole genome and whole exome sequencing data", + "keywords": ["cna", "cnv", "somatic", "single", "tumor-only"], + "tools": [ + { + "controlfreec/freec": { + "description": "Copy number and genotype annotation from whole genome and whole exome sequencing data.", + "homepage": "http://boevalab.inf.ethz.ch/FREEC", + "documentation": "http://boevalab.inf.ethz.ch/FREEC/tutorial.html", + "tool_dev_url": "https://github.com/BoevaLab/FREEC/", + "doi": "10.1093/bioinformatics/btq635", + "licence": ["GPL >=2"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "mpileup_normal": { + "type": "file", + "description": "miniPileup file", + "ontologies": [] + } + }, + { + "mpileup_tumor": { + "type": "file", + "description": "miniPileup file", + "ontologies": [] + } + }, + { + "cpn_normal": { + "type": "file", + "description": "Raw copy number profiles (optional)", + "pattern": "*.cpn", + "ontologies": [] + } + }, + { + "cpn_tumor": { + "type": "file", + "description": "Raw copy number profiles (optional)", + "pattern": "*.cpn", + "ontologies": [] + } + }, + { + "minipileup_normal": { + "type": "file", + "description": "miniPileup file from previous run (optional)", + "pattern": "*.pileup", + "ontologies": [] + } + }, + { + "minipileup_tumor": { + "type": "file", + "description": "miniPileup file from previous run (optional)", + "pattern": "*.pileup", + "ontologies": [] + } + } + ], + { + "fasta": { + "type": "file", + "description": "Reference file (optional; required if args 'makePileup' is set)", + "pattern": "*.{fasta,fna,fa}", + "ontologies": [] + } + }, + { + "fai": { + "type": "file", + "description": "Fasta index", + "pattern": "*.fai", + "ontologies": [] + } + }, + { + "snp_position": { + "type": "file", + "description": "Path to a BED or VCF file with SNP positions to create a mini pileup file from the initial BAM file provided in mateFile (optional)", + "pattern": "*.{bed,vcf}", + "ontologies": [] + } + }, + { + "known_snps": { + "type": "file", + "description": "File with known SNPs", + "pattern": "*.{vcf,vcf.gz}", + "ontologies": [] + } + }, + { + "known_snps_tbi": { + "type": "file", + "description": "Index of known_snps", + "pattern": "*.tbi", + "ontologies": [] + } + }, + { + "chr_directory": { + "type": "file", + "description": "Path to directory with chromosome fasta files (optional, required if gccontentprofile is not provided)", + "pattern": "*/", + "ontologies": [] + } + }, + { + "mappability": { + "type": "file", + "description": "Contains information of mappable positions (optional)", + "pattern": "*.gem", + "ontologies": [] + } + }, + { + "target_bed": { + "type": "file", + "description": "Sorted bed file containing capture regions (optional)", + "pattern": "*.bed", + "ontologies": [] + } + }, + { + "gccontent_profile": { + "type": "file", + "description": "File with GC-content profile", + "ontologies": [] + } + } + ], + "output": { + "bedgraph": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_ratio.BedGraph": { + "type": "file", + "description": "Bedgraph format for the UCSC genome browser", + "pattern": ".bedgraph", + "ontologies": [] + } + } + ] + ], + "control_cpn": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_control.cpn": { + "type": "file", + "description": "files with raw copy number profiles", + "pattern": "*_control.cpn", + "ontologies": [] + } + } + ] + ], + "sample_cpn": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_sample.cpn": { + "type": "file", + "description": "files with raw copy number profiles", + "pattern": "*_sample.cpn", + "ontologies": [] + } + } + ] + ], + "gcprofile_cpn": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "GC_profile.*.cpn": { + "type": "file", + "description": "file with GC-content profile.", + "pattern": "GC_profile.*.cpn", + "ontologies": [] + } + } + ] + ], + "BAF": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_BAF.txt": { + "type": "file", + "description": "file B-allele frequencies for each possibly heterozygous SNP position", + "pattern": "*_BAF.txt", + "ontologies": [] + } + } + ] + ], + "CNV": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_CNVs": { + "type": "file", + "description": "file with coordinates of predicted copy number alterations.", + "pattern": "*_CNVs", + "ontologies": [] + } + } + ] + ], + "info": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_info.txt": { + "type": "file", + "description": "parsable file with information about FREEC run", + "pattern": "*_info.txt", + "ontologies": [] + } + } + ] + ], + "ratio": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_ratio.txt": { + "type": "file", + "description": "file with ratios and predicted copy number alterations for each window", + "pattern": "*_ratio.txt", + "ontologies": [] + } + } + ] + ], + "config": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "config.txt": { + "type": "file", + "description": "Config file used to run Control-FREEC", + "pattern": "config.txt", + "ontologies": [] + } + } + ] + ], + "versions_controlfreec": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "controlfreec": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "11.6b": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "controlfreec": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "11.6b": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@FriederikeHanssen"], + "maintainers": ["@FriederikeHanssen"] }, - { - "bcl": { - "type": "file", - "description": "Base call files", - "pattern": "*.bcl.bgzf", - "ontologies": [] - } - } - ], - { - "csv": { - "type": "file", - "description": "Sample sheet", - "pattern": "*.csv", - "ontologies": [ + "pipelines": [ { - "edam": "http://edamontology.org/format_3752" + "name": "sarek", + "version": "3.8.1" } - ] - } - } - ], - "output": { - "fastq": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}/outs/fastq_path/*.fastq.gz": { - "type": "file", - "description": "Unaligned FastQ files", - "pattern": "${prefix}/outs/fastq_path/*.fastq.gz", - "ontologies": [] - } - } - ] - ], - "versions_cellrangerarc": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cellrangerarc": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cellranger-arc --version 2>&1 | sed 's/cellranger-arc cellranger-arc-//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cellrangerarc": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cellranger-arc --version 2>&1 | sed 's/cellranger-arc cellranger-arc-//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@ggabernet", - "@edmundmiller", - "@RHReynolds", - "@heylf" - ] - } - }, - { - "name": "cellrangerarc_mkgtf", - "path": "modules/nf-core/cellrangerarc/mkgtf/meta.yml", - "type": "module", - "meta": { - "name": "cellrangerarc_mkgtf", - "description": "Module to build a filtered gtf needed by the 10x Genomics Cell Ranger Arc tool. Uses the cellranger-arc mkgtf command.", - "keywords": [ - "reference", - "mkref", - "index" - ], - "tools": [ - { - "cellrangerarc": { - "description": "Cell Ranger Arc by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.", - "homepage": "https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc", - "documentation": "https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc", - "tool_dev_url": "https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc", - "licence": [ - "10x Genomics EULA" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "gtf": { - "type": "file", - "description": "The reference GTF transcriptome file", - "pattern": "*.gtf", - "ontologies": [] - } - } - ] - ], - "output": { - "gtf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.gtf": { - "type": "directory", - "description": "The filtered GTF transcriptome file", - "pattern": "${prefix}.gtf" - } - } - ] - ], - "versions_cellrangerarc": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cellrangerarc": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cellranger-arc --version 2>&1 | sed 's/cellranger-arc cellranger-arc-//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cellrangerarc": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cellranger-arc --version 2>&1 | sed 's/cellranger-arc cellranger-arc-//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@ggabernet", - "@edmundmiller", - "@heylf" - ] - }, - "pipelines": [ - { - "name": "scrnaseq", - "version": "4.1.0" - } - ] - }, - { - "name": "cellrangerarc_mkref", - "path": "modules/nf-core/cellrangerarc/mkref/meta.yml", - "type": "module", - "meta": { - "name": "cellrangerarc_mkref", - "description": "Module to build the reference needed by the 10x Genomics Cell Ranger Arc tool. Uses the cellranger-arc mkref command.", - "keywords": [ - "reference", - "mkref", - "index" - ], - "tools": [ - { - "cellrangerarc": { - "description": "Cell Ranger Arc is a set of analysis pipelines that process Chromium Single Cell Arc data.", - "homepage": "https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc", - "documentation": "https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc", - "tool_dev_url": "https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc", - "licence": [ - "10x Genomics EULA" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing genome information\ne.g. `[ id:'genome' ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome FASTA file", - "pattern": "*.{fasta,fa}", - "ontologies": [] - } - }, - { - "gtf": { - "type": "file", - "description": "Reference transcriptome GTF file", - "pattern": "*.gtf", - "ontologies": [] - } - }, - { - "motifs": { - "type": "file", - "description": "Sequence motif file (e.g., from transcription factors)", - "pattern": "*.txt", - "ontologies": [] - } - }, - { - "reference_config": { - "type": "file", - "description": "JSON-like file holding organism, genome, reference fasta path, reference annotation gtf path, contigs that should be excluded and sequence format motif file path", - "pattern": "config", - "ontologies": [] - } - } - ] - ], - "output": { - "reference": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing genome information\ne.g. `[ id:'genome' ]`\n" - } - }, - { - "${prefix}": { - "type": "directory", - "description": "Folder called like the reference_name containing all the reference indices needed by Cell Ranger Arc" - } - } ] - ], - "config": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing genome information\ne.g. `[ id:'genome' ]`\n" - } - }, - { - "config": { - "type": "file", - "description": "Configuration file", - "ontologies": [] - } - } - ] - ], - "versions_cellrangerarc": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cellrangerarc": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cellranger-arc --version 2>&1 | sed 's/cellranger-arc cellranger-arc-//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cellrangerarc": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cellranger-arc --version 2>&1 | sed 's/cellranger-arc cellranger-arc-//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] }, - "authors": [ - "@ggabernet", - "@heylf" - ] - }, - "pipelines": [ { - "name": "scrnaseq", - "version": "4.1.0" - } - ] - }, - { - "name": "cellrangeratac_count", - "path": "modules/nf-core/cellrangeratac/count/meta.yml", - "type": "module", - "meta": { - "name": "cellrangeratac_count", - "description": "Module to use Cell Ranger's ATAC pipelines analyze sequencing data produced from Chromium Single Cell ATAC.", - "keywords": [ - "align", - "count", - "reference" - ], - "tools": [ - { - "cellranger-atac": { - "description": "Cell Ranger ATAC is a set of analysis pipelines that process Chromium Single Cell ATAC data.", - "homepage": "https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac", - "documentation": "https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac", - "tool_dev_url": "https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac", - "licence": [ - "10x Genomics EULA" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + "name": "controlfreec_freec2bed", + "path": "modules/nf-core/controlfreec/freec2bed/meta.yml", + "type": "module", + "meta": { + "name": "controlfreec_freec2bed", + "description": "Plot Freec output", + "keywords": ["cna", "cnv", "somatic", "single", "tumor-only"], + "tools": [ + { + "controlfreec": { + "description": "Copy number and genotype annotation from whole genome and whole exome sequencing data.", + "homepage": "http://boevalab.inf.ethz.ch/FREEC", + "documentation": "http://boevalab.inf.ethz.ch/FREEC/tutorial.html", + "tool_dev_url": "https://github.com/BoevaLab/FREEC/", + "doi": "10.1093/bioinformatics/btq635", + "licence": ["GPL >=2"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "ratio": { + "type": "file", + "description": "ratio file generated by FREEC", + "pattern": "*.ratio.txt", + "ontologies": [] + } + } + ] + ], + "output": { + "bed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "Bed file", + "pattern": "*.bed", + "ontologies": [] + } + } + ] + ], + "versions_controlfreec": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "controlfreec": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "11.6b": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "controlfreec": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "11.6b": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@FriederikeHanssen"], + "maintainers": ["@FriederikeHanssen"] }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively, plus an additional FastQ for the barcodes\n", - "ontologies": [] - } - } - ], - { - "reference": { - "type": "directory", - "description": "Directory containing all the reference indices needed by Cell Ranger ATAC" - } - } - ], - "output": { - "outs": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "${meta.id}/outs/*": { - "type": "file", - "description": "Files containing the outputs of Cell Ranger ATAC", - "pattern": "sample-${meta.gem}/outs/*", - "ontologies": [] - } - } - ] - ], - "versions_cellrangeratac": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cellrangeratac": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cellranger-atac --version | sed 's/.*cellranger-atac-//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cellrangeratac": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cellranger-atac --version | sed 's/.*cellranger-atac-//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@ggabernet", - "@edmundmiller", - "@heylf" - ], - "maintainers": [ - "@ggabernet", - "@edmundmiller", - "@heylf" - ] - } - }, - { - "name": "cellrangeratac_mkfastq", - "path": "modules/nf-core/cellrangeratac/mkfastq/meta.yml", - "type": "module", - "meta": { - "name": "cellrangeratac_mkfastq", - "description": "Module to create fastqs needed by the 10x Genomics Cell Ranger ATAC tool. Uses the cellranger-atac mkfastq command.", - "keywords": [ - "reference", - "mkfastq", - "fastq", - "illumina", - "bcl2fastq" - ], - "tools": [ - { - "cellranger-atac": { - "description": "Cell Ranger ATAC by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.", - "homepage": "https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac", - "documentation": "https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac", - "tool_dev_url": "https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac", - "licence": [ - "10x Genomics EULA" - ], - "identifier": "" - } - } - ], - "input": [ - { - "bcl": { - "type": "file", - "description": "Base call files", - "pattern": "*.bcl.bgzf", - "ontologies": [] - } - }, - { - "csv": { - "type": "file", - "description": "Sample sheet", - "pattern": "*.csv", - "ontologies": [ + "pipelines": [ { - "edam": "http://edamontology.org/format_3752" + "name": "sarek", + "version": "3.8.1" } - ] - } - } - ], - "output": { - "fastq": [ - { - "${bcl.getSimpleName()}/outs/fastq_path/*.fastq.gz": { - "type": "file", - "description": "Unaligned FastQ files", - "pattern": "*.fastq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ], - "versions_cellrangeratac": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cellrangeratac": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cellranger-atac --version | sed 's/.*cellranger-atac-//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cellrangeratac": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cellranger-atac --version | sed 's/.*cellranger-atac-//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@ggabernet", - "@edmundmiller", - "@RHReynolds", - "@heylf" - ], - "maintainers": [ - "@ggabernet", - "@edmundmiller", - "@RHReynolds", - "@heylf" - ] - } - }, - { - "name": "cellrangeratac_mkref", - "path": "modules/nf-core/cellrangeratac/mkref/meta.yml", - "type": "module", - "meta": { - "name": "cellrangeratac_mkref", - "description": "Module to build the reference needed by the 10x Genomics Cell Ranger ATAC tool. Uses the cellranger-atac mkref command.", - "keywords": [ - "reference", - "mkref", - "index" - ], - "tools": [ - { - "cellranger-atac": { - "description": "Cell Ranger ATAC is a set of analysis pipelines that process Chromium Single Cell ATAC data.", - "homepage": "https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac", - "documentation": "https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac", - "tool_dev_url": "https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac", - "licence": [ - "10x Genomics EULA" - ], - "identifier": "" - } - } - ], - "input": [ - { - "fasta": { - "type": "file", - "description": "Reference genome FASTA file", - "pattern": "*.{fasta,fa}", - "ontologies": [] - } - }, - { - "gtf": { - "type": "file", - "description": "Reference transcriptome GTF file", - "pattern": "*.gtf", - "ontologies": [] - } - }, - { - "motifs": { - "type": "file", - "description": "Sequence motif file (e.g., of transcription factors)", - "pattern": "*.txt", - "ontologies": [] - } - }, - { - "reference_config": { - "type": "file", - "description": "JSON-like config file holding organism, genome, reference fasta path, reference annotation gtf path, contigs that should be excluded and sequence format motif file path", - "pattern": "config", - "ontologies": [] - } - }, - { - "reference_name": { - "type": "string", - "description": "The name to give the new reference folder", - "pattern": "str" - } - } - ], - "output": { - "reference": [ - { - "${reference_name}": { - "type": "directory", - "description": "Folder called regarding reference_name containing all the reference indices needed by Cell Ranger ATAC" - } - } - ], - "versions_cellrangeratac": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cellrangeratac": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cellranger-atac --version 2>&1 | sed 's/.*cellranger-atac-//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cellrangeratac": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cellranger-atac --version 2>&1 | sed 's/.*cellranger-atac-//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@ggabernet", - "@heylf" - ], - "maintainers": [ - "@ggabernet", - "@heylf" - ] - } - }, - { - "name": "cellsnp_modea", - "path": "modules/nf-core/cellsnp/modea/meta.yml", - "type": "module", - "meta": { - "name": "cellsnp_modea", - "description": "Cellsnp-lite is a C/C++ tool for efficient genotyping bi-allelic SNPs on single cells. You can use the mode A of cellsnp-lite after read alignment to obtain the snp x cell pileup UMI or read count matrices for each alleles of given or detected SNPs for droplet based single cell data.", - "keywords": [ - "genotyping", - "single cell", - "SNP", - "droplet based single cells" - ], - "tools": [ - { - "cellsnp": { - "description": "Efficient genotyping bi-allelic SNPs on single cells", - "homepage": "https://github.com/single-cell-genetics/cellsnp-lite", - "documentation": "https://cellsnp-lite.readthedocs.io", - "tool_dev_url": "https://github.com/single-cell-genetics/cellsnp-lite", - "doi": "10.1093/bioinformatics/btab358", - "licence": [ - "Apache-2.0" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "A single BAM/SAM/CRAM file, e.g., from CellRanger.", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } - }, - { - "bai": { - "type": "file", - "description": "The index of the BAM/CRAM file.", - "pattern": "*.{bai,crai}", - "ontologies": [] - } - }, - { - "region_vcf": { - "type": "file", - "description": "A optional vcf file listing all candidate SNPs for genotyping.", - "pattern": "*.{vcf, vcf.gz}", - "ontologies": [] - } - }, - { - "barcode": { - "type": "file", - "description": "A plain file listing all effective cell barcodes.", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "output": { - "base": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.base.vcf.gz": { - "type": "file", - "description": "A VCF file listing genotyped SNPs and aggregated AD & DP information (without GT).", - "pattern": "*.base.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "cell": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.cells.vcf.gz": { - "type": "file", - "description": "A VCF file listing genotyped SNPs and aggregated AD & DP information & genotype (GT) information for each cell or sample.", - "pattern": "*.cells.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "sample": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.samples.tsv": { - "type": "file", - "description": "A TSV file listing cell barcodes or sample IDs.", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "allele_depth": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.tag.AD.mtx": { - "type": "file", - "description": "A file in “Matrix Market exchange formats”, containing the allele depths of the alternative (ALT) alleles.", - "pattern": "*.tag.AD.mtx", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3916" - } - ] - } - } - ] - ], - "depth_coverage": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.tag.DP.mtx": { - "type": "file", - "description": "A file in “Matrix Market exchange formats”, containing the sum of allele depths of the reference and alternative alleles (REF + ALT).", - "pattern": "*.tag.DP.mtx", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3916" - } - ] - } - } - ] - ], - "depth_other": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.tag.OTH.mtx": { - "type": "file", - "description": "A file in “Matrix Market exchange formats”, containing the sum of allele depths of all the alleles other than REF and ALT.", - "pattern": "*.tag.OTH.mtx", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3916" - } - ] - } - } ] - ], - "versions_cellsnp": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cellsnp": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cellsnp-lite --v | cut -f2 -d ' '": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cellsnp": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cellsnp-lite --v | cut -f2 -d ' '": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@wxicu" - ], - "maintainers": [ - "@wxicu" - ] - } - }, - { - "name": "centrifuge_build", - "path": "modules/nf-core/centrifuge/build/meta.yml", - "type": "module", - "meta": { - "name": "centrifuge_build", - "description": "Build centrifuge database for taxonomic profiling", - "keywords": [ - "database", - "metagenomics", - "build", - "db", - "fasta" - ], - "tools": [ - { - "centrifuge": { - "description": "Classifier for metagenomic sequences", - "homepage": "https://ccb.jhu.edu/software/centrifuge/", - "documentation": "https://ccb.jhu.edu/software/centrifuge/manual.shtml", - "doi": "10.1101/gr.210641.116", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:centrifuge" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Fasta file containing sequences to be used in centrifuge database.", - "pattern": "*.{fasta,fna}", - "ontologies": [] - } - } - ], - { - "conversion_table": { - "type": "file", - "description": "A tab-separated file with sequence ID to taxonomy ID mapping", - "pattern": "*.{map}", - "ontologies": [] - } - }, - { - "taxonomy_tree": { - "type": "file", - "description": "A \\t|\\t-separated file mapping taxonomy. Typically nodes.dmp from the NCBI taxonomy dump. Links taxonomy IDs to their parents", - "pattern": "*.{dmp}", - "ontologies": [] - } - }, - { - "name_table": { - "type": "file", - "description": "A '|'-separated file mapping taxonomy IDs to a name. Typically names.dmp from the NCBI taxonomy dump. Links taxonomy IDs to their scientific name", - "pattern": "*.{dmp}", - "ontologies": [] - } - }, - { - "size_table": { - "type": "file", - "description": "Optional list of taxonomic IDs and lengths of the sequences belonging to the same taxonomic IDs.", - "pattern": "*", - "ontologies": [] - } - } - ], - "output": { - "cf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", - "pattern": "${prefix}/" - } - }, - { - "${prefix}/": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", - "pattern": "${prefix}/" - } - } - ] - ], - "versions_centrifuge": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "centrifuge": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "centrifuge --version 2>&1 | sed '1!d;s/.* version //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "centrifuge": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "centrifuge --version 2>&1 | sed '1!d;s/.* version //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] }, - "authors": [ - "@sarah-buddle", - "@jfy133" - ] - }, - "pipelines": [ { - "name": "createtaxdb", - "version": "3.0.0" - } - ] - }, - { - "name": "centrifuge_centrifuge", - "path": "modules/nf-core/centrifuge/centrifuge/meta.yml", - "type": "module", - "meta": { - "name": "centrifuge_centrifuge", - "description": "Classifies metagenomic sequence data", - "keywords": [ - "classify", - "metagenomics", - "fastq", - "db" - ], - "tools": [ - { - "centrifuge": { - "description": "Centrifuge is a classifier for metagenomic sequences.", - "homepage": "https://ccb.jhu.edu/software/centrifuge/", - "documentation": "https://ccb.jhu.edu/software/centrifuge/manual.shtml", - "doi": "10.1101/gr.210641.116", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:centrifuge" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", - "ontologies": [] - } - } - ], - { - "db": { - "type": "directory", - "description": "Path to directory containing centrifuge database files" - } - }, - { - "save_unaligned": { - "type": "boolean", - "description": "If true unmapped fastq files are saved" - } - }, - { - "save_aligned": { - "type": "boolean", - "description": "If true mapped fastq files are saved" - } - } - ], - "output": { - "report": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*report.txt": { - "type": "file", - "description": "File containing a classification summary\n", - "pattern": "*.{report.txt}", - "ontologies": [] - } - } - ] - ], - "results": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*results.txt": { - "type": "file", - "description": "File containing classification results\n", - "pattern": "*.{results.txt}", - "ontologies": [] - } - } - ] - ], - "sam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.{sam,tab}": { - "type": "file", - "description": "Optional output file containing read alignments (SAM format )or a table of per-read hit information (TAB)s\n", - "pattern": "*.{sam,tab}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "fastq_mapped": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.mapped.fastq{,.1,.2}.gz": { - "type": "file", - "description": "Mapped fastq files", - "pattern": "*.mapped.fastq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "fastq_unmapped": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.unmapped.fastq{,.1,.2}.gz": { - "type": "file", - "description": "Unmapped fastq files", - "pattern": "*.unmapped.fastq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "versions_centrifuge": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" 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"meta": { - "name": "centrifuge_kreport", - "description": "Creates Kraken-style reports from centrifuge out files", - "keywords": [ - "classify", - "metagenomics", - "fastq", - "db", - "report", - "kraken" - ], - "tools": [ - { - "centrifuge": { - "description": "Centrifuge is a classifier for metagenomic sequences.", - "homepage": "https://ccb.jhu.edu/software/centrifuge/", - "documentation": "https://ccb.jhu.edu/software/centrifuge/manual.shtml", - "doi": "10.1101/gr.210641.116", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:centrifuge" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + "name": "controlfreec_freec2circos", + "path": "modules/nf-core/controlfreec/freec2circos/meta.yml", + "type": "module", + "meta": { + "name": "controlfreec_freec2circos", + "description": "Format Freec output to circos input format", + "keywords": ["cna", "cnv", "somatic", 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"*.{fastq,fq,fastq.gz,fq.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information. e.g. `[ id:'sample1', single_end:false ]`" - } + }, + { + "name": "cooler_digest", + "path": "modules/nf-core/cooler/digest/meta.yml", + "type": "module", + "meta": { + "name": "cooler_digest", + "description": "Generate fragment-delimited genomic bins", + "keywords": ["digest", "enzyme", "cooler"], + "tools": [ + { + "cooler": { + "description": "Sparse binary format for genomic interaction matrices", + "homepage": "https://open2c.github.io/cooler/", + "documentation": "https://cooler.readthedocs.io/en/latest/index.html", + "tool_dev_url": "https://github.com/open2c/cooler", + "doi": "10.1093/bioinformatics/btz540", + "licence": ["BSD-3-Clause"], + "identifier": "" + } + } + ], + "input": [ + { + "fasta": { + "type": "file", + "description": "Genome assembly FASTA file or folder containing FASTA files (uncompressed).", + "pattern": "*.{fasta,fa}", + "ontologies": [] + } + }, + { + "chromsizes": { + "type": "file", + "description": "Path to a chromsizes file.", + "ontologies": [] + } + }, + { + "enzyme": { + "type": "string", + "description": "Name of restriction enzyme. e.g. CviQI.", + "documentation": "http://biopython.org/DIST/docs/cookbook/Restriction.html" + } + } + ], + "output": { + "bed": [ + { + "*.bed": { + "type": "file", + "description": "A genome segmentation of restriction fragments as a BED file.", + "pattern": "*.{bed}", + "ontologies": [] + } + } + ], + "versions_cooler": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cooler": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cooler --version 2>&1 | sed \"s/cooler, version //\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cooler": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cooler --version 2>&1 | sed \"s/cooler, version //\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@jianhong"], + "maintainers": ["@jianhong"] }, - { - "db": { - "type": "directory", - "description": "Path to directory containing Centrifuger database files (that end in `.cfr`)." - } - } - ], - { - "save_unclassified": { - "type": "boolean", - "description": "Optional - if true, output unclassified reads.\n" - } - }, - { - "save_classified": { - "type": "boolean", - "description": "Optional - if true, output classified reads.\n" - } - }, - { - "barcode": { - "type": "file", - "description": "Optional barcode file.\n" - } - }, - { - "umi": { - "type": "file", - "description": "Optional UMI file.\n" - } - } - ], - "output": { - "classification_file": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information. e.g. `[ id:'sample1', single_end:false ]`" - } - }, - { - "*.tsv": { - "type": "file", - "description": "File containing classification results\n", - "pattern": "${prefix}.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "fastq_classified": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.classified*.fq.gz": { - "type": "file", - "description": "FASTQ file(s) containing classified reads", - "pattern": "*.{fastq,fq,fastq.gz,fq.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "fastq_unclassified": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.unclassified*.fq.gz": { - "type": "file", - "description": "FASTQ file(s) containing unclassified reads", - "pattern": "*.{fastq,fq,fastq.gz,fq.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "versions_centrifuger": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "centrifuger": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "centrifuger -v 2>&1 | sed 's/Centrifuger v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "centrifuger": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "centrifuger -v 2>&1 | sed 's/Centrifuger v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "hicar", + "version": "1.0.0" + } ] - ] - }, - "authors": [ - "@haris18s" - ], - "maintainers": [ - "@haris18s", - "@sofstam", - "@jfy133" - ] - } - }, - { - "name": "centrifuger_quantification", - "path": "modules/nf-core/centrifuger/quantification/meta.yml", - "type": "module", - "meta": { - "name": "centrifuger_quantification", - "description": "Quantification (taxonomic profiling) of Centrifuger model", - "keywords": [ - "metagenomics", - "quantification", - "Centrifuger" - ], - "tools": [ - { - "centrifuger": { - "description": "Centrifuger is an efficient taxonomic classification method that compares sequencing reads against a microbial genome database.", - "homepage": "https://github.com/mourisl/centrifuger", - "documentation": "https://github.com/mourisl/centrifuger", - "tool_dev_url": "https://github.com/mourisl/centrifuger", - "doi": "10.1186/s13059-024-03244-4", - "licence": [ - "MIT" - ], - "identifier": "biotools:centrifuger" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' single_end:false ]`" - } - }, - { - "classification_file": { - "type": "file", - "description": "Path to file containing classification results" - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information. e.g. `[ id:'sample1', single_end:false ]`" - } + }, + { + "name": "cooler_dump", + "path": "modules/nf-core/cooler/dump/meta.yml", + "type": "module", + "meta": { + "name": "cooler_dump", + "description": "Dump a cooler’s data to a text stream.", + "keywords": ["dump", "text", "cooler"], + "tools": [ + { + "cooler": { + "description": "Sparse binary format for genomic interaction matrices", + "homepage": "https://open2c.github.io/cooler/", + "documentation": "https://cooler.readthedocs.io/en/latest/index.html", + "tool_dev_url": "https://github.com/open2c/cooler", + "doi": "10.1093/bioinformatics/btz540", + "licence": ["BSD-3-Clause"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "cool": { + "type": "file", + "description": "Path to COOL file", + "pattern": "*.{cool,mcool}", + "ontologies": [] + } + }, + { + "resolution": { + "type": "integer", + "description": "Resolution" + } + } + ] + ], + "output": { + "bedpe": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bedpe": { + "type": "file", + "description": "Output text file", + "pattern": "*.bedpe", + "ontologies": [] + } + } + ] + ], + "versions_cooler": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cooler": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cooler --version 2>&1 | sed \"s/cooler, version //\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cooler": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cooler --version 2>&1 | sed \"s/cooler, version //\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@jianhong", "@muffato"], + "maintainers": ["@jianhong", "@muffato"] }, - { - "db": { - "type": "directory", - "description": "Path to directory containing Centrifuger database files (that end in `.cfr`)." - } - } - ], - { - "taxonomy_nodes": { - "type": "file", - "description": "File describing parent-child relationships of a taxonomic tree in NCBI nodes.dmp format", - "ontologies": [ + "pipelines": [ { - "edam": "http://edamontology.org/format_1964" - } - ] - } - }, - { - "taxonomy_names": { - "type": "file", - "description": "File describing individual members of a taxonomic tree in NCBI names.dmp format", - "ontologies": [ + "name": "hic", + "version": "2.1.0" + }, { - "edam": "http://edamontology.org/format_1964" + "name": "hicar", + "version": "1.0.0" } - ] - } - }, - { - "size_table": { - "type": "file", - "description": "Optional - Table of contig (or genome) sizes." - } - } - ], - "output": { - "report_file": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" - } - }, - { - "${meta.id}.tsv": { - "type": "file", - "description": "File containing taxonomic profiling results\n", - "pattern": "${prefix}.tsv" - } - } - ] - ], - "versions_centrifuger": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "centrifuger": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "centrifuger -v 2>&1 | sed 's/Centrifuger v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "centrifuger": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "centrifuger -v 2>&1 | sed 's/Centrifuger v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@haris18s" - ], - "maintainers": [ - "@haris18s", - "@sofstam", - "@jfy133" - ] - } - }, - { - "name": "checkm2_databasedownload", - "path": "modules/nf-core/checkm2/databasedownload/meta.yml", - "type": "module", - "meta": { - "name": "checkm2_databasedownload", - "description": "CheckM2 database download", - "keywords": [ - "checkm", - "mag", - "metagenome", - "quality", - "completeness", - "contamination", - "bins" - ], - "tools": [ - { - "checkm2": { - "description": "CheckM2 - Rapid assessment of genome bin quality using machine learning", - "homepage": "https://github.com/chklovski/CheckM2", - "doi": "10.1038/s41592-023-01940-w", - "licence": [ - "GPL v3" - ], - "identifier": "" - } - } - ], - "input": [ - { - "db_zenodo_id": { - "type": "integer", - "description": "Zenodo ID of the CheckM2 database to download" - } - } - ], - "output": { - "database": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing database information\ne.g. `[ id:'test', version:1 ]`\n" - } - }, - { - "checkm2_db_v${db_version}.dmnd": { - "type": "file", - "description": "CheckM2 database file", - "pattern": "checkm2_db_v*.dmnd", - "ontologies": [] - } - } - ] - ], - "versions_checkm2_databasedownload": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "aria2": { - "type": "string", - "description": "The tool name" - } - }, - { - "aria2c --version 2>&1 | sed '1s/[^ ]* [^ ]* //; q'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "aria2": { - "type": "string", - "description": "The tool name" - } - }, - { - "aria2c --version 2>&1 | sed '1s/[^ ]* [^ ]* //; q'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@dialvarezs", - "@eit-maxlcummins" - ] - }, - "pipelines": [ - { - "name": "mag", - "version": "5.4.2" }, { - "name": "seqsubmit", - "version": "dev" - } - ] - }, - { - "name": "checkm2_predict", - "path": "modules/nf-core/checkm2/predict/meta.yml", - "type": "module", - "meta": { - "name": "checkm2_predict", - "description": "CheckM2 bin quality prediction", - "keywords": [ - "checkm", - "mag", - "metagenome", - "quality", - "completeness", - "contamination", - "bins" - ], - "tools": [ - { - "checkm2": { - "description": "CheckM2 - Rapid assessment of genome bin quality using machine learning", - "homepage": "https://github.com/chklovski/CheckM2", - "doi": "10.1038/s41592-023-01940-w", - "licence": [ - "GPL v3" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "One or multiple FASTA files of each bin", - "pattern": "*.{fasta,fna,fa}", - "ontologies": [] - } - } - ], - [ - { - "dbmeta": { - "type": "map", - "description": "Groovy Map containing database information\ne.g. `[ id:'test', version:1 ]`\n" - } + "name": "cooler_makebins", + "path": "modules/nf-core/cooler/makebins/meta.yml", + "type": "module", + "meta": { + "name": "cooler_makebins", + "description": "Generate fixed-width genomic bins", + "keywords": ["makebins", "cooler", "genomic bins"], + "tools": [ + { + "cooler": { + "description": "Sparse binary format for genomic interaction matrices", + "homepage": "https://open2c.github.io/cooler/", + "documentation": "https://cooler.readthedocs.io/en/latest/index.html", + "tool_dev_url": "https://github.com/open2c/cooler", + "doi": "10.1093/bioinformatics/btz540", + "licence": ["BSD-3-Clause"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "chromsizes": { + "type": "file", + "description": "Path to a chromsizes file.", + "ontologies": [] + } + }, + { + "cool_bin": { + "type": "integer", + "description": "Resolution (bin size) in base pairs" + } + } + ] + ], + "output": { + "bed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.bed": { + "type": "file", + "description": "Genome segmentation at a fixed resolution as a BED file.", + "pattern": "*.bed", + "ontologies": [] + } + } + ] + ], + "versions_cooler": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cooler": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cooler --version 2>&1 | sed \"s/cooler, version //\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cooler": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cooler --version 2>&1 | sed \"s/cooler, version //\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@nservant", "@muffato"], + "maintainers": ["@nservant", "@muffato"] }, - { - "db": { - "type": "file", - "description": "CheckM2 database", - "ontologies": [] - } - } - ] - ], - "output": { - "checkm2_output": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "${prefix}": { - "type": "directory", - "description": "CheckM2 output directory", - "pattern": "${prefix}/" - } - } - ] - ], - "checkm2_tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "${prefix}_checkm2_report.tsv": { - "type": "file", - "description": "CheckM2 summary completeness statistics table", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_checkm2_predict": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "checkm2": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "checkm2 --version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "checkm2": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "checkm2 --version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "hic", + "version": "2.1.0" + } ] - ] }, - "authors": [ - "@dialvarezs", - "@eit-maxlcummins" - ] - }, - "pipelines": [ { - "name": "mag", - "version": "5.4.2" + "name": "cooler_merge", + "path": "modules/nf-core/cooler/merge/meta.yml", + "type": "module", + "meta": { + "name": "cooler_merge", + "description": "Merge multiple coolers with identical axes", + "keywords": ["merge", "cooler", "hic"], + "tools": [ + { + "cooler": { + "description": "Sparse binary format for genomic interaction matrices", + "homepage": "https://open2c.github.io/cooler/", + "documentation": "https://cooler.readthedocs.io/en/latest/index.html", + "tool_dev_url": "https://github.com/open2c/cooler", + "doi": "10.1093/bioinformatics/btz540", + "licence": ["BSD-3-clause"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "cool": { + "type": "file", + "description": "Path to COOL file", + "pattern": "*.{cool,mcool}", + "ontologies": [] + } + } + ] + ], + "output": { + "cool": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.cool": { + "type": "file", + "description": "Path to COOL file", + "pattern": "*.cool", + "ontologies": [] + } + } + ] + ], + "versions_cooler": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cooler": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cooler --version 2>&1 | sed \"s/cooler, version //\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cooler": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cooler --version 2>&1 | sed \"s/cooler, version //\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@jianhong"], + "maintainers": ["@jianhong"] + } }, { - "name": "seqsubmit", - "version": "dev" - } - ] - }, - { - "name": "checkm_lineagewf", - "path": "modules/nf-core/checkm/lineagewf/meta.yml", - "type": "module", - "meta": { - "name": "checkm_lineagewf", - "description": "CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.", - "keywords": [ - "checkm", - "mag", - "metagenome", - "quality", - "isolates", - "microbes", - "single cells", - "completeness", - "contamination", - "bins", - "genome bins" - ], - "tools": [ - { - "checkm": { - "description": "Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes.", - "homepage": "https://ecogenomics.github.io/CheckM/", - "documentation": "https://github.com/Ecogenomics/CheckM/wiki", - "tool_dev_url": "https://github.com/Ecogenomics/CheckM", - "doi": "10.1101/gr.186072.114", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:checkm" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": 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"description": "Lineage file", - "pattern": "*.ms", - "ontologies": [] - } - } - ] - ], - "checkm_tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample', bin:'1' ]\n" - } - }, - { - "${prefix}.tsv": { - "type": "file", - "description": "CheckM summary completeness statistics table", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_checkm": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "checkm": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "checkm 2>&1 | grep '...:::' | sed 's/.*CheckM v//;s/ .*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - 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"${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cooltools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cooltools --version | sed -n 's/cooltools, version //p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cooltools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cooltools --version | sed -n 's/cooltools, version //p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@nservant"] + } }, { - "name": "viralmetagenome", - "version": "1.1.1" - } - ] - }, - { - "name": "checkv_endtoend", - "path": "modules/nf-core/checkv/endtoend/meta.yml", - "type": "module", - "meta": { - "name": "checkv_endtoend", 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peak-to-through ratio (PTR) from metagenomic sequence data", + "keywords": ["coptr", "mapping", "ptr"], + "tools": [ + { + "coptr": { + "description": "Accurate and robust inference of microbial growth dynamics from metagenomic sequencing reads.", + "homepage": "https://github.com/tyjo/coptr", + "documentation": "https://coptr.readthedocs.io/", + "tool_dev_url": "https://github.com/tyjo/coptr", + "doi": "10.1101/gr.275533.121", + "licence": ["GPL v3"], + "identifier": "biotools:coptr" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "pkl": { + "type": "file", + "description": "Python pickle file containing coverage maps", + "pattern": "*.pkl", + "ontologies": [ + { + "edam": "http://edamontology.org/format_4002" + } + ] + } + } + ] + ], + "output": { + "ptr": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample 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{ + "coptr |& sed -E '11!d ; s/CoPTR.*?\\(v(.*?)\\).*/\\1/'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + } + } + }, + { + "name": "coptr_extract", + "path": "modules/nf-core/coptr/extract/meta.yml", + "type": "module", + "meta": { + "name": "coptr_extract", + "description": "Computes the coverage map along the reference genome", + "keywords": ["coptr", "mapping", "ptr"], + "tools": [ + { + "coptr": { + "description": "Accurate and robust inference of microbial growth dynamics from metagenomic sequencing reads.", + "homepage": "https://github.com/tyjo/coptr", + "documentation": "https://coptr.readthedocs.io/", + "tool_dev_url": "https://github.com/tyjo/coptr", + "doi": "10.1101/gr.275533.121", + "licence": ["GPL v3"], + "identifier": "biotools:coptr" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "bam": { + "type": "file", + "description": "bam file with the mapping of the reads on the reference genome", + "pattern": "*.{.bam}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + } + ] + ], + "output": { + "coverage": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.pkl": { + "type": "file", + "description": "Python pickle (pkl) file containing coverage along the reference genome", + "pattern": "*.{pkl}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_4002" + } + ] + } + } + ] + ], + "versions_coptr": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "coptr": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "coptr |& sed -E '11!d ; s/CoPTR.*?\\(v(.*?)\\).*/\\1/'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@ramirobarrantes"], + "maintainers": ["@ramirobarrantes"], + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "coptr": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "coptr |& sed -E '11!d ; s/CoPTR.*?\\(v(.*?)\\).*/\\1/'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + } + } + }, + { + "name": "coptr_index", + "path": "modules/nf-core/coptr/index/meta.yml", + "type": "module", + "meta": { + "name": "coptr_index", + "description": "Indexes a directory of fasta files for use with CoPTR", + "keywords": ["coptr", "index", "ptr"], + "tools": [ + { + "coptr": { + "description": "Accurate and robust inference of microbial growth dynamics from metagenomic sequencing reads.", + "homepage": "https://github.com/tyjo/coptr", + "documentation": 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"description": "The name of the process" + } + }, + { + "coptr": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "coptr |& sed -E '11!d ; s/CoPTR.*?\\(v(.*?)\\).*/\\1/'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@ramirobarrantes"], + "maintainers": ["@ramirobarrantes"], + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "coptr": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "coptr |& sed -E '11!d ; s/CoPTR.*?\\(v(.*?)\\).*/\\1/'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + } + } + }, + { + "name": "coptr_map", + "path": "modules/nf-core/coptr/map/meta.yml", + "type": "module", + "meta": { + "name": "coptr_map", + "description": "Maps the reads to the reference database", + "keywords": ["coptr", "mapping", "ptr"], + "tools": [ + { + "coptr": { + "description": "Accurate and robust inference of microbial growth dynamics from metagenomic sequencing reads.", + "homepage": "https://github.com/tyjo/coptr", + "documentation": "https://coptr.readthedocs.io/", + "tool_dev_url": "https://github.com/tyjo/coptr", + "doi": "10.1101/gr.275533.121", + "licence": ["GPL v3"], + "identifier": "biotools:coptr" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "fastq file with reads", + "pattern": "*.{.fastq,.fq,.fastq.gz,fq.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing index genome id and path\ne.g. [ id:'test', 'bowtie2' ]\n" + } + }, + { + "index": { + "type": "file", + "description": 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"versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "coptr": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "coptr |& sed -E '11!d ; s/CoPTR.*?\\(v(.*?)\\).*/\\1/'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + } + } + }, + { + "name": "coptr_merge", + "path": "modules/nf-core/coptr/merge/meta.yml", + "type": "module", + "meta": { + "name": "coptr_merge", + "description": "Merge reads that were mapped to multiple indices", + "keywords": ["coptr", "mapping", "merging", "ptr"], + "tools": [ + { + "coptr": { + "description": "Accurate and robust inference of microbial growth dynamics from metagenomic sequencing reads.", + "homepage": "https://github.com/tyjo/coptr", + "documentation": "https://coptr.readthedocs.io/", + "tool_dev_url": "https://github.com/tyjo/coptr", + "doi": "10.1101/gr.275533.121", + "licence": ["GPL v3"], + "identifier": "biotools:coptr" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "bams": { + "type": "file", + "description": "bam files to merge. Assumes that the reads were mapped to different indices.", + "pattern": "*.bam", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + } + ] + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Merged BAM file", + "pattern": "*.{bam}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + } + ] + ], + "versions_coptr": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "coptr": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "coptr |& sed -E '11!d ; s/CoPTR.*?\\(v(.*?)\\).*/\\1/'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@ramirobarrantes"], + "maintainers": ["@ramirobarrantes"], + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "coptr": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "coptr |& sed -E '11!d ; s/CoPTR.*?\\(v(.*?)\\).*/\\1/'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + } + } + }, + { + "name": "coreograph", + "path": "modules/nf-core/coreograph/meta.yml", + "type": "module", + "meta": { + "name": "coreograph", + "description": "Great....yet another TMA dearray program. What does this one do? Coreograph uses UNet, a deep learning model, to identify complete/incomplete tissue cores on a tissue microarray. It has been trained on 9 TMA slides of different sizes and tissue types.", + "keywords": ["UNet", "TMA dearray", "Segmentation", "Cores"], + "tools": [ + { + "coreograph": { + "description": "A TMA dearray program that uses UNet, a deep learning model, to identify complete/incomplete tissue cores on a tissue microarray.", + "homepage": "https://mcmicro.org/parameters/core.html#coreograph", + "documentation": "https://mcmicro.org/troubleshooting/tuning/coreograph.html", + "tool_dev_url": "https://github.com/HMS-IDAC/UNetCoreograph", + "doi": "10.1038/s41592-021-01308-y", + "license": ["MIT License"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\n" + } + }, + { + "image": { + "type": "file", + "description": "OME-TIFF or TIFF file for core detection and extraction.", + "pattern": "*.{ome.tif,tif,tiff}", + "ontologies": [] + } + } + ] + ], + "output": { + "cores": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*[0-9]*.tif": { + "type": "file", + "description": "Complete/Incomplete tissue cores", + "pattern": "*.{tif}", + "ontologies": [] + } + } + ] + ], + "masks": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "masks/*.tif": { + "type": "file", + "description": "Binary masks for the Complete/Incomplete tissue cores", + "pattern": "./masks/*.{tif}", + "ontologies": [] + } + } + ] + ], + "tma_map": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "TMA_MAP.tif": { + "type": "file", + "description": "A TMA map showing labels and outlines", + "pattern": "TMA_MAP.tif", + "ontologies": [] + } + } + ] + ], + "centroids": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "centroidsY-X.txt": { + "type": "file", + "description": "A text file listing centroids of each core in format Y, X", + "pattern": "centroidsY-X.txt", + "ontologies": [] + } + } + ] + ], + "versions_coreograph": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "coreograph": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "2.2.9": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "coreograph": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "2.2.9": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@arozhada", "@MargotCh"], + "maintainers": ["@arozhada", "@MargotCh"] }, - { - "fasta": { - "type": "file", - "description": "fasta file", - "pattern": "*.{fasta,fna,fa}", - "ontologies": [] - } - } - ], - { - "db": { - "type": "directory", - "description": "Directory pointing to checkV database" - } - } - ], - "output": { - "quality_summary": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample', bin:'1' ]\n" - } - }, - { - "${prefix}/quality_summary.tsv": { - "type": "file", - "description": "CheckV's main output containing integrated results from the three main modules (contamination, completeness, complete genomes) with overall quality of contigs", - "pattern": "${prefix}/quality_summary.tsv", - "ontologies": [] - } - } - ] - ], - "completeness": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample', bin:'1' ]\n" - } - }, - { - "${prefix}/completeness.tsv": { - "type": "file", - "description": "CheckV's detailed overview table on estimating completeness", - 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} - }, - { - "${prefix}/proviruses.fna": { - "type": "file", - "description": "CheckV's extracted proviruses contigs", - "pattern": "${prefix}/proviruses.fna", - "ontologies": [] - } - } - ] - ], - "viruses": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample', bin:'1' ]\n" - } - }, - { - "${prefix}/viruses.fna": { - "type": "file", - "description": "CheckV's extracted virus contigs", - "pattern": "${prefix}/viruses.fna", - "ontologies": [] - } - } - ] - ], - "versions_checkv": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "checkv": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "checkv -h 2>&1 | sed '1!d;s/^.*CheckV v//;s/:.*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "checkv": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "checkv -h 2>&1 | sed '1!d;s/^.*CheckV v//;s/:.*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "mcmicro", + "version": "dev" + } ] - ] - }, - "authors": [ - "@Joon-Klaps" - ], - "maintainers": [ - "@Joon-Klaps" - ] - }, - "pipelines": [ - { - "name": "phageannotator", - "version": "dev" }, { - "name": "viralmetagenome", - "version": "1.1.1" - } - ] - }, - { - "name": "checkv_updatedatabase", - "path": "modules/nf-core/checkv/updatedatabase/meta.yml", - "type": "module", - "meta": { - "name": "checkv_updatedatabase", - "description": "Construct the database necessary for checkv's quality assessment", - "keywords": [ - "checkv", - "checkm", - "mag", - "metagenome", - "quality", - "isolates", - "virus", - "completeness", - "contamination" - ], - "tools": [ - { - "checkv": { - "description": "Assess the quality of metagenome-assembled viral genomes.", - 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"description": "File contains the loci coordinates in the genomes analyzed", - "pattern": "*_results_contigsInfo.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "alleles": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "*_results_alleles.tsv": { - "type": "file", - "description": "File contains the allelic profiles determined for the input sample", - "pattern": "*_results_alleles.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "*_logging_info.txt": { - "type": "file", - "description": "File contains the log information", - "pattern": "*_logging_info.txt", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2330" - } - ] - } - } - ] - ], - "paralogous_counts": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "*_paralogous_counts.tsv": { - "type": "file", - "description": "File contains the list of paralogous loci and the number of times those loci matched a CDS that was also similar to other loci in the schema", - "pattern": "*_paralogous_counts.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "paralogous_loci": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "*_paralogous_loci.tsv": { - "type": "file", - "description": "File contains the sets of paralogous loci identified in the input sample", - "pattern": "*_paralogous_loci.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "cds_coordinates": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "*_cds_coordinates.tsv": { - "type": "file", - "description": "File contains the coordinates of the CDS in the input sample", - "pattern": "*_cds_coordinates.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "invalid_cds": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "*_invalid_cds.txt": { - "type": "file", - "description": "File contains the list of alleles predicted by Prodigal that were excluded", - "pattern": "*_invalid_cds.txt", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2330" - } - ] - } - } - ] - ], - "loci_summary_stats": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "*_loci_summary_stats.tsv": { - "type": "file", - "description": "File contains summary statistics for each locus", - "pattern": "*_loci_summary_stats.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_chewbbaca": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "chewbbaca": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "chewie --version 2>&1 | sed 's/chewBBACA version: //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "chewbbaca": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "chewie --version 2>&1 | sed 's/chewBBACA version: //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@anwarMZ" - ] - } - }, - { - "name": "chewbbaca_createschema", - "path": "modules/nf-core/chewbbaca/createschema/meta.yml", - "type": "module", - "meta": { - "name": "chewbbaca_createschema", - "description": "Create a schema to determine the allelic profiles of a genome", - "keywords": [ - "cgMLST", - "WGS", - "genomics" - ], - "tools": [ - { - "chewbbaca": { - "description": "A complete suite for gene-by-gene schema creation and strain identification.", - "homepage": "https://chewbbaca.readthedocs.io/en/latest/index.html", - "documentation": "https://chewbbaca.readthedocs.io/en/latest/index.html", - "tool_dev_url": "https://github.com/B-UMMI/chewBBACA", - "doi": "10.1099/mgen.0.000166", - "licence": [ - "GPL v3" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "fasta": { - "type": "directory", - "description": "One or multiple FASTA files to create schema from", - "pattern": "*.{fasta,fa,fas,fna,fasta.gz,fa.gz,fas.gz,fna.gz}" - } - } - ], - { - "prodigal_tf": { - "type": "file", - "description": "File containing the prodigal training file", - "pattern": "*.ptf", - "ontologies": [] - } - }, - { - "cds": { - "type": "file", - "description": "File containing the prodigal cds file", - "pattern": "*.cds", - "ontologies": [] - } - } - ], - "output": { - "schema": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "results/$meta.id": { - "type": "directory", - "description": "Schema directory", - "pattern": "*/" - } - } - ] - ], - "cds_coordinates": [ - { - "results/cds_coordinates.tsv": { - "type": "file", - "description": "File containing the coordinates of the CDS in the input sample", - "pattern": "*_cds_coordinates.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - "invalid_cds": [ - { - "results/invalid_cds.txt": { - "type": "file", - "description": "File containing the list of alleles predicted by Prodigal that were excluded", - "pattern": "*_invalid_cds.txt", - "ontologies": [] - } - } - ], - "versions_chewbbaca": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "chewbbaca": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "chewie --version 2>&1 | sed 's/chewBBACA version: //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "chewbbaca": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "chewie --version 2>&1 | sed 's/chewBBACA version: //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@anwarMZ" - ] - } - }, - { - "name": "chopper", - "path": "modules/nf-core/chopper/meta.yml", - "type": "module", - "meta": { - "name": "chopper", - "description": "Filter and trim long read data.", - "keywords": [ - "filter", - "trimming", - "fastq", - "nanopore", - "qc" - ], - "tools": [ - { - "zcat": { - "description": "zcat uncompresses either a list of files on the command line or its standard input and writes the uncompressed data on standard output.", - "documentation": "https://linux.die.net/man/1/zcat", - "args_id": "$args", - "identifier": "" - } - }, - { - "chopper": { - "description": "A rust command line for filtering and trimming long reads.", - "homepage": "https://github.com/wdecoster/chopper", - "documentation": "https://github.com/wdecoster/chopper", - "tool_dev_url": "https://github.com/wdecoster/chopper", - "doi": "10.1093/bioinformatics/bty149", - "licence": [ - "MIT" - ], - "args_id": "$args2", - "identifier": "" - } - }, - { - "gzip": { - "description": "Gzip reduces the size of the named files using Lempel-Ziv coding (LZ77).", - "documentation": "https://linux.die.net/man/1/gzip", - "args_id": "$args3", - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + "name": "coverm_contig", + "path": "modules/nf-core/coverm/contig/meta.yml", + "type": "module", + "meta": { + "name": "coverm_contig", + "description": "Map reads to contigs and estimate coverage", + "keywords": ["mapping", "genomics", "metagenomics", "coverage"], + "tools": [ + { + "coverm": { + "description": "CoverM aims to be a configurable, easy to use and fast DNA read coverage and relative abundance calculator focused on metagenomics applications", + "homepage": "https://github.com/wwood/CoverM", + "documentation": "https://wwood.github.io/CoverM/coverm-contig.html", + "tool_dev_url": "https://github.com/wwood/CoverM", + "doi": "10.5281/zenodo.10531253", + "licence": ["GPL v3"], + "identifier": "biotools:coverm" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "input": { + "type": "file", + "description": "FASTA/FASTQ containing reads (can be gzipped), or sorted BAM files of reads mapped to a reference.\nIf supplying PE fasta for multiple samples, should be in the order \"sample1_1, sample1_2, sample2_1, sample2_2...\".\n", + "pattern": "*.{fa,fq,fa.gz,fq.gz,bam}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + }, + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "reference": { + "type": "file", + "description": "Reference FASTA file to map reads to, or minimap2/strobealign index.\nNot required if using BAM input.\n", + "pattern": "*.{fasta,fasta.gz,mmi,sti}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + { + "bam_input": { + "type": "boolean", + "description": "True if input is bam files" + } + }, + { + "interleaved": { + "type": "boolean", + "description": "True if input is interleaved fastq file" + } + }, + { + "enable_bam_output": { + "type": "boolean", + "description": "True to enable BAM output of aligned reads" + } + } + ], + "output": { + "coverage": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.depth.tsv": { + "type": "file", + "description": "Tab-delimited file containing coverage information for each contig and sample.", + "pattern": "*.depth.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "BAM file containing aligned reads.", + "pattern": "*.bam", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + } + ] + ], + "versions_coverm": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "coverm": { + "type": "string", + "description": "The tool name" + } + }, + { + "coverm --version | sed \"s/coverm //\"": { + "type": "string", + "description": "Command used to collect the version" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "coverm": { + "type": "string", + "description": "The tool name" + } + }, + { + "coverm --version | sed \"s/coverm //\"": { + "type": "string", + "description": "Command used to collect the version" + } + } + ] + ] + }, + "authors": ["@prototaxites"], + "maintainers": ["@prototaxites"] }, - { - "fastq": { - "type": "file", - "description": "FastQ with reads from long read sequencing e.g. PacBio or ONT", - "pattern": "*.{fastq.gz}", - "ontologies": [] - } - } - ], - { - "fasta": { - "type": "file", - "description": "An optional reference fasta file against which to remove reads that align to it.", - "pattern": "*.fasta", - "ontologies": [] - } - } - ], - "output": { - "fastq": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.fastq.gz": { - "type": "file", - "description": "Filtered and trimmed FastQ file", - "pattern": "*.{fastq.gz}", - "ontologies": [] - } - } - ] - ], - "versions_chopper": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "chopper": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "chopper --version 2>&1 | cut -d ' ' -f 2": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "chopper": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "chopper --version 2>&1 | cut -d ' ' -f 2": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "seqsubmit", + "version": "dev" + } ] - ] - }, - "authors": [ - "@FynnFreyer" - ], - "maintainers": [ - "@FynnFreyer" - ] - }, - "pipelines": [ - { - "name": "mag", - "version": "5.4.2" - } - ] - }, - { - "name": "chromap_chromap", - "path": "modules/nf-core/chromap/chromap/meta.yml", - "type": "module", - "meta": { - "name": "chromap_chromap", - "description": "Performs preprocessing and alignment of chromatin fastq files to fasta reference files using chromap.\n", - "keywords": [ - "chromap", - "alignment", - "map", - "fastq", - "bam", - "sam", - "hi-c", - "atac-seq", - "chip-seq", - "trimming", - "duplicate removal" - ], - "tools": [ - { - "chromap": { - "description": "Fast alignment and preprocessing of chromatin profiles\n", - "homepage": "https://github.com/haowenz/chromap", - "documentation": "https://github.com/haowenz/chromap", - "tool_dev_url": "https://github.com/haowenz/chromap", - "licence": [ - "GPL v3" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing information for the fasta\ne.g. [ id:'test' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome FASTA file", - "pattern": "*.{fa,fasta,fna}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing information for the index\ne.g. [ id:'test' ]\n" - } + }, + { + "name": "coverm_genome", + "path": "modules/nf-core/coverm/genome/meta.yml", + "type": "module", + "meta": { + "name": "coverm_genome", + "description": "Calculate read coverage per-genome", + "keywords": ["mapping", "genomics", "metagenomics", "coverage"], + "tools": [ + { + "coverm": { + "description": "CoverM aims to be a configurable, easy to use and fast DNA read coverage and relative abundance calculator focused on metagenomics applications", + "homepage": "https://github.com/wwood/CoverM", + "documentation": "https://wwood.github.io/CoverM/coverm-contig.html", + "tool_dev_url": "https://github.com/wwood/CoverM", + "doi": "10.5281/zenodo.10531253", + "licence": ["GPL v3"], + "identifier": "biotools:coverm" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "input": { + "type": "file", + "description": "FASTA/FASTQ containing reads (can be gzipped), or sorted BAM files of reads mapped to a reference.\nIf supplying PE fasta for multiple samples, should be in the order \"sample1_1, sample1_2, sample2_1, sample2_2...\".\n", + "pattern": "*.{fa,fq,fa.gz,fq.gz,bam}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + }, + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "reference": { + "type": "file", + "description": "Genome FASTA file(s) to map reads to, or a directory containing genome FASTA files.", + "pattern": "*.{fasta,fasta.gz,mmi,sti,fna,fna.gz,fa,fa.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + { + "bam_input": { + "type": "boolean", + "description": "True if input is bam files" + } + }, + { + "interleaved": { + "type": "boolean", + "description": "True if input is interleaved fastq file" + } + }, + { + "ref_mode": { + "type": "string", + "description": "How to interpret the `reference` input:\n - `\"dir\"`: Treat as a directory containing one or more FASTA files.\n - `\"file\"`: Treat as a single FASTA file.\n - `\"auto\"`: Automatically detect based on whether the `reference` path is a directory or file.\nDefaults to `\"auto\"` if not provided.\n", + "pattern": "^(dir|file|auto)$" + } + }, + { + "enable_bam_output": { + "type": "boolean", + "description": "True to enable BAM output of aligned reads" + } + } + ], + "output": { + "coverage": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.depth.tsv": { + "type": "map", + "description": "Tab-delimited file containing coverage information for each contig and sample.", + "pattern": "*.depth.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "BAM file containing aligned reads.", + "pattern": "*.bam", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + } + ] + ], + "versions_coverm": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "coverm": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "coverm --version | sed 's/coverm //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "coverm": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "coverm --version | sed 's/coverm //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@vinisalazar"], + "maintainers": ["@vinisalazar"] }, - { - "index": { - "type": "file", - "description": "Chromap genome index files (*.index)\n", - "ontologies": [] - } - } - ], - { - "barcodes": { - "type": "file", - "description": "Cell barcode files\n", - "ontologies": [] - } - }, - { - "whitelist": { - "type": "file", - "description": "Cell barcode whitelist file\n", - "ontologies": [] - } - }, - { - "chr_order": { - "type": "file", - "description": "Custom chromosome order\n", - "ontologies": [] - } - }, - { - "pairs_chr_order": { - "type": "file", - "description": "Natural chromosome order for pairs flipping\n", - "ontologies": [] - } - } - ], - "output": { - "bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bed.gz": { - "type": "file", - "description": "BED file", - "pattern": "*.bed.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "BAM file", - "pattern": "*.bam", - "ontologies": [] - } - } - ] - ], - "tagAlign": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tagAlign.gz": { - "type": "file", - "description": "tagAlign file", - "pattern": "*.tagAlign.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "pairs": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.pairs.gz": { - "type": "file", - "description": "pairs file", - "pattern": "*.pairs.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "versions_chromap": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "chromap": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "chromap --version 2>&1": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_samtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "chromap": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "chromap --version 2>&1": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - 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], - { - "annotation_genome_version": { - "type": "string", - "description": "Reference genome version passed to civicpy (e.g. GRCh38)" + }, + { + "name": "crabz_decompress", + "path": "modules/nf-core/crabz/decompress/meta.yml", + "type": "module", + "meta": { + "name": "crabz_decompress", + "description": "Decompress files with crabz", + "keywords": ["decompression", "gzip", "zlib"], + "tools": [ + { + "crabz": { + "description": "Like pigz, but rust", + "homepage": "https://github.com/sstadick/crabz", + "documentation": "https://github.com/sstadick/crabz", + "tool_dev_url": "https://github.com/sstadick/crabz", + "licence": ["MIT"], + "identifier": "biotools:crabz" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "archive": { + "type": "file", + "description": "File to be decompressed", + "pattern": "*.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "output": { + "file": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.*": { + "type": "file", + "description": "The decompressed file", + "pattern": "*.*", + "ontologies": [] + } + } + ] + ], + "versions_crabz": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "crabz": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "0.10.0": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "crabz": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "0.10.0": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@camlloyd"], + "maintainers": ["@camlloyd"] } - }, - { - "cache": { - "type": "file", - "description": "Optional civicpy cache file (*.pkl). If not provided, civicpy will download and cache data locally.", - "pattern": "*.pkl", - "ontologies": [] + }, + { + "name": "cramino", + "path": "modules/nf-core/cramino/meta.yml", + "type": "module", + "meta": { + "name": "cramino", + "description": "Quality assessment of long-read bam files using cramino.", + "keywords": ["quality assessment", "bam", "long-read", "genomics"], + "tools": [ + { + "cramino": { + "description": "A tool for very fast quality assessment of long read cram/bam files.", + "homepage": "https://github.com/wdecoster/cramino", + "documentation": "https://github.com/wdecoster/cramino#readme", + "tool_dev_url": "https://github.com/wdecoster/cramino", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM file", + "pattern": "*.{bam,cram}", + "ontologies": [] + } + }, + { + "bai": { + "type": "file", + "description": "Index of BAM/CRAM file", + "pattern": "*.{bai,crai,csi}", + "ontologies": [] + } + } + ] + ], + "output": { + "stats": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "Text file containing summary statistics of the long-read data", + "pattern": "*.txt", + "ontologies": [] + } + } + ] + ], + "arrow": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.arrow": { + "type": "file", + "description": "Arrow file containing summary statistics of the long-read data", + "pattern": "*.arrow", + "ontologies": [] + } + } + ] + ], + "versions_cramino": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cramino": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cramino -V | sed 's/cramino //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cramino": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cramino -V | sed 's/cramino //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@inemesb"], + "maintainers": ["@inemesb"] } - } - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.vcf.gz": { - "type": "file", - "description": "Annotated bgzipped VCF file", - "pattern": "*.vcf.gz", - "ontologies": [ + }, + { + "name": "crisprcleanr_normalize", + "path": "modules/nf-core/crisprcleanr/normalize/meta.yml", + "type": "module", + "meta": { + "name": "crisprcleanr_normalize", + "description": "remove false positives of functional crispr genomics due to CNVs", + "keywords": ["sort", "CNV", "correction", "CRISPR"], + "tools": [ + { + "crisprcleanr": { + "description": "Analysis of CRISPR functional genomics, remove false positive due to CNVs.", + "homepage": "https://github.com/francescojm/CRISPRcleanR", + "documentation": "https://github.com/francescojm/CRISPRcleanR/blob/master/Quick_start.pdf", + "tool_dev_url": "https://github.com/francescojm/CRISPRcleanR/tree/v3.0.0", + "doi": "10.1186/s12864-018-4989-y", + "licence": ["MIT"], + "identifier": "biotools:crisprcleanr" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "count_file": { + "type": "file", + "description": "sgRNA raw counts", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, + { + "library_file": { + "type": "file", + "description": "sgRNA library", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], { - "edam": "http://edamontology.org/format_3016" + "min_reads": { + "type": "integer", + "description": "Minimum number of reads" + } }, { - "edam": "http://edamontology.org/format_3989" + "min_targeted_genes": { + "type": "integer", + "description": "Minimum number of targeted genes" + } } - ] - } - } - ] - ], - "versions_civicpy": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "civicpy": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "civicpy --version | sed 's/.*version //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_htslib": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "htslib": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bgzip --version 2>&1 | head -1 | sed 's/bgzip (htslib) //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "civicpy": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "civicpy --version | sed 's/.*version //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "htslib": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bgzip --version 2>&1 | head -1 | sed 's/bgzip (htslib) //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@emmcauley" - ], - "maintainers": [ - "@emmcauley" - ] - } - }, - { - "name": "clair3", - "path": "modules/nf-core/clair3/meta.yml", - "type": "module", - "meta": { - "name": "clair3", - "description": "Clair3 is a germline small variant caller for long-reads", - "keywords": [ - "germline", - "variant", - "Indel", - "SNV" - ], - "tools": [ - { - "clair3": { - "description": "Clair3 is a small variant caller for long-reads. Compare to PEPPER (r0.4), Clair3 (v0.1) shows a better SNP F1-score with ≤30-fold of ONT data (precisionFDA Truth Challenge V2), and a better Indel F1-score, while runs generally four times faster. Clair3 makes the best of both worlds of using pileup or full-alignment as input for deep-learning based long-read small variant calling. Clair3 is simple and modular for easy deployment and integration.", - "homepage": "https://github.com/HKU-BAL/Clair3", - "documentation": "https://github.com/HKU-BAL/Clair3", - "tool_dev_url": "https://github.com/HKU-BAL/Clair3", - "doi": "10.1038/s43588-022-00387-x", - "licence": [ - "BSD-3-clause" - ], - "identifier": "biotools:clair3" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_25722" - }, - { - "edam": "http://edamontology.org/format_2573" - }, - { - "edam": "http://edamontology.org/format_3462" - } - ] - } - }, - { - "bai": { - "type": "file", - "description": "BAM index file", - "pattern": "*.bai", - "ontologies": [] - } - }, - { - "packaged_model": { - "type": "string", - "description": "string containing the name of a prepackaged Clair3 model full list of models and their descriptions is provided at https://github.com/HKU-BAL/Clair3?tab=readme-ov-file#pre-trained-models" - 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} - }, - { - "*.emsim.txt": { - "type": "file", - "description": "Bootstrapped values for the three parameters R/theta, nu and delta", - "pattern": "*.emsim.txt", - "ontologies": [] - } - } - ] - ], - "em": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.em.txt": { - "type": "file", - "description": "Point estimates for R/theta, nu, delta and the branch lengths", - "pattern": "*.em.txt", - "ontologies": [] - } - } - ] - ], - "status": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.importation_status.txt": { - "type": "file", - "description": "List of reconstructed recombination events", - "pattern": "*.importation_status.txt", - "ontologies": [] - } - } - ] - ], - "newick": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.labelled_tree.newick": { - "type": "file", - "description": "Tree with all nodes labelled", - "pattern": "*.labelled_tree.newick", - "ontologies": [] - } - } - ] - ], - "fasta": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.ML_sequence.fasta": { - "type": "file", - "description": "Sequence reconstructed by maximum likelihood", - "pattern": "*.ML_sequence.fasta", - "ontologies": [] - } - } - ] - ], - "pos_ref": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.position_cross_reference.txt": { - "type": "file", - "description": "CSV mapping input sequence files to the sequences in the *.ML_sequence.fasta", - "pattern": "*.position_cross_reference.txt", - "ontologies": [] - } - } - ] - ], - "versions_clonalframeml": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "clonalframeml": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "ClonalFrameML -version 2>&1 | sed 's/^.*ClonalFrameML v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "clonalframeml": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "ClonalFrameML -version 2>&1 | sed 's/^.*ClonalFrameML v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@rpetit3" - ], - "maintainers": [ - "@rpetit3" - ] - } - }, - { - "name": "clustalo_align", - "path": "modules/nf-core/clustalo/align/meta.yml", - "type": "module", - "meta": { - "name": "clustalo_align", - "description": "Align sequences using Clustal Omega", - 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} - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing tree information\ne.g. `[ id:'test_tree']`\n" - } - }, - { - "tree": { - "type": "file", - "description": "Input guide tree in Newick format", - "pattern": "*.{dnd}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2006" - } - ] - } - } - ], - { - "hmm_in": { - "type": "file", - "description": "HMM file for profile alignment", - "pattern": "*.hmm", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1391" - } - ] - } - }, - { - "hmm_batch": { - "type": "file", - "description": "specify HMMs for individual sequences", - "pattern": "*.hmm", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1391" - } - ] + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "optional filtered/compressed BAM file", + "pattern": "*.{bam}", + "ontologies": [] + } + } + ] + ], + "cram": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.cram": { + "type": "file", + "description": "optional filtered/compressed CRAM file", + "pattern": "*.{cram}", + "ontologies": [] + } + } + ] + ], + "sam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.sam": { + "type": "file", + "description": "optional filtered/compressed SAM file", + "pattern": "*.{sam}", + "ontologies": [] + } + } + ] + ], + "bed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "optional suspicious regions BED file", + "pattern": "*{bed}", + "ontologies": [] + } + } + ] + ], + "versions_crumble": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "crumble": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "0.9.1": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "crumble": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "0.9.1": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@priyanka-surana"], + "maintainers": ["@priyanka-surana"] } - }, - { - "profile1": { - "type": "file", - "description": "Pre-aligned multiple sequence file 1", - "pattern": "*.{alnfaa,faa,fa,fasta}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" + }, + { + "name": "csvtk_concat", + "path": "modules/nf-core/csvtk/concat/meta.yml", + "type": "module", + "meta": { + "name": "csvtk_concat", + "description": "Concatenate two or more CSV (or TSV) tables into a single table", + "keywords": ["concatenate", "tsv", "csv"], + "tools": [ + { + "csvtk": { + "description": "A cross-platform, efficient, practical CSV/TSV toolkit", + "homepage": "http://bioinf.shenwei.me/csvtk", + "documentation": "http://bioinf.shenwei.me/csvtk", + "tool_dev_url": "https://github.com/shenwei356/csvtk", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "csv": { + "type": "file", + "description": "CSV/TSV formatted files", + "pattern": "*.{csv,tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + }, + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + { + "in_format": { + "type": "string", + "description": "Input format (csv, tab, or a delimiting character)", + "pattern": "*" + } + }, + { + "out_format": { + "type": "string", + "description": "Output format (csv, tab, or a delimiting character)", + "pattern": "*" + } + } + ], + "output": { + "csv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.${out_extension}": { + "type": "file", + "description": "Concatenated CSV/TSV file", + "pattern": "*.{csv,tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + }, + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_csvtk": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "csvtk": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "csvtk version | sed -e 's/csvtk v//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "csvtk": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "csvtk version | sed -e 's/csvtk v//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] }, + "authors": ["@rpetit3"], + "maintainers": ["@rpetit3"] + }, + "pipelines": [ { - "edam": "http://edamontology.org/format_2554" + "name": "deepmodeloptim", + "version": "dev" }, { - "edam": "http://edamontology.org/format_1921" + "name": "multiplesequencealign", + "version": "1.1.1" }, { - "edam": "http://edamontology.org/format_1984" + "name": "reportho", + "version": "1.1.0" } - ] - } - }, - { - "profile2": { - "type": "file", - "description": "Pre-aligned multiple sequence file 2", - "pattern": "*.{alnfaa,faa,fa,fasta}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" + ] + }, + { + "name": "csvtk_join", + "path": "modules/nf-core/csvtk/join/meta.yml", + "type": "module", + "meta": { + "name": "csvtk_join", + "description": "Join two or more CSV (or TSV) tables by selected fields into a single table", + "keywords": ["join", "tsv", "csv"], + "tools": [ + { + "csvtk": { + "description": "A cross-platform, efficient, practical CSV/TSV toolkit", + "homepage": "http://bioinf.shenwei.me/csvtk", + "documentation": "http://bioinf.shenwei.me/csvtk", + "tool_dev_url": "https://github.com/shenwei356/csvtk", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "csv": { + "type": "file", + "description": "CSV/TSV formatted files", + "pattern": "*.{csv,tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + }, + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "output": { + "csv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.${out_extension}": { + "type": "file", + "description": "Joined CSV/TSV file", + "pattern": "*.{csv,tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + }, + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_csvtk": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "csvtk": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "csvtk version | sed -e 's/csvtk v//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "csvtk": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "csvtk version | sed -e 's/csvtk v//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@anoronh4"], + "maintainers": ["@anoronh4"] + }, + "pipelines": [ { - "edam": "http://edamontology.org/format_2554" + "name": "circrna", + "version": "dev" }, { - "edam": "http://edamontology.org/format_1921" + "name": "multiplesequencealign", + "version": "1.1.1" }, { - "edam": "http://edamontology.org/format_1984" - } - ] - } - }, - { - "compress": { - "type": "boolean", - "description": "Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded." - } - } - ], - "output": { - "alignment": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" + "name": "reportho", + "version": "1.1.0" } - }, - { - "*.aln{.gz,}": { - "type": "file", - "description": "Alignment file, in gzipped fasta format", - "pattern": "*.aln{.gz,}", - "ontologies": [ + ] + }, + { + "name": "csvtk_mutate2", + "path": "modules/nf-core/csvtk/mutate2/meta.yml", + "type": "module", + "meta": { + "name": "csvtk_mutate2", + "description": "Create a new column from selected fields by awk-like arithmetic/string expressions", + "keywords": ["mutate", "tsv", "csv"], + "tools": [ + { + "csvtk": { + "description": "A cross-platform, efficient, practical CSV/TSV toolkit", + "homepage": "http://bioinf.shenwei.me/csvtk", + "documentation": "http://bioinf.shenwei.me/csvtk", + "tool_dev_url": "https://github.com/shenwei356/csvtk", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "CSV/TSV formatted files, or files with a custom delimiter", + "pattern": "*.{csv,tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + }, + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], { - "edam": "http://edamontology.org/format_2554" + "in_format": { + "type": "string", + "description": "Input format (csv, tsv, or a delimiting character)", + "pattern": "*" + } }, { - "edam": "http://edamontology.org/format_1921" + "out_format": { + "type": "string", + "description": "Output format (csv, tsv, or a delimiting character)", + "pattern": "*" + } + } + ], + "output": { + "output": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.${out_extension}": { + "type": "file", + "description": "Mutated CSV/TSV file", + "pattern": "*.{csv,tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + }, + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_csvtk": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "csvtk": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "csvtk version | sed -e 's/csvtk v//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "csvtk": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "csvtk version | sed -e 's/csvtk v//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@fellen31"], + "maintainers": ["@fellen31"] + } + }, + { + "name": "csvtk_sort", + "path": "modules/nf-core/csvtk/sort/meta.yml", + "type": "module", + "meta": { + "name": "csvtk_sort", + "description": "Sort CSV (or TSV) tables", + "keywords": ["sort", "tsv", "csv"], + "tools": [ + { + "csvtk": { + "description": "A cross-platform, efficient, practical CSV/TSV toolkit", + "homepage": "http://bioinf.shenwei.me/csvtk", + "documentation": "http://bioinf.shenwei.me/csvtk", + "tool_dev_url": "https://github.com/shenwei356/csvtk", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "csv": { + "type": "file", + "description": "CSV/TSV formatted file", + "pattern": "*.{csv,tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + }, + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + { + "in_format": { + "type": "string", + "description": "Input format (csv, tab, or a delimiting character)", + "pattern": "*" + } }, { - "edam": "http://edamontology.org/format_1984" + "out_format": { + "type": "string", + "description": "Output format (csv, tab, or a delimiting character)", + "pattern": "*" + } } - ] + ], + "output": { + "sorted": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.${out_extension}": { + "type": "file", + "description": "Sorted CSV/TSV file", + "pattern": "*.{csv,tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + }, + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_csvtk": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "csvtk": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "csvtk version | sed -e 's/csvtk v//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "csvtk": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "csvtk version | sed -e 's/csvtk v//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@LeonHafner"], + "maintainers": ["@LeonHafner"] + }, + "pipelines": [ + { + "name": "tfactivity", + "version": "dev" } - } - ] - ], - "versions_clustalo": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "clustalo": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "clustalo --version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } ] - ], - "versions_pigz": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pigz": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pigz --version 2>&1 | sed \"s/^.*pigz[[:space:]]*//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "clustalo": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "clustalo --version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pigz": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pigz --version 2>&1 | sed \"s/^.*pigz[[:space:]]*//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@luisas", - "@joseespinosa" - ], - "maintainers": [ - "@luisas", - "@joseespinosa", - "@lrauschning" - ] - }, - "pipelines": [ - { - "name": "ampliseq", - "version": "2.17.0" }, { - "name": "multiplesequencealign", - "version": "1.1.1" - }, - { - "name": "phyloplace", - "version": "2.0.0" - } - ] - }, - { - "name": "clustalo_guidetree", - "path": "modules/nf-core/clustalo/guidetree/meta.yml", - "type": "module", - "meta": { - "name": "clustalo_guidetree", - "description": "Renders a guidetree in clustalo", - "keywords": [ - "guide tree", - "msa", - "newick" - ], - "tools": [ - { - "clustalo": { - "description": "Latest version of Clustal: a multiple sequence alignment program for DNA or proteins", - "homepage": "http://www.clustal.org/omega/", - "documentation": "http://www.clustal.org/omega/", - "tool_dev_url": "http://www.clustal.org/omega/", - "doi": "10.1038/msb.2011.75", - "licence": [ - "GPL v2" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" - } + "name": "csvtk_split", + "path": "modules/nf-core/csvtk/split/meta.yml", + "type": "module", + "meta": { + "name": "csvtk_split", + "description": "Splits CSV/TSV into multiple files according to column values", + "keywords": ["split", "csv", "tsv"], + "tools": [ + { + "csvtk": { + "description": "CSVTK is a cross-platform, efficient and practical CSV/TSV toolkit that allows rapid data investigation and manipulation.", + "homepage": "https://bioinf.shenwei.me/csvtk/", + "documentation": "https://bioinf.shenwei.me/csvtk/", + "tool_dev_url": "https://github.com/shenwei356/csvtk", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "csv": { + "type": "file", + "description": "CSV/TSV file", + "pattern": "*.{csv,tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + }, + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + { + "in_format": { + "type": "string", + "description": "Input format (csv, tab, or a delimiting character)", + "pattern": "*" + } + }, + { + "out_format": { + "type": "string", + "description": "Output format (csv, tab, or a delimiting character)", + "pattern": "*" + } + } + ], + "output": { + "split_csv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.${out_extension}": { + "type": "file", + "description": "Split CSV/TSV file", + "pattern": "*.{csv,tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + }, + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_csvtk": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "csvtk": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "csvtk version | sed -e 's/csvtk v//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "csvtk": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "csvtk version | sed -e 's/csvtk v//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@SusiJo"], + "maintainers": ["@SusiJo"] }, - { - "fasta": { - "type": "file", - "description": "Input sequences in FASTA format", - "pattern": "*.{fa,fasta}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1919" - }, - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ], - "output": { - "tree": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" - } - }, - { - "*.dnd": { - "type": "file", - "description": "Guide tree file in Newick format", - "pattern": "*.{dnd}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2006" - } - ] - } - } - ] - ], - "versions_clustalo": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "clustalo": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "clustalo --version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "clustalo": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "clustalo --version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "circrna", + "version": "dev" + } ] - ] - }, - "authors": [ - "@luisas", - "@JoseEspinosa" - ], - "maintainers": [ - "@luisas", - "@JoseEspinosa" - ] - }, - "pipelines": [ - { - "name": "multiplesequencealign", - "version": "1.1.1" - } - ] - }, - { - "name": "clusty", - "path": "modules/nf-core/clusty/meta.yml", - "type": "module", - "meta": { - "name": "clusty", - "description": "Clusty is a tool for large-scale clustering using sparse distance matrices, suitable for datasets with millions of objects.", - "keywords": [ - "cluster", - "network", - "contig", - "scaffold", - "alignment", - "protein" - ], - "tools": [ - { - "clusty": { - "description": "Clusty is a tool for large-scale data clustering.", - "homepage": "https://github.com/refresh-bio/clusty", - "documentation": "https://github.com/refresh-bio/clusty", - "tool_dev_url": "https://github.com/refresh-bio/clusty", - "doi": "10.1038/s41592-025-02701-7", - "licence": [ - "GPL v3-or-later" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "distances": { - "type": "file", - "description": "pairwise distances file (e.g., TSV format)", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } + }, + { + "name": "ctatsplicing_prepgenomelib", + "path": "modules/nf-core/ctatsplicing/prepgenomelib/meta.yml", + "type": "module", + "meta": { + "name": "ctatsplicing_prepgenomelib", + "description": "Reference preparation for CTAT-splicing", + "keywords": ["splicing", "cancer", "rna", "rnaseq"], + "tools": [ + { + "ctatsplicing": { + "description": "Detection and annotation of cancer splicing aberrations", + "homepage": "https://github.com/TrinityCTAT/CTAT-SPLICING", + "documentation": "https://github.com/TrinityCTAT/CTAT-SPLICING", + "tool_dev_url": "https://github.com/TrinityCTAT/CTAT-SPLICING", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "genome_lib": { + "type": "file", + "description": "CTAT genome library reference", + "pattern": "*", + "ontologies": [] + } + } + ], + { + "cancer_intron_tsv": { + "type": "file", + "description": "CTAT-splicing data resource supplement", + "ontologies": [] + } + } + ], + "output": { + "reference": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "genome_lib": { + "type": "file", + "description": "Modified CTAT genome library reference", + "pattern": "*", + "ontologies": [] + } + } + ] + ], + "versions_ctatsplicing": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "ctatsplicing": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "0.0.3": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "ctatsplicing": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "0.0.3": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@anoronh4", "@nvnieuwk"], + "maintainers": ["@anoronh4"], + "long_description": "This module prepares the CTAT genome library reference for splicing analysis by integrating cancer intron annotations.\nIt takes a CTAT genome library and a cancer intron TSV file as input, and outputs a modified genome library reference.\nThe output can be used in subsequent CTAT-splicing analyses to detect and annotate cancer splicing aberrations.\nMake sure to provide the correct genome library and cancer intron data resource.\n" }, - { - "objects": { - "type": "file", - "description": "Optional TSV file containing object identifiers", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "output": { - "assignments": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "TSV file with cluster assignments", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_clusty": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "clusty": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "echo $(clusty --version 2>&1": { - "type": "string", - "description": "The version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "clusty": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "echo $(clusty --version 2>&1": { - "type": "string", - "description": "The version of the tool" - } - } + "pipelines": [ + { + "name": "rnafusion", + "version": "4.1.2" + } ] - ] - }, - "authors": [ - "@Joon-Klaps" - ], - "maintainers": [ - "@Joon-Klaps" - ] - }, - "pipelines": [ - { - "name": "viralmetagenome", - "version": "1.1.1" - } - ] - }, - { - "name": "cmaple", - "path": "modules/nf-core/cmaple/meta.yml", - "type": "module", - "meta": { - "name": "cmaple", - "description": "Efficient phylogenetic tree reconstruction for sequences using the CMAPLE algorithm", - "keywords": [ - "phylogeny", - "phylogenetic tree", - "maximum likelihood", - "dna", - "amino acid", - "alignment", - "tree reconstruction", - "cmaple", - "iqtree" - ], - "tools": [ - { - "cmaple": { - "description": "CMAPLE (Comprehensive Maximum-likelihood Analysis for Phylogenetic Likelihood Estimation)\nis an efficient implementation of the MAPLE algorithm for phylogenetic tree reconstruction,\nparticularly optimized for pathogen sequences with low divergence such as SARS-CoV-2.\nIt is integrated within IQ-TREE.\n", - "homepage": "https://github.com/iqtree/cmaple", - "documentation": "https://github.com/iqtree/cmaple/wiki/User-Manual", - "tool_dev_url": "https://github.com/iqtree/cmaple", - "doi": "10.1093/molbev/msae134", - "licence": [ - "GPL-2.0" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "aln": { - "type": "file", - "description": "Multiple sequence alignment file in FASTA, PHYLIP, or MAPLE format.\nCan be gzipped on uncompressed.\n", - "pattern": "*.{fa,fasta,faa,fna,fas,aln,afa,phy,phylip,maple}{.gz,}", - "ontologies": [ - { - "edam": "http://edamontology.org/data_0863" - }, - { - "edam": "http://edamontology.org/format_1929" - }, - { - "edam": "http://edamontology.org/format_1997" - }, - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - }, - { - "newick": { - "type": "file", - "description": "A Newick formatted tree based on multiple sequence alignment", - "pattern": "*.{newick,nwk,treefile}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1910" - } - ] - } - } - ] - ], - "output": { - "treefile": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.treefile": { - "type": "file", - "description": "Maximum likelihood phylogenetic tree in Newick format", - "pattern": "*.treefile", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1910" - } - ] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.log": { - "type": "file", - "description": "Log file containing detailed information about the tree reconstruction process", - "pattern": "*.log", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2330" - } - ] - } - } - ] - ], - "versions_cmaple": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cmaple": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cmaple --help | grep -m1 -oE \"[0-9]+(\\.[0-9]+)+\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cmaple": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cmaple --help | grep -m1 -oE \"[0-9]+(\\.[0-9]+)+\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@vagkaratzas" - ], - "maintainers": [ - "@vagkaratzas" - ] - }, - "pipelines": [ - { - "name": "proteinfamilies", - "version": "2.3.0" - } - ] - }, - { - "name": "cmseq_polymut", - "path": "modules/nf-core/cmseq/polymut/meta.yml", - "type": "module", - "meta": { - "name": "cmseq_polymut", - "description": "Calculates polymorphic site rates over protein coding genes", - "keywords": [ - "polymut", - "polymorphic", - "mags", - "assembly", - "polymorphic sites", - "estimation", - "protein coding genes", - "cmseq", - "bam", - "coverage" - ], - "tools": [ - { - "cmseq": { - "description": "Set of utilities on sequences and BAM files", - "homepage": "https://github.com/SegataLab/cmseq", - "documentation": "https://github.com/SegataLab/cmseq", - "tool_dev_url": "https://github.com/SegataLab/cmseq", - "licence": [ - "MIT License" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file", - "pattern": "*.bam", - "ontologies": [] - } - }, - { - "bai": { - "type": "file", - "description": "BAM index file", - "pattern": "*.bai", - "ontologies": [] - } - }, - { - "gff": { - "type": "file", - "description": "GFF file used to extract protein-coding genes", - "pattern": "*.gff", - "ontologies": [] - } + }, + { + "name": "ctatsplicing_startocancerintrons", + "path": "modules/nf-core/ctatsplicing/startocancerintrons/meta.yml", + "type": "module", + "meta": { + "name": "ctatsplicing_startocancerintrons", + "description": "Detection and annotation of aberrant splicing isoforms in cancer transcriptomes", + "keywords": ["splicing", "cancer", "rna", "rnaseq"], + "tools": [ + { + "ctatsplicing": { + "description": "Detection and annotation of cancer splicing aberrations", + "homepage": "https://github.com/TrinityCTAT/CTAT-SPLICING", + "documentation": "https://github.com/TrinityCTAT/CTAT-SPLICING", + "tool_dev_url": "https://github.com/TrinityCTAT/CTAT-SPLICING", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "split_junction": { + "type": "file", + "description": "STAR alignment splice junction tab file", + "pattern": "*.SJ.out.tab", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, + { + "junction": { + "type": "file", + "description": "STAR alignment chimeric junction file", + "pattern": "*.out.junction", + "ontologies": [] + } + }, + { + "bam": { + "type": "file", + "description": "Sorted BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + }, + { + "edam": "http://edamontology.org/format_2573" + }, + { + "edam": "http://edamontology.org/format_3462" + } + ] + } + }, + { + "bai": { + "type": "file", + "description": "BAM/CRAM/SAM index file", + "pattern": "*.{bai,crai,sai}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3327" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "genome_lib": { + "type": "file", + "description": "CTAT genome library reference with integrated cancer intron annotation", + "pattern": "*", + "ontologies": [] + } + } + ] + ], + "output": { + "cancer_introns_sorted_bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.cancer_intron_reads.sorted.bam": { + "type": "file", + "description": "Sorted BAM file containing reads mapped to cancer introns", + "pattern": "*.cancer_intron_reads.sorted.bam", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + } + ] + ], + "cancer_introns_sorted_bai": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.cancer_intron_reads.sorted.bam.bai": { + "type": "file", + "description": "Index file for the sorted BAM of cancer introns", + "pattern": "*.cancer_intron_reads.sorted.bam.bai", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3327" + } + ] + } + } + ] + ], + "gene_reads_sorted_bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.gene_reads.sorted.sifted.bam": { + "type": "file", + "description": "Sorted BAM file containing reads mapped to gene regions after downsampling coverage", + "pattern": "*.gene_reads.sorted.sifted.bam", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + } + ] + ], + "gene_reads_sorted_bai": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.gene_reads.sorted.sifted.bam.bai": { + "type": "file", + "description": "Index file for the sorted BAM of gene reads after filtering", + "pattern": "*.gene_reads.sorted.sifted.bam.bai", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3327" + } + ] + } + } + ] + ], + "cancer_introns": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.cancer.introns": { + "type": "file", + "description": "File containing detected and filtered introns that are found to be enriched in cancer transcriptomes", + "pattern": "*.cancer.introns", + "ontologies": [] + } + } + ] + ], + "cancer_introns_prelim": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.cancer.introns.prelim": { + "type": "file", + "description": "File containing detected introns that have at least one supporting read and are found to be enriched in cancer transcriptomes", + "pattern": "*.cancer.introns.prelim", + "ontologies": [] + } + } + ] + ], + "introns": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*${prefix}.introns": { + "type": "file", + "description": "File containing all detected introns", + "pattern": "*${prefix}.introns", + "ontologies": [] + } + } + ] + ], + "introns_igv_bed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.introns.for_IGV.bed": { + "type": "file", + "description": "Bed file used as input for IGV-report visualization, containing cancer introns", + "pattern": "*.introns.for_IGV.bed", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3586" + } + ] + } + } + ] + ], + "igv_html": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.ctat-splicing.igv.html": { + "type": "file", + "description": "Self-contained IGV-report in HTML format for visualization of cancer introns", + "pattern": "*.ctat-splicing.igv.html", + "ontologies": [] + } + } + ] + ], + "igv_tracks": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.igv.tracks": { + "type": "file", + "description": "IGV tracks file for visualizing cancer introns in IGV", + "pattern": "*.igv.tracks", + "ontologies": [] + } + } + ] + ], + "chckpts": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.chckpts": { + "type": "file", + "description": "Checkpoint files for CTAT-SPLICING, useful for debugging or resuming interrupted runs", + "pattern": "*.chckpts", + "ontologies": [] + } + } + ] + ], + "versions_ctatsplicing": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "ctatsplicing": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "0.0.3": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "ctatsplicing": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "0.0.3": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@anoronh4", "@nvnieuwk"], + "maintainers": ["@anoronh4"], + "long_description": "This module detects and annotates aberrant splicing isoforms in cancer transcriptomes using CTAT-splicing.\nIt takes STAR alignment files, a sorted BAM file, and a CTAT genome library reference as input, and outputs various files related to cancer introns.\nThe output can be used for further analysis of splicing aberrations in cancer.\nMake sure to provide the correct STAR alignment files and CTAT genome library reference.\n" }, - { - "fasta": { - "type": "file", - "description": "Optional fasta file to run on a subset of references in the BAM file.", - "pattern": ".{fa,fasta,fas,fna}", - "ontologies": [] - } - } - ] - ], - "output": { - "polymut": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.txt": { - "type": "file", - "description": "Polymut report in `.txt` format.", - "pattern": "*.txt", - "ontologies": [] - } - } - ] - ], - "versions_cmseq": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "cmseq": { - "type": "string", - "description": "The tool name" - } - }, - { - "VERSION": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "cmseq": { - "type": "string", - "description": "The tool name" - } - }, - { - "VERSION": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "rnafusion", + "version": "4.1.2" + } ] - ] - }, - "authors": [ - "@maxibor" - ], - "maintainers": [ - "@maxibor" - ] - } - }, - { - "name": "cnaqc", - "path": "modules/nf-core/cnaqc/meta.yml", - "type": "module", - "meta": { - "name": "cnaqc", - "description": "Quality control of copy number data from bulk WGS assays", - "keywords": [ - "WGS", - "copy number", - "quality control" - ], - "tools": [ - { - "cnaqc": { - "description": "Copy number quality control", - "homepage": "https://caravagnalab.github.io/CNAqc/", - "documentation": "https://caravagnalab.github.io/CNAqc/", - "tool_dev_url": "https://github.com/caravagnalab/CNAqc", - "licence": [ - "GPL v3-or-later" - ], - "identifier": "biotools:cnaqc" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "snv_rds": { - "type": "file", - "description": "R object with mutation data", - "pattern": "*.rds", - "ontologies": [] - } - }, - { - "cna_rds": { - "type": "file", - "description": "R object with copy number data", - "pattern": "*.rds", - "ontologies": [] - } + }, + { + "name": "ctree", + "path": "modules/nf-core/ctree/meta.yml", + "type": "module", + "meta": { + "name": "ctree", + "description": "Clone trees for Cancer Evolution studies from bulk sequencing data.", + "keywords": ["phylogenetic-trees", "cancer-genomics", "cancer-evolution", "clonal-evolution"], + "tools": [ + { + "ctree": { + "description": "The ctree package implements clones trees for cancer evolutionary studies. These models are built from\nCancer Cell Franctions (CCFs) clusters computed via tumour subclonal deconvolution, using either one or\nmore tumour biopsies at once. They can be used to model evolutionary trajectories from bulk sequencing\ndata, especially if whole-genome sequencing is available.\n", + "homepage": "https://caravagnalab.github.io/ctree/", + "documentation": "https://caravagnalab.github.io/ctree/", + "tool_dev_url": "https://github.com/caravagnalab/ctree", + "doi": "10.1038/s41592-018-0108-x", + "licence": ["GPL v3-or-later"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "ctree_input": { + "type": "file", + "description": "Either a .rds object of class `vb_bmm` or `dbpmm`, or a `.tsv` mutations table obtained after running the `pyclonevi` module\n", + "pattern": "*.{rds,tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "output": { + "ctree_rds": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "**ctree_{mobster,VIBER,pyclonevi}.rds": { + "type": "file", + "description": "The output varies based on the input. If the input is an object of class `dbpmm`,\nthe module outputs one object per sample as follows: `SampleID/ctree_mobster.rds`.\nIf the input is an object of class `vb_bmm`, the output will be one ctree object\nnamed `ctree_VIBER.rds`. If the input is the `pyclonevi` `.tsv` file, the output will\nbe one ctree object named `ctree_pyclonevi.rds`\n", + "pattern": "**ctree_{mobster,VIBER,pyclonevi}.rds", + "ontologies": [] + } + } + ] + ], + "ctree_plots_rds": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "**ctree_{mobster,VIBER,pyclonevi}_plots.rds": { + "type": "file", + "description": "Final plots as an .rds object. The module outputs one file for each ctree object\n", + "pattern": "**ctree_{mobster,VIBER,pyclonevi}_plots.rds", + "ontologies": [] + } + } + ] + ], + "ctree_report_rds": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "**ctree_{mobster,VIBER,pyclonevi}_report.rds": { + "type": "file", + "description": "Final report plots as an .rds object. The module outputs one file for each ctree object\n", + "pattern": "**ctree_{mobster,VIBER,pyclonevi}_report.rds", + "ontologies": [] + } + } + ] + ], + "ctree_report_pdf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "**ctree_{mobster,VIBER,pyclonevi}_report.pdf": { + "type": "file", + "description": "Final report plots as a pdf object. The module outputs one file for each ctree object\n", + "pattern": "**ctree_{mobster,VIBER,pyclonevi}_report.pdf", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3508" + } + ] + } + } + ] + ], + "ctree_report_png": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "**ctree_{mobster,VIBER,pyclonevi}_report.png": { + "type": "file", + "description": "Final report plots as a png object. The module outputs one file for each ctree object\n", + "pattern": "**ctree_{mobster,VIBER,pyclonevi}_report.png", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3603" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "topics": { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@elena-buscaroli"], + "maintainers": ["@elena-buscaroli"] }, - { - "tumour_sample": { - "type": "string", - "description": "string containing sample name", - "ontologies": [] - } - } - ] - ], - "output": { - "qc_rds": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', tumour_sample:'tumour_sample1_name' ]`\n" - } - }, - { - "*_qc.rds": { - "type": "file", - "description": "R object containing quality control results for the sample", - "pattern": "*{_qc.rds}", - "ontologies": [] - } - } - ] - ], - "data_plot_rds": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', tumour_sample:'tumour_sample1_name' ]`\n" - } - }, - { - "*_data_plot.rds": { - "type": "file", - "description": "R object containing plots of the CNA statistics for the sample", - "pattern": "*{_data_plot.rds}", - "ontologies": [] - } - }, - { - "*_qc_plot.rds": { - "type": "file", - "description": "R object containing plots of the quality control results for the sample", - "pattern": "*{_qc_plot.rds}", - "ontologies": [] - } - } - ] - ], - "qc_plot_rds": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', tumour_sample:'tumour_sample1_name' ]`\n" - } - }, - { - "*_qc_plot.rds": { - "type": "file", - "description": "R object containing plots of the quality control results for the sample", - "pattern": "*{_qc_plot.rds}", - "ontologies": [] - } - } - ] - ], - "plot_pdf_data": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', tumour_sample:'tumour_sample1_name' ]`\n" - } - }, - { - "*_data.pdf": { - "type": "file", - "description": "plots of the CNA statistics for the sample", - "pattern": "*{_data.pdf}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3508" - } - ] - } - } - ] - ], - "plot_pdf_qc": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', tumour_sample:'tumour_sample1_name' ]`\n" - } - }, - { - "*_qc.pdf": { - "type": "file", - "description": "plots of the quality control results for the sample", - "pattern": "*{_qc.pdf}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3508" - } - ] - } - } + "pipelines": [ + { + "name": "tumourevo", + "version": "dev" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "YAML file containing versions of tools used in the module", - "ontologies": [] - } - } - ] - }, - "topics": { - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "YAML file containing versions of tools used in the module", - "ontologies": [] - } - } - ] - }, - "authors": [ - "@vvvirgy" - ], - "maintainers": [ - "@vvvirgy" - ] - }, - "pipelines": [ - { - "name": "tumourevo", - "version": "dev" - } - ] - }, - { - "name": "cnvkit_access", - "path": "modules/nf-core/cnvkit/access/meta.yml", - "type": "module", - "meta": { - "name": "cnvkit_access", - "description": "Calculate the sequence-accessible coordinates in chromosomes from the given reference genome, output as a BED file.", - "keywords": [ - "cvnkit", - "access", - "fasta", - "copy number" - ], - "tools": [ - { - "cnvkit": { - "description": "CNVkit is a Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data.\nIt is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent.\n", - "homepage": "https://cnvkit.readthedocs.io/en/stable/index.html", - "documentation": "https://cnvkit.readthedocs.io/en/stable/index.html", - "tool_dev_url": "https://github.com/etal/cnvkit", - "doi": "10.1371/journal.pcbi.1004873", - "licence": [ - "Apache-2.0" - ], - "identifier": "biotools:cnvkit" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Genome FASTA.", - "pattern": "*.fasta", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "exclude_bed": { - "type": "file", - "description": "Additional regions to exclude, in BED format. Can be used multiple times.", - "ontologies": [] - } + }, + { + "name": "custom_addmostsevereconsequence", + "path": "modules/nf-core/custom/addmostsevereconsequence/meta.yml", + "type": "module", + "meta": { + "name": "custom_addmostsevereconsequence", + "description": "Annotate a VEP annotated VCF with the most severe consequence field", + "keywords": ["annotation", "vep", "consequence", "vcf"], + "tools": [ + { + "custom": { + "description": "Custom module to annotate a VEP annotated VCF with the most severe consequence field", + "tool_dev_url": "https://github.com/nf-core/modules/blob/master/modules/nf-core/custom/addmostsevereconsequence/main.nf", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VEP annotated VCF file", + "pattern": "*.{vcf,vcf.gz}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "variant_consequences": { + "type": "file", + "description": "File with VEP variant consequences, one per line.", + "pattern": "*", + "ontologies": [] + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "Annotated VCF file", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "versions_addmostsevereconsequence": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "addmostsevereconsequence": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "1.2.0": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_bgzip": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bgzip": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bgzip --version | sed '1!d;s/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "addmostsevereconsequence": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "1.2.0": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bgzip": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bgzip --version | sed '1!d;s/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@ramprasadn", "@fellen31"], + "maintainers": ["@ramprasadn", "@fellen31"] } - ] - ], - "output": { - "bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bed": { - "type": "file", - "description": "File containing accessible regions.", - "pattern": "*.{bed}", - "ontologies": [] - } - } - ] - ], - "versions_cnvkit": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "cnvkit": { - "type": "string", - "description": "The tool name" - } - }, - { - "cnvkit.py version | sed -e \"s/cnvkit v//g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "cnvkit": { - "type": "string", - "description": "The tool name" - } - }, - { - "cnvkit.py version | sed -e \"s/cnvkit v//g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@adamrtalbot", - "@priesgo" - ], - "maintainers": [ - "@adamrtalbot", - "@priesgo" - ] - } - }, - { - "name": "cnvkit_antitarget", - "path": "modules/nf-core/cnvkit/antitarget/meta.yml", - "type": "module", - "meta": { - "name": "cnvkit_antitarget", - "description": "Derive off-target (“antitarget”) bins from target regions.", - "keywords": [ - "cvnkit", - "antitarget", - "cnv", - "copy number" - ], - "tools": [ - { - "cnvkit": { - "description": "CNVkit is a Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data.\nIt is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent.\n", - "homepage": "https://cnvkit.readthedocs.io/en/stable/index.html", - "documentation": "https://cnvkit.readthedocs.io/en/stable/index.html", - "tool_dev_url": "https://github.com/etal/cnvkit", - "doi": "10.1371/journal.pcbi.1004873", - "licence": [ - "Apache-2.0" - ], - "identifier": "biotools:cnvkit" + }, + { + "name": "custom_addmostseverepli", + "path": "modules/nf-core/custom/addmostseverepli/meta.yml", + "type": "module", + "meta": { + "name": "custom_addmostseverepli", + "description": "Annotate a VEP annotated VCF with the most severe pLi field", + "keywords": ["annotation", "vep", "pli", "vcf"], + "tools": [ + { + "custom": { + "description": "Custom module to annotate a VEP annotated VCF with the most severe pLi field", + "tool_dev_url": "https://github.com/nf-core/modules/blob/master/modules/nf-core/custom/addmostseverepli/main.nf", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VEP annotated VCF file", + "pattern": "*.{vcf,vcf.gz}", + "ontologies": [] + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "Annotated VCF file", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "versions_addmostseverepli": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "addmostseverepli": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "1.2.0": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_bgzip": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bgzip": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bgzip --version | sed '1!d;s/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "addmostseverepli": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "1.2.0": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bgzip": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bgzip --version | sed '1!d;s/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@ramprasadn", "@fellen31"], + "maintainers": ["@ramprasadn", "@fellen31"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + }, + { + "name": "custom_catadditionalfasta", + "path": "modules/nf-core/custom/catadditionalfasta/meta.yml", + "type": "module", + "meta": { + "name": "custom_catadditionalfasta", + "description": "Custom module to Add a new fasta file to an old one and update an associated GTF", + "keywords": ["fasta", "gtf", "genomics"], + "tools": [ + { + "custom": { + "description": "Custom module to Add a new fasta file to an old one and update an associated GTF", + "tool_dev_url": "https://github.com/nf-core/modules/blob/master/modules/nf-core/custom/catadditionalfasta/main.nf", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing fasta information\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA-format sequence file", + "pattern": "*.{fasta,fa}", + "ontologies": [] + } + }, + { + "gtf": { + "type": "file", + "description": "GTF-format annotation file for fasta", + "pattern": "*.gtf", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing additional fasta information\n" + } + }, + { + "add_fasta": { + "type": "file", + "description": "FASTA-format file of additional sequences", + "pattern": "*.fa", + "ontologies": [] + } + } + ], + { + "biotype": { + "type": "string", + "description": "Biotype to apply to new GTF entries" + } + } + ], + "output": { + "fasta": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing fasta information\n" + } + }, + { + "out/${prefix}.fasta": { + "type": "file", + "description": "FASTA-format combined sequence file", + "pattern": "*.{fasta,fa}", + "ontologies": [] + } + } + ] + ], + "gtf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing fasta information\n" + } + }, + { + "out/${prefix}.gtf": { + "type": "file", + "description": "GTF-format combined annotation file", + "pattern": "*.gtf", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "topics": { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@pinin4fjords"], + "maintainers": ["@pinin4fjords"] }, - { - "targets": { - "type": "file", - "description": "File containing genomic regions", - "pattern": "*.{bed}", - "ontologies": [] - } - } - ] - ], - "output": { - "bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bed": { - "type": "file", - "description": "File containing off-target regions", - "pattern": "*.{bed}", - "ontologies": [] - } - } - ] - ], - "versions_cnvkit": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cnvkit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cnvkit.py version | sed -e \"s/cnvkit v//g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cnvkit": { - "type": "string", - 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It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent.\n", - "homepage": "https://cnvkit.readthedocs.io/en/stable/index.html", - "documentation": "https://cnvkit.readthedocs.io/en/stable/index.html", - "licence": [ - "Apache-2.0" - ], - "identifier": "biotools:cnvkit" + }, + { + "name": "custom_clustermetrics", + "path": "modules/nf-core/custom/clustermetrics/meta.yml", + "type": "module", + "meta": { + "name": "CUSTOM_CLUSTERMETRICS", + "description": "Computes clustering quality metrics (silhouette, Calinski-Harabasz, Davies-Bouldin) and performs k-sweep analysis", + "keywords": [ + "clustering", + "metrics", + "silhouette", + "calinski-harabasz", + "davies-bouldin", + "evaluation" + ], + "tools": [ + { + "scikit-learn": { + "description": "Machine learning library for clustering metrics", + "homepage": "https://scikit-learn.org/", + "documentation": "https://scikit-learn.org/stable/modules/clustering.html", + "licence": ["BSD-3-Clause"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "features": { + "type": "file", + "description": "Tab-separated feature matrix with a `sample_id` column and one\ncolumn per numeric feature (e.g. PCA scores).\n", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, + { + "clusters": { + "type": "file", + "description": "Comma-separated cluster assignments with `sample_id` and integer\n`cluster` columns. Label -1 is treated as DBSCAN noise.\n", + "pattern": "*.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "output": { + "metrics": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.metrics.tsv": { + "type": "file", + "description": "TSV with selected cluster quality metrics", + "pattern": "*.metrics.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "k_sweep": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.k_sweep.csv": { + "type": "file", + "description": "CSV with metrics for different values of k", + "pattern": "*.k_sweep.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "selected": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.selected.json": { + "type": "file", + "description": "JSON with the selected/best metrics", + "pattern": "*.selected.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "plots": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.png": { + "type": "file", + "description": "Optional PNG plots (elbow, silhouette, etc.)", + "pattern": "*.png", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "topics": { + "versions": [ + { + "versions.yml": { + "type": "string", + "description": "The name of the process" + } + } + ] + }, + "authors": ["@dbaku42"], + "maintainers": ["@dbaku42"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "tumor": { - "type": "file", - "description": "Input tumour sample bam file (or cram)\n", - "pattern": "*.{bam,cram}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - }, - { - "edam": "http://edamontology.org/format_3462" - } - ] - } - }, - { - "tumor_index": { - "type": "file", - "description": "Input tumour sample bam/cram index file (only needed for bam input)\n", - "pattern": "*.{bai,crai}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3327" - } - ] - } - }, - { - "normal": { - "type": "file", - "description": "Input normal sample bam file (or cram)\n", - "pattern": "*.{bam,cram}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - }, - { - "edam": "http://edamontology.org/format_3462" - } - ] - } - }, - { - "normal_index": { - "type": "file", - "description": "Input normal sample bam/cram index file (only needed for bam input)\n", - "pattern": "*.{bai,crai}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3327" - } - ] - } + }, + { + "name": "custom_clustervisualization", + "path": "modules/nf-core/custom/clustervisualization/meta.yml", + "type": "module", + "meta": { + "name": "CUSTOM_CLUSTERVISUALIZATION", + "description": "Generates UMAP and t-SNE visualizations colored by cluster", + "keywords": ["clustering", "visualization", "pca", "umap", "tsne", "dimension-reduction"], + "tools": [ + { + "scikit-learn": { + "description": "Machine learning library for dimension reduction (PCA, t-SNE)", + "homepage": "https://scikit-learn.org/", + "documentation": "https://scikit-learn.org/stable/modules/clustering.html", + "licence": ["BSD-3-Clause"], + "identifier": "" + } + }, + { + "umap-learn": { + "description": "Uniform Manifold Approximation and Projection for dimension reduction", + "homepage": "https://umap-learn.readthedocs.io/", + "documentation": "https://umap-learn.readthedocs.io/en/latest/", + "licence": ["BSD-3-Clause"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "features": { + "type": "file", + "description": "Tab-separated feature matrix with a `sample_id` column and one\ncolumn per numeric feature (e.g. PCA scores).\n", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, + { + "clusters": { + "type": "file", + "description": "Comma-separated cluster assignments with `sample_id` and integer\n`cluster` columns. Label -1 is treated as DBSCAN noise.\n", + "pattern": "*.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "output": { + "umap_tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.umap.tsv": { + "type": "file", + "description": "UMAP coordinates per sample", + "pattern": "*.umap.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/operation_2432" + }, + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "tsne_tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.tsne.tsv": { + "type": "file", + "description": "t-SNE coordinates per sample", + "pattern": "*.tsne.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/operation_2432" + }, + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "umap_png": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.umap.png": { + "type": "file", + "description": "UMAP visualization coloured by cluster", + "pattern": "*.umap.png", + "ontologies": [] + } + } + ] + ], + "tsne_png": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.tsne.png": { + "type": "file", + "description": "t-SNE visualization coloured by cluster", + "pattern": "*.tsne.png", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "Software versions used in the module", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "topics": { + "versions": [ + { + "versions.yml": { + "type": "string", + "description": "The name of the process" + } + } + ] + }, + "authors": ["@dbaku42"], + "maintainers": ["@dbaku42"] } - ], - [ - { - "meta2": { - "type": 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"identifier": "" + } + } + ], + "input": [ + { + "versions": { + "type": "file", + "description": "YML file containing software versions", + "pattern": "*.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ], + "output": { + "yml": [ + { + "software_versions.yml": { + "type": "file", + "description": "Standard YML file containing software versions", + "pattern": "software_versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ], + "mqc_yml": [ + { + "software_versions_mqc.yml": { + "type": "file", + "description": "MultiQC custom content YML file containing software versions", + "pattern": "software_versions_mqc.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": 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"module", + "meta": { + "name": "custom_filterdifferentialtable", + "description": "Filters a differential expression table based on logFC and adjusted p-value thresholds", + "keywords": ["filter", "differential expression", "logFC", "significance statistic", "p-value"], + "tools": [ + { + "pandas": { + "description": "Python library for data manipulation and analysis", + "homepage": "https://pandas.pydata.org/", + "documentation": "https://pandas.pydata.org/docs/", + "tool_dev_url": "https://github.com/pandas-dev/pandas", + "doi": "10.5281/zenodo.3509134", + "licence": ["BSD-3-Clause"], + "identifiers": ["biotools:pandas", "conda:pandas"], + "identifier": "biotools:pandas" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input_file": { + "type": "file", + "description": "Input differential expression table (CSV, TSV, or TXT format)", + "pattern": "*.{csv,tsv,txt}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + }, + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + [ + { + "logfc_column": { + "type": "string", + "description": "Name of the column containing log fold change values" + } + }, + { + "fc_threshold": { + "type": "float", + "description": "Fold change threshold for filtering" + } + }, + { + "fc_cardinality": { + "type": "string", + "description": "Operator to compare the fold change values with the threshold.\nValid values are: \">=\", \"<=\", \">\", \"<\".\n" + } + } + ], + [ + { + "stat_column": { + "type": "string", + "description": "Name of the column containing the significance statistic values\n(eg. adjusted p-values).\n" + } + }, + { + "stat_threshold": { + "type": "float", + "description": "Statistic threshold for filtering" + } + }, + { + "stat_cardinality": { + "type": "string", + "description": "Operator to compare the column values with the threshold.\nValid values are: \">=\", \"<=\", \">\", \"<\".\n" + } + } + ] + ], + "output": { + "filtered": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_filtered.tsv": { + "type": "file", + "description": "Filtered differential expression table", + "pattern": "*_filtered.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "filtered_up": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_filtered_up.tsv": { + "type": "file", + "description": "Filtered differential expression table for overexpressed genes", + "pattern": "*_filtered_up.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "filtered_down": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_filtered_down.tsv": { + "type": "file", + "description": "Filtered differential expression table for underexpressed genes", + "pattern": "*_filtered_down.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "topics": { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@pinin4fjords", "@WackerO"], + "maintainers": ["@pinin4fjords", "@WackerO"] } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing information about target file\ne.g. [ id:'test' ]\n" - } - }, - { - "targets": { - "type": "file", - "description": "Input target bed file\n", - "pattern": "*.{bed}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3003" - } - ] - } + }, + { + "name": "custom_geneticmapconvert", + "path": "modules/nf-core/custom/geneticmapconvert/meta.yml", + "type": "module", + "meta": { + "name": "custom_geneticmapconvert", + "description": "This R script allows to automatically detect the different genetic map format and\nconvert the input file in all the other format type.\n", + "keywords": ["map", "convertion", "R"], + "tools": [ + { + "custom": { + "description": "Custom script to convert any genetic map format", + "homepage": "https://github.com/nf-core/tools", + "documentation": "https://github.com/nf-core/tools", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "map_file": { + "type": "file", + "description": "Genomic map file to process.\nThis file should contain the data of only one chromosome.\nIt should be a flat file (comma, semicolon, tab or space delimited) with\nat least the physical position and its corresponding recombination\ndistance in centiMorgans.\nThe columns names will be normalised (no space, extra character transformed to \"_\")\nand then automatically recognise as:\n - chr: _chr, chrom, chromosome\n - pos: position, bp\n - id: snp, marker, rsid\n - cm: genetic_map_cm\n - rate: combined_rate, combined_rate_cm_mb, cm_mb\nIf no header present, then it will try for 3 columns table with chr, pos, cm format\nand for 4 columns table with chr, id, cm, pos format.\n", + "ontologies": [] + } + } + ] + ], + "output": { + "glimpse_map": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "${prefix}.glimpse.map": { + "type": "file", + "description": "File containing the map in Glimpse format:\ntab-delimited file with header and columns:\npos, chr, cM\n", + "pattern": "*.glimpse.map" + } + } + ] + ], + "plink_map": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "${prefix}.plink.map": { + "type": "file", + "description": "File containing the map in PLINK format:\nspace-delimited file without header and columns:\nchr, id, cM, pos\n", + "pattern": "*.plink.map" + } + } + ] + ], + "stitch_map": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "${prefix}.stitch.map": { + "type": "file", + "description": "File containing the map in STITCH format:\nspace-delimited file with header and columns:\npos, rate, cM\n", + "pattern": "*.stitch.map" + } + } + ] + ], + "minimac_map": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "${prefix}.minimac.map": { + "type": "file", + "description": "File containing the map in Minimac format:\ntab-delimited file with header and columns:\nchr, pos, cM\n", + "pattern": "*.minimac.map" + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "topics": { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@LouisLeNezet"], + "maintainers": ["@LouisLeNezet"] } - ], - [ - { - "meta5": { - "type": "map", - "description": "Groovy Map containing information about reference file\ne.g. [ id:'test' ]\n" - } + }, + { + "name": "custom_getchromsizes", + "path": "modules/nf-core/custom/getchromsizes/meta.yml", + "type": "module", + "meta": { + "name": "custom_getchromsizes", + "description": "Generates a FASTA file of chromosome sizes and a fasta index file", + "deprecated": true, + "keywords": ["fasta", "chromosome", "indexing"], + "tools": [ + { + "samtools": { + "description": "Tools for dealing with SAM, BAM and CRAM files", + "homepage": "http://www.htslib.org/", + "documentation": "http://www.htslib.org/doc/samtools.html", + "tool_dev_url": "https://github.com/samtools/samtools", + "doi": "10.1093/bioinformatics/btp352", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA file", + "pattern": "*.{fa,fasta,fna,fas}", + "ontologies": [] + } + } + ] + ], + "output": { + "sizes": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.sizes": { + "type": "file", + "description": "File containing chromosome lengths", + "pattern": "*.{sizes}", + "ontologies": [] + } + } + ] + ], + "fai": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fai": { + "type": "file", + "description": "FASTA index file", + "pattern": "*.{fai}", + "ontologies": [] + } + } + ] + ], + "gzi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.gzi": { + "type": "file", + "description": "Optional gzip index file for compressed inputs", + "pattern": "*.gzi", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "topics": { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@tamara-hodgetts", "@chris-cheshire", "@muffato"], + "maintainers": ["@tamara-hodgetts", "@chris-cheshire", "@muffato"] }, - { - "reference": { - "type": "file", - "description": "Input reference cnn-file (only for germline and tumor-only running)\n", - "pattern": "*.{cnn}", - "ontologies": [] - } - } - ], - { - "panel_of_normals": { - "type": "file", - "description": "Input panel of normals file\n", - "pattern": "*.{cnn}", - "ontologies": [] - } - } - ], - "output": { - "bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bed": { - "type": "file", - "description": "File containing genomic regions", - "pattern": "*.{bed}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3003" - } - ] - } - } - ] - ], - "cnn": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.cnn": { - "type": "file", - "description": "File containing coverage information", - "pattern": "*.{cnn}", - "ontologies": [] - } - } - ] - ], - "cnr": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.cnr": { - "type": "file", - "description": "File containing copy number ratio information", - "pattern": "*.{cnr}", - "ontologies": [] - } - } - ] - ], - "cns": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.cns": { - "type": "file", - "description": "File containing copy number segment information", - "pattern": "*.{cns}", - "ontologies": [] - } - } - ] - ], - "pdf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.pdf": { - "type": "file", - "description": "File with plot of copy numbers or segments on chromosomes", - "pattern": "*.{pdf}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3508" - } - ] - } - } - ] - ], - "png": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.png": { - "type": "file", - "description": "File with plot of bin-level log2 coverages and segmentation calls", - "pattern": "*.{png}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3603" - } - ] - } - } - ] - ], - "versions_cnvkit": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cnvkit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cnvkit.py version | sed -e \"s/cnvkit v//g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_samtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cnvkit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cnvkit.py version | sed -e \"s/cnvkit v//g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "atacseq", + "version": "2.1.2" + }, + { + "name": "chipseq", + "version": "2.1.0" + }, + { + "name": "cutandrun", + "version": "3.2.2" + }, + { + "name": "deepmodeloptim", + "version": "dev" + }, + { + "name": "hic", + "version": "2.1.0" + }, + { + "name": "lncpipe", + "version": "dev" + }, + { + "name": "nascent", + "version": "2.3.0" + }, + { + "name": "riboseq", + "version": "1.2.0" + }, + { + "name": "rnasplice", + "version": "1.0.4" + }, + { + "name": "viralrecon", + "version": "3.0.0" + } ] - ] - }, - "authors": [ - "@adamrtalbot", - "@drpatelh", - "@fbdtemme", - "@kaurravneet4123", - "@KevinMenden", - "@lassefolkersen", - "@MaxUlysse", - "@priesgo", - "@SusiJo" - ], - "maintainers": [ - "@adamrtalbot", - "@drpatelh", - "@fbdtemme", - "@kaurravneet4123", - "@KevinMenden", - "@lassefolkersen", - "@MaxUlysse", - "@priesgo", - "@SusiJo" - ] - }, - "pipelines": [ - { - "name": "createpanelrefs", - "version": "dev" - }, - { - "name": "pacsomatic", - "version": "dev" - }, - { - "name": "sarek", - "version": "3.8.1" - } - ] - }, - { - "name": "cnvkit_call", - "path": "modules/nf-core/cnvkit/call/meta.yml", - "type": "module", - "meta": { - "name": "cnvkit_call", - "description": "Given segmented log2 ratio estimates (.cns), derive each segment’s absolute integer copy number", - "keywords": [ - "cnvkit", - "bam", - "fasta", - "copy number" - ], - "tools": [ - { - "cnvkit": { - "description": "CNVkit is a Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent.\n", - "homepage": "https://cnvkit.readthedocs.io/en/stable/index.html", - "documentation": "https://cnvkit.readthedocs.io/en/stable/index.html", - "licence": [ - "Apache-2.0" - ], - "identifier": "biotools:cnvkit" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "cns": { - "type": "file", - "description": "CNVKit CNS file.", - "pattern": "*.cns", - "ontologies": [] - } + }, + { + "name": "custom_gtffilter", + "path": "modules/nf-core/custom/gtffilter/meta.yml", + "type": "module", + "meta": { + "name": "custom_gtffilter", + "description": "Filter a gtf file to keep only regions that are located on a chromosome represented in a given fasta file", + "keywords": ["gtf", "fasta", "filter"], + "tools": [ + { + "gtffilter": { + "description": "Filter a gtf file to keep only regions that are located on a chromosome represented in a given fasta file", + "tool_dev_url": "https://github.com/nf-core/modules/blob/master/modules/nf-core/custom/gtffilter/main.nf", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "gtf": { + "type": "file", + "description": "GTF file", + "pattern": "*.{gtf}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Genome fasta file", + "pattern": "*.{fasta,fa}", + "ontologies": [] + } + } + ] + ], + "output": { + "gtf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}.${suffix}": { + "type": "file", + "description": "Filtered GTF file", + "pattern": "*.{gtf}", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "topics": { + "versions": [ + { + "versions.yml": { + "type": "string", + "description": "The name of the process" + } + } + ] + }, + "authors": ["@nictru"], + "maintainers": ["@nictru"] }, - { - "vcf": { - "type": "file", - "description": "Germline VCF file for BAF.", - "pattern": "*.vcf{,.gz}", - "ontologies": [] - } - } - ] - ], - "output": { - "cns": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.cns": { - "type": "file", - "description": "CNS file.", - "pattern": "*.cns", - "ontologies": [] - } - } - ] - ], - "versions_cnvkit": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cnvkit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cnvkit.py version | sed -e \"s/cnvkit v//g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cnvkit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cnvkit.py version | sed -e \"s/cnvkit v//g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "circrna", + "version": "dev" + }, + { + "name": "rnaseq", + "version": "3.26.0" + } ] - ] }, - "authors": [ - "@adamrtalbot", - "@priesgo" - ], - "maintainers": [ - "@adamrtalbot", - "@priesgo" - ] - }, - "pipelines": [ { - "name": "pacsomatic", - "version": "dev" + "name": "custom_matrixfilter", + "path": "modules/nf-core/custom/matrixfilter/meta.yml", + "type": "module", + "meta": { + "name": "custom_matrixfilter", + "description": "filter a matrix based on a minimum value and numbers of samples that must pass.", + "keywords": ["matrix", "filter", "abundance", "na"], + "tools": [ + { + "matrixfilter": { + "description": "filter a matrix based on a minimum value and numbers of samples", + "tool_dev_url": "https://github.com/nf-core/modules/blob/master/modules/nf-core/custom/matrixfilter/main.nf", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information on matrix to be filtered, at a\nminimum an id. e.g. [ id:'test' ]\n" + } + }, + { + "abundance": { + "type": "file", + "description": "Raw TSV or CSV format abundance matrix with features (e.g.\ngenes) by row and observations (e.g. samples) by column. All rownames\nfrom the sample sheet should be present in the columns.\n", + "ontologies": [] + } + } + ], + [ + { + "samplesheet_meta": { + "type": "map", + "description": "Where samplesheet is provided, aroovy Map containing information on\nsample sheet, at a minimum an id. e.g. [ id:'test' ]\n" + } + }, + { + "samplesheet": { + "type": "file", + "description": "Optional CSV or TSV format sample sheet with sample metadata. If\nprovided this is used to infer minimum passing samples from group sizes\npresent (see grouping_variable), but also to validate matrix columns.\nIf not provided, all numeric columns are selected.\n", + "ontologies": [] + } + } + ] + ], + "output": { + "filtered": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information on experiment.\ne.g. [ id:'test' ]\n" + } + }, + { + "*.filtered.tsv": { + "type": "file", + "description": "Filtered version of input matrix", + "pattern": "*.filtered.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "tests": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information on experiment.\ne.g. [ id:'test' ]\n" + } + }, + { + "*.tests.tsv": { + "type": "file", + "description": "Boolean matrix with pass/ fail status for each test on each feature", + "pattern": "*.tests.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "thresholds": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information on experiment.\ne.g. [ id:'test' ]\n" + } + }, + { + "*.thresholds.tsv": { + "type": "file", + "description": "Table of filtering thresholds applied in matrix filtering", + "pattern": "*.thresholds.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "session_info": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information on experiment.\ne.g. [ id:'test' ]\n" + } + }, + { + "*R_sessionInfo.log": { + "type": "file", + "description": "Log file containing R session information", + "pattern": "*.log", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "topics": { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@pinin4fjords"], + "maintainers": ["@pinin4fjords"] + }, + "pipelines": [ + { + "name": "differentialabundance", + "version": "1.5.0" + } + ] }, { - "name": "sarek", - "version": "3.8.1" - } - ] - }, - { - "name": "cnvkit_coverage", - "path": "modules/nf-core/cnvkit/coverage/meta.yml", - "type": "module", - "meta": { - "name": "cnvkit_coverage", - "description": "Calculate coverage in the given regions from BAM/CRAM or bedGraph files read depths.", - "keywords": [ - "cnvkit", - "coverage", - "BAM", - "CRAM", - "bedGraph", - "read depth", - "genomics" - ], - "tools": [ - { - "cnvkit": { - "description": "Copy number variant detection from high-throughput sequencing.", - "homepage": "https://cnvkit.readthedocs.io/en/stable", - "documentation": "https://cnvkit.readthedocs.io/en/stable", - "tool_dev_url": "https://github.com/etal/cnvkit", - "doi": "10.1371/journal.pcbi.1004873", - "licence": [ - "Apache-2.0" - ], - "identifier": "biotools:cnvkit" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "alignment_file": { - "type": "file", - "description": "Sorted BAM/CRAM, or bedGraph file containing read alignements.", - "pattern": "*.{bam,cram,bed.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - }, - { - "edam": "http://edamontology.org/format_2573" - }, - { - "edam": "http://edamontology.org/format_3583" - } - ] - } + "name": "custom_multiqccustombiotype", + "path": "modules/nf-core/custom/multiqccustombiotype/meta.yml", + "type": "module", + "meta": { + "name": "custom_multiqccustombiotype", + "description": "Generate MultiQC-compatible biotype count summaries from featureCounts output", + "keywords": ["biotype", "featurecounts", "multiqc", "rnaseq", "qc"], + "tools": [ + { + "custom": { + "description": "Summarise featureCounts biotype assignments for MultiQC reporting", + "tool_dev_url": "https://github.com/nf-core/modules/blob/master/modules/nf-core/custom/multiqccustombiotype/main.nf", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "count": { + "type": "file", + "description": "featureCounts output count file", + "pattern": "*.featureCounts.txt", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\n" + } + }, + { + "header": { + "type": "file", + "description": "Header file for the biotype counts MultiQC table", + "pattern": "*.txt", + "ontologies": [] + } + } + ] + ], + "output": { + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\n" + } + }, + { + "*biotype_counts_mqc.tsv": { + "type": "file", + "description": "Biotype counts formatted for MultiQC. The process fails if the\nnumber of biotype rows exceeds the threshold passed via\n`ext.args = '--max_biotypes N'` (default 100), since MultiQC\ncannot render a bar plot with that many categories.\n", + "pattern": "*biotype_counts_mqc.tsv", + "ontologies": [] + } + } + ] + ], + "rrna": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\n" + } + }, + { + "*biotype_counts_rrna_mqc.tsv": { + "type": "file", + "description": "rRNA percentage for MultiQC general stats", + "pattern": "*biotype_counts_rrna_mqc.tsv", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "topics": { + "versions": [ + { + "versions.yml": { + "type": "string", + "description": "The name of the process" + } + } + ] + }, + "authors": ["@pinin4fjords"], + "maintainers": ["@pinin4fjords"] }, - { - "interval": { - "type": "file", - "description": "bed file containing the target or antitarget regions.", - "pattern": "*.{target,antitarget}.bed", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3003" - } - ] - } - } - ] - ], - "output": { - "coverage": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.cnn": { - "type": "file", - "description": "Coverage bedfile with .cnn extension.", - "pattern": "*.{targetcoverage,antitargetcoverage}.cnn", - "ontologies": [] - } - } - ] - ], - "versions_cnvkit": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cnvkit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cnvkit.py version | sed -e \"s/cnvkit v//g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cnvkit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cnvkit.py version | sed -e \"s/cnvkit v//g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "rnaseq", + "version": "3.26.0" + } ] - ] - }, - "authors": [ - "@aadecock" - ], - "maintainers": [ - "@aadecock" - ] - } - }, - { - "name": "cnvkit_export", - "path": "modules/nf-core/cnvkit/export/meta.yml", - "type": "module", - "meta": { - "name": "cnvkit_export", - "description": "Convert copy number ratio tables (.cnr files) or segments (.cns) to another format.", - "keywords": [ - "cnvkit", - "copy number", - "export" - ], - "tools": [ - { - "cnvkit": { - "description": "CNVkit is a Python library and command-line software toolkit to infer and\nvisualize copy number from high-throughput DNA sequencing data.\nIt is designed for use with hybrid capture, including both whole-exome and custom\ntarget panels, and short-read sequencing platforms such as Illumina and Ion Torrent.\n", - "homepage": "https://cnvkit.readthedocs.io/en/stable/index.html", - "documentation": "https://cnvkit.readthedocs.io/en/stable/index.html", - "licence": [ - "Apache-2.0" - ], - "identifier": "biotools:cnvkit" + }, + { + "name": "custom_pcaclustering", + "path": "modules/nf-core/custom/pcaclustering/meta.yml", + "type": "module", + "meta": { + "name": "CUSTOM_PCACLUSTERING", + "description": "Performs KMeans or DBSCAN clustering on a sample-by-feature numeric matrix (e.g. principal components, embeddings)", + "keywords": ["clustering", "kmeans", "dbscan", "pca", "embeddings"], + "tools": [ + { + "scikit-learn": { + "description": "Machine learning library for clustering", + "homepage": "https://scikit-learn.org/", + "documentation": "https://scikit-learn.org/stable/modules/clustering.html", + "licence": ["BSD-3-Clause"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "features": { + "type": "file", + "description": "Tab-separated file whose first column is sample IDs (any column\nname) and remaining columns are numeric features (e.g. PLINK2 PCA\ncomponents with `FID` dropped, scikit-learn embeddings, etc.).\n", + "pattern": "*.{tsv,txt}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + { + "algorithm": { + "type": "string", + "description": "Clustering algorithm to use (kmeans or dbscan)" + } + }, + { + "n_clusters": { + "type": "integer", + "description": "Number of clusters for KMeans" + } + }, + { + "dbscan_eps": { + "type": "float", + "description": "Epsilon parameter for DBSCAN" + } + }, + { + "dbscan_min_samples": { + "type": "integer", + "description": "Minimum samples parameter for DBSCAN" + } + } + ], + "output": { + "clusters": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.clusters.csv": { + "type": "file", + "description": "CSV file with sample_id and assigned cluster", + "pattern": "*.clusters.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "info": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.clustering_info.json": { + "type": "file", + "description": "JSON file with clustering parameters and statistics", + "pattern": "*.clustering_info.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "topics": { + "versions": [ + { + "versions.yml": { + "type": "string", + "description": "The name of the process" + } + } + ] + }, + "authors": ["@dbaku42"], + "maintainers": ["@dbaku42"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + }, + { + "name": "custom_rsemmergecounts", + "path": "modules/nf-core/custom/rsemmergecounts/meta.yml", + "type": "module", + "meta": { + "name": "custom_rsemmergecounts", + "description": "Merge per-sample RSEM results into wide and long format TSV matrices", + "keywords": ["rsem", "merge", "counts", "gene expression"], + "tools": [ + { + "custom": { + "description": "Custom module to merge RSEM gene and isoform count results across\nsamples into count/TPM matrices and long-format tables.\n", + "tool_dev_url": "https://github.com/nf-core/modules/blob/master/modules/nf-core/custom/rsemmergecounts/main.nf", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information. e.g. [ id:'all_samples' ].\n" + } + }, + { + "genes/*": { + "type": "file", + "description": "Collected RSEM gene-level results files across all samples.\n", + "pattern": "*.genes.results", + "ontologies": [] + } + } + ], + { + "isoforms/*": { + "type": "file", + "description": "Collected RSEM isoform-level results files across all samples.\n", + "pattern": "*.isoforms.results", + "ontologies": [] + } + } + ], + "output": { + "counts_gene": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information. e.g. [ id:'all_samples' ].\n" + } + }, + { + "${prefix}.gene_counts.tsv": { + "type": "file", + "description": "Wide-format gene-level count matrix (expected_count column from\nRSEM) with samples as columns.\n", + "pattern": "*.gene_counts.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "tpm_gene": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information. e.g. [ id:'all_samples' ].\n" + } + }, + { + "${prefix}.gene_tpm.tsv": { + "type": "file", + "description": "Wide-format gene-level TPM matrix with samples as columns.\n", + "pattern": "*.gene_tpm.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "counts_transcript": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information. e.g. [ id:'all_samples' ].\n" + } + }, + { + "${prefix}.transcript_counts.tsv": { + "type": "file", + "description": "Wide-format transcript-level count matrix (expected_count column\nfrom RSEM) with samples as columns.\n", + "pattern": "*.transcript_counts.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "tpm_transcript": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information. e.g. [ id:'all_samples' ].\n" + } + }, + { + "${prefix}.transcript_tpm.tsv": { + "type": "file", + "description": "Wide-format transcript-level TPM matrix with samples as columns.\n", + "pattern": "*.transcript_tpm.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "genes_long": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information. e.g. [ id:'all_samples' ].\n" + } + }, + { + "${prefix}.genes_long.tsv": { + "type": "file", + "description": "Long-format gene-level results with all RSEM fields and a\nsample_name column.\n", + "pattern": "*.genes_long.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "isoforms_long": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information. e.g. [ id:'all_samples' ].\n" + } + }, + { + "${prefix}.isoforms_long.tsv": { + "type": "file", + "description": "Long-format isoform-level results with all RSEM fields and a\nsample_name column.\n", + "pattern": "*.isoforms_long.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_sed": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "sed": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "sed --version 2>&1 | sed '1!d;s/^.*) //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "sed": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "sed --version 2>&1 | sed '1!d;s/^.*) //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@pinin4fjords"], + "maintainers": ["@pinin4fjords"] }, - { - "cns": { - "type": "file", - "description": "CNVKit CNS file.", - "pattern": "*.cns", - "ontologies": [] - } - } - ] - ], - "output": { - "output": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.${suffix}": { - "type": "file", - "description": "Output file", - "ontologies": [] - } - } - ] - ], - "versions_cnvkit": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cnvkit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cnvkit.py version | sed -e \"s/cnvkit v//g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cnvkit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cnvkit.py version | sed -e \"s/cnvkit v//g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "rnaseq", + "version": "3.26.0" + } ] - ] - }, - "authors": [ - "@adamrtalbot", - "@priesgo" - ], - "maintainers": [ - "@adamrtalbot", - "@priesgo" - ] - }, - "pipelines": [ - { - "name": "sarek", - "version": "3.8.1" - } - ] - }, - { - "name": "cnvkit_genemetrics", - "path": "modules/nf-core/cnvkit/genemetrics/meta.yml", - "type": "module", - "meta": { - "name": "cnvkit_genemetrics", - "description": "Copy number variant detection from high-throughput sequencing data", - "keywords": [ - "cnvkit", - "bam", - "fasta", - "copy number" - ], - "tools": [ - { - "cnvkit": { - "description": "CNVkit is a Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent.\n", - "homepage": "https://cnvkit.readthedocs.io/en/stable/index.html", - "documentation": "https://cnvkit.readthedocs.io/en/stable/index.html", - "licence": [ - "Apache-2.0" - ], - "identifier": "biotools:cnvkit" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "cnr": { - "type": "file", - "description": "CNR file", - "pattern": "*.cnr", - "ontologies": [] - } + }, + { + "name": "custom_sratoolsncbisettings", + "path": "modules/nf-core/custom/sratoolsncbisettings/meta.yml", + "type": "module", + "meta": { + "name": "custom_sratoolsncbisettings", + "description": "Test for the presence of suitable NCBI settings or create them on the fly.", + "keywords": ["NCBI", "settings", "sra-tools", "prefetch", "fasterq-dump"], + "tools": [ + { + "sratools": { + "description": "SRA Toolkit and SDK from NCBI", + "homepage": "https://github.com/ncbi/sra-tools", + "documentation": "https://github.com/ncbi/sra-tools/wiki", + "tool_dev_url": "https://github.com/ncbi/sra-tools", + "licence": ["Public Domain"], + "identifier": "" + } + } + ], + "input": [ + { + "ids": { + "type": "string", + "description": "List of id settings" + } + } + ], + "output": { + "ncbi_settings": [ + { + "*.mkfg": { + "type": "file", + "description": "An NCBI user settings file.", + "pattern": "*.mkfg", + "ontologies": [] + } + } + ], + "versions_sratools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "sratools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "prefetch --version 2>&1 | grep -Eo '[0-9.]+'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "sratools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "prefetch --version 2>&1 | grep -Eo '[0-9.]+'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@Midnighter"], + "maintainers": ["@Midnighter"] }, - { - "cns": { - "type": "file", - "description": "CNS file [Optional]", - "pattern": "*.cns", - "ontologies": [] - } - } - ] - ], - "output": { - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "TSV file", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_cnvkit": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cnvkit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cnvkit.py version | sed -e \"s/cnvkit v//g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cnvkit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cnvkit.py version | sed -e \"s/cnvkit v//g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "fetchngs", + "version": "1.12.0" + } ] - ] - }, - "authors": [ - "@adamrtalbot", - "@marrip", - "@priesgo" - ], - "maintainers": [ - "@adamrtalbot", - "@marrip", - "@priesgo" - ] - }, - "pipelines": [ - { - "name": "sarek", - "version": "3.8.1" - } - ] - }, - { - "name": "cnvkit_reference", - "path": "modules/nf-core/cnvkit/reference/meta.yml", - "type": "module", - "meta": { - "name": "cnvkit_reference", - "description": "Compile a coverage reference from the given files (normal samples).", - "keywords": [ - "cnvkit", - "reference", - "cnv", - "copy number" - ], - "tools": [ - { - "cnvkit": { - "description": "CNVkit is a Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data.\nIt is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent.\n", - "homepage": "https://cnvkit.readthedocs.io/en/stable/index.html", - "documentation": "https://cnvkit.readthedocs.io/en/stable/index.html", - "tool_dev_url": "https://github.com/etal/cnvkit", - "doi": "10.1371/journal.pcbi.1004873", - "licence": [ - "Apache-2.0" - ], - "identifier": "biotools:cnvkit" - } - } - ], - "input": [ - { - "fasta": { - "type": "file", - "description": "File containing reference genome", - "pattern": "*.{fasta}", - "ontologies": [] - } - }, - { - "targets": { - "type": "file", - "description": "File containing genomic regions", - "pattern": "*.{bed}", - "ontologies": [] - } - }, - { - "antitargets": { - "type": "file", - "description": "File containing off-target genomic regions", - "pattern": "*.{bed}", - "ontologies": [] - } - } - ], - "output": { - "cnn": [ - { - "*.cnn": { - "type": "file", - "description": "File containing a copy-number reference (required for CNV calling in tumor_only mode)", - "pattern": "*.{cnn}", - "ontologies": [] - } + }, + { + "name": "custom_summarisetelomereestimation", + "path": "modules/nf-core/custom/summarisetelomereestimation/meta.yml", + "type": "module", + "meta": { + "name": "custom_summarisetelomereestimation", + "description": "Normalise and combine telomere length and content estimates from telseq, telogator2, and telomerehunter into a unified summary", + "keywords": ["telomere", "summary", "telseq", "telogator2", "telomerehunter"], + "tools": [ + { + "pandas": { + "description": "Python Data Analysis Library", + "homepage": "https://pandas.pydata.org/", + "documentation": "https://pandas.pydata.org/docs/", + "licence": ["BSD-3-Clause"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "length_tsv": { + "type": "file", + "description": "TSV file from telseq or telogator2 with telomere length estimates", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, + { + "content_tsv": { + "type": "file", + "description": "Optional TSV file from telomerehunter with telomere content estimates", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, + { + "length_tool": { + "type": "string", + "description": "Which tool produced the length TSV ('telseq' or 'telogator2')" + } + } + ] + ], + "output": { + "summary": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*_telomere_summary.tsv": { + "type": "file", + "description": "Unified summary TSV with normalised telomere length (kb) and content metrics", + "pattern": "*_telomere_summary.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "YAML file containing versions of tools used in the module", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "topics": { + "versions": [ + { + "versions.yml": { + "type": "string", + "description": "The name of the process" + } + } + ] + }, + "authors": ["@pinin4fjords"], + "maintainers": ["@pinin4fjords"] } - ], - "versions_cnvkit": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cnvkit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cnvkit.py version | sed -e \"s/cnvkit v//g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cnvkit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cnvkit.py version | sed -e \"s/cnvkit v//g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@adamrtalbot", - "@priesgo", - "@SusiJo" - ], - "maintainers": [ - "@adamrtalbot", - "@priesgo", - "@SusiJo" - ] - }, - "pipelines": [ - { - "name": "sarek", - "version": "3.8.1" - } - ] - }, - { - "name": "cnvkit_target", - "path": "modules/nf-core/cnvkit/target/meta.yml", - "type": "module", - "meta": { - "name": "cnvkit_target", - "description": "Transform bait intervals into targets more suitable for CNVkit.", - "keywords": [ - "cnvkit", - "target", - "cnv", - "copy number" - ], - "tools": [ - { - "cnvkit": { - "description": "CNVkit is a Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data.\nIt is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent.\n", - "homepage": "https://cnvkit.readthedocs.io/en/stable/index.html", - "documentation": "https://cnvkit.readthedocs.io/en/stable/index.html", - "tool_dev_url": "https://github.com/etal/cnvkit", - "doi": "10.1371/journal.pcbi.1004873", - "licence": [ - "Apache-2.0" - ], - "identifier": "biotools:cnvkit" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "baits": { - "type": "file", - "description": "BED or interval file listing the targeted regions.", - "pattern": "*.{bed}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "annotation": { - "type": "file", - "description": "Use gene models from this file to assign names to the target regions.", - "pattern": "*.{txt,bed,gff3,pil}", - "ontologies": [] - } - } - ] - ], - "output": { - "bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bed": { - "type": "file", - "description": "File containing target regions", - "pattern": "*.{bed}", - "ontologies": [] - } - } - ] - ], - "versions_cnvkit": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cnvkit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cnvkit.py version | sed -e \"s/cnvkit v//g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cnvkit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cnvkit.py version | sed -e \"s/cnvkit v//g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@adamrtalbot", - "@priesgo" - ], - "maintainers": [ - "@adamrtalbot", - "@priesgo" - ] - } - }, - { - "name": "cnvnator_cnvnator", - "path": "modules/nf-core/cnvnator/cnvnator/meta.yml", - "type": "module", - "meta": { - "name": "cnvnator_cnvnator", - "description": "CNVnator is a command line tool for CNV/CNA analysis from depth-of-coverage by mapped reads.", - "keywords": [ - "cnvnator", - "cnv", - "cna" - ], - "tools": [ - { - "cnvnator": { - "description": "Tool for calling copy number variations.", - "homepage": "https://github.com/abyzovlab/CNVnator", - "documentation": "https://github.com/abyzovlab/CNVnator/blob/master/README.md", - "tool_dev_url": "https://github.com/abyzovlab/CNVnator", - "licence": [ - "MIT" - ], - "identifier": "biotools:cnvnator" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM/CRAM/SAM file", - "pattern": "*.bam", - "ontologies": [] - } - }, - { - "bai": { - "type": "file", - "description": "Sorted BAM/CRAM/SAM file", - "pattern": "*.bam", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "root": { - "type": "file", - "description": "ROOT file", - "pattern": "*.root", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Path to a directory containing fasta files or a fasta file", - "pattern": "*.fa", - "ontologies": [] - } + }, + { + "name": "custom_tabulartogseachip", + "path": "modules/nf-core/custom/tabulartogseachip/meta.yml", + "type": "module", + "meta": { + "name": "custom_tabulartogseachip", + "description": "Make a GSEA class file (.chip) from tabular inputs", + "keywords": ["gsea", "chip", "convert", "tabular"], + "tools": [ + { + "custom": { + "description": "Make a GSEA annotation file (.chip) from tabular inputs", + "tool_dev_url": "https://github.com/nf-core/modules/blob/master/modules/nf-core/custom/tabulartogseachip/main.nf", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing data information.\nThis can be used at the workflow level to pass optional parameters to the module.\n[id: 'test', ...]\n" + } + }, + { + "tabular": { + "type": "file", + "description": "Tabular (NOTE that for the moment it only works for TSV file) containing a column with the\nfeatures ids, and another column with the features symbols.\n", + "pattern": "*.{tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + [ + { + "id": { + "type": "string", + "description": "The name of the column containing feature ids" + } + }, + { + "symbol": { + "type": "string", + "description": "The name of the column containing feature symbols" + } + } + ] + ], + "output": { + "chip": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing metadata e.g. [ id:'test', ... ]" + } + }, + { + "*.chip": { + "type": "file", + "description": "A categorical class format file (.chip) as defined by the Broad\ndocumentation at\nhttps://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats\n", + "pattern": "*.chip", + "ontologies": [] + } + } + ] + ], + "versions_gawk": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gawk": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gawk --version 2>&1 | sed '1!d;s/^.*GNU Awk //; s/, .*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gawk": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gawk --version 2>&1 | sed '1!d;s/^.*GNU Awk //; s/, .*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@pinin4fjords", "@suzannejin"], + "maintainers": ["@pinin4fjords"] } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. `[ id:'test' ]`\n" - } + }, + { + "name": "custom_tabulartogseacls", + "path": "modules/nf-core/custom/tabulartogseacls/meta.yml", + "type": "module", + "meta": { + "name": "custom_tabulartogseacls", + "description": "Make a GSEA class file (.cls) from tabular inputs", + "keywords": ["gsea", "cls", "convert", "tabular"], + "tools": [ + { + "custom": { + "description": "Make a GSEA class file (.cls) from tabular inputs", + "tool_dev_url": "https://github.com/nf-core/modules/blob/master/modules/nf-core/custom/tabulartogseacls/main.nf", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing metadata including an id, the sample sheet column\nused to define groups, and optionally a separator to override defaults e.g. [\n id:'test', variable:'treatment', separator:',' ]. The way these values are\npassed to the associated module parameters is then defined via an ext.args\nspecification for the process from the workflow, like: ext.args = { [\n \"separator\": \"\\t\", \"variable\": \"$meta.variable\" ] } ('variable' is\ncompulsory here).\n" + } + }, + { + "samples": { + "type": "file", + "description": "Tabular (e.g. TSV/CSV) samples file with sample IDs by row and variables by column.", + "pattern": "*.{csv,tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + }, + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "output": { + "cls": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing metadata e.g. [ id:'test', variable:'treatment',\nseparator:',' ]\n" + } + }, + { + "*.cls": { + "type": "file", + "description": "A categorical class format file (.cls) as defined by the Broad\ndocumentation at\nhttps://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats\n", + "ontologies": [] + } + } + ] + ], + "versions_mawk": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "mawk": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "mawk --version | sed '1!d;s/mawk //;s/ .*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "mawk": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "mawk --version | sed '1!d;s/mawk //;s/ .*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@pinin4fjords"], + "maintainers": ["@pinin4fjords"] }, - { - "fai": { - "type": "file", - "description": "Path to a fasta file index", - "pattern": "*.fai", - "ontologies": [] - } - } - ], - { - "step": { - "type": "string", - "description": "One of \"his\", \"rd\", \"call\", \"stat\", and \"partition\"" - } - } - ], - "output": { - "root": [ - [ - { - "output_meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "${prefix}.root": { - "type": "file", - "description": "A ROOT file", - "pattern": "*.root", - "ontologies": [] - } - } - ] - ], - "tab": [ - [ - { - "output_meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "${prefix}.tab": { - "type": "file", - "description": "A tab file containing cnvnator calls", - "pattern": "*.tab", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_cnvnator": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cnvnator": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cnvnator 2>&1 | sed -n '3s/CNVnator v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cnvnator": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cnvnator 2>&1 | sed -n '3s/CNVnator v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "differentialabundance", + "version": "1.5.0" + } ] - ] - }, - "authors": [ - "@ramprasadn" - ], - "maintainers": [ - "@ramprasadn" - ] - }, - "pipelines": [ - { - "name": "raredisease", - "version": "3.0.0" - } - ] - }, - { - "name": "cnvnator_convert2vcf", - "path": "modules/nf-core/cnvnator/convert2vcf/meta.yml", - "type": "module", - "meta": { - "name": "cnvnator_convert2vcf", - "description": "convert2vcf.pl is command line tool to convert CNVnator calls to vcf format.", - "keywords": [ - "cnvnator", - "cnv", - "cna" - ], - "tools": [ - { - "cnvnator": { - "description": "Tool for calling copy number variations.", - "homepage": "https://github.com/abyzovlab/CNVnator", - "documentation": "https://github.com/abyzovlab/CNVnator/blob/master/README.md", - "tool_dev_url": "https://github.com/abyzovlab/CNVnator", - "licence": [ - "MIT" - ], - "identifier": "biotools:cnvnator" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } + }, + { + "name": "custom_tabulartogseagct", + "path": "modules/nf-core/custom/tabulartogseagct/meta.yml", + "type": "module", + "meta": { + "name": "custom_tabulartogseagct", + "description": "Convert a TSV or CSV with features by row and observations by column to a GCT format file as consumed by GSEA", + "keywords": ["gsea", "gct", "tabular"], + "tools": [ + { + "tabulartogseagct": { + "description": "Convert a TSV or CSV with features by row and observations by column to a GCT format file as consumed by GSEA", + "tool_dev_url": "https://github.com/nf-core/modules/blob/master/modules/nf-core/custom/tabulartogseagct/main.nf", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing matrix information\ne.g. [ id:'test' ]\n" + } + }, + { + "tabular": { + "type": "file", + "description": "Tabular (e.g. TSV or CSV file) containing a numeric matrix with features (e.g. genes) by row and samples by column.", + "pattern": "*.{tsv,csv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + }, + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "output": { + "gct": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing matrix information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.gct": { + "type": "file", + "description": "GCT format version of input TSV", + "pattern": "*.{gct}", + "ontologies": [] + } + } + ] + ], + "versions_mawk": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "mawk": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "mawk --version | sed '1!d;s/mawk //;s/ .*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "mawk": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "mawk --version | sed '1!d;s/mawk //;s/ .*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@pinin4fjords"], + "maintainers": ["@pinin4fjords"] }, - { - "calls": { - "type": "file", - "description": "A tab file containing CNVnator calls", - "pattern": "*.tab", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*.vcf": { - "type": "file", - "description": "CNVnator calls in vcf format", - "pattern": "*.vcf", - "ontologies": [] - } - } - ] - ], - "versions_cnvnator": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cnvnator": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cnvnator 2>&1 | sed -n '3s/CNVnator v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cnvnator": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cnvnator 2>&1 | sed -n '3s/CNVnator v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "differentialabundance", + "version": "1.5.0" + } ] - ] - }, - "authors": [ - "@ramprasadn" - ], - "maintainers": [ - "@ramprasadn" - ] - }, - "pipelines": [ - { - "name": "raredisease", - "version": "3.0.0" - } - ] - }, - { - "name": "cnvpytor_callcnvs", - "path": "modules/nf-core/cnvpytor/callcnvs/meta.yml", - "type": "module", - "meta": { - "name": "cnvpytor_callcnvs", - "description": "Command line tool for calling CNVs in whole genome sequencing data", - "keywords": [ - "CNV", - "call", - "wgs" - ], - "tools": [ - { - "cnvpytor": { - "description": "calling CNVs using read depth", - "homepage": "https://github.com/abyzovlab/CNVpytor", - "documentation": "https://github.com/abyzovlab/CNVpytor", - "tool_dev_url": "https://github.com/abyzovlab/CNVpytor", - "doi": "10.1101/2021.01.27.428472v1", - "licence": [ - "MIT" - ], - "identifier": "biotools:cnvpytor" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } + }, + { + "name": "custom_tx2gene", + "path": "modules/nf-core/custom/tx2gene/meta.yml", + "type": "module", + "meta": { + "name": "custom_tx2gene", + "description": "Make a transcript/gene mapping from a GTF and cross-reference with transcript quantifications.", + "keywords": ["gene", "gtf", "pseudoalignment", "rsem", "transcript"], + "tools": [ + { + "custom": { + "description": "\"Custom module to create a transcript to gene mapping from a GTF and\ncheck it against transcript quantifications\"\n", + "tool_dev_url": "https://github.com/nf-core/modules/blob/master/modules/nf-core/custom/tx2gene/main.nf", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information related to the GTF file\ne.g. `[ id:'yeast' ]`\n" + } + }, + { + "gtf": { + "type": "file", + "description": "An annotation file of the reference genome in GTF format", + "pattern": "*.gtf", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing information related to the experiment as a whole\ne.g. `[ id:'SRP123456' ]`\n" + } + }, + { + "quants/*": { + "type": "file", + "description": "quants file" + } + } + ], + { + "quant_type": { + "type": "string", + "description": "Quantification type, 'kallisto', 'salmon', or 'rsem'" + } + }, + { + "id": { + "type": "string", + "description": "Gene ID attribute in the GTF file (default= gene_id)" + } + }, + { + "extra": { + "type": "string", + "description": "Extra gene attribute(s) in the GTF file, comma-separated for multiple (default= gene_name)" + } + } + ], + "output": { + "tx2gene": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information related to the GTF file\ne.g. `[ id:'yeast' ]`\n" + } + }, + { + "*tx2gene.tsv": { + "type": "file", + "description": "A transcript/ gene mapping table in TSV format", + "pattern": "*.tx2gene.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "YAML file containing versions of tools used in the module", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "topics": { + "versions": [ + { + "versions.yml": { + "type": "string", + "description": "The name of the process" + } + } + ] + }, + "authors": ["@pinin4fjords"], + "maintainers": ["@pinin4fjords"] }, - { - "pytor": { - "type": "file", - "description": "pytor file containing partitions of read depth histograms using mean-shift method", - "pattern": "*.{pytor}", - "ontologies": [] - } - } - ], - { - "bin_sizes": { - "type": "string", - "description": "list of binsizes separated by space e.g. \"1000 10000\" and \"1000\"" - } - } - ], - "output": { - "pytor": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "${pytor.baseName}.pytor": { - "type": "file", - "description": "pytor files containing cnv calls", - "pattern": "*.{pytor}", - "ontologies": [] - } - } - ] - ], - "versions_cnvpytor": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cnvpytor": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cnvpytor --version | sed -n 's/.*CNVpytor \\(.*\\)/\\1/p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cnvpytor": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cnvpytor --version | sed -n 's/.*CNVpytor \\(.*\\)/\\1/p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "circrna", + "version": "dev" + }, + { + "name": "riboseq", + "version": "1.2.0" + }, + { + "name": "rnaseq", + "version": "3.26.0" + } ] - ] - }, - "authors": [ - "@sima-r" - ], - "maintainers": [ - "@sima-r" - ] - } - }, - { - "name": "cnvpytor_histogram", - "path": "modules/nf-core/cnvpytor/histogram/meta.yml", - "type": "module", - "meta": { - "name": "cnvpytor_histogram", - "description": "calculates read depth histograms", - "keywords": [ - "cnv calling", - "histogram", - "read depth" - ], - "tools": [ - { - "cnvpytor": { - "description": "calling CNVs using read depth", - "homepage": "https://github.com/abyzovlab/CNVpytor", - "documentation": "https://github.com/abyzovlab/CNVpytor", - "tool_dev_url": "https://github.com/abyzovlab/CNVpytor", - "doi": "10.1101/2021.01.27.428472v1", - "licence": [ - "MIT" - ], - "identifier": "biotools:cnvpytor" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } + }, + { + "name": "cutadapt", + "path": "modules/nf-core/cutadapt/meta.yml", + "type": "module", + "meta": { + "name": "cutadapt", + "description": "Removes adapter sequences from sequencing reads", + "keywords": ["adapter", "primers", "poly-A tails", "trimming", "fastq"], + "tools": [ + { + "cutadapt": { + "description": "Cutadapt finds and removes adapter sequences, primers, poly-A tails\nand other types of unwanted sequence from your high-throughput sequencing reads.\n", + "homepage": "https://cutadapt.readthedocs.io/en/stable/index.html", + "documentation": "https://github.com/marcelm/cutadapt", + "doi": "10.14806/ej.17.1.200", + "licence": ["MIT"], + "identifier": "biotools:cutadapt" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", + "pattern": "*.{fq,fastq,fq.gz,fastq.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ] + ], + "output": { + "reads": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.trim.fastq.gz": { + "type": "file", + "description": "The trimmed/modified fastq reads", + "pattern": "*fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "cutadapt log file", + "pattern": "*cutadapt.log", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + } + ] + ], + "versions_cutadapt": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cutadapt": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cutadapt --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cutadapt": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cutadapt --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@drpatelh", "@kevinmenden"], + "maintainers": ["@drpatelh", "@kevinmenden", "@vagkaratzas"] }, - { - "pytor": { - "type": "file", - "description": "pytor file containing read depth data", - "pattern": "*.{pytor}", - "ontologies": [] - } - } - ], - { - "bin_sizes": { - "type": "string", - "description": "list of binsizes separated by space e.g. \"1000 10000\" and \"1000\"" - } - } - ], - "output": { - "pytor": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "${pytor.baseName}.pytor": { - "type": "file", - "description": "pytor file containing read depth histograms binned based on given bin size(s)", - "pattern": "*.{pytor}", - "ontologies": [] - } - } - ] - ], - "versions_cnvpytor": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cnvpytor": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "1.3.2": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cnvpytor": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "1.3.2": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "ampliseq", + "version": "2.17.0" + }, + { + "name": "crisprseq", + "version": "2.3.0" + }, + { + "name": "evexplorer", + "version": "dev" + }, + { + "name": "hicar", + "version": "1.0.0" + }, + { + "name": "marsseq", + "version": "1.0.3" + }, + { + "name": "panoramaseq", + "version": "dev" + }, + { + "name": "riboseq", + "version": "1.2.0" + }, + { + "name": "viralrecon", + "version": "3.0.0" + } ] - ] - }, - "authors": [ - "@sima-r", - "@ramprasadn" - ], - "maintainers": [ - "@sima-r", - "@ramprasadn" - ] - } - }, - { - "name": "cnvpytor_importreaddepth", - "path": "modules/nf-core/cnvpytor/importreaddepth/meta.yml", - "type": "module", - "meta": { - "name": "cnvpytor_importreaddepth", - "description": "command line tool for CNV/CNA analysis. This step imports the read depth data into a root pytor file.", - "keywords": [ - "read depth", - "cnv", - "cna", - "call" - ], - "tools": [ - { - "cnvpytor -rd": { - "description": "calling CNVs using read depth", - "homepage": "https://github.com/abyzovlab/CNVpytor", - "documentation": "https://github.com/abyzovlab/CNVpytor", - "tool_dev_url": "https://github.com/abyzovlab/CNVpytor", - "doi": "10.1101/2021.01.27.428472v1", - "licence": [ - "MIT" - ], - "identifier": "biotools:cnvpytor" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "input_file": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram}", - "ontologies": [] - } - }, - { - "index": { - "type": "file", - "description": "bam file index", - "pattern": "*.{bai,crai}", - "ontologies": [] - } + }, + { + "name": "cutesv", + "path": "modules/nf-core/cutesv/meta.yml", + "type": "module", + "meta": { + "name": "cutesv", + "description": "structural-variant calling with cutesv", + "keywords": ["cutesv", "structural-variant calling", "sv"], + "tools": [ + { + "cutesv": { + "description": "a clustering-and-refinement method to analyze the signatures to implement sensitive SV detection.", + "homepage": "https://github.com/tjiangHIT/cuteSV", + "documentation": "https://github.com/tjiangHIT/cuteSV#readme", + "tool_dev_url": "https://github.com/tjiangHIT/cuteSV", + "licence": ["MIT"], + "identifier": "biotools:cuteSV" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file", + "pattern": "*.bam", + "ontologies": [] + } + }, + { + "bai": { + "type": "file", + "description": "Index of BAM file", + "pattern": "*.bai", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'fasta' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference database in FASTA format\n", + "ontologies": [] + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.vcf": { + "type": "file", + "description": "VCF file containing called variants from CuteSV", + "pattern": "*.vcf", + "ontologies": [] + } + } + ] + ], + "versions_cutesv": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cuteSV": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cuteSV --version 2>&1 | sed 's/cuteSV //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cuteSV": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cuteSV --version 2>&1 | sed 's/cuteSV //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@christopher-hakkaart", "@yuukiiwa"], + "maintainers": ["@christopher-hakkaart", "@yuukiiwa"] } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing genome information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "specifies reference genome file (only for cram file without reference genome)", - "pattern": "*.{fasta,fasta.gz,fa,fa.gz}", - "ontologies": [] - } + }, + { + "name": "damageprofiler", + "path": "modules/nf-core/damageprofiler/meta.yml", + "type": "module", + "meta": { + "name": "damageprofiler", + "description": "A Java based tool to determine damage patterns on ancient DNA as a replacement for mapDamage", + "keywords": [ + "damage", + "deamination", + "miscoding lesions", + "C to T", + "ancient DNA", + "aDNA", + "palaeogenomics", + "archaeogenomics", + "palaeogenetics", + "archaeogenetics" + ], + "tools": [ + { + "damageprofiler": { + "description": "A Java based tool to determine damage patterns on ancient DNA as a replacement for mapDamage", + "homepage": "https://github.com/Integrative-Transcriptomics/DamageProfiler", + "documentation": "https://damageprofiler.readthedocs.io/", + "tool_dev_url": "https://github.com/Integrative-Transcriptomics/DamageProfiler", + "doi": "10.1093/bioinformatics/btab190", + "licence": ["GPL v3"], + "identifier": "biotools:damageprofiler" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + }, + { + "edam": "http://edamontology.org/format_3462" + }, + { + "edam": "http://edamontology.org/format_2573" + } + ] + } + } + ], + { + "fasta": { + "type": "file", + "description": "OPTIONAL FASTA reference file", + "pattern": "*.{fasta,fna,fa}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1332" + } + ] + } + }, + { + "fai": { + "type": "file", + "description": "OPTIONAL FASTA index file from samtools faidx", + "pattern": "*.{fai}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1332" + } + ] + } + }, + { + "specieslist": { + "type": "file", + "description": "OPTIONAL text file with list of target reference headers", + "pattern": "*.{txt}", + "ontologies": [] + } + } + ], + "output": { + "results": [ + [ + { + "meta": { + "type": "directory", + "description": "DamageProfiler results directory", + "pattern": "*/*" + } + }, + { + "${prefix}": { + "type": "directory", + "description": "DamageProfiler results directory", + "pattern": "*/*" + } + } + ] + ], + "versions_damageprofiler": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "damageprofiler": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "damageprofiler -v | sed 's/^DamageProfiler v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "damageprofiler": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "damageprofiler -v | sed 's/^DamageProfiler v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@jfy133"], + "maintainers": ["@jfy133"] }, - { - "fai": { - "type": "file", - "description": "Index of reference fasta file", - "pattern": "*.fai", - "ontologies": [] - } - } - ] - ], - "output": { - "pytor": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.pytor": { - "type": "file", - "description": "read depth root file in which read depth data binned to 100 base pair bins will be stored.", - "pattern": "*.{pytor}", - "ontologies": [] - } - } - ] - ], - "versions_cnvpytor": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cnvpytor": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cnvpytor --version 2>&1 | sed -n 's/.*CNVpytor //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cnvpytor": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cnvpytor --version 2>&1 | sed -n 's/.*CNVpytor //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "coproid", + "version": "2.0.1" + } ] - ] - }, - "authors": [ - "@sima-r", - "@ramprasadn" - ], - "maintainers": [ - "@sima-r", - "@ramprasadn" - ] - } - }, - { - "name": "cnvpytor_partition", - "path": "modules/nf-core/cnvpytor/partition/meta.yml", - "type": "module", - "meta": { - "name": "cnvpytor_partition", - "description": "Calculate segmentation for specified bin size (multiple bin sizes separate by space)", - "keywords": [ - "cnv", - "call", - "partition", - "histogram" - ], - "tools": [ - { - "cnvpytor": { - "description": "Calling CNVs using read depth", - "homepage": "https://github.com/abyzovlab/CNVpytor", - "documentation": "https://github.com/abyzovlab/CNVpytor", - "tool_dev_url": "https://github.com/abyzovlab/CNVpytor", - "doi": "10.1101/2021.01.27.428472v1", - "licence": [ - "MIT" - ], - "identifier": "biotools:cnvpytor" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } + }, + { + "name": "dastool_dastool", + "path": "modules/nf-core/dastool/dastool/meta.yml", + "type": "module", + "meta": { + "name": "dastool_dastool", + "description": "DAS Tool binning step.", + "keywords": ["binning", "das tool", "table", "de novo", "bins", "contigs", "assembly", "das_tool"], + "tools": [ + { + "dastool": { + "description": "DAS Tool is an automated method that integrates the results\nof a flexible number of binning algorithms to calculate an optimized, non-redundant\nset of bins from a single assembly.\n", + "homepage": "https://github.com/cmks/DAS_Tool", + "documentation": "https://github.com/cmks/DAS_Tool", + "tool_dev_url": "https://github.com/cmks/DAS_Tool", + "doi": "10.1038/s41564-018-0171-1", + "licence": ["BSD"], + "identifier": "biotools:dastool" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "contigs": { + "type": "file", + "description": "fasta file", + "pattern": "*.{fa.gz,fas.gz,fasta.gz}", + "ontologies": [] + } + }, + { + "bins": { + "type": "file", + "description": "FastaToContig2Bin tabular file generated with dastool/fastatocontig2bin", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, + { + "proteins": { + "type": "file", + "description": "Predicted proteins in prodigal fasta format (>scaffoldID_geneNo)", + "pattern": "*.{fa.gz,fas.gz,fasta.gz}", + "ontologies": [] + } + } + ], + { + "db_directory": { + "type": "file", + "description": "(optional) Directory of single copy gene database.", + "ontologies": [] + } + } + ], + "output": { + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "Log file of the run", + "pattern": "*.log", + "ontologies": [] + } + } + ] + ], + "summary": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_summary.tsv": { + "type": "file", + "description": "Summary of output bins including quality and completeness estimates", + "pattern": "*summary.txt", + "ontologies": [] + } + } + ] + ], + "contig2bin": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_DASTool_contig2bin.tsv": { + "type": "file", + "description": "Scaffolds to bin file of output bins", + "pattern": "*.contig2bin.txt", + "ontologies": [] + } + } + ] + ], + "eval": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.eval": { + "type": "file", + "description": "Quality and completeness estimates of input bin sets", + "pattern": "*.eval", + "ontologies": [] + } + } + ] + ], + "bins": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_DASTool_bins/*.fa": { + "type": "file", + "description": "Final refined bins in fasta format", + "pattern": "*.fa", + "ontologies": [] + } + } + ] + ], + "pdfs": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.pdf": { + "type": "file", + "description": "Plots showing the amount of high quality bins and score distribution of bins per method", + "pattern": "*.pdf", + "ontologies": [] + } + } + ] + ], + "candidates_faa": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.candidates.faa": { + "type": "file", + "description": "FAA file", + "pattern": "*.candidates.faa", + "ontologies": [] + } + } + ] + ], + "fasta_proteins": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_proteins.faa": { + "type": "file", + "description": "Output from prodigal if not already supplied", + "pattern": "*_proteins.faa", + "ontologies": [] + } + } + ] + ], + "fasta_archaea_scg": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.archaea.scg": { + "type": "file", + "description": "Results of archaeal single-copy-gene prediction", + "pattern": "*.archaea.scg", + "ontologies": [] + } + } + ] + ], + "fasta_bacteria_scg": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bacteria.scg": { + "type": "file", + "description": "Results of bacterial single-copy-gene prediction", + "pattern": "*.bacteria.scg", + "ontologies": [] + } + } + ] + ], + "b6": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.b6": { + "type": "file", + "description": "Results in b6 format", + "pattern": "*.b6", + "ontologies": [] + } + } + ] + ], + "seqlength": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.seqlength": { + "type": "file", + "description": "Summary of contig lengths", + "pattern": "*.seqlength", + "ontologies": [] + } + } + ] + ], + "versions_dastool": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "dastool": { + "type": "string", + "description": "The tool name" + } + }, + { + "DAS_Tool --version 2>&1 | grep \"DAS Tool\" | sed \"s/DAS Tool //\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "dastool": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "DAS_Tool --version 2>&1 | grep \"DAS Tool\" | sed \"s/DAS Tool //\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@maxibor", "@jfy133"], + "maintainers": ["@maxibor", "@jfy133"] }, - { - "pytor": { - "type": "file", - "description": "pytor file containing read depth data", - "pattern": "*.{pytor}", - "ontologies": [] - } - } - ], - { - "bin_sizes": { - "type": "string", - "description": "list of binsizes separated by space e.g. \"1000 10000\" default is \"1000\"" - } - } - ], - "output": { - "pytor": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "${prefix}.pytor": { - "type": "file", - "description": "pytor file", - "pattern": "*.pytor", - "ontologies": [] - } - } - ] - ], - "versions_cnvpytor": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "cnvpytor": { - "type": "string", - "description": "The tool name" - } - }, - { - "cnvpytor --version 2>&1 | sed -n 's/.*CNVpytor //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "cnvpytor": { - "type": "string", - "description": "The tool name" - } - }, - { - "cnvpytor --version 2>&1 | sed -n 's/.*CNVpytor //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "mag", + "version": "5.4.2" + } ] - ] - }, - "authors": [ - "@sima-r", - "@ramprasadn" - ], - "maintainers": [ - "@sima-r", - "@ramprasadn" - ] - } - }, - { - "name": "cnvpytor_view", - "path": "modules/nf-core/cnvpytor/view/meta.yml", - "type": "module", - "meta": { - "name": "cnvpytor_view", - "description": "view function to generate vcfs", - "keywords": [ - "cnv", - "calling", - "vcf" - ], - "tools": [ - { - "cnvpytor": { - "description": "calling CNVs using read depth", - "homepage": "https://github.com/abyzovlab/CNVpytor", - "documentation": "https://github.com/abyzovlab/CNVpytor", - "tool_dev_url": "https://github.com/abyzovlab/CNVpytor", - "doi": "10.1101/2021.01.27.428472v1", - "licence": [ - "MIT" - ], - "identifier": "biotools:cnvpytor" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } + }, + { + "name": "dastool_fastatocontig2bin", + "path": "modules/nf-core/dastool/fastatocontig2bin/meta.yml", + "type": "module", + "meta": { + "name": "dastool_fastatocontig2bin", + "description": "Helper script to convert a set of bins in fasta format to tabular scaffolds2bin format", + "keywords": ["binning", "das tool", "table", "de novo", "bins", "contigs", "assembly", "das_tool"], + "tools": [ + { + "dastool": { + "description": "DAS Tool is an automated method that integrates the results\nof a flexible number of binning algorithms to calculate an optimized, non-redundant\nset of bins from a single assembly.\n", + "homepage": "https://github.com/cmks/DAS_Tool", + "documentation": "https://github.com/cmks/DAS_Tool", + "tool_dev_url": "https://github.com/cmks/DAS_Tool", + "doi": "10.1038/s41564-018-0171-1", + "licence": ["BSD"], + "identifier": "biotools:dastool" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Fasta of list of fasta files recommended to be gathered via with .collect() of bins", + "pattern": "*.{fa,fa.gz,fas,fas.gz,fna,fna.gz,fasta,fasta.gz}", + "ontologies": [] + } + } + ], + { + "extension": { + "type": "string", + "description": "Fasta file extension (fa | fas | fasta | ...), without .gz suffix, if gzipped input." + } + } + ], + "output": { + "fastatocontig2bin": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "tabular contig2bin file for DAS tool input", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_dastool": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "dastool": { + "type": "string", + "description": "The tool name" + } + }, + { + "DAS_Tool --version 2>&1 | grep \"DAS Tool\" | sed \"s/DAS Tool //\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "dastool": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "DAS_Tool --version 2>&1 | grep \"DAS Tool\" | sed \"s/DAS Tool //\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@maxibor", "@jfy133"], + "maintainers": ["@maxibor", "@jfy133"] }, - { - "pytor_files": { - "type": "file", - "description": "pytor file containing cnv calls. To merge calls from multiple samples use a list of files.", - "pattern": "*.{pytor}", - "ontologies": [] - } - } - ], - { - "bin_sizes": { - "type": "string", - "description": "list of binsizes separated by space e.g. \"1000 10000\" and \"1000\"" - } - }, - { - "output_format": { - "type": "string", - "description": "output format of the cnv calls. Valid entries are \"tsv\", \"vcf\", and \"xls\"" - } - } - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.vcf": { - "type": "file", - "description": "vcf file containing cnv calls", - "pattern": "*.{vcf}", - "ontologies": [] - } - } - ] - ], - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "tsv file containing cnv calls", - "pattern": "*.{tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "xls": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.xls": { - "type": "file", - "description": "xls file containing cnv calls", - "pattern": "*.{xls}", - "ontologies": [] - } - } - ] - ], - "versions_cnvpytor": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cnvpytor": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "1.3.2": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cnvpytor": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "1.3.2": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "mag", + "version": "5.4.2" + } ] - ] - }, - "authors": [ - "@sima-r", - "@ramprasadn" - ], - "maintainers": [ - "@sima-r", - "@ramprasadn" - ] - } - }, - { - "name": "cobiontid_kmercounter", - "path": "modules/nf-core/cobiontid/kmercounter/meta.yml", - "type": "module", - "meta": { - "name": "cobiontid_kmercounter", - "description": "A rust based tool based on Needletail's FASTA parser tallies k-mer counts\nfor large sequencing rounds. Written with downstream processing with Tensorflow\nor numpy in mind.\n", - "keywords": [ - "cobiontid", - "kmer", - "counts", - "npy", - "fasta" - ], - "tools": [ - { - "kmer-counter": { - "description": "A rust based tool based on Needletail's FASTA parser tallies k-mer counts\nfor large sequencing rounds. Written with downstream processing with Tensorflow\nor numpy in mind.\n", - "homepage": "https://github.com/CobiontID/kmer-counter", - "documentation": "https://github.com/CobiontID/kmer-counter", - "license": [ - "MIT" - ], - "identifier": "" + }, + { + "name": "dastool_scaffolds2bin", + "path": "modules/nf-core/dastool/scaffolds2bin/meta.yml", + "type": "module", + "meta": { + "name": "dastool_scaffolds2bin", + "description": "Helper script to convert a set of bins in fasta format to tabular scaffolds2bin format", + "deprecated": true, + "keywords": ["binning", "das tool", "table", "de novo", "bins", "contigs", "assembly", "das_tool"], + "tools": [ + { + "dastool": { + "description": "DAS Tool is an automated method that integrates the results\nof a flexible number of binning algorithms to calculate an optimized, non-redundant\nset of bins from a single assembly.\n", + "homepage": "https://github.com/cmks/DAS_Tool", + "documentation": "https://github.com/cmks/DAS_Tool", + "tool_dev_url": "https://github.com/cmks/DAS_Tool", + "doi": "10.1038/s41564-018-0171-1", + "licence": ["BSD"], + "identifier": "biotools:dastool" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Fasta or list of fasta files recommended to be gathered via with .collect() of bins", + "pattern": "*.{fa,fa.gz,fas,fas.gz,fna,fna.gz,fasta,fasta.gz}", + "ontologies": [] + } + } + ], + { + "extension": { + "type": "string", + "description": "Fasta file extension (fa | fas | fasta | ...), but without .gz suffix, even if gzipped input." + } + } + ], + "output": { + "scaffolds2bin": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "tabular scaffolds2bin file for DAS tool input", + "pattern": "*.scaffolds2bin.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@maxibor"], + "maintainers": ["@maxibor"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } + }, + { + "name": "datavzrd", + "path": "modules/nf-core/datavzrd/meta.yml", + "type": "module", + "meta": { + "name": "datavzrd", + "description": "Datavzrd is a tool to create visual HTML reports from collections of CSV/TSV tables.", + "keywords": ["visualisation", "tsv", "csv"], + "tools": [ + { + "datavzrd": { + "description": "Datavzrd is a tool to create visual HTML reports from collections of CSV/TSV tables.", + "homepage": "https://datavzrd.github.io/", + "documentation": "https://datavzrd.github.io/docs/index.html", + "tool_dev_url": "https://github.com/datavzrd/datavzrd", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "config_file": { + "type": "file", + "description": "Path to a config file in YAML format", + "pattern": "*.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + }, + { + "table": { + "type": "file", + "description": "Path to a CSV/TSV file", + "pattern": "*.{csv,tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + }, + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "output": { + "report": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "${prefix}": { + "type": "directory", + "description": "directory with HTML report of provided CSV/TSV files", + "pattern": "${prefix}" + } + } + ] + ], + "versions_datavzrd": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "datavzrd": { + "type": "string", + "description": "The tool name" + } + }, + { + "datavzrd --version | sed -e 's/[^0-9.]//g'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "datavzrd": { + "type": "string", + "description": "The tool name" + } + }, + { + "datavzrd --version | sed -e 's/[^0-9.]//g'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@vickylaram", "@famosab"], + "maintainers": ["@famosab"] }, - { - "fasta": { - "type": "file", - "description": "Input fasta assembly file\n", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - { - "kmer_size": { - "type": "integer", - "description": "Size of kmer to scan the genome for.\n" - } - } - ], - "output": { - "npy": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.npy": { - "type": "file", - "description": "A Numpy file containing the kmer counts.\n", - "ontologies": [ - { - "edam": "http://edamontology.org/format_4003" - } - ] - } - } - ] - ], - "versions_kmercounter": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "kmer-counter": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "kmer-counter --version | sed -e \"s/K-mer counter //g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "kmer-counter": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "kmer-counter --version | sed -e \"s/K-mer counter //g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "variantbenchmarking", + "version": "1.5.0" + } ] - ] - }, - "authors": [ - "@DLBPointon" - ], - "maintainers": [ - "@DLBPointon" - ] - } - }, - { - "name": "cobrameta", - "path": "modules/nf-core/cobrameta/meta.yml", - "type": "module", - "meta": { - "name": "cobrameta", - "description": "A tool to raise the quality of viral genomes assembled from short-read metagenomes via resolving and joining of contigs fragmented during de novo assembly.", - "keywords": [ - "cobra", - "contig", - "scaffold", - "assembly", - "extension", - "virus", - "phage" - ], - "tools": [ - { - "cobra-meta": { - "description": "COBRA is a tool to get higher quality viral genomes assembled from metagenomes.", - "homepage": "https://github.com/linxingchen/cobra", - "documentation": "https://github.com/linxingchen/cobra", - "tool_dev_url": "https://github.com/linxingchen/cobra", - "doi": "10.1038/s41564-023-01598-2", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Assembly file (contigs/scaffolds) in FASTA format\n", - "pattern": "*.{fa,fasta,fna,fa.gz,fasta.gz,fna.gz}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "coverage": { - "type": "file", - "description": "TSV file with 2 columns containing 1) the contig/scaffold id and\n2) the coverage depth of the sequence specified in column 1\n", - "pattern": "*.{tsv,txt}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "query": { - "type": "file", - "description": "File containing the query contigs that the user wants COBRA to extend. This\ncan be provided in one-column TXT or FASTA format. (The IDs must match the IDs\nin the `--fasta` file exactly)\n", - "pattern": "*.{txt,fasta}", - "ontologies": [] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM/CRAM/SAM file resulting from mapping reads used in assembly\nto the resulting assembly FASTA\n", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } - } - ], - { - "assembler": { - "type": "string", - "description": "The name of the tool used to assemble contigs", - "pattern": "{metaspades,megahit,idba}" + }, + { + "name": "deacon_filter", + "path": "modules/nf-core/deacon/filter/meta.yml", + "type": "module", + "meta": { + "name": "deacon_filter", + "description": "Filter DNA sequences using index of reference genome", + "keywords": [ + "filter", + "index", + "fasta", + "fastq", + "genome", + "reference", + "minimizer", + "decontamination" + ], + "tools": [ + { + "deacon": { + "description": "Fast alignment-free sequence filter", + "homepage": "https://github.com/bede/deacon", + "documentation": "https://github.com/bede/deacon#readme", + "tool_dev_url": "https://github.com/bede/deacon", + "doi": "10.1093/bioinformatics/btae004", + "licence": ["MIT"], + "identifier": "biotools:deacon" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "index": { + "type": "file", + "description": "Deacon minimizer index file", + "pattern": "*.idx", + "ontologies": [ + { + "edam": "http://edamontology.org/data_3210" + } + ] + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively.", + "pattern": "*.{fastq,fastq.gz,fqs,fqs.gz,fq,fq.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ] + ], + "output": { + "fastq_filtered": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}*.fq.gz": { + "type": "file", + "description": "List of output filtered FastQ files of size 1 and 2, for single-end and paired-end data, respectively.", + "pattern": "*.fq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.json": { + "type": "file", + "description": "JSON file containing summary of results.", + "pattern": "*.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "versions_deacon": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "deacon": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "deacon --version | head -n1 | sed \"s/deacon //g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "deacon": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "deacon --version | head -n1 | sed \"s/deacon //g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@Baksic-Ivan", "@Omer0191"], + "maintainers": ["@Baksic-Ivan", "@Omer0191", "@vagkaratzas"] } - }, - { - "mink": { - "type": "integer", - "description": "The minimum kmer size used to assemble contigs", - "pattern": "[0-9]+" + }, + { + "name": "deacon_index", + "path": "modules/nf-core/deacon/index/meta.yml", + "type": "module", + "meta": { + "name": "deacon_index", + "description": "Create deacon index for reference genome", + "keywords": ["index", "fasta", "genome", "reference", "minimizer", "decontamination"], + "tools": [ + { + "deacon": { + "description": "Fast alignment-free sequence filter", + "homepage": "https://github.com/bede/deacon", + "documentation": "https://github.com/bede/deacon#readme", + "tool_dev_url": "https://github.com/bede/deacon", + "doi": "10.1093/bioinformatics/btae004", + "licence": ["MIT"], + "identifier": "biotools:deacon" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input genome fasta file", + "pattern": "*.{fasta,fasta.gz,fas,fas.gz,fa,fa.gz,fna,fna.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/data_2044" + }, + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ] + ], + "output": { + "index": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.idx": { + "type": "file", + "description": "Deacon minimizer index file", + "pattern": "*.idx", + "ontologies": [ + { + "edam": "http://edamontology.org/data_3210" + } + ] + } + } + ] + ], + "versions_deacon": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "deacon": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "deacon --version | head -n1 | sed \"s/deacon //g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "deacon": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "deacon --version | head -n1 | sed \"s/deacon //g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@mberacochea"], + "maintainers": ["@mberacochea"] } - }, - { - "maxk": { - "type": "integer", - "description": "The maximum kmer size used to assemble contigs", - "pattern": "[0-9]+" + }, + { + "name": "decoupler_decoupler", + "path": "modules/nf-core/decoupler/decoupler/meta.yml", + "type": "module", + "meta": { + "name": "decoupler_decoupler", + "description": "decoupler is a package containing different statistical methods\nto extract biological activities from omics data within a unified framework.\nIt allows to flexibly test any enrichment method with any prior knowledge\nresource and incorporates methods that take into account the sign and weight.\nIt can be used with any omic, as long as its features can be linked to a\nbiological process based on prior knowledge. For example, in transcriptomics\ngene sets regulated by a transcription factor, or in phospho-proteomics\nphosphosites that are targeted by a kinase.\n", + "keywords": ["enrichment", "omics", "biological activity", "functional analysis", "prior knowledge"], + "tools": [ + { + "decoupler": { + "description": "Ensemble of methods to infer biological activities from omics data", + "homepage": "https://github.com/saezlab/decoupler-py", + "documentation": "https://decoupler-py.readthedocs.io/en/latest/api.html", + "tool_dev_url": "https://decoupler-py.readthedocs.io", + "doi": "10.1093/bioadv/vbac016", + "licence": ["GPL v3"], + "identifier": "biotools:decoupler" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:‘test’, single_end ]\n" + } + }, + { + "mat": { + "type": "file", + "description": "Path to the matrix file (e.g. gene/protein expression, etc.).\nShould be in in tab-separated format (`*.tab`)\n", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy map" + } + }, + { + "net": { + "type": "file", + "description": "The prior knowledge network linking the features of the\nexpression matrix to a process/component (e.g. gene set,\ntranscription factor, kinase, etc.)\n", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy map" + } + }, + { + "annot": { + "type": "file", + "description": "Annotation file in TSV format containing gene ID to gene name mappings.\nUsed specifically for mapping Ensembl IDs to gene names.\nExpected format: two columns with gene_id and gene_name headers.\n", + "pattern": "*.tsv", + "required": false, + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "output": { + "dc_estimate": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:‘test’, single_end ]\n" + } + }, + { + "*estimate_decoupler.tsv": { + "type": "file", + "description": "The file containing the estimation results of the enrichment(s)\n", + "pattern": "*estimate_decoupler.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "dc_pvals": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:‘test’, single_end ]\n" + } + }, + { + "*pvals_decoupler.tsv": { + "type": "file", + "description": "The file containing the p-value associated to the estimation\nresults of the enrichment(s)\n", + "pattern": "*pvals_decoupler.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "png": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:‘test’, single_end ]\n" + } + }, + { + "*estimate_decoupler_plot.png": { + "type": "file", + "description": "The file containing the plots associated to the estimation\nresults of the enrichment(s)\n", + "pattern": "*estimate_decoupler_plot.png", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "YAML file containing versions of tools used in the module", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "topics": { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "YAML file containing versions of tools used in the module", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@gabora", "@vicpaton", "@Nic-Nic"] } - } - ], - "output": { - "self_circular": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "${prefix}/COBRA_category_i_self_circular.fasta.gz": { - "type": "file", - "description": "fasta file", - "pattern": "*/COBRA_category_i_self_circular.fasta.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "extended_circular": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "${prefix}/COBRA_category_ii-a_extended_circular_unique.fasta.gz": { - "type": "file", - "description": "Gzipped FASTA file containing query contigs that were joined and extended\ninto a circular genome\n", - "pattern": "${prefix}/COBRA_category_ii-a_extended_circular_unique.fasta.gz", - "ontologies": [] - } - } - ] - ], - "extended_partial": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "${prefix}/COBRA_category_ii-b_extended_partial_unique.fasta.gz": { - "type": "file", - "description": "Gzipped FASTA file containing query contigs were joined and extended, but\nnot into circular sequences\n", - "pattern": "${prefix}/COBRA_category_ii-b_extended_partial_unique.fasta.gz", - "ontologies": [] - } - } - ] - ], - "extended_failed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "${prefix}/COBRA_category_ii-c_extended_failed.fasta.gz": { - "type": "file", - "description": "Gzipped FASTA file containing query contigs that could not be extended due\nto COBRA rules\n", - "pattern": "${prefix}/COBRA_category_ii-c_extended_failed.fasta.gz", - "ontologies": [] - } - } - ] - ], - "orphan_end": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "${prefix}/COBRA_category_iii_orphan_end.fasta.gz": { - "type": "file", - "description": "Gzipped FASTA file containing query contigs that do not shared the\n\"expected overlap length\" with other contigs\n", - "pattern": "${prefix}/COBRA_category_iii_orphan_end.fasta.gz", - "ontologies": [] - } - } - ] - ], - "all_cobra_assemblies": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "${prefix}/COBRA_all_assemblies.fasta.gz": { - "type": "file", - "description": "Gzipped FASTA file containing all the assemblies generated by COBRA", - "pattern": "*/COBRA_all_assemblies.fasta.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "joining_summary": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "${prefix}/COBRA_joining_summary.txt": { - "type": "file", - "description": "TSV file containing information regarding COBRA's extension results\n", - "pattern": "${prefix}/COBRA_joining_summary.txt", - "ontologies": [] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "${prefix}/log": { - "type": "file", - "description": "Log file containing the contents of each processing\n", - "pattern": "${prefix}/log", - "ontologies": [] - } - } - ] - ], - "versions_cobra": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cobra": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cobra-meta --version 2>&1 | sed 's/^.*cobra v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cobra": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cobra-meta --version 2>&1 | sed 's/^.*cobra v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@CarsonJM" - ], - "maintainers": [ - "@CarsonJM" - ] - }, - "pipelines": [ - { - "name": "phageannotator", - "version": "dev" - } - ] - }, - { - "name": "cobs_classicconstruct", - "path": "modules/nf-core/cobs/classicconstruct/meta.yml", - "type": "module", - "meta": { - "name": "cobs_classicconstruct", - "description": "Builds a classic bloom filter COBS index", - "keywords": [ - "COBS", - "index", - "k-mer index", - "bloom filter" - ], - "tools": [ - { - "cobs": { - "description": "Compact Bit-Sliced Signature Index (for Genomic k-Mer Data or q-Grams)", - "homepage": "https://panthema.net/cobs", - "documentation": "https://github.com/iqbal-lab-org/cobs", - "tool_dev_url": "https://github.com/iqbal-lab-org/cobs", - "doi": "10.1007/978-3-030-32686-9_21", - "licence": [ - "MIT" - ], - "identifier": "" + }, + { + "name": "dedup", + "path": "modules/nf-core/dedup/meta.yml", + "type": "module", + "meta": { + "name": "dedup", + "description": "DeDup is a tool for read deduplication in paired-end read merging (e.g. for ancient DNA experiments).", + "keywords": ["dedup", "deduplication", "pcr duplicates", "ancient DNA", "paired-end", "bam"], + "tools": [ + { + "dedup": { + "description": "DeDup is a tool for read deduplication in paired-end read merging (e.g. for ancient DNA experiments).", + "homepage": "https://github.com/apeltzer/DeDup", + "documentation": "https://dedup.readthedocs.io/en/latest/", + "tool_dev_url": "https://github.com/apeltzer/DeDup", + "doi": "10.1186/s13059-016-0918-z", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/SAM file", + "pattern": "*.{bam,sam}", + "ontologies": [] + } + } + ] + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.bam": { + "type": "file", + "description": "Deduplicated BAM file", + "pattern": "${prefix}.bam", + "ontologies": [] + } + } + ] + ], + "json": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.json": { + "type": "file", + "description": "JSON file for MultiQC", + "pattern": "${prefix}.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "hist": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.hist": { + "type": "file", + "description": "Histogram data of amount of deduplication", + "pattern": "${prefix}.hist", + "ontologies": [] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.log": { + "type": "file", + "description": "Dedup log information", + "pattern": "${prefix}.log", + "ontologies": [] + } + } + ] + ], + "versions_dedup": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "dedup": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "dedup --version | grep -oE '[0-9]+\\.[0-9]+\\.[0-9]+'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "dedup": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "dedup --version | grep -oE '[0-9]+\\.[0-9]+\\.[0-9]+'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@jfy133"], + "maintainers": ["@jfy133"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } + }, + { + "name": "deeparg_downloaddata", + "path": "modules/nf-core/deeparg/downloaddata/meta.yml", + "type": "module", + "meta": { + "name": "deeparg_downloaddata", + "description": "A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes", + "keywords": [ + "download", + "database", + "deeparg", + "antimicrobial resistance genes", + "deep learning", + "prediction" + ], + "tools": [ + { + "deeparg": { + "description": "A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes", + "homepage": "https://github.com/gaarangoa/deeparg", + "documentation": "https://github.com/gaarangoa/deeparg", + "tool_dev_url": "https://github.com/gaarangoa/deeparg", + "doi": "10.1186/s40168-018-0401-z", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [], + "output": { + "db": [ + { + "db/": { + "type": "directory", + "description": "Directory containing database required for deepARG.", + "pattern": "db/" + } + } + ], + "versions_deeparg": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "deeparg": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "1.0.4": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "deeparg": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "1.0.4": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@jfy133"], + "maintainers": ["@jfy133"] }, - { - "input": { - "type": "file", - "description": "The file or directory to be indexed.\nCOBS can read:\n 1. FASTA files (*.fa, *.fasta, *.fna, *.ffn, *.faa, *.frn, *.fa.gz, *.fasta.gz, *.fna.gz, *.ffn.gz, *.faa.gz, *.frn.gz),\n 2. FASTQ files (*.fq, *.fastq, *.fq.gz., *.fastq.gz),\n 3. \"Multi-FASTA\" and \"Multi-FASTQ\" files (*.mfasta, *.mfastq),\n 4. McCortex files (*.ctx),\n 5. or text files (*.txt).\nYou can either recursively scan a directory for all files matching any of these files,\nor pass a *.list file which lists all paths COBS should index.\n", - "pattern": "*.*", - "ontologies": [] - } - } - ] - ], - "output": { - "index": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.index.cobs_classic": { - "type": "file", - "description": "The COBS classic index", - "pattern": "*.index.cobs_classic", - "ontologies": [] - } - } - ] - ], - "versions_cobs": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cobs": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cobs version 2>&1 | grep -Eo '[0-9]+\\.[0-9]+\\.[0-9]+'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cobs": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cobs version 2>&1 | grep -Eo '[0-9]+\\.[0-9]+\\.[0-9]+'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "funcscan", + "version": "3.0.0" + } ] - ] - }, - "authors": [ - "@leoisl" - ], - "maintainers": [ - "@leoisl" - ] - } - }, - { - "name": "cobs_compactconstruct", - "path": "modules/nf-core/cobs/compactconstruct/meta.yml", - "type": "module", - "meta": { - "name": "cobs_compactconstruct", - "description": "Builds a compact bloom filter COBS index", - "keywords": [ - "COBS", - "index", - "k-mer index", - "bloom filter" - ], - "tools": [ - { - "cobs": { - "description": "Compact Bit-Sliced Signature Index (for Genomic k-Mer Data or q-Grams)", - "homepage": "https://panthema.net/cobs", - "documentation": "https://github.com/iqbal-lab-org/cobs", - "doi": "10.1007/978-3-030-32686-9_21", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } + }, + { + "name": "deeparg_predict", + "path": "modules/nf-core/deeparg/predict/meta.yml", + "type": "module", + "meta": { + "name": "deeparg_predict", + "description": "A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes", + "keywords": [ + "deeparg", + "antimicrobial resistance", + "antimicrobial resistance genes", + "arg", + "deep learning", + "prediction", + "contigs", + "metagenomes" + ], + "tools": [ + { + "deeparg": { + "description": "A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes", + "homepage": "https://github.com/gaarangoa/deeparg", + "documentation": "https://github.com/gaarangoa/deeparg", + "tool_dev_url": "https://github.com/gaarangoa/deeparg", + "doi": "10.1186/s40168-018-0401-z", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA file containing gene-like sequences", + "pattern": "*.{fasta,fa,fna}", + "ontologies": [] + } + }, + { + "model": { + "type": "string", + "description": "Which model to use, depending on input data. Either 'LS' or 'SS' for long or short sequences respectively", + "pattern": "LS|LS" + } + } + ], + { + "db": { + "type": "directory", + "description": "Path to a directory containing the deepARG pre-built models", + "pattern": "*/" + } + } + ], + "output": { + "daa": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.align.daa": { + "type": "file", + "description": "Sequences of ARG-like sequences from DIAMOND alignment", + "pattern": "*.align.daa", + "ontologies": [] + } + } + ] + ], + "daa_tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.align.daa.tsv": { + "type": "file", + "description": "Alignments scores against ARG-like sequences from DIAMOND alignment", + "pattern": "*.align.daa.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "arg": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.mapping.ARG": { + "type": "file", + "description": "Table containing sequences with an ARG-like probability of more than specified thresholds", + "pattern": "*.mapping.ARG", + "ontologies": [] + } + } + ] + ], + "potential_arg": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.mapping.potential.ARG": { + "type": "file", + "description": "Table containing sequences with an ARG-like probability of less than specified thresholds, and requires manual inspection", + "pattern": "*.mapping.potential.ARG", + "ontologies": [] + } + } + ] + ], + "versions_deeparg": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "deeparg": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "1.0.4": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "deeparg": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "1.0.4": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@jfy133"], + "maintainers": ["@jfy133"] }, - { - "input": { - "type": "file", - "description": "The file or directory to be indexed.\nCOBS can read:\n 1. FASTA files (`*.fa`, `*.fasta`, `*.fna`, `*.ffn`, `*.faa`, `*.frn`, `*.fa.gz`, `*.fasta.gz`, `*.fna.gz`, `*.ffn.gz`, `*.faa.gz`, `*.frn.gz`),\n 2. FASTQ files (`*.fq`, `*.fastq`, `*.fq.gz.`, `*.fastq.gz`),\n 3. \"Multi-FASTA\" and \"Multi-FASTQ\" files (`*.mfasta`, `*.mfastq`),\n 4. McCortex files (`*.ctx`),\n 5. or text files (`*.txt`).\nYou can either recursively scan a directory for all files matching any of these files,\nor pass a `*.list` file which lists all paths COBS should index.\n", - "pattern": "*.*", - "ontologies": [] - } - } - ] - ], - "output": { - "index": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.index.cobs_compact": { - "type": "file", - "description": "The COBS compact index", - "pattern": "*.index.cobs_compact", - "ontologies": [] - } - } - ] - ], - "versions_cobs": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cobs": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cobs version 2>&1 | grep -Eo '[0-9]+\\.[0-9]+\\.[0-9]+'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cobs": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cobs version 2>&1 | grep -Eo '[0-9]+\\.[0-9]+\\.[0-9]+'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "funcscan", + "version": "3.0.0" + } ] - ] - }, - "authors": [ - "@leoisl" - ], - "maintainers": [ - "@leoisl" - ] - } - }, - { - "name": "comebin_runcomebin", - "path": "modules/nf-core/comebin/runcomebin/meta.yml", - "type": "module", - "meta": { - "name": "comebin_runcomebin", - "description": "Effective binning of metagenomic contigs using COntrastive Multi-viEw representation learning", - "keywords": [ - "metagenomics", - "binning", - "clustering" - ], - "tools": [ - { - "comebin": { - "description": "COMEBin allows effective binning of metagenomic contigs using COntrastive Multi-viEw representation learning", - "homepage": "https://github.com/ziyewang/COMEBin", - "documentation": "https://github.com/ziyewang/COMEBin", - "tool_dev_url": "https://github.com/ziyewang/COMEBin", - "doi": "10.1038/s41467-023-44290-z", - "licence": [ - "GPL v3" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "assembly": { - "type": "file", - "description": "FASTA file of contigs for binning", - "pattern": "*.{fa,fas,fasta,fna,fa.gz,fas.gz,fasta.gz,fna.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } + }, + { + "name": "deepbgc_download", + "path": "modules/nf-core/deepbgc/download/meta.yml", + "type": "module", + "meta": { + "name": "deepbgc_download", + "description": "Database download module for DeepBGC which detects BGCs in bacterial and fungal genomes using deep learning.", + "keywords": [ + "database", + "download", + "BGC", + "biosynthetic gene cluster", + "deep learning", + "neural network", + "random forest", + "genomes", + "bacteria", + "fungi" + ], + "tools": [ + { + "deepbgc": { + "description": "DeepBGC - Biosynthetic Gene Cluster detection and classification", + "homepage": "https://github.com/Merck/deepbgc", + "documentation": "https://github.com/Merck/deepbgc", + "tool_dev_url": "https://github.com/Merck/deepbgc", + "doi": "10.1093/nar/gkz654", + "licence": ["MIT"], + "identifier": "biotools:DeepBGC" + } + } + ], + "output": { + "db": [ + { + "deepbgc_db/": { + "type": "directory", + "description": "Directory containing the DeepBGC database", + "pattern": "deepbgc_db/" + } + } + ], + "versions_deepbgc": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "deepbgc": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "deepbgc info 2>&1 | sed '6!d;s/.*= version //;s/ .*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "deepbgc": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "deepbgc info 2>&1 | sed '6!d;s/.*= version //;s/ .*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@louperelo"], + "maintainers": ["@louperelo"] }, - { - "bam": { - "type": "file", - "description": "List of sorted bam files of reads mapped to the reference assembly. Not compatible with TSV input.\n", - "pattern": "*.bam", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - } - ] - ], - "output": { - "bins": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" + "pipelines": [ + { + "name": "funcscan", + "version": "3.0.0" } - }, - { - "${prefix}/comebin_res_bins/*.fa.gz": { - "type": "file", - "description": "List of FASTA files of binned contigs", - "pattern": "*.fna.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - }, + ] + }, + { + "name": "deepbgc_pipeline", + "path": "modules/nf-core/deepbgc/pipeline/meta.yml", + "type": "module", + "meta": { + "name": "deepbgc_pipeline", + "description": "DeepBGC detects BGCs in bacterial and fungal genomes using deep learning.", + "keywords": [ + "BGC", + "biosynthetic gene cluster", + "deep learning", + "neural network", + "random forest", + "genomes", + "bacteria", + "fungi" + ], + "tools": [ + { + "deepbgc": { + "description": "DeepBGC - Biosynthetic Gene Cluster detection and classification", + "homepage": "https://github.com/Merck/deepbgc", + "documentation": "https://github.com/Merck/deepbgc", + "tool_dev_url": "https://github.com/Merck/deepbgc", + "doi": "10.1093/nar/gkz654", + "licence": ["MIT"], + "identifier": "biotools:DeepBGC" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "genome": { + "type": "file", + "description": "FASTA/GenBank/Pfam CSV file", + "pattern": "*.{fasta,fa,fna,gbk,csv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ], { - "edam": "http://edamontology.org/format_3989" + "db": { + "type": "directory", + "description": "Database path" + } } - ] + ], + "output": { + "readme": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ 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+ "blacklist": { + "type": "file", + "description": "BED/GTF file containing regions to exclude from analysis", + "pattern": "*.{bed,gtf}", + "ontologies": [ + { + "edam": "http://edamontology.org/data_3002" + }, + { + "edam": "http://edamontology.org/format_3003" + } + ], + "optional": true + } + } + ] + ], + "output": { + "matrix": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.npz": { + "type": "file", + "description": "compressed numpy array of read coverage data used by plotCorrelation and plotPCA\ndeeptool utilities\n", + "pattern": "all_bam.bamSummary.npz", + "ontologies": [] + } + } + ] + ], + "versions_deeptools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "deeptools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "multiBamSummary --version | sed \"s/multiBamSummary 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- ], - "CNV": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_CNVs": { - "type": "file", - "description": "file with coordinates of predicted copy number alterations.", - "pattern": "*_CNVs", - "ontologies": [] - } - } - ] - ], - "info": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_info.txt": { - "type": "file", - "description": "parsable file with information about FREEC run", - "pattern": "*_info.txt", - "ontologies": [] - } - } - ] - ], - "ratio": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_ratio.txt": { - "type": "file", - "description": "file with ratios and predicted copy number alterations for each window", - "pattern": "*_ratio.txt", - "ontologies": 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"description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "bigwigs": { + "type": "file", + "description": "Two or more bigWig files", + "pattern": "*.{bigWig,bw}", + "ontologies": [] + } + }, + { + "labels": { + "type": "list", + "description": "Labels for the bigWig files used in the matrix" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing blacklist metadata\ne.g. [ id:'blacklist' ]\n" + } + }, + { + "blacklist": { + "type": "file", + "description": "BED/GTF file containing regions to exclude from analysis", + "pattern": "*.{bed,gtf}", + "ontologies": [ + { + "edam": "http://edamontology.org/data_3002" + }, + { + "edam": "http://edamontology.org/format_3003" + } + ], + "optional": true + } + } + ] + ], + "output": { + "matrix": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.npz": { + "type": "file", + "description": "Matrix file from multiBigwigSummary", + "pattern": "*.npz", + "ontologies": [] + } + } + ] + ], + "versions_deeptools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "deeptools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "multiBigwigSummary --version | sed \"s/multiBigwigSummary //g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "deeptools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "multiBigwigSummary --version | sed \"s/multiBigwigSummary //g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@ugoiannacchero", "@daisymut"], + "maintainers": 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"string", - "description": "The name of the tool" - } - }, - { - "11.6b": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "sammyseq", + "version": "dev" + } ] - ] - }, - "authors": [ - "@FriederikeHanssen" - ], - "maintainers": [ - "@FriederikeHanssen" - ] - }, - "pipelines": [ - { - "name": "sarek", - "version": "3.8.1" - } - ] - }, - { - "name": "controlfreec_freec2circos", - "path": "modules/nf-core/controlfreec/freec2circos/meta.yml", - "type": "module", - "meta": { - "name": "controlfreec_freec2circos", - "description": "Format Freec output to circos input format", - "keywords": [ - "cna", - "cnv", - "somatic", - "single", - "tumor-only" - ], - "tools": [ - { - "controlfreec": { - "description": "Copy number and genotype annotation from whole genome and whole exome sequencing data.", - "homepage": "http://boevalab.inf.ethz.ch/FREEC", - "documentation": 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"https://github.com/deeptools/deepTools", + "doi": "10.1093/nar/gku365", + "licence": ["GPL v3"], + "identifier": "biotools:deeptools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "matrix": { + "type": "file", + "description": "compressed matrix file produced by\nmutlibamsummary or multibigwigsummary\n", + "pattern": "*.{npz}", + "ontologies": [] + } + } + ], + { + "method": { + "type": "string", + "description": "Correlation coefficient to use for heatmap or scatterplot generation\n", + "pattern": "{spearman,pearson}" + } + }, + { + "plot_type": { + "type": "string", + "description": "Type of output plot to display sample correlation\n", + "pattern": "{heatmap,scatterplot}" + } + } + ], + "output": { + "pdf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, 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containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.csv": { - "type": "file", - "description": "CSV table with rows as reference genomes, columns samples and entries as log2 PTR", - "pattern": "*.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "versions_coptr": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "coptr": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "coptr |& sed -E '11!d ; s/CoPTR.*?\\(v(.*?)\\).*/\\1/'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@ramirobarrantes" - ], - "maintainers": [ - "@ramirobarrantes" - ], - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "coptr": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "coptr |& sed -E '11!d ; s/CoPTR.*?\\(v(.*?)\\).*/\\1/'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - } - } - }, - { - "name": "coptr_extract", - "path": "modules/nf-core/coptr/extract/meta.yml", - "type": "module", - "meta": { - "name": "coptr_extract", - "description": "Computes the coverage map along the reference genome", - "keywords": [ - "coptr", - "mapping", - "ptr" - ], - "tools": [ - { - "coptr": { - "description": "Accurate and robust inference of microbial growth dynamics from metagenomic sequencing reads.", - "homepage": "https://github.com/tyjo/coptr", - "documentation": "https://coptr.readthedocs.io/", - "tool_dev_url": "https://github.com/tyjo/coptr", - "doi": "10.1101/gr.275533.121", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:coptr" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "bam file with the mapping of the reads on the reference genome", - "pattern": "*.{.bam}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - } - ] - ], - "output": { - "coverage": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.pkl": { - "type": "file", - "description": "Python pickle (pkl) file containing coverage along the reference genome", - "pattern": "*.{pkl}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_4002" - } - ] - } - } - ] - ], - "versions_coptr": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "coptr": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "coptr |& sed -E '11!d ; s/CoPTR.*?\\(v(.*?)\\).*/\\1/'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@ramirobarrantes" - ], - "maintainers": [ - "@ramirobarrantes" - ], - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "coptr": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "coptr |& sed -E '11!d ; s/CoPTR.*?\\(v(.*?)\\).*/\\1/'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - } - } - }, - { - "name": "coptr_index", - "path": "modules/nf-core/coptr/index/meta.yml", - "type": "module", - "meta": { - "name": "coptr_index", - "description": "Indexes a directory of fasta files for use with CoPTR", - "keywords": [ - "coptr", - "index", - "ptr" - ], - "tools": [ - { - "coptr": { - "description": "Accurate and robust inference of microbial growth dynamics from metagenomic sequencing reads.", - "homepage": "https://github.com/tyjo/coptr", - "documentation": "https://coptr.readthedocs.io/", - "tool_dev_url": "https://github.com/tyjo/coptr", - "doi": "10.1101/gr.275533.121", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:coptr" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing genome information\n" - } - }, - { - "indexfasta": { - "type": "file", - "description": "Fasta file(s) ending in [.fasta, .fna, .fa] to be used to create the index.", - "pattern": "*.{.fasta,.fna,.fa}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ], - "output": { - "index_dir": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing genome information\n" - } - }, - { - "bowtie2": { - "type": "map", - "description": "index genome directory", - "ontologies": [ - { - "edam": "http://edamontology.org/data_3210" - } - ], - "pattern": "*.{genome}" - } - } - ] - ], - "versions_coptr": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "coptr": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "coptr |& sed -E '11!d ; s/CoPTR.*?\\(v(.*?)\\).*/\\1/'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@ramirobarrantes" - ], - "maintainers": [ - "@ramirobarrantes" - ], - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "coptr": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "coptr |& sed -E '11!d ; s/CoPTR.*?\\(v(.*?)\\).*/\\1/'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - } - } - }, - { - "name": "coptr_map", - "path": "modules/nf-core/coptr/map/meta.yml", - "type": "module", - "meta": { - "name": "coptr_map", - "description": "Maps the reads to the reference database", - "keywords": [ - "coptr", - "mapping", - "ptr" - ], - "tools": [ - { - "coptr": { - "description": "Accurate and robust inference of microbial growth dynamics from metagenomic sequencing reads.", - "homepage": "https://github.com/tyjo/coptr", - "documentation": "https://coptr.readthedocs.io/", - "tool_dev_url": "https://github.com/tyjo/coptr", - "doi": "10.1101/gr.275533.121", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:coptr" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "fastq file with reads", - "pattern": "*.{.fastq,.fq,.fastq.gz,fq.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing index genome id and path\ne.g. [ id:'test', 'bowtie2' ]\n" - } - }, - { - "index": { - "type": "file", - "description": "Directory with Bowtie2 genome index files", - "pattern": "*.ebwt", - "ontologies": [] - } - } - ] - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "Alignment (BAM) file of reads mapped to the reference database", - "pattern": "*.{bam}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - } - ] - ], - "versions_coptr": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "coptr": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "coptr |& sed -E '11!d ; s/CoPTR.*?\\(v(.*?)\\).*/\\1/'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@ramirobarrantes" - ], - "maintainers": [ - "@ramirobarrantes" - ], - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "coptr": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "coptr |& sed -E '11!d ; s/CoPTR.*?\\(v(.*?)\\).*/\\1/'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - } - } - }, - { - "name": "coptr_merge", - "path": "modules/nf-core/coptr/merge/meta.yml", - "type": "module", - "meta": { - "name": "coptr_merge", - "description": "Merge reads that were mapped to multiple indices", - "keywords": [ - "coptr", - "mapping", - "merging", - "ptr" - ], - "tools": [ - { - "coptr": { - "description": "Accurate and robust inference of microbial growth dynamics from metagenomic sequencing reads.", - "homepage": "https://github.com/tyjo/coptr", - "documentation": "https://coptr.readthedocs.io/", - "tool_dev_url": "https://github.com/tyjo/coptr", - "doi": "10.1101/gr.275533.121", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:coptr" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "bams": { - "type": "file", - "description": "bam files to merge. Assumes that the reads were mapped to different indices.", - "pattern": "*.bam", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - } - ] - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "Merged BAM file", - "pattern": "*.{bam}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - } - ] - ], - "versions_coptr": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "coptr": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "coptr |& sed -E '11!d ; s/CoPTR.*?\\(v(.*?)\\).*/\\1/'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@ramirobarrantes" - ], - "maintainers": [ - "@ramirobarrantes" - ], - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "coptr": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "coptr |& sed -E '11!d ; s/CoPTR.*?\\(v(.*?)\\).*/\\1/'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - } - } - }, - { - "name": "coreograph", - "path": "modules/nf-core/coreograph/meta.yml", - "type": "module", - "meta": { - "name": "coreograph", - "description": "Great....yet another TMA dearray program. What does this one do? Coreograph uses UNet, a deep learning model, to identify complete/incomplete tissue cores on a tissue microarray. It has been trained on 9 TMA slides of different sizes and tissue types.", - "keywords": [ - "UNet", - "TMA dearray", - "Segmentation", - "Cores" - ], - "tools": [ - { - "coreograph": { - "description": "A TMA dearray program that uses UNet, a deep learning model, to identify complete/incomplete tissue cores on a tissue microarray.", - "homepage": "https://mcmicro.org/parameters/core.html#coreograph", - "documentation": "https://mcmicro.org/troubleshooting/tuning/coreograph.html", - "tool_dev_url": "https://github.com/HMS-IDAC/UNetCoreograph", - "doi": "10.1038/s41592-021-01308-y", - "license": [ - "MIT License" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\n" - } - }, - { - "image": { - "type": "file", - "description": "OME-TIFF or TIFF file for core detection and extraction.", - "pattern": "*.{ome.tif,tif,tiff}", - "ontologies": [] - } - } - ] - ], - "output": { - "cores": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*[0-9]*.tif": { - "type": "file", - "description": "Complete/Incomplete tissue cores", - "pattern": "*.{tif}", - "ontologies": [] - } - } - ] - ], - "masks": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "masks/*.tif": { - "type": "file", - "description": "Binary masks for the Complete/Incomplete tissue cores", - "pattern": "./masks/*.{tif}", - "ontologies": [] - } - } - ] - ], - "tma_map": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "TMA_MAP.tif": { - "type": "file", - "description": "A TMA map showing labels and outlines", - "pattern": "TMA_MAP.tif", - "ontologies": [] - } - } - ] - ], - "centroids": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "centroidsY-X.txt": { - "type": "file", - "description": "A text file listing centroids of each core in format Y, X", - "pattern": "centroidsY-X.txt", - "ontologies": [] - } - } - ] - ], - "versions_coreograph": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "coreograph": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "2.2.9": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "coreograph": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "2.2.9": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@arozhada", - "@MargotCh" - ], - "maintainers": [ - "@arozhada", - "@MargotCh" - ] - }, - "pipelines": [ - { - "name": "mcmicro", - "version": "dev" - } - ] - }, - { - "name": "coverm_contig", - "path": "modules/nf-core/coverm/contig/meta.yml", - "type": "module", - "meta": { - "name": "coverm_contig", - "description": "Map reads to contigs and estimate coverage", - "keywords": [ - "mapping", - "genomics", - "metagenomics", - "coverage" - ], - "tools": [ - { - "coverm": { - "description": "CoverM aims to be a configurable, easy to use and fast DNA read coverage and relative abundance calculator focused on metagenomics applications", - "homepage": "https://github.com/wwood/CoverM", - "documentation": "https://wwood.github.io/CoverM/coverm-contig.html", - "tool_dev_url": "https://github.com/wwood/CoverM", - "doi": "10.5281/zenodo.10531253", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:coverm" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "input": { - "type": "file", - "description": "FASTA/FASTQ containing reads (can be gzipped), or sorted BAM files of reads mapped to a reference.\nIf supplying PE fasta for multiple samples, should be in the order \"sample1_1, sample1_2, sample2_1, sample2_2...\".\n", - "pattern": "*.{fa,fq,fa.gz,fq.gz,bam}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - }, - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "reference": { - "type": "file", - "description": "Reference FASTA file to map reads to, or minimap2/strobealign index.\nNot required if using BAM input.\n", - "pattern": "*.{fasta,fasta.gz,mmi,sti}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - { - "bam_input": { - "type": "boolean", - "description": "True if input is bam files" - } - }, - { - "interleaved": { - "type": "boolean", - "description": "True if input is interleaved fastq file" - } - }, - { - "enable_bam_output": { - "type": "boolean", - "description": "True to enable BAM output of aligned reads" - } - } - ], - "output": { - "coverage": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.depth.tsv": { - "type": "file", - "description": "Tab-delimited file containing coverage information for each contig and sample.", - "pattern": "*.depth.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "BAM file containing aligned reads.", - "pattern": "*.bam", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - } - ] - ], - "versions_coverm": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "coverm": { - "type": "string", - "description": "The tool name" - } - }, - { - "coverm --version | sed \"s/coverm //\"": { - "type": "string", - "description": "Command used to collect the version" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "coverm": { - "type": "string", - "description": "The tool name" - } - }, - { - "coverm --version | sed \"s/coverm //\"": { - "type": "string", - "description": "Command used to collect the version" - } - } - ] - ] - }, - "authors": [ - "@prototaxites" - ], - "maintainers": [ - "@prototaxites" - ] - }, - "pipelines": [ - { - "name": "seqsubmit", - "version": "dev" - } - ] - }, - { - "name": "coverm_genome", - "path": "modules/nf-core/coverm/genome/meta.yml", - "type": "module", - "meta": { - "name": "coverm_genome", - "description": "Calculate read coverage per-genome", - "keywords": [ - "mapping", - "genomics", - "metagenomics", - "coverage" - ], - "tools": [ - { - "coverm": { - "description": "CoverM aims to be a configurable, easy to use and fast DNA read coverage and relative abundance calculator focused on metagenomics applications", - "homepage": "https://github.com/wwood/CoverM", - "documentation": "https://wwood.github.io/CoverM/coverm-contig.html", - "tool_dev_url": "https://github.com/wwood/CoverM", - "doi": "10.5281/zenodo.10531253", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:coverm" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "input": { - "type": "file", - "description": "FASTA/FASTQ containing reads (can be gzipped), or sorted BAM files of reads mapped to a reference.\nIf supplying PE fasta for multiple samples, should be in the order \"sample1_1, sample1_2, sample2_1, sample2_2...\".\n", - "pattern": "*.{fa,fq,fa.gz,fq.gz,bam}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - }, - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "reference": { - "type": "file", - "description": "Genome FASTA file(s) to map reads to, or a directory containing genome FASTA files.", - "pattern": "*.{fasta,fasta.gz,mmi,sti,fna,fna.gz,fa,fa.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - { - "bam_input": { - "type": "boolean", - "description": "True if input is bam files" - } - }, - { - "interleaved": { - "type": "boolean", - "description": "True if input is interleaved fastq file" - } - }, - { - "ref_mode": { - "type": "string", - "description": "How to interpret the `reference` input:\n - `\"dir\"`: Treat as a directory containing one or more FASTA files.\n - `\"file\"`: Treat as a single FASTA file.\n - `\"auto\"`: Automatically detect based on whether the `reference` path is a directory or file.\nDefaults to `\"auto\"` if not provided.\n", - "pattern": "^(dir|file|auto)$" - } - }, - { - "enable_bam_output": { - "type": "boolean", - "description": "True to enable BAM output of aligned reads" - } - } - ], - "output": { - "coverage": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.depth.tsv": { - "type": "map", - "description": "Tab-delimited file containing coverage information for each contig and sample.", - "pattern": "*.depth.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "BAM file containing aligned reads.", - 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} - ] - }, - { - "name": "cowpy", - "path": "modules/nf-core/cowpy/meta.yml", - "type": "module", - "meta": { - "name": "cowpy", - "description": "Print any text in a cow or other characters", - "keywords": [ - "cowpy", - "hello", - "ascii_art" - ], - "tools": [ - { - "cowpy": { - "description": "Print any text in a cow or other characters", - "homepage": "https://github.com/jeffbuttars/cowpy", - "documentation": "https://github.com/jeffbuttars/cowpy", - "tool_dev_url": "https://github.com/jeffbuttars/cowpy", - "licence": [ - "Apache-2.0" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "text": { - "type": "file", - "description": "text file", - "pattern": "*.{txt}", - "ontologies": [] - } - } - ] - ], - "output": { - "txt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n", - "pattern": "*.txt" - } - }, - { - "${prefix}.txt": { - "type": "file", - "description": "test file", - "pattern": "*.txt", - "ontologies": [] - } - } - ] - ], - "versions_cowpy": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cowpy": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "1.1.5": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cowpy": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "1.1.5": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@maxulysse" - ], - "maintainers": [ - "@maxulysse" - ] - } - }, - { - "name": "crabs_import", - "path": "modules/nf-core/crabs/import/meta.yml", - "type": "module", - "meta": { - "name": "crabs_import", - "description": "In-house generated or curated data can be imported into CRABS.", - "keywords": [ - "insilico", - "amplicon", - "sequencing", - "inhouse" - ], - "tools": [ - { - "crabs": { - "description": "Crabs (Creating Reference databases for Amplicon-Based Sequencing)\nis a program to download and curate reference databases\nfor eDNA metabarcoding analyses\n", - "homepage": "https://github.com/gjeunen/reference_database_creator", - "documentation": "https://github.com/gjeunen/reference_database_creator?tab=readme-ov-file#running-crabs", - "tool_dev_url": "https://github.com/gjeunen/reference_database_creator", - "doi": "10.1111/1755-0998.13741", - "licence": [ - "MIT License" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "In-house sequencing data", - "pattern": "*.{fa,fasta}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "accession2taxid": { - "type": "file", - "description": "Linking accession numbers to taxonomic IDs", - "pattern": "*.accession2taxid", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "names": { - "type": "file", - "description": "Containing information about the phylogenetic name associated with each taxonomic ID", - "pattern": "*.dmp", - "ontologies": [] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "nodes": { - "type": "file", - "description": "Containing information how taxonomic IDs are linked", - "pattern": "*.dmp", - "ontologies": [] - } - } - ], - { - "import_format": { - "type": "string", - "description": "Name of the repository from which the data was downloaded, i.e., BOLD, EMBL, GreenGenes, MIDORI, MITOFISH, NCBI, SILVA, or UNITE.", - "choices": [ - "bold", - "embl", - "greengenes", - "midori", - "mitofish", - "ncbi", - "silva", - "unite" - ] - } - } - ], - "output": { - "crabsdb": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.txt": { - "type": "file", - "description": "Reverse complemented Sequence", - "pattern": "*.txt", - "ontologies": [] - } - } - ] - ], - "versions_crabs": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "crabs": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "crabs --help 2>/dev/null | grep -oE 'v[0-9.]+' | cut -c2-": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "crabs": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "crabs --help 2>/dev/null | grep -oE 'v[0-9.]+' | cut -c2-": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@famosab", - "@a4000" - ], - "maintainers": [ - "@famosab", - "@a4000" - ] - } - }, - { - "name": "crabs_insilicopcr", - "path": "modules/nf-core/crabs/insilicopcr/meta.yml", - "type": "module", - "meta": { - "name": "crabs_insilicopcr", - "description": "CRABS extracts the amplicon region of the primer set by conducting an in silico PCR.", - "keywords": [ - "insilico", - "PCR", - "amplicon", - "sequencing" - ], - "tools": [ - { - "crabs": { - "description": "Crabs (Creating Reference databases for Amplicon-Based Sequencing)\nis a program to download and curate reference databases\nfor eDNA metabarcoding analyses\n", - "homepage": "https://github.com/gjeunen/reference_database_creator", - "documentation": "https://github.com/gjeunen/reference_database_creator?tab=readme-ov-file#running-crabs", - "tool_dev_url": "https://github.com/gjeunen/reference_database_creator", - "doi": "10.1111/1755-0998.13741", - "licence": [ - "MIT License" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "crabsdb": { - "type": "file", - "description": "CRABSDB to conduct in silico PCR on", - "pattern": "*.txt", - "ontologies": [] - } - } - ] - ], - "output": { - "txt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}.txt": { - "type": "file", - "description": "Extracted amplicon regions", - "pattern": "*.insilicopcr.txt", - "ontologies": [] - } - } - ] - ], - "versions_crabs": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "crabs": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "crabs --help 2>/dev/null | grep -oE 'v[0-9.]+' | cut -c2-": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "crabs": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "crabs --help 2>/dev/null | grep -oE 'v[0-9.]+' | cut -c2-": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@famosab", - "@a4000" - ], - "maintainers": [ - "@famosab", - "@a4000" - ] - } - }, - { - "name": "crabz_compress", - "path": "modules/nf-core/crabz/compress/meta.yml", - "type": "module", - "meta": { - "name": "crabz_compress", - "description": "Compress files with crabz", - "keywords": [ - "compression", - "gzip", - "zlib" - ], - "tools": [ - { - "crabz": { - "description": "Like pigz, but rust", - "homepage": "https://github.com/sstadick/crabz", - "documentation": "https://github.com/sstadick/crabz", - "tool_dev_url": "https://github.com/sstadick/crabz", - "licence": [ - "MIT" - ], - "identifier": "biotools:crabz" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "file": { - "type": "file", - "description": "File to be compressed", - "pattern": "*.*", - "ontologies": [] - } - } - ] - ], - "output": { - "archive": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.gz": { - "type": "file", - "description": "The compressed file", - "pattern": "*.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "versions_crabz": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "crabz": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "0.10.0": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "crabz": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "0.10.0": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@camlloyd" - ], - "maintainers": [ - "@camlloyd" - ] - } - }, - { - "name": "crabz_decompress", - "path": "modules/nf-core/crabz/decompress/meta.yml", - "type": "module", - "meta": { - "name": "crabz_decompress", - "description": "Decompress files with crabz", - "keywords": [ - "decompression", - "gzip", - "zlib" - ], - "tools": [ - { - "crabz": { - "description": "Like pigz, but rust", - "homepage": "https://github.com/sstadick/crabz", - "documentation": "https://github.com/sstadick/crabz", - "tool_dev_url": "https://github.com/sstadick/crabz", - "licence": [ - "MIT" - ], - "identifier": "biotools:crabz" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "archive": { - "type": "file", - "description": "File to be decompressed", - "pattern": "*.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "output": { - "file": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.*": { - "type": "file", - "description": "The decompressed file", - "pattern": "*.*", - "ontologies": [] - } - } - ] - ], - "versions_crabz": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "crabz": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "0.10.0": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "crabz": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "0.10.0": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@camlloyd" - ], - "maintainers": [ - "@camlloyd" - ] - } - }, - { - "name": "cramino", - "path": "modules/nf-core/cramino/meta.yml", - "type": "module", - "meta": { - "name": "cramino", - "description": "Quality assessment of long-read bam files using cramino.", - "keywords": [ - "quality assessment", - 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"description": "Text file containing summary statistics of the long-read data", - "pattern": "*.txt", - "ontologies": [] - } - } - ] - ], - "arrow": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.arrow": { - "type": "file", - "description": "Arrow file containing summary statistics of the long-read data", - "pattern": "*.arrow", - "ontologies": [] - } - } - ] - ], - "versions_cramino": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cramino": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cramino -V | sed 's/cramino //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cramino": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cramino -V | sed 's/cramino //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@inemesb" - ], - "maintainers": [ - "@inemesb" - ] - } - }, - { - "name": "crisprcleanr_normalize", - "path": "modules/nf-core/crisprcleanr/normalize/meta.yml", - "type": "module", - "meta": { - "name": "crisprcleanr_normalize", - "description": "remove false positives of functional crispr genomics due to CNVs", - "keywords": [ - "sort", - "CNV", - "correction", - "CRISPR" - ], - "tools": [ - { - "crisprcleanr": { - "description": "Analysis of CRISPR functional genomics, remove false positive due to CNVs.", - "homepage": "https://github.com/francescojm/CRISPRcleanR", - "documentation": "https://github.com/francescojm/CRISPRcleanR/blob/master/Quick_start.pdf", - "tool_dev_url": "https://github.com/francescojm/CRISPRcleanR/tree/v3.0.0", - "doi": "10.1186/s12864-018-4989-y", - "licence": [ - "MIT" - ], - "identifier": "biotools:crisprcleanr" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "count_file": { - "type": "file", - "description": "sgRNA raw counts", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - }, - { - "library_file": { - "type": "file", - "description": "sgRNA library", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - { - "min_reads": { - "type": "integer", - "description": "Minimum number of reads" - } - }, - { - "min_targeted_genes": { - "type": "integer", - "description": "Minimum number of targeted genes" - } - } - ], - "output": { - "norm_count_file": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_norm_table.tsv": { - "type": "file", - "description": "normalized count file", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "topics": { - "versions": [ - { - "versions.yml": { - "type": "string", - "description": "The name of the process" - } - } - ] - }, - "authors": [ - "@LaurenceKuhl" - ], - "maintainers": [ - "@LaurenceKuhl" - ] - }, - "pipelines": [ - { - "name": "crisprseq", - "version": "2.3.0" - } - ] - }, - { - "name": "crispresso2", - "path": "modules/nf-core/crispresso2/meta.yml", - "type": "module", - "meta": { - "name": "crispresso2", - "description": "A software pipeline for the analysis of genome editing outcomes from deep sequencing data", - "keywords": [ - "genome editing", - "CRISPR", - "sequencing", - "amplicon" - ], - "tools": [ - { - "crispresso2": { - "description": "CRISPResso2 is a software pipeline designed to enable rapid and intuitive interpretation of genome editing experiments.", - "homepage": "https://crispresso.pinellolab.partners.org/", - "documentation": "https://docs.crispresso.com", - "tool_dev_url": "https://github.com/pinellolab/CRISPResso2", - "doi": "10.1038/s41587-019-0032-3", - "licence": [ - "MIT" - ], - "identifier": "biotools:crispresso2" + }, + { + "name": "deepvariant_vcfstatsreport", + "path": "modules/nf-core/deepvariant/vcfstatsreport/meta.yml", + "type": "module", + "meta": { + "name": "deepvariant_vcfstatsreport", + "description": "DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data", + "keywords": ["variant calling", "machine learning", "neural network"], + "tools": [ + { + "deepvariant": { + "description": "DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data", + "homepage": "https://github.com/google/deepvariant", + "documentation": "https://github.com/google/deepvariant", + "tool_dev_url": "https://github.com/google/deepvariant", + "doi": "10.1038/nbt.4235", + "licence": ["BSD-3-clause"], + "identifier": "biotools:deepvariant" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF file", + "pattern": "{*.vcf,vcf.gz,bcf,bcf.gz}", + "ontologies": [] + } + } + ] + ], + "output": { + "report": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.visual_report.html": { + "type": "file", + "description": "Visual report in HTML format", + "pattern": "*.html", + "ontologies": [] + } + } + ] + ], + "versions_deepvariant": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "deepvariant": { + "type": "string", + "description": "The tool name" + } + }, + { + "/opt/deepvariant/bin/run_deepvariant --version | sed 's/^.*version //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "deepvariant": { + "type": "string", + "description": "The tool name" + } + }, + { + "/opt/deepvariant/bin/run_deepvariant --version | sed 's/^.*version //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@fellen31"], + "maintainers": ["@fellen31"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } + }, + { + "name": "delly_call", + "path": "modules/nf-core/delly/call/meta.yml", + "type": "module", + "meta": { + "name": "delly_call", + "description": "Call structural variants", + "keywords": ["genome", "structural", "variants", "bcf"], + "tools": [ + { + "delly": { + "description": "Structural variant discovery by integrated paired-end and split-read analysis", + "homepage": "https://github.com/dellytools/delly", + "documentation": "https://github.com/dellytools/delly/blob/master/README.md", + "doi": "10.1093/bioinformatics/bts378", + "licence": ["BSD-3-Clause"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM file from alignment must be sorted, indexed, and duplicate marked", + "pattern": "*.{bam,cram}", + "ontologies": [] + } + }, + { + "input_index": { + "type": "file", + "description": "Index of the BAM/CRAM file", + "pattern": "*.{bai,crai}", + "ontologies": [] + } + }, + { + "vcf": { + "type": "file", + "description": "A BCF/VCF file to genotype with Delly. If this is supplied, the variant calling will be skipped", + "pattern": "*.{vcf.gz,bcf}", + "ontologies": [] + } + }, + { + "vcf_index": { + "type": "file", + "description": "The index of the BCF/VCF file", + "pattern": "*.{tbi,csi}", + "ontologies": [] + } + }, + { + "exclude_bed": { + "type": "file", + "description": "An optional bed file containing regions to exclude from the called VCF", + "pattern": "*.bed", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing fasta information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The reference fasta file", + "pattern": "*.{fasta,fa}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing fasta index information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Index of reference fasta file to identify split-reads", + "pattern": "*.fai", + "ontologies": [] + } + } + ], + { + "suffix": { + "type": "string", + "description": "A flag to specify whether the output should be in BCF or VCF format", + "enum": ["bcf", "vcf"] + } + } + ], + "output": { + "bcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{bcf,vcf.gz}": { + "type": "file", + "description": "Called variants in BCF/VCF format. Set suffix to either \"bcf\" or \"vcf\" to define the output type", + "pattern": "*.{bcf,vcf.gz}", + "ontologies": [] + } + } + ] + ], + "csi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{csi,tbi}": { + "type": "file", + "description": "A generated csi index that matches the bcf output (not generated for vcf files)", + "pattern": "*.{bcf.csi}", + "ontologies": [] + } + } + ] + ], + "versions_delly": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "delly": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "delly --version |& sed -n '1s/Delly version: *v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "delly": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "delly --version |& sed -n '1s/Delly version: *v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@projectoriented", "@nvnieuwk"], + "maintainers": ["@projectoriented", "@nvnieuwk"] }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively.", - "pattern": "*.{fastq,fq,fastq.gz,fq.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "output": { - "results": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "CRISPResso_on_*": { - "type": "directory", - "description": "CRISPResso output directory", - "pattern": "CRISPResso_on_*" - } - } - ] - ], - "html": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*.html": { - "type": "file", - "description": "CRISPResso HTML report", - "pattern": "*.html", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2331" - } - ] - } - } - ] - ], - "txt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "CRISPResso_on_*/*.txt": { - "type": "file", - "description": "CRISPResso text output files", - "pattern": "CRISPResso_on_*/*.txt", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2330" - } - ] - } - } - ] - ], - "versions_crispresso2": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "crispresso2": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "CRISPResso --version 2>&1 | sed 's/CRISPResso //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "crispresso2": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "CRISPResso --version 2>&1 | sed 's/CRISPResso //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "tbanalyzer", + "version": "dev" + } ] - ] - }, - "authors": [ - "@sathyasjali" - ], - "maintainers": [ - "@sathyasjali" - ] - } - }, - { - "name": "crumble", - "path": "modules/nf-core/crumble/meta.yml", - "type": "module", - "meta": { - "name": "crumble", - "description": "Controllable lossy compression of BAM/CRAM files", - "keywords": [ - "compress", - "bam", - "sam", - "cram" - ], - "tools": [ - { - "crumble": { - "description": "Controllable lossy compression of BAM/CRAM files", - "homepage": "https://github.com/jkbonfield/crumble", - "documentation": "https://github.com/jkbonfield/crumble", - "tool_dev_url": "https://github.com/jkbonfield/crumble", - "doi": "10.1093/bioinformatics/bty608", - "licence": [ - "multiple BSD style licenses" - ], - "identifier": "" + }, + { + "name": "demuxem", + "path": "modules/nf-core/demuxem/meta.yml", + "type": "module", + "meta": { + "name": "demuxem", + "description": "Demultiplexing cell nucleus hashing data, using the estimated antibody background probability.", + "keywords": ["demultiplexing", "hashing-based deconvoltion", "single-cell"], + "tools": [ + { + "demuxem": { + "description": "DemuxEM is the demultiplexing module of Pegasus, which works on cell-hashing and nucleus-hashing genomics data.", + "homepage": "https://demuxEM.readthedocs.io", + "documentation": "https://demuxEM.readthedocs.io", + "tool_dev_url": "https://github.com/lilab-bcb/pegasus/tree/master", + "doi": "10.1038/s41467-019-10756-2", + "licence": ["BSD-3-clause"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "input_raw_gene_bc_matrices_h5": { + "type": "string", + "description": "Path to file containing input raw RNA expression matrix in 10x hdf5 format\npattern: \"*.{h5}\"\n" + } + }, + { + "input_hto_csv_file": { + "type": "string", + "description": "Path to file containing input HTO (antibody tag) count matrix in CSV format.\n", + "pattern": "*.{csv}" + } + } + ], + { + "generate_gender_plot": { + "type": "string", + "description": "Generate violin plots using gender-specific genes (e.g. Xist). It is a comma-separated list of gene names.\n" + } + }, + { + "genome": { + "type": "string", + "description": "Reference genome name. If not provided, the tools infers it from the expression matrix file\n" + } + }, + { + "generate_diagnostic_plots": { + "type": "string", + "description": "Generate diagnostic plots, including the background/signal between HTO counts, estimated background probabilities, HTO distributions.\n" + } + } + ], + "output": { + "zarr": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample1' ]\n" + } + }, + { + "*_demux.zarr.zip": { + "type": "file", + "description": "RNA expression matrix with demultiplexed sample identities in Zarr format.\n", + "pattern": "*_demux.zarr.zip", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3987" + } + ] + } + } + ] + ], + "out_zarr": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample1' ]\n" + } + }, + { + "*.out.demuxEM.zarr.zip": { + "type": "file", + "description": "DemuxEM-calculated results in Zarr format, containing two datasets, one for HTO and one for RNA.\n", + "pattern": "*.out.demuxEM.zarr.zip", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3987" + } + ] + } + } + ] + ], + "versions_demuxem": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "demuxEM": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "demuxEM --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "demuxEM": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "demuxEM --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@mari-ga", "@maxozo", "@wxicu", "@Zethson"], + "maintainers": ["@mari-ga", "@maxozo", "@wxicu", "@Zethson"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + }, + { + "name": "deseq2_differential", + "path": "modules/nf-core/deseq2/differential/meta.yml", + "type": "module", + "meta": { + "name": "deseq2_differential", + "description": "runs a differential expression analysis with DESeq2", + "keywords": ["differential", "expression", "rna-seq", "deseq2"], + "tools": [ + { + "deseq2": { + "description": "Differential gene expression analysis based on the negative binomial distribution", + "homepage": "https://bioconductor.org/packages/release/bioc/html/DESeq2.html", + "documentation": "https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html", + "tool_dev_url": "https://github.com/mikelove/DESeq2", + "doi": "10.1186/s13059-014-0550-8", + "licence": ["LGPL >=3"], + "identifier": "biotools:deseq2" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing contrast information. This can be used at the\nworkflow level to pass optional parameters to the module, e.g.\n[ id:'contrast1', blocking:'patient' ] passed in as ext.args like:\n'--blocking_variable $meta.blocking'.\n" + } + }, + { + "contrast_variable": { + "type": "string", + "description": "The column in the sample sheet that should be used to define groups for\ncomparison\n" + } + }, + { + "reference": { + "type": "string", + "description": "The value within the contrast_variable column of the sample sheet that\nshould be used to derive the reference samples\n" + } + }, + { + "target": { + "type": "string", + "description": "The value within the contrast_variable column of the sample sheet that\nshould be used to derive the target samples\n" + } + }, + { + "formula": { + "type": "string", + "description": "(Optional) R formula string used for modeling, e.g. '~ treatment'." + } + }, + { + "comparison": { + "type": "string", + "description": "(Optional, mandatory if formula is provided) Literal string for contrasts, e.g. 'treatmenthND6'." + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy map containing study-wide metadata related to the sample sheet\nand matrix\n" + } + }, + { + "samplesheet": { + "type": "file", + "description": "CSV or TSV format sample sheet with sample metadata\n", + "ontologies": [] + } + }, + { + "counts": { + "type": "file", + "description": "Raw TSV or CSV format expression matrix as output from the nf-core\nRNA-seq workflow\n", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Meta map describing control genes, e.g. [ id: 'ERCC' ]\n", + "ontologies": [] + } + }, + { + "control_genes_file": { + "type": "file", + "description": "Text file listing control genes, one per line\n", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy map containing study-wide metadata related to the transcript\nlengths file\n" + } + }, + { + "transcript_lengths_file": { + "type": "file", + "description": "Optional file of transcript lengths, with the same sample columns as\ncounts. If supplied, lengths will be supplied to DESeq2 to correct for\ndifferences in average transcript lengths across samples.\n", + "ontologies": [] + } + } + ] + ], + "output": { + "results": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing contrast information, same as input meta\n" + } + }, + { + "*.deseq2.results.tsv": { + "type": "file", + "description": "TSV-format table of differential expression information as output by DESeq2", + "pattern": "*.deseq2.results.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "dispersion_plot_png": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing contrast information, same as input meta\n" + } + }, + { + "*.deseq2.dispersion.png": { + "type": "file", + "description": "DESeq2 dispersion plot in PNG format", + "pattern": "*.deseq2.dispersion.png", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3603" + } + ] + } + } + ] + ], + "dispersion_plot_pdf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing contrast information, same as input meta\n" + } + }, + { + "*.deseq2.dispersion.pdf": { + "type": "file", + "description": "DESeq2 dispersion plot in PDF format", + "pattern": "*.deseq2.dispersion.pdf", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3508" + } + ] + } + } + ] + ], + "rdata": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing contrast information, same as input meta\n" + } + }, + { + "*.dds.rld.rds": { + "type": "file", + "description": "Serialised DESeq2 object", + "pattern": "*.dds.rld.rds", + "ontologies": [] + } + } + ] + ], + "size_factors": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing contrast information, same as input meta\n" + } + }, + { + "*.deseq2.sizefactors.tsv": { + "type": "file", + "description": "TSV-format table containing DESeq2 size factors", + "pattern": "*.deseq2.sizefactors.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "normalised_counts": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing contrast information, same as input meta\n" + } + }, + { + "*.normalised_counts.tsv": { + "type": "file", + "description": "TSV-format counts matrix, normalised to size factors", + "pattern": "*.normalised_counts.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "rlog_counts": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing contrast information, same as input meta\n" + } + }, + { + "*.rlog.tsv": { + "type": "file", + "description": "Optional, TSV-format counts matrix, normalised to size factors, with\nvariance stabilisation applied via `rlog()`.\n", + "pattern": "*.rlog.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "vst_counts": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing contrast information, same as input meta\n" + } + }, + { + "*.vst.tsv": { + "type": "file", + "description": "Optional, TSV-format counts matrix, normalised to size factors, with\nvariance stabilisation applied via `vst()`.\n", + "pattern": "*.vst.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "model": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing contrast information, same as input meta\n" + } + }, + { + "*.deseq2.model.txt": { + "type": "file", + "description": "TXT-format DESeq2 model", + "pattern": "*.deseq2.model.txt", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + } + ] + ], + "session_info": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing contrast information, same as input meta\n" + } + }, + { + "*.R_sessionInfo.log": { + "type": "file", + "description": "Dump of R SessionInfo", + "pattern": "*.R_sessionInfo.log", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "YAML file containing versions of tools used in the module", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "topics": { + "versions": [ + { + "versions.yml": { + "type": "string", + "description": "The name of the process" + } + } + ] + }, + "authors": ["@pinin4fjords"], + "maintainers": ["@pinin4fjords"] }, - { - "input": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } - } - ], - { - "keepbed": { - "type": "file", - "description": "BED file defining regions to keep quality", - "ontologies": [] - } - }, - { - "bedout": { - "type": "boolean", - "description": "set to true to output suspicious regions to a BED file" - } - } - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "optional filtered/compressed BAM file", - "pattern": "*.{bam}", - "ontologies": [] - } - } - ] - ], - "cram": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.cram": { - "type": "file", - "description": "optional filtered/compressed CRAM file", - "pattern": "*.{cram}", - "ontologies": [] - } - } - ] - ], - "sam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.sam": { - "type": "file", - "description": "optional filtered/compressed SAM file", - "pattern": "*.{sam}", - "ontologies": [] - } - } - ] - ], - "bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bed": { - "type": "file", - "description": "optional suspicious regions BED file", - "pattern": "*{bed}", - "ontologies": [] - } - } - ] - ], - "versions_crumble": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "crumble": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "0.9.1": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "crumble": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "0.9.1": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "differentialabundance", + "version": "1.5.0" + }, + { + "name": "tfactivity", + "version": "dev" + } ] - ] - }, - "authors": [ - "@priyanka-surana" - ], - "maintainers": [ - "@priyanka-surana" - ] - } - }, - { - "name": "csvtk_concat", - "path": "modules/nf-core/csvtk/concat/meta.yml", - "type": "module", - "meta": { - "name": "csvtk_concat", - "description": "Concatenate two or more CSV (or TSV) tables into a single table", - "keywords": [ - "concatenate", - "tsv", - "csv" - ], - "tools": [ - { - "csvtk": { - "description": "A cross-platform, efficient, practical CSV/TSV toolkit", - "homepage": "http://bioinf.shenwei.me/csvtk", - "documentation": "http://bioinf.shenwei.me/csvtk", - "tool_dev_url": "https://github.com/shenwei356/csvtk", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "csv": { - "type": "file", - "description": "CSV/TSV formatted files", - "pattern": "*.{csv,tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - }, - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - { - "in_format": { - "type": "string", - "description": "Input format (csv, tab, or a delimiting character)", - "pattern": "*" - } - }, - { - "out_format": { - "type": "string", - "description": "Output format (csv, tab, or a delimiting character)", - "pattern": "*" + }, + { + "name": "diamond_blastp", + "path": "modules/nf-core/diamond/blastp/meta.yml", + "type": "module", + "meta": { + "name": "diamond_blastp", + "description": "Queries a DIAMOND database using blastp mode", + "keywords": ["fasta", "diamond", "blastp", "DNA sequence"], + "tools": [ + { + "diamond": { + "description": "Accelerated BLAST compatible local sequence aligner", + "homepage": "https://github.com/bbuchfink/diamond", + "documentation": "https://github.com/bbuchfink/diamond/wiki", + "tool_dev_url": "https://github.com/bbuchfink/diamond", + "doi": "10.1038/s41592-021-01101-x", + "licence": ["GPL v3.0"], + "identifier": "biotools:diamond" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input fasta file containing query sequences", + "pattern": "*.{fa,fasta,fa.gz,fasta.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing db information\ne.g. [ id:'test2' ]\n" + } + }, + { + "db": { + "type": "file", + "description": "File of the indexed DIAMOND database", + "pattern": "*.dmnd", + "ontologies": [] + } + } + ], + { + "outfmt": { + "type": "integer", + "description": "Specify the type of output file to be generated.\n0, .blast, BLAST pairwise format.\n5, .xml, BLAST XML format.\n6, .txt, BLAST tabular format (default). This format can be customized, the 6 may be followed by a space-separated list of the blast_columns keywords, each specifying a field of the output.\n100, .daa, DIAMOND alignment archive (DAA). The DAA format is a proprietary binary format that can subsequently be used to generate other output formats using the view command. It is also supported by MEGAN and allows a quick import of results.\n101, .sam, SAM format.\n102, .tsv, Taxonomic classification. This format will not print alignments but only a taxonomic classification for each query using the LCA algorithm.\n103, .paf, PAF format. The custom fields in the format are AS (bit score), ZR (raw score) and ZE (e-value).\n", + "pattern": "0|5|6|100|101|102|103" + } + }, + { + "blast_columns": { + "type": "string", + "description": "Optional space separated list of DIAMOND tabular BLAST output keywords\nused in conjunction with the --outfmt 6 option (txt).\nOptions:\nqseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore\n" + } + } + ], + "output": { + "blast": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', db:'ncbi-refseq' ]\n" + } + }, + { + "*.{blast,blast.gz}": { + "type": "file", + "description": "File containing blastp hits", + "pattern": "*.{blast,blast.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3836" + } + ] + } + } + ] + ], + "xml": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', db:'ncbi-refseq' ]\n" + } + }, + { + "*.{xml,xml.gz}": { + "type": "file", + "description": "File containing blastp hits", + "pattern": "*.{xml,xml.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2332" + } + ] + } + } + ] + ], + "txt": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', db:'ncbi-refseq' ]\n" + } + }, + { + "*.{txt,txt.gz}": { + "type": "file", + "description": "File containing hits in tabular BLAST format.", + "pattern": "*.{txt,txt.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1333" + } + ] + } + } + ] + ], + "daa": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', db:'ncbi-refseq' ]\n" + } + }, + { + "*.{daa,daa.gz}": { + "type": "file", + "description": "File containing hits DAA format", + "pattern": "*.{daa,daa.gz}", + "ontologies": [] + } + } + ] + ], + "sam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', db:'ncbi-refseq' ]\n" + } + }, + { + "*.{sam,sam.gz}": { + "type": "file", + "description": "File containing aligned reads in SAM format", + "pattern": "*.{sam,sam.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2573" + } + ] + } + } + ] + ], + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', db:'ncbi-refseq' ]\n" + } + }, + { + "*.{tsv,tsv.gz}": { + "type": "file", + "description": "Tab separated file containing taxonomic classification of hits", + "pattern": "*.{tsv,tsv.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "paf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', db:'ncbi-refseq' ]\n" + } + }, + { + "*.{paf,paf.gz}": { + "type": "file", + "description": "File containing aligned reads in pairwise mapping format format", + "pattern": "*.{paf,paf.gz}", + "ontologies": [] + } + } + ] + ], + "versions_diamond": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "diamond": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "diamond --version 2>&1 | tail -n 1 | sed \"s/^diamond version //\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "diamond": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "diamond --version 2>&1 | tail -n 1 | sed \"s/^diamond version //\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@spficklin", "@jfy133"], + "maintainers": ["@spficklin", "@jfy133", "@vagkaratzas"] } - } - ], - "output": { - "csv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.${out_extension}": { - "type": "file", - "description": "Concatenated CSV/TSV file", - "pattern": "*.{csv,tsv}", - "ontologies": [ + }, + { + "name": "diamond_blastx", + "path": "modules/nf-core/diamond/blastx/meta.yml", + "type": "module", + "meta": { + "name": "diamond_blastx", + "description": "Queries a DIAMOND database using blastx mode", + "keywords": ["fasta", "diamond", "blastx", "DNA sequence"], + "tools": [ + { + "diamond": { + "description": "Accelerated BLAST compatible local sequence aligner", + "homepage": "https://github.com/bbuchfink/diamond", + "documentation": "https://github.com/bbuchfink/diamond/wiki", + "tool_dev_url": "https://github.com/bbuchfink/diamond", + "doi": "10.1038/s41592-021-01101-x", + "licence": ["GPL v3.0"], + "identifier": "biotools:diamond" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input fasta file containing query sequences", + "pattern": "*.{fa,fasta,fa.gz,fasta.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing db information\ne.g. [ id:'test2', single_end:false ]\n" + } + }, + { + "db": { + "type": "file", + "description": "File of the indexed DIAMOND database", + "pattern": "*.dmnd", + "ontologies": [] + } + } + ], { - "edam": "http://edamontology.org/format_3752" + "out_ext": { + "type": "string", + "description": "Specify the type of output file to be generated. `blast` corresponds to\nBLAST pairwise format. `xml` corresponds to BLAST xml format.\n`txt` corresponds to to BLAST tabular format. `tsv` corresponds to\ntaxonomic classification format.\n", + "pattern": "blast|xml|txt|daa|sam|tsv|paf" + } }, { - "edam": "http://edamontology.org/format_3475" + "blast_columns": { + "type": "string", + "description": "Optional space separated list of DIAMOND tabular BLAST output keywords\nused for in conjunction with the 'txt' out_ext option (--outfmt 6). Options:\nqseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore\n" + } } - ] + ], + "output": { + "blast": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.blast": { + "type": "file", + "description": "File containing blastp hits", + "pattern": "*.{blast}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3836" + } + ] + } + } + ] + ], + "xml": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.xml": { + "type": "file", + "description": "File containing blastp hits", + "pattern": "*.{xml}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2332" + } + ] + } + } + ] + ], + "txt": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "File containing hits in tabular BLAST format.", + "pattern": "*.{txt}", + "ontologies": [] + } + } + ] + ], + "daa": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.daa": { + "type": "file", + "description": "File containing hits DAA format", + "pattern": "*.{daa}", + "ontologies": [] + } + } + ] + ], + "sam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.sam": { + "type": "file", + "description": "File containing aligned reads in SAM format", + "pattern": "*.{sam}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2573" + } + ] + } + } + ] + ], + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "Tab separated file containing taxonomic classification of hits", + "pattern": "*.{tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "paf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.paf": { + "type": "file", + "description": "File containing aligned reads in pairwise mapping format format", + "pattern": "*.{paf}", + "ontologies": [] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "Log file containing stdout information", + "pattern": "*.{log}", + "ontologies": [] + } + } + ] + ], + "versions_diamond": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "diamond": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "diamond --version | sed 's/diamond version //g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "diamond": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "diamond --version | sed 's/diamond version //g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@spficklin", "@jfy133", "@mjamy"], + "maintainers": ["@spficklin", "@jfy133", "@mjamy", "@vagkaratzas"] + }, + "pipelines": [ + { + "name": "funcprofiler", + "version": "dev" + }, + { + "name": "taxprofiler", + "version": "2.0.0" } - } - ] - ], - "versions_csvtk": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "csvtk": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "csvtk version | sed -e 's/csvtk v//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "csvtk": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "csvtk version | sed -e 's/csvtk v//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] }, - "authors": [ - "@rpetit3" - ], - "maintainers": [ - "@rpetit3" - ] - }, - "pipelines": [ { - "name": "deepmodeloptim", - "version": "dev" + "name": "diamond_cluster", + "path": "modules/nf-core/diamond/cluster/meta.yml", + "type": "module", + "meta": { + "name": "diamond_cluster", + "description": "calculate clusters of highly similar sequences", + "keywords": ["clustering", "alignment", "genomics", "proteomics"], + "tools": [ + { + "diamond": { + "description": "Accelerated BLAST compatible local sequence aligner", + "homepage": "https://github.com/bbuchfink/diamond/wiki", + "documentation": "https://github.com/bbuchfink/diamond/wiki", + "tool_dev_url": "https://github.com/bbuchfink/diamond", + "doi": "10.1038/s41592-021-01101-x", + "licence": ["GPL v3-or-later"], + "identifier": "biotools:diamond" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "db": { + "type": "file", + "description": "The input sequence database. Supported formats are FASTA and DIAMOND (.dmnd) format.", + "pattern": "*.{dmnd,fa,faa,fasta}(.gz)", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ] + ], + "output": { + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "a 2-column tabular file with the representative accession as the first column and the member sequence accession as the second column", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_diamond": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "diamond": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "diamond --version | sed 's/diamond version //g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "diamond": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "diamond --version | sed 's/diamond version //g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@itrujnara"], + "maintainers": ["@itrujnara"] + }, + "pipelines": [ + { + "name": "reportho", + "version": "1.1.0" + } + ] }, { - "name": "multiplesequencealign", - "version": "1.1.1" + "name": "diamond_deepclust", + "path": "modules/nf-core/diamond/deepclust/meta.yml", + "type": "module", + "meta": { + "name": "diamond_deepclust", + "description": "Fast graph-based protein sequence clustering using DIAMOND deepclust", + "keywords": ["clustering", "protein", "diamond", "deepclust", "proteomics"], + "tools": [ + { + "diamond": { + "description": "Accelerated BLAST compatible local sequence aligner", + "homepage": "https://github.com/bbuchfink/diamond", + "documentation": "https://github.com/bbuchfink/diamond/wiki", + "tool_dev_url": "https://github.com/bbuchfink/diamond", + "doi": "10.1038/s41592-021-01101-x", + "licence": ["GPL v3-or-later"], + "identifier": "biotools:diamond" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input protein FASTA file to be clustered", + "pattern": "*.{fa,faa,fasta,fa.gz,faa.gz,fasta.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + { + "save_aln": { + "type": "boolean", + "description": "Whether to save clustering alignments to a file (--aln-out)\nWARNING: unusable in this version (2.1.24) of diamond due to bug, leaving as placeholder\n" + } + } + ], + "output": { + "clusters": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}.tsv": { + "type": "file", + "description": "Tab-separated file mapping each member sequence to its cluster\nrepresentative. The first column contains the representative\naccession and the second column contains the member sequence\naccession.\n", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "alignment": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}.aln": { + "type": "file", + "description": "Optional. Tab-separated file containing the clustering alignments,\nproduced when save_aln is true (--aln-out).\n", + "pattern": "*.aln", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_diamond": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "diamond": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "diamond --version | sed 's/.* //g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "diamond": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "diamond --version | sed 's/.* //g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@vagkaratzas"], + "maintainers": ["@vagkaratzas"] + } }, { - "name": "reportho", - "version": "1.1.0" - } - ] - }, - { - "name": "csvtk_join", - "path": "modules/nf-core/csvtk/join/meta.yml", - "type": "module", - "meta": { - "name": "csvtk_join", - "description": "Join two or more CSV (or TSV) tables by selected fields into a single table", - "keywords": [ - "join", - "tsv", - "csv" - ], - "tools": [ - { - "csvtk": { - "description": "A cross-platform, efficient, practical CSV/TSV toolkit", - "homepage": "http://bioinf.shenwei.me/csvtk", - "documentation": "http://bioinf.shenwei.me/csvtk", - "tool_dev_url": "https://github.com/shenwei356/csvtk", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "csv": { - "type": "file", - "description": "CSV/TSV formatted files", - "pattern": "*.{csv,tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - }, - { - "edam": "http://edamontology.org/format_3475" - } - ] - } + "name": "diamond_linclust", + "path": "modules/nf-core/diamond/linclust/meta.yml", + "type": "module", + "meta": { + "name": "diamond_linclust", + "description": "Fast protein sequence clustering using a greedy incremental approach", + "keywords": ["clustering", "protein", "diamond", "linclust", "proteomics"], + "tools": [ + { + "diamond": { + "description": "Accelerated BLAST compatible local sequence aligner", + "homepage": "https://github.com/bbuchfink/diamond", + "documentation": "https://github.com/bbuchfink/diamond/wiki", + "tool_dev_url": "https://github.com/bbuchfink/diamond", + "doi": "10.1038/s41592-021-01101-x", + "licence": ["GPL v3-or-later"], + "identifier": "biotools:diamond" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input protein FASTA file to be clustered", + "pattern": "*.{fa,faa,fasta,fa.gz,faa.gz,fasta.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ] + ], + "output": { + "clusters": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}.tsv": { + "type": "file", + "description": "Tab-separated file mapping each member sequence to its cluster\nrepresentative. The first column contains the representative\naccession and the second column contains the member sequence\naccession.\n", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_diamond": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "diamond": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "diamond --version | sed 's/diamond version //g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "diamond": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "diamond --version | sed 's/diamond version //g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@vagkaratzas"], + "maintainers": ["@vagkaratzas"] } - ] - ], - "output": { - "csv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.${out_extension}": { - "type": "file", - "description": "Joined CSV/TSV file", - "pattern": "*.{csv,tsv}", - "ontologies": [ + }, + { + "name": "diamond_makedb", + "path": "modules/nf-core/diamond/makedb/meta.yml", + "type": "module", + "meta": { + "name": "diamond_makedb", + "description": "Builds a DIAMOND database", + "keywords": ["fasta", "diamond", "index", "database"], + "tools": [ + { + "diamond": { + "description": "Accelerated BLAST compatible local sequence aligner", + "homepage": "https://github.com/bbuchfink/diamond", + "documentation": "https://github.com/bbuchfink/diamond/wiki", + "tool_dev_url": "https://github.com/bbuchfink/diamond", + "doi": "10.1038/s41592-021-01101-x", + "licence": ["GPL v3.0"], + "identifier": "biotools:diamond" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input fasta file", + "pattern": "*.{fa,fasta,fa.gz,fasta.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + { + "taxonmap": { + "type": "file", + "description": "Optional mapping file of NCBI protein accession numbers to taxon ids (gzip compressed), required for taxonomy functionality.", + "pattern": "*.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + }, { - "edam": "http://edamontology.org/format_3752" + "taxonnodes": { + "type": "file", + "description": "Optional NCBI taxonomy nodes.dmp file, required for taxonomy functionality.", + "pattern": "*.dmp", + "ontologies": [] + } }, { - "edam": "http://edamontology.org/format_3475" + "taxonnames": { + "type": "file", + "description": "Optional NCBI taxonomy names.dmp file, required for taxonomy functionality.", + "pattern": "*.dmp", + "ontologies": [] + } } - ] + ], + "output": { + "db": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.dmnd": { + "type": "file", + "description": "File of the indexed DIAMOND database", + "pattern": "*.dmnd", + "ontologies": [] + } + } + ] + ], + "versions_diamond": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "diamond": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "diamond --version | sed 's/diamond version //g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "diamond": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "diamond --version | sed 's/diamond version //g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@spficklin"], + "maintainers": ["@spficklin", "@vagkaratzas", "@jfy133"] + }, + "pipelines": [ + { + "name": "createtaxdb", + "version": "3.0.0" } - } - ] - ], - "versions_csvtk": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "csvtk": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "csvtk version | sed -e 's/csvtk v//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "csvtk": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "csvtk version | sed -e 's/csvtk v//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } ] - ] }, - "authors": [ - "@anoronh4" - ], - "maintainers": [ - "@anoronh4" - ] - }, - "pipelines": [ { - "name": "circrna", - "version": "dev" + "name": "diann", + "path": "modules/nf-core/diann/meta.yml", + "type": "module", + "meta": { + "name": "diann", + "description": "Generic DIA-NN module for running any DIA-NN operation including in-silico library generation, preliminary analysis, empirical library assembly, individual analysis, and final quantification", + "keywords": ["proteomics", "mass spectrometry", "DIA", "spectral library", "quantification"], + "tools": [ + { + "diann": { + "description": "DIA-NN - a fast and easy to use tool for processing data independent acquisition (DIA) proteomics data", + "homepage": "https://github.com/vdemichev/DiaNN", + "documentation": "https://github.com/vdemichev/DiaNN#readme", + "tool_dev_url": "https://github.com/vdemichev/DiaNN", + "licence": [ + "Custom", + "https://raw.githubusercontent.com/vdemichev/DiaNN/master/LICENSE.txt" + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "ms_files": { + "type": "file", + "description": "MS data file(s) in mzML or Bruker .d format (can be single file or list).\nThermo RAW files are only supported on Linux with DIA-NN 2.0+; older versions\nrequire conversion to mzML or .d format first.\nFor preliminary/assembly/individual analysis, these are actual file paths.\nFor final quantification with --use-quant, this should be an empty list.\n", + "pattern": "*.{mzML,raw,d}", + "ontologies": [] + } + }, + { + "ms_file_names": { + "type": "string", + "description": "MS file basenames (not paths) as strings (can be single name or list).\nUsed for final quantification step with --use-quant where only filenames are needed.\nFor other analysis steps, this should be an empty list.\nExample: ['sample1.mzML', 'sample2.mzML'] or []\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA database file for peptide searches.\nUse a placeholder file (e.g., 'NO_FASTA_FILE') if not needed for the specific analysis step.\n", + "pattern": "*.{fasta,fa}", + "ontologies": [] + } + }, + { + "library": { + "type": "file", + "description": "Spectral library file in .speclib or .tsv format.\nUse a placeholder file (e.g., 'NO_LIB_FILE') if not needed for the specific analysis step.\n", + "pattern": "*.{speclib,tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, + { + "quant": { + "type": "directory", + "description": "Directory containing .quant files from previous DIA-NN analysis.\nWhen provided, enables --use-quant mode to reuse cached quantification results,\nimproving performance for empirical library assembly and final quantification.\nPass empty list [] if not needed. Files are staged as 'quant/*' in the work directory.\n" + } + } + ] + ], + "output": { + "predict_speclib": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}.predicted.speclib": { + "type": "file", + "description": "Predicted spectral library from in-silico generation.\nFilename is determined by the prefix (task.ext.prefix or meta.id).\n", + "pattern": "*.predicted.speclib", + "ontologies": [] + } + } + ] + ], + "final_speclib": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}.speclib": { + "type": "file", + "description": "Empirical spectral library refined from experimental data.\nProduced by the library assembly step, which combines predicted library\ninformation with actual MS measurements to improve search accuracy.\n", + "pattern": "*.speclib", + "ontologies": [] + } + } + ] + ], + "skyline_speclib": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}.tsv.skyline.speclib": { + "type": "file", + "description": "Spectral library in Skyline format for use with Skyline software.\nFilename is determined by the prefix (task.ext.prefix or meta.id).\n", + "pattern": "*.tsv.skyline.speclib", + "ontologies": [] + } + } + ] + ], + "diann_quant": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.quant": { + "type": "file", + "description": "Quantification results in .quant format (intermediate output for empirical library assembly and final quantification)", + "pattern": "*.quant", + "ontologies": [] + } + } + ] + ], + "main_report": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}.tsv": { + "type": "file", + "description": "Main DIA-NN report in TSV format containing peptide and protein quantification.\nFilename is determined by the prefix (task.ext.prefix or meta.id).\n", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "report_parquet": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}.parquet": { + "type": "file", + "description": "Main DIA-NN report in Parquet format for efficient data access.\nFilename is determined by the prefix (task.ext.prefix or meta.id).\n", + "pattern": "*.parquet", + "ontologies": [] + } + } + ] + ], + "report_manifest": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}.manifest.txt": { + "type": "file", + "description": "Report manifest file listing all output files.\nFilename is determined by the prefix (task.ext.prefix or meta.id).\n", + "pattern": "*.manifest.txt", + "ontologies": [] + } + } + ] + ], + "protein_description": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}.protein_description.tsv": { + "type": "file", + "description": "Protein descriptions extracted from FASTA headers.\nFilename is determined by the prefix (task.ext.prefix or meta.id).\n", + "pattern": "*.protein_description.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "report_stats": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}.stats.tsv": { + "type": "file", + "description": "Report statistics including identification and quantification metrics.\nFilename is determined by the prefix (task.ext.prefix or meta.id).\n", + "pattern": "*.stats.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "pr_matrix": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}.pr_matrix.tsv": { + "type": "file", + "description": "Precursor-level quantification matrix (peptides across runs).\nFilename is determined by the prefix (task.ext.prefix or meta.id).\n", + "pattern": "*.pr_matrix.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "pg_matrix": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}.pg_matrix.tsv": { + "type": "file", + "description": "Protein group-level quantification matrix.\nFilename is determined by the prefix (task.ext.prefix or meta.id).\n", + "pattern": "*.pg_matrix.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "gg_matrix": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}.gg_matrix.tsv": { + "type": "file", + "description": "Gene group-level quantification matrix.\nFilename is determined by the prefix (task.ext.prefix or meta.id).\n", + "pattern": "*.gg_matrix.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "unique_gene_matrix": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}.unique_genes_matrix.tsv": { + "type": "file", + "description": "Unique genes quantification matrix.\nFilename is determined by the prefix (task.ext.prefix or meta.id).\n", + "pattern": "*.unique_genes_matrix.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.log.txt": { + "type": "file", + "description": "DIA-NN log file containing run information and recommended settings", + "pattern": "*.log.txt", + "ontologies": [] + } + } + ] + ], + "versions_diann": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "diann": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "diann | grep \"DIA-NN\" | grep -oP \"\\d+\\.\\d+(\\.\\w+)*(\\.[\\d]+)?\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "diann": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "diann | grep \"DIA-NN\" | grep -oP \"\\d+\\.\\d+(\\.\\w+)*(\\.[\\d]+)?\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@pinin4fjords"], + "maintainers": ["@pinin4fjords"] + } }, { - "name": "multiplesequencealign", - "version": "1.1.1" + "name": "diann_insilicolibrarygeneration", + "path": "modules/nf-core/diann/insilicolibrarygeneration/meta.yml", + "type": "module", + "meta": { + "name": "diann_insilicolibrarygeneration", + "description": "Generate in silico predicted spectral library using DIA-NN deep learning predictor.\nThis module uses DIA-NN software for data-independent acquisition (DIA) proteomics data processing.\nOutput materials should include attribution: \"Generated using DIA-NN\".\n", + "keywords": ["diann", "spectral library", "proteomics", "deep learning", "dia"], + "tools": [ + { + "diann": { + "description": "DIA-NN is a universal software for data-independent acquisition (DIA) proteomics data processing.\nIt uses deep learning to predict spectral libraries and perform peptide identification and quantification.\n", + "homepage": "https://github.com/vdemichev/DiaNN", + "documentation": "https://github.com/vdemichev/DiaNN", + "tool_dev_url": "https://github.com/vdemichev/DiaNN", + "doi": "10.1038/s41592-020-01009-0", + "licence": ["https://github.com/vdemichev/DiaNN/blob/1.8.1/LICENSE.txt"], + "identifier": "biotools:diann" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA sequence database", + "pattern": "*.{fasta,fa}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ] + ], + "output": { + "predict_speclib": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.predicted.speclib": { + "type": "file", + "description": "In silico predicted spectral library by DIA-NN deep learning predictor", + "pattern": "*.predicted.speclib", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3240" + } + ] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.log": { + "type": "file", + "description": "DIA-NN log file", + "pattern": "*.log", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + } + ] + ], + "versions_diann": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "diann": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "diann | grep \"DIA-NN\" | grep -oP \"\\d+\\.\\d+(\\.\\w+)*(\\.[\\d]+)?\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "diann": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "diann | grep \"DIA-NN\" | grep -oP \"\\d+\\.\\d+(\\.\\w+)*(\\.[\\d]+)?\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@daichengxin", "@pinin4fjords"], + "maintainers": ["@daichengxin"] + } }, { - "name": "reportho", - "version": "1.1.0" - } - ] - }, - { - "name": "csvtk_mutate2", - "path": "modules/nf-core/csvtk/mutate2/meta.yml", - "type": "module", - "meta": { - "name": "csvtk_mutate2", - "description": "Create a new column from selected fields by awk-like arithmetic/string expressions", - "keywords": [ - "mutate", - "tsv", - "csv" - ], - "tools": [ - { - "csvtk": { - "description": "A cross-platform, efficient, practical CSV/TSV toolkit", - "homepage": "http://bioinf.shenwei.me/csvtk", - "documentation": "http://bioinf.shenwei.me/csvtk", - "tool_dev_url": "https://github.com/shenwei356/csvtk", - "licence": [ - "MIT" - ], - "identifier": "" + "name": "disambiguate", + "path": "modules/nf-core/disambiguate/meta.yml", + "type": "module", + "meta": { + "name": "disambiguate", + "description": "Disambiguates reads aligned to two different organisms (e.g. human and mouse)\nfrom the same source of FASTQ files. Useful in explant RNA/DNA-Seq workflows\nwhere reads from two species are present. For reads aligned to both organisms,\nthe algorithm compares alignment quality scores to determine the most likely\nspecies of origin. Produces four BAM files (uniquely assigned to species A or B,\nambiguous for species A or B) and a summary file.\n", + "keywords": ["disambiguation", "xenograft", "explant", "rna-seq", "alignment", "bam"], + "tools": [ + { + "ngs-disambiguate": { + "description": "Disambiguation algorithm for reads aligned to two different organisms using Tophat, Hisat2, BWA or STAR alignments.", + "homepage": "https://github.com/AstraZeneca-NGS/disambiguate", + "documentation": "https://github.com/AstraZeneca-NGS/disambiguate", + "tool_dev_url": "https://github.com/AstraZeneca-NGS/disambiguate", + "doi": "10.12688/f1000research.10082.2", + "licence": ["MIT"], + "identifier": "biotools:disambiguate", + "args_id": "$args" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "bam_a": { + "type": "file", + "description": "BAM file with alignments to species A (e.g. human). Mandatory.", + "pattern": "*.{bam}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + }, + { + "bam_b": { + "type": "file", + "description": "BAM file with alignments to species B (e.g. mouse). Mandatory.", + "pattern": "*.{bam}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + } + ] + ], + "output": { + "disambiguated_bam_a": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*disambiguatedSpeciesA.bam": { + "type": "file", + "description": "Reads uniquely assigned to species A.", + "pattern": "*disambiguatedSpeciesA.bam", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + } + ] + ], + "disambiguated_bam_b": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*disambiguatedSpeciesB.bam": { + "type": "file", + "description": "Reads uniquely assigned to species B.", + "pattern": "*disambiguatedSpeciesB.bam", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + } + ] + ], + "ambiguous_bam_a": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*ambiguousSpeciesA.bam": { + "type": "file", + "description": "Reads aligned to species A that also aligned to species B but could not be uniquely assigned.", + "pattern": "*ambiguousSpeciesA.bam", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + } + ] + ], + "ambiguous_bam_b": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*ambiguousSpeciesB.bam": { + "type": "file", + "description": "Reads aligned to species B that also aligned to species A but could not be uniquely assigned.", + "pattern": "*ambiguousSpeciesB.bam", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + } + ] + ], + "summary": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_summary.txt": { + "type": "file", + "description": "Summary of read counts uniquely assigned to species A, species B, and ambiguous reads.", + "pattern": "*_summary.txt", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + } + ] + ], + "versions_ngs_disambiguate": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "ngs-disambiguate": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "2018.05.03": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "ngs-disambiguate": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "2018.05.03": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@ctuni"], + "maintainers": ["@ctuni"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + }, + { + "name": "doubletdetection", + "path": "modules/nf-core/doubletdetection/meta.yml", + "type": "module", + "meta": { + "name": "doubletdetection", + "description": "Doublet detection in single-cell RNA-seq data", + "keywords": ["single-cell", "doublets", "doublet_detection"], + "tools": [ + { + "doubletdetection": { + "description": "Doublet detection in single-cell RNA-seq data", + "tool_dev_url": "https://github.com/JonathanShor/DoubletDetection", + "doi": "10.5281/zenodo.6349517", + "licence": ["MIT"], + "identifier": "biotools:DoubletDetection" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "h5ad": { + "type": "file", + "description": "H5AD anndata object", + "pattern": "*.h5ad", + "ontologies": [] + } + } + ] + ], + "output": { + "h5ad": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.h5ad": { + "type": "file", + "description": "H5AD anndata object", + "pattern": "*.h5ad", + "ontologies": [] + } + } + ] + ], + "predictions": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.pkl": { + "type": "file", + "description": "pandas dataframe containing the doublet classification", + "pattern": "*.pkl", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "topics": { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@LeonHafner"], + "maintainers": ["@LeonHafner"] }, - { - "input": { - "type": "file", - "description": "CSV/TSV formatted files, or files with a custom delimiter", - "pattern": "*.{csv,tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - }, - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - { - "in_format": { - "type": "string", - "description": "Input format (csv, tsv, or a delimiting character)", - "pattern": "*" - } - }, - { - "out_format": { - "type": "string", - "description": "Output format (csv, tsv, or a delimiting character)", - "pattern": "*" - } - } - ], - "output": { - "output": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + "pipelines": [ + { + "name": "scdownstream", + "version": "dev" } - }, - { - "${prefix}.${out_extension}": { - "type": "file", - "description": "Mutated CSV/TSV file", - "pattern": "*.{csv,tsv}", - "ontologies": [ + ] + }, + { + "name": "dragen_germline", + "path": "modules/nf-core/dragen/germline/meta.yml", + "type": "module", + "meta": { + "name": "dragen", + "description": "The DRAGEN DNA Germline Pipeline accelerates the secondary analysis of NGS data by harnessing the tremendous power available on the DRAGEN Platform. The pipeline includes highly optimized algorithms for mapping, aligning, sorting, duplicate marking, and haplotype variant calling. In addition to haplotype variant calling, the pipeline supports calling of copy number and structural variants as well as detection of repeat expansions and targeted calls.", + "keywords": [ + "check fingerprint", + "copy number variation", + "fastqc", + "genomics", + "germline", + "quality control", + "repeat expansion detection", + "structural variation", + "trimming", + "variable number tandem repeat detection", + "variant annotation", + "variant calling", + "variant deduplication" + ], + "tools": [ + { + "dragen": { + "description": "The Illumina DRAGEN™ Bio-IT Platform is based on the highly reconfigurable DRAGEN Bio-IT Processor, which is integrated on a Field Programmable Gate Array (FPGA) card and is available in a preconfigured server that can be seamlessly integrated into bioinformatics workflows. The platform can be loaded with highly optimized algorithms for many different NGS secondary analysis pipelines.", + "homepage": "https://support-docs.illumina.com/SW/dragen_v42/Content/SW/FrontPages/DRAGEN.htm?searchText=explify-ref-db-dir", + "documentation": "https://support-docs.illumina.com/SW/dragen_v42/Content/SW/FrontPages/DRAGEN.htm?searchText=explify-ref-db-dir", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false]`\n" + } + }, + { + "input": { + "type": "file", + "description": "FASTQ (may be gzipped), ora, BAM or CRAM files", + "pattern": "*.{fastq,fq,ora,bam,cram}{,.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + }, + { + "sex": { + "type": "string", + "description": "Sample's sex.\nRecognize options: male, female, none, auto\n" + } + } + ], { - "edam": "http://edamontology.org/format_3752" + "checkfingerprint_expected_vcf": { + "type": "file", + "description": "Input expected genotypes (VCF) for checkfingerprint comparison", + "pattern": "*.vcf", + "ontologies": [] + } }, { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_csvtk": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "csvtk": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "csvtk version | sed -e 's/csvtk v//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "csvtk": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "csvtk version | sed -e 's/csvtk v//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@fellen31" - ], - "maintainers": [ - "@fellen31" - ] - } - }, - { - "name": "csvtk_sort", - "path": "modules/nf-core/csvtk/sort/meta.yml", - "type": "module", - "meta": { - "name": "csvtk_sort", - "description": "Sort CSV (or TSV) tables", - "keywords": [ - "sort", - "tsv", - "csv" - ], - "tools": [ - { - "csvtk": { - "description": "A cross-platform, efficient, practical CSV/TSV toolkit", - "homepage": "http://bioinf.shenwei.me/csvtk", - "documentation": "http://bioinf.shenwei.me/csvtk", - "tool_dev_url": "https://github.com/shenwei356/csvtk", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "csv": { - "type": "file", - "description": "CSV/TSV formatted file", - "pattern": "*.{csv,tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - }, - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - { - "in_format": { - "type": "string", - "description": "Input format (csv, tab, or a delimiting character)", - "pattern": "*" - } - }, - { - "out_format": { - "type": "string", - "description": "Output format (csv, tab, or a delimiting character)", - "pattern": "*" - } - } - ], - "output": { - "sorted": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.${out_extension}": { - "type": "file", - "description": "Sorted CSV/TSV file", - "pattern": "*.{csv,tsv}", - "ontologies": [ + "cnv_combined_counts": { + "type": "file", + "description": "Specify combined PON file", + "pattern": "*.combined.counts.txt.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + }, { - "edam": "http://edamontology.org/format_3752" + "cnv_exclude_bed": { + "type": "file", + "description": "Regions to exclude for CNV processing", + "pattern": "*.bed", + "ontologies": [] + } }, { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_csvtk": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "csvtk": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "csvtk version | sed -e 's/csvtk v//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "csvtk": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "csvtk version | sed -e 's/csvtk v//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@LeonHafner" - ], - "maintainers": [ - "@LeonHafner" - ] - }, - "pipelines": [ - { - "name": "tfactivity", - "version": "dev" - } - ] - }, - { - "name": "csvtk_split", - "path": "modules/nf-core/csvtk/split/meta.yml", - "type": "module", - "meta": { - "name": "csvtk_split", - "description": "Splits CSV/TSV into multiple files according to column values", - "keywords": [ - "split", - "csv", - "tsv" - ], - "tools": [ - { - "csvtk": { - "description": "CSVTK is a cross-platform, efficient and practical CSV/TSV toolkit that allows rapid data investigation and manipulation.", - "homepage": "https://bioinf.shenwei.me/csvtk/", - "documentation": "https://bioinf.shenwei.me/csvtk/", - "tool_dev_url": "https://github.com/shenwei356/csvtk", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "csv": { - "type": "file", - "description": "CSV/TSV file", - "pattern": "*.{csv,tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - }, - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - { - "in_format": { - "type": "string", - "description": "Input format (csv, tab, or a delimiting character)", - "pattern": "*" - } - }, - { - "out_format": { - "type": "string", - "description": "Output format (csv, tab, or a delimiting character)", - "pattern": "*" - } - } - ], - "output": { - "split_csv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.${out_extension}": { - "type": "file", - "description": "Split CSV/TSV file", - "pattern": "*.{csv,tsv}", - "ontologies": [ + "cnv_population_b_allele_vcf": { + "type": "file", + "description": "CNV population SNP input VCF file", + "pattern": "*.vcf", + "ontologies": [] + } + }, { - "edam": "http://edamontology.org/format_3752" + "cnv_segmentation_bed": { + "type": "file", + "description": "Intervals to limit segmentation to", + "pattern": "*.bed", + "ontologies": [] + } }, { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_csvtk": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "csvtk": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "csvtk version | sed -e 's/csvtk v//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "csvtk": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "csvtk version | sed -e 's/csvtk v//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@SusiJo" - ], - "maintainers": [ - "@SusiJo" - ] - }, - "pipelines": [ - { - "name": "circrna", - "version": "dev" - } - ] - }, - { - "name": "ctatsplicing_prepgenomelib", - "path": "modules/nf-core/ctatsplicing/prepgenomelib/meta.yml", - "type": "module", - "meta": { - "name": "ctatsplicing_prepgenomelib", - "description": "Reference preparation for CTAT-splicing", - "keywords": [ - "splicing", - "cancer", - "rna", - "rnaseq" - ], - "tools": [ - { - "ctatsplicing": { - "description": "Detection and annotation of cancer splicing aberrations", - "homepage": "https://github.com/TrinityCTAT/CTAT-SPLICING", - "documentation": "https://github.com/TrinityCTAT/CTAT-SPLICING", - "tool_dev_url": "https://github.com/TrinityCTAT/CTAT-SPLICING", - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "genome_lib": { - "type": "file", - "description": "CTAT genome library reference", - "pattern": "*", - "ontologies": [] - } - } - ], - { - "cancer_intron_tsv": { - "type": "file", - "description": "CTAT-splicing data resource supplement", - "ontologies": [] - } - } - ], - "output": { - "reference": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "genome_lib": { - "type": "file", - "description": "Modified CTAT genome library reference", - "pattern": "*", - "ontologies": [] - } - } - ] - ], - "versions_ctatsplicing": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "ctatsplicing": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "0.0.3": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "ctatsplicing": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "0.0.3": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@anoronh4", - "@nvnieuwk" - ], - "maintainers": [ - "@anoronh4" - ], - "long_description": "This module prepares the CTAT genome library reference for splicing analysis by integrating cancer intron annotations.\nIt takes a CTAT genome library and a cancer intron TSV file as input, and outputs a modified genome library reference.\nThe output can be used in subsequent CTAT-splicing analyses to detect and annotate cancer splicing aberrations.\nMake sure to provide the correct genome library and cancer intron data resource.\n" - }, - "pipelines": [ - { - "name": "rnafusion", - "version": "4.1.2" - } - ] - }, - { - "name": "ctatsplicing_startocancerintrons", - "path": "modules/nf-core/ctatsplicing/startocancerintrons/meta.yml", - "type": "module", - "meta": { - "name": "ctatsplicing_startocancerintrons", - "description": "Detection and annotation of aberrant splicing isoforms in cancer transcriptomes", - "keywords": [ - "splicing", - "cancer", - "rna", - "rnaseq" - ], - "tools": [ - { - "ctatsplicing": { - "description": "Detection and annotation of cancer splicing aberrations", - "homepage": "https://github.com/TrinityCTAT/CTAT-SPLICING", - "documentation": "https://github.com/TrinityCTAT/CTAT-SPLICING", - "tool_dev_url": "https://github.com/TrinityCTAT/CTAT-SPLICING", - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "split_junction": { - "type": "file", - "description": "STAR alignment splice junction tab file", - "pattern": "*.SJ.out.tab", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - }, - { - "junction": { - "type": "file", - "description": "STAR alignment chimeric junction file", - "pattern": "*.out.junction", - "ontologies": [] - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - }, - { - "edam": "http://edamontology.org/format_2573" - }, - { - "edam": "http://edamontology.org/format_3462" - } - ] - } - }, - { - "bai": { - "type": "file", - "description": "BAM/CRAM/SAM index file", - "pattern": "*.{bai,crai,sai}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3327" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "genome_lib": { - "type": "file", - "description": "CTAT genome library reference with integrated cancer intron annotation", - "pattern": "*", - "ontologies": [] - } - } - ] - ], - "output": { - "cancer_introns_sorted_bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.cancer_intron_reads.sorted.bam": { - "type": "file", - "description": "Sorted BAM file containing reads mapped to cancer introns", - "pattern": "*.cancer_intron_reads.sorted.bam", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - } - ] - ], - "cancer_introns_sorted_bai": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.cancer_intron_reads.sorted.bam.bai": { - "type": "file", - "description": "Index file for the sorted BAM of cancer introns", - "pattern": "*.cancer_intron_reads.sorted.bam.bai", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3327" - } - ] - } - } - ] - ], - "gene_reads_sorted_bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.gene_reads.sorted.sifted.bam": { - "type": "file", - "description": "Sorted BAM file containing reads mapped to gene regions after downsampling coverage", - "pattern": "*.gene_reads.sorted.sifted.bam", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - } - ] - ], - "gene_reads_sorted_bai": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.gene_reads.sorted.sifted.bam.bai": { - "type": "file", - "description": "Index file for the sorted BAM of gene reads after filtering", - "pattern": "*.gene_reads.sorted.sifted.bam.bai", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3327" - } - ] - } - } - ] - ], - "cancer_introns": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.cancer.introns": { - "type": "file", - "description": "File containing detected and filtered introns that are found to be enriched in cancer transcriptomes", - "pattern": "*.cancer.introns", - "ontologies": [] - } - } - ] - ], - "cancer_introns_prelim": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.cancer.introns.prelim": { - "type": "file", - "description": "File containing detected introns that have at least one supporting read and are found to be enriched in cancer transcriptomes", - "pattern": "*.cancer.introns.prelim", - "ontologies": [] - } - } - ] - ], - "introns": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*${prefix}.introns": { - "type": "file", - "description": "File containing all detected introns", - "pattern": "*${prefix}.introns", - "ontologies": [] - } - } - ] - ], - "introns_igv_bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.introns.for_IGV.bed": { - "type": "file", - "description": "Bed file used as input for IGV-report visualization, containing cancer introns", - "pattern": "*.introns.for_IGV.bed", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3586" - } - ] - } - } - ] - ], - "igv_html": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.ctat-splicing.igv.html": { - "type": "file", - "description": "Self-contained IGV-report in HTML format for visualization of cancer introns", - "pattern": "*.ctat-splicing.igv.html", - "ontologies": [] - } - } - ] - ], - "igv_tracks": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.igv.tracks": { - "type": "file", - "description": "IGV tracks file for visualizing cancer introns in IGV", - "pattern": "*.igv.tracks", - "ontologies": [] - } - } - ] - ], - "chckpts": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.chckpts": { - "type": "file", - "description": "Checkpoint files for CTAT-SPLICING, useful for debugging or resuming interrupted runs", - "pattern": "*.chckpts", - "ontologies": [] - } - } - ] - ], - "versions_ctatsplicing": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "ctatsplicing": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "0.0.3": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "ctatsplicing": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "0.0.3": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@anoronh4", - "@nvnieuwk" - ], - "maintainers": [ - "@anoronh4" - ], - "long_description": "This module detects and annotates aberrant splicing isoforms in cancer transcriptomes using CTAT-splicing.\nIt takes STAR alignment files, a sorted BAM file, and a CTAT genome library reference as input, and outputs various files related to cancer introns.\nThe output can be used for further analysis of splicing aberrations in cancer.\nMake sure to provide the correct STAR alignment files and CTAT genome library reference.\n" - }, - "pipelines": [ - { - "name": "rnafusion", - "version": "4.1.2" - } - ] - }, - { - "name": "ctree", - "path": "modules/nf-core/ctree/meta.yml", - "type": "module", - "meta": { - "name": "ctree", - "description": "Clone trees for Cancer Evolution studies from bulk sequencing data.", - "keywords": [ - "phylogenetic-trees", - "cancer-genomics", - "cancer-evolution", - "clonal-evolution" - ], - "tools": [ - { - "ctree": { - "description": "The ctree package implements clones trees for cancer evolutionary studies. These models are built from\nCancer Cell Franctions (CCFs) clusters computed via tumour subclonal deconvolution, using either one or\nmore tumour biopsies at once. They can be used to model evolutionary trajectories from bulk sequencing\ndata, especially if whole-genome sequencing is available.\n", - "homepage": "https://caravagnalab.github.io/ctree/", - "documentation": "https://caravagnalab.github.io/ctree/", - "tool_dev_url": "https://github.com/caravagnalab/ctree", - "doi": "10.1038/s41592-018-0108-x", - "licence": [ - "GPL v3-or-later" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "ctree_input": { - "type": "file", - "description": "Either a .rds object of class `vb_bmm` or `dbpmm`, or a `.tsv` mutations table obtained after running the `pyclonevi` module\n", - "pattern": "*.{rds,tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "output": { - "ctree_rds": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "**ctree_{mobster,VIBER,pyclonevi}.rds": { - "type": "file", - "description": "The output varies based on the input. If the input is an object of class `dbpmm`,\nthe module outputs one object per sample as follows: `SampleID/ctree_mobster.rds`.\nIf the input is an object of class `vb_bmm`, the output will be one ctree object\nnamed `ctree_VIBER.rds`. If the input is the `pyclonevi` `.tsv` file, the output will\nbe one ctree object named `ctree_pyclonevi.rds`\n", - "pattern": "**ctree_{mobster,VIBER,pyclonevi}.rds", - "ontologies": [] - } - } - ] - ], - "ctree_plots_rds": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "**ctree_{mobster,VIBER,pyclonevi}_plots.rds": { - "type": "file", - "description": "Final plots as an .rds object. The module outputs one file for each ctree object\n", - "pattern": "**ctree_{mobster,VIBER,pyclonevi}_plots.rds", - "ontologies": [] - } - } - ] - ], - "ctree_report_rds": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "**ctree_{mobster,VIBER,pyclonevi}_report.rds": { - "type": "file", - "description": "Final report plots as an .rds object. The module outputs one file for each ctree object\n", - "pattern": "**ctree_{mobster,VIBER,pyclonevi}_report.rds", - "ontologies": [] - } - } - ] - ], - "ctree_report_pdf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "**ctree_{mobster,VIBER,pyclonevi}_report.pdf": { - "type": "file", - "description": "Final report plots as a pdf object. The module outputs one file for each ctree object\n", - "pattern": "**ctree_{mobster,VIBER,pyclonevi}_report.pdf", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3508" - } - ] - } - } - ] - ], - "ctree_report_png": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "**ctree_{mobster,VIBER,pyclonevi}_report.png": { - "type": "file", - "description": "Final report plots as a png object. The module outputs one file for each ctree object\n", - "pattern": "**ctree_{mobster,VIBER,pyclonevi}_report.png", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3603" - } - ] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "topics": { - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@elena-buscaroli" - ], - "maintainers": [ - "@elena-buscaroli" - ] - }, - "pipelines": [ - { - "name": "tumourevo", - "version": "dev" - } - ] - }, - { - "name": "custom_addmostsevereconsequence", - "path": "modules/nf-core/custom/addmostsevereconsequence/meta.yml", - "type": "module", - "meta": { - "name": "custom_addmostsevereconsequence", - "description": "Annotate a VEP annotated VCF with the most severe consequence field", - "keywords": [ - "annotation", - "vep", - "consequence", - "vcf" - ], - "tools": [ - { - "custom": { - "description": "Custom module to annotate a VEP annotated VCF with the most severe consequence field", - "tool_dev_url": "https://github.com/nf-core/modules/blob/master/modules/nf-core/custom/addmostsevereconsequence/main.nf", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VEP annotated VCF file", - "pattern": "*.{vcf,vcf.gz}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "variant_consequences": { - "type": "file", - "description": "File with VEP variant consequences, one per line.", - "pattern": "*", - "ontologies": [] - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.vcf.gz": { - "type": "file", - "description": "Annotated VCF file", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "versions_addmostsevereconsequence": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "addmostsevereconsequence": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "1.2.0": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_bgzip": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bgzip": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bgzip --version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "addmostsevereconsequence": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "1.2.0": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bgzip": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bgzip --version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@ramprasadn", - "@fellen31" - ], - "maintainers": [ - "@ramprasadn", - "@fellen31" - ] - } - }, - { - "name": "custom_addmostseverepli", - "path": "modules/nf-core/custom/addmostseverepli/meta.yml", - "type": "module", - "meta": { - "name": "custom_addmostseverepli", - "description": "Annotate a VEP annotated VCF with the most severe pLi field", - "keywords": [ - "annotation", - "vep", - "pli", - "vcf" - ], - "tools": [ - { - "custom": { - "description": "Custom module to annotate a VEP annotated VCF with the most severe pLi field", - "tool_dev_url": "https://github.com/nf-core/modules/blob/master/modules/nf-core/custom/addmostseverepli/main.nf", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VEP annotated VCF file", - "pattern": "*.{vcf,vcf.gz}", - "ontologies": [] - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.vcf.gz": { - "type": "file", - "description": "Annotated VCF file", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "versions_addmostseverepli": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "addmostseverepli": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "1.2.0": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_bgzip": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bgzip": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bgzip --version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "addmostseverepli": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "1.2.0": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bgzip": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bgzip --version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@ramprasadn", - "@fellen31" - ], - "maintainers": [ - "@ramprasadn", - "@fellen31" - ] - } - }, - { - "name": "custom_catadditionalfasta", - "path": "modules/nf-core/custom/catadditionalfasta/meta.yml", - "type": "module", - "meta": { - "name": "custom_catadditionalfasta", - "description": "Custom module to Add a new fasta file to an old one and update an associated GTF", - "keywords": [ - "fasta", - "gtf", - "genomics" - ], - "tools": [ - { - "custom": { - "description": "Custom module to Add a new fasta file to an old one and update an associated GTF", - "tool_dev_url": "https://github.com/nf-core/modules/blob/master/modules/nf-core/custom/catadditionalfasta/main.nf", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing fasta information\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA-format sequence file", - "pattern": "*.{fasta,fa}", - "ontologies": [] - } - }, - { - "gtf": { - "type": "file", - "description": "GTF-format annotation file for fasta", - "pattern": "*.gtf", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing additional fasta information\n" - } - }, - { - "add_fasta": { - "type": "file", - "description": "FASTA-format file of additional sequences", - "pattern": "*.fa", - "ontologies": [] - } - } - ], - { - "biotype": { - "type": "string", - "description": "Biotype to apply to new GTF entries" - } - } - ], - "output": { - "fasta": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing fasta information\n" - } - }, - { - "out/${prefix}.fasta": { - "type": "file", - "description": "FASTA-format combined sequence file", - "pattern": "*.{fasta,fa}", - "ontologies": [] - } - } - ] - ], - "gtf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing fasta information\n" - } - }, - { - "out/${prefix}.gtf": { - "type": "file", - "description": "GTF-format combined annotation file", - "pattern": "*.gtf", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "topics": { - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@pinin4fjords" - ], - "maintainers": [ - "@pinin4fjords" - ] - }, - "pipelines": [ - { - "name": "lncpipe", - "version": "dev" - }, - { - "name": "references", - "version": "0.1" - }, - { - "name": "riboseq", - "version": "1.2.0" - }, - { - "name": "rnaseq", - "version": "3.26.0" - } - ] - }, - { - "name": "custom_clustermetrics", - "path": "modules/nf-core/custom/clustermetrics/meta.yml", - "type": "module", - "meta": { - "name": "CUSTOM_CLUSTERMETRICS", - "description": "Computes clustering quality metrics (silhouette, Calinski-Harabasz, Davies-Bouldin) and performs k-sweep analysis", - "keywords": [ - "clustering", - "metrics", - "silhouette", - "calinski-harabasz", - "davies-bouldin", - "evaluation" - ], - "tools": [ - { - "scikit-learn": { - "description": "Machine learning library for clustering metrics", - "homepage": "https://scikit-learn.org/", - "documentation": "https://scikit-learn.org/stable/modules/clustering.html", - "licence": [ - "BSD-3-Clause" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "features": { - "type": "file", - "description": "Tab-separated feature matrix with a `sample_id` column and one\ncolumn per numeric feature (e.g. PCA scores).\n", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - }, - { - "clusters": { - "type": "file", - "description": "Comma-separated cluster assignments with `sample_id` and integer\n`cluster` columns. Label -1 is treated as DBSCAN noise.\n", - "pattern": "*.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "output": { - "metrics": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*.metrics.tsv": { - "type": "file", - "description": "TSV with selected cluster quality metrics", - "pattern": "*.metrics.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "k_sweep": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*.k_sweep.csv": { - "type": "file", - "description": "CSV with metrics for different values of k", - "pattern": "*.k_sweep.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "selected": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*.selected.json": { - "type": "file", - "description": "JSON with the selected/best metrics", - "pattern": "*.selected.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "plots": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*.png": { - "type": "file", - "description": "Optional PNG plots (elbow, silhouette, etc.)", - "pattern": "*.png", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "topics": { - "versions": [ - { - "versions.yml": { - "type": "string", - "description": "The name of the process" - } - } - ] - }, - "authors": [ - "@dbaku42" - ], - "maintainers": [ - "@dbaku42" - ] - } - }, - { - "name": "custom_clustervisualization", - "path": "modules/nf-core/custom/clustervisualization/meta.yml", - "type": "module", - "meta": { - "name": "CUSTOM_CLUSTERVISUALIZATION", - "description": "Generates UMAP and t-SNE visualizations colored by cluster", - "keywords": [ - "clustering", - "visualization", - "pca", - "umap", - "tsne", - "dimension-reduction" - ], - "tools": [ - { - "scikit-learn": { - "description": "Machine learning library for dimension reduction (PCA, t-SNE)", - "homepage": "https://scikit-learn.org/", - "documentation": "https://scikit-learn.org/stable/modules/clustering.html", - "licence": [ - "BSD-3-Clause" - ], - "identifier": "" - } - }, - { - "umap-learn": { - "description": "Uniform Manifold Approximation and Projection for dimension reduction", - "homepage": "https://umap-learn.readthedocs.io/", - "documentation": "https://umap-learn.readthedocs.io/en/latest/", - "licence": [ - "BSD-3-Clause" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "features": { - "type": "file", - "description": "Tab-separated feature matrix with a `sample_id` column and one\ncolumn per numeric feature (e.g. PCA scores).\n", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - }, - { - "clusters": { - "type": "file", - "description": "Comma-separated cluster assignments with `sample_id` and integer\n`cluster` columns. Label -1 is treated as DBSCAN noise.\n", - "pattern": "*.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "output": { - "umap_tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*.umap.tsv": { - "type": "file", - "description": "UMAP coordinates per sample", - "pattern": "*.umap.tsv", - "ontologies": [ + "cnv_target_bed": { + "type": "file", + "description": "CNV target BED file", + "pattern": "*.bed", + "ontologies": [] + } + }, { - "edam": "http://edamontology.org/operation_2432" + "cram_reference": { + "type": "file", + "description": "Reference file in FASTA format (only used for decompression)", + "pattern": "*.{fasta,fa}", + "ontologies": [] + } }, { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "tsne_tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*.tsne.tsv": { - "type": "file", - "description": "t-SNE coordinates per sample", - "pattern": "*.tsne.tsv", - "ontologies": [ + "dbsnp": { + "type": "file", + "description": "Variant annotation database VCF (or .vcf.gz) file", + "pattern": "*.vcf{,.gz}", + "ontologies": [] + } + }, + { + "fastqc_adapter_file": { + "type": "file", + "description": "FASTA file containing adapter sequences", + "pattern": "*.{fasta,fa}", + "ontologies": [] + } + }, + { + "fastqc_kmer_file": { + "type": "file", + "description": "FASTA file containing kmers of interest", + "pattern": "*.{fasta,fa}", + "ontologies": [] + } + }, + { + "ora_reference": { + "type": "directory", + "description": "Path to the directory that contains the compression reference and index file" + } + }, + { + "qc_coverage_region": { + "type": "file", + "description": "bed files to report coverage on, max 3", + "pattern": "*.bed", + "ontologies": [] + } + }, + { + "qc_cross_cont_vcf": { + "type": "file", + "description": "Variant file (.vcf/.vcf.gz) with population allele frequencies to estimate sample contamination", + "pattern": "*.vcf{,.gz}", + "ontologies": [] + } + }, + { + "ref_dir": { + "type": "directory", + "description": "Directory with reference and hash tables" + } + }, + { + "repeat_genotype_ref_fasta": { + "type": "file", + "description": "FASTA file containing repeat genotypes", + "pattern": "*.{fasta,fa}", + "ontologies": [] + } + }, + { + "repeat_genotype_specs": { + "type": "file", + "description": "Repeat variant catalog file", + "ontologies": [] + } + }, + { + "sv_call_regions_bed": { + "type": "file", + "description": "BED file containing the set of regions to call (optionally gzip or bgzip compressed)", + "pattern": "*.bed{,.gz}", + "ontologies": [] + } + }, + { + "sv_exclusion_bed": { + "type": "file", + "description": "BED file containing the set of exclusion regions for SV calling (optionally gzip or bzip compressed)", + "pattern": "*.bed", + "ontologies": [] + } + }, + { + "sv_forcegt_vcf": { + "type": "file", + "description": "Specify a VCF of structural variants for forced genotyping, meaning these variants will be scored and emitted in the output VCF even if not found in the sample data. These variants will be merged with any additional variants discovered directly from the sample data.", + "pattern": "*.vcf", + "ontologies": [] + } + }, + { + "sv_systematic_noise": { + "type": "file", + "description": "Systematic noise BEDPE file containing the set of noisy paired regions for SV calling (optionally gzip or bzip compressed).", + "pattern": "*.bed{,.gz}", + "ontologies": [] + } + }, + { + "trim_adapter_read": { + "type": "file", + "description": "Files of adapter sequences to trim from the 3' end of read 1 and 2", + "pattern": "*.{fasta,fa}", + "ontologies": [] + } + }, + { + "trim_adapter_read_5prime": { + "type": "file", + "description": "FASTA files that contains adapter sequences to trim from the 5' end of Read 1 and 2; The sequences should be in reverse order (with respect to their appearance in the FASTQ) but not complemented", + "pattern": "*.{fasta,fa}", + "ontologies": [] + } + }, + { + "variant_annotation_data": { + "type": "directory", + "description": "Location of downloaded Nirvana annotation files" + } + }, + { + "vc_combine_phased_variants_distance_bed": { + "type": "file", + "description": "Combine variants in the same phase set bed file.", + "pattern": "*.bed", + "ontologies": [] + } + }, + { + "vc_excluded_regions_bed": { + "type": "file", + "description": "Excluded regions bed specifying where variants will be hard filtered", + "pattern": "*.bed", + "ontologies": [] + } + }, + { + "vc_forcegt_vcf": { + "type": "file", + "description": "List of small variants to force genotype. Can be .vcf or .vcf.gz file", + "pattern": "*.vcf{,.gz}", + "ontologies": [] + } + }, + { + "vc_log_bed": { + "type": "file", + "description": "Log information for regions in this BED file", + "pattern": "*.bed", + "ontologies": [] + } + }, + { + "vc_mapping_metrics": { + "type": "file", + "description": "File containing mapping metrics", + "ontologies": [] + } + }, + { + "vc_ml_dir": { + "type": "directory", + "description": "directory containing machine learning package" + } + }, + { + "vc_ntd_error_params": { + "type": "file", + "description": "Params file for per-nucleotide error rate calibration", + "ontologies": [] + } + }, + { + "vc_roh_blacklist_bed": { + "type": "file", + "description": "Blacklist BED file for ROH", + "pattern": "*.bed", + "ontologies": [] + } + }, + { + "vc_snp_error_cal_bed": { + "type": "file", + "description": "BED file containing regions from which to estimate nucleotide substitution biases", + "pattern": "*.bed", + "ontologies": [] + } + }, + { + "vc_systematic_noise": { + "type": "file", + "description": "Site specific noise file. This file enables the systematic-noise filter and improves specificity during somatic variant calling", + "ontologies": [] + } + }, + { + "vc_target_bed": { + "type": "file", + "description": "Target BED file", + "pattern": "*.bed", + "ontologies": [] + } + }, + { + "vd_eh_vcf": { + "type": "file", + "description": "Expansion hunter vcf (optionally .gzip compressed)", + "pattern": "*.vcf{,.gz}", + "ontologies": [] + } + }, + { + "vd_small_variant_vcf": { + "type": "file", + "description": "Small variant vcf (optionally .gzip compressed)", + "pattern": "*.vcf{,.gz}", + "ontologies": [] + } + }, { - "edam": "http://edamontology.org/operation_2432" + "vd_sv_vcf": { + "type": "file", + "description": "Structural variant vcf (optionally .gzip compressed)", + "pattern": "*.vcf{,.gz}", + "ontologies": [] + } }, { - "edam": "http://edamontology.org/format_3475" + "vntr_catalog_bed": { + "type": "file", + "description": "BED file specifying the TR regions for the VNTR Caller to act upon", + "pattern": "*.bed", + "ontologies": [] + } } - ] - } - } - ] - ], - "umap_png": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*.umap.png": { - "type": "file", - "description": "UMAP visualization coloured by cluster", - "pattern": "*.umap.png", - "ontologies": [] - } - } - ] - ], - "tsne_png": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*.tsne.png": { - "type": "file", - "description": "t-SNE visualization coloured by cluster", - "pattern": "*.tsne.png", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "Software versions used in the module", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "topics": { - "versions": [ - { - "versions.yml": { - "type": "string", - "description": "The name of the process" - } - } - ] - }, - "authors": [ - "@dbaku42" - ], - "maintainers": [ - "@dbaku42" - ] - } - }, - { - "name": "custom_dumpsoftwareversions", - "path": "modules/nf-core/custom/dumpsoftwareversions/meta.yml", - "type": "module", - "meta": { - "name": "custom_dumpsoftwareversions", - "description": "Custom module used to dump software versions within the nf-core pipeline template", - "deprecated": true, - "keywords": [ - "custom", - "dump", - "version" - ], - "tools": [ - { - "custom": { - "description": "Custom module used to dump software versions within the nf-core pipeline template", - "homepage": "https://github.com/nf-core/tools", - "documentation": "https://github.com/nf-core/tools", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - { - "versions": { - "type": "file", - "description": "YML file containing software versions", - "pattern": "*.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ], - "output": { - "yml": [ - { - 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It is designed for accurate and efficient detection of structural variations.", + "keywords": ["structural variants", "sv", "vcf"], + "tools": [ + { + "dysgu": { + "description": "Structural variant caller for mapped sequencing data", + "homepage": "https://github.com/kcleal/dysgu", + "documentation": "https://github.com/kcleal/dysgu/blob/master/README.rst", + "tool_dev_url": "https://github.com/kcleal/dysgu", + "doi": "10.1093/nar/gkac039", + "licence": ["GPL-3.0-or-later"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "input": { + "type": "file", + "description": "Input BAM file", + "pattern": "*.bam", + "ontologies": [] + } + }, + { + "index": { + "type": "file", + "description": "BAM index file", + "pattern": "*.bai", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Genome reference FASTA file", + "pattern": "*.{fa,fasta}", + "ontologies": [] + } + }, + { + "fai": { + "type": "file", + "description": "Genome reference FASTA index file", + "pattern": "*.{fa.fai,fasta.fai}", + "ontologies": [] + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample1' ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "VCF file with identified structural variants", + "pattern": "*.{vcf.gz}", + "ontologies": [] + } + } + ] + ], + "tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample1' ]\n" + } + }, + { + "*.vcf.gz.tbi": { + "type": "file", + "description": "The index of the BCF/VCF file", + "pattern": "*.{vcf.gz.tbi}", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@famosab", "@poddarharsh15"], + "maintainers": ["@poddarharsh15"] + } }, { - "name": "scnanoseq", - "version": "1.2.2" + "name": "dysgu_run", + "path": "modules/nf-core/dysgu/run/meta.yml", + "type": "module", + "meta": { + "name": "dysgu_run", + "description": "Dysgu calls structural variants (SVs) from mapped sequencing reads. It is designed for accurate and efficient detection of structural variations.", + "keywords": ["structural variants", "sv", "vcf"], + "tools": [ + { + "dysgu": { + "description": "Structural variant caller for mapped sequencing data", + "homepage": "https://github.com/kcleal/dysgu", + "documentation": "https://github.com/kcleal/dysgu/blob/master/README.rst", + "tool_dev_url": "https://github.com/kcleal/dysgu", + "doi": "10.1093/nar/gkac039", + "licence": ["GPL-3.0-or-later"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "input": { + "type": "file", + "description": "Input BAM file", + "pattern": "*.{bam,cram}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + }, + { + "edam": "http://edamontology.org/format_3462" + } + ] + } + }, + { + "index": { + "type": "file", + "description": "BAM index file", + "pattern": "*.{bai,crai}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3327" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Genome reference FASTA file", + "pattern": "*.{fa,fasta}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Genome reference FASTA index file", + "pattern": "*.{fa.fai,fasta.fai}", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "sites": { + "type": "file", + "description": "Known sites VCF file", + "pattern": "*.{vcf,vcf.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + } + ] + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "bed": { + "type": "file", + "description": "Regions to include BED file", + "pattern": "*.bed", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3003" + } + ] + } + } + ], + [ + { + "meta6": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "search_bed": { + "type": "file", + "description": "Regions to search BED file", + "pattern": "*.bed", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3003" + } + ] + } + } + ], + [ + { + "meta7": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "exclude_bed": { + "type": "file", + "description": "Regions to exclude BED file", + "pattern": "*.bed", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3003" + } + ] + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample1' ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "VCF file with identified structural variants", + "pattern": "*.{vcf.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + } + ] + } + } + ] + ], + "tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample1' ]\n" + } + }, + { + "*.vcf.gz.tbi": { + "type": "file", + "description": "The index of the BCF/VCF file", + "pattern": "*.vcf.gz.tbi", + "ontologies": [] + } + } + ] + ], + "versions_dysgu": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "dysgu": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "dysgu --version 2>&1 | sed 's/.*version //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "dysgu": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "dysgu --version 2>&1 | sed 's/.*version //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@famosab", "@poddarharsh15"], + "maintainers": ["@poddarharsh15", "@nvnieuwk"] + } }, { - "name": "ssds", - "version": "dev" - }, - { - "name": "variantcatalogue", - "version": "dev" - }, - { - "name": "viralintegration", - "version": "0.1.1" - } - ] - }, - { - "name": "custom_filterdifferentialtable", - "path": "modules/nf-core/custom/filterdifferentialtable/meta.yml", - "type": "module", - "meta": { - "name": "custom_filterdifferentialtable", - "description": "Filters a differential expression table based on logFC and adjusted p-value thresholds", - "keywords": [ - "filter", - "differential expression", - "logFC", - "significance statistic", - "p-value" - ], - "tools": [ - { - "pandas": { - "description": "Python library for data manipulation and analysis", - "homepage": "https://pandas.pydata.org/", - "documentation": "https://pandas.pydata.org/docs/", - "tool_dev_url": "https://github.com/pandas-dev/pandas", - "doi": "10.5281/zenodo.3509134", - "licence": [ - "BSD-3-Clause" - ], - "identifiers": [ - "biotools:pandas", - "conda:pandas" - ], - "identifier": "biotools:pandas" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input_file": { - "type": "file", - "description": "Input differential expression table (CSV, TSV, or TXT format)", - "pattern": "*.{csv,tsv,txt}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - }, - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - [ - { - "logfc_column": { - "type": "string", - "description": "Name of the column containing log fold change values" - } - }, - { - "fc_threshold": { - "type": "float", - "description": "Fold change threshold for filtering" - } - }, - { - "fc_cardinality": { - "type": "string", - "description": "Operator to compare the fold change values with the threshold.\nValid values are: \">=\", \"<=\", \">\", \"<\".\n" - } - } - ], - [ - { - "stat_column": { - "type": "string", - "description": "Name of the column containing the significance statistic values\n(eg. adjusted p-values).\n" - } - }, - { - "stat_threshold": { - "type": "float", - "description": "Statistic threshold for filtering" - } - }, - { - "stat_cardinality": { - "type": "string", - "description": "Operator to compare the column values with the threshold.\nValid values are: \">=\", \"<=\", \">\", \"<\".\n" - } - } - ] - ], - "output": { - "filtered": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_filtered.tsv": { - "type": "file", - "description": "Filtered differential expression table", - "pattern": "*_filtered.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "filtered_up": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_filtered_up.tsv": { - "type": "file", - "description": "Filtered differential expression table for overexpressed genes", - "pattern": "*_filtered_up.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "filtered_down": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_filtered_down.tsv": { - "type": "file", - "description": "Filtered differential expression table for underexpressed genes", - "pattern": "*_filtered_down.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "topics": { - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@pinin4fjords", - "@WackerO" - ], - "maintainers": [ - "@pinin4fjords", - "@WackerO" - ] - } - }, - { - "name": "custom_geneticmapconvert", - "path": "modules/nf-core/custom/geneticmapconvert/meta.yml", - "type": "module", - "meta": { - "name": "custom_geneticmapconvert", - "description": "This R script allows to automatically detect the different genetic map format and\nconvert the input file in all the other format type.\n", - "keywords": [ - "map", - "convertion", - "R" - ], - "tools": [ - { - "custom": { - "description": "Custom script to convert any genetic map format", - "homepage": "https://github.com/nf-core/tools", - "documentation": "https://github.com/nf-core/tools", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "map_file": { - "type": "file", - "description": "Genomic map file to process.\nThis file should contain the data of only one chromosome.\nIt should be a flat file (comma, semicolon, tab or space delimited) with\nat least the physical position and its corresponding recombination\ndistance in centiMorgans.\nThe columns names will be normalised (no space, extra character transformed to \"_\")\nand then automatically recognise as:\n - chr: _chr, chrom, chromosome\n - pos: position, bp\n - id: snp, marker, rsid\n - cm: genetic_map_cm\n - rate: combined_rate, combined_rate_cm_mb, cm_mb\nIf no header present, then it will try for 3 columns table with chr, pos, cm format\nand for 4 columns table with chr, id, cm, pos format.\n", - "ontologies": [] - } - } - ] - ], - "output": { - "glimpse_map": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "${prefix}.glimpse.map": { - "type": "file", - "description": "File containing the map in Glimpse format:\ntab-delimited file with header and columns:\npos, chr, cM\n", - "pattern": "*.glimpse.map" - } - } - ] - ], - "plink_map": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "${prefix}.plink.map": { - "type": "file", - "description": "File containing the map in PLINK format:\nspace-delimited file without header and columns:\nchr, id, cM, pos\n", - "pattern": "*.plink.map" - } - } - ] - ], - "stitch_map": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "${prefix}.stitch.map": { - "type": "file", - "description": "File containing the map in STITCH format:\nspace-delimited file with header and columns:\npos, rate, cM\n", - "pattern": "*.stitch.map" - } - } - ] - ], - "minimac_map": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "${prefix}.minimac.map": { - "type": "file", - "description": "File containing the map in Minimac format:\ntab-delimited file with header and columns:\nchr, pos, cM\n", - "pattern": "*.minimac.map" - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "topics": { - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@LouisLeNezet" - ], - "maintainers": [ - "@LouisLeNezet" - ] - } - }, - { - "name": "custom_getchromsizes", - "path": "modules/nf-core/custom/getchromsizes/meta.yml", - "type": "module", - "meta": { - "name": "custom_getchromsizes", - "description": "Generates a FASTA file of chromosome sizes and a fasta index file", - "deprecated": true, - "keywords": [ - "fasta", - "chromosome", - "indexing" - ], - "tools": [ - { - "samtools": { - "description": "Tools for dealing with SAM, BAM and CRAM files", - "homepage": "http://www.htslib.org/", - "documentation": "http://www.htslib.org/doc/samtools.html", - "tool_dev_url": "https://github.com/samtools/samtools", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + "name": "ea-utils_gtf2bed", + "path": "modules/nf-core/ea-utils/gtf2bed/meta.yml", + "type": "module", + "meta": { + "name": "eautils_gtf2bed", + "description": "Convert a GTF/GFF annotation file to BED12 format", + "keywords": ["gtf", "gff", "bed", "bed12", "annotation", "conversion"], + "tools": [ + { + "gtf2bed": { + "description": "Perl script from the ea-utils package that converts GTF/GFF annotation\nfiles to BED12 format, handling exons, start/stop codons, and miRNAs.\nProduces UCSC-compatible BED with proper thin/thick regions.\n", + "homepage": "https://expressionanalysis.github.io/ea-utils/", + "documentation": "https://github.com/ExpressionAnalysis/ea-utils/blob/master/clipper/gtf2bed", + "tool_dev_url": "https://github.com/ExpressionAnalysis/ea-utils", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'genome' ]`\n" + } + }, + { + "gtf": { + "type": "file", + "description": "GTF or GFF annotation file", + "pattern": "*.{gtf,gff,gtf.gz,gff.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2306" + } + ] + } + } + ] + ], + "output": { + "bed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'genome' ]`\n" + } + }, + { + "${prefix}.bed": { + "type": "file", + "description": "BED12 format annotation file with one entry per transcript", + "pattern": "*.bed", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3003" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "topics": { + "versions": [ + { + "versions.yml": { + "type": "string", + "description": "The name of the process" + } + } + ] + }, + "authors": ["@pinin4fjords"], + "maintainers": ["@pinin4fjords"] }, - { - "fasta": { - "type": "file", - "description": "FASTA file", - "pattern": "*.{fa,fasta,fna,fas}", - "ontologies": [] - } - } - ] - ], - "output": { - "sizes": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.sizes": { - "type": "file", - "description": "File containing chromosome lengths", - "pattern": "*.{sizes}", - "ontologies": [] - } - } - ] - ], - "fai": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.fai": { - "type": "file", - "description": "FASTA index file", - "pattern": "*.{fai}", - "ontologies": [] - } - } - ] - ], - "gzi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.gzi": { - "type": "file", - "description": "Optional gzip index file for compressed inputs", - "pattern": "*.gzi", - "ontologies": [] - } - } + "pipelines": [ + { + "name": "rnaseq", + "version": "3.26.0" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "topics": { - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@tamara-hodgetts", - "@chris-cheshire", - "@muffato" - ], - "maintainers": [ - "@tamara-hodgetts", - "@chris-cheshire", - "@muffato" - ] - }, - "pipelines": [ - { - "name": "atacseq", - "version": "2.1.2" - }, - { - "name": "chipseq", - "version": "2.1.0" - }, - { - "name": "cutandrun", - "version": "3.2.2" - }, - { - "name": "deepmodeloptim", - "version": "dev" }, { - "name": "hic", - "version": "2.1.0" - }, - { - "name": "lncpipe", - "version": "dev" - }, - { - "name": "nascent", - "version": "2.3.0" - }, - { - "name": "riboseq", - "version": "1.2.0" + "name": "eagle2", + "path": "modules/nf-core/eagle2/meta.yml", + "type": "module", + "meta": { + "name": "eagle2", + "description": "Perform phasing of genotyped data with or without a reference panel", + "keywords": ["phasing", "haplotypes", "reference panel", "genomics"], + "tools": [ + { + "eagle2": { + "description": "The Eagle software estimates haplotype phase either within a genotyped cohort or using a phased reference panel.", + "homepage": "https://alkesgroup.broadinstitute.org/Eagle/", + "documentation": "https://alkesgroup.broadinstitute.org/Eagle/", + "tool_dev_url": "https://github.com/poruloh/Eagle", + "doi": "10.1038/ng.3679", + "licence": ["GPL v3-or-later"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "input": { + "type": "file", + "description": "Vcf file containing genotyped cohort or target samples to phase", + "pattern": "*.{vcf,vcf.gz,bcf}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + }, + { + "edam": "http://edamontology.org/format_3020" + } + ] + } + }, + { + "index": { + "type": "file", + "description": "Input file index", + "pattern": "*.{csi,tbi}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3700" + } + ] + } + }, + { + "ref_vcf": { + "type": "file", + "description": "Reference panel to phase the genotyped cohort", + "pattern": "*.{vcf,vcf.gz,bcf}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + }, + { + "edam": "http://edamontology.org/format_3020" + } + ] + } + }, + { + "ref_index": { + "type": "file", + "description": "Reference panel index", + "pattern": "*.{csi,tbi}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3700" + } + ] + } + }, + { + "map": { + "type": "file", + "description": "Genetic map file", + "pattern": "*.{txt,txt.gz,map,map.gz}", + "ontologies": [] + } + } + ] + ], + "output": { + "phased_variants": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.{vcf,vcf.gz,bcf}": { + "type": "file", + "description": "Input phased variants", + "pattern": "*.{vcf,vcf.gz,bcf}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + }, + { + "edam": "http://edamontology.org/format_3020" + } + ] + } + } + ] + ], + "versions_eagle2": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "eagle2": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "eagle --help | sed -n 's/.*Eagle v\\([0-9.]\\+\\).*/\\1/p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "eagle2": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "eagle --help | sed -n 's/.*Eagle v\\([0-9.]\\+\\).*/\\1/p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@LouisLeNezet"], + "maintainers": ["@LouisLeNezet"] + } }, { - "name": "rnasplice", - "version": "1.0.4" + "name": "ectyper", + "path": "modules/nf-core/ectyper/meta.yml", + "type": "module", + "meta": { + "name": "ectyper", + "description": "In silico prediction of E. coli serotype", + "keywords": ["escherichia coli", "fasta", "serotype"], + "tools": [ + { + "ectyper": { + "description": "ECtyper is a python program for serotyping E. coli genomes", + "homepage": "https://github.com/phac-nml/ecoli_serotyping", + "documentation": "https://github.com/phac-nml/ecoli_serotyping", + "tool_dev_url": "https://github.com/phac-nml/ecoli_serotyping", + "licence": ["Apache 2"], + "identifier": "biotools:ectyper" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA formatted assembly file", + "pattern": "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}", + "ontologies": [] + } + } + ] + ], + "output": { + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "ectyper log output", + "pattern": "*.log", + "ontologies": [] + } + } + ] + ], + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "ectyper serotyping results in TSV format", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "txt": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "Allele report generated from BLAST results", + "pattern": "*.txt", + "ontologies": [] + } + } + ] + ], + "versions_ectyper": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "ectyper": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "ectyper --version 2>&1 | sed 's/.*ectyper //; s/ .*$//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "ectyper": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "ectyper --version 2>&1 | sed 's/.*ectyper //; s/ .*$//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@rpetit3"], + "maintainers": ["@rpetit3"] + } }, { - "name": "viralrecon", - "version": "3.0.0" - } - ] - }, - { - "name": "custom_gtffilter", - "path": "modules/nf-core/custom/gtffilter/meta.yml", - "type": "module", - "meta": { - "name": "custom_gtffilter", - "description": "Filter a gtf file to keep only regions that are located on a chromosome represented in a given fasta file", - "keywords": [ - "gtf", - "fasta", - "filter" - ], - "tools": [ - { - "gtffilter": { - "description": "Filter a gtf file to keep only regions that are located on a chromosome represented in a given fasta file", - "tool_dev_url": "https://github.com/nf-core/modules/blob/master/modules/nf-core/custom/gtffilter/main.nf", - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "gtf": { - "type": "file", - "description": "GTF file", - "pattern": "*.{gtf}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } + "name": "eggnogmapper", + "path": "modules/nf-core/eggnogmapper/meta.yml", + "type": "module", + "meta": { + "name": "eggnogmapper", + "description": "Fast genome-wide functional annotation through orthology assignment.", + "keywords": ["annotation", "functional annotation", "orthology", "genomics", "eggnog"], + "tools": [ + { + "eggnogmapper": { + "description": "EggNOG-mapper is a tool for fast functional annotation of novel sequences.\nIt uses precomputed orthologous groups and phylogenies from the eggNOG database\nto transfer functional information from fine-grained orthologs only.\n", + "homepage": "https://github.com/eggnogdb/eggnog-mapper", + "documentation": "https://github.com/eggnogdb/eggnog-mapper/wiki", + "tool_dev_url": "https://github.com/eggnogdb/eggnog-mapper", + "doi": "10.1093/molbev/msab293", + "licence": ["AGPL v3"], + "identifier": "biotools:eggnog-mapper-v2" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input sequences in FASTA format (plain or gzip-compressed)", + "pattern": "*.{fasta,faa,fa}(.gz)?", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + [ + { + "search_mode": { + "type": "string", + "description": "Search mode passed to emapper.py via -m. Determines which backend\nis used and which database flag is applied internally.\nSupported modes:\n - diamond: DIAMOND-based homology search (--dmnd_db)\n - novel_fams: DIAMOND search against novel families (--dmnd_db)\n - mmseqs: MMseqs2-based search (--mmseqs_db)\n - hmmer: HMMER-based search (--database)\n - no_search: Skip search step and annotate from a precomputed\n *.emapper.seed_orthologs file (--annotate_hits_table)\n - cache: Reuse a previously generated hits table (--cache)\n", + "enum": ["diamond", "novel_fams", "mmseqs", "hmmer", "no_search", "cache"] + } + }, + { + "db": { + "type": "file", + "description": "Database file, directory, or precomputed results file required by the\nselected search_mode. The module automatically assigns the correct\nflag depending on search_mode:\n - diamond / novel_fams: DIAMOND database (*.dmnd)\n - mmseqs: MMseqs2 database directory or prefix\n - hmmer: HMM database (*.hmm, *.h3m)\n - no_search: Precomputed *.emapper.seed_orthologs file\n - cache: Previously generated *.emapper.hits file\nThis input is mandatory but its expected format depends on search_mode.\n", + "pattern": "*", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1370" + }, + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + { + "eggnog_data_dir": { + "type": "directory", + "description": "Directory containing eggnog-mapper database files\n(e.g. can be downloaded via download_eggnog_data.py,\nfound in the eggnog-mapper repository)\n", + "pattern": "*" + } + } + ], + "output": { + "annotations": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.emapper.annotations": { + "type": "file", + "description": "TSV file with the results from the annotation phase, including functional annotations, GO terms, KEGG pathways, and COG categories", + "pattern": "*.emapper.annotations", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "orthologs": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.emapper.seed_orthologs": { + "type": "file", + "description": "TSV file with the results from parsing the hits, linking queries with their best seed orthologs (includes commented metadata header)", + "pattern": "*.emapper.seed_orthologs", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "hits": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.emapper.hits": { + "type": "file", + "description": "TSV file with the raw search hits from the Diamond/MMseqs2/HMMER search phase before annotation", + "pattern": "*.emapper.hits", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_eggnogmapper": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "eggnog-mapper": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "emapper.py --version 2>&1 | grep -o 'emapper-[0-9]\\+\\.[0-9]\\+\\.[0-9]\\+' | sed 's/emapper-//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "eggnog-mapper": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "emapper.py --version 2>&1 | grep -o 'emapper-[0-9]\\+\\.[0-9]\\+\\.[0-9]\\+' | sed 's/emapper-//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@vagkaratzas"], + "maintainers": ["@vagkaratzas", "@gallvp"] }, - { - "fasta": { - "type": "file", - "description": "Genome fasta file", - "pattern": "*.{fasta,fa}", - "ontologies": [] - } - } - ] - ], - "output": { - "gtf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}.${suffix}": { - "type": "file", - "description": "Filtered GTF file", - "pattern": "*.{gtf}", - "ontologies": [] - } - } + "pipelines": [ + { + "name": "funcprofiler", + "version": "dev" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "topics": { - "versions": [ - { - "versions.yml": { - "type": "string", - "description": "The name of the process" - } - } - ] }, - "authors": [ - "@nictru" - ], - "maintainers": [ - "@nictru" - ] - }, - "pipelines": [ { - "name": "circrna", - "version": "dev" + "name": "eido_convert", + "path": "modules/nf-core/eido/convert/meta.yml", + "type": "module", + "meta": { + "name": "eido_convert", + "description": "Convert any PEP project or Nextflow samplesheet to any format", + "keywords": ["eido", "convert", "PEP", "format", "samplesheet"], + "tools": [ + { + "eido": { + "description": "Convert any PEP project or Nextflow samplesheet to any format", + "homepage": "http://eido.databio.org/en/latest/", + "documentation": "http://eido.databio.org/en/latest/", + "doi": "10.1093/gigascience/giab077", + "licence": ["BSD-2-Clause"], + "identifier": "biotools:eido-python-package" + } + } + ], + "input": [ + { + "samplesheet": { + "type": "file", + "description": "Nextflow samplesheet or PEP project", + "pattern": "*.{yaml,yml,csv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + }, + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + }, + { + "format": { + "type": "string", + "description": "Extension of an output file" + } + } + ], + "output": { + "samplesheet_converted": [ + { + "${prefix}.${format}": { + "type": "file", + "description": "PEP project or samplesheet converted to csv file", + "ontologies": [] + } + } + ], + "versions_eido": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "eido": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "eido --version 2>&1 | sed 's/^.*eido //;s/ .*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "eido": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "eido --version 2>&1 | sed 's/^.*eido //;s/ .*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@rafalstepien"], + "maintainers": ["@rafalstepien", "@khoroshevskyi"] + } }, { - "name": "rnaseq", - "version": "3.26.0" - } - ] - }, - { - "name": "custom_matrixfilter", - "path": "modules/nf-core/custom/matrixfilter/meta.yml", - "type": "module", - "meta": { - "name": "custom_matrixfilter", - "description": "filter a matrix based on a minimum value and numbers of samples that must pass.", - "keywords": [ - "matrix", - "filter", - "abundance", - "na" - ], - "tools": [ - { - "matrixfilter": { - "description": "filter a matrix based on a minimum value and numbers of samples", - "tool_dev_url": "https://github.com/nf-core/modules/blob/master/modules/nf-core/custom/matrixfilter/main.nf", - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing information on matrix to be filtered, at a\nminimum an id. e.g. [ id:'test' ]\n" - } - }, - { - "abundance": { - "type": "file", - "description": "Raw TSV or CSV format abundance matrix with features (e.g.\ngenes) by row and observations (e.g. samples) by column. All rownames\nfrom the sample sheet should be present in the columns.\n", - "ontologies": [] - } - } - ], - [ - { - "samplesheet_meta": { - "type": "map", - "description": "Where samplesheet is provided, aroovy Map containing information on\nsample sheet, at a minimum an id. e.g. [ id:'test' ]\n" - } - }, - { - "samplesheet": { - "type": "file", - "description": "Optional CSV or TSV format sample sheet with sample metadata. If\nprovided this is used to infer minimum passing samples from group sizes\npresent (see grouping_variable), but also to validate matrix columns.\nIf not provided, all numeric columns are selected.\n", - "ontologies": [] - } - } - ] - ], - "output": { - "filtered": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing information on experiment.\ne.g. [ id:'test' ]\n" - } - }, - { - "*.filtered.tsv": { - "type": "file", - "description": "Filtered version of input matrix", - "pattern": "*.filtered.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "tests": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing information on experiment.\ne.g. [ id:'test' ]\n" - } - }, - { - "*.tests.tsv": { - "type": "file", - "description": "Boolean matrix with pass/ fail status for each test on each feature", - "pattern": "*.tests.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "thresholds": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing information on experiment.\ne.g. [ id:'test' ]\n" - } - }, - { - "*.thresholds.tsv": { - "type": "file", - "description": "Table of filtering thresholds applied in matrix filtering", - "pattern": "*.thresholds.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "session_info": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing information on experiment.\ne.g. [ id:'test' ]\n" - } - }, - { - "*R_sessionInfo.log": { - "type": "file", - "description": "Log file containing R session information", - "pattern": "*.log", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "topics": { - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@pinin4fjords" - ], - "maintainers": [ - "@pinin4fjords" - ] - }, - "pipelines": [ - { - "name": "differentialabundance", - "version": "1.5.0" - } - ] - }, - { - "name": "custom_multiqccustombiotype", - "path": "modules/nf-core/custom/multiqccustombiotype/meta.yml", - "type": "module", - "meta": { - "name": "custom_multiqccustombiotype", - "description": "Generate MultiQC-compatible biotype count summaries from featureCounts output", - "keywords": [ - "biotype", - "featurecounts", - "multiqc", - "rnaseq", - "qc" - ], - "tools": [ - { - "custom": { - "description": "Summarise featureCounts biotype assignments for MultiQC reporting", - "tool_dev_url": "https://github.com/nf-core/modules/blob/master/modules/nf-core/custom/multiqccustombiotype/main.nf", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "count": { - "type": "file", - "description": "featureCounts output count file", - "pattern": "*.featureCounts.txt", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\n" - } - }, - { - "header": { - "type": "file", - "description": "Header file for the biotype counts MultiQC table", - "pattern": "*.txt", - "ontologies": [] - } - } - ] - ], - "output": { - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\n" - } - }, - { - "*biotype_counts_mqc.tsv": { - "type": "file", - "description": "Biotype counts formatted for MultiQC. The process fails if the\nnumber of biotype rows exceeds the threshold passed via\n`ext.args = '--max_biotypes N'` (default 100), since MultiQC\ncannot render a bar plot with that many categories.\n", - "pattern": "*biotype_counts_mqc.tsv", - "ontologies": [] - } - } - ] - ], - "rrna": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\n" - } - }, - { - "*biotype_counts_rrna_mqc.tsv": { - "type": "file", - "description": "rRNA percentage for MultiQC general stats", - "pattern": "*biotype_counts_rrna_mqc.tsv", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "topics": { - "versions": [ - { - "versions.yml": { - "type": "string", - "description": "The name of the process" - } - } - ] - }, - "authors": [ - "@pinin4fjords" - ], - "maintainers": [ - "@pinin4fjords" - ] - }, - "pipelines": [ - { - "name": "rnaseq", - "version": "3.26.0" - } - ] - }, - { - "name": "custom_pcaclustering", - "path": "modules/nf-core/custom/pcaclustering/meta.yml", - "type": "module", - "meta": { - "name": "CUSTOM_PCACLUSTERING", - "description": "Performs KMeans or DBSCAN clustering on a sample-by-feature numeric matrix (e.g. principal components, embeddings)", - "keywords": [ - "clustering", - "kmeans", - "dbscan", - "pca", - "embeddings" - ], - "tools": [ - { - "scikit-learn": { - "description": "Machine learning library for clustering", - "homepage": "https://scikit-learn.org/", - "documentation": "https://scikit-learn.org/stable/modules/clustering.html", - "licence": [ - "BSD-3-Clause" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "features": { - "type": "file", - "description": "Tab-separated file whose first column is sample IDs (any column\nname) and remaining columns are numeric features (e.g. PLINK2 PCA\ncomponents with `FID` dropped, scikit-learn embeddings, etc.).\n", - "pattern": "*.{tsv,txt}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - { - "algorithm": { - "type": "string", - "description": "Clustering algorithm to use (kmeans or dbscan)" - } - }, - { - "n_clusters": { - "type": "integer", - "description": "Number of clusters for KMeans" - } - }, - { - "dbscan_eps": { - "type": "float", - "description": "Epsilon parameter for DBSCAN" - } - }, - { - "dbscan_min_samples": { - "type": "integer", - "description": "Minimum samples parameter for DBSCAN" - } - } - ], - "output": { - "clusters": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*.clusters.csv": { - "type": "file", - "description": "CSV file with sample_id and assigned cluster", - "pattern": "*.clusters.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "info": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*.clustering_info.json": { - "type": "file", - "description": "JSON file with clustering parameters and statistics", - "pattern": "*.clustering_info.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "topics": { - "versions": [ - { - "versions.yml": { - "type": "string", - "description": "The name of the process" - } - } - ] - }, - "authors": [ - "@dbaku42" - ], - "maintainers": [ - "@dbaku42" - ] - } - }, - { - "name": "custom_rsemmergecounts", - "path": "modules/nf-core/custom/rsemmergecounts/meta.yml", - "type": "module", - "meta": { - "name": "custom_rsemmergecounts", - "description": "Merge per-sample RSEM results into wide and long format TSV matrices", - "keywords": [ - "rsem", - "merge", - "counts", - "gene expression" - ], - "tools": [ - { - "custom": { - "description": "Custom module to merge RSEM gene and isoform count results across\nsamples into count/TPM matrices and long-format tables.\n", - "tool_dev_url": "https://github.com/nf-core/modules/blob/master/modules/nf-core/custom/rsemmergecounts/main.nf", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information. e.g. [ id:'all_samples' ].\n" - } - }, - { - "genes/*": { - "type": "file", - "description": "Collected RSEM gene-level results files across all samples.\n", - "pattern": "*.genes.results", - "ontologies": [] - } - } - ], - { - "isoforms/*": { - "type": "file", - "description": "Collected RSEM isoform-level results files across all samples.\n", - "pattern": "*.isoforms.results", - "ontologies": [] - } - } - ], - "output": { - "counts_gene": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information. e.g. [ id:'all_samples' ].\n" - } - }, - { - "${prefix}.gene_counts.tsv": { - "type": "file", - "description": "Wide-format gene-level count matrix (expected_count column from\nRSEM) with samples as columns.\n", - "pattern": "*.gene_counts.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "tpm_gene": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information. e.g. [ id:'all_samples' ].\n" - } - }, - { - "${prefix}.gene_tpm.tsv": { - "type": "file", - "description": "Wide-format gene-level TPM matrix with samples as columns.\n", - "pattern": "*.gene_tpm.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "counts_transcript": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information. e.g. [ id:'all_samples' ].\n" - } - }, - { - "${prefix}.transcript_counts.tsv": { - "type": "file", - "description": "Wide-format transcript-level count matrix (expected_count column\nfrom RSEM) with samples as columns.\n", - "pattern": "*.transcript_counts.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "tpm_transcript": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information. e.g. [ id:'all_samples' ].\n" - } - }, - { - "${prefix}.transcript_tpm.tsv": { - "type": "file", - "description": "Wide-format transcript-level TPM matrix with samples as columns.\n", - "pattern": "*.transcript_tpm.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "genes_long": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information. e.g. [ id:'all_samples' ].\n" - } - }, - { - "${prefix}.genes_long.tsv": { - "type": "file", - "description": "Long-format gene-level results with all RSEM fields and a\nsample_name column.\n", - "pattern": "*.genes_long.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "isoforms_long": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information. e.g. [ id:'all_samples' ].\n" - } - }, - { - "${prefix}.isoforms_long.tsv": { - "type": "file", - "description": "Long-format isoform-level results with all RSEM fields and a\nsample_name column.\n", - "pattern": "*.isoforms_long.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_sed": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "sed": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "sed --version 2>&1 | sed '1!d;s/^.*) //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "sed": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "sed --version 2>&1 | sed '1!d;s/^.*) //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@pinin4fjords" - ], - "maintainers": [ - "@pinin4fjords" - ] - }, - "pipelines": [ - { - "name": "rnaseq", - "version": "3.26.0" - } - ] - }, - { - "name": "custom_sratoolsncbisettings", - "path": "modules/nf-core/custom/sratoolsncbisettings/meta.yml", - "type": "module", - "meta": { - "name": "custom_sratoolsncbisettings", - "description": "Test for the presence of suitable NCBI settings or create them on the fly.", - "keywords": [ - "NCBI", - "settings", - "sra-tools", - "prefetch", - "fasterq-dump" - ], - "tools": [ - { - "sratools": { - "description": "SRA Toolkit and SDK from NCBI", - "homepage": "https://github.com/ncbi/sra-tools", - "documentation": "https://github.com/ncbi/sra-tools/wiki", - "tool_dev_url": "https://github.com/ncbi/sra-tools", - "licence": [ - "Public Domain" - ], - "identifier": "" - } - } - ], - "input": [ - { - "ids": { - "type": "string", - "description": "List of id settings" - } - } - ], - "output": { - "ncbi_settings": [ - { - "*.mkfg": { - "type": "file", - "description": "An NCBI user settings file.", - "pattern": "*.mkfg", - "ontologies": [] - } - } - ], - "versions_sratools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "sratools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "prefetch --version 2>&1 | grep -Eo '[0-9.]+'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "sratools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "prefetch --version 2>&1 | grep -Eo '[0-9.]+'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@Midnighter" - ], - "maintainers": [ - "@Midnighter" - ] - }, - "pipelines": [ - { - "name": "fetchngs", - "version": "1.12.0" - } - ] - }, - { - "name": "custom_summarisetelomereestimation", - "path": "modules/nf-core/custom/summarisetelomereestimation/meta.yml", - "type": "module", - "meta": { - "name": "custom_summarisetelomereestimation", - "description": "Normalise and combine telomere length and content estimates from telseq, telogator2, and telomerehunter into a unified summary", - "keywords": [ - "telomere", - "summary", - "telseq", - "telogator2", - "telomerehunter" - ], - "tools": [ - { - "pandas": { - "description": "Python Data Analysis Library", - "homepage": "https://pandas.pydata.org/", - "documentation": "https://pandas.pydata.org/docs/", - "licence": [ - "BSD-3-Clause" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "length_tsv": { - "type": "file", - "description": "TSV file from telseq or telogator2 with telomere length estimates", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - }, - { - "content_tsv": { - "type": "file", - "description": "Optional TSV file from telomerehunter with telomere content estimates", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - }, - { - "length_tool": { - "type": "string", - "description": "Which tool produced the length TSV ('telseq' or 'telogator2')" - } - } - ] - ], - "output": { - "summary": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*_telomere_summary.tsv": { - "type": "file", - "description": "Unified summary TSV with normalised telomere length (kb) and content metrics", - "pattern": "*_telomere_summary.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "YAML file containing versions of tools used in the module", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "topics": { - "versions": [ - { - "versions.yml": { - "type": "string", - "description": "The name of the process" - } - } - ] - }, - "authors": [ - "@pinin4fjords" - ], - "maintainers": [ - "@pinin4fjords" - ] - } - }, - { - "name": "custom_tabulartogseachip", - "path": "modules/nf-core/custom/tabulartogseachip/meta.yml", - "type": "module", - "meta": { - "name": "custom_tabulartogseachip", - "description": "Make a GSEA class file (.chip) from tabular inputs", - "keywords": [ - "gsea", - "chip", - "convert", - "tabular" - ], - "tools": [ - { - "custom": { - "description": "Make a GSEA annotation file (.chip) from tabular inputs", - "tool_dev_url": "https://github.com/nf-core/modules/blob/master/modules/nf-core/custom/tabulartogseachip/main.nf", - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing data information.\nThis can be used at the workflow level to pass optional parameters to the module.\n[id: 'test', ...]\n" - } - }, - { - "tabular": { - "type": "file", - "description": "Tabular (NOTE that for the moment it only works for TSV file) containing a column with the\nfeatures ids, and another column with the features symbols.\n", - "pattern": "*.{tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - [ - { - "id": { - "type": "string", - "description": "The name of the column containing feature ids" - } - }, - { - "symbol": { - "type": "string", - "description": "The name of the column containing feature symbols" - } - } - ] - ], - "output": { - "chip": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing metadata e.g. [ id:'test', ... ]" - } - }, - { - "*.chip": { - "type": "file", - "description": "A categorical class format file (.chip) as defined by the Broad\ndocumentation at\nhttps://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats\n", - "pattern": "*.chip", - "ontologies": [] - } - } - ] - ], - "versions_gawk": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gawk": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gawk --version 2>&1 | sed '1!d;s/^.*GNU Awk //; s/, .*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gawk": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gawk --version 2>&1 | sed '1!d;s/^.*GNU Awk //; s/, .*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@pinin4fjords", - "@suzannejin" - ], - "maintainers": [ - "@pinin4fjords" - ] - } - }, - { - "name": "custom_tabulartogseacls", - "path": "modules/nf-core/custom/tabulartogseacls/meta.yml", - "type": "module", - "meta": { - "name": "custom_tabulartogseacls", - "description": "Make a GSEA class file (.cls) from tabular inputs", - "keywords": [ - "gsea", - "cls", - "convert", - "tabular" - ], - "tools": [ - { - "custom": { - "description": "Make a GSEA class file (.cls) from tabular inputs", - "tool_dev_url": "https://github.com/nf-core/modules/blob/master/modules/nf-core/custom/tabulartogseacls/main.nf", - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing metadata including an id, the sample sheet column\nused to define groups, and optionally a separator to override defaults e.g. [\n id:'test', variable:'treatment', separator:',' ]. The way these values are\npassed to the associated module parameters is then defined via an ext.args\nspecification for the process from the workflow, like: ext.args = { [\n \"separator\": \"\\t\", \"variable\": \"$meta.variable\" ] } ('variable' is\ncompulsory here).\n" - } - }, - { - "samples": { - "type": "file", - "description": "Tabular (e.g. TSV/CSV) samples file with sample IDs by row and variables by column.", - "pattern": "*.{csv,tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - }, - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "output": { - "cls": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing metadata e.g. [ id:'test', variable:'treatment',\nseparator:',' ]\n" - } - }, - { - "*.cls": { - "type": "file", - "description": "A categorical class format file (.cls) as defined by the Broad\ndocumentation at\nhttps://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats\n", - "ontologies": [] - } - } - ] - ], - "versions_mawk": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "mawk": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "mawk --version | sed '1!d;s/mawk //;s/ .*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "mawk": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "mawk --version | sed '1!d;s/mawk //;s/ .*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@pinin4fjords" - ], - "maintainers": [ - "@pinin4fjords" - ] - }, - "pipelines": [ - { - "name": "differentialabundance", - "version": "1.5.0" - } - ] - }, - { - "name": "custom_tabulartogseagct", - "path": "modules/nf-core/custom/tabulartogseagct/meta.yml", - "type": "module", - "meta": { - "name": "custom_tabulartogseagct", - "description": "Convert a TSV or CSV with features by row and observations by column to a GCT format file as consumed by GSEA", - "keywords": [ - "gsea", - "gct", - "tabular" - ], - "tools": [ - { - "tabulartogseagct": { - "description": "Convert a TSV or CSV with features by row and observations by column to a GCT format file as consumed by GSEA", - "tool_dev_url": "https://github.com/nf-core/modules/blob/master/modules/nf-core/custom/tabulartogseagct/main.nf", - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing matrix information\ne.g. [ id:'test' ]\n" - } - }, - { - "tabular": { - "type": "file", - "description": "Tabular (e.g. TSV or CSV file) containing a numeric matrix with features (e.g. genes) by row and samples by column.", - "pattern": "*.{tsv,csv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - }, - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "output": { - "gct": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing matrix information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.gct": { - "type": "file", - "description": "GCT format version of input TSV", - "pattern": "*.{gct}", - "ontologies": [] - } - } - ] - ], - "versions_mawk": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "mawk": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "mawk --version | sed '1!d;s/mawk //;s/ .*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "mawk": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "mawk --version | sed '1!d;s/mawk //;s/ .*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@pinin4fjords" - ], - "maintainers": [ - "@pinin4fjords" - ] - }, - "pipelines": [ - { - "name": "differentialabundance", - "version": "1.5.0" - } - ] - }, - { - "name": "custom_tx2gene", - "path": "modules/nf-core/custom/tx2gene/meta.yml", - "type": "module", - "meta": { - "name": "custom_tx2gene", - "description": "Make a transcript/gene mapping from a GTF and cross-reference with transcript quantifications.", - "keywords": [ - "gene", - "gtf", - "pseudoalignment", - "rsem", - "transcript" - ], - "tools": [ - { - "custom": { - "description": "\"Custom module to create a transcript to gene mapping from a GTF and\ncheck it against transcript quantifications\"\n", - "tool_dev_url": "https://github.com/nf-core/modules/blob/master/modules/nf-core/custom/tx2gene/main.nf", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information related to the GTF file\ne.g. `[ id:'yeast' ]`\n" - } - }, - { - "gtf": { - "type": "file", - "description": "An annotation file of the reference genome in GTF format", - "pattern": "*.gtf", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing information related to the experiment as a whole\ne.g. `[ id:'SRP123456' ]`\n" - } - }, - { - "quants/*": { - "type": "file", - "description": "quants file" - } - } - ], - { - "quant_type": { - "type": "string", - "description": "Quantification type, 'kallisto', 'salmon', or 'rsem'" - } - }, - { - "id": { - "type": "string", - "description": "Gene ID attribute in the GTF file (default= gene_id)" - } - }, - { - "extra": { - "type": "string", - "description": "Extra gene attribute(s) in the GTF file, comma-separated for multiple (default= gene_name)" - } - } - ], - "output": { - "tx2gene": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information related to the GTF file\ne.g. `[ id:'yeast' ]`\n" - } - }, - { - "*tx2gene.tsv": { - "type": "file", - "description": "A transcript/ gene mapping table in TSV format", - "pattern": "*.tx2gene.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "YAML file containing versions of tools used in the module", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "topics": { - "versions": [ - { - "versions.yml": { - "type": "string", - "description": "The name of the process" - } + "name": "eido_validate", + "path": "modules/nf-core/eido/validate/meta.yml", + "type": "module", + "meta": { + "name": "eido_validate", + "description": "Validate samplesheet or PEP config against a schema", + "keywords": ["eido", "validate", "schema", "format", "pep"], + "tools": [ + { + "validate": { + "description": "Validate samplesheet or PEP config against a schema.", + "homepage": "http://eido.databio.org/en/latest/", + "documentation": "http://eido.databio.org/en/latest/", + "doi": "10.1093/gigascience/giab077", + "licence": ["BSD-2-Clause"], + "identifier": "biotools:eido-python-package" + } + } + ], + "input": [ + { + "samplesheet": { + "type": "file", + "description": "Samplesheet or PEP file to be validated", + "pattern": "*.{yaml,yml,csv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + }, + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + }, + { + "schema": { + "type": "file", + "description": "Schema that the samplesheet will be validated against", + "pattern": "*.{yaml,yml}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ], + "output": { + "log": [ + { + "*.log": { + "type": "file", + "description": "File containing validation log.", + "pattern": "*.log", + "ontologies": [] + } + } + ], + "versions_eido": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "eido": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "eido --version 2>&1 | sed 's/^.*eido //;s/ .*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "eido": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "eido --version 2>&1 | sed 's/^.*eido //;s/ .*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@rafalstepien"], + "maintainers": ["@rafalstepien", "@khoroshevskyi"] } - ] }, - "authors": [ - "@pinin4fjords" - ], - "maintainers": [ - "@pinin4fjords" - ] - }, - "pipelines": [ { - "name": "circrna", - "version": "dev" + "name": "eigenstratdatabasetools_eigenstratsnpcoverage", + "path": "modules/nf-core/eigenstratdatabasetools/eigenstratsnpcoverage/meta.yml", + "type": "module", + "meta": { + "name": "eigenstratdatabasetools_eigenstratsnpcoverage", + "description": "Provide the SNP coverage of each individual in an eigenstrat formatted dataset.", + "keywords": ["coverage", "eigenstrat", "eigenstratdatabasetools", "snp", "snps"], + "tools": [ + { + "eigenstratdatabasetools": { + "description": "A set of tools to compare and manipulate the contents of EingenStrat databases, and to calculate SNP coverage statistics in such databases.", + "documentation": "https://github.com/TCLamnidis/EigenStratDatabaseTools/README.md", + "tool_dev_url": "https://github.com/TCLamnidis/EigenStratDatabaseTools", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "geno": { + "type": "file", + "description": "An Eigenstrat formatted genotype file", + "pattern": "*.{geno}", + "ontologies": [] + } + }, + { + "snp": { + "type": "file", + "description": "An Eigenstrat formatted snp file", + "pattern": "*.{snp}", + "ontologies": [] + } + }, + { + "ind": { + "type": "file", + "description": "An Eigenstrat formatted individual file", + "pattern": "*.{ind}", + "ontologies": [] + } + } + ] + ], + "output": { + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "A TSV table with the number of covered SNPs per individual.", + "pattern": "*.{tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "json": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.json": { + "type": "file", + "description": "A json table with the number of covered SNPs per individual.", + "pattern": "*.{json}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "versions_eigenstratdatabasetools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "eigenstratdatabasetools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "eigenstrat_snp_coverage --version 2>&1 | sed 's/^.*eigenstrat_snp_coverage //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "eigenstratdatabasetools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "eigenstrat_snp_coverage --version 2>&1 | sed 's/^.*eigenstrat_snp_coverage //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@TCLamnidis"], + "maintainers": ["@TCLamnidis"] + } }, { - "name": "riboseq", - "version": "1.2.0" + "name": "eklipse", + "path": "modules/nf-core/eklipse/meta.yml", + "type": "module", + "meta": { + "name": "eklipse", + "description": "tool for detection and quantification of large mtDNA rearrangements.", + "keywords": ["eklipse", "mitochondria", "mtDNA", "circos", "deletion", "SV"], + "tools": [ + { + "eklipse": { + "description": "tool for detection and quantification of large mtDNA rearrangements.", + "homepage": "https://github.com/dooguypapua/eKLIPse/tree/master", + "documentation": "https://github.com/dooguypapua/eKLIPse/tree/master", + "tool_dev_url": "https://github.com/dooguypapua/eKLIPse/tree/master", + "doi": "10.1038/s41436-018-0350-8", + "licence": ["GNU General Public v3 or later (GPL v3+)"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "MT BAM/SAM file", + "pattern": "*.{bam,sam}", + "ontologies": [] + } + }, + { + "bai": { + "type": "file", + "description": "MT BAM/SAM index file", + "pattern": "*.{bai,sai}", + "ontologies": [] + } + } + ], + { + "ref_gb": { + "type": "file", + "description": "mtDNA reference genome in Genbank format, optional if empty NC_012920.1.gb will be used", + "pattern": "*.{gb}", + "ontologies": [] + } + } + ], + "output": { + "deletions": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*deletions.csv": { + "type": "file", + "description": "csv file with deletion information", + "pattern": "*deletions.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "genes": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*genes.csv": { + "type": "file", + "description": "csv file with gene information", + "pattern": "*genes.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "circos": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.png": { + "type": "file", + "description": "png file with circos plot of mt", + "pattern": "*.{png}", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@Lucpen"], + "maintainers": ["@Lucpen"] + } }, { - "name": "rnaseq", - "version": "3.26.0" - } - ] - }, - { - "name": "cutadapt", - "path": "modules/nf-core/cutadapt/meta.yml", - "type": "module", - "meta": { - "name": "cutadapt", - "description": "Removes adapter sequences from sequencing reads", - "keywords": [ - "adapter", - "primers", - "poly-A tails", - "trimming", - "fastq" - ], - "tools": [ - { - "cutadapt": { - "description": "Cutadapt finds and removes adapter sequences, primers, poly-A tails\nand other types of unwanted sequence from your high-throughput sequencing reads.\n", - "homepage": "https://cutadapt.readthedocs.io/en/stable/index.html", - "documentation": "https://github.com/marcelm/cutadapt", - "doi": "10.14806/ej.17.1.200", - "licence": [ - "MIT" - ], - "identifier": "biotools:cutadapt" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", - "pattern": "*.{fq,fastq,fq.gz,fastq.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } + "name": "elprep_fastatoelfasta", + "path": "modules/nf-core/elprep/fastatoelfasta/meta.yml", + "type": "module", + "meta": { + "name": "elprep_fastatoelfasta", + "description": "Convert a file in FASTA format to the ELFASTA format", + "keywords": ["fasta", "elfasta", "elprep"], + "tools": [ + { + "elprep": { + "description": "elPrep is a high-performance tool for preparing .sam/.bam files for variant calling in sequencing pipelines. It can be used as a drop-in replacement for SAMtools/Picard/GATK4.", + "homepage": "https://github.com/ExaScience/elprep", + "documentation": "https://github.com/ExaScience/elprep", + "tool_dev_url": "https://github.com/ExaScience/elprep", + "doi": "10.1371/journal.pone.0244471", + "licence": ["AGPL v3"], + "identifier": "biotools:elprep" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA file", + "pattern": "*.{fasta,fa,fna}", + "ontologies": [] + } + } + ] + ], + "output": { + "elfasta": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n", + "pattern": "*.elfasta" + } + }, + { + "*.elfasta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n", + "pattern": "*.elfasta" + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n", + "pattern": "*.elfasta" + } + }, + { + "logs/elprep/elprep*": { + "type": "file", + "description": "ELFasta log file", + "pattern": "*.log", + "ontologies": [] + } + } + ] + ], + "versions_elprep": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "elprep": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "elprep 2>&1 | sed -n '2s/^.*version //;s/ compiled.*$//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "elprep": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "elprep 2>&1 | sed -n '2s/^.*version //;s/ compiled.*$//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@nvnieuwk"], + "maintainers": ["@nvnieuwk"] } - ] - ], - "output": { - "reads": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.trim.fastq.gz": { - "type": "file", - "description": "The trimmed/modified fastq reads", - "pattern": "*fastq.gz", - "ontologies": [ + }, + { + "name": "elprep_filter", + "path": "modules/nf-core/elprep/filter/meta.yml", + "type": "module", + "meta": { + "name": "elprep_filter", + "description": "Filter, sort and markdup sam/bam files, with optional BQSR and variant calling.", + "keywords": ["sort", "bam", "sam", "filter", "variant calling"], + "tools": [ + { + "elprep": { + "description": "elPrep is a high-performance tool for preparing .sam/.bam files for variant calling in sequencing pipelines. It can be used as a drop-in replacement for SAMtools/Picard/GATK4.", + "homepage": "https://github.com/ExaScience/elprep", + "documentation": "https://github.com/ExaScience/elprep", + "tool_dev_url": "https://github.com/ExaScience/elprep", + "doi": "10.1371/journal.pone.0244471", + "licence": ["AGPL v3"], + "identifier": "biotools:elprep" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "Input SAM/BAM file", + "pattern": "*.{bam,sam}", + "ontologies": [] + } + }, + { + "bai": { + "type": "file", + "description": "Input BAM file index", + "pattern": "*.bai", + "ontologies": [] + } + }, + { + "target_regions_bed": { + "type": "file", + "description": "Optional BED file containing target regions for BQSR and variant calling.", + "pattern": "*.bed", + "ontologies": [] + } + }, + { + "filter_regions_bed": { + "type": "file", + "description": "Optional BED file containing regions to filter.", + "pattern": "*.bed", + "ontologies": [] + } + }, + { + "intermediate_bqsr_tables": { + "type": "file", + "description": "Optional list of BQSR tables, used when parsing files created by `elprep split`", + "pattern": "*.table", + "ontologies": [] + } + }, + { + "recall_file": { + "type": "file", + "description": "Recall file with intermediate results for bqsr", + "pattern": "*.recall", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reference_sequences": { + "type": "file", + "description": "Optional SAM header to replace existing header.", + "pattern": "*.sam", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reference_elfasta": { + "type": "file", + "description": "Elfasta file, required for BQSR and variant calling.", + "pattern": "*.elfasta", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "known_sites_elsites": { + "type": "file", + "description": "Optional elsites file containing known SNPs for BQSR.", + "pattern": "*.elsites", + "ontologies": [] + } + } + ], + { + "run_haplotypecaller": { + "type": "boolean", + "description": "Run variant calling on the input files. Needed to generate gvcf output." + } + }, + { + "run_bqsr": { + "type": "boolean", + "description": "Run BQSR on the input files. Needed to generate recall metrics." + } + }, + { + "bqsr_tables_only": { + "type": "boolean", + "description": "Write intermediate BQSR tables, used when parsing files created by `elprep split`." + } + }, { - "edam": "http://edamontology.org/format_1930" + "get_activity_profile": { + "type": "boolean", + "description": "Get the activity profile calculated by the haplotypecaller to the given file in IGV format." + } }, { - "edam": "http://edamontology.org/format_3989" + "get_assembly_regions": { + "type": "boolean", + "description": "Get the assembly regions calculated by haplotypecaller to the specified file in IGV format." + } } - ] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.log": { - "type": "file", - "description": "cutadapt log file", - "pattern": "*cutadapt.log", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2330" - } - ] - } - } - ] - ], - "versions_cutadapt": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cutadapt": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cutadapt --version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cutadapt": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cutadapt --version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{bam,sam}": { + "type": "file", + "description": "BAM/SAM file", + "pattern": "*.{bam,sam}", + "ontologies": [] + } + } + ] + ], + "logs": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "Log file", + "pattern": "elprep-*.log", + "ontologies": [] + } + } + ] + ], + "metrics": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.metrics.txt": { + "type": "file", + "description": "Metrics file", + "pattern": "*.{metrics.txt}", + "ontologies": [] + } + } + ] + ], + "recall": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.recall": { + "type": "file", + "description": "Recall file", + "pattern": "*.{recall}", + "ontologies": [] + } + } + ] + ], + "gvcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "VCF file", + "pattern": "*.{vcf.gz}", + "ontologies": [] + } + } + ] + ], + "table": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.table": { + "type": "file", + "description": "Table", + "pattern": "*.{table}", + "ontologies": [] + } + } + ] + ], + "activity_profile": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.activity_profile.igv": { + "type": "file", + "description": "Activity profile", + "pattern": "*.{activity_profile.igv}", + "ontologies": [] + } + } + ] + ], + "assembly_regions": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.assembly_regions.igv": { + "type": "file", + "description": "Assembly regions", + "pattern": "*.{assembly_regions.igv}", + "ontologies": [] + } + } + ] + ], + "versions_elprep": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "elprep": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "elprep 2>&1 | sed -n '2s/^.*version //;s/ compiled.*$//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "elprep": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "elprep 2>&1 | sed -n '2s/^.*version //;s/ compiled.*$//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@matthdsm"], + "maintainers": ["@matthdsm"] + } }, - "authors": [ - "@drpatelh", - "@kevinmenden" - ], - "maintainers": [ - "@drpatelh", - "@kevinmenden", - "@vagkaratzas" - ] - }, - "pipelines": [ { - "name": "ampliseq", - "version": "2.17.0" + "name": "elprep_merge", + "path": "modules/nf-core/elprep/merge/meta.yml", + "type": "module", + "meta": { + "name": "elprep_merge", + "description": "Merge split bam/sam chunks in one file", + "keywords": ["bam", "sam", "merge"], + "tools": [ + { + "elprep": { + "description": "elPrep is a high-performance tool for preparing .sam/.bam files for variant calling in sequencing pipelines. It can be used as a drop-in replacement for SAMtools/Picard/GATK4.", + "homepage": "https://github.com/ExaScience/elprep", + "documentation": "https://github.com/ExaScience/elprep", + "tool_dev_url": "https://github.com/ExaScience/elprep", + "doi": "10.1371/journal.pone.0244471", + "licence": ["AGPL v3"], + "identifier": "biotools:elprep" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "List of BAM/SAM chunks to merge", + "pattern": "*.{bam,sam}", + "ontologies": [] + } + } + ] + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "output/**.{bam,sam}": { + "type": "file", + "description": "Merged BAM/SAM file", + "pattern": "*.{bam,sam}", + "ontologies": [] + } + } + ] + ], + "versions_elprep": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "elprep": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "elprep 2>&1 | sed -n '2s/^.*version //;s/ compiled.*$//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "elprep": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "elprep 2>&1 | sed -n '2s/^.*version //;s/ compiled.*$//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@matthdsm"], + "maintainers": ["@matthdsm"] + } }, { - "name": "crisprseq", - "version": "2.3.0" + "name": "elprep_split", + "path": "modules/nf-core/elprep/split/meta.yml", + "type": "module", + "meta": { + "name": "elprep_split", + "description": "Split bam file into manageable chunks", + "keywords": ["bam", "split by chromosome", "chunk"], + "tools": [ + { + "elprep": { + "description": "elPrep is a high-performance tool for preparing .sam/.bam files for variant calling in sequencing pipelines. It can be used as a drop-in replacement for SAMtools/Picard/GATK4.", + "homepage": "https://github.com/ExaScience/elprep", + "documentation": "https://github.com/ExaScience/elprep", + "tool_dev_url": "https://github.com/ExaScience/elprep", + "doi": "10.1371/journal.pone.0244471", + "licence": ["AGPL v3"], + "identifier": "biotools:elprep" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "List of BAM/SAM files", + "pattern": "*.{bam,sam}", + "ontologies": [] + } + } + ] + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "output/**.{bam,sam}": { + "type": "file", + "description": "List of split BAM/SAM files", + "pattern": "*.{bam,sam}", + "ontologies": [] + } + } + ] + ], + "versions_elprep": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "elprep": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "elprep 2>&1 | sed -n '2s/^.*version //;s/ compiled.*$//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "elprep": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "elprep 2>&1 | sed -n '2s/^.*version //;s/ compiled.*$//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@matthdsm"], + "maintainers": ["@matthdsm"] + } }, { - "name": "evexplorer", - "version": "dev" + "name": "emboss_cons", + "path": "modules/nf-core/emboss/cons/meta.yml", + "type": "module", + "meta": { + "name": "emboss_cons", + "description": "cons calculates a consensus sequence from a multiple sequence alignment. To obtain the consensus, the sequence weights and a scoring matrix are used to calculate a score for each amino acid residue or nucleotide at each position in the alignment.", + "keywords": ["emboss", "consensus", "fasta", "multiple sequence alignment", "MSA"], + "tools": [ + { + "emboss": { + "description": "The European Molecular Biology Open Software Suite", + "homepage": "https://www.ebi.ac.uk/Tools/sfc/emboss_seqret/", + "documentation": "https://emboss.bioinformatics.nl/cgi-bin/emboss/help/seqret", + "tool_dev_url": "http://emboss.open-bio.org/", + "doi": "10.1016/s0168-9525(00)02024-2 ", + "licence": ["GPL"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Multiple sequence alignment (unzipped)", + "pattern": "*.{fasta,fa,fas,fsa,seq,mpfa,aln,clustal,clw,msf,phy,phylip,stockholm,sto,msf,afa,afa,a}", + "ontologies": [] + } + } + ] + ], + "output": { + "consensus": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fa": { + "type": "file", + "description": "Consensus sequence calculated from multiple sequence alignment", + "pattern": "*.fa", + "ontologies": [] + } + } + ] + ], + "versions_emboss": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "emboss": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cons -version 2>&1 | sed \"s/EMBOSS://\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "emboss": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cons -version 2>&1 | sed \"s/EMBOSS://\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@Joon-Klaps"], + "maintainers": ["@Joon-Klaps"] + } }, { - "name": "hicar", - "version": "1.0.0" + "name": "emboss_revseq", + "path": "modules/nf-core/emboss/revseq/meta.yml", + "type": "module", + "meta": { + "name": "emboss_revseq", + "description": "the revseq program from emboss reverse complements a nucleotide sequence", + "keywords": ["nucleotides", "reverse complement", "sequences"], + "tools": [ + { + "emboss": { + "description": "The European Molecular Biology Open Software Suite", + "homepage": "https://www.ebi.ac.uk/Tools/sfc/emboss_seqret/", + "documentation": "https://emboss.bioinformatics.nl/cgi-bin/emboss/help/seqret", + "tool_dev_url": "http://emboss.open-bio.org/", + "doi": "10.1016/s0168-9525(00)02024-2 ", + "licence": ["GPL"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "sequences": { + "type": "file", + "description": "Input sequences", + "pattern": "*.{fasta,fna,fa,fst,aln,phy}", + "ontologies": [] + } + } + ] + ], + "output": { + "revseq": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.${sequences.name - ~/.*\\./}": { + "type": "file", + "description": "File with reverse complemented sequences", + "pattern": "*.{fasta,fna,fa,fst,aln,phy}", + "ontologies": [] + } + } + ] + ], + "versions_emboss": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "emboss": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "revseq -version 2>&1 | sed 's/EMBOSS://'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "emboss": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "revseq -version 2>&1 | sed 's/EMBOSS://'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@erikrikarddaniel"], + "maintainers": ["@erikrikarddaniel"] + } }, { - "name": "marsseq", - "version": "1.0.3" + "name": "emboss_seqret", + "path": "modules/nf-core/emboss/seqret/meta.yml", + "type": "module", + "meta": { + "name": "emboss_seqret", + "description": "Reads in one or more sequences, converts, filters, or transforms them and writes them out again", + "keywords": ["emboss", "gff", "embl", "genbank", "fasta", "convert", "swissprot"], + "tools": [ + { + "emboss": { + "description": "The European Molecular Biology Open Software Suite", + "homepage": "https://www.ebi.ac.uk/Tools/sfc/emboss_seqret/", + "documentation": "https://emboss.bioinformatics.nl/cgi-bin/emboss/help/seqret", + "tool_dev_url": "http://emboss.open-bio.org/", + "doi": "10.1016/s0168-9525(00)02024-2 ", + "licence": ["GPL"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "sequence": { + "type": "file", + "description": "Input sequence query", + "pattern": "*.{gff,em,gb,refseq,pir,swiss,sw,txt}", + "ontologies": [] + } + } + ], + { + "out_ext": { + "type": "string", + "description": "File extension of the output file. Unless otherwise set by a flag in `ext.args`, the extension dictates the output file format." + } + } + ], + "output": { + "outseq": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.${out_ext}": { + "type": "file", + "description": "Converted sequence file", + "pattern": "*", + "ontologies": [] + } + } + ] + ], + "versions_emboss": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "emboss": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "revseq -version 2>&1 | sed 's/EMBOSS://'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "emboss": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "revseq -version 2>&1 | sed 's/EMBOSS://'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@MillironX"], + "maintainers": ["@MillironX"] + } }, { - "name": "panoramaseq", - "version": "dev" + "name": "emmtyper", + "path": "modules/nf-core/emmtyper/meta.yml", + "type": "module", + "meta": { + "name": "emmtyper", + "description": "EMM typing of Streptococcus pyogenes assemblies", + "keywords": ["fasta", "Streptococcus pyogenes", "typing"], + "tools": [ + { + "emmtyper": { + "description": "Streptococcus pyogenes in silico EMM typer", + "homepage": "https://github.com/MDU-PHL/emmtyper", + "documentation": "https://github.com/MDU-PHL/emmtyper", + "tool_dev_url": "https://github.com/MDU-PHL/emmtyper", + "licence": ["GNU General Public v3 (GPL v3)"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA assembly file", + "pattern": "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}", + "ontologies": [] + } + } + ] + ], + "output": { + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "Tab-delimited result file", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_emmtyper": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "emmtyper": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python -c \"import emmtyper; print(emmtyper.__version__)\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "emmtyper": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python -c \"import emmtyper; print(emmtyper.__version__)\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@rpetit3"], + "maintainers": ["@rpetit3"] + } }, { - "name": "riboseq", - "version": "1.2.0" + "name": "emu_abundance", + "path": "modules/nf-core/emu/abundance/meta.yml", + "type": "module", + "meta": { + "name": "emu_abundance", + "description": "A taxonomic profiler for metagenomic 16S data optimized for error prone long reads.", + "keywords": ["metagenomics", "16S", "nanopore"], + "tools": [ + { + "emu": { + "description": "Emu is a relative abundance estimator for 16s genomic data.", + "homepage": "https://gitlab.com/treangenlab/emu", + "documentation": "https://gitlab.com/treangenlab/emu", + "doi": "10.1038/s41592-022-01520-4", + "licence": ["MIT"], + "identifier": "biotools:emu" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "fastq.gz file containing 16S metagenomics data", + "pattern": "*.{fastq.gz}", + "ontologies": [] + } + } + ], + { + "db": { + "type": "directory", + "description": "Emu database" + } + } + ], + "output": { + "report": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}_rel-abundance.tsv": { + "type": "file", + "description": "Output file containing relative abundances for reads", + "pattern": "*{.tsv}" + } + } + ] + ], + "assignment_report": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}_read-assignment-distributions.tsv": { + "type": "file", + "description": "Output file with read assignment distributions.", + "pattern": "*{.tsv}" + } + } + ] + ], + "samfile": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}_emu_alignments.sam": { + "type": "file", + "description": "Sam alignment file", + "pattern": "*{.sam}" + } + } + ] + ], + "unclassified": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}_unclassified_mapped.*": { + "type": "file", + "description": "Output file with unclassified sequences", + "pattern": "*{.fasta,.fastq}" + } + } + ] + ], + "unmapped": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}_unmapped.*": { + "type": "file", + "description": "Output file with unmapped sequences", + "pattern": "*{.fasta,.fastq}" + } + } + ] + ], + "versions_emu": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "emu": { + "type": "string", + "description": "The tool name" + } + }, + { + "emu --version 2>&1 | sed \"s/^.*emu //; s/Using.*$//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "emu": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "emu --version 2>&1 | sed \"s/^.*emu //; s/Using.*$//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@fwa93", "@sofstam"] + } }, { - "name": "viralrecon", - "version": "3.0.0" - } - ] - }, - { - "name": "cutesv", - "path": "modules/nf-core/cutesv/meta.yml", - "type": "module", - "meta": { - "name": "cutesv", - "description": "structural-variant calling with cutesv", - "keywords": [ - "cutesv", - "structural-variant calling", - "sv" - ], - "tools": [ - { - "cutesv": { - "description": "a clustering-and-refinement method to analyze the signatures to implement sensitive SV detection.", - "homepage": "https://github.com/tjiangHIT/cuteSV", - "documentation": "https://github.com/tjiangHIT/cuteSV#readme", - "tool_dev_url": "https://github.com/tjiangHIT/cuteSV", - "licence": [ - "MIT" - ], - "identifier": "biotools:cuteSV" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file", - "pattern": "*.bam", - "ontologies": [] - } - }, - { - "bai": { - "type": "file", - "description": "Index of BAM file", - "pattern": "*.bai", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'fasta' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference database in FASTA format\n", - "ontologies": [] - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.vcf": { - "type": "file", - "description": "VCF file containing called variants from CuteSV", - "pattern": "*.vcf", - "ontologies": [] - } - } - ] - ], - "versions_cutesv": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cuteSV": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cuteSV --version 2>&1 | sed 's/cuteSV //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cuteSV": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cuteSV --version 2>&1 | sed 's/cuteSV //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@christopher-hakkaart", - "@yuukiiwa" - ], - "maintainers": [ - "@christopher-hakkaart", - "@yuukiiwa" - ] - } - }, - { - "name": "damageprofiler", - "path": "modules/nf-core/damageprofiler/meta.yml", - "type": "module", - "meta": { - "name": "damageprofiler", - "description": "A Java based tool to determine damage patterns on ancient DNA as a replacement for mapDamage", - "keywords": [ - "damage", - "deamination", - "miscoding lesions", - "C to T", - "ancient DNA", - "aDNA", - "palaeogenomics", - "archaeogenomics", - "palaeogenetics", - "archaeogenetics" - ], - "tools": [ - { - "damageprofiler": { - "description": "A Java based tool to determine damage patterns on ancient DNA as a replacement for mapDamage", - "homepage": "https://github.com/Integrative-Transcriptomics/DamageProfiler", - "documentation": "https://damageprofiler.readthedocs.io/", - "tool_dev_url": "https://github.com/Integrative-Transcriptomics/DamageProfiler", - "doi": "10.1093/bioinformatics/btab190", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:damageprofiler" + "name": "endorspy", + "path": "modules/nf-core/endorspy/meta.yml", + "type": "module", + "meta": { + "name": "endorspy", + "description": "endorS.py calculates endogenous DNA from samtools flagstat files and print to screen", + "keywords": ["endogenous DNA", "ancient DNA", "percent on target", "statistics"], + "tools": [ + { + "endorspy": { + "description": "endorS.py calculates percent on target and/or clonality from samtools flagstat files and print to screen", + "homepage": "https://github.com/aidaanva/endorS.py", + "documentation": "https://github.com/aidaanva/endorS.py", + "tool_dev_url": "https://github.com/aidaanva/endorS.py", + "doi": "10.7717/peerj.10947", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "stats_raw": { + "type": "file", + "description": "output of samtools flagstat in a txt file, assumes no quality filtering nor duplicate removal performed", + "ontologies": [] + } + }, + { + "stats_qualityfiltered": { + "type": "file", + "description": "output of samtools flagstat in a txt file, assumes some form of quality or length filtering has been performed, must be provided with at least one of the options -r or -d", + "ontologies": [] + } + }, + { + "stats_deduplicated": { + "type": "file", + "description": "output of samtools flagstat in a txt file, whereby duplicate removal has been performed on the input reads", + "ontologies": [] + } + } + ] + ], + "output": { + "json": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_mqc.json": { + "type": "file", + "description": "file with the endogenous DNA calculation tailored for multiQC", + "pattern": "*_mqc.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "versions_endorspy": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "endorspy": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "endorspy --version 2>&1 | sed 's/^endorS.py //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "endorspy": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "endorspy --version 2>&1 | sed 's/^endorS.py //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@aidaanva"], + "maintainers": ["@aidaanva"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + }, + { + "name": "ensemblvep_download", + "path": "modules/nf-core/ensemblvep/download/meta.yml", + "type": "module", + "meta": { + "name": "ensemblvep_download", + "description": "Ensembl Variant Effect Predictor (VEP). The cache downloading options are controlled through `task.ext.args`.", + "keywords": ["annotation", "cache", "download"], + "tools": [ + { + "ensemblvep": { + "description": "VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs\nor structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.\n", + "homepage": "https://www.ensembl.org/info/docs/tools/vep/index.html", + "documentation": "https://www.ensembl.org/info/docs/tools/vep/script/index.html", + "licence": ["Apache-2.0"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "assembly": { + "type": "string", + "description": "Genome assembly\n" + } + }, + { + "species": { + "type": "string", + "description": "Specie\n" + } + }, + { + "cache_version": { + "type": "string", + "description": "cache version\n" + } + } + ], + { + "preflight_check": { + "type": "boolean", + "description": "Whether to check that the expected cache file is listed in the Ensembl CHECKSUMS file before downloading\n" + } + } + ], + "output": { + "cache": [ + [ + { + "meta": { + "type": "file", + "description": "cache", + "pattern": "*", + "ontologies": [] + } + }, + { + "prefix": { + "type": "file", + "description": "cache", + "pattern": "*", + "ontologies": [] + } + } + ] + ], + "versions_ensemblvep": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "ensemblvep": { + "type": "string", + "description": "The tool name" + } + }, + { + "vep --help | sed -n '/ensembl-vep/s/.*: //p'": { + "type": "eval", + "description": "The command used to generate the version of the tool" + } + } + ] + ], + "versions_perlmathcdf": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "perl-math-cdf": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "perl -MMath::CDF -e 'print \\$Math::CDF::VERSION'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "ensemblvep": { + "type": "string", + "description": "The tool name" + } + }, + { + "vep --help | sed -n '/ensembl-vep/s/.*: //p'": { + "type": "eval", + "description": "The command used to generate the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "perl-math-cdf": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "perl -MMath::CDF -e 'print \\$Math::CDF::VERSION'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@maxulysse"], + "maintainers": ["@maxulysse"] }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - }, - { - "edam": "http://edamontology.org/format_3462" - }, - { - "edam": "http://edamontology.org/format_2573" - } - ] - } - } - ], - { - "fasta": { - "type": "file", - "description": "OPTIONAL FASTA reference file", - "pattern": "*.{fasta,fna,fa}", - "ontologies": [ + "pipelines": [ { - "edam": "http://edamontology.org/format_1332" - } - ] - } - }, - { - "fai": { - "type": "file", - "description": "OPTIONAL FASTA index file from samtools faidx", - "pattern": "*.{fai}", - "ontologies": [ + "name": "pacsomatic", + "version": "dev" + }, + { + "name": "rnadnavar", + "version": "dev" + }, { - "edam": "http://edamontology.org/format_1332" + "name": "rnavar", + "version": "1.2.3" + }, + { + "name": "sarek", + "version": "3.8.1" + }, + { + "name": "tumourevo", + "version": "dev" } - ] - } - }, - { - "specieslist": { - "type": "file", - "description": "OPTIONAL text file with list of target reference headers", - "pattern": "*.{txt}", - "ontologies": [] - } - } - ], - "output": { - "results": [ - [ - { - "meta": { - "type": "directory", - "description": "DamageProfiler results directory", - "pattern": "*/*" - } - }, - { - "${prefix}": { - "type": "directory", - "description": "DamageProfiler results directory", - "pattern": "*/*" - } - } - ] - ], - "versions_damageprofiler": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "damageprofiler": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "damageprofiler -v | sed 's/^DamageProfiler v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "damageprofiler": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "damageprofiler -v | sed 's/^DamageProfiler v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } ] - ] - }, - "authors": [ - "@jfy133" - ], - "maintainers": [ - "@jfy133" - ] - }, - "pipelines": [ - { - "name": "coproid", - "version": "2.0.1" - } - ] - }, - { - "name": "dastool_dastool", - "path": "modules/nf-core/dastool/dastool/meta.yml", - "type": "module", - "meta": { - "name": "dastool_dastool", - "description": "DAS Tool binning step.", - "keywords": [ - "binning", - "das tool", - "table", - "de novo", - "bins", - "contigs", - "assembly", - "das_tool" - ], - "tools": [ - { - "dastool": { - "description": "DAS Tool is an automated method that integrates the results\nof a flexible number of binning algorithms to calculate an optimized, non-redundant\nset of bins from a single assembly.\n", - "homepage": "https://github.com/cmks/DAS_Tool", - "documentation": "https://github.com/cmks/DAS_Tool", - "tool_dev_url": "https://github.com/cmks/DAS_Tool", - "doi": "10.1038/s41564-018-0171-1", - "licence": [ - "BSD" - ], - "identifier": "biotools:dastool" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "contigs": { - "type": "file", - "description": "fasta file", - "pattern": "*.{fa.gz,fas.gz,fasta.gz}", - "ontologies": [] - } - }, - { - "bins": { - "type": "file", - "description": "FastaToContig2Bin tabular file generated with dastool/fastatocontig2bin", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } + }, + { + "name": "ensemblvep_filtervep", + "path": "modules/nf-core/ensemblvep/filtervep/meta.yml", + "type": "module", + "meta": { + "name": "ensemblvep_filtervep", + "description": "Filter variants based on Ensembl Variant Effect Predictor (VEP) annotations.", + "keywords": ["annotation", "vcf", "tab", "filter"], + "tools": [ + { + "ensemblvep": { + "description": "VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs\nor structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.\n", + "homepage": "https://www.ensembl.org/info/docs/tools/vep/index.html", + "documentation": "https://www.ensembl.org/info/docs/tools/vep/script/index.html", + "licence": ["Apache-2.0"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "input": { + "type": "file", + "description": "VCF/TAB file annotated with vep", + "pattern": "*.{vcf,tab,tsv,txt}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + { + "feature_file": { + "type": "file", + "description": "File containing features on separate lines. To be used with --filter option.", + "ontologies": [] + } + } + ], + "output": { + "output": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.${extension}": { + "type": "file", + "description": "VCF/TAB file", + "pattern": "*.{vcf,tab,txt,tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_ensemblvep": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "ensemblvep": { + "type": "string", + "description": "The tool name" + } + }, + { + "vep --help | sed -n '/ensembl-vep/s/.*: //p'": { + "type": "eval", + "description": "The command used to generate the version of the tool" + } + } + ] + ], + "versions_perlmathcdf": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "perl-math-cdf": { + "type": "string", + "description": "The tool name" + } + }, + { + "perl -MMath::CDF -e 'print \\\\$Math::CDF::VERSION'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "ensemblvep": { + "type": "string", + "description": "The tool name" + } + }, + { + "vep --help | sed -n '/ensembl-vep/s/.*: //p'": { + "type": "eval", + "description": "The command used to generate the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "perl-math-cdf": { + "type": "string", + "description": "The tool name" + } + }, + { + "perl -MMath::CDF -e 'print \\\\$Math::CDF::VERSION'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@ramprasadn"], + "maintainers": ["@ramprasadn"] }, - { - "proteins": { - "type": "file", - "description": "Predicted proteins in prodigal fasta format (>scaffoldID_geneNo)", - "pattern": "*.{fa.gz,fas.gz,fasta.gz}", - "ontologies": [] - } - } - ], - { - "db_directory": { - "type": "file", - "description": "(optional) Directory of single copy gene database.", - "ontologies": [] - } - } - ], - "output": { - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.log": { - "type": "file", - "description": "Log file of the run", - "pattern": "*.log", - "ontologies": [] - } - } - ] - ], - "summary": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_summary.tsv": { - "type": "file", - "description": "Summary of output bins including quality and completeness estimates", - "pattern": "*summary.txt", - "ontologies": [] - } - } - ] - ], - "contig2bin": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_DASTool_contig2bin.tsv": { - "type": "file", - "description": "Scaffolds to bin file of output bins", - "pattern": "*.contig2bin.txt", - "ontologies": [] - } - } - ] - ], - "eval": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.eval": { - "type": "file", - "description": "Quality and completeness estimates of input bin sets", - "pattern": "*.eval", - "ontologies": [] - } - } - ] - ], - "bins": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_DASTool_bins/*.fa": { - "type": "file", - "description": "Final refined bins in fasta format", - "pattern": "*.fa", - "ontologies": [] - } - } - ] - ], - "pdfs": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.pdf": { - "type": "file", - "description": "Plots showing the amount of high quality bins and score distribution of bins per method", - "pattern": "*.pdf", - "ontologies": [] - } - } - ] - ], - "candidates_faa": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.candidates.faa": { - "type": "file", - "description": "FAA file", - "pattern": "*.candidates.faa", - "ontologies": [] - } - } - ] - ], - "fasta_proteins": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_proteins.faa": { - "type": "file", - "description": "Output from prodigal if not already supplied", - "pattern": "*_proteins.faa", - "ontologies": [] - } - } - ] - ], - "fasta_archaea_scg": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.archaea.scg": { - "type": "file", - "description": "Results of archaeal single-copy-gene prediction", - "pattern": "*.archaea.scg", - "ontologies": [] - } - } + "pipelines": [ + { + "name": "raredisease", + "version": "3.0.0" + } ] - ], - "fasta_bacteria_scg": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bacteria.scg": { - "type": "file", - "description": "Results of bacterial single-copy-gene prediction", - "pattern": "*.bacteria.scg", - "ontologies": [] - } - } - ] - ], - "b6": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.b6": { - "type": "file", - "description": "Results in b6 format", - "pattern": "*.b6", - "ontologies": [] - } - } - ] - ], - "seqlength": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.seqlength": { - "type": "file", - "description": "Summary of contig lengths", - "pattern": "*.seqlength", - "ontologies": [] - } - } - ] - ], - "versions_dastool": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "dastool": { - "type": "string", - "description": "The tool name" - } - }, - { - "DAS_Tool --version 2>&1 | grep \"DAS Tool\" | sed \"s/DAS Tool //\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "dastool": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "DAS_Tool --version 2>&1 | grep \"DAS Tool\" | sed \"s/DAS Tool //\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@maxibor", - "@jfy133" - ], - "maintainers": [ - "@maxibor", - "@jfy133" - ] - }, - "pipelines": [ - { - "name": "mag", - "version": "5.4.2" - } - ] - }, - { - "name": "dastool_fastatocontig2bin", - "path": "modules/nf-core/dastool/fastatocontig2bin/meta.yml", - "type": "module", - "meta": { - "name": "dastool_fastatocontig2bin", - "description": "Helper script to convert a set of bins in fasta format to tabular scaffolds2bin format", - "keywords": [ - "binning", - "das tool", - "table", - "de novo", - "bins", - "contigs", - "assembly", - "das_tool" - ], - "tools": [ - { - "dastool": { - "description": "DAS Tool is an automated method that integrates the results\nof a flexible number of binning algorithms to calculate an optimized, non-redundant\nset of bins from a single assembly.\n", - "homepage": "https://github.com/cmks/DAS_Tool", - "documentation": "https://github.com/cmks/DAS_Tool", - "tool_dev_url": "https://github.com/cmks/DAS_Tool", - "doi": "10.1038/s41564-018-0171-1", - "licence": [ - "BSD" - ], - "identifier": "biotools:dastool" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Fasta of list of fasta files recommended to be gathered via with .collect() of bins", - "pattern": "*.{fa,fa.gz,fas,fas.gz,fna,fna.gz,fasta,fasta.gz}", - "ontologies": [] - } - } - ], - { - "extension": { - "type": "string", - "description": "Fasta file extension (fa | fas | fasta | ...), without .gz suffix, if gzipped input." - } - } - ], - "output": { - "fastatocontig2bin": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "tabular contig2bin file for DAS tool input", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_dastool": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "dastool": { - "type": "string", - "description": "The tool name" - } - }, - { - "DAS_Tool --version 2>&1 | grep \"DAS Tool\" | sed \"s/DAS Tool //\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "dastool": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "DAS_Tool --version 2>&1 | grep \"DAS Tool\" | sed \"s/DAS Tool //\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@maxibor", - "@jfy133" - ], - "maintainers": [ - "@maxibor", - "@jfy133" - ] - }, - "pipelines": [ - { - "name": "mag", - "version": "5.4.2" - } - ] - }, - { - "name": "dastool_scaffolds2bin", - "path": "modules/nf-core/dastool/scaffolds2bin/meta.yml", - "type": "module", - "meta": { - "name": "dastool_scaffolds2bin", - "description": "Helper script to convert a set of bins in fasta format to tabular scaffolds2bin format", - "deprecated": true, - "keywords": [ - "binning", - "das tool", - "table", - "de novo", - "bins", - "contigs", - "assembly", - "das_tool" - ], - "tools": [ - { - "dastool": { - "description": "DAS Tool is an automated method that integrates the results\nof a flexible number of binning algorithms to calculate an optimized, non-redundant\nset of bins from a single assembly.\n", - "homepage": "https://github.com/cmks/DAS_Tool", - "documentation": "https://github.com/cmks/DAS_Tool", - "tool_dev_url": "https://github.com/cmks/DAS_Tool", - "doi": "10.1038/s41564-018-0171-1", - "licence": [ - "BSD" - ], - "identifier": "biotools:dastool" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Fasta or list of fasta files recommended to be gathered via with .collect() of bins", - "pattern": "*.{fa,fa.gz,fas,fas.gz,fna,fna.gz,fasta,fasta.gz}", - "ontologies": [] - } - } - ], - { - "extension": { - "type": "string", - "description": "Fasta file extension (fa | fas | fasta | ...), but without .gz suffix, even if gzipped input." - } - } - ], - "output": { - "scaffolds2bin": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "tabular scaffolds2bin file for DAS tool input", - "pattern": "*.scaffolds2bin.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@maxibor" - ], - "maintainers": [ - "@maxibor" - ] - } - }, - { - "name": "datavzrd", - "path": "modules/nf-core/datavzrd/meta.yml", - "type": "module", - "meta": { - "name": "datavzrd", - "description": "Datavzrd is a tool to create visual HTML reports from collections of CSV/TSV tables.", - "keywords": [ - "visualisation", - "tsv", - "csv" - ], - "tools": [ - { - "datavzrd": { - "description": "Datavzrd is a tool to create visual HTML reports from collections of CSV/TSV tables.", - "homepage": "https://datavzrd.github.io/", - "documentation": "https://datavzrd.github.io/docs/index.html", - "tool_dev_url": "https://github.com/datavzrd/datavzrd", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "config_file": { - "type": "file", - "description": "Path to a config file in YAML format", - "pattern": "*.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - }, - { - "table": { - "type": "file", - "description": "Path to a CSV/TSV file", - "pattern": "*.{csv,tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - }, - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "output": { - "report": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "${prefix}": { - "type": "directory", - "description": "directory with HTML report of provided CSV/TSV files", - "pattern": "${prefix}" - } - } - ] - ], - "versions_datavzrd": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "datavzrd": { - "type": "string", - "description": "The tool name" - } - }, - { - "datavzrd --version | sed -e 's/[^0-9.]//g'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "datavzrd": { - "type": "string", - "description": "The tool name" - } - }, - { - "datavzrd --version | sed -e 's/[^0-9.]//g'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@vickylaram", - "@famosab" - ], - "maintainers": [ - "@famosab" - ] - }, - "pipelines": [ - { - "name": "variantbenchmarking", - "version": "1.5.0" - } - ] - }, - { - "name": "deacon_filter", - "path": "modules/nf-core/deacon/filter/meta.yml", - "type": "module", - "meta": { - "name": "deacon_filter", - "description": "Filter DNA sequences using index of reference genome", - "keywords": [ - "filter", - "index", - "fasta", - "fastq", - "genome", - "reference", - "minimizer", - "decontamination" - ], - "tools": [ - { - "deacon": { - "description": "Fast alignment-free sequence filter", - "homepage": "https://github.com/bede/deacon", - "documentation": "https://github.com/bede/deacon#readme", - "tool_dev_url": "https://github.com/bede/deacon", - "doi": "10.1093/bioinformatics/btae004", - "licence": [ - "MIT" - ], - "identifier": "biotools:deacon" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "index": { - "type": "file", - "description": "Deacon minimizer index file", - "pattern": "*.idx", - "ontologies": [ - { - "edam": "http://edamontology.org/data_3210" - } - ] - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively.", - "pattern": "*.{fastq,fastq.gz,fqs,fqs.gz,fq,fq.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "output": { - "fastq_filtered": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}*.fq.gz": { - "type": "file", - "description": "List of output filtered FastQ files of size 1 and 2, for single-end and paired-end data, respectively.", - "pattern": "*.fq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.json": { - "type": "file", - "description": "JSON file containing summary of results.", - "pattern": "*.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "versions_deacon": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "deacon": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "deacon --version | head -n1 | sed \"s/deacon //g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "deacon": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "deacon --version | head -n1 | sed \"s/deacon //g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@Baksic-Ivan", - "@Omer0191" - ], - "maintainers": [ - "@Baksic-Ivan", - "@Omer0191", - "@vagkaratzas" - ] - } - }, - { - "name": "deacon_index", - "path": "modules/nf-core/deacon/index/meta.yml", - "type": "module", - "meta": { - "name": "deacon_index", - "description": "Create deacon index for reference genome", - "keywords": [ - "index", - "fasta", - "genome", - "reference", - "minimizer", - "decontamination" - ], - "tools": [ - { - "deacon": { - "description": "Fast alignment-free sequence filter", - "homepage": "https://github.com/bede/deacon", - "documentation": "https://github.com/bede/deacon#readme", - "tool_dev_url": "https://github.com/bede/deacon", - "doi": "10.1093/bioinformatics/btae004", - "licence": [ - "MIT" - ], - "identifier": "biotools:deacon" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input genome fasta file", - "pattern": "*.{fasta,fasta.gz,fas,fas.gz,fa,fa.gz,fna,fna.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/data_2044" - }, - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ], - "output": { - "index": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.idx": { - "type": "file", - "description": "Deacon minimizer index file", - "pattern": "*.idx", - "ontologies": [ - { - "edam": "http://edamontology.org/data_3210" - } - ] - } - } - ] - ], - "versions_deacon": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "deacon": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "deacon --version | head -n1 | sed \"s/deacon //g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "deacon": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "deacon --version | head -n1 | sed \"s/deacon //g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@mberacochea" - ], - "maintainers": [ - "@mberacochea" - ] - } - }, - { - "name": "decoupler_decoupler", - "path": "modules/nf-core/decoupler/decoupler/meta.yml", - "type": "module", - "meta": { - "name": "decoupler_decoupler", - "description": "decoupler is a package containing different statistical methods\nto extract biological activities from omics data within a unified framework.\nIt allows to flexibly test any enrichment method with any prior knowledge\nresource and incorporates methods that take into account the sign and weight.\nIt can be used with any omic, as long as its features can be linked to a\nbiological process based on prior knowledge. For example, in transcriptomics\ngene sets regulated by a transcription factor, or in phospho-proteomics\nphosphosites that are targeted by a kinase.\n", - "keywords": [ - "enrichment", - "omics", - "biological activity", - "functional analysis", - "prior knowledge" - ], - "tools": [ - { - "decoupler": { - "description": "Ensemble of methods to infer biological activities from omics data", - "homepage": "https://github.com/saezlab/decoupler-py", - "documentation": "https://decoupler-py.readthedocs.io/en/latest/api.html", - "tool_dev_url": "https://decoupler-py.readthedocs.io", - "doi": "10.1093/bioadv/vbac016", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:decoupler" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:‘test’, single_end ]\n" - } - }, - { - "mat": { - "type": "file", - "description": "Path to the matrix file (e.g. gene/protein expression, etc.).\nShould be in in tab-separated format (`*.tab`)\n", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy map" - } - }, - { - "net": { - "type": "file", - "description": "The prior knowledge network linking the features of the\nexpression matrix to a process/component (e.g. gene set,\ntranscription factor, kinase, etc.)\n", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy map" - } - }, - { - "annot": { - "type": "file", - "description": "Annotation file in TSV format containing gene ID to gene name mappings.\nUsed specifically for mapping Ensembl IDs to gene names.\nExpected format: two columns with gene_id and gene_name headers.\n", - "pattern": "*.tsv", - "required": false, - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "output": { - "dc_estimate": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:‘test’, single_end ]\n" - } - }, - { - "*estimate_decoupler.tsv": { - "type": "file", - "description": "The file containing the estimation results of the enrichment(s)\n", - "pattern": "*estimate_decoupler.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "dc_pvals": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:‘test’, single_end ]\n" - } - }, - { - "*pvals_decoupler.tsv": { - "type": "file", - "description": "The file containing the p-value associated to the estimation\nresults of the enrichment(s)\n", - "pattern": "*pvals_decoupler.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "png": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:‘test’, single_end ]\n" - } - }, - { - "*estimate_decoupler_plot.png": { - "type": "file", - "description": "The file containing the plots associated to the estimation\nresults of the enrichment(s)\n", - "pattern": "*estimate_decoupler_plot.png", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "YAML file containing versions of tools used in the module", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "topics": { - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "YAML file containing versions of tools used in the module", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@gabora", - "@vicpaton", - "@Nic-Nic" - ] - } - }, - { - "name": "dedup", - "path": "modules/nf-core/dedup/meta.yml", - "type": "module", - "meta": { - "name": "dedup", - "description": "DeDup is a tool for read deduplication in paired-end read merging (e.g. for ancient DNA experiments).", - "keywords": [ - "dedup", - "deduplication", - "pcr duplicates", - "ancient DNA", - "paired-end", - "bam" - ], - "tools": [ - { - "dedup": { - "description": "DeDup is a tool for read deduplication in paired-end read merging (e.g. for ancient DNA experiments).", - "homepage": "https://github.com/apeltzer/DeDup", - "documentation": "https://dedup.readthedocs.io/en/latest/", - "tool_dev_url": "https://github.com/apeltzer/DeDup", - "doi": "10.1186/s13059-016-0918-z", - "licence": [ - "GPL v3" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/SAM file", - "pattern": "*.{bam,sam}", - "ontologies": [] - } - } - ] - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.bam": { - "type": "file", - "description": "Deduplicated BAM file", - "pattern": "${prefix}.bam", - "ontologies": [] - } - } - ] - ], - "json": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.json": { - "type": "file", - "description": "JSON file for MultiQC", - "pattern": "${prefix}.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "hist": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.hist": { - "type": "file", - "description": "Histogram data of amount of deduplication", - "pattern": "${prefix}.hist", - "ontologies": [] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.log": { - "type": "file", - "description": "Dedup log information", - "pattern": "${prefix}.log", - "ontologies": [] - } - } - ] - ], - "versions_dedup": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "dedup": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "dedup --version | grep -oE '[0-9]+\\.[0-9]+\\.[0-9]+'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "dedup": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "dedup --version | grep -oE '[0-9]+\\.[0-9]+\\.[0-9]+'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@jfy133" - ], - "maintainers": [ - "@jfy133" - ] - } - }, - { - "name": "deeparg_downloaddata", - "path": "modules/nf-core/deeparg/downloaddata/meta.yml", - "type": "module", - "meta": { - "name": "deeparg_downloaddata", - "description": "A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes", - "keywords": [ - "download", - "database", - "deeparg", - "antimicrobial resistance genes", - "deep learning", - "prediction" - ], - "tools": [ - { - "deeparg": { - "description": "A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes", - "homepage": "https://github.com/gaarangoa/deeparg", - "documentation": "https://github.com/gaarangoa/deeparg", - "tool_dev_url": "https://github.com/gaarangoa/deeparg", - "doi": "10.1186/s40168-018-0401-z", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [], - "output": { - "db": [ - { - "db/": { - "type": "directory", - "description": "Directory containing database required for deepARG.", - "pattern": "db/" - } - } - ], - "versions_deeparg": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "deeparg": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "1.0.4": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "deeparg": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "1.0.4": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@jfy133" - ], - "maintainers": [ - "@jfy133" - ] - }, - "pipelines": [ - { - "name": "funcscan", - "version": "3.0.0" - } - ] - }, - { - "name": "deeparg_predict", - "path": "modules/nf-core/deeparg/predict/meta.yml", - "type": "module", - "meta": { - "name": "deeparg_predict", - "description": "A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes", - "keywords": [ - "deeparg", - "antimicrobial resistance", - "antimicrobial resistance genes", - "arg", - "deep learning", - "prediction", - "contigs", - "metagenomes" - ], - "tools": [ - { - "deeparg": { - "description": "A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes", - "homepage": "https://github.com/gaarangoa/deeparg", - "documentation": "https://github.com/gaarangoa/deeparg", - "tool_dev_url": "https://github.com/gaarangoa/deeparg", - "doi": "10.1186/s40168-018-0401-z", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA file containing gene-like sequences", - "pattern": "*.{fasta,fa,fna}", - "ontologies": [] - } - }, - { - "model": { - "type": "string", - "description": "Which model to use, depending on input data. Either 'LS' or 'SS' for long or short sequences respectively", - "pattern": "LS|LS" - } - } - ], - { - "db": { - "type": "directory", - "description": "Path to a directory containing the deepARG pre-built models", - "pattern": "*/" - } - } - ], - "output": { - "daa": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.align.daa": { - "type": "file", - "description": "Sequences of ARG-like sequences from DIAMOND alignment", - "pattern": "*.align.daa", - "ontologies": [] - } - } - ] - ], - "daa_tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.align.daa.tsv": { - "type": "file", - "description": "Alignments scores against ARG-like sequences from DIAMOND alignment", - "pattern": "*.align.daa.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "arg": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.mapping.ARG": { - "type": "file", - "description": "Table containing sequences with an ARG-like probability of more than specified thresholds", - "pattern": "*.mapping.ARG", - "ontologies": [] - } - } - ] - ], - "potential_arg": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.mapping.potential.ARG": { - "type": "file", - "description": "Table containing sequences with an ARG-like probability of less than specified thresholds, and requires manual inspection", - "pattern": "*.mapping.potential.ARG", - "ontologies": [] - } - } - ] - ], - "versions_deeparg": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "deeparg": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "1.0.4": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "deeparg": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "1.0.4": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@jfy133" - ], - "maintainers": [ - "@jfy133" - ] - }, - "pipelines": [ - { - "name": "funcscan", - "version": "3.0.0" - } - ] - }, - { - "name": "deepbgc_download", - "path": "modules/nf-core/deepbgc/download/meta.yml", - "type": "module", - "meta": { - "name": "deepbgc_download", - "description": "Database download module for DeepBGC which detects BGCs in bacterial and fungal genomes using deep learning.", - "keywords": [ - "database", - "download", - "BGC", - "biosynthetic gene cluster", - "deep learning", - "neural network", - "random forest", - "genomes", - "bacteria", - "fungi" - ], - "tools": [ - { - "deepbgc": { - "description": "DeepBGC - Biosynthetic Gene Cluster detection and classification", - "homepage": "https://github.com/Merck/deepbgc", - "documentation": "https://github.com/Merck/deepbgc", - "tool_dev_url": "https://github.com/Merck/deepbgc", - "doi": "10.1093/nar/gkz654", - "licence": [ - "MIT" - ], - "identifier": "biotools:DeepBGC" - } - } - ], - "output": { - "db": [ - { - "deepbgc_db/": { - "type": "directory", - "description": "Directory containing the DeepBGC database", - "pattern": "deepbgc_db/" - } - } - ], - "versions_deepbgc": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "deepbgc": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "deepbgc info 2>&1 | sed '6!d;s/.*= version //;s/ .*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "deepbgc": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "deepbgc info 2>&1 | sed '6!d;s/.*= version //;s/ .*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@louperelo" - ], - "maintainers": [ - "@louperelo" - ] - }, - "pipelines": [ - { - "name": "funcscan", - "version": "3.0.0" - } - ] - }, - { - "name": "deepbgc_pipeline", - "path": "modules/nf-core/deepbgc/pipeline/meta.yml", - "type": "module", - "meta": { - "name": "deepbgc_pipeline", - "description": "DeepBGC detects BGCs in bacterial and fungal genomes using deep learning.", - "keywords": [ - "BGC", - "biosynthetic gene cluster", - "deep learning", - "neural network", - "random forest", - "genomes", - "bacteria", - "fungi" - ], - "tools": [ - { - "deepbgc": { - "description": "DeepBGC - Biosynthetic Gene Cluster detection and classification", - "homepage": "https://github.com/Merck/deepbgc", - "documentation": "https://github.com/Merck/deepbgc", - "tool_dev_url": "https://github.com/Merck/deepbgc", - "doi": "10.1093/nar/gkz654", - "licence": [ - "MIT" - ], - "identifier": "biotools:DeepBGC" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "genome": { - "type": "file", - "description": "FASTA/GenBank/Pfam CSV file", - "pattern": "*.{fasta,fa,fna,gbk,csv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ], - { - "db": { - "type": "directory", - "description": "Database path" - } - } - ], - "output": { - "readme": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "${prefix}/README.txt": { - "type": "file", - "description": "txt file containing description of output files", - "pattern": "*.{txt}", - "ontologies": [] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "${prefix}/LOG.txt": { - "type": "file", - "description": "Log output of DeepBGC", - "pattern": "*.{txt}", - "ontologies": [] - } - } - ] - ], - "json": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "${prefix}/${prefix}.antismash.json": { - "type": "file", - "description": "AntiSMASH JSON file for sideloading", - "pattern": "*.{json}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "bgc_gbk": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "${prefix}/${prefix}.bgc.gbk": { - "type": "file", - "description": "Sequences and features of all detected BGCs in GenBank format", - "pattern": "*.{bgc.gbk}", - "ontologies": [] - } - } - ] - ], - "bgc_tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "${prefix}/${prefix}.bgc.tsv": { - "type": "file", - "description": "Table of detected BGCs and their properties", - "pattern": "*.{bgc.tsv}", - "ontologies": [] - } - } - ] - ], - "full_gbk": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "${prefix}/${prefix}.full.gbk": { - "type": "file", - "description": "Fully annotated input sequence with proteins, Pfam domains (PFAM_domain features) and BGCs (cluster features)", - "pattern": "*.{full.gbk}", - "ontologies": [] - } - } - ] - ], - "pfam_tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "${prefix}/${prefix}.pfam.tsv": { - "type": "file", - "description": "Table of Pfam domains (pfam_id) from given sequence (sequence_id) in genomic order, with BGC detection scores", - "pattern": "*.{pfam.tsv}", - "ontologies": [] - } - } - ] - ], - "bgc_png": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "${prefix}/evaluation/${prefix}.bgc.png": { - "type": "file", - "description": "Detected BGCs plotted by their nucleotide coordinates", - "pattern": "*.{bgc.png}", - "ontologies": [] - } - } - ] - ], - "pr_png": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "${prefix}/evaluation/${prefix}.pr.png": { - "type": "file", - "description": "Precision-Recall curve based on predicted per-Pfam BGC scores", - "pattern": "*.{pr.png}", - "ontologies": [] - } - } - ] - ], - "roc_png": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "${prefix}/evaluation/${prefix}.roc.png": { - "type": "file", - "description": "ROC curve based on predicted per-Pfam BGC scores", - "pattern": "*.{roc.png}", - "ontologies": [] - } - } - ] - ], - "score_png": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "${prefix}/evaluation/${prefix}.score.png": { - "type": "file", - "description": "BGC detection scores of each Pfam domain in genomic order", - "pattern": "*.{score.png}", - "ontologies": [] - } - } - ] - ], - "versions_deepbgc": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "deepbgc": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "deepbgc info 2>&1 | sed '6!d;s/.*= version //;s/ .*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_prodigal": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "prodigal": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "prodigal -v 2>&1 | sed '2!d;s/Prodigal V//;s/:.*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "deepbgc": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "deepbgc info 2>&1 | sed '6!d;s/.*= version //;s/ .*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "prodigal": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "prodigal -v 2>&1 | sed '2!d;s/Prodigal V//;s/:.*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@louperelo", - "@jfy133" - ], - "maintainers": [ - "@louperelo", - "@jfy133" - ] - }, - "pipelines": [ - { - "name": "funcscan", - "version": "3.0.0" - } - ] - }, - { - "name": "deepcell_mesmer", - "path": "modules/nf-core/deepcell/mesmer/meta.yml", - "type": "module", - "meta": { - "name": "deepcell_mesmer", - "description": "Deepcell/mesmer segmentation for whole-cell", - "keywords": [ - "imaging", - "spatial_omics", - "segmentation" - ], - "tools": [ - { - "mesmer": { - "description": "Deep cell is a collection of tools to segment imaging data", - "homepage": "https://github.com/vanvalenlab/deepcell-tf", - "documentation": "https://github.com/vanvalenlab/intro-to-deepcell/tree/master/pretrained_models", - "tool_dev_url": "https://githu/b.com/vanvalenlab/deepcell-tf", - "doi": "10.1038/s41587-021-01094-0", - "licence": [ - "APACHE2" - ], - "identifier": "biotools:deepcell" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "img": { - 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} - }, - { - "input": { - "type": "file", - "description": "BAM file", - "pattern": "*.{bam}", - "ontologies": [] - } - }, - { - "input_index": { - "type": "file", - "description": "BAM index file", - "pattern": "*.{bai}", - "ontologies": [] - } - } - ] - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_as.bam": { - "type": "file", - "description": "BAM file", - "pattern": "*.bam", - "ontologies": [] - } - } - ] - ], - "logs": [ - { - "*_log.txt": { - "type": "file", - "description": "TXT file", - "pattern": "*.txt", - "ontologies": [] - } - } - ], - "versions_deeptools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "deeptools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "alignmentSieve --version | sed \"s/alignmentSieve //g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_samtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "deeptools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "alignmentSieve --version | sed \"s/alignmentSieve //g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@lpantano" - ], - "maintainers": [ - "@lpantano" - ] - } - }, - { - "name": "deeptools_bamcompare", - "path": "modules/nf-core/deeptools/bamcompare/meta.yml", - "type": "module", - "meta": { - "name": "deeptools_bamcompare", - "description": "Compares two BAM files based on the number of mapped reads and generates a bigWig or bedGraph file with the log2 ratio, ratio, difference or other operations.", - "keywords": [ - "bam", - "bigwig", - "bedgraph", - "normalization", - "comparison" - ], - "tools": [ - { - "deeptools": { - "description": "A set of user-friendly tools for normalization and visualization of deep-sequencing data", - "homepage": "https://deeptools.readthedocs.io/en/latest/", - "documentation": "https://deeptools.readthedocs.io/en/latest/content/tools/bamCompare.html", - "tool_dev_url": "https://github.com/deeptools/deepTools", - "doi": "10.1093/nar/gkw257", - 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"type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "deeptools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bamCompare --version | sed \"s/bamCompare //g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@seqeraai", - "@oliverdrechsel" - ], - "maintainers": [ - "@oliverdrechsel" - ] - } - }, - { - "name": "deeptools_bamcoverage", - "path": "modules/nf-core/deeptools/bamcoverage/meta.yml", - "type": "module", - "meta": { - "name": "deeptools_bamcoverage", - "description": "This tool takes an alignment of reads or fragments as input (BAM file) and generates a coverage track (bigWig or bedGraph) as output.", - "keywords": [ - "coverage", - "depth", - "track" - ], - "tools": [ - { - "deeptools": { - "description": "A set of user-friendly tools for normalization and visualization of deep-sequencing data", - "homepage": "https://deeptools.readthedocs.io/en/develop/content/tools/bamCoverage.html", - "documentation": "https://deeptools.readthedocs.io/en/develop/content/tools/bamCoverage.html", - "tool_dev_url": "https://github.com/deeptools/deepTools/", - "doi": "10.1093/nar/gkw257", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:deeptools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM file", - "pattern": "*.{bam,cram}", - "ontologies": [] - } - }, - { - "input_index": { - "type": "file", - "description": "BAM/CRAM index file", - "pattern": "*.{bai,crai}", - "ontologies": [] - } - } - ], - { - "fasta": { - "type": "file", - "description": "Reference file the CRAM file was created with (required with CRAM input)", - "pattern": "*.{fasta,fa}", - "ontologies": [] - } - }, - { - "fasta_fai": { - "type": "file", - "description": "Index of the reference file (optional, but recommended)", - "pattern": "*.{fai}", - "ontologies": [] - } - }, - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing blacklist metadata\ne.g. [ id:'blacklist' ]\n" - } + "name": "ensemblvep_vep", + "path": "modules/nf-core/ensemblvep/vep/meta.yml", + "type": "module", + "meta": { + "name": "ensemblvep_vep", + "description": "Ensembl Variant Effect Predictor (VEP). The output-file-format is controlled through `task.ext.args`.", + "keywords": ["annotation", "vcf", "json", "tab"], + "tools": [ + { + "ensemblvep": { + "description": "VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs\nor structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.\n", + "homepage": "https://www.ensembl.org/info/docs/tools/vep/index.html", + "documentation": "https://www.ensembl.org/info/docs/tools/vep/script/index.html", + "licence": ["Apache-2.0"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "vcf to annotate\n", + "ontologies": [] + } + }, + { + "custom_extra_files": { + "type": "file", + "description": "extra sample-specific files to be used with the `--custom` flag to be configured with ext.args\n(optional)\n", + "ontologies": [] + } + } + ], + { + "genome": { + "type": "string", + "description": "which genome to annotate with\n" + } + }, + { + "species": { + "type": "string", + "description": "which species to annotate with\n" + } + }, + { + "cache_version": { + "type": "integer", + "description": "which version of the cache to annotate with\n" + } + }, + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing cache information\ne.g. [ id:'test' ]\n" + } + }, + { + "cache": { + "type": "file", + "description": "path to VEP cache (optional)\n", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing fasta reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "reference FASTA file (optional)\n", + "pattern": "*.{fasta,fa}", + "ontologies": [] + } + } + ], + { + "extra_files": { + "type": "file", + "description": "path to file(s) needed for plugins (optional)\n", + "ontologies": [] + } + } + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Map with sample information\n" + } + }, + { + "${prefix}.vcf.gz": { + "type": "file", + "description": "annotated vcf (optional)\n", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Map with sample information\n" + } + }, + { + "${prefix}.vcf.gz.tbi": { + "type": "file", + "description": "annotated vcf index (optional)\n", + "pattern": "*.vcf.gz.tbi", + "ontologies": [] + } + } + ] + ], + "tab": [ + [ + { + "meta": { + "type": "map", + "description": "Map with sample information\n" + } + }, + { + "${prefix}.tab.gz": { + "type": "file", + "description": "tab file with annotated variants (optional)\n", + "pattern": "*.ann.tab.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "json": [ + [ + { + "meta": { + "type": "map", + "description": "Map with sample information\n" + } + }, + { + "${prefix}.json.gz": { + "type": "file", + "description": "json file with annotated variants (optional)\n", + "pattern": "*.ann.json.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "report": [ + [ + { + "meta": { + "type": "map", + "description": "Map with sample information\n" + } + }, + { + "${task.process}": { + "type": "string", + "description": "The process" + } + }, + { + "ensemblvep": { + "type": "string", + "description": "The tool name" + } + }, + { + "*.html": { + "type": "file", + "description": "VEP report file", + "pattern": "*.html", + "ontologies": [] + } + } + ] + ], + "versions_ensemblvep": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process" + } + }, + { + "ensemblvep": { + "type": "string", + "description": "The tool name" + } + }, + { + "vep --help | sed -n '/ensembl-vep/s/.*: //p'": { + "type": "eval", + "description": "The command used to generate the version of the tool" + } + } + ] + ], + "versions_tabix": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process" + } + }, + { + "tabix": { + "type": "string", + "description": "The tool name" + } + }, + { + "tabix -h 2>&1 | grep -oP 'Version:\\s*\\K[^\\s]+'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_perlmathcdf": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process" + } + }, + { + "perl-math-cdf": { + "type": "string", + "description": "The tool name" + } + }, + { + "perl -MMath::CDF -e 'print \\\\$Math::CDF::VERSION'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "multiqc_files": [ + [ + { + "meta": { + "type": "string", + "description": "Map with sample information\n" + } + }, + { + "${task.process}": { + "type": "string", + "description": "The process" + } + }, + { + "ensemblvep": { + "type": "string", + "description": "The tool name" + } + }, + { + "*.html": { + "type": "file", + "description": "VEP report file", + "pattern": "*.html", + "ontologies": [] + } + } + ] + ], + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process" + } + }, + { + "ensemblvep": { + "type": "string", + "description": "The tool name" + } + }, + { + "vep --help | sed -n '/ensembl-vep/s/.*: //p'": { + "type": "eval", + "description": "The command used to generate the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The process" + } + }, + { + "tabix": { + "type": "string", + "description": "The tool name" + } + }, + { + "tabix -h 2>&1 | grep -oP 'Version:\\s*\\K[^\\s]+'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The process" + } + }, + { + "perl-math-cdf": { + "type": "string", + "description": "The tool name" + } + }, + { + "perl -MMath::CDF -e 'print \\\\$Math::CDF::VERSION'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@maxulysse", "@matthdsm", "@nvnieuwk"], + "maintainers": ["@maxulysse", "@matthdsm", "@nvnieuwk"] }, - { - "blacklist": { - "type": "file", - "description": "BED/GTF file containing regions to exclude from analysis", - "pattern": "*.{bed,gtf}", - "ontologies": [ - { - "edam": "http://edamontology.org/data_3002" - }, - { - "edam": "http://edamontology.org/format_3003" - } - ], - "optional": true - } - } - ] - ], - "output": { - "bigwig": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bigWig": { - "type": "file", - "description": "BigWig file", - "pattern": "*.bigWig", - "ontologies": [] - } - } - ] - ], - "bedgraph": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bedgraph": { - "type": "file", - "description": "Bedgraph file", - "pattern": "*.bedgraph", - "ontologies": [] - } - } - ] - ], - "versions_deeptools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "deeptools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bamCoverage --version | sed \"s/bamCoverage //g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_samtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "deeptools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bamCoverage --version | sed \"s/bamCoverage //g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "pacsomatic", + "version": "dev" + }, + { + "name": "raredisease", + "version": "3.0.0" + }, + { + "name": "rnadnavar", + 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window. Functions\ntake search terms from command line arguments. Individual operations\nare combined to build multi-step queries. Record retrieval and\nformatting normally complete the process.\n", + "homepage": "https://www.ncbi.nlm.nih.gov/books/NBK179288/", + "documentation": "https://www.ncbi.nlm.nih.gov/books/NBK25501/", + "tool_dev_url": "https://www.ncbi.nlm.nih.gov/books/NBK25498/", + "doi": "10.1016/S0076-6879(96)66012-1", + "licence": ["PUBLIC DOMAIN"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "term": { + "type": "string", + "description": "Entrez text query. All special characters must be URL encoded.\nSpaces may be replaced by '+' signs.\n" + } + } + ], + { + "database": { + "type": "string", + "description": "Value must be a valid Entrez database name." + } + } + ], + "output": { + "xml": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.xml": { + "type": "file", + "description": "XML file containing search results", + "pattern": "*.xml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2332" + } + ] + } + } + ] + ], + "versions_esearch": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "ENTREZDIRECT": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "esearch -version 2>&1": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "ENTREZDIRECT": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "esearch -version 2>&1": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@alxndrdiaz"], + "maintainers": ["@alxndrdiaz"] + } }, { - "name": "pacsomatic", - "version": "dev" + "name": "entrezdirect_esummary", + "path": "modules/nf-core/entrezdirect/esummary/meta.yml", + "type": "module", + "meta": { + "name": "entrezdirect_esummary", + "description": "Queries an NCBI database using Unique Identifier(s)", + "keywords": ["public datasets", "ncbi", "entrez", "metadata", "query", "database"], + "tools": [ + { + "entrezdirect": { + "description": "Entrez Direct (EDirect) is a method for accessing the NCBI's set of\ninterconnected databases (publication, sequence, structure, gene,\nvariation, expression, etc.) from a UNIX terminal window. Functions\ntake search terms from command line arguments. Individual operations\nare combined to build multi-step queries. Record retrieval and\nformatting normally complete the process.\n", + "homepage": "https://www.ncbi.nlm.nih.gov/books/NBK179288/", + "documentation": "https://www.ncbi.nlm.nih.gov/books/NBK25501/", + "tool_dev_url": "https://www.ncbi.nlm.nih.gov/books/NBK25498/", + "doi": "10.1016/S0076-6879(96)66012-1", + "licence": ["PUBLIC DOMAIN"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "uid": { + "type": "string", + "description": "Unique Identifier (UID) of record in NCBI database. Cannot be used at the same time as uids_file" + } + }, + { + "uids_file": { + "type": "file", + "description": "Text file containing multiple UIDs. Cannot be used at the same time as uid.", + "ontologies": [] + } + } + ], + { + "database": { + "type": "string", + "description": "Value must be a valid Entrez database name ('assembly', etc)." + } + } + ], + "output": { + "xml": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.xml": { + "type": "file", + "description": "Query result in XML format", + "pattern": "*.xml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2332" + } + ] + } + } + ] + ], + "versions_esummary": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "ENTREZDIRECT": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "esummary -version 2>&1": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "ENTREZDIRECT": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "esummary -version 2>&1": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@alxndrdiaz"], + "maintainers": ["@alxndrdiaz"] + } }, { - "name": "sammyseq", - "version": "dev" - } - ] - }, - { - "name": "deeptools_bigwigcompare", - "path": "modules/nf-core/deeptools/bigwigcompare/meta.yml", - "type": "module", - "meta": { - "name": "deeptools_bigwigcompare", - "description": "Compare two bigWig files based on the number of mapped reads", - "keywords": [ - "bigwig", - "compare", - "genomics", - "deeptools", - "coverage" - ], - "tools": [ - { - "deeptools": { - "description": "A set of user-friendly tools for normalization and visualization of deep-sequencing data", - "homepage": "https://deeptools.readthedocs.io/en/develop/", - "documentation": "https://deeptools.readthedocs.io/en/develop/content/tools/bigwigCompare.html", - "tool_dev_url": "https://github.com/deeptools/deepTools", - "doi": "10.1093/nar/gku365", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:deeptools", - "args_id": "$args" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "bigwig1": { - "type": "file", - "description": "First bigWig file (usually treatment)", - "pattern": "*.{bw,bigwig,bigWig}", - "ontologies": [ - { - "edam": "http://edamontology.org/data_3002" - }, - { - "edam": "http://edamontology.org/format_3006" - } - ] - } - }, - { - "bigwig2": { - "type": "file", - "description": "Second bigWig file (usually control)", - "pattern": "*.{bw,bigwig,bigWig}", - "ontologies": [ - { - "edam": "http://edamontology.org/data_3002" - }, - { - "edam": "http://edamontology.org/format_3006" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing blacklist metadata\ne.g. [ id:'blacklist' ]\n" - } - }, - { - "blacklist": { - "type": "file", - "description": "BED/GTF file containing regions to exclude from analysis", - "pattern": "*.{bed,gtf}", - "ontologies": [ - { - "edam": "http://edamontology.org/data_3002" - }, - { - "edam": "http://edamontology.org/format_3003" - } - ], - "optional": true - } - } - ] - ], - "output": { - "output": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.{bigWig,bedgraph}": { - "type": "file", - "description": "Output bigWig or bedGraph file with comparison results", - "pattern": "*.{bigWig,bedgraph}", - "ontologies": [ + "name": "entrezdirect_xtract", + "path": "modules/nf-core/entrezdirect/xtract/meta.yml", + "type": "module", + "meta": { + "name": "entrezdirect_xtract", + "description": "Queries an NCBI database using an UID", + "keywords": ["public datasets", "entrez", "search", "ncbi", "database"], + "tools": [ + { + "entrezdirect": { + "description": "Entrez Direct (EDirect) is a method for accessing the NCBI's set of\ninterconnected databases (publication, sequence, structure, gene,\nvariation, expression, etc.) from a UNIX terminal window. Functions\ntake search terms from command line arguments. Individual operations\nare combined to build multi-step queries. Record retrieval and\nformatting normally complete the process.\n", + "homepage": "https://www.ncbi.nlm.nih.gov/books/NBK179288/", + "documentation": "https://www.ncbi.nlm.nih.gov/books/NBK25501/", + "tool_dev_url": "https://www.ncbi.nlm.nih.gov/books/NBK25498/", + "doi": "10.1016/S0076-6879(96)66012-1", + "licence": ["PUBLIC DOMAIN"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "xml_input": { + "type": "file", + "description": "XML text file containing query results from database.", + "ontologies": [] + } + } + ], + { + "pattern": { + "type": "string", + "description": "String in xml_input that encloses element to search." + } + }, { - "edam": "http://edamontology.org/format_3583" + "element": { + "type": "string", + "description": "Space-delimited strings that will be converted to columns." + } }, { - "edam": 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"modules/nf-core/deeptools/plotcorrelation/meta.yml", - "type": "module", - "meta": { - "name": "deeptools_plotcorrelation", - "description": "Visualises sample correlations using a compressed matrix generated by mutlibamsummary or multibigwigsummary as input.", - "keywords": [ - "corrrelation", - "matrix", - "heatmap", - "scatterplot" - ], - "tools": [ - { - "deeptools": { - "description": "A set of user-friendly tools for normalization and visualization of deep-sequencing data", - "documentation": "https://deeptools.readthedocs.io/en/develop/index.html", - "tool_dev_url": "https://github.com/deeptools/deepTools", - "doi": "10.1093/nar/gku365", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:deeptools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "matrix": { - "type": "file", - "description": "compressed matrix file produced by\nmutlibamsummary or multibigwigsummary\n", - "pattern": "*.{npz}", - "ontologies": [] - } - } - ], - { - "method": { - "type": "string", - "description": "Correlation coefficient to use for heatmap or scatterplot generation\n", - "pattern": "{spearman,pearson}" - } - }, - { - "plot_type": { - "type": "string", - "description": "Type of output plot to display sample correlation\n", - "pattern": "{heatmap,scatterplot}" - } - } - ], - "output": { - "pdf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.pdf": { - "type": "file", - "description": "Output figure containing resulting plot\n", - "pattern": "*.{plotCorrelation.pdf}", - "ontologies": [] - } - } - ] - ], - "matrix": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tab": { - "type": "file", - "description": "Tab-separated file containing a matrix of pairwise correlations\n", - "pattern": "*.{plotCorrelation.mat.tab}", - "ontologies": [] - } - } - ] - ], - "versions_deeptools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "deeptools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "plotCorrelation --version | sed \"s/plotCorrelation //g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "deeptools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "plotCorrelation --version | sed \"s/plotCorrelation //g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@tamara-hodgetts", - "@chris-cheshire", - "@joseespinosa" - 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"description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "bams": { - "type": "file", - "description": "BAM files", - "pattern": "*.bam", - "ontologies": [] - } + "name": "evigene_tr2aacds", + "path": "modules/nf-core/evigene/tr2aacds/meta.yml", + "type": "module", + "meta": { + "name": "evigene_tr2aacds", + "description": "Uses evigene/scripts/prot/tr2aacds.pl to filter a transcript assembly", + "keywords": [ + "genomics", + "transcript", + "assembly", + "clean", + "polish", + "filter", + "redundant", + "duplicate" + ], + "tools": [ + { + "evigene": { + "description": "EvidentialGene is a genome informatics project for \"Evidence Directed Gene Construction\nfor Eukaryotes\", for constructing high quality, accurate gene sets for animals and\nplants (any eukaryotes), being developed by Don Gilbert at Indiana University, gilbertd at indiana edu.\n", + "homepage": "http://arthropods.eugenes.org/EvidentialGene/evigene/", + "documentation": "http://arthropods.eugenes.org/EvidentialGene/evigene/", + "tool_dev_url": "http://arthropods.eugenes.org/EvidentialGene/evigene/", + "doi": "10.7490/f1000research.1112594.1 ", + "licence": ["Don Gilbert, gilbertd At indiana edu, 2018"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Transcript assembly in fasta format", + "pattern": "*.{fsa,fa,fasta,fsa.gz,fa.gz,fasta.gz}", + "ontologies": [] + } + } + ] + ], + "output": { + "dropset": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "dropset": { + "type": "directory", + "description": "Directory containing dropped transcripts and associated files", + "pattern": "dropset" + } + } + ] + ], + "okayset": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "okayset": { + "type": "directory", + "description": "Directory containing included transcripts and associated files", + "pattern": "okayset" + } + } + ] + ], + "versions_tr2aacds": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "tr2aacds": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "\\$EVIGENEHOME/scripts/prot/tr2aacds.pl 2>&1 | sed '1!d;s/.*VERSION //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "tr2aacds": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "\\$EVIGENEHOME/scripts/prot/tr2aacds.pl 2>&1 | sed '1!d;s/.*VERSION //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@GallVp"], + "maintainers": ["@GallVp"] }, - { - "bais": { - "type": "file", - "description": "Corresponding BAM file indexes", - "pattern": "*.bam.bai", - "ontologies": [] - } - } - ] - ], - "output": { - "pdf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.pdf": { - "type": "file", - "description": "Output figure containing resulting plot\n", - "pattern": "*.{plotFingerprint.pdf}", - "ontologies": [] - } - } - ] - ], - "matrix": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.raw.txt": { - "type": "file", - "description": "Output file summarizing the read counts per bin\n", - "pattern": "*.{plotFingerprint.raw.txt}", - "ontologies": [] - } - } - ] - ], - "metrics": [ - [ - { - "meta": { - "type": 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"description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "denovotranscript", + "version": "1.2.1" + } ] - ] }, - "authors": [ - "@edmundmiller", - "@drpatelh", - "@joseespinosa" - ], - "maintainers": [ - "@edmundmiller", - "@drpatelh", - "@joseespinosa" - ] - }, - "pipelines": [ { - "name": "atacseq", - "version": "2.1.2" - }, - { - "name": "chipseq", - "version": "2.1.0" - }, - { - "name": "cutandrun", - "version": "3.2.2" + "name": "expansionhunter", + "path": "modules/nf-core/expansionhunter/meta.yml", + "type": "module", + "meta": { + "name": "expansionhunter", + "description": "Estimate repeat sizes using NGS data", + "keywords": ["STR", "repeat_expansions", "bam", "cram", "vcf", "json"], + "tools": [ + { + "expansionhunter": { + "description": "A tool for estimating repeat sizes", + "homepage": "https://github.com/Illumina/ExpansionHunter", + "documentation": "https://github.com/Illumina/ExpansionHunter/blob/master/docs/01_Introduction.md", + "doi": "10.1093/bioinformatics/btz431", + "licence": ["Apache-2.0"], + "identifier": "biotools:ExpansionHunter" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM file", + "pattern": "*.{bam,cram}", + "ontologies": [] + } + }, + { + "bai": { + "type": "file", + "description": "Index of BAM/CRAM file", + "pattern": "*.{bai,crai}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference genome", + "pattern": "*.{fna,fa,fasta}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta_fai": { + "type": "file", + "description": "Reference genome index", + "pattern": "*.fai", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "variant_catalog": { + "type": "file", + "description": "JSON file with repeat expansion sites to genotype", + "pattern": "*.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', gender:'female' ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "VCF with repeat expansions", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "json": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', gender:'female' ]\n" + } + }, + { + "*.json.gz": { + "type": "file", + "description": "JSON with repeat expansions", + "pattern": "*.json.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', gender:'female' ]\n" + } + }, + { + "*_realigned.bam": { + "type": "file", + "description": "BAM/CRAM file", + "pattern": "*.{bam,cram}", + "ontologies": [] + } + } + ] + ], + "versions_expansionhunter": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "expansionhunter": { + "type": "string", + "description": "The tool name" + } + }, + { + "ExpansionHunter --version | head -1 | sed -n 's/^.*ExpansionHunter v//; s/]//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_bgzip": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bgzip": { + "type": "string", + "description": "The tool name" + } + }, + { + "bgzip --version | sed '1!d;s/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "expansionhunter": { + "type": "string", + "description": "The tool name" + } + }, + { + "ExpansionHunter --version | head -1 | sed -n 's/^.*ExpansionHunter v//; s/]//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bgzip": { + "type": "string", + "description": "The tool name" + } + }, + { + "bgzip --version | sed '1!d;s/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@jemten"], + "maintainers": ["@jemten"] + }, + "pipelines": [ + { + "name": "raredisease", + "version": "3.0.0" + } + ] }, { - "name": "sammyseq", - "version": "dev" + "name": "expansionhunterdenovo_merge", + "path": "modules/nf-core/expansionhunterdenovo/merge/meta.yml", + "type": "module", + "meta": { + "name": "expansionhunterdenovo_merge", + "description": "Merge STR profiles into a multi-sample STR profile", + "keywords": ["expansionhunterdenovo", "merge", "str"], + "tools": [ + { + "expansionhunterdenovo": { + "description": "ExpansionHunter Denovo (EHdn) is a suite of tools for detecting novel expansions of short tandem repeats (STRs).", + "homepage": "https://github.com/Illumina/ExpansionHunterDenovo", + "documentation": "https://github.com/Illumina/ExpansionHunterDenovo/blob/master/documentation/00_Introduction.md", + "tool_dev_url": "https://github.com/Illumina/ExpansionHunterDenovo", + "licence": ["Apache License 2.0"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "manifest": { + "type": "file", + "description": "A tab-delimited file containing the sample name, whether it's case or control\nand the paths to the corresponding STR profiles.\nSee here for an example: https://github.com/Illumina/ExpansionHunterDenovo/blob/master/documentation/06_Merging_profiles.md#manifest-files\n", + "pattern": "*.{tsv,txt}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The reference FASTA file", + "pattern": "*.{fasta,fa}", + "ontologies": [] + } + }, + { + "fasta_fai": { + "type": "file", + "description": "The index of the reference FASTA file", + "pattern": "*.fai", + "ontologies": [] + } + } + ] + ], + "output": { + "merged_profiles": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.multisample_profile.json": { + "type": "file", + "description": "The merged STR profiles", + "pattern": "*.multisample_profile.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "versions_expansionhunterdenovo": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "expansionhunterdenovo": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "ExpansionHunterDenovo --help |& sed '1!d;s/ExpansionHunter Denovo v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "expansionhunterdenovo": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "ExpansionHunterDenovo --help |& sed '1!d;s/ExpansionHunter Denovo v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@nvnieuwk"], + "maintainers": ["@nvnieuwk"] + } }, { - "name": "ssds", - "version": "dev" - } - ] - }, - { - "name": "deeptools_plotheatmap", - "path": "modules/nf-core/deeptools/plotheatmap/meta.yml", - "type": "module", - "meta": { - "name": "deeptools_plotheatmap", - "description": "plots values produced by deeptools_computematrix as a heatmap", - "keywords": [ - "plot", - "heatmap", - "scores", - "matrix" - 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Set to true to enable/false to disable compression. Compression is handled by passing '-gz' to FAMSA along with any other options specified in task.ext.args." + } + } + ], + "output": { + "alignment": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" + } + }, + { + "${prefix}.aln{.gz,}": { + "type": "file", + "description": "Alignment file, in FASTA format. May be gzipped or uncompressed, depending on if compress is set to true or false", + "pattern": "*.aln{.gz,}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2554" + }, + { + "edam": "http://edamontology.org/format_1921" + }, + { + "edam": "http://edamontology.org/format_1984" + } + ] + } + } + ] + ], + "versions_famsa": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "famsa": { + "type": "string", + "description": "The tool name" + } + }, + { + "famsa -help 2>&1 | sed '2!d;s/.*version //;s/ .*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "famsa": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "famsa -help 2>&1 | sed '2!d;s/.*version //;s/ .*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@luisas", "@JoseEspinosa"], + "maintainers": ["@luisas", "@JoseEspinosa", "@vagkaratzas"] }, - { - "matrix": { - "type": "file", - "description": "gzipped matrix file produced by deeptools_\ncomputematrix deeptools utility\n", - "pattern": "*.{mat.gz}", - "ontologies": [] - } - } - ] - ], - "output": { - "pdf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.pdf": { - "type": "file", - "description": "Output figure containing resulting plot\n", - "pattern": "*.{plotProfile.pdf}", - "ontologies": [] - } - } - ] - ], - "table": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tab": { - "type": "file", - "description": "Output table", - "pattern": "*.tab", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_deeptools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "deeptools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "plotProfile --version | sed \"s/plotProfile //g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "deeptools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "plotProfile --version | sed \"s/plotProfile //g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "multiplesequencealign", + "version": "1.1.1" + }, + { + "name": "proteinfamilies", + "version": "2.3.0" + } ] - ] }, - "authors": [ - "@edmundmiller", - "@drpatelh", - "@joseespinosa" - ], - "maintainers": [ - "@edmundmiller", - "@drpatelh", - "@joseespinosa" - ] - }, - "pipelines": [ { - "name": "atacseq", - "version": "2.1.2" + "name": "famsa_guidetree", + "path": "modules/nf-core/famsa/guidetree/meta.yml", + "type": "module", + "meta": { + "name": "famsa_guidetree", + "description": "Renders a guidetree in famsa", + "keywords": ["guide tree", "msa", "newick"], + "tools": [ + { + "famsa": { + "description": "Algorithm for large-scale multiple sequence alignments", + "homepage": "https://github.com/refresh-bio/FAMSA", + "documentation": "https://github.com/refresh-bio/FAMSA", + "tool_dev_url": "https://github.com/refresh-bio/FAMSA", + "doi": "10.1038/srep33964", + "licence": ["GPL v3"], + "identifier": "biotools:famsa" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input sequences in FASTA format", + "pattern": "*.{fa,fasta}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1919" + }, + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ] + ], + "output": { + "tree": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" + } + }, + { + "*.dnd": { + "type": "file", + "description": "Guide tree file in Newick format", + "pattern": "*.{dnd}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2006" + } + ] + } + } + ] + ], + "versions_famsa": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "famsa": { + "type": "string", + "description": "The tool name" + } + }, + { + "famsa -help 2>&1 | sed '2!d;s/.*version //;s/ .*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "famsa": { + "type": "string", + "description": "The tool name" + } + }, + { + "famsa -help 2>&1 | sed '2!d;s/.*version //;s/ .*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@luisas", "@JoseEspinosa"], + "maintainers": ["@luisas", "@JoseEspinosa"] + }, + "pipelines": [ + { + "name": "multiplesequencealign", + "version": "1.1.1" + } + ] }, { - "name": "chipseq", - "version": "2.1.0" + "name": "faqcs", + "path": "modules/nf-core/faqcs/meta.yml", + "type": "module", + "meta": { + "name": "faqcs", + "description": "Perform adapter and quality trimming on sequencing reads with reporting", + "keywords": ["trimming", "quality control", "fastq", "faqcs"], + "tools": [ + { + "faqcs": { + "description": "FaQCs combines several features of currently available applications into a single, user-friendly process, and includes additional unique capabilities such as filtering the PhiX control sequences, conversion of FASTQ formats, and multi-threading. The original data and trimmed summaries are reported within a variety of graphics and reports, providing a simple way to do data quality control and assurance.\n", + "homepage": "https://github.com/LANL-Bioinformatics/FaQCs", + "documentation": "https://github.com/LANL-Bioinformatics/FaQCs", + "tool_dev_url": "https://github.com/LANL-Bioinformatics/FaQCs", + "doi": "10.1186/s12859-014-0366-2", + "licence": ["GPLv3 License"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for\nsingle-end and paired-end data, respectively.\n", + "ontologies": [] + } + } + ] + ], + "output": { + "reads": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.trimmed.fastq.gz": { + "type": "file", + "description": "The trimmed/modified fastq reads", + "pattern": "*trimmed.fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "stats": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.stats.txt": { + "type": "file", + "description": "trimming/qc text stats file", + "pattern": "*.stats.txt", + "ontologies": [] + } + } + ] + ], + "debug": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "./debug": { + "type": "directory", + "description": "trimming/qc files from --debug option", + "pattern": "./debug" + } + } + ] + ], + "statspdf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_qc_report.pdf": { + "type": "file", + "description": "trimming/qc pdf report file", + "pattern": "*_qc_report.pdf", + "ontologies": [] + } + } + ] + ], + "reads_fail": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.discard.fastq.gz": { + "type": "file", + "description": "Reads that failed the preprocessing (Optional with --discard args setting)", + "pattern": "*discard.fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "reads_unpaired": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.trimmed.unpaired.fastq.gz": { + "type": "file", + "description": "Reads without matching mates in paired-end files (Optional)", + "pattern": "*trimmed.unpaired.fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "fastq log file", + "pattern": "*.log", + "ontologies": [] + } + } + ] + ], + "versions_faqcs": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "faqcs": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "FaQCs --version 2>&1 | sed 's/^.*Version: //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "faqcs": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "FaQCs --version 2>&1 | sed 's/^.*Version: //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@mjcipriano", "@sateeshperi", "@hseabolt"], + "maintainers": ["@mjcipriano", "@sateeshperi", "@hseabolt"] + } }, { - "name": "sammyseq", - "version": "dev" - } - ] - }, - { - "name": "deepvariant", - "path": "modules/nf-core/deepvariant/meta.yml", - "type": "module", - "meta": { - "name": "deepvariant", - "description": "(DEPRECATED - see main.nf) DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data", - "deprecated": true, - "keywords": [ - "variant calling", - "machine learning", - "neural network" - ], - "tools": [ - { - "deepvariant": { - "description": "DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data", - "homepage": "https://github.com/google/deepvariant", - "documentation": "https://github.com/google/deepvariant", - "tool_dev_url": "https://github.com/google/deepvariant", - "doi": "10.1038/nbt.4235", - "licence": [ - "BSD-3-clause" - ], - "identifier": "biotools:deepvariant" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM file", - "pattern": "*.bam/cram", - "ontologies": [] - } - }, - { - "index": { - "type": "file", - "description": "Index of BAM/CRAM file", - "pattern": "*.bai/crai", - "ontologies": [] - } - }, - { - "intervals": { - "type": "file", - "description": "file containing intervals", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference fasta file", - "pattern": "*.fasta", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fai": { - "type": "file", - "description": "Index of reference fasta file", - "pattern": "*.fai", - "ontologies": [] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "gzi": { - "type": "file", - "description": "GZI index of reference fasta file", - "pattern": "*.gzi", - "ontologies": [] - } - } - ], - [ - { - "meta5": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } + "name": "fargene", + "path": "modules/nf-core/fargene/meta.yml", + "type": "module", + "meta": { + "name": "fargene", + "description": "tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output.", + "keywords": ["antibiotic resistance genes", "ARGs", "identifier", "metagenomic", "contigs"], + "tools": [ + { + "fargene": { + "description": "Fragmented Antibiotic Resistance Gene Identifier takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output", + "homepage": "https://github.com/fannyhb/fargene", + "documentation": "https://github.com/fannyhb/fargene", + "tool_dev_url": "https://github.com/fannyhb/fargene", + "licence": ["MIT"], + "identifier": "biotools:fargene" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "uncompressed fasta file or paired-end fastq files containing either genomes or longer contigs as nucleotide or protein sequences (fasta) or fragmented metagenomic reads (fastq)", + "pattern": "*.{fasta}", + "ontologies": [] + } + } + ], + { + "hmm_model": { + "type": "string", + "description": "name of custom hidden markov model to be used [pre-defined class_a, class_b_1_2, class_b_3, class_c, class_d_1, class_d_2, qnr, tet_efflux, tet_rpg, tet_enzyme]" + } + } + ], + "output": { + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "log file", + "pattern": "*.{log}", + "ontologies": [] + } + } + ] + ], + "txt": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/results_summary.txt": { + "type": "file", + "description": "analysis summary text file", + "pattern": "*.{txt}", + "ontologies": [] + } + } + ] + ], + "hmm": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/hmmsearchresults/*.out": { + "type": "file", + "description": "output from hmmsearch (both single gene annotations + contigs)", + "pattern": "*.{out}", + "ontologies": [] + } + } + ] + ], + "hmm_genes": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/hmmsearchresults/retrieved-*.out": { + "type": "file", + "description": "output from hmmsearch (single gene annotations only)", + "pattern": "retrieved-*.{out}", + "ontologies": [] + } + } + ] + ], + "orfs": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/predictedGenes/predicted-orfs.fasta": { + "type": "file", + "description": "open reading frames (ORFs)", + "pattern": "*.{fasta}", + "ontologies": [] + } + } + ] + ], + "orfs_amino": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/predictedGenes/predicted-orfs-amino.fasta": { + "type": "file", + "description": "protein translation of open reading frames (ORFs)", + "pattern": "*.{fasta}", + "ontologies": [] + } + } + ] + ], + "contigs": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/predictedGenes/retrieved-contigs.fasta": { + "type": "file", + "description": "(complete) contigs that passed the final full-length classification", + "pattern": "*.{fasta}", + "ontologies": [] + } + } + ] + ], + "contigs_pept": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/predictedGenes/retrieved-contigs-peptides.fasta": { + "type": "file", + "description": "parts of the contigs that passed the final classification step that aligned with the HMM, as amino acid sequences", + "pattern": "*.{fasta}", + "ontologies": [] + } + } + ] + ], + "filtered": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/predictedGenes/*filtered.fasta": { + "type": "file", + "description": "sequences that passed the final classification step, but only the parts that where predicted by the HMM to be part of the gene", + "pattern": "*.{fasta}", + "ontologies": [] + } + } + ] + ], + "filtered_pept": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/predictedGenes/*filtered-peptides.fasta": { + "type": "file", + "description": "sequences from filtered.fasta, translated in the same frame as the gene is predicted to be located", + "pattern": "*.{fasta}", + "ontologies": [] + } + } + ] + ], + "fragments": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/retrievedFragments/all_retrieved_*.fastq": { + "type": "file", + "description": "All quality controlled retrieved fragments that were classified as positive, together with its read-pair, gathered in two files", + "pattern": "*.{fastq}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ] + ], + "trimmed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/retrievedFragments/trimmedReads/*.fasta": { + "type": "file", + "description": "The quality controlled retrieved fragments from each input file.", + "pattern": "*.{fasta}", + "ontologies": [] + } + } + ] + ], + "spades": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/spades_assembly/*": { + "type": "directory", + "description": "The output from the SPAdes assembly", + "pattern": "spades_assembly" + } + } + ] + ], + "metagenome": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/tmpdir/*.fasta": { + "type": "file", + "description": "The FASTQ to FASTA converted input files from metagenomic reads.", + "pattern": "*.{fasta}", + "ontologies": [] + } + } + ] + ], + "tmp": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/tmpdir/*.out": { + "type": "file", + "description": "The from FASTQ to FASTA converted input files and their translated input sequences. Are only saved if option --store-peptides is used.", + "pattern": "*.{fasta}", + "ontologies": [] + } + } + ] + ], + "versions_fargene": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "fargene": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "0.1": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "fargene": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "0.1": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@louperelo"], + "maintainers": ["@louperelo"] }, - { - "par_bed": { - "type": "file", - "description": "BED file containing PAR regions", - "pattern": "*.bed", - "ontologies": [] - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.vcf.gz": { - "type": "file", - "description": "Compressed VCF file", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "vcf_tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.vcf.gz.tbi": { - "type": "file", - "description": "Tabix index of compressed VCF file", - "pattern": "*.vcf.gz.tbi", - "ontologies": [] - } - } - ] - ], - "gvcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.g.vcf.gz": { - "type": "file", - "description": "Compressed GVCF file", - "pattern": "*.g.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "gvcf_tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.g.vcf.gz.tbi": { - "type": "file", - "description": "Tabix index of compressed GVCF file", - "pattern": "*.g.vcf.gz.tbi", - "ontologies": [] - } - } + "pipelines": [ + { + "name": "funcscan", + "version": "3.0.0" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] }, - "authors": [ - "@abhi18av", - "@ramprasadn" - ], - "maintainers": [ - "@abhi18av", - "@ramprasadn" - ] - }, - "pipelines": [ { - "name": "pacvar", - "version": "1.0.1" + "name": "fast2q", + "path": "modules/nf-core/fast2q/meta.yml", + "type": "module", + "meta": { + "name": "fast2q", + "description": "A program that counts sequence occurrences in FASTQ files.", + "keywords": ["CRISPRi", "FASTQ", "genomics"], + "tools": [ + { + "2FAST2Q": { + "description": "2FAST2Q is ideal for CRISPRi-Seq, and for extracting and counting any kind of information from reads in the fastq format, such as barcodes in Bar-seq experiments.\n2FAST2Q can work with sequence mismatches, Phred-score, and be used to find and extract unknown sequences delimited by known sequences.\n2FAST2Q can extract multiple features per read using either fixed positions or delimiting search sequences.\n", + "homepage": "https://github.com/afombravo/2FAST2Q", + "doi": "10.7717/peerj.14041", + "licence": ["GPL-3.0-or-later"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing output name.\ne.g. [ id:'test']\n" + } + }, + { + "fastq": { + "type": "directory", + "description": "Folder with FASTQ file(s). 2FAST2Q automatically picks up all the FASTQ files inside the provided folder.", + "pattern": "*.{fastq,gz}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'library_name', multiple_features_per_read:false ]\n" + } + }, + { + "library": { + "type": "file", + "description": ".csv library file following the ´Feature_name,sequence´ or ´Feature_name,sequence1:sequence2´ format. See 2FAST2Q instructions for more information.", + "pattern": "*.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "output": { + "count_matrix": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing output name.\ne.g. [ id:'test' ]\n" + } + }, + { + "${prefix}.csv": { + "type": "file", + "description": "Count matrix csv file\n", + "ontologies": [] + } + } + ] + ], + "stats": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing output name.\ne.g. [ id:'test' ]\n" + } + }, + { + "${prefix}_stats.csv": { + "type": "file", + "description": "File containing all the relevant statistics such as quality passing reads, aligned reads, total reads, and sample run times.\n", + "ontologies": [] + } + } + ] + ], + "distribution_plot": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing output name.\ne.g. [ id:'test' ]\n" + } + }, + { + "${prefix}_distribution_plot.png": { + "type": "file", + "description": "Violin plot of the distribution of reads per feature across all samples.\n", + "ontologies": [] + } + } + ] + ], + "reads_plot": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing output name.\ne.g. [ id:'test' ]\n" + } + }, + { + "${prefix}_reads_plot.png": { + "type": "file", + "description": "Bar plot with the distribution of reads, in absolute numbers, binned to the different quality metrics indicated in the statistics.csv\n", + "ontologies": [] + } + } + ] + ], + "reads_plot_percentage": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing output name.\ne.g. [ id:'test' ]\n" + } + }, + { + "${prefix}_reads_plot_percentage.png": { + "type": "file", + "description": "Bar plot with the distribution of reads, in percentage, binned to the different quality metrics indicated in the statistics.csv\n", + "ontologies": [] + } + } + ] + ], + "versions_fast2q": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "fast2q": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "2fast2q -v | sed -n \"s/Version: //p\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "fast2q": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "2fast2q -v | sed -n \"s/Version: //p\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@afombravo"], + "maintainers": ["@afombravo"] + } }, { - "name": "variantcatalogue", - "version": "dev" - } - ] - }, - { - "name": "deepvariant_callvariants", - "path": "modules/nf-core/deepvariant/callvariants/meta.yml", - "type": "module", - "meta": { - "name": "deepvariant_callvariants", - "description": "Call variants from the examples produced by make_examples", - "keywords": [ - "variant calling", - "machine learning", - "neural network" - ], - "tools": [ - { - "deepvariant": { - "description": "DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data", - "homepage": "https://github.com/google/deepvariant", - "documentation": "https://github.com/google/deepvariant", - "tool_dev_url": "https://github.com/google/deepvariant", - "doi": "10.1038/nbt.4235", - "licence": [ - "BSD-3-clause" - ], - "identifier": "biotools:deepvariant" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "make_examples_tfrecords": { - "type": "file", - "description": "The actual sharded input files, from DEEPVARIANT_MAKEEXAMPLES process", - "pattern": "*.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "output": { - "call_variants_tfrecords": [ - [ - { - "meta": { - "type": "list", - "description": "Each output contains: unique ID string from input channel, meta, tfrecord file with variant calls.\n" - } - }, - { - "${prefix}.call-*-of-*.tfrecord.gz": { - "type": "list", - "description": "Each output contains: unique ID string from input channel, meta, tfrecord file with variant calls.\n" - } - } - ] - ], - "versions_deepvariant": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "deepvariant": { - "type": "string", - "description": "The tool name" - } - }, - { - "/opt/deepvariant/bin/run_deepvariant --version | sed 's/^.*version //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "deepvariant": { - "type": "string", - "description": "The tool name" - } - }, - { - "/opt/deepvariant/bin/run_deepvariant --version | sed 's/^.*version //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@abhi18av", - "@ramprasadn", - "@fa2k" - ], - "maintainers": [ - "@abhi18av", - "@ramprasadn" - ] - }, - "pipelines": [ - { - "name": "pacvar", - "version": "1.0.1" - } - ] - }, - { - "name": "deepvariant_makeexamples", - "path": "modules/nf-core/deepvariant/makeexamples/meta.yml", - "type": "module", - "meta": { - "name": "deepvariant_makeexamples", - "description": "Transforms the input alignments to a format suitable for the deep neural network variant caller", - "keywords": [ - "variant calling", - "machine learning", - "neural network" - ], - "tools": [ - { - "deepvariant": { - "description": "DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data", - "homepage": "https://github.com/google/deepvariant", - "documentation": "https://github.com/google/deepvariant", - "tool_dev_url": "https://github.com/google/deepvariant", - "doi": "10.1038/nbt.4235", - "licence": [ - "BSD-3-clause" - ], - "identifier": "biotools:deepvariant" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM file", - "pattern": "*.bam/cram", - "ontologies": [] - } - }, - { - "index": { - "type": "file", - "description": "Index of BAM/CRAM file", - "pattern": "*.bai/crai", - "ontologies": [] - } - }, - { - "intervals": { - "type": "file", - "description": "Interval file for targeted regions", - "pattern": "*.bed", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference fasta file", - "pattern": "*.fasta", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fai": { - "type": "file", - "description": "Index of reference fasta file", - "pattern": "*.fai", - "ontologies": [] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "gzi": { - "type": "file", - "description": "GZI index of reference fasta file", - "ontologies": [] - } - } - ], - [ - { - "meta5": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n", - "pattern": "*.gzi" - } - }, - { - "par_bed": { - "type": "file", - "description": "BED file containing PAR regions", - "pattern": "*.bed", - "ontologies": [] - } - } - ] - ], - "output": { - "examples": [ - [ - { - "meta": { - "type": "list", - "description": "Tuple containing sample metadata and examples that can be used for calling\n" - } - }, - { - "${prefix}.examples.tfrecord-*-of-*.gz{,.example_info.json}": { - "type": "list", - "description": "Tuple containing sample metadata and examples that can be used for calling\n" - } - } - ] - ], - "gvcf": [ - [ - { - "meta": { - "type": "list", - "description": "Tuple containing sample metadata and examples that can be used for calling\n" - } - }, - { - "${prefix}.gvcf.tfrecord-*-of-*.gz": { - "type": "list", - "description": "Tuple containing sample metadata and the GVCF data in tfrecord format\n" - } - } - ] - ], - "small_model_calls": [ - [ - { - "meta": { - "type": "list", - "description": "Tuple containing sample metadata and examples that can be used for calling\n" - } - }, - { - "${prefix}_call_variant_outputs.examples.tfrecord-*-of-*.gz": { - "type": "list", - "description": "Optional variant calls from the small model, if enabled, in tfrecord format\n" - } - } - ] - ], - "versions_deepvariant": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "deepvariant": { - "type": "string", - "description": "The tool name" - } - }, - { - "/opt/deepvariant/bin/run_deepvariant --version | sed 's/^.*version //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "deepvariant": { - "type": "string", - "description": "The tool name" - } - }, - { - "/opt/deepvariant/bin/run_deepvariant --version | sed 's/^.*version //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@abhi18av", - "@ramprasadn", - "@fa2k" - ], - "maintainers": [ - "@abhi18av", - "@ramprasadn" - ] - }, - "pipelines": [ - { - "name": "pacvar", - "version": "1.0.1" - } - ] - }, - { - "name": "deepvariant_postprocessvariants", - "path": "modules/nf-core/deepvariant/postprocessvariants/meta.yml", - "type": "module", - "meta": { - "name": "deepvariant_postprocessvariants", - "description": "DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data", - "keywords": [ - "variant calling", - "machine learning", - "neural network" - ], - "tools": [ - { - "deepvariant": { - "description": "DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data", - "homepage": "https://github.com/google/deepvariant", - "documentation": "https://github.com/google/deepvariant", - "tool_dev_url": "https://github.com/google/deepvariant", - "doi": "10.1038/nbt.4235", - "licence": [ - "BSD-3-clause" - ], - "identifier": "biotools:deepvariant" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "variant_calls_tfrecord_files": { - "type": "file", - "description": "One or more data files containing variant calls from DEEPVARIANT_CALLVARIANTS\n", - "pattern": "*.tfrecord.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - }, - { - "gvcf_tfrecords": { - "type": "file", - "description": "Sharded tfrecord file from DEEPVARIANT_MAKEEXAMPLES with the coverage information used for GVCF output\n", - "pattern": "*.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - }, - { - "small_model_calls": { - "type": "file", - "description": "Sharded tfrecord file from DEEPVARIANT_MAKEEXAMPLES with variant calls from the small model\n", - "pattern": "*.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - }, - { - "intervals": { - "type": "file", - "description": "Interval file for targeted regions", - "pattern": "*.bed", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference fasta file", - "pattern": "*.fasta", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fai": { - "type": "file", - "description": "Index of reference fasta file", - "pattern": "*.fai", - "ontologies": [] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "gzi": { - "type": "file", - "description": "GZI index of reference fasta file", - "pattern": "*.gzi", - "ontologies": [] - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.vcf.gz": { - "type": "file", - "description": "Compressed VCF file", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "vcf_index": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.vcf.gz.{tbi,csi}": { - "type": "file", - "description": "Index for VCF", - "pattern": "$*.vcf.gz.{tbi,csi}", - "ontologies": [] - } - } - ] - ], - "gvcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.g.vcf.gz": { - "type": "file", - "description": "Compressed GVCF file", - "pattern": "*.g.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "gvcf_index": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.g.vcf.gz.{tbi,csi}": { - "type": "file", - "description": "Index for GVCF", - "pattern": "*.g.vcf.gz.{tbi,csi}", - "ontologies": [] - } - } - ] - ], - "versions_deepvariant": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "deepvariant": { - "type": "string", - "description": "The tool name" - } - }, - { - "/opt/deepvariant/bin/run_deepvariant --version | sed 's/^.*version //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "deepvariant": { - "type": "string", - "description": "The tool name" - } - }, - { - "/opt/deepvariant/bin/run_deepvariant --version | sed 's/^.*version //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@abhi18av", - "@ramprasadn", - "@fa2k" - ], - "maintainers": [ - "@abhi18av", - "@ramprasadn" - ] - }, - "pipelines": [ - { - "name": "pacvar", - "version": "1.0.1" - } - ] - }, - { - "name": "deepvariant_rundeepvariant", - "path": "modules/nf-core/deepvariant/rundeepvariant/meta.yml", - "type": "module", - "meta": { - "name": "deepvariant_rundeepvariant", - "description": "DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data", - "keywords": [ - "variant calling", - "machine learning", - "neural network" - ], - "tools": [ - { - "deepvariant": { - "description": "DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data", - "homepage": "https://github.com/google/deepvariant", - "documentation": "https://github.com/google/deepvariant", - "tool_dev_url": "https://github.com/google/deepvariant", - "doi": "10.1038/nbt.4235", - "licence": [ - "BSD-3-clause" - ], - "identifier": "biotools:deepvariant" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM file", - "pattern": "*.bam/cram", - "ontologies": [] - } - }, - { - "index": { - "type": "file", - "description": "Index of BAM/CRAM file", - "pattern": "*.bai/crai", - "ontologies": [] - } - }, - { - "intervals": { - "type": "file", - "description": "file containing intervals", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference fasta file", - 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If provided, ql will be ignored.", + "pattern": "*.{fasta,fna,fa}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information for the reference" + } + }, + { + "reference": { + "type": "file", + "description": "Fasta file to be used as the reference. If provided, rl will be ignored.", + "pattern": "*.{fasta,fna,fa}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + { + "ql": { + "type": "file", + "description": "File containing a list of query fasta paths. query input takes precedence over this list if both are provided.", + "pattern": "*.txt", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + }, + { + "rl": { + "type": "file", + "description": "File containing a list of reference fasta paths. reference input takes precedence over this list if both are provided.", + "pattern": "*.txt", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + } + ], + "output": { + "ani": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "ANI results file", + "pattern": "*.txt", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + } + ] + ], + "visual": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.visual": { + "type": "file", + "optional": true, + "description": "FastANI visualization output", + "pattern": "*.visual", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "matrix": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.matrix": { + "type": "file", + "optional": true, + "description": "ANI matrix output", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3033" + } + ] + } + } + ] + ], + "versions_fastani": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "fastani": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "fastANI --version 2>&1 | head -1 | sed \"s/version\\ //\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "fastani": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "fastANI --version 2>&1 | head -1 | sed \"s/version\\ //\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@abhi18av", "@Ethan-Hetrick"], + "maintainers": ["@abhi18av", "@Ethan-Hetrick"] } - ], - [ - { - "meta5": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } + }, + { + "name": "fastavalidator", + "path": "modules/nf-core/fastavalidator/meta.yml", + "type": "module", + "meta": { + "name": "fastavalidator", + "description": "\"Python C-extension for a simple validator for fasta files. 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{ - "par_bed": { - "type": "file", - "description": "BED file containing PAR regions", - "pattern": "*.bed", - "ontologies": [] - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.vcf.gz": { - "type": "file", - "description": "Compressed VCF file", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "vcf_index": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.vcf.gz.{tbi,csi}": { - "type": "file", - "description": "Tabix index file of compressed VCF", - "pattern": "*.vcf.gz.{tbi,csi}", - "ontologies": [] - } - } - ] - ], - "gvcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.g.vcf.gz": { - "type": "file", - "description": "Compressed GVCF file", - "pattern": "*.g.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "gvcf_index": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.g.vcf.gz.{tbi,csi}": { - "type": "file", - "description": "Tabix index file of compressed GVCF", - "pattern": "*.g.vcf.gz.{tbi,csi}", - "ontologies": [] - } - } - ] - ], - "report": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.visual_report.html": { - "type": "file", - "description": "Visual report in HTML format", - "pattern": "*.html", - "optional": true, - "ontologies": [] - } - } - ] - ], - "versions_deepvariant": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - 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The executable takes a fasta formatted file and calculates some statistics of interest in windows", + "homepage": "https://github.com/tolkit/fasta_windows", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA file", + "pattern": "*.{fa,fasta,fna}", + "ontologies": [] + } + } + ] + ], + "output": { + "freq": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fw_out/*_freq_windows.tsv": { + "type": "file", + "description": "TSV file with frequencies and statistics", + "pattern": "*.{tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "mononuc": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fw_out/*_mononuc_windows.tsv": { + "type": "file", + "description": "TSV file with mononucleotide counts", + "pattern": "*.{tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "dinuc": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fw_out/*_dinuc_windows.tsv": { + "type": "file", + "description": "TSV file with dinucleotide counts", + "pattern": "*.{tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "trinuc": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fw_out/*_trinuc_windows.tsv": { + "type": "file", + "description": "TSV file with trinucleotide counts", + "pattern": "*.{tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "tetranuc": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fw_out/*_tetranuc_windows.tsv": { + "type": "file", + "description": "TSV file with tetranucleotide counts", + "pattern": "*.{tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_fasta_windows": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "fasta_windows": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "fasta_windows --version | cut -d\" \" -f3": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "fasta_windows": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "fasta_windows --version | cut -d\" \" -f3": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@muffato"], + "maintainers": ["@muffato"] + } }, { - 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"description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF file", - "pattern": "{*.vcf,vcf.gz,bcf,bcf.gz}", - "ontologies": [] - } - } - ] - ], - "output": { - "report": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.visual_report.html": { - "type": "file", - "description": "Visual report in HTML format", - "pattern": "*.html", - "ontologies": [] - } - } - ] - ], - "versions_deepvariant": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "deepvariant": { - "type": "string", - "description": "The tool name" - } - }, - { - "/opt/deepvariant/bin/run_deepvariant --version | sed 's/^.*version //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "deepvariant": { - "type": "string", - "description": "The tool name" - } - }, - { - "/opt/deepvariant/bin/run_deepvariant --version | sed 's/^.*version //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@fellen31" - ], - "maintainers": [ - "@fellen31" - ] - } - }, - { - "name": "delly_call", - "path": "modules/nf-core/delly/call/meta.yml", - "type": "module", - "meta": { - "name": "delly_call", - "description": "Call structural variants", - "keywords": [ - "genome", - "structural", - "variants", - "bcf" - ], - "tools": [ - { - "delly": { - "description": "Structural variant discovery by integrated paired-end and split-read analysis", - "homepage": "https://github.com/dellytools/delly", - "documentation": "https://github.com/dellytools/delly/blob/master/README.md", - "doi": "10.1093/bioinformatics/bts378", - "licence": [ - "BSD-3-Clause" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM file from alignment must be sorted, indexed, and duplicate marked", - "pattern": "*.{bam,cram}", - "ontologies": [] - } - }, - { - "input_index": { - "type": "file", - "description": "Index of the BAM/CRAM file", - "pattern": "*.{bai,crai}", - "ontologies": [] - } - }, - { - "vcf": { - "type": "file", - "description": "A BCF/VCF file to genotype with Delly. If this is supplied, the variant calling will be skipped", - "pattern": "*.{vcf.gz,bcf}", - "ontologies": [] - } - }, - { - "vcf_index": { - "type": "file", - "description": "The index of the BCF/VCF file", - "pattern": "*.{tbi,csi}", - "ontologies": [] - } - }, - { - "exclude_bed": { - "type": "file", - "description": "An optional bed file containing regions to exclude from the called VCF", - "pattern": "*.bed", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing fasta information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference fasta file", - "pattern": "*.{fasta,fa}", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing fasta index information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fai": { - "type": "file", - "description": "Index of reference fasta file to identify split-reads", - "pattern": "*.fai", - "ontologies": [] - } - } - ], - { - "suffix": { - "type": "string", - "description": "A flag to specify whether the output should be in BCF or VCF format", - "enum": [ - "bcf", - "vcf" - ] - } - } - ], - "output": { - "bcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.{bcf,vcf.gz}": { - "type": "file", - "description": "Called variants in BCF/VCF format. Set suffix to either \"bcf\" or \"vcf\" to define the output type", - "pattern": "*.{bcf,vcf.gz}", - "ontologies": [] - } - } - ] - ], - "csi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.{csi,tbi}": { - "type": "file", - "description": "A generated csi index that matches the bcf output (not generated for vcf files)", - "pattern": "*.{bcf.csi}", - "ontologies": [] - } - } - ] - ], - "versions_delly": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "delly": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "delly --version |& sed -n '1s/Delly version: *v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "delly": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "delly --version |& sed -n '1s/Delly version: *v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@projectoriented", - "@nvnieuwk" - ], - "maintainers": [ - "@projectoriented", - "@nvnieuwk" - ] - }, - "pipelines": [ - { - "name": "tbanalyzer", - "version": "dev" - } - ] - }, - { - "name": "demuxem", - "path": "modules/nf-core/demuxem/meta.yml", - "type": "module", - "meta": { - "name": "demuxem", - "description": "Demultiplexing cell nucleus hashing data, using the estimated antibody background probability.", - "keywords": [ - "demultiplexing", - "hashing-based deconvoltion", - "single-cell" - ], - "tools": [ - { - "demuxem": { - "description": "DemuxEM is the demultiplexing module of Pegasus, which works on cell-hashing and nucleus-hashing genomics data.", - "homepage": "https://demuxEM.readthedocs.io", - "documentation": "https://demuxEM.readthedocs.io", - "tool_dev_url": "https://github.com/lilab-bcb/pegasus/tree/master", - "doi": "10.1038/s41467-019-10756-2", - "licence": [ - "BSD-3-clause" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "input_raw_gene_bc_matrices_h5": { - "type": "string", - "description": "Path to file containing input raw RNA expression matrix in 10x hdf5 format\npattern: \"*.{h5}\"\n" - } - }, - { - "input_hto_csv_file": { - "type": "string", - "description": "Path to file containing input HTO (antibody tag) count matrix in CSV format.\n", - "pattern": "*.{csv}" - } - } - ], - { - "generate_gender_plot": { - "type": "string", - "description": "Generate violin plots using gender-specific genes (e.g. Xist). It is a comma-separated list of gene names.\n" - } - }, - { - "genome": { - "type": "string", - "description": "Reference genome name. If not provided, the tools infers it from the expression matrix file\n" - } - }, - { - "generate_diagnostic_plots": { - "type": "string", - "description": "Generate diagnostic plots, including the background/signal between HTO counts, estimated background probabilities, HTO distributions.\n" - } - } - ], - "output": { - "zarr": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample1' ]\n" - } - }, - { - "*_demux.zarr.zip": { - "type": "file", - "description": "RNA expression matrix with demultiplexed sample identities in Zarr format.\n", - "pattern": "*_demux.zarr.zip", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3987" - } - ] - } - } - ] - ], - "out_zarr": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample1' ]\n" - } - }, - { - "*.out.demuxEM.zarr.zip": { - "type": "file", - "description": "DemuxEM-calculated results in Zarr format, containing two datasets, one for HTO and one for RNA.\n", - "pattern": "*.out.demuxEM.zarr.zip", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3987" - } - ] - } - } - ] - ], - "versions_demuxem": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "demuxEM": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "demuxEM --version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "demuxEM": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "demuxEM --version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@mari-ga", - "@maxozo", - "@wxicu", - "@Zethson" - ], - "maintainers": [ - "@mari-ga", - "@maxozo", - "@wxicu", - "@Zethson" - ] - } - }, - { - "name": "deseq2_differential", - "path": "modules/nf-core/deseq2/differential/meta.yml", - "type": "module", - "meta": { - "name": "deseq2_differential", - "description": "runs a differential expression analysis with DESeq2", - "keywords": [ - "differential", - "expression", - "rna-seq", - "deseq2" - ], - "tools": [ - { - "deseq2": { - "description": "Differential gene expression analysis based on the negative binomial distribution", - "homepage": "https://bioconductor.org/packages/release/bioc/html/DESeq2.html", - "documentation": "https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html", - "tool_dev_url": "https://github.com/mikelove/DESeq2", - "doi": "10.1186/s13059-014-0550-8", - "licence": [ - "LGPL >=3" - ], - "identifier": "biotools:deseq2" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing contrast information. This can be used at the\nworkflow level to pass optional parameters to the module, e.g.\n[ id:'contrast1', blocking:'patient' ] passed in as ext.args like:\n'--blocking_variable $meta.blocking'.\n" - } - }, - { - "contrast_variable": { - "type": "string", - "description": "The column in the sample sheet that should be used to define groups for\ncomparison\n" - } - }, - { - "reference": { - "type": "string", - "description": "The value within the contrast_variable column of the sample sheet that\nshould be used to derive the reference samples\n" - } - }, - { - "target": { - "type": "string", - "description": "The value within the contrast_variable column of the sample sheet that\nshould be used to derive the target samples\n" - } - }, - { - "formula": { - "type": "string", - "description": "(Optional) R formula string used for modeling, e.g. '~ treatment'." - } - }, - { - "comparison": { - "type": "string", - "description": "(Optional, mandatory if formula is provided) Literal string for contrasts, e.g. 'treatmenthND6'." - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy map containing study-wide metadata related to the sample sheet\nand matrix\n" - } - }, - { - "samplesheet": { - "type": "file", - "description": "CSV or TSV format sample sheet with sample metadata\n", - "ontologies": [] - } - }, - { - "counts": { - "type": "file", - "description": "Raw TSV or CSV format expression matrix as output from the nf-core\nRNA-seq workflow\n", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Meta map describing control genes, e.g. [ id: 'ERCC' ]\n", - "ontologies": [] - } - }, - { - "control_genes_file": { - "type": "file", - "description": "Text file listing control genes, one per line\n", - "ontologies": [] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy map containing study-wide metadata related to the transcript\nlengths file\n" - } - }, - { - "transcript_lengths_file": { - "type": "file", - "description": "Optional file of transcript lengths, with the same sample columns as\ncounts. If supplied, lengths will be supplied to DESeq2 to correct for\ndifferences in average transcript lengths across samples.\n", - "ontologies": [] - } - } - ] - ], - "output": { - "results": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing contrast information, same as input meta\n" - } - }, - { - "*.deseq2.results.tsv": { - "type": "file", - "description": "TSV-format table of differential expression information as output by DESeq2", - "pattern": "*.deseq2.results.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "dispersion_plot_png": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing contrast information, same as input meta\n" - } - }, - { - "*.deseq2.dispersion.png": { - "type": "file", - "description": "DESeq2 dispersion plot in PNG format", - "pattern": "*.deseq2.dispersion.png", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3603" - } - ] - } - } - ] - ], - "dispersion_plot_pdf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing contrast information, same as input meta\n" - } - }, - { - "*.deseq2.dispersion.pdf": { - "type": "file", - "description": "DESeq2 dispersion plot in PDF format", - "pattern": "*.deseq2.dispersion.pdf", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3508" - } - ] - } - } - ] - ], - "rdata": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing contrast information, same as input meta\n" - } - }, - { - "*.dds.rld.rds": { - "type": "file", - "description": "Serialised DESeq2 object", - "pattern": "*.dds.rld.rds", - "ontologies": [] - } - } - ] - ], - "size_factors": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing contrast information, same as input meta\n" - } - }, - { - "*.deseq2.sizefactors.tsv": { - "type": "file", - "description": "TSV-format table containing DESeq2 size factors", - "pattern": "*.deseq2.sizefactors.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "normalised_counts": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing contrast information, same as input meta\n" - } - }, - { - "*.normalised_counts.tsv": { - "type": "file", - "description": "TSV-format counts matrix, normalised to size factors", - "pattern": "*.normalised_counts.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "rlog_counts": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing contrast information, same as input meta\n" - } - }, - { - "*.rlog.tsv": { - "type": "file", - "description": "Optional, TSV-format counts matrix, normalised to size factors, with\nvariance stabilisation applied via `rlog()`.\n", - "pattern": "*.rlog.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "vst_counts": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing contrast information, same as input meta\n" - } - }, - { - "*.vst.tsv": { - "type": "file", - "description": "Optional, TSV-format counts matrix, normalised to size factors, with\nvariance stabilisation applied via `vst()`.\n", - "pattern": "*.vst.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "model": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing contrast information, same as input meta\n" - } - }, - { - "*.deseq2.model.txt": { - "type": "file", - "description": "TXT-format DESeq2 model", - "pattern": "*.deseq2.model.txt", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2330" - } - ] - } - } - ] - ], - "session_info": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing contrast information, same as input meta\n" - } - }, - { - "*.R_sessionInfo.log": { - "type": "file", - "description": "Dump of R SessionInfo", - "pattern": "*.R_sessionInfo.log", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "YAML file containing versions of tools used in the module", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "topics": { - "versions": [ - { - "versions.yml": { - "type": "string", - "description": "The name of the process" - } + "name": "fastk_fastk", + "path": "modules/nf-core/fastk/fastk/meta.yml", + "type": "module", + "meta": { + "name": "fastk_fastk", + "description": "A fast K-mer counter for high-fidelity shotgun datasets", + "keywords": ["k-mer", "count", "histogram"], + "tools": [ + { + "fastk": { + "description": "A fast K-mer counter for high-fidelity shotgun datasets", + "homepage": "https://github.com/thegenemyers/FASTK", + "tool_dev_url": "https://github.com/thegenemyers/FASTK", + "license": ["https://github.com/thegenemyers/FASTK/blob/master/LICENSE"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FASTA, FASTQ, SAM, BAM or CRAM files. All must be of the same type.\n", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + }, + { + "edam": "http://edamontology.org/format_2545" + }, + { + "edam": "http://edamontology.org/format_2573" + }, + { + "edam": "http://edamontology.org/format_2572" + }, + { + "edam": "http://edamontology.org/format_3462" + } + ] + } + } + ] + ], + "output": { + "hist": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.hist": { + "type": "file", + "description": "Histogram of k-mers", + "pattern": "*.hist", + "ontologies": [] + } + } + ] + ], + "ktab": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.ktab*": { + "type": "file", + "description": "A sorted table of all canonical k‑mers along with their counts.", + "pattern": "*.ktab*", + "ontologies": [] + } + } + ] + ], + "prof": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{prof,pidx}*": { + "type": "file", + "description": "A k‑mer count profile of each sequence in the input data set.", + "pattern": "*.{prof,pidx}*", + "ontologies": [] + } + } + ] + ], + "versions_fastk": [ + [ + { + "${task.process}": { + "type": "string", + "description": "Name of the process" + } + }, + { + "fastk": { + "type": "string", + "description": "Name of the tool" + } + }, + { + "1.2": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "FastK command stdout/stderr log file", + "pattern": "*.log", + "ontologies": [] + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "Name of the process" + } + }, + { + "fastk": { + "type": "string", + "description": "Name of the tool" + } + }, + { + "1.2": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@mahesh-panchal"], + "maintainers": ["@mahesh-panchal", "@gallvp"] } - ] }, - "authors": [ - "@pinin4fjords" - ], - "maintainers": [ - "@pinin4fjords" - ] - }, - "pipelines": [ { - "name": "differentialabundance", - "version": "1.5.0" + "name": "fastk_histex", + "path": "modules/nf-core/fastk/histex/meta.yml", + "type": "module", + "meta": { + "name": "fastk_histex", + "description": "A fast K-mer counter for high-fidelity shotgun datasets", + "keywords": ["k-mer", "histogram", "fastk"], + "tools": [ + { + "fastk": { + "description": "A fast K-mer counter for high-fidelity shotgun datasets", + "homepage": "https://github.com/thegenemyers/FASTK", + "tool_dev_url": "https://github.com/thegenemyers/FASTK", + "license": ["https://github.com/thegenemyers/FASTK/blob/master/LICENSE"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "histogram": { + "type": "file", + "description": "A FastK histogram file", + "pattern": "*.hist", + "ontologies": [] + } + } + ] + ], + "output": { + "hist": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.hist.txt": { + "type": "file", + "description": "A formatted histogram file", + "pattern": "*.hist", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_fastk": [ + [ + { + "${task.process}": { + "type": "string", + "description": "Name of the process" + } + }, + { + "fastk": { + "type": "string", + "description": "Name of the tool" + } + }, + { + "1.2": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "Name of the process" + } + }, + { + "fastk": { + "type": "string", + "description": "Name of the tool" + } + }, + { + "1.2": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@mahesh-panchal"], + "maintainers": ["@mahesh-panchal"] + } }, { - "name": "tfactivity", - "version": "dev" - } - ] - }, - { - "name": "diamond_blastp", - "path": "modules/nf-core/diamond/blastp/meta.yml", - "type": "module", - "meta": { - "name": "diamond_blastp", - "description": "Queries a DIAMOND database using blastp mode", - "keywords": [ - "fasta", - "diamond", - "blastp", - "DNA sequence" - ], - "tools": [ - { - "diamond": { - "description": "Accelerated BLAST compatible local sequence aligner", - "homepage": "https://github.com/bbuchfink/diamond", - "documentation": "https://github.com/bbuchfink/diamond/wiki", - "tool_dev_url": "https://github.com/bbuchfink/diamond", - "doi": "10.1038/s41592-021-01101-x", - "licence": [ - "GPL v3.0" - ], - "identifier": "biotools:diamond" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input fasta file containing query sequences", - "pattern": "*.{fa,fasta,fa.gz,fasta.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing db information\ne.g. [ id:'test2' ]\n" - } - }, - { - "db": { - "type": "file", - "description": "File of the indexed DIAMOND database", - "pattern": "*.dmnd", - "ontologies": [] - } - } - ], - { - "outfmt": { - "type": "integer", - "description": "Specify the type of output file to be generated.\n0, .blast, BLAST pairwise format.\n5, .xml, BLAST XML format.\n6, .txt, BLAST tabular format (default). This format can be customized, the 6 may be followed by a space-separated list of the blast_columns keywords, each specifying a field of the output.\n100, .daa, DIAMOND alignment archive (DAA). The DAA format is a proprietary binary format that can subsequently be used to generate other output formats using the view command. It is also supported by MEGAN and allows a quick import of results.\n101, .sam, SAM format.\n102, .tsv, Taxonomic classification. This format will not print alignments but only a taxonomic classification for each query using the LCA algorithm.\n103, .paf, PAF format. The custom fields in the format are AS (bit score), ZR (raw score) and ZE (e-value).\n", - "pattern": "0|5|6|100|101|102|103" - } - }, - { - "blast_columns": { - "type": "string", - "description": "Optional space separated list of DIAMOND tabular BLAST output keywords\nused in conjunction with the --outfmt 6 option (txt).\nOptions:\nqseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore\n" - } - } - ], - "output": { - "blast": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', db:'ncbi-refseq' ]\n" - } - }, - { - "*.{blast,blast.gz}": { - "type": "file", - "description": "File containing blastp hits", - "pattern": "*.{blast,blast.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3836" - } - ] - } - } - ] - ], - "xml": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', db:'ncbi-refseq' ]\n" - } - }, - { - "*.{xml,xml.gz}": { - "type": "file", - "description": "File containing blastp hits", - "pattern": "*.{xml,xml.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2332" - } - ] - } - } - ] - ], - "txt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', db:'ncbi-refseq' ]\n" - } - }, - { - "*.{txt,txt.gz}": { - "type": "file", - "description": "File containing hits in tabular BLAST format.", - "pattern": "*.{txt,txt.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1333" - } - ] - } - } - ] - ], - "daa": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', db:'ncbi-refseq' ]\n" - } - }, - { - "*.{daa,daa.gz}": { - "type": "file", - "description": "File containing hits DAA format", - "pattern": "*.{daa,daa.gz}", - "ontologies": [] - } - } - ] - ], - "sam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', db:'ncbi-refseq' ]\n" - } - }, - { - "*.{sam,sam.gz}": { - "type": "file", - "description": "File containing aligned reads in SAM format", - "pattern": "*.{sam,sam.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2573" - } - ] - } - } - ] - ], - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', db:'ncbi-refseq' ]\n" - } - }, - { - "*.{tsv,tsv.gz}": { - "type": "file", - "description": "Tab separated file containing taxonomic classification of hits", - "pattern": "*.{tsv,tsv.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "paf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', db:'ncbi-refseq' ]\n" - } - }, - { - "*.{paf,paf.gz}": { - "type": "file", - "description": "File containing aligned reads in pairwise mapping format format", - "pattern": "*.{paf,paf.gz}", - "ontologies": [] - } - } - ] - ], - "versions_diamond": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "diamond": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "diamond --version 2>&1 | tail -n 1 | sed \"s/^diamond version //\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "diamond": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "diamond --version 2>&1 | tail -n 1 | sed \"s/^diamond version //\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@spficklin", - "@jfy133" - ], - "maintainers": [ - "@spficklin", - "@jfy133", - "@vagkaratzas" - ] - } - }, - { - "name": "diamond_blastx", - "path": "modules/nf-core/diamond/blastx/meta.yml", - "type": "module", - "meta": { - "name": "diamond_blastx", - "description": "Queries a DIAMOND database using blastx mode", - "keywords": [ - "fasta", - "diamond", - "blastx", - "DNA sequence" - ], - "tools": [ - { - "diamond": { - "description": "Accelerated BLAST compatible local sequence aligner", - "homepage": "https://github.com/bbuchfink/diamond", - "documentation": "https://github.com/bbuchfink/diamond/wiki", - "tool_dev_url": "https://github.com/bbuchfink/diamond", - "doi": "10.1038/s41592-021-01101-x", - "licence": [ - "GPL v3.0" - ], - "identifier": "biotools:diamond" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input fasta file containing query sequences", - "pattern": "*.{fa,fasta,fa.gz,fasta.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing db information\ne.g. [ id:'test2', single_end:false ]\n" - } - }, - { - "db": { - "type": "file", - "description": "File of the indexed DIAMOND database", - "pattern": "*.dmnd", - "ontologies": [] - } - } - ], - { - "out_ext": { - "type": "string", - "description": "Specify the type of output file to be generated. `blast` corresponds to\nBLAST pairwise format. `xml` corresponds to BLAST xml format.\n`txt` corresponds to to BLAST tabular format. `tsv` corresponds to\ntaxonomic classification format.\n", - "pattern": "blast|xml|txt|daa|sam|tsv|paf" - } - }, - { - "blast_columns": { - "type": "string", - "description": "Optional space separated list of DIAMOND tabular BLAST output keywords\nused for in conjunction with the 'txt' out_ext option (--outfmt 6). Options:\nqseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore\n" - } - } - ], - "output": { - "blast": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.blast": { - "type": "file", - "description": "File containing blastp hits", - "pattern": "*.{blast}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3836" - } - ] - } - } - ] - ], - "xml": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.xml": { - "type": "file", - "description": "File containing blastp hits", - "pattern": "*.{xml}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2332" - } - ] - } - } - ] - ], - "txt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.txt": { - "type": "file", - "description": "File containing hits in tabular BLAST format.", - "pattern": "*.{txt}", - "ontologies": [] - } - } - ] - ], - "daa": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.daa": { - "type": "file", - "description": "File containing hits DAA format", - "pattern": "*.{daa}", - "ontologies": [] - } - } - ] - ], - "sam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.sam": { - "type": "file", - "description": "File containing aligned reads in SAM format", - "pattern": "*.{sam}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2573" - } - ] - } - } - ] - ], - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "Tab separated file containing taxonomic classification of hits", - "pattern": "*.{tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "paf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.paf": { - "type": "file", - "description": "File containing aligned reads in pairwise mapping format format", - "pattern": "*.{paf}", - "ontologies": [] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.log": { - "type": "file", - "description": "Log file containing stdout information", - "pattern": "*.{log}", - "ontologies": [] - } - } - ] - ], - "versions_diamond": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "diamond": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "diamond --version | sed 's/diamond version //g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "diamond": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "diamond --version | sed 's/diamond version //g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@spficklin", - "@jfy133", - "@mjamy" - ], - "maintainers": [ - "@spficklin", - "@jfy133", - "@mjamy", - "@vagkaratzas" - ] - }, - "pipelines": [ - { - "name": "funcprofiler", - "version": "dev" - }, - { - "name": "taxprofiler", - "version": "2.0.0" - } - ] - }, - { - "name": "diamond_cluster", - "path": "modules/nf-core/diamond/cluster/meta.yml", - "type": "module", - "meta": { - "name": "diamond_cluster", - "description": "calculate clusters of highly similar sequences", - "keywords": [ - "clustering", - "alignment", - "genomics", - "proteomics" - ], - "tools": [ - { - "diamond": { - "description": "Accelerated BLAST compatible local sequence aligner", - "homepage": "https://github.com/bbuchfink/diamond/wiki", - "documentation": "https://github.com/bbuchfink/diamond/wiki", - "tool_dev_url": "https://github.com/bbuchfink/diamond", - "doi": "10.1038/s41592-021-01101-x", - "licence": [ - "GPL v3-or-later" - ], - "identifier": "biotools:diamond" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "db": { - "type": "file", - "description": "The input sequence database. Supported formats are FASTA and DIAMOND (.dmnd) format.", - "pattern": "*.{dmnd,fa,faa,fasta}(.gz)", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ], - "output": { - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "a 2-column tabular file with the representative accession as the first column and the member sequence accession as the second column", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_diamond": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "diamond": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "diamond --version | sed 's/diamond version //g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "diamond": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "diamond --version | sed 's/diamond version //g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@itrujnara" - ], - "maintainers": [ - "@itrujnara" - ] - }, - "pipelines": [ - { - "name": "reportho", - "version": "1.1.0" - } - ] - }, - { - "name": "diamond_deepclust", - "path": "modules/nf-core/diamond/deepclust/meta.yml", - "type": "module", - "meta": { - "name": "diamond_deepclust", - "description": "Fast graph-based protein sequence clustering using DIAMOND deepclust", - "keywords": [ - "clustering", - "protein", - "diamond", - "deepclust", - "proteomics" - ], - "tools": [ - { - "diamond": { - "description": "Accelerated BLAST compatible local sequence aligner", - "homepage": "https://github.com/bbuchfink/diamond", - "documentation": "https://github.com/bbuchfink/diamond/wiki", - "tool_dev_url": "https://github.com/bbuchfink/diamond", - "doi": "10.1038/s41592-021-01101-x", - "licence": [ - "GPL v3-or-later" - ], - "identifier": "biotools:diamond" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input protein FASTA file to be clustered", - "pattern": "*.{fa,faa,fasta,fa.gz,faa.gz,fasta.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - { - "save_aln": { - "type": "boolean", - "description": "Whether to save clustering alignments to a file (--aln-out)\nWARNING: unusable in this version (2.1.24) of diamond due to bug, leaving as placeholder\n" - } - } - ], - "output": { - "clusters": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}.tsv": { - "type": "file", - "description": "Tab-separated file mapping each member sequence to its cluster\nrepresentative. The first column contains the representative\naccession and the second column contains the member sequence\naccession.\n", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "alignment": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}.aln": { - "type": "file", - "description": "Optional. Tab-separated file containing the clustering alignments,\nproduced when save_aln is true (--aln-out).\n", - "pattern": "*.aln", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_diamond": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "diamond": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "diamond --version | sed 's/.* //g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "diamond": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "diamond --version | sed 's/.* //g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@vagkaratzas" - ], - "maintainers": [ - "@vagkaratzas" - ] - } - }, - { - "name": "diamond_linclust", - "path": "modules/nf-core/diamond/linclust/meta.yml", - "type": "module", - "meta": { - "name": "diamond_linclust", - "description": "Fast protein sequence clustering using a greedy incremental approach", - "keywords": [ - "clustering", - "protein", - "diamond", - "linclust", - "proteomics" - ], - "tools": [ - { - "diamond": { - "description": "Accelerated BLAST compatible local sequence aligner", - "homepage": "https://github.com/bbuchfink/diamond", - "documentation": "https://github.com/bbuchfink/diamond/wiki", - "tool_dev_url": "https://github.com/bbuchfink/diamond", - "doi": "10.1038/s41592-021-01101-x", - "licence": [ - "GPL v3-or-later" - ], - "identifier": "biotools:diamond" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input protein FASTA file to be clustered", - "pattern": "*.{fa,faa,fasta,fa.gz,faa.gz,fasta.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } + "name": "fastk_merge", + "path": "modules/nf-core/fastk/merge/meta.yml", + "type": "module", + "meta": { + "name": "fastk_merge", + "description": "A tool to merge FastK histograms", + "keywords": ["merge", "k-mer", "histogram", "fastk"], + "tools": [ + { + "fastk": { + "description": "A fast K-mer counter for high-fidelity shotgun datasets", + "homepage": "https://github.com/thegenemyers/FASTK", + "tool_dev_url": "https://github.com/thegenemyers/FASTK", + "license": ["https://github.com/thegenemyers/FASTK/blob/master/LICENSE"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "hist": { + "type": "file", + "description": "FastK histogram file", + "ontologies": [] + } + }, + { + "ktab": { + "type": "file", + "description": "FastK ktab file", + "ontologies": [] + } + }, + { + "prof": { + "type": "file", + "description": "FastK prof file", + "ontologies": [] + } + } + ] + ], + "output": { + "hist": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.hist": { + "type": "file", + "description": "FastK histogram file", + "pattern": "*.hist", + "ontologies": [] + } + } + ] + ], + "ktab": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.ktab*": { + "type": "file", + "description": "FastK ktab file", + "pattern": "*.ktab" + } + } + ] + ], + "prof": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{prof,pidx}*": { + "type": "file", + "description": "FastK prof file", + "pattern": "*.{prof,pidx}" + } + } + ] + ], + "versions_fastk": [ + [ + { + "${task.process}": { + "type": "string", + "description": "Name of the process" + } + }, + { + "fastk": { + "type": "string", + "description": "Name of the tool" + } + }, + { + "1.2": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "Name of the process" + } + }, + { + "fastk": { + "type": "string", + "description": "Name of the tool" + } + }, + { + "1.2": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@mahesh-panchal"], + "maintainers": ["@mahesh-panchal"] } - ] - ], - "output": { - "clusters": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}.tsv": { - "type": "file", - "description": "Tab-separated file mapping each member sequence to its cluster\nrepresentative. The first column contains the representative\naccession and the second column contains the member sequence\naccession.\n", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_diamond": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "diamond": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "diamond --version | sed 's/diamond version //g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "diamond": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "diamond --version | sed 's/diamond version //g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@vagkaratzas" - ], - "maintainers": [ - "@vagkaratzas" - ] - } - }, - { - "name": "diamond_makedb", - "path": "modules/nf-core/diamond/makedb/meta.yml", - "type": "module", - "meta": { - "name": "diamond_makedb", - "description": "Builds a DIAMOND database", - "keywords": [ - "fasta", - "diamond", - "index", - "database" - ], - "tools": [ - { - "diamond": { - "description": "Accelerated BLAST compatible local sequence aligner", - "homepage": "https://github.com/bbuchfink/diamond", - "documentation": "https://github.com/bbuchfink/diamond/wiki", - "tool_dev_url": "https://github.com/bbuchfink/diamond", - "doi": "10.1038/s41592-021-01101-x", - "licence": [ - "GPL v3.0" - ], - "identifier": "biotools:diamond" + }, + { + "name": "fastme", + "path": "modules/nf-core/fastme/meta.yml", + "type": "module", + "meta": { + "name": "fastme", + "description": "Distance-based phylogeny with FastME", + "keywords": ["phylogenetics", "newick", "minimum_evolution", "distance-based"], + "tools": [ + { + "fastme": { + "description": "A comprehensive, accurate and fast distance-based phylogeny inference program.", + "homepage": "http://www.atgc-montpellier.fr/fastme", + "documentation": "http://www.atgc-montpellier.fr/fastme/usersguide.php", + "tool_dev_url": "https://gite.lirmm.fr/atgc/FastME/", + "doi": "10.1093/molbev/msv150", + "licence": ["GPL v3"], + "args_id": "$args", + "identifier": "biotools:fastme" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "A Groovy map containing sample information,\ne.g. [ id: \"test\" ]\n" + } + }, + { + "infile": { + "type": "file", + "description": "MSA or distance matrix in Phylip format", + "pattern": "*", + "ontologies": [] + } + }, + { + "initial_tree": { + "type": "file", + "description": "Initial tree", + "ontologies": [] + } + } + ] + ], + "output": { + "nwk": [ + [ + { + "meta": { + "type": "map", + "description": "A Groovy map containing sample information" + } + }, + { + "*.nwk": { + "type": "file", + "description": "Final phylogeny in Newick format", + "pattern": "*.nwk", + "ontologies": [] + } + } + ] + ], + "stats": [ + [ + { + "meta": { + "type": "map", + "description": "A Groovy map containing sample information" + } + }, + { + "*_stat.txt": { + "type": "file", + "description": "A text file with the statistics of the phylogeny", + "pattern": "*_stat.txt", + "ontologies": [] + } + } + ] + ], + "matrix": [ + [ + { + "meta": { + "type": "map", + "description": "A Groovy map containing sample information" + } + }, + { + "*.matrix.phy": { + "type": "file", + "description": "Optional; the distance matrix in Phylip matrix format; it is generated if the -O option is passed in ext.args, although the provided file name will be overwritten", + "pattern": "*.matrix.phy", + "ontologies": [] + } + } + ] + ], + "bootstrap": [ + [ + { + "meta": { + "type": "map", + "description": "A Groovy map containing sample information" + } + }, + { + "*.bootstrap": { + "type": "file", + "description": "A file containing all bootstrap trees in Newick format; it is generated if the -B option is passed in ext.args (and bootstrap is used), although the provided file name will be overwritten", + "pattern": "*.bootstrap", + "ontologies": [] + } + } + ] + ], + "versions_fastme": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "fastme": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "fastme --version |& sed '1!d ; s/FastME //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "fastme": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "fastme --version |& sed '1!d ; s/FastME //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@itrujnara"], + "maintainers": ["@itrujnara"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + }, + { + "name": "fastp", + "path": "modules/nf-core/fastp/meta.yml", + "type": "module", + "meta": { + "name": "fastp", + "description": "Perform adapter/quality trimming on sequencing reads", + "keywords": ["trimming", "quality control", "fastq"], + "tools": [ + { + "fastp": { + "description": "A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.\n", + "documentation": "https://github.com/OpenGene/fastp", + "doi": "10.1093/bioinformatics/bty560", + "licence": ["MIT"], + "identifier": "biotools:fastp" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information. Use 'single_end: true' to specify single ended or interleaved FASTQs. Use 'single_end: false' for paired-end reads.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively. If you wish to run interleaved paired-end data, supply as single-end data\nbut with `--interleaved_in` in your `modules.conf`'s `ext.args` for the module.\n", + "ontologies": [] + } + }, + { + "adapter_fasta": { + "type": "file", + "description": "File in FASTA format containing possible adapters to remove.", + "pattern": "*.{fasta,fna,fas,fa}", + "ontologies": [] + } + } + ], + { + "discard_trimmed_pass": { + "type": "boolean", + "description": "Specify true to not write any reads that pass trimming thresholds.\nThis can be used to use fastp for the output report only.\n" + } + }, + { + "save_trimmed_fail": { + "type": "boolean", + "description": "Specify true to save files that failed to pass trimming thresholds ending in `*.fail.fastq.gz`" + } + }, + { + "save_merged": { + "type": "boolean", + "description": "Specify true to save all merged reads to a file ending in `*.merged.fastq.gz`" + } + } + ], + "output": { + "reads": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fastp.fastq.gz": { + "type": "file", + "description": "The trimmed/modified/unmerged fastq reads", + "pattern": "*fastp.fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "json": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.json": { + "type": "file", + "description": "Results in JSON format", + "pattern": "*.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "html": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.html": { + "type": "file", + "description": "Results in HTML format", + "pattern": "*.html", + "ontologies": [] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "fastq log file", + "pattern": "*.log", + "ontologies": [] + } + } + ] + ], + "reads_fail": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fail.fastq.gz": { + "type": "file", + "description": "Reads the failed the preprocessing", + "pattern": "*fail.fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "reads_merged": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.merged.fastq.gz": { + "type": "file", + "description": "Reads that were successfully merged", + "pattern": "*.{merged.fastq.gz}", + "ontologies": [] + } + } + ] + ], + "versions_fastp": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "fastp": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "fastp --version 2>&1 | sed -e \"s/fastp //g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "fastp": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "fastp --version 2>&1 | sed -e \"s/fastp //g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@drpatelh", "@kevinmenden", "@eit-maxlcummins"], + "maintainers": ["@drpatelh", "@kevinmenden"] }, - { - "fasta": { - "type": "file", - "description": "Input fasta file", - "pattern": "*.{fa,fasta,fa.gz,fasta.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - { - "taxonmap": { - "type": "file", - "description": "Optional mapping file of NCBI protein accession numbers to taxon ids (gzip compressed), required for taxonomy functionality.", - "pattern": "*.gz", - "ontologies": [ + "pipelines": [ + { + "name": "airrflow", + "version": "5.0.0" + }, + { + "name": "bacass", + "version": "2.6.0" + }, + { + "name": "circrna", + "version": "dev" + }, + { + "name": "coproid", + "version": "2.0.1" + }, + { + "name": "dartseq", + "version": "dev" + }, + { + "name": "demultiplex", + "version": "1.7.1" + }, + { + "name": "denovotranscript", + "version": "1.2.1" + }, + { + "name": "detaxizer", + "version": "1.3.0" + }, + { + "name": "genomicrelatedness", + "version": "dev" + }, + { + "name": "lncpipe", + "version": "dev" + }, + { + "name": "mag", + "version": "5.4.2" + }, + { + "name": "nascent", + "version": "2.3.0" + }, + { + "name": "pathogensurveillance", + "version": "1.1.0" + }, + { + "name": "radseq", + "version": "dev" + }, + { + "name": "raredisease", + "version": "3.0.0" + }, { - "edam": "http://edamontology.org/format_3989" + "name": "riboseq", + "version": "1.2.0" + }, + { + "name": "rnadnavar", + "version": "dev" + }, + { + "name": "rnafusion", + "version": "4.1.2" + }, + { + "name": "rnaseq", + "version": "3.26.0" + }, + { + "name": "sarek", + "version": "3.8.1" + }, + { + "name": "smrnaseq", + "version": "2.4.1" + }, + { + "name": "taxprofiler", + "version": "2.0.0" + }, + { + "name": "viralmetagenome", + "version": "1.1.1" + }, + { + "name": "viralrecon", + "version": "3.0.0" } - ] - } - }, - { - "taxonnodes": { - "type": "file", - "description": "Optional NCBI taxonomy nodes.dmp file, required for taxonomy functionality.", - "pattern": "*.dmp", - "ontologies": [] - } - }, - { - "taxonnames": { - "type": "file", - "description": "Optional NCBI taxonomy names.dmp file, required for taxonomy functionality.", - "pattern": "*.dmp", - "ontologies": [] - } - } - ], - "output": { - "db": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.dmnd": { - "type": "file", - "description": "File of the indexed DIAMOND database", - "pattern": "*.dmnd", - "ontologies": [] - } - } - ] - ], - "versions_diamond": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "diamond": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "diamond --version | sed 's/diamond version //g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "diamond": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "diamond --version | sed 's/diamond version //g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@spficklin" - ], - "maintainers": [ - "@spficklin", - "@vagkaratzas", - "@jfy133" - ] - }, - "pipelines": [ - { - "name": "createtaxdb", - "version": "3.0.0" - } - ] - }, - { - "name": "diann", - "path": "modules/nf-core/diann/meta.yml", - "type": "module", - "meta": { - "name": "diann", - "description": "Generic DIA-NN module for running any DIA-NN operation including in-silico library generation, preliminary analysis, empirical library assembly, individual analysis, and final quantification", - "keywords": [ - "proteomics", - "mass spectrometry", - "DIA", - "spectral library", - "quantification" - ], - "tools": [ - { - "diann": { - "description": "DIA-NN - a fast and easy to use tool for processing data independent acquisition (DIA) proteomics data", - "homepage": "https://github.com/vdemichev/DiaNN", - "documentation": "https://github.com/vdemichev/DiaNN#readme", - "tool_dev_url": "https://github.com/vdemichev/DiaNN", - "licence": [ - "Custom", - "https://raw.githubusercontent.com/vdemichev/DiaNN/master/LICENSE.txt" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "ms_files": { - "type": "file", - "description": "MS data file(s) in mzML or Bruker .d format (can be single file or list).\nThermo RAW files are only supported on Linux with DIA-NN 2.0+; older versions\nrequire conversion to mzML or .d format first.\nFor preliminary/assembly/individual analysis, these are actual file paths.\nFor final quantification with --use-quant, this should be an empty list.\n", - "pattern": "*.{mzML,raw,d}", - "ontologies": [] - } - }, - { - "ms_file_names": { - "type": "string", - "description": "MS file basenames (not paths) as strings (can be single name or list).\nUsed for final quantification step with --use-quant where only filenames are needed.\nFor other analysis steps, this should be an empty list.\nExample: ['sample1.mzML', 'sample2.mzML'] or []\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA database file for peptide searches.\nUse a placeholder file (e.g., 'NO_FASTA_FILE') if not needed for the specific analysis step.\n", - "pattern": "*.{fasta,fa}", - "ontologies": [] - } - }, - { - "library": { - "type": "file", - "description": "Spectral library file in .speclib or .tsv format.\nUse a placeholder file (e.g., 'NO_LIB_FILE') if not needed for the specific analysis step.\n", - "pattern": "*.{speclib,tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - }, - { - "quant": { - "type": "directory", - "description": "Directory containing .quant files from previous DIA-NN analysis.\nWhen provided, enables --use-quant mode to reuse cached quantification results,\nimproving performance for empirical library assembly and final quantification.\nPass empty list [] if not needed. Files are staged as 'quant/*' in the work directory.\n" - } - } - ] - ], - "output": { - "predict_speclib": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}.predicted.speclib": { - "type": "file", - "description": "Predicted spectral library from in-silico generation.\nFilename is determined by the prefix (task.ext.prefix or meta.id).\n", - "pattern": "*.predicted.speclib", - "ontologies": [] - } - } - ] - ], - "final_speclib": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}.speclib": { - "type": "file", - "description": "Empirical spectral library refined from experimental data.\nProduced by the library assembly step, which combines predicted library\ninformation with actual MS measurements to improve search accuracy.\n", - "pattern": "*.speclib", - "ontologies": [] - } - } ] - ], - "skyline_speclib": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}.tsv.skyline.speclib": { - "type": "file", - "description": "Spectral library in Skyline format for use with Skyline software.\nFilename is determined by the prefix (task.ext.prefix or meta.id).\n", - "pattern": "*.tsv.skyline.speclib", - "ontologies": [] - } - } - ] - ], - "diann_quant": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.quant": { - "type": "file", - "description": "Quantification results in .quant format (intermediate output for empirical library assembly and final quantification)", - "pattern": "*.quant", - "ontologies": [] - } - } - ] - ], - "main_report": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}.tsv": { - "type": "file", - "description": "Main DIA-NN report in TSV format containing peptide and protein quantification.\nFilename is determined by the prefix (task.ext.prefix or meta.id).\n", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "report_parquet": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}.parquet": { - "type": "file", - "description": "Main DIA-NN report in Parquet format for efficient data access.\nFilename is determined by the prefix (task.ext.prefix or meta.id).\n", - "pattern": "*.parquet", - "ontologies": [] - } - } - ] - ], - "report_manifest": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}.manifest.txt": { - "type": "file", - "description": "Report manifest file listing all output files.\nFilename is determined by the prefix (task.ext.prefix or meta.id).\n", - "pattern": "*.manifest.txt", - "ontologies": [] - } - } - ] - ], - "protein_description": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}.protein_description.tsv": { - "type": "file", - "description": "Protein descriptions extracted from FASTA headers.\nFilename is determined by the prefix (task.ext.prefix or meta.id).\n", - "pattern": "*.protein_description.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "report_stats": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}.stats.tsv": { - "type": "file", - "description": "Report statistics including identification and quantification metrics.\nFilename is determined by the prefix (task.ext.prefix or meta.id).\n", - "pattern": "*.stats.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "pr_matrix": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}.pr_matrix.tsv": { - "type": "file", - "description": "Precursor-level quantification matrix (peptides across runs).\nFilename is determined by the prefix (task.ext.prefix or meta.id).\n", - "pattern": "*.pr_matrix.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "pg_matrix": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}.pg_matrix.tsv": { - "type": "file", - "description": "Protein group-level quantification matrix.\nFilename is determined by the prefix (task.ext.prefix or meta.id).\n", - "pattern": "*.pg_matrix.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "gg_matrix": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}.gg_matrix.tsv": { - "type": "file", - "description": "Gene group-level quantification matrix.\nFilename is determined by the prefix (task.ext.prefix or meta.id).\n", - "pattern": "*.gg_matrix.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "unique_gene_matrix": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}.unique_genes_matrix.tsv": { - "type": "file", - "description": "Unique genes quantification matrix.\nFilename is determined by the prefix (task.ext.prefix or meta.id).\n", - "pattern": "*.unique_genes_matrix.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.log.txt": { - "type": "file", - "description": "DIA-NN log file containing run information and recommended settings", - "pattern": "*.log.txt", - "ontologies": [] - } - } - ] - ], - "versions_diann": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "diann": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "diann | grep \"DIA-NN\" | grep -oP \"\\d+\\.\\d+(\\.\\w+)*(\\.[\\d]+)?\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "diann": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "diann | grep \"DIA-NN\" | grep -oP \"\\d+\\.\\d+(\\.\\w+)*(\\.[\\d]+)?\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@pinin4fjords" - ], - "maintainers": [ - "@pinin4fjords" - ] - } - }, - { - "name": "diann_insilicolibrarygeneration", - "path": "modules/nf-core/diann/insilicolibrarygeneration/meta.yml", - "type": "module", - "meta": { - "name": "diann_insilicolibrarygeneration", - "description": "Generate in silico predicted spectral library using DIA-NN deep learning predictor.\nThis module uses DIA-NN software for data-independent acquisition (DIA) proteomics data processing.\nOutput materials should include attribution: \"Generated using DIA-NN\".\n", - "keywords": [ - "diann", - "spectral library", - "proteomics", - "deep learning", - "dia" - ], - "tools": [ - { - "diann": { - "description": "DIA-NN is a universal software for data-independent acquisition (DIA) proteomics data processing.\nIt uses deep learning to predict spectral libraries and perform peptide identification and quantification.\n", - "homepage": "https://github.com/vdemichev/DiaNN", - "documentation": "https://github.com/vdemichev/DiaNN", - "tool_dev_url": "https://github.com/vdemichev/DiaNN", - "doi": "10.1038/s41592-020-01009-0", - "licence": [ - "https://github.com/vdemichev/DiaNN/blob/1.8.1/LICENSE.txt" - ], - "identifier": "biotools:diann" + }, + { + "name": "fastplong", + "path": "modules/nf-core/fastplong/meta.yml", + "type": "module", + "meta": { + "name": "fastplong", + "description": "Perform adapter/quality trimming and QC on long sequencing reads (ONT, PacBio, etc.)", + "keywords": ["trimming", "quality control", "fastq", "long reads"], + "tools": [ + { + "fastplong": { + "description": "Ultra-fast preprocessing and quality control for long-read sequencing data.", + "homepage": "https://github.com/OpenGene/fastplong/blob/v0.4.1/README.md", + "documentation": "https://github.com/OpenGene/fastplong/blob/v0.4.1/README.md", + "tool_dev_url": "https://github.com/OpenGene/fastplong", + "doi": "10.1002/imt2.107", + "licence": ["MIT"], + "identifier": "biotools:fastplong" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information. Use 'single_end: true' for single-end reads.\ne.g. [ id:'test', single_end:true ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "Input FASTQ file. Gzip-compressed files are supported.\n", + "pattern": "*.{fastq.gz,fastq}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ], + { + "adapter_fasta": { + "type": "file", + "description": "Optional FASTA file containing adapter sequences to trim.\n", + "pattern": "*.{fasta,fa,fna}", + "ontologies": [] + } + }, + { + "discard_trimmed_pass": { + "type": "boolean", + "description": "If true, no reads that pass trimming thresholds will be written. Only reports will be generated.\n" + } + }, + { + "save_trimmed_fail": { + "type": "boolean", + "description": "If true, reads that fail filtering will be saved to a file ending in `*.fail.fastq.gz`.\n" + } + } + ], + "output": { + "reads": [ + [ + { + "meta": { + "type": "map", + "description": "Sample information map" + } + }, + { + "*.fastplong.fastq.gz": { + "type": "file", + "description": "Trimmed and filtered reads", + "pattern": "*fastplong.fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "json": [ + [ + { + "meta": { + "type": "map", + "description": "Sample information map" + } + }, + { + "*.json": { + "type": "file", + "description": "QC report in JSON format", + "pattern": "*.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "html": [ + [ + { + "meta": { + "type": "map", + "description": "Sample information map" + } + }, + { + "*.html": { + "type": "file", + "description": "QC report in HTML format", + "pattern": "*.html", + "ontologies": [] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Sample information map" + } + }, + { + "*.log": { + "type": "file", + "description": "Log file generated during trimming", + "pattern": "*.log", + "ontologies": [] + } + } + ] + ], + "reads_fail": [ + [ + { + "meta": { + "type": "map", + "description": "Sample information map" + } + }, + { + "*.fail.fastq.gz": { + "type": "file", + "description": "Reads that failed quality/trimming filters", + "pattern": "*fail.fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "versions_fastplong": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "fastplong": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "fastplong --version 2>&1 | sed -e \"s/fastplong //g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "fastplong": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "fastplong --version 2>&1 | sed -e \"s/fastplong //g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@Lupphes", "@eit-maxlcummins"], + "maintainers": ["@Lupphes"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } + }, + { + "name": "fastqc", + "path": "modules/nf-core/fastqc/meta.yml", + "type": "module", + "meta": { + "name": "fastqc", + "description": "Run FastQC on sequenced reads", + "keywords": ["quality control", "qc", "adapters", "fastq"], + "tools": [ + { + "fastqc": { + "description": "FastQC gives general quality metrics about your reads.\nIt provides information about the quality score distribution\nacross your reads, the per base sequence content (%A/C/G/T).\n\nYou get information about adapter contamination and other\noverrepresented sequences.\n", + "homepage": "https://www.bioinformatics.babraham.ac.uk/projects/fastqc/", + "documentation": "https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/", + "licence": ["GPL-2.0-only"], + "identifier": "biotools:fastqc" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", + "ontologies": [] + } + } + ] + ], + "output": { + "html": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.html": { + "type": "file", + "description": "FastQC report", + "pattern": "*_{fastqc.html}", + "ontologies": [] + } + } + ] + ], + "zip": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.zip": { + "type": "file", + "description": "FastQC report archive", + "pattern": "*_{fastqc.zip}", + "ontologies": [] + } + } + ] + ], + "versions_fastqc": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "fastqc": { + "type": "string", + "description": "The tool name" + } + }, + { + "fastqc --version | sed \"/FastQC v/!d; s/.*v//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "fastqc": { + "type": "string", + "description": "The tool name" + } + }, + { + "fastqc --version | sed \"/FastQC v/!d; s/.*v//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@drpatelh", "@grst", "@ewels", "@FelixKrueger"], + "maintainers": ["@drpatelh", "@grst", "@ewels", "@FelixKrueger"], + "containers": { + "docker": { + "linux/arm64": { + "name": "community.wave.seqera.io/library/fastqc:0.12.1--e455e32f745abe68", + "build_id": "bd-e455e32f745abe68_1", + "scan_id": "sc-f102f736465af88c_1" + }, + "linux/amd64": { + "name": "community.wave.seqera.io/library/fastqc:0.12.1--5cb1a2fa2f18c7c2", + "build_id": "bd-5cb1a2fa2f18c7c2_1", + "scan_id": "sc-0c0466326b6b77d2_1" + } + }, + "singularity": { + "linux/amd64": { + "name": "oras://community.wave.seqera.io/library/fastqc:0.12.1--5c4bd442468d75dd", + "build_id": "bd-5c4bd442468d75dd_1", + "https": "https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f2/f20b021476d1d87658820f971ebecc1e8cdbde0f338eb0d9cea2b0a8fc54a54b/data" + }, + "linux/arm64": { + "name": "oras://community.wave.seqera.io/library/fastqc:0.12.1--127a87fc06499035", + "build_id": "bd-127a87fc06499035_1", + "https": "https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/46/46daf2dad0169afd2ae047c3e50ed3776259f664bf07e5e06b045dc23449e994/data" + } + }, + "conda": { + "linux/amd64": { + "lock_file": "modules/nf-core/fastqc/.conda-lock/linux_amd64-bd-5cb1a2fa2f18c7c2_1.txt" + }, + "linux/arm64": { + "lock_file": "modules/nf-core/fastqc/.conda-lock/linux_arm64-bd-e455e32f745abe68_1.txt" + } + } + } }, - { - "fasta": { - "type": "file", - "description": "FASTA sequence database", - "pattern": "*.{fasta,fa}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ], - "output": { - "predict_speclib": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.predicted.speclib": { - "type": "file", - "description": "In silico predicted spectral library by DIA-NN deep learning predictor", - "pattern": "*.predicted.speclib", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3240" - } - ] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.log": { - "type": "file", - "description": "DIA-NN log file", - "pattern": "*.log", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2330" - } - ] - } - } - ] - ], - "versions_diann": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "diann": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "diann | grep \"DIA-NN\" | grep -oP \"\\d+\\.\\d+(\\.\\w+)*(\\.[\\d]+)?\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "diann": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "diann | grep \"DIA-NN\" | grep -oP \"\\d+\\.\\d+(\\.\\w+)*(\\.[\\d]+)?\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "abotyper", + "version": "dev" + }, + { + "name": "airrflow", + "version": "5.0.0" + }, + { + "name": "alleleexpression", + "version": "dev" + }, + { + "name": "ampliseq", + "version": "2.17.0" + }, + { + "name": "atacseq", + "version": "2.1.2" + }, + { + "name": "bacass", + "version": "2.6.0" + }, + { + "name": "bamtofastq", + "version": "2.2.1" + }, + { + "name": "callingcards", + "version": "1.0.0" + }, + { + "name": "chipseq", + "version": "2.1.0" + }, + { + "name": "circdna", + "version": "1.1.0" + }, + { + "name": "circrna", + "version": "dev" + }, + { + "name": "coproid", + "version": "2.0.1" + }, + { + "name": "crisprseq", + "version": "2.3.0" + }, + { + "name": "cutandrun", + "version": "3.2.2" + }, + { + "name": "dartseq", + "version": "dev" + }, + { + "name": "deepmutscan", + "version": "dev" + }, + { + "name": "demo", + "version": "1.1.0" + }, + { + "name": "demultiplex", + "version": "1.7.1" + }, + { + "name": "denovotranscript", + "version": "1.2.1" + }, + { + "name": "detaxizer", + "version": "1.3.0" + }, + { + "name": "evexplorer", + "version": "dev" + }, + { + "name": "fastqrepair", + "version": "1.0.0" + }, + { + "name": "fastquorum", + "version": "1.2.0" + }, + { + "name": "funcprofiler", + "version": "dev" + }, + { + "name": "genomeannotator", + "version": "dev" + }, + { + "name": "genomeassembler", + "version": "1.1.0" + }, + { + "name": "genomeqc", + "version": "dev" + }, + { + "name": "genomeskim", + "version": "dev" + }, + { + "name": "hgtseq", + "version": "1.1.0" + }, + { + "name": "hic", + "version": "2.1.0" + }, + { + "name": "hicar", + "version": "1.0.0" + }, + { + "name": "hlatyping", + "version": "2.2.0" + }, + { + "name": "liverctanalysis", + "version": "dev" + }, + { + "name": "lncpipe", + "version": "dev" + }, + { + "name": "mag", + "version": "5.4.2" + }, + { + "name": "magmap", + "version": "1.0.0" + }, + { + "name": "marsseq", + "version": "1.0.3" + }, + { + "name": "metaboigniter", + "version": "2.0.1" + }, + { + "name": "metatdenovo", + "version": "1.3.0" + }, + { + "name": "methylarray", + "version": "dev" + }, + { + "name": "methylong", + "version": "2.0.0" + }, + { + "name": "methylseq", + "version": "4.2.0" + }, + { + "name": "mitodetect", + "version": "dev" + }, + { + "name": "multiplesequencealign", + "version": "1.1.1" + }, + { + "name": "nanoseq", + "version": "3.1.0" + }, + { + "name": "nascent", + "version": "2.3.0" + }, + { + "name": "omicsgenetraitassociation", + "version": "dev" + }, + { + "name": "pacvar", + "version": "1.0.1" + }, + { + "name": "panoramaseq", + "version": "dev" + }, + { + "name": "pathogensurveillance", + "version": "1.1.0" + }, + { + "name": "phageannotator", + "version": "dev" + }, + { + "name": "radseq", + "version": "dev" + }, + { + "name": "raredisease", + "version": "3.0.0" + }, + { + "name": "readsimulator", + "version": "1.0.1" + }, + { + "name": "riboseq", + "version": "1.2.0" + }, + { + "name": "rnadnavar", + "version": "dev" + }, + { + "name": "rnafusion", + "version": "4.1.2" + }, + { + "name": "rnaseq", + "version": "3.26.0" + }, + { + "name": "rnasplice", + "version": "1.0.4" + }, + { + "name": "rnavar", + "version": "1.2.3" + }, + { + "name": "sammyseq", + "version": "dev" + }, + { + "name": "sarek", + "version": "3.8.1" + }, + { + "name": "scnanoseq", + "version": "1.2.2" + }, + { + "name": "scrnaseq", + "version": "4.1.0" + }, + { + "name": "seqinspector", + "version": "1.0.1" + }, + { + "name": "smrnaseq", + "version": "2.4.1" + }, + { + "name": "spatialvi", + "version": "dev" + }, + { + "name": "ssds", + "version": "dev" + }, + { + "name": "taxprofiler", + "version": "2.0.0" + }, + { + "name": "tbanalyzer", + "version": "dev" + }, + { + "name": "troughgraph", + "version": "dev" + }, + { + "name": "variantcatalogue", + "version": "dev" + }, + { + "name": "viralintegration", + "version": "0.1.1" + }, + { + "name": "viralmetagenome", + "version": "1.1.1" + }, + { + "name": "viralrecon", + "version": "3.0.0" + } ] - ] - }, - "authors": [ - "@daichengxin", - "@pinin4fjords" - ], - "maintainers": [ - "@daichengxin" - ] - } - }, - { - "name": "disambiguate", - "path": "modules/nf-core/disambiguate/meta.yml", - "type": "module", - "meta": { - "name": "disambiguate", - "description": "Disambiguates reads aligned to two different organisms (e.g. human and mouse)\nfrom the same source of FASTQ files. Useful in explant RNA/DNA-Seq workflows\nwhere reads from two species are present. For reads aligned to both organisms,\nthe algorithm compares alignment quality scores to determine the most likely\nspecies of origin. Produces four BAM files (uniquely assigned to species A or B,\nambiguous for species A or B) and a summary file.\n", - "keywords": [ - "disambiguation", - "xenograft", - "explant", - "rna-seq", - "alignment", - "bam" - ], - "tools": [ - { - "ngs-disambiguate": { - "description": "Disambiguation algorithm for reads aligned to two different organisms using Tophat, Hisat2, BWA or STAR alignments.", - "homepage": "https://github.com/AstraZeneca-NGS/disambiguate", - "documentation": "https://github.com/AstraZeneca-NGS/disambiguate", - "tool_dev_url": "https://github.com/AstraZeneca-NGS/disambiguate", - "doi": "10.12688/f1000research.10082.2", - "licence": [ - "MIT" - ], - "identifier": "biotools:disambiguate", - "args_id": "$args" + }, + { + "name": "fastqdl", + "path": "modules/nf-core/fastqdl/meta.yml", + "type": "module", + "meta": { + "name": "fastqdl", + "description": "Download FASTQ files from SRA or ENA repositories.", + "keywords": ["download", "ena", "fastq", "sra"], + "tools": [ + { + "fastqdl": { + "description": "A tool to download FASTQs associated with Study, Experiment, or Run accessions.", + "homepage": "https://github.com/rpetit3/fastq-dl", + "documentation": "https://github.com/rpetit3/fastq-dl", + "tool_dev_url": "https://github.com/rpetit3/fastq-dl", + "doi": "10.5281/zenodo.13957735", + "licence": ["MIT"], + "identifier": "biotools:fastq-dl" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "accession": { + "type": "string", + "description": "ENA/SRA accession to query" + } + } + ] + ], + "output": { + "fastq": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.fastq.gz": { + "type": "file", + "description": "FASTQ files downloaded from ENA or SRA", + "pattern": "*.fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "runinfo": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*-run-info.tsv": { + "type": "file", + "description": "Tab-delimited file containing metadata for each Run downloaded", + "pattern": "*-run-info.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "runmergers": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*-run-mergers.tsv": { + "type": "file", + "description": "Tab-delimited file merge information from --group-by-experiment or --group-by-sample", + "pattern": "*-run-mergers.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_fastqdl": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "fastq-dl": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "fastq-dl --version |& sed \"s/.* //\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "fastq-dl": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "fastq-dl --version |& sed \"s/.* //\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@camlloyd"], + "maintainers": ["@camlloyd"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "bam_a": { - "type": "file", - "description": "BAM file with alignments to species A (e.g. human). Mandatory.", - "pattern": "*.{bam}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - }, - { - "bam_b": { - "type": "file", - "description": "BAM file with alignments to species B (e.g. mouse). Mandatory.", - "pattern": "*.{bam}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } + }, + { + "name": "fastqe", + "path": "modules/nf-core/fastqe/meta.yml", + "type": "module", + "meta": { + "name": "fastqe", + "description": "fastqe is a bioinformatics command line tool that uses emojis to represent and analyze genomic data.", + "keywords": ["quality control", "fastq", "emoji", "visualization"], + "tools": [ + { + "fastqe": { + "description": "A tool for visualizing FASTQ file quality using emoji", + "homepage": "https://github.com/fastqe/fastqe", + "documentation": "https://github.com/fastqe/fastqe#readme", + "tool_dev_url": "https://github.com/fastqe/fastqe", + "doi": "10.21105/joss.02400", + "licence": ["MIT"], + "identifier": "biotools:fastqe" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "fastq": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", + "ontologies": [] + } + } + ] + ], + "output": { + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "Text file containing emoji", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_fastqe": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "fastqe": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "0.5.2": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "fastqe": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "0.5.2": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@adamrtalbot"], + "maintainers": ["@adamrtalbot"] } - ] - ], - "output": { - "disambiguated_bam_a": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*disambiguatedSpeciesA.bam": { - "type": "file", - "description": "Reads uniquely assigned to species A.", - "pattern": "*disambiguatedSpeciesA.bam", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - } - ] - ], - "disambiguated_bam_b": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*disambiguatedSpeciesB.bam": { - "type": "file", - "description": "Reads uniquely assigned to species B.", - "pattern": "*disambiguatedSpeciesB.bam", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - } - ] - ], - "ambiguous_bam_a": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*ambiguousSpeciesA.bam": { - "type": "file", - "description": "Reads aligned to species A that also aligned to species B but could not be uniquely assigned.", - "pattern": "*ambiguousSpeciesA.bam", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - } - ] - ], - "ambiguous_bam_b": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*ambiguousSpeciesB.bam": { - "type": "file", - "description": "Reads aligned to species B that also aligned to species A but could not be uniquely assigned.", - "pattern": "*ambiguousSpeciesB.bam", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - } - ] - ], - "summary": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*_summary.txt": { - "type": "file", - "description": "Summary of read counts uniquely assigned to species A, species B, and ambiguous reads.", - "pattern": "*_summary.txt", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2330" - } - ] - } - } - ] - ], - "versions_ngs_disambiguate": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "ngs-disambiguate": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "2018.05.03": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "ngs-disambiguate": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "2018.05.03": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@ctuni" - ], - "maintainers": [ - "@ctuni" - ] - } - }, - { - "name": "doubletdetection", - "path": "modules/nf-core/doubletdetection/meta.yml", - 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} - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "h5ad": { - "type": "file", - "description": "H5AD anndata object", - "pattern": "*.h5ad", - "ontologies": [] - } + }, + { + "name": "fastqscreen_buildfromindex", + "path": "modules/nf-core/fastqscreen/buildfromindex/meta.yml", + "type": "module", + "meta": { + "name": "fastqscreen_buildfromindex", + "description": "Build fastq screen config file from bowtie index files", + "keywords": ["build", "index", "genome", "reference"], + "tools": [ + { + "fastqscreen": { + "description": "FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect.", + "homepage": "https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/", + "documentation": "https://stevenwingett.github.io/FastQ-Screen/", + "tool_dev_url": "https://github.com/StevenWingett/FastQ-Screen/archive/refs/tags/v0.15.3.zip", + "doi": "10.5281/zenodo.5838377", + "licence": ["GPL-3.0-or-later"], + "identifier": "" + } + } + ], + "input": [ + { + "genome_names": { + "type": "string", + "description": "List of names for each index" + } + }, + { + "indexes": { + "type": "directory", + "description": "Bowtie2 genome directories containing index files" + } + } + ], + "output": { + "database": [ + { + "FastQ_Screen_Genomes": { + "type": "directory", + "description": "fastq screen database folder containing config file and index folders", + "pattern": "FastQ_Screen_Genomes" + } + } + ], + "versions_fastqscreen": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "fastqscreen": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "fastq_screen --version 2>&1 | sed \"s/^.*FastQ Screen v//;\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "fastqscreen": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "fastq_screen --version 2>&1 | sed \"s/^.*FastQ Screen v//;\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@snesic", "@JPejovicApis"] } - ] - ], - "output": { - "h5ad": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.h5ad": { - "type": "file", - "description": "H5AD anndata object", - "pattern": "*.h5ad", - "ontologies": [] - } - } + }, + { + "name": "fastqscreen_fastqscreen", + "path": "modules/nf-core/fastqscreen/fastqscreen/meta.yml", + "type": "module", + "meta": { + "name": "fastqscreen_fastqscreen", + "description": "Align reads to multiple reference genomes using fastq-screen", + "keywords": ["align", "map", "fasta", "fastq", "genome", "reference"], + "tools": [ + { + "fastqscreen": { + "description": "FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect.", + "homepage": "https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/", + "documentation": "https://stevenwingett.github.io/FastQ-Screen/", + "tool_dev_url": "https://github.com/StevenWingett/FastQ-Screen/archive/refs/tags/v0.15.3.zip", + "doi": "10.5281/zenodo.5838377", + "licence": ["GPL-3.0-or-later"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", + "ontologies": [] + } + } + ], + { + "database": { + "type": "directory", + "description": "fastq screen database folder containing config file and index folders", + "pattern": "FastQ_Screen_Genomes" + } + } + ], + "output": { + "txt": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.txt": { + "type": "file", + "description": "TXT file containing alignment statistics", + "pattern": "*.txt", + "ontologies": [] + } + } + ] + ], + "png": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.png": { + "type": "file", + "description": "PNG file with graphical representation of alignments", + "pattern": "*.png", + "ontologies": [] + } + } + ] + ], + "html": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.html": { + "type": "file", + "description": "HTML file containing mapping results as a table and graphical representation", + "pattern": "*.html", + "ontologies": [] + } + } + ] + ], + "fastq": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.fastq.gz": { + "type": "file", + "description": "FastQ file containing reads that did not align to any database (optional)", + "pattern": "*.fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "versions_fastqscreen": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "fastqscreen": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "fastq_screen --version 2>&1 | sed \"s/^.*FastQ Screen v//;\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "fastqscreen": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "fastq_screen --version 2>&1 | sed \"s/^.*FastQ Screen v//;\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@snesic", "@JPejovicApis"] + }, + "pipelines": [ + { + "name": "seqinspector", + "version": "1.0.1" + } ] - ], - "predictions": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.pkl": { - "type": "file", - "description": "pandas dataframe containing the doublet classification", - "pattern": "*.pkl", - "ontologies": [] - } - } + }, + { + "name": "fastqutils_info", + "path": "modules/nf-core/fastqutils/info/meta.yml", + "type": "module", + "meta": { + "name": "fastqutils_info", + "description": "Performs quality control of FASTQ files", + "keywords": ["fastq", "qualitycontrol", "genomics", "sequencing"], + "tools": [ + { + "fastqutils": { + "description": "Validation and manipulation of FASTQ files, scRNA-seq barcode pre-processing and UMI quantification.", + "homepage": "https://github.com/nunofonseca/fastq_utils", + "documentation": "https://github.com/nunofonseca/fastq_utils", + "tool_dev_url": "https://github.com/nunofonseca/fastq_utils", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", + "pattern": "*.{fastq,fastq.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_25722" + }, + { + "edam": "http://edamontology.org/format_2573" + }, + { + "edam": "http://edamontology.org/format_3462" + }, + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ] + ], + "output": { + "info": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.txt": { + "type": "file", + "description": "Contains info if process ran successfully", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + } + ] + ], + "versions_fastqutils": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "fastqutils": { + "type": "string", + "description": "The tool name" + } + }, + { + "fastq_info -h 2>&1 | head -n 1 | sed 's/^fastq_utils //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "fastqutils": { + "type": "string", + "description": "The tool name" + } + }, + { + "fastq_info -h 2>&1 | head -n 1 | sed 's/^fastq_utils //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@famosab"], + "maintainers": ["@famosab"] + }, + "pipelines": [ + { + "name": "bamtofastq", + "version": "2.2.1" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "topics": { - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } + }, + { + "name": "fasttree", + "path": "modules/nf-core/fasttree/meta.yml", + "type": "module", + "meta": { + "name": "fasttree", + "description": "Produces a Newick format phylogeny from a multiple sequence alignment. Capable of bacterial genome size alignments.", + "keywords": ["phylogeny", "newick", "alignment"], + "tools": [ + { + "fasttree": { + "description": "FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences", + "homepage": "http://www.microbesonline.org/fasttree/", + "documentation": "http://www.microbesonline.org/fasttree/#Usage", + "licence": ["GPL v2"], + "identifier": "biotools:fasttree" + } + } + ], + "input": [ + { + "alignment": { + "type": "file", + "description": "A FASTA format multiple sequence alignment file", + "pattern": "*.{fasta,fas,fa,mfa}", + "ontologies": [] + } + } + ], + "output": { + "phylogeny": [ + { + "*.tre": { + "type": "file", + "description": "A phylogeny in Newick format", + "pattern": "*.{tre}", + "ontologies": [] + } + } + ], + "versions_fasttree": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "fasttree": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "fasttree -help 2>&1 | head -1 | sed 's/^FastTree \\([0-9.]*\\) .*$/\\1/'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "fasttree": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "fasttree -help 2>&1 | head -1 | sed 's/^FastTree \\([0-9.]*\\) .*$/\\1/'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@aunderwo"], + "maintainers": ["@aunderwo"] } - ] - }, - "authors": [ - "@LeonHafner" - ], - "maintainers": [ - "@LeonHafner" - ] - }, - "pipelines": [ - { - "name": "scdownstream", - "version": "dev" - } - ] - }, - { - "name": "dragen_germline", - "path": "modules/nf-core/dragen/germline/meta.yml", - "type": "module", - "meta": { - "name": "dragen", - "description": "The DRAGEN DNA Germline Pipeline accelerates the secondary analysis of NGS data by harnessing the tremendous power available on the DRAGEN Platform. The pipeline includes highly optimized algorithms for mapping, aligning, sorting, duplicate marking, and haplotype variant calling. In addition to haplotype variant calling, the pipeline supports calling of copy number and structural variants as well as detection of repeat expansions and targeted calls.", - "keywords": [ - "check fingerprint", - "copy number variation", - "fastqc", - "genomics", - "germline", - "quality control", - "repeat expansion detection", - "structural variation", - "trimming", - "variable number tandem repeat detection", - "variant annotation", - "variant calling", - "variant deduplication" - ], - "tools": [ - { - "dragen": { - "description": "The Illumina DRAGEN™ Bio-IT Platform is based on the highly reconfigurable DRAGEN Bio-IT Processor, which is integrated on a Field Programmable Gate Array (FPGA) card and is available in a preconfigured server that can be seamlessly integrated into bioinformatics workflows. The platform can be loaded with highly optimized algorithms for many different NGS secondary analysis pipelines.", - "homepage": "https://support-docs.illumina.com/SW/dragen_v42/Content/SW/FrontPages/DRAGEN.htm?searchText=explify-ref-db-dir", - "documentation": "https://support-docs.illumina.com/SW/dragen_v42/Content/SW/FrontPages/DRAGEN.htm?searchText=explify-ref-db-dir", - "identifier": "" + }, + { + "name": "fastx_collapser", + "path": "modules/nf-core/fastx/collapser/meta.yml", + "type": "module", + "meta": { + "name": "fastx_collapser", + "description": "Collapses identical sequences in a FASTQ/A file into a single sequence (while maintaining reads counts)", + "keywords": ["collapse", "genomics", "fasta", "fastq"], + "tools": [ + { + "fastx": { + "description": "A collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing", + "homepage": "http://hannonlab.cshl.edu/fastx_toolkit/", + "documentation": "http://hannonlab.cshl.edu/fastx_toolkit/commandline.html", + "tool_dev_url": "https://github.com/agordon/fastx_toolkit", + "licence": ["AGPL"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "fastx": { + "type": "file", + "description": "Decompressed FASTA/FASTQ input file", + "pattern": "*.{fastq,fasta}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ] + ], + "output": { + "fasta": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}.fasta": { + "type": "file", + "description": "Collapsed FASTA file", + "pattern": "*.fasta", + "ontologies": [] + } + } + ] + ], + "versions_fastx": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "fastx": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "fastx_collapser -h 2>&1 | grep -oE '[0-9]+\\.[0-9]+\\.[0-9]+' | head -1": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "fastx": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "fastx_collapser -h 2>&1 | grep -oE '[0-9]+\\.[0-9]+\\.[0-9]+' | head -1": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@jvfe"], + "maintainers": ["@jvfe"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false]`\n" - } - }, - { - "input": { - "type": "file", - "description": "FASTQ (may be gzipped), ora, BAM or CRAM files", - "pattern": "*.{fastq,fq,ora,bam,cram}{,.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } + }, + { + "name": "fcs_fcsadaptor", + "path": "modules/nf-core/fcs/fcsadaptor/meta.yml", + "type": "module", + "meta": { + "name": "fcs_fcsadaptor", + "description": "Run NCBI's FCS adaptor on assembled genomes", + "keywords": ["assembly", "genomics", "quality control", "contamination", "NCBI"], + "tools": [ + { + "fcs": { + "description": "The Foreign Contamination Screening (FCS) tool rapidly detects contaminants from foreign\norganisms in genome assemblies to prepare your data for submission. Therefore, the\nsubmission process to NCBI is faster and fewer contaminated genomes are submitted.\nThis reduces errors in analyses and conclusions, not just for the original data submitter\nbut for all subsequent users of the assembly.\n", + "homepage": "https://www.ncbi.nlm.nih.gov/data-hub/cgr/data-quality-tools/", + "documentation": "https://github.com/ncbi/fcs/wiki/FCS-adaptor", + "tool_dev_url": "https://github.com/ncbi/fcs", + "licence": ["NCBI-PD"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "assembly": { + "type": "file", + "description": "assembly fasta file", + "ontologies": [] + } + } + ] + ], + "output": { + "cleaned_assembly": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.cleaned_sequences.fa.gz": { + "type": "file", + "description": "Cleaned assembly in fasta format", + "pattern": "*.{cleaned_sequences.fa.gz}", + "ontologies": [] + } + } + ] + ], + "adaptor_report": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fcs_adaptor_report.txt": { + "type": "file", + "description": "Report of identified adaptors", + "pattern": "*.{fcs_adaptor_report.txt}", + "ontologies": [] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fcs_adaptor.log": { + "type": "file", + "description": "Log file", + "pattern": "*.{fcs_adaptor.log}", + "ontologies": [] + } + } + ] + ], + "pipeline_args": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.pipeline_args.yaml": { + "type": "file", + "description": "Run arguments", + "pattern": "*.{pipeline_args.yaml}", + "ontologies": [] + } + } + ] + ], + "skipped_trims": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.skipped_trims.jsonl": { + "type": "file", + "description": "Skipped trim information", + "pattern": "*.{skipped_trims.jsonl}", + "ontologies": [] + } + } + ] + ], + "versions_fcsadaptor": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "fcsadaptor": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "0.5.0": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "fcsadaptor": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "0.5.0": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@d4straub"], + "maintainers": ["@d4straub", "@gallvp"] }, - { - "sex": { - "type": "string", - "description": "Sample's sex.\nRecognize options: male, female, none, auto\n" - } - } - ], - { - "checkfingerprint_expected_vcf": { - "type": "file", - "description": "Input expected genotypes (VCF) for checkfingerprint comparison", - "pattern": "*.vcf", - "ontologies": [] - } - }, - { - "cnv_combined_counts": { - "type": "file", - "description": "Specify combined PON file", - "pattern": "*.combined.counts.txt.gz", - "ontologies": [ + "pipelines": [ { - "edam": "http://edamontology.org/format_3989" + "name": "genomeqc", + "version": "dev" } - ] - } - }, - { - "cnv_exclude_bed": { - "type": "file", - "description": "Regions to exclude for CNV processing", - "pattern": "*.bed", - "ontologies": [] - } - }, - { - "cnv_population_b_allele_vcf": { - "type": "file", - "description": "CNV population SNP input VCF file", - "pattern": "*.vcf", - "ontologies": [] - } - }, - { - "cnv_segmentation_bed": { - "type": "file", - "description": "Intervals to limit segmentation to", - "pattern": "*.bed", - "ontologies": [] - } - }, - { - "cnv_target_bed": { - "type": "file", - "description": "CNV target BED file", - "pattern": "*.bed", - "ontologies": [] - } - }, - { - "cram_reference": { - "type": "file", - "description": "Reference file in FASTA format (only used for decompression)", - "pattern": "*.{fasta,fa}", - "ontologies": [] - } - }, - { - "dbsnp": { - "type": "file", - "description": "Variant annotation database VCF (or .vcf.gz) file", - "pattern": "*.vcf{,.gz}", - "ontologies": [] - } - }, - { - "fastqc_adapter_file": { - "type": "file", - "description": "FASTA file containing adapter sequences", - "pattern": "*.{fasta,fa}", - "ontologies": [] - } - }, - { - "fastqc_kmer_file": { - "type": "file", - "description": "FASTA file containing kmers of interest", - "pattern": "*.{fasta,fa}", - "ontologies": [] - } - }, - { - "ora_reference": { - "type": "directory", - "description": "Path to the directory that contains the compression reference and index file" - } - }, - { - "qc_coverage_region": { - "type": "file", - "description": "bed files to report coverage on, max 3", - "pattern": "*.bed", - "ontologies": [] - } - }, - { - "qc_cross_cont_vcf": { - "type": "file", - "description": "Variant file (.vcf/.vcf.gz) with population allele frequencies to estimate sample contamination", - "pattern": "*.vcf{,.gz}", - "ontologies": [] - } - }, - { - "ref_dir": { - "type": "directory", - "description": "Directory with reference and hash tables" - } - }, - { - "repeat_genotype_ref_fasta": { - "type": "file", - "description": "FASTA file containing repeat genotypes", - "pattern": "*.{fasta,fa}", - "ontologies": [] - } - }, - { - "repeat_genotype_specs": { - "type": "file", - "description": "Repeat variant catalog file", - "ontologies": [] - } - }, - { - "sv_call_regions_bed": { - "type": "file", - "description": "BED file containing the set of regions to call (optionally gzip or bgzip compressed)", - "pattern": "*.bed{,.gz}", - "ontologies": [] - } - }, - { - "sv_exclusion_bed": { - "type": "file", - "description": "BED file containing the set of exclusion regions for SV calling (optionally gzip or bzip compressed)", - "pattern": "*.bed", - "ontologies": [] - } - }, - { - "sv_forcegt_vcf": { - "type": "file", - "description": "Specify a VCF of structural variants for forced genotyping, meaning these variants will be scored and emitted in the output VCF even if not found in the sample data. These variants will be merged with any additional variants discovered directly from the sample data.", - "pattern": "*.vcf", - "ontologies": [] - } - }, - { - "sv_systematic_noise": { - "type": "file", - "description": "Systematic noise BEDPE file containing the set of noisy paired regions for SV calling (optionally gzip or bzip compressed).", - "pattern": "*.bed{,.gz}", - "ontologies": [] - } - }, - { - "trim_adapter_read": { - "type": "file", - "description": "Files of adapter sequences to trim from the 3' end of read 1 and 2", - "pattern": "*.{fasta,fa}", - "ontologies": [] - } - }, - { - "trim_adapter_read_5prime": { - "type": "file", - "description": "FASTA files that contains adapter sequences to trim from the 5' end of Read 1 and 2; The sequences should be in reverse order (with respect to their appearance in the FASTQ) but not complemented", - "pattern": "*.{fasta,fa}", - "ontologies": [] - } - }, - { - "variant_annotation_data": { - "type": "directory", - "description": "Location of downloaded Nirvana annotation files" - } - }, - { - "vc_combine_phased_variants_distance_bed": { - "type": "file", - "description": "Combine variants in the same phase set bed file.", - "pattern": "*.bed", - "ontologies": [] - } - }, - { - "vc_excluded_regions_bed": { - "type": "file", - "description": "Excluded regions bed specifying where variants will be hard filtered", - "pattern": "*.bed", - "ontologies": [] - } - }, - { - "vc_forcegt_vcf": { - "type": "file", - "description": "List of small variants to force genotype. Can be .vcf or .vcf.gz file", - "pattern": "*.vcf{,.gz}", - "ontologies": [] - } - }, - { - "vc_log_bed": { - "type": "file", - "description": "Log information for regions in this BED file", - "pattern": "*.bed", - "ontologies": [] - } - }, - { - "vc_mapping_metrics": { - "type": "file", - "description": "File containing mapping metrics", - "ontologies": [] - } - }, - { - "vc_ml_dir": { - "type": "directory", - "description": "directory containing machine learning package" - } - }, - { - "vc_ntd_error_params": { - "type": "file", - "description": "Params file for per-nucleotide error rate calibration", - "ontologies": [] - } - }, - { - "vc_roh_blacklist_bed": { - "type": "file", - "description": "Blacklist BED file for ROH", - "pattern": "*.bed", - "ontologies": [] - } - }, - { - "vc_snp_error_cal_bed": { - "type": "file", - "description": "BED file containing regions from which to estimate nucleotide substitution biases", - "pattern": "*.bed", - "ontologies": [] - } - }, - { - "vc_systematic_noise": { - "type": "file", - "description": "Site specific noise file. This file enables the systematic-noise filter and improves specificity during somatic variant calling", - "ontologies": [] - } - }, - { - "vc_target_bed": { - "type": "file", - "description": "Target BED file", - "pattern": "*.bed", - "ontologies": [] - } - }, - { - "vd_eh_vcf": { - "type": "file", - "description": "Expansion hunter vcf (optionally .gzip compressed)", - "pattern": "*.vcf{,.gz}", - "ontologies": [] - } - }, - { - "vd_small_variant_vcf": { - "type": "file", - "description": "Small variant vcf (optionally .gzip compressed)", - "pattern": "*.vcf{,.gz}", - "ontologies": [] - } - }, - { - "vd_sv_vcf": { - "type": "file", - "description": "Structural variant vcf (optionally .gzip compressed)", - "pattern": "*.vcf{,.gz}", - "ontologies": [] - } - }, - { - "vntr_catalog_bed": { - "type": "file", - "description": "BED file specifying the TR regions for the VNTR Caller to act upon", - "pattern": "*.bed", - "ontologies": [] - } - } - ], - "output": { - "replay_json": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false, sex:'female' ]`\n" - } - }, - { - "${prefix}-replay.json": { - "type": "file", - "description": "Contains the exact set of parameters that specifies the analysis", - "pattern": "*-replay.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "coverage_metrics_csv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false, sex:'female' ]`\n" - } - }, - { - "${prefix}.*_coverage_metrics.csv": { - "type": "file", - "description": "Provides metrics over a region, a target region, or a QC coverage region", - "pattern": "*.*_coverage_metrics.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "SJ_saturation_txt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false, sex:'female' ]`\n" - 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} - } - ] - ], - "baf_seg": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false, sex:'female' ]`\n" - } - }, - { - "${prefix}.baf.seg": { - "type": "file", - "description": "Contains segmentation of b-allele loci", - "pattern": "*.baf.seg", - "ontologies": [] - } - } - ] - ], - "baf_seq_bw": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false, sex:'female' ]`\n" - } - }, - { - "${prefix}.baf.seq.bw": { - "type": "file", - "description": "BigWig representation of the BAF segments", - "pattern": "*.baf.seq.bw", - "ontologies": [] - } - } - ] - ], - "ballele_counts_gz": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false, sex:'female' ]`\n" - } - }, - { - "${prefix}.ballele.counts.gz": { - "type": "file", - "description": "TSV-file containing b-allele counts", - 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Therefore, the\nsubmission process to NCBI is faster and fewer contaminated genomes are submitted.\nThis reduces errors in analyses and conclusions, not just for the original data submitter\nbut for all subsequent users of the assembly.\"\n", + "homepage": "https://www.ncbi.nlm.nih.gov/data-hub/cgr/data-quality-tools/", + "documentation": "https://github.com/ncbi/fcs/wiki/FCS-GX", + "tool_dev_url": "https://github.com/ncbi/fcs", + "license": ["United States Government Work"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "assembly": { + "type": "file", + "description": "assembly fasta file", + "ontologies": [] + } + }, + { + "taxid": { + "type": "string", + "description": "Taxonomic id (e.g. \"6973\")" + } + } + ], { - "edam": "http://edamontology.org/format_3989" + "gxdb": { + "type": "file", + "description": "The NCBI GenBank database to search against.", + "ontologies": [] + } + } + ], + "output": { + "fcs_gx_report": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "out/*.fcs_gx_report.txt": { + "type": "file", + "description": "Report containing the contig identifier and recommended action (EXCLUDE, TRIM, FIX, REVIEW)", + "pattern": "*.fcs_gx_report.txt", + "ontologies": [] + } + } + ] + ], + "taxonomy_report": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "out/*.taxonomy.rpt": { + "type": "file", + "description": "Report containing the contig identifier and mapped contaminant species", + "pattern": "*.taxonomy.rpt", + "ontologies": [] + } + } + ] + ], + "versions_fcsadaptor": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "fcsadaptor": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "0.4.0": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_python": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "python": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python3 --version |& sed 's/Python //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "fcsadaptor": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "0.4.0": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "python": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python3 --version |& sed 's/Python //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@tillenglert"], + "maintainers": ["@tillenglert"] + } + }, + { + "name": "fcsgx_cleangenome", + "path": "modules/nf-core/fcsgx/cleangenome/meta.yml", + "type": "module", + "meta": { + "name": "fcsgx_cleangenome", + "description": "Runs FCS-GX (Foreign Contamination Screen - Genome eXtractor) to remove foreign contamination from genome assemblies", + "keywords": ["genome", "assembly", "contamination", "screening", "cleaning", "fcs-gx"], + "tools": [ + { + "fcsgx": { + "description": "The NCBI Foreign Contamination Screen. 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} - }, - { - "${prefix}.quant.transcript_coverage.txt": { - "type": "file", - "description": "Contains transcript coverage information", - "pattern": "*.quant.transcript_coverage.txt", - "ontologies": [] - } - } - ] - ], - "quant_transcript_fragment_lengths_txt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false, sex:'female' ]`\n" - } - }, - { - "${prefix}.quant.transcript_fragment_lengths.txt": { - "type": "file", - "description": "Contains transcript fragment lengths", - "pattern": "*.quant.transcript_fragment_lengths.txt", - "ontologies": [] - } - } - ] - ], - "realigned_regions_bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false, sex:'female' ]`\n" - } - }, - { - "${prefix}.realigned-regions.bed": { - "type": "file", - "description": "Contains regions that have been realigned", - "pattern": "*.realigned-regions.bed", - 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"pattern": "*.repeats.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "repeats_vcf_gz_tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false, sex:'female' ]`\n" - } - }, - { - "${prefix}.repeats.vcf.gz.tbi": { - "type": "file", - "description": "Index file for the gzipped repeats VCF", - "pattern": "*.repeats.vcf.gz.tbi", - "ontologies": [] - } - } - ] - ], - "roh_bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false, sex:'female' ]`\n" - } - }, - { - "${prefix}.roh.bed": { - "type": "file", - "description": "Contains regions of homozygosity", - "pattern": "*.roh.bed", - "ontologies": [] - } - } - ] - ], - "roh_metrics_csv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false, sex:'female' ]`\n" - } - }, - { - "${prefix}.roh_metrics.csv": { - "type": "file", - "description": "Contains metrics related to regions of homozygosity", - "pattern": "*.roh_metrics.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "sam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false, sex:'female' ]`\n" - } - }, - { - "${prefix}.sam": { - "type": "file", - "description": "Contains aligned read data in SAM format", - "pattern": "*.sam", - "ontologies": [] - } - } - ] - ], - "seg": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false, sex:'female' ]`\n" - } - }, - { - "${prefix}.seg": { - "type": "file", - "description": "Contains segmentation of genomic regions", - "pattern": "*.seg", - "ontologies": [] - } - } - ] - ], - "seg_bw": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false, sex:'female' ]`\n" - 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} - }, - { - "${prefix}.seg.called.merged": { - "type": "file", - "description": "Contains merged segmentation data", - "pattern": "*.seg.called.merged", - "ontologies": [] - } - } - ] - ], - "select_gvcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false, sex:'female' ]`\n" - } - }, - { - "${prefix}.select.gvcf": { - "type": "file", - "description": "Contains selected genomic variants in GVCF format", - "pattern": "*.select.gvcf", - "ontologies": [] - } - } - ] - ], - "small_indel_dedup": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false, sex:'female' ]`\n" - } - }, - { - "${prefix}.small_indel_dedup": { - "type": "file", - "description": "Contains deduplicated small indel variants", - "pattern": "*.small_indel_dedup", - "ontologies": [] - } - } - ] - ], - "smn_dedup": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false, sex:'female' ]`\n" - } - }, - { - "${prefix}.smn_dedup": { - "type": "file", - "description": "Contains deduplicated SMN variants", - "pattern": "*.smn_dedup", - "ontologies": [] - } - } - ] - ], - "snperror_samples_log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false, sex:'female' ]`\n" - } - }, - { - "${prefix}.snperror-sampler.log": { - "type": "file", - "description": "Log file containing information about SNP error sampling", - "pattern": "*.snperror-sampler.log", - "ontologies": [] - } - } - ] - ], - "sv_vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false, sex:'female' ]`\n" - } - }, - { - "${prefix}.sv.vcf": { - "type": "file", - "description": "VCF file containing structural variants", - "pattern": "*.sv.vcf", - "ontologies": [] - } - } - ] - ], - "sv_vcf_gz_tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false, sex:'female' ]`\n" - } - }, - { - "${prefix}.sv.vcf.gz.tbi": { - "type": "file", - "description": "Index file for the gzipped SV VCF", - "pattern": "*.sv.vcf.gz.tbi", - "ontologies": [] - } - } - ] - ], - "sv_metrics_csv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false, sex:'female' ]`\n" - } - }, - { - "${prefix}.sv_metrics.csv": { - "type": "file", - "description": "Contains metrics related to structural variants", - "pattern": "*.sv_metrics.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "target_counts_bw": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false, sex:'female' ]`\n" - } - }, - { - "${prefix}.target.counts.bw": { - "type": "file", - "description": "BigWig file containing target counts", - "pattern": "*.target.counts.bw", - "ontologies": [] - } - } - ] - ], - "target_counts_diploid_bw": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false, sex:'female' ]`\n" - } - }, - { - "${prefix}.target.counts.diploid.bw": { - "type": "file", - "description": "BigWig file containing diploid target counts", - "pattern": "*.target.counts.diploid.bw", - "ontologies": [] - } - } - ] - ], - "target_counts_gc_corrected_gz": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false, sex:'female' ]`\n" - } - }, - { - "${prefix}.target.counts.gc-corrected.gz": { - "type": "file", - "description": "Gzipped file containing GC-corrected target counts", - "pattern": "*.target.counts.gc-corrected.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "target_counts_gz": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false, sex:'female' ]`\n" - } - }, - { - "${prefix}.target.counts.gz": { - "type": "file", - "description": "Gzipped file containing target counts", - "pattern": "*.target.counts.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "targeted_json": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false, sex:'female' ]`\n" - } - }, - { - "${prefix}.targeted.json": { - "type": "file", - "description": "JSON file containing targeted sequencing information", - "pattern": "*.targeted.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "targeted_vcf_gz": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false, sex:'female' ]`\n" - } - }, - { - "${prefix}.targeted.vcf.gz": { - "type": "file", - "description": "Gzipped VCF file containing targeted variants", - "pattern": "*.targeted.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "time_metrics_csv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false, sex:'female' ]`\n" - } - }, - { - "${prefix}.time_metrics.csv": { - "type": "file", - "description": "Contains time metrics for the workflow", - "pattern": "*.time_metrics.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "tn_bw": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false, sex:'female' ]`\n" - } - }, - { - "${prefix}.tn.bw": { - "type": "file", - "description": "BigWig file containing TN (Tumor Normal) data", - "pattern": "*.tn.bw", - "ontologies": [] - } - } - ] - ], - "tn_tsv_gz": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false, sex:'female' ]`\n" - } - }, - { - "${prefix}.tn.tsv.gz": { - "type": "file", - "description": "Contains TN data in gzipped TSV format", - "pattern": "*.tn.tsv.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "trimmer_metrics_csv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false, sex:'female' ]`\n" - } - }, - { - "${prefix}.trimmer_metrics.csv": { - "type": "file", - "description": "Contains metrics from the trimmer", - "pattern": "*.trimmer_metrics.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "vc_hethom_ratio_metrics_csv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false, sex:'female' ]`\n" - } - }, - { - "${prefix}.vc_hethom_ratio_metrics.csv": { - "type": "file", - "description": "Contains heterozygous to homozygous ratio metrics", - "pattern": "*.vc_hethom_ratio_metrics.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "vc_metrics_csv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false, sex:'female' ]`\n" - } - }, - { - "${prefix}.vc_metrics.csv": { - "type": "file", - "description": "Contains variant calling metrics", - "pattern": "*.vc_metrics.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "vcf_gz": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false, sex:'female' ]`\n" - } - }, - { - "${prefix}.vcf.gz": { - "type": "file", - "description": "Gzipped VCF file containing genomic variants", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "vcf_gz_md5sum": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false, sex:'female' ]`\n" - } - }, - { - "${prefix}.vcf.gz.md5sum": { - "type": "file", - "description": "MD5 checksum file for the gzipped VCF", - "pattern": "*.vcf.gz.md5sum", - "ontologies": [] - } - } - ] - ], - "vcf_gz_tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false, sex:'female' ]`\n" - } - }, - { - "${prefix}.vcf.gz.tbi": { - "type": "file", - "description": "Index file for the gzipped VCF", - "pattern": "*.vcf.gz.tbi", - "ontologies": [] - } - } - ] - ], - "wgs_contig_mean_cov_csv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false, sex:'female' ]`\n" - } - }, - { - "${prefix}.wgs_contig_mean_cov.csv": { - "type": "file", - "description": "Contains WGS contig mean coverage metrics", - "pattern": "*.wgs_contig_mean_cov.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "wgs_coverage_metrics_csv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false, sex:'female' ]`\n" - } - }, - { - "${prefix}.wgs_coverage_metrics.csv": { - "type": "file", - "description": "Contains WGS coverage metrics", - "pattern": "*.wgs_coverage_metrics.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "wgs_fine_hist_csv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false, sex:'female' ]`\n" - } - }, - { - "${prefix}.wgs_fine_hist.csv": { - "type": "file", - "description": "Contains WGS fine histogram data", - "pattern": "*.wgs_fine_hist.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "wgs_hist_csv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false, sex:'female' ]`\n" - } - }, - { - "${prefix}.wgs_hist.csv": { - "type": "file", - "description": "Contains WGS histogram data", - "pattern": "*.wgs_hist.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "wgs_overall_mean_cov_csv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false, sex:'female' ]`\n" - } - }, - { - "${prefix}.wgs_overall_mean_cov.csv": { - "type": "file", - "description": "Contains WGS overall mean coverage metrics", - "pattern": "*.wgs_overall_mean_cov.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "callability_bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false, sex:'female' ]`\n" - } - }, - { - "${prefix}_callability.bed": { - "type": "file", - "description": "BED file containing callability regions", - "pattern": "*_callability.bed", - "ontologies": [] - } - } - ] - ], - "chr_start_end_impute_phase_vcf_gz": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false, sex:'female' ]`\n" - } - }, - { - "${prefix}_chr_start-end.impute.phase.vcf.gz": { - "type": "file", - "description": "Gzipped VCF file containing phased imputed variants", - "pattern": "*_chr_start-end.impute.phase.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "contig_mean_cov_csv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false, sex:'female' ]`\n" - } - }, - { - "${prefix}_contig_mean_cov.csv": { - "type": "file", - "description": "Contains WGS contig mean coverage metrics", - "pattern": "*_contig_mean_cov.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "cov_report_bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false, sex:'female' ]`\n" - } - }, - { - "${prefix}_cov_report.bed": { - "type": "file", - "description": "BED file containing coverage report", - "pattern": "*_cov_report.bed", - "ontologies": [] - } - } - ] - ], - "evidence": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false, sex:'female' ]`\n" - } - }, - { - "${prefix}_evidence.{b,cr,s}am": { - "type": "file", - "description": "Sorted BAM, CRAM or SAM file containing evidence reads", - "pattern": "*_evidence.{b,cr,s}am", - "ontologies": [ + }, + { + "name": "ffq", + "path": "modules/nf-core/ffq/meta.yml", + "type": "module", + "meta": { + "name": "ffq", + "description": "A command line tool that makes it easier to find sequencing data from the SRA / GEO / ENA.", + "keywords": ["SRA", "ENA", "GEO", "metadata", "fetch", "public", "databases"], + "tools": [ + { + "ffq": { + "description": "A command line tool that makes it easier to find sequencing data from the SRA / GEO / ENA.", + "homepage": "https://github.com/pachterlab/ffq", + "documentation": "https://github.com/pachterlab/ffq#usage", + "tool_dev_url": "https://github.com/pachterlab/ffq", + "doi": "10.1101/2022.05.18.492548", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ { - "edam": "http://edamontology.org/format_2572" - }, + "ids": { + "type": "list", + "description": "List of supported database ids e.g. SRA / GEO / ENA" + } + } + ], + "output": { + "json": [ + { + "*.json": { + "type": "file", + "description": "JSON file containing metadata for ids", + "pattern": "*.{json}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ], + "versions_ffq": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "ffq": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "ffq --help 2>&1 | sed 's/^.*ffq //; s/: A command.*\\$//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "ffq": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "ffq --help 2>&1 | sed 's/^.*ffq //; s/: A command.*\\$//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@drpatelh"], + "maintainers": ["@drpatelh"] + } + }, + { + "name": "fgbio_callduplexconsensusreads", + "path": "modules/nf-core/fgbio/callduplexconsensusreads/meta.yml", + "type": "module", + "meta": { + "name": "fgbio_callduplexconsensusreads", + "description": "Uses FGBIO CallDuplexConsensusReads to call duplex consensus sequences from reads generated from the same double-stranded source molecule.", + "keywords": ["umi", "duplex", "fgbio"], + "tools": [ + { + "fgbio": { + "description": "A set of tools for working with genomic and high throughput sequencing data, including UMIs", + "homepage": "http://fulcrumgenomics.github.io/fgbio/", + "documentation": "http://fulcrumgenomics.github.io/fgbio/tools/latest/CallDuplexConsensusReads.html", + "tool_dev_url": "https://github.com/fulcrumgenomics/fgbio", + "licence": ["MIT"], + "identifier": "biotools:fgbio" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "grouped_bam": { + "type": "file", + "description": "Grouped BAM file", + "pattern": "*.bam", + "ontologies": [] + } + } + ], { - "edam": "http://edamontology.org/format_3462" + "min_reads": { + "type": "string", + "description": "Minimum number of raw/original reads to build each consensus read. Can be a space delimited list of 1-3 values. See fgbio documentation for more details." + } }, { - "edam": "http://edamontology.org/format_2573" + "min_baseq": { + "type": "integer", + "description": "Ignore bases in raw reads that have Q below this value" + } } - ] - } - } - ] - ], - "fine_hist_csv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false, sex:'female' ]`\n" - } - }, - { - "${prefix}_fine_hist.csv": { - "type": "file", - "description": "Contains fine histogram data", - "pattern": "*_fine_hist.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "full_res_bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false, sex:'female' ]`\n" - } - }, - { - "${prefix}_full_res.bed": { - "type": "file", - "description": "BED file containing full resolution data", - "pattern": "*_full_res.bed", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3003" - } - ] - } - } - ] - ], - "hist_csv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false, sex:'female' ]`\n" - } - }, - { - "${prefix}_hist.csv": { - "type": "file", - "description": "Contains histogram data", - "pattern": "*_hist.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "overall_mean_cov_csv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false, sex:'female' ]`\n" - } - }, - { - "${prefix}_overall_mean_cov.csv": { - "type": "file", - "description": "Contains overall mean coverage metrics", - "pattern": "*_overall_mean_cov.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "read_cov_report_bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false, sex:'female' ]`\n" - } - }, - { - "${prefix}_read_cov_report.bed": { - "type": "file", - "description": "BED file containing read coverage report", - "pattern": "*_read_cov_report.bed", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3003" - } - ] - } - } - ] - ], - "partitions_txt": [ - { - "./sort_spill/partitions.txt": { - "type": "file", - "description": "Partitions file for sort spill", - "pattern": "./sort_spill/partitions.txt", - "ontologies": [] - } - } - ], - "alignmentStatsSummary_txt": [ - { - "./sv/results/stats/alignmentStatsSummary.txt": { - "type": "file", - "description": "Alignment statistics summary", - "pattern": "./sv/results/stats/alignmentStatsSummary.txt", - "ontologies": [] - } - } - ], - "candidate_metrics_csv": [ - { - "./sv/results/stats/candidate_metrics.csv": { - "type": "file", - "description": "Candidate metrics", - "pattern": "./sv/results/stats/candidate_metrics.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ], - "diploidSV_sv_metrics_csv": [ - { - "./sv/results/stats/diploidSV.sv_metrics.csv": { - "type": "file", - "description": "Diploid SV metrics", - "pattern": "./sv/results/stats/diploidSV.sv_metrics.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ], - "graph_metrics_csv": [ - { - "./sv/results/stats/graph_metrics.csv": { - "type": "file", - "description": "Graph metrics", - "pattern": "./sv/results/stats/graph_metrics.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ], - "svCandidateGenerationStats_tsv": [ - { - "./sv/results/stats/svCandidateGenerationStats.tsv": { - "type": "file", - "description": "Structural variant candidate generation statistics", - "pattern": "./sv/results/stats/svCandidateGenerationStats.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - "svCandidateGenerationStats_xml": [ - { - "./sv/results/stats/svCandidateGenerationStats.xml": { - "type": "file", - "description": "Structural variant candidate generation statistics (XML format)", - "pattern": "./sv/results/stats/svCandidateGenerationStats.xml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2332" - } - ] - } - } - ], - "svLocusGraphStats_tsv": [ - { - "./sv/results/stats/svLocusGraphStats.tsv": { - "type": "file", - "description": "Structural variant locus graph statistics", - "pattern": "./sv/results/stats/svLocusGraphStats.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - "candidateSV_vcf_gz": [ - { - "./sv/results/variants/candidateSV.vcf.gz": { - "type": "file", - "description": "Candidate structural variants (VCF format)", - "pattern": "./sv/results/variants/candidateSV.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ], - "candidateSV_vcf_gz_tbi": [ - { - "./sv/results/variants/candidateSV.vcf.gz.tbi": { - "type": "file", - "description": "Candidate structural variants index (VCF format)", - "pattern": "./sv/results/variants/candidateSV.vcf.gz.tbi", - "ontologies": [] - } - } - ], - "diploidSV_vcf_gz": [ - { - "./sv/results/variants/diploidSV.vcf.gz": { - "type": "file", - "description": "Gzipped VCF file containing diploid structural variants", - "pattern": "./sv/results/variants/diploidSV.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ], - "diploidSV_vcf_gz_tbi": [ - { - "./sv/results/variants/diploidSV.vcf.gz.tbi": { - "type": "file", - "description": "Candidate structural variants index (VCF format)", - "pattern": "./sv/results/variants/diploidSV.vcf.gz.tbi", - "ontologies": [] - } - } - ], - "alignmentStats_xml": [ - { - "./sv/workspace/alignmentStats.xml": { - "type": "file", - "description": "Alignment statistics in XML format", - "pattern": "./sv/workspace/alignmentStats.xml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2332" - } - ] - } - } - ], - "chromDepth_txt": [ - { - "./sv/workspace/chromDepth.txt": { - "type": "file", - "description": "Chromosome depth statistics", - "pattern": "./sv/workspace/chromDepth.txt", - "ontologies": [] - } - } - ], - "edgeRuntimeLog_txt": [ - { - "./sv/workspace/edgeRuntimeLog.txt": { - "type": "file", - "description": "Edge runtime log file", - "pattern": "./sv/workspace/edgeRuntimeLog.txt", - "ontologies": [] - } - } - ], - "genomeSegmentScanDebugInfo_txt": [ - { - "./sv/workspace/genomeSegmentScanDebugInfo.txt": { - "type": "file", - "description": "Genome segment scan debug information", - "pattern": "./sv/workspace/genomeSegmentScanDebugInfo.txt", - "ontologies": [] - } - } - ], - "config_log_txt": [ - { - "./sv/workspace/logs/config_log.txt": { - "type": "file", - "description": "Configuration log file", - "pattern": "./sv/workspace/logs/config_log.txt", - "ontologies": [] - } - } - ], - "svLocusGraph_bin": [ - { - "./sv/workspace/svLocusGraph.bin": { - "type": "file", - "description": "Binary file containing the SV locus graph", - "pattern": "./sv/workspace/svLocusGraph.bin", - "ontologies": [] - } - } - ], - "body_txt": [ - { - "body.txt": { - "type": "file", - "description": "Body log file", - "pattern": "body.txt", - "ontologies": [] - } - } - ], - "dragen_time_metrics_csv": [ - { - "dragen.time_metrics.csv": { - "type": "file", - "description": "Dragen time metrics", - "pattern": "dragen.time_metrics.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ], - "header_txt": [ - { - "header.txt": { - "type": "file", - "description": "Header log file", - "pattern": "header.txt", - "ontologies": [] - } - } - ], - "match_log_small_indel_dedup_txt": [ - { - "match_log.small_indel_dedup.txt": { - "type": "file", - "description": "Small indel deduplication log file", - "pattern": "match_log.small_indel_dedup.txt", - "ontologies": [] - } - } - ], - "match_log_smn_dedup_txt": [ - { - "match_log.smn_dedup.txt": { - "type": "file", - "description": "SMN deduplication log file", - "pattern": "match_log.smn_dedup.txt", - "ontologies": [] - } - } - ], - "streaming_log_csv": [ - { - "streaming_log_*.csv": { - "type": "file", - "description": "Streaming log files", - "pattern": "streaming_log_*.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ], - "usage_txt": [ - { - "*_usage.txt": { - "type": "file", - "description": "Usage log files", - "pattern": "*_usage.txt", - "ontologies": [] - } - } - ], - "all": [ - { - "**": { - "type": "file", - "description": "all output files", - "pattern": "**", - "ontologies": [] - } - } - ], - "versions_dragen": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "dragen": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "dragen --version 2>&1 | sed 's/^dragen Version //;q'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "dragen": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "dragen --version 2>&1 | sed 's/^dragen Version //;q'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@asr081", - "@marrip", - "@xuyangyuio" - ], - "maintainers": [ - "@marrip" - ] - } - }, - { - "name": "dragmap_align", - "path": "modules/nf-core/dragmap/align/meta.yml", - "type": "module", - "meta": { - "name": "dragmap_align", - "description": "Performs fastq alignment to a reference using DRAGMAP", - "keywords": [ - "alignment", - "map", - "fastq", - "bam", - "sam" - ], - "tools": [ - { - "dragmap": { - "description": "Dragmap is the Dragen mapper/aligner Open Source Software.", - "homepage": "https://github.com/Illumina/dragmap", - "documentation": "https://github.com/Illumina/dragmap", - "tool_dev_url": "https://github.com/Illumina/dragmap#basic-command-line-usage", - "licence": [ - "GPL v3" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "hashmap": { - "type": "file", - "description": "DRAGMAP hash table", - "pattern": "Directory containing DRAGMAP hash table *.{cmp,.bin,.txt}", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome']\n" - } + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.bam": { + "type": "file", + "description": "consensus BAM file", + "pattern": "${prefix}.bam", + "ontologies": [] + } + } + ] + ], + "versions_fgbio": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "fgbio": { + "type": "string", + "description": "The tool name" + } + }, + { + "fgbio --version 2>&1 | tr -d \"[:cntrl:]\" | sed -e \"s/^.*Version: //;s/\\[.*$//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "fgbio": { + "type": "string", + "description": "The tool name" + } + }, + { + "fgbio --version 2>&1 | tr -d \"[:cntrl:]\" | sed -e \"s/^.*Version: //;s/\\[.*$//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@lescai"], + "maintainers": ["@lescai"] }, - { - "fasta": { - "type": "file", - "description": "Genome fasta reference files", - "pattern": "*.{fa,fasta,fna}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - { - "sort_bam": { - "type": "boolean", - "description": "Sort the BAM file" - } - } - ], - "output": { - "sam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.sam": { - "type": "file", - "description": "Output SAM file containing read alignments", - "pattern": "*.{sam}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2571" - } - ] - } - } - ] - ], - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "Output BAM file containing read alignments", - "pattern": "*.{bam}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - } - ] - ], - "cram": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.cram": { - "type": "file", - "description": "Output CRAM file containing read alignments", - "pattern": "*.{cram}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2573" - } - ] - } - } - ] - ], - "crai": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.crai": { - "type": "file", - "description": "Index file for CRAM file", - "pattern": "*.{crai}", - "ontologies": [] - } - } - ] - ], - "csi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.csi": { - "type": "file", - "description": "Index file for CRAM file", - "pattern": "*.{csi}", - "ontologies": [] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.log": { - "type": "file", - "description": "Log file", - "pattern": "*.{log}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3888" - } - ] - } - } - ] - ], - "versions_dragmap": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "dragmap": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "dragen-os --version 2>&1": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_samtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_pigz": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pigz": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pigz --version 2>&1 | sed 's/pigz //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "dragmap": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "dragen-os --version 2>&1": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pigz": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pigz --version 2>&1 | sed 's/pigz //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "radseq", + "version": "dev" + } ] - ] }, - "authors": [ - "@edmundmiller" - ], - "maintainers": [ - "@edmundmiller" - ] - }, - "pipelines": [ { - "name": "nascent", - "version": "2.3.0" + "name": "fgbio_callmolecularconsensusreads", + "path": "modules/nf-core/fgbio/callmolecularconsensusreads/meta.yml", + "type": "module", + "meta": { + "name": "fgbio_callmolecularconsensusreads", + "description": "Calls consensus sequences from reads with the same unique molecular tag.", + "keywords": ["UMIs", "consensus sequence", "bam"], + "tools": [ + { + "fgbio": { + "description": "Tools for working with genomic and high throughput sequencing data.", + "homepage": "https://github.com/fulcrumgenomics/fgbio", + "documentation": "http://fulcrumgenomics.github.io/fgbio/", + "licence": ["MIT"], + "identifier": "biotools:fgbio" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false, collapse:false ]\n" + } + }, + { + "grouped_bam": { + "type": "file", + "description": "The input SAM or BAM file, grouped by UMIs\n", + "pattern": "*.{bam,sam}", + "ontologies": [] + } + } + ], + { + "min_reads": { + "type": "integer", + "description": "Minimum number of original reads to build each consensus read." + } + }, + { + "min_baseq": { + "type": "integer", + "description": "Ignore bases in raw reads that have Q below this value." + } + } + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Output SAM or BAM file to write consensus reads.\n", + "pattern": "*.{bam,sam}", + "ontologies": [] + } + } + ] + ], + "versions_fgbio": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "fgbio": { + "type": "string", + "description": "The tool name" + } + }, + { + "fgbio --version 2>&1 | tr -d \"[:cntrl:]\" | sed -e \"s/^.*Version: //;s/\\[.*$//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "fgbio": { + "type": "string", + "description": "The tool name" + } + }, + { + "fgbio --version 2>&1 | tr -d \"[:cntrl:]\" | sed -e \"s/^.*Version: //;s/\\[.*$//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@sruthipsuresh"], + "maintainers": ["@sruthipsuresh"] + }, + "pipelines": [ + { + "name": "radseq", + "version": "dev" + }, + { + "name": "sarek", + "version": "3.8.1" + } + ] }, { - "name": "rnadnavar", - "version": "dev" + "name": "fgbio_collectduplexseqmetrics", + "path": "modules/nf-core/fgbio/collectduplexseqmetrics/meta.yml", + "type": "module", + "meta": { + "name": "fgbio_collectduplexseqmetrics", + "description": "Collects a suite of metrics to QC duplex sequencing data.", + "keywords": ["UMIs", "QC", "bam", "duplex"], + "tools": [ + { + "fgbio": { + "description": "A set of tools for working with genomic and high throughput sequencing data, including UMIs", + "homepage": "http://fulcrumgenomics.github.io/fgbio/", + "documentation": "http://fulcrumgenomics.github.io/fgbio/", + "tool_dev_url": "https://github.com/fulcrumgenomics/fgbio", + "licence": ["MIT"], + "identifier": "biotools:fgbio" + } + }, + { + "r-ggplot2": { + "description": "ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics. ", + "homepage": "https://ggplot2.tidyverse.org/", + "documentation": "https://ggplot2.tidyverse.org/", + "tool_dev_url": "https://github.com/tidyverse/ggplot2", + "licence": ["MIT"], + "identifier": "biotools:fgbio" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "grouped_bam": { + "type": "file", + "description": "It has to be either 1)The exact BAM output by the GroupReadsByUmi tool (in the sort-order it was produced in) 2)A BAM file that has MI tags present on all reads (usually set by GroupReadsByUmi and has been sorted with SortBam into TemplateCoordinate order.", + "pattern": "*.bam", + "ontologies": [] + } + }, + { + "interval_list": { + "type": "file", + "description": "Calculation of metrics may be restricted to a set of regions using the --intervals parameter. The file format is descripted here https://samtools.github.io/htsjdk/javadoc/htsjdk/index.html?htsjdk/samtools/util/Interval.html", + "pattern": "*.{tsv|txt|interval_list}", + "ontologies": [] + } + } + ] + ], + "output": { + "family_sizes": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "**.family_sizes.txt": { + "type": "file", + "description": "Metrics on the frequency of different types of families of different sizes", + "pattern": "*.txt", + "ontologies": [] + } + } + ] + ], + "duplex_family_sizes": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "**.duplex_family_sizes.txt": { + "type": "file", + "description": "Metrics on the frequency of duplex tag families by the number of observations from each strand", + "pattern": "*.txt", + "ontologies": [] + } + } + ] + ], + "duplex_yield_metrics": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "**.duplex_yield_metrics.txt": { + "type": "file", + "description": "Summary QC metrics produced using 5%, 10%, 15%...100% of the data", + "pattern": "*.txt", + "ontologies": [] + } + } + ] + ], + "umi_counts": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "**.umi_counts.txt": { + "type": "file", + "description": "Metrics on the frequency of observations of UMIs within reads and tag families", + "pattern": "*.txt", + "ontologies": [] + } + } + ] + ], + "duplex_qc": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "**.duplex_qc.pdf": { + "type": "file", + "description": "A series of plots generated from the preceding metrics files for visualization", + "pattern": "*.pdf", + "ontologies": [] + } + } + ] + ], + "duplex_umi_counts": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "**.duplex_umi_counts.txt": { + "type": "file", + "description": "Metrics on the frequency of observations of duplex UMIs within reads and tag families.", + "pattern": "*.txt", + "ontologies": [] + } + } + ] + ], + "versions_fgbio": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "fgbio": { + "type": "string", + "description": "The tool name" + } + }, + { + "fgbio --version 2>&1 | tr -d \"[:cntrl:]\" | sed -e \"s/^.*Version: //;s/\\[.*$//\"": { + "type": "eval", + "description": "The command used to generate the version of the tool" + } + } + ] + ], + "versions_ggplot2": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "ggplot2": { + "type": "string", + "description": "The tool name" + } + }, + { + "Rscript -e \"cat(as.character(packageVersion('ggplot2')))\"": { + "type": "eval", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "fgbio": { + "type": "string", + "description": "The tool name" + } + }, + { + "fgbio --version 2>&1 | tr -d \"[:cntrl:]\" | sed -e \"s/^.*Version: //;s/\\[.*$//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "ggplot2": { + "type": "string", + "description": "The tool name" + } + }, + { + "Rscript -e \"cat(as.character(packageVersion('ggplot2')))\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@georgiakes"], + "maintainers": ["@georgiakes"] + } }, { - "name": "sammyseq", - "version": "dev" + "name": "fgbio_copyumifromreadname", + "path": "modules/nf-core/fgbio/copyumifromreadname/meta.yml", + "type": "module", + "meta": { + "name": "fgbio_copyumifromreadname", + "description": "Copies the UMI at the end of a bam files read name to the RX tag.", + "keywords": ["fgbio", "copy", "umi", "readname"], + "tools": [ + { + "fgbio": { + "description": "A set of tools for working with genomic and high throughput sequencing data, including UMIs", + "homepage": "http://fulcrumgenomics.github.io/fgbio/", + "documentation": "http://fulcrumgenomics.github.io/fgbio/tools/latest/CallDuplexConsensusReads.html", + "tool_dev_url": "https://github.com/fulcrumgenomics/fgbio", + "licence": ["MIT"], + "identifier": "biotools:fgbio" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "bam": { + "type": "file", + "description": "Sorted BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + }, + { + "edam": "http://edamontology.org/format_2573" + }, + { + "edam": "http://edamontology.org/format_3462" + } + ] + } + }, + { + "bai": { + "type": "file", + "description": "Index for bam file", + "pattern": "*.{bai}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + }, + { + "edam": "http://edamontology.org/format_2573" + }, + { + "edam": "http://edamontology.org/format_3462" + } + ] + } + } + ] + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Sorted BAM file", + "pattern": "*.{bam}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + } + ] + ], + "bai": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.bai": { + "type": "file", + "description": "Index for bam file", + "pattern": "*.{bai}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3327" + } + ] + } + } + ] + ], + "versions_fgbio": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "fgbio": { + "type": "string", + "description": "The tool name" + } + }, + { + "fgbio --version 2>&1 | tr -d \"[:cntrl:]\" | sed -e \"s/^.*Version: //;s/\\[.*$//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "fgbio": { + "type": "string", + "description": "The tool name" + } + }, + { + "fgbio --version 2>&1 | tr -d \"[:cntrl:]\" | sed -e \"s/^.*Version: //;s/\\[.*$//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@sppearce"], + "maintainers": ["@sppearce"] + }, + "pipelines": [ + { + "name": "sarek", + "version": "3.8.1" + } + ] }, { - "name": "sarek", - "version": "3.8.1" - } - ] - }, - { - "name": "dragmap_hashtable", - "path": "modules/nf-core/dragmap/hashtable/meta.yml", - "type": "module", - "meta": { - "name": "dragmap_hashtable", - "description": "Create DRAGEN hashtable for reference genome", - "keywords": [ - "index", - "fasta", - "genome", - "reference" - ], - "tools": [ - { - "dragmap": { - "description": "Dragmap is the Dragen mapper/aligner Open Source Software.", - "homepage": "https://github.com/Illumina/dragmap", - "documentation": "https://github.com/Illumina/dragmap", - "tool_dev_url": "https://github.com/Illumina/dragmap#basic-command-line-usage", - "licence": [ - "GPL v3" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test', single_end:false ]\n" - } + "name": "fgbio_fastqtobam", + "path": "modules/nf-core/fgbio/fastqtobam/meta.yml", + "type": "module", + "meta": { + "name": "fgbio_fastqtobam", + "description": "Using the fgbio tools, converts FASTQ files sequenced into unaligned BAM or CRAM files possibly moving the UMI barcode into the RX field of the reads\n", + "keywords": ["unaligned", "bam", "cram"], + "tools": [ + { + "fgbio": { + "description": "A set of tools for working with genomic and high throughput sequencing data, including UMIs", + "homepage": "http://fulcrumgenomics.github.io/fgbio/", + "documentation": "http://fulcrumgenomics.github.io/fgbio/tools/latest/", + "tool_dev_url": "https://github.com/fulcrumgenomics/fgbio", + "licence": ["MIT"], + "identifier": "biotools:fgbio" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "pair of reads to be converted into BAM file", + "pattern": "*.{fastq.gz}", + "ontologies": [] + } + } + ] + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{bam,cram}": { + "type": "file", + "description": "Unaligned, unsorted BAM or CRAM file", + "pattern": "*.{bam,cram}", + "ontologies": [] + } + } + ] + ], + "versions_fgbio": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "fgbio": { + "type": "string", + "description": "The tool name" + } + }, + { + "fgbio --version 2>&1 | tr -d \"[:cntrl:]\" | sed -e \"s/^.*Version: //;s/\\[.*$//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "fgbio": { + "type": "string", + "description": "The tool name" + } + }, + { + "fgbio --version 2>&1 | tr -d \"[:cntrl:]\" | sed -e \"s/^.*Version: //;s/\\[.*$//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@lescai", "@matthdsm", "@nvnieuwk"], + "maintainers": ["@lescai", "@matthdsm", "@nvnieuwk"] }, - { - "fasta": { - "type": "file", - "description": "Input genome fasta file", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ], - "output": { - "hashmap": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "dragmap": { - "type": "string", - "description": "DRAGMAP hash table", - "pattern": "*.{cmp,.bin,.txt}", - "ontologies": [] - } - } - ] - ], - "versions_dragmap": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "dragmap": { - "type": "string", - "description": "DRAGMAP hash table", - "pattern": "*.{cmp,.bin,.txt}", - "ontologies": [] - } - }, - { - "dragen-os --version 2>&1": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "dragmap": { - "type": "string", - "description": "DRAGMAP hash table", - "pattern": "*.{cmp,.bin,.txt}", - "ontologies": [] - } - }, - { - "dragen-os --version 2>&1": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "radseq", + "version": "dev" + }, + { + "name": "sarek", + "version": "3.8.1" + } ] - ] }, - "authors": [ - "@edmundmiller" - ], - "maintainers": [ - "@edmundmiller" - ] - }, - "pipelines": [ { - "name": "nascent", - "version": "2.3.0" + "name": "fgbio_filterconsensusreads", + "path": "modules/nf-core/fgbio/filterconsensusreads/meta.yml", + "type": "module", + "meta": { + "name": "fgbio_filterconsensusreads", + "description": "Uses FGBIO FilterConsensusReads to filter consensus reads generated by CallMolecularConsensusReads or CallDuplexConsensusReads.", + "keywords": ["fgbio", "filter", "consensus", "umi", "duplexumi"], + "tools": [ + { + "fgbio": { + "description": "A set of tools for working with genomic and high throughput sequencing data, including UMIs", + "homepage": "http://fulcrumgenomics.github.io/fgbio/", + "documentation": "http://fulcrumgenomics.github.io/fgbio/tools/latest/FilterConsensusReads.html", + "tool_dev_url": "https://github.com/fulcrumgenomics/fgbio", + "licence": ["MIT"], + "identifier": "biotools:fgbio" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file", + "pattern": "*.bam", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing genome information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Fasta file containing genomic sequence information", + "pattern": "*.{fa,fasta,fna}", + "ontologies": [] + } + }, + { + "index": { + "type": "file", + "description": "Fasta index file", + "pattern": "*.fai", + "ontologies": [] + } + }, + { + "dict": { + "type": "file", + "description": "Fasta dictionary file", + "pattern": "*.dict", + "ontologies": [] + } + } + ], + { + "min_reads": { + "type": "integer", + "description": "Minimum number of reads required to keep a consensus read" + } + }, + { + "min_baseq": { + "type": "file", + "description": "Minimum base quality to consider", + "ontologies": [] + } + }, + { + "max_base_error_rate": { + "type": "file", + "description": "Maximum base error rate for a position before it is replaced with an N.", + "ontologies": [] + } + } + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.bam": { + "type": "file", + "description": "Filtered consensus BAM file", + "pattern": "*.bam", + "ontologies": [] + } + } + ] + ], + "versions_fgbio": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "fgbio": { + "type": "string", + "description": "The tool name" + } + }, + { + "fgbio --version 2>&1 | tr -d \"[:cntrl:]\" | sed -e \"s/^.*Version: //;s/\\[.*$//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "fgbio": { + "type": "string", + "description": "The tool name" + } + }, + { + "fgbio --version 2>&1 | tr -d \"[:cntrl:]\" | sed -e \"s/^.*Version: //;s/\\[.*$//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@lescai"], + "maintainers": ["@lescai"] + }, + "pipelines": [ + { + "name": "radseq", + "version": "dev" + } + ] }, { - "name": "references", - "version": "0.1" + "name": "fgbio_groupreadsbyumi", + "path": "modules/nf-core/fgbio/groupreadsbyumi/meta.yml", + "type": "module", + "meta": { + "name": "fgbio_groupreadsbyumi", + "description": "Groups reads together that appear to have come from the same original molecule.\nReads are grouped by template, and then templates are sorted by the 5’ mapping positions\nof the reads from the template, used from earliest mapping position to latest.\nReads that have the same end positions are then sub-grouped by UMI sequence.\n(!) Note: the MQ tag is required on reads with mapped mates (!)\nThis can be added using samblaster with the optional argument --addMateTags.\n", + "keywords": ["UMI", "groupreads", "fgbio"], + "tools": [ + { + "fgbio": { + "description": "A set of tools for working with genomic and high throughput sequencing data, including UMIs", + "homepage": "http://fulcrumgenomics.github.io/fgbio/", + "documentation": "http://fulcrumgenomics.github.io/fgbio/tools/latest/", + "tool_dev_url": "https://github.com/fulcrumgenomics/fgbio", + "licence": ["MIT"], + "identifier": "biotools:fgbio" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file. Note: the MQ tag is required on reads with mapped mates (!)\n", + "pattern": "*.bam", + "ontologies": [] + } + } + ], + { + "strategy": { + "type": "string", + "enum": ["Identity", "Edit", "Adjacency", "Paired"], + "description": "Required argument: defines the UMI assignment strategy.\nMust be chosen among: Identity, Edit, Adjacency, Paired.\n" + } + } + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "UMI-grouped BAM", + "pattern": "*.bam", + "ontologies": [] + } + } + ] + ], + "histogram": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*histogram.txt": { + "type": "file", + "description": "A text file containing the tag family size counts", + "pattern": "*.txt", + "ontologies": [] + } + } + ] + ], + "read_metrics": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*read-metrics.txt": { + "type": "file", + "description": "A text file containing the read count metrics from grouping", + "pattern": "*.txt", + "ontologies": [] + } + } + ] + ], + "versions_fgbio": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "fgbio": { + "type": "string", + "description": "The tool name" + } + }, + { + "fgbio --version 2>&1 | tr -d \"[:cntrl:]\" | sed -e \"s/^.*Version: //;s/\\[.*$//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "fgbio": { + "type": "string", + "description": "The tool name" + } + }, + { + "fgbio --version 2>&1 | tr -d \"[:cntrl:]\" | sed -e \"s/^.*Version: //;s/\\[.*$//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@lescai"], + "maintainers": ["@lescai"] + }, + "pipelines": [ + { + "name": "radseq", + "version": "dev" + }, + { + "name": "sarek", + "version": "3.8.1" + } + ] }, { - "name": "rnadnavar", - "version": "dev" + "name": "fgbio_sortbam", + "path": "modules/nf-core/fgbio/sortbam/meta.yml", + "type": "module", + "meta": { + "name": "fgbio_sortbam", + "description": "Sorts a SAM or BAM file. Several sort orders are available, including coordinate, queryname, random, and randomquery.", + "keywords": ["sort", "bam", "sam"], + "tools": [ + { + "fgbio": { + "description": "Tools for working with genomic and high throughput sequencing data.", + "homepage": "https://github.com/fulcrumgenomics/fgbio", + "documentation": "http://fulcrumgenomics.github.io/fgbio/", + "licence": ["MIT"], + "identifier": "biotools:fgbio" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false, collapse:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "The input SAM or BAM file to be sorted.\n", + "pattern": "*.{bam,sam}", + "ontologies": [] + } + } + ] + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Output SAM or BAM file.\n", + "pattern": "*.{bam,sam}", + "ontologies": [] + } + } + ] + ], + "versions_fgbio": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "fgbio": { + "type": "string", + "description": "The tool name" + } + }, + { + "fgbio --version 2>&1 | tr -d \"[:cntrl:]\" | sed -e \"s/^.*Version: //;s/\\[.*$//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "fgbio": { + "type": "string", + "description": "The tool name" + } + }, + { + "fgbio --version 2>&1 | tr -d \"[:cntrl:]\" | sed -e \"s/^.*Version: //;s/\\[.*$//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@sruthipsuresh"], + "maintainers": ["@sruthipsuresh"] + } }, { - "name": "sarek", - "version": "3.8.1" - } - ] - }, - { - "name": "dragonflye", - "path": "modules/nf-core/dragonflye/meta.yml", - "type": "module", - "meta": { - "name": "dragonflye", - "description": "Assemble bacterial isolate genomes from Nanopore reads", - "keywords": [ - "bacterial", - "assembly", - "nanopore" - ], - "tools": [ - { - "dragonflye": { - "description": "Microbial assembly pipeline for Nanopore reads", - "homepage": "https://github.com/rpetit3/dragonflye", - "documentation": "https://github.com/rpetit3/dragonflye/blob/main/README.md", - "licence": [ - "GPL v2" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "shortreads": { - "type": "file", - "description": "Optional. List of FastQ files of short reads (paired-end data) that will be used to polish the draft genome.\n", - "pattern": "*.fastq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - }, - { - "longreads": { - "type": "file", - "description": "Input Nanopore FASTQ file", - "pattern": "*.fastq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "output": { - "contigs": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.fa": { - "type": "file", - "description": "The final assembly produced by Dragonflye", - "pattern": "*.fa", - "ontologies": [] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "dragonflye.log": { - "type": "file", - "description": "Full log file for bug reporting", - "pattern": "dragonflye.log", - "ontologies": [] - } - } - ] - ], - "raw_contigs": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "{flye,miniasm,raven}.fasta": { - "type": "file", - "description": "Raw assembly produced by the assembler (Flye, Miniasm, or Raven)", - "pattern": "{flye,miniasm,raven}.fasta", - "ontologies": [] - } - } - ] - ], - "gfa": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "{flye,miniasm,raven}-unpolished.gfa": { - "type": "file", - "description": "Assembly graph produced by Miniasm, or Raven", - "pattern": "{flye,miniasm,raven}-unpolished.gfa", - "ontologies": [] - } - } - ] - ], - "txt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "flye-info.txt": { - "type": "file", - "description": "Assembly information output by Flye", - "pattern": "flye-info.txt", - "ontologies": [] - } - } - ] - ], - "versions_dragonflye": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "dragonflye": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "dragonflye --version 2>&1 | sed 's/^.*dragonflye //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "dragonflye": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "dragonflye --version 2>&1 | sed 's/^.*dragonflye //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@rpetit3" - ], - "maintainers": [ - "@rpetit3" - ] - }, - "pipelines": [ - { - "name": "bacass", - "version": "2.6.0" - } - ] - }, - { - "name": "drep_compare", - "path": "modules/nf-core/drep/compare/meta.yml", - "type": "module", - "meta": { - "name": "drep_compare", - "description": "Performs rapid genome comparisons for a group of genomes and visualize their relatedness", - "keywords": [ - "drep", - "genome", - "fasta", - "compare", - "comparison", - "visualisation", - "metagenomics", - "assembly", - "microbial genomics", - "dereplication" - ], - "tools": [ - { - "drep": { - "description": "De-replication of microbial genomes assembled from multiple samples", - "homepage": "https://drep.readthedocs.io/en/latest/", - "documentation": "https://drep.readthedocs.io/en/latest/", - "tool_dev_url": "https://github.com/MrOlm/drep", - "doi": "10.1038/ismej.2017.126", - "licence": [ - "MIT" - ], - "identifier": "biotools:drep" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "fastas/*": { - "type": "file", - "description": "List of FASTA files to compare", - "pattern": "*.{fasta,fa,fna,fas}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ], - "output": { - "directory": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "${prefix}": { - "type": "directory", - "description": "Directory containing output files, such as PDF figures and intermediate tables for use in dRep dereplicate", - "pattern": "${prefix}/", - "ontologies": [ - { - "edam": "http://edamontology.org/data_1049" - } - ] - } - } - ] - ], - "versions_drep": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "drep": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "dRep | sed '2!d;s/.*v//g;s/ .*//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "drep": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "dRep | sed '2!d;s/.*v//g;s/ .*//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@jfy133" - ], - "maintainers": [ - "@jfy133" - ] - } - }, - { - "name": "drep_dereplicate", - "path": "modules/nf-core/drep/dereplicate/meta.yml", - "type": "module", - "meta": { - "name": "drep_dereplicate", - "description": "Dereplicates a genome set by identifying highly similar genomes and choose the best representative genome", - "keywords": [ - "drep", - "genome", - "fasta", - "compare", - "comparison", - "visualisation", - "metagenomics", - "assembly", - "microbial genomics", - "dereplication" - ], - "tools": [ - { - "drep": { - "description": "De-replication of microbial genomes assembled from multiple samples", - "homepage": "https://drep.readthedocs.io/en/latest/", - "documentation": "https://drep.readthedocs.io/en/latest/", - "tool_dev_url": "https://github.com/MrOlm/drep", - "doi": "10.1038/ismej.2017.126", - "licence": [ - "MIT" - ], - "identifier": "biotools:drep" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "fastas": { - "type": "file", - "description": "List of FASTA files to dereplicate", - "pattern": "*.{fasta,fa,fna,fas}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "drep_work": { - "type": "directory", - "description": "Optional existing dRep working directory containing pre-computed clustering results (e.g. output from dRep compare)", - "ontologies": [ - { - "edam": "http://edamontology.org/data_1049" - } - ] - } - } - ] - ], - "output": { - "fastas": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "dereplicated_genomes/*": { - "type": "file", - "description": "Representative genomes for each cluster of similar genomes", - "pattern": "*.{fasta,fa,fna,fas}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ], - "summary_tables": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "data_tables/*.csv": { - "type": "file", - "description": "Summary tables containing information about the dereplication process including cluster membership of each genome", - "pattern": "*.{csv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "figures": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "figures/*pdf": { - "type": "file", - "description": "Figures visualising the dereplication process, such as clustering results and representative genome selection", - "pattern": "*.{pdf}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3508" - } - ] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "logger.log": { - "type": "file", - "description": "logging file containing information about the dereplication process", - "pattern": "*.{log}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1964" - } - ] - } - } - ] - ], - "versions_drep": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "drep": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "dRep | sed '2!d;s/.*v//g;s/ .*//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "drep": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "dRep | sed '2!d;s/.*v//g;s/ .*//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@jfy133" - ], - "maintainers": [ - "@jfy133" - ] - } - }, - { - "name": "dshbio_exportsegments", - "path": "modules/nf-core/dshbio/exportsegments/meta.yml", - "type": "module", - "meta": { - "name": "dshbio_exportsegments", - "description": "Export assembly segment sequences in GFA 1.0 format to FASTA format", - "keywords": [ - "gfa", - "assembly", - "segment" - ], - "tools": [ - { - "dshbio": { - "description": "Reads, features, variants, assemblies, alignments, genomic range trees, pangenome\ngraphs, and a bunch of random command line tools for bioinformatics. LGPL version 3\nor later.\n", - "homepage": "https://github.com/heuermh/dishevelled-bio", - "documentation": "https://github.com/heuermh/dishevelled-bio", - "licence": [ - "LGPL-3.0-or-later" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + "name": "fgbio_zipperbams", + "path": "modules/nf-core/fgbio/zipperbams/meta.yml", + "type": "module", + "meta": { + "name": "fgbio_zipperbams", + "description": "FGBIO tool to zip together an unmapped and mapped BAM to transfer metadata into the output BAM", + "keywords": ["fgbio", "umi", "unmapped", "ubam", "zipperbams"], + "tools": [ + { + "fgbio": { + "description": "A set of tools for working with genomic and high throughput sequencing data, including UMIs", + "homepage": "http://fulcrumgenomics.github.io/fgbio/", + "documentation": "http://fulcrumgenomics.github.io/fgbio/tools/latest/", + "tool_dev_url": "https://github.com/fulcrumgenomics/fgbio", + "licence": ["MIT"], + "identifier": "biotools:fgbio" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "mapped_bam": { + "type": "file", + "description": "mapped BAM/SAM file", + "pattern": "*.{bam,sam}", + "ontologies": [] + } + }, + { + "unmapped_bam": { + "type": "file", + "description": "unmapped BAM file", + "pattern": "*.bam", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'GRCh38' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "fasta file containing genomic sequence information", + "pattern": "*.{fasta,fna,fa}", + "ontologies": [] + } + }, + { + "index": { + "type": "file", + "description": "fasta index file", + "pattern": "*.fai", + "ontologies": [] + } + }, + { + "dict": { + "type": "file", + "description": "dict file containing a sequence dictionary for the fasta file", + "pattern": "*.dict", + "ontologies": [] + } + } + ] + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.bam": { + "type": "file", + "description": "Zipped BAM file", + "pattern": "*.bam", + "ontologies": [] + } + } + ] + ], + "versions_fgbio": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "fgbio": { + "type": "string", + "description": "The tool name" + } + }, + { + "fgbio --version 2>&1 | tr -d \"[:cntrl:]\" | sed -e \"s/^.*Version: //;s/\\[.*$//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "fgbio": { + "type": "string", + "description": "The tool name" + } + }, + { + "fgbio --version 2>&1 | tr -d \"[:cntrl:]\" | sed -e \"s/^.*Version: //;s/\\[.*$//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@lescai"], + "maintainers": ["@lescai"] }, - { - "gfa": { - "type": "file", - "description": "Assembly segments in uncompressed or compressed GFA 1.0 format", - "pattern": "*.{gfa|gfa.bgz|gfa.gz|gfa.zst}", - "ontologies": [] - } - } - ] - ], - "output": { - "fasta": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.fa.gz": { - "type": "file", - "description": "Assembly segment sequences in gzipped FASTA format", - "pattern": "*.{fa.gz}", - "ontologies": [] - } - } - ] - ], - "versions_dshbio": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "dsh-bio": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "dsh-bio --version | sed '1!d;s/dsh-bio-tools //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "dsh-bio": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "dsh-bio --version | sed '1!d;s/dsh-bio-tools //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "radseq", + "version": "dev" + } ] - ] - }, - "authors": [ - "@heuermh" - ], - "maintainers": [ - "@heuermh" - ] - } - }, - { - "name": "dshbio_filterbed", - "path": "modules/nf-core/dshbio/filterbed/meta.yml", - "type": "module", - "meta": { - "name": "dshbio_filterbed", - "description": "Filter features in gzipped BED format", - "keywords": [ - "bed", - "filter", - "feature" - ], - "tools": [ - { - "dshbio": { - "description": "Reads, features, variants, assemblies, alignments, genomic range trees, pangenome\ngraphs, and a bunch of random command line tools for bioinformatics. 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], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Genome reference FASTA file", - "pattern": "*.{fa,fasta}", - "ontologies": [] - } + }, + { + "name": "foldmason_createdb", + "path": "modules/nf-core/foldmason/createdb/meta.yml", + "type": "module", + "meta": { + "name": "foldmason_createdb", + "description": "Creates a database for Foldmason.", + "keywords": ["alignment", "MSA", "genomics", "structure"], + "tools": [ + { + "foldmason": { + "description": "Multiple Protein Structure Alignment at Scale with FoldMason", + "homepage": "https://github.com/steineggerlab/foldmason", + "documentation": "https://github.com/steineggerlab/foldmason", + "tool_dev_url": "https://github.com/steineggerlab/foldmason", + "doi": "10.1101/2024.08.01.606130", + "licence": ["GPL v3"], + "identifier": "biotools:foldmason" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "structures": { + "type": "file", + "description": "Input protein structures in `PDB` or `mmCIF` format.", + "pattern": "*.{pdb,mmcif}", + "ontologies": [] + } + } + ] + ], + "output": { + "db": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}*": { + "type": "file", + "description": "All database files created by Foldmason", + "pattern": "*", + "ontologies": [] + } + } + ] + ], + "versions_foldmason": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "foldmason": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "foldmason version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "foldmason": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "foldmason version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@luisas"], + "maintainers": ["@luisas"] }, - { - "fai": { - "type": "file", - "description": "Genome reference FASTA index file", - "pattern": "*.{fa.fai,fasta.fai}", - "ontologies": [] - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample1' ]\n" - } - }, - { - "*.vcf.gz": { - "type": "file", - "description": "VCF file with identified structural variants", - "pattern": "*.{vcf.gz}", - "ontologies": [] - } - } - ] - ], - "tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample1' ]\n" - } - }, - { - "*.vcf.gz.tbi": { - "type": "file", - "description": "The index of the BCF/VCF file", - "pattern": "*.{vcf.gz.tbi}", - "ontologies": [] - } - } + "pipelines": [ + { + "name": "multiplesequencealign", + "version": "1.1.1" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@famosab", - "@poddarharsh15" - ], - "maintainers": [ - "@poddarharsh15" - ] - } - }, - { - "name": "dysgu_run", - "path": "modules/nf-core/dysgu/run/meta.yml", - "type": "module", - "meta": { - "name": "dysgu_run", - "description": "Dysgu calls structural variants (SVs) from mapped sequencing reads. It is designed for accurate and efficient detection of structural variations.", - "keywords": [ - "structural variants", - "sv", - "vcf" - ], - "tools": [ - { - "dysgu": { - "description": "Structural variant caller for mapped sequencing data", - "homepage": "https://github.com/kcleal/dysgu", - "documentation": "https://github.com/kcleal/dysgu/blob/master/README.rst", - "tool_dev_url": "https://github.com/kcleal/dysgu", - "doi": "10.1093/nar/gkac039", - "licence": [ - "GPL-3.0-or-later" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "input": { - "type": "file", - "description": "Input BAM file", - "pattern": "*.{bam,cram}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - }, - { - "edam": "http://edamontology.org/format_3462" - } - ] - } - }, - { - "index": { - "type": "file", - "description": "BAM index file", - "pattern": "*.{bai,crai}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3327" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Genome reference FASTA file", - "pattern": "*.{fa,fasta}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fai": { - "type": "file", - "description": "Genome reference FASTA index file", - "pattern": "*.{fa.fai,fasta.fai}", - "ontologies": [] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "sites": { - "type": "file", - "description": "Known sites VCF file", - "pattern": "*.{vcf,vcf.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - } - ] - } - } - ], - [ - { - "meta5": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "bed": { - "type": "file", - "description": "Regions to include BED file", - "pattern": "*.bed", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3003" - } - ] - } - } - ], - [ - { - "meta6": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "search_bed": { - "type": "file", - "description": "Regions to search BED file", - "pattern": "*.bed", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3003" - } - ] - } - } - ], - [ - { - "meta7": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } + }, + { + "name": "foldmason_easymsa", + "path": "modules/nf-core/foldmason/easymsa/meta.yml", + "type": "module", + "meta": { + "name": "foldmason_easymsa", + "description": "Aligns protein structures using foldmason", + "keywords": ["alignment", "MSA", "genomics", "structure"], + "tools": [ + { + "foldmason": { + "description": "Multiple Protein Structure Alignment at Scale with FoldMason", + "homepage": "https://github.com/steineggerlab/foldmason", + "documentation": "https://github.com/steineggerlab/foldmason", + "tool_dev_url": "https://github.com/steineggerlab/foldmason", + "doi": "10.1101/2024.08.01.606130", + "licence": ["GPL v3"], + "identifier": "biotools:foldmason" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "pdbs": { + "type": "file", + "description": "Input protein structures in PDB format.", + "pattern": "*.{pdb,mmcif}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1476" + }, + { + "edam": "http://edamontology.org/format_1477" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "tree": { + "type": "file", + "description": "Input guide tree in Newick format.", + "pattern": "*.{dnd,nwk}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2006" + }, + { + "edam": "http://edamontology.org/format_1910" + } + ] + } + } + ], + { + "compress": { + "type": "boolean", + "description": "Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded." + } + } + ], + "output": { + "msa_3di": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}_3di.fa${compress ? '.gz' : ''}": { + "type": "file", + "description": "Fasta file containing the multiple sequence alignment with 3Di alphabet", + "pattern": "*.{fa}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2554" + }, + { + "edam": "http://edamontology.org/format_1921" + }, + { + "edam": "http://edamontology.org/format_1984" + } + ] + } + } + ] + ], + "msa_aa": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}_aa.fa${compress ? '.gz' : ''}": { + "type": "file", + "description": "Fasta file containing the multiple sequence alignment with Amino Acid alphabet", + "pattern": "*.{fa}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2554" + }, + { + "edam": "http://edamontology.org/format_1921" + }, + { + "edam": "http://edamontology.org/format_1984" + } + ] + } + } + ] + ], + "versions_foldmason": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "foldmason": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "foldmason version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_pigz": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "pigz": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pigz --version 2>&1 | sed \"s/^.*pigz[[:space:]]*//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "foldmason": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "foldmason version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "pigz": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pigz --version 2>&1 | sed \"s/^.*pigz[[:space:]]*//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@luisas"], + "maintainers": ["@luisas"] }, - { - "exclude_bed": { - "type": "file", - "description": "Regions to exclude BED file", - "pattern": "*.bed", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3003" - } - ] - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample1' ]\n" - } - }, - { - "*.vcf.gz": { - "type": "file", - "description": "VCF file with identified structural variants", - "pattern": "*.{vcf.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - } - ] - } - } - ] - ], - "tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample1' ]\n" - } - }, - { - "*.vcf.gz.tbi": { - "type": "file", - "description": "The index of the BCF/VCF file", - "pattern": "*.vcf.gz.tbi", - "ontologies": [] - } - } - ] - ], - "versions_dysgu": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - 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Required if aoi is a shapefile.", + "pattern": "*.{dbf}", + "ontologies": [] + } }, { - "edam": "http://edamontology.org/format_3020" + "shapefile_prj": { + "type": "file", + "description": "Optional projection for shapefiles. Required if aoi is a shapefile.", + "pattern": "*.{prj}", + "ontologies": [] + } + }, + { + "shapefile_shx": { + "type": "file", + "description": "Optional shape index for shapefiles. 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Directory names indicate corresponding datacube tile. Pixel values indicate usable pixels in downstream analysis.", + "pattern": "*.tif", + "ontologies": [] + } + } + ], + "versions_force": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "force": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "force-cube -v": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "force": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "force-cube -v": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@Felix-Kummer"], + "maintainers": ["@Felix-Kummer"] } - ] - ], - "output": { - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.log": { - "type": "file", - "description": "ectyper log output", - "pattern": "*.log", - "ontologies": [] - } - } - ] - ], - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "ectyper serotyping results in TSV format", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "txt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.txt": { - "type": "file", - "description": "Allele report generated from BLAST results", - "pattern": "*.txt", - "ontologies": [] - } - } - ] - ], - "versions_ectyper": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "ectyper": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "ectyper --version 2>&1 | sed 's/.*ectyper //; s/ .*$//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "ectyper": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "ectyper --version 2>&1 | sed 's/.*ectyper //; s/ .*$//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@rpetit3" - ], - "maintainers": [ - "@rpetit3" - ] - } - }, - { - "name": "eggnogmapper", - "path": "modules/nf-core/eggnogmapper/meta.yml", - "type": "module", - "meta": { - "name": "eggnogmapper", - "description": "Fast genome-wide functional annotation through orthology assignment.", - "keywords": [ - "annotation", - "functional annotation", - "orthology", - "genomics", - "eggnog" - ], - "tools": [ - { - "eggnogmapper": { - "description": "EggNOG-mapper is a tool for fast functional annotation of novel sequences.\nIt uses precomputed orthologous groups and phylogenies from the eggNOG database\nto transfer functional information from fine-grained orthologs only.\n", - "homepage": "https://github.com/eggnogdb/eggnog-mapper", - "documentation": "https://github.com/eggnogdb/eggnog-mapper/wiki", - "tool_dev_url": "https://github.com/eggnogdb/eggnog-mapper", - "doi": "10.1093/molbev/msab293", - "licence": [ - "AGPL v3" - ], - "identifier": "biotools:eggnog-mapper-v2" + }, + { + "name": "force_tileextent", + "path": "modules/nf-core/force/tileextent/meta.yml", + "type": "module", + "meta": { + "name": "force_tileextent", + "description": "Compute valid tiles for a given datacube definition and area of interest.\nThis list can be used by downstream analysis tasks to limit processing to the area of interest when satellite data covers a larger region.\n", + "keywords": ["satellite data", "extent", "tile", "datacube"], + "tools": [ + { + "force": { + "description": "A all-in-one tool for processing satellite data.\nSpecialized on medium resolution data such as Landsat or Sentinel imagery.\n", + "homepage": "https://davidfrantz.github.io/code/force/", + "documentation": "https://force-eo.readthedocs.io/en/latest/index.html", + "tool_dev_url": "https://github.com/davidfrantz/force", + "doi": "10.3390/rs11091124", + "licence": ["GPL-3.0"], + "identifier": "" + } + } + ], + "input": [ + { + "aoi": { + "type": "file", + "description": "Vector file (either shapefile geometry or geopackage) defining the area of interest.", + "pattern": "*.{shp,gpkg}", + "ontologies": [] + } + }, + { + "datacube_definition": { + "type": "file", + "description": "Datacube file in FORCE format defining the properties of the targeted datacube.", + "pattern": "*.{prj}", + "ontologies": [] + } + }, + { + "shapefile_dbf": { + "type": "file", + "description": "Optional attribute table for shapefiles. Required if aoi is a shapefile.", + "pattern": "*.{dbf}", + "ontologies": [] + } + }, + { + "shapefile_prj": { + "type": "file", + "description": "Optional projection for shapefiles. Required if aoi is a shapefile.", + "pattern": "*.{prj}", + "ontologies": [] + } + }, + { + "shapefile_shx": { + "type": "file", + "description": "Optional shape index for shapefiles. Required if aoi is a shapefile.", + "pattern": "*.{shx}", + "ontologies": [] + } + } + ], + "output": { + "tile_allow": [ + { + "tile_allow.txt": { + "type": "file", + "description": "List of allowed datacube tiles. Each line contains an tile identifier.", + "pattern": "tile_allow.txt", + "ontologies": [] + } + } + ], + "versions_force": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "force": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "force-tile-extent -v": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "force": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "force-tile-extent -v": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@Felix-Kummer"], + "maintainers": ["@Felix-Kummer"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input sequences in FASTA format (plain or gzip-compressed)", - "pattern": "*.{fasta,faa,fa}(.gz)?", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } + }, + { + "name": "fq_generate", + "path": "modules/nf-core/fq/generate/meta.yml", + "type": "module", + "meta": { + "name": "fq_generate", + "description": "fq generate is a FASTQ file pair generator. It creates two reads, formatting names as described by Illumina. While generate creates \"valid\" FASTQ reads, the content of the files are completely random. The sequences do not align to any genome. This requires a seed (--seed) to be supplied in ext.args.\n", + "keywords": ["generate", "fastq", "random", "sequence"], + "tools": [ + { + "fq": { + "description": "fq is a library to generate and validate FASTQ file pairs.", + "homepage": "https://github.com/stjude-rust-labs/fq", + "documentation": "https://github.com/stjude-rust-labs/fq", + "tool_dev_url": "https://github.com/stjude-rust-labs/fq", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + } + ], + "output": { + "fastq": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fastq.gz": { + "type": "file", + "description": "Random generated FASTQ files.", + "pattern": "*_R[12].fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "versions_fq": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "fq": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "fq generate --version | sed 's/fq-generate //;s/ .*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "fq": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "fq generate --version | sed 's/fq-generate //;s/ .*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@adamrtalbot"], + "maintainers": ["@adamrtalbot"] } - ], - [ - { - "search_mode": { - "type": "string", - "description": "Search mode passed to emapper.py via -m. Determines which backend\nis used and which database flag is applied internally.\nSupported modes:\n - diamond: DIAMOND-based homology search (--dmnd_db)\n - novel_fams: DIAMOND search against novel families (--dmnd_db)\n - mmseqs: MMseqs2-based search (--mmseqs_db)\n - hmmer: HMMER-based search (--database)\n - no_search: Skip search step and annotate from a precomputed\n *.emapper.seed_orthologs file (--annotate_hits_table)\n - cache: Reuse a previously generated hits table (--cache)\n", - "enum": [ - "diamond", - "novel_fams", - "mmseqs", - "hmmer", - "no_search", - "cache" - ] - } + }, + { + "name": "fq_lint", + "path": "modules/nf-core/fq/lint/meta.yml", + "type": "module", + "meta": { + "name": "fq_lint", + "description": "fq lint is a FASTQ file pair validator.", + "keywords": ["lint", "fastq", "validate"], + "tools": [ + { + "fq": { + "description": "fq is a library to generate and validate FASTQ file pairs.", + "homepage": "https://github.com/stjude-rust-labs/fq", + "documentation": "https://github.com/stjude-rust-labs/fq", + "tool_dev_url": "https://github.com/stjude-rust-labs/fq", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fastq": { + "type": "file", + "description": "FASTQ file list", + "pattern": "*.fastq{,.gz}", + "ontologies": [] + } + } + ] + ], + "output": { + "lint": [ + [ + { + "meta": { + "type": "file", + "description": "Lint output", + "pattern": "*.fq_lint.txt", + "ontologies": [] + } + }, + { + "*.fq_lint.txt": { + "type": "file", + "description": "Lint output", + "pattern": "*.fq_lint.txt", + "ontologies": [] + } + } + ] + ], + "versions_fq": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "fq": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "fq lint --version | sed 's/fq-lint //; s/ .*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "fq": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "fq lint --version | sed 's/fq-lint //; s/ .*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@adamrtalbot"], + "maintainers": ["@adamrtalbot"] }, - { - "db": { - "type": "file", - "description": "Database file, directory, or precomputed results file required by the\nselected search_mode. The module automatically assigns the correct\nflag depending on search_mode:\n - diamond / novel_fams: DIAMOND database (*.dmnd)\n - mmseqs: MMseqs2 database directory or prefix\n - hmmer: HMM database (*.hmm, *.h3m)\n - no_search: Precomputed *.emapper.seed_orthologs file\n - cache: Previously generated *.emapper.hits file\nThis input is mandatory but its expected format depends on search_mode.\n", - "pattern": "*", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1370" - }, - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - { - "eggnog_data_dir": { - "type": "directory", - "description": "Directory containing eggnog-mapper database files\n(e.g. can be downloaded via download_eggnog_data.py,\nfound in the eggnog-mapper repository)\n", - "pattern": "*" - } - } - ], - "output": { - "annotations": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.emapper.annotations": { - "type": "file", - "description": "TSV file with the results from the annotation phase, including functional annotations, GO terms, KEGG pathways, and COG categories", - "pattern": "*.emapper.annotations", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "orthologs": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.emapper.seed_orthologs": { - "type": "file", - "description": "TSV file with the results from parsing the hits, linking queries with their best seed orthologs (includes commented metadata header)", - "pattern": "*.emapper.seed_orthologs", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "hits": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.emapper.hits": { - "type": "file", - "description": "TSV file with the raw search hits from the Diamond/MMseqs2/HMMER search phase before annotation", - "pattern": "*.emapper.hits", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_eggnogmapper": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "eggnog-mapper": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "emapper.py --version 2>&1 | grep -o 'emapper-[0-9]\\+\\.[0-9]\\+\\.[0-9]\\+' | sed 's/emapper-//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "eggnog-mapper": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "emapper.py --version 2>&1 | grep -o 'emapper-[0-9]\\+\\.[0-9]\\+\\.[0-9]\\+' | sed 's/emapper-//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@vagkaratzas" - ], - "maintainers": [ - "@vagkaratzas", - "@gallvp" - ] - }, - "pipelines": [ - { - "name": "funcprofiler", - "version": "dev" - } - ] - }, - { - "name": "eido_convert", - "path": "modules/nf-core/eido/convert/meta.yml", - "type": "module", - "meta": { - "name": "eido_convert", - "description": "Convert any PEP project or Nextflow samplesheet to any format", - "keywords": [ - "eido", - "convert", - "PEP", - "format", - "samplesheet" - ], - "tools": [ - { - "eido": { - "description": "Convert any PEP project or Nextflow samplesheet to any format", - "homepage": "http://eido.databio.org/en/latest/", - "documentation": "http://eido.databio.org/en/latest/", - "doi": "10.1093/gigascience/giab077", - "licence": [ - "BSD-2-Clause" - ], - "identifier": "biotools:eido-python-package" - } - } - ], - "input": [ - { - "samplesheet": { - "type": "file", - "description": "Nextflow samplesheet or PEP project", - "pattern": "*.{yaml,yml,csv}", - "ontologies": [ + "pipelines": [ + { + "name": "lncpipe", + "version": "dev" + }, { - "edam": "http://edamontology.org/format_3750" + "name": "riboseq", + "version": "1.2.0" }, { - "edam": "http://edamontology.org/format_3752" + "name": "rnaseq", + "version": "3.26.0" } - ] - } - }, - { - "format": { - "type": "string", - "description": "Extension of an output file" - } - } - ], - "output": { - "samplesheet_converted": [ - { - "${prefix}.${format}": { - "type": "file", - "description": "PEP project or samplesheet converted to csv file", - "ontologies": [] - } - } - ], - "versions_eido": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "eido": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "eido --version 2>&1 | sed 's/^.*eido //;s/ .*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "eido": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "eido --version 2>&1 | sed 's/^.*eido //;s/ .*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@rafalstepien" - ], - "maintainers": [ - "@rafalstepien", - "@khoroshevskyi" - ] - } - }, - { - "name": "eido_validate", - "path": "modules/nf-core/eido/validate/meta.yml", - "type": "module", - "meta": { - "name": "eido_validate", - "description": "Validate samplesheet or PEP config against a schema", - "keywords": [ - "eido", - "validate", - "schema", - "format", - "pep" - ], - "tools": [ - { - "validate": { - "description": "Validate samplesheet or PEP config against a schema.", - "homepage": "http://eido.databio.org/en/latest/", - "documentation": "http://eido.databio.org/en/latest/", - "doi": "10.1093/gigascience/giab077", - "licence": [ - "BSD-2-Clause" - ], - "identifier": "biotools:eido-python-package" - } - } - ], - "input": [ - { - "samplesheet": { - "type": "file", - "description": "Samplesheet or PEP file to be validated", - "pattern": "*.{yaml,yml,csv}", - "ontologies": [ + }, + { + "name": "fq_subsample", + "path": "modules/nf-core/fq/subsample/meta.yml", + "type": "module", + "meta": { + "name": "fq_subsample", + "description": "fq subsample outputs a subset of records from single or paired FASTQ files. This requires a seed (--seed) to be set in ext.args.", + "keywords": ["fastq", "fq", "subsample"], + "tools": [ + { + "fq": { + "description": "fq is a library to generate and validate FASTQ file pairs.", + "homepage": "https://github.com/stjude-rust-labs/fq", + "documentation": "https://github.com/stjude-rust-labs/fq", + "tool_dev_url": "https://github.com/stjude-rust-labs/fq", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fastq": { + "type": "file", + "description": "FASTQ file", + "pattern": "*.{fq,fastq}{,.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ] + ], + "output": { + "fastq": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fastq.gz": { + "type": "file", + "description": "Randomly sampled FASTQ files.", + "pattern": "*_R[12].fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "versions_fq": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "fq": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "fq subsample --version | sed 's/fq-subsample //; s/ .*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "fq": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "fq subsample --version | sed 's/fq-subsample //; s/ .*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@adamrtalbot"], + "maintainers": ["@adamrtalbot"] + }, + "pipelines": [ { - "edam": "http://edamontology.org/format_3750" + "name": "lncpipe", + "version": "dev" }, { - "edam": "http://edamontology.org/format_3752" - } - ] - } - }, - { - "schema": { - "type": "file", - "description": "Schema that the samplesheet will be validated against", - "pattern": "*.{yaml,yml}", - "ontologies": [ + "name": "riboseq", + "version": "1.2.0" + }, { - "edam": "http://edamontology.org/format_3750" + "name": "rnaseq", + "version": "3.26.0" } - ] - } - } - ], - "output": { - "log": [ - { - "*.log": { - "type": "file", - "description": "File containing validation log.", - "pattern": "*.log", - "ontologies": [] - } - } - ], - "versions_eido": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "eido": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "eido --version 2>&1 | sed 's/^.*eido //;s/ .*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "eido": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "eido --version 2>&1 | sed 's/^.*eido //;s/ .*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@rafalstepien" - ], - "maintainers": [ - "@rafalstepien", - "@khoroshevskyi" - ] - } - }, - { - "name": "eigenstratdatabasetools_eigenstratsnpcoverage", - "path": "modules/nf-core/eigenstratdatabasetools/eigenstratsnpcoverage/meta.yml", - "type": "module", - "meta": { - "name": "eigenstratdatabasetools_eigenstratsnpcoverage", - "description": "Provide the SNP coverage of each individual in an eigenstrat formatted dataset.", - "keywords": [ - "coverage", - "eigenstrat", - "eigenstratdatabasetools", - "snp", - "snps" - ], - "tools": [ - { - "eigenstratdatabasetools": { - "description": "A set of tools to compare and manipulate the contents of EingenStrat databases, and to calculate SNP coverage statistics in such databases.", - "documentation": "https://github.com/TCLamnidis/EigenStratDatabaseTools/README.md", - "tool_dev_url": "https://github.com/TCLamnidis/EigenStratDatabaseTools", - "licence": [ - "GPL v3" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "geno": { - "type": "file", - "description": "An Eigenstrat formatted genotype file", - "pattern": "*.{geno}", - "ontologies": [] - } - }, - { - "snp": { - "type": "file", - "description": "An Eigenstrat formatted snp file", - "pattern": "*.{snp}", - "ontologies": [] - } - }, - { - "ind": { - "type": "file", - "description": "An Eigenstrat formatted individual file", - "pattern": "*.{ind}", - "ontologies": [] - } - } - ] - ], - "output": { - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "A TSV table with the number of covered SNPs per individual.", - "pattern": "*.{tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "json": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.json": { - "type": "file", - "description": "A json table with the number of covered SNPs per individual.", - "pattern": "*.{json}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "versions_eigenstratdatabasetools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "eigenstratdatabasetools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "eigenstrat_snp_coverage --version 2>&1 | sed 's/^.*eigenstrat_snp_coverage //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "eigenstratdatabasetools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "eigenstrat_snp_coverage --version 2>&1 | sed 's/^.*eigenstrat_snp_coverage //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@TCLamnidis" - ], - "maintainers": [ - "@TCLamnidis" - ] - } - }, - { - "name": "eklipse", - "path": "modules/nf-core/eklipse/meta.yml", - "type": "module", - "meta": { - "name": "eklipse", - "description": "tool for detection and quantification of large mtDNA rearrangements.", - "keywords": [ - "eklipse", - "mitochondria", - "mtDNA", - "circos", - "deletion", - "SV" - ], - "tools": [ - { - "eklipse": { - "description": "tool for detection and quantification of large mtDNA rearrangements.", - "homepage": "https://github.com/dooguypapua/eKLIPse/tree/master", - "documentation": "https://github.com/dooguypapua/eKLIPse/tree/master", - "tool_dev_url": "https://github.com/dooguypapua/eKLIPse/tree/master", - "doi": "10.1038/s41436-018-0350-8", - "licence": [ - "GNU General Public v3 or later (GPL v3+)" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "MT BAM/SAM file", - "pattern": "*.{bam,sam}", - "ontologies": [] - } + }, + { + "name": "fqtk", + "path": "modules/nf-core/fqtk/meta.yml", + "type": "module", + "meta": { + "name": "fqtk", + "description": "Demultiplex fastq files", + "keywords": ["demultiplex", "fastq", "rust"], + "tools": [ + { + "fqtk": { + "description": "A toolkit for working with FASTQ files, written in Rust.", + "homepage": "https://github.com/fulcrumgenomics/fqtk", + "documentation": "https://github.com/fulcrumgenomics/fqtk", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "sample_sheet": { + "type": "file", + "description": "Tsv file, with two columns sample_id and barcode", + "pattern": "*.{tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, + { + "fastq_folder": { + "type": "file", + "description": "Directory containing fastq files that will be staged as 'input' folder", + "pattern": "*", + "ontologies": [] + } + }, + { + "fastq_readstructure_pairs": { + "type": "map", + "description": "List of lists i.e. [[, ],...]" + } + } + ] + ], + "output": { + "sample_fastq": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "output/*.fq.gz": { + "type": "file", + "description": "Demultiplexed per-sample FASTQ files", + "pattern": "output/*R*.fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "metrics": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "output/demux-metrics.txt": { + "type": "file", + "description": "Demultiplexing summary stats; sample_id, barcode templates, frac_templates, ratio_to_mean, ratio_to_best\n", + "pattern": "output/demux-metrics.txt", + "ontologies": [] + } + } + ] + ], + "most_frequent_unmatched": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "output/unmatched*.fq.gz": { + "type": "file", + "description": "File containing unmatched fastq records\n", + "pattern": "output/unmatched*.fq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "versions_fqtk": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "fqtk": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "fqtk --version 2>&1 | cut -d \" \" -f2": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "fqtk": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "fqtk --version 2>&1 | cut -d \" \" -f2": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@nh13", "@sam-white04"], + "maintainers": ["@nh13", "@sam-white04"] }, - { - "bai": { - "type": "file", - "description": "MT BAM/SAM index file", - "pattern": "*.{bai,sai}", - "ontologies": [] - } - } - ], - { - "ref_gb": { - "type": "file", - "description": "mtDNA reference genome in Genbank format, optional if empty NC_012920.1.gb will be used", - "pattern": "*.{gb}", - "ontologies": [] - } - } - ], - "output": { - "deletions": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*deletions.csv": { - "type": "file", - "description": "csv file with deletion information", - "pattern": "*deletions.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "genes": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*genes.csv": { - "type": "file", - "description": "csv file with gene information", - "pattern": "*genes.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "circos": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.png": { - "type": "file", - "description": "png file with circos plot of mt", - "pattern": "*.{png}", - "ontologies": [] - } - } + "pipelines": [ + { + "name": "demultiplex", + "version": "1.7.1" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@Lucpen" - ], - "maintainers": [ - "@Lucpen" - ] - } - }, - { - "name": "elprep_fastatoelfasta", - "path": "modules/nf-core/elprep/fastatoelfasta/meta.yml", - "type": "module", - "meta": { - "name": "elprep_fastatoelfasta", - "description": "Convert a file in FASTA format to the ELFASTA format", - "keywords": [ - "fasta", - "elfasta", - "elprep" - ], - "tools": [ - { - "elprep": { - "description": "elPrep is a high-performance tool for preparing .sam/.bam files for variant calling in sequencing pipelines. It can be used as a drop-in replacement for SAMtools/Picard/GATK4.", - "homepage": "https://github.com/ExaScience/elprep", - "documentation": "https://github.com/ExaScience/elprep", - "tool_dev_url": "https://github.com/ExaScience/elprep", - "doi": "10.1371/journal.pone.0244471", - "licence": [ - "AGPL v3" - ], - "identifier": "biotools:elprep" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } + }, + { + "name": "freebayes", + "path": "modules/nf-core/freebayes/meta.yml", + "type": "module", + "meta": { + "name": "freebayes", + "description": "A haplotype-based variant detector", + "keywords": [ + "variant caller", + "SNP", + "genotyping", + "somatic variant calling", + "germline variant calling", + "bacterial variant calling", + "bayesian" + ], + "tools": [ + { + "freebayes": { + "description": "Bayesian haplotype-based polymorphism discovery and genotyping", + "homepage": "https://github.com/freebayes/freebayes", + "documentation": "https://github.com/freebayes/freebayes", + "tool_dev_url": "https://github.com/freebayes/freebayes", + "doi": "10.48550/arXiv.1207.3907", + "licence": ["MIT"], + "identifier": "biotools:freebayes" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input_1": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}", + "ontologies": [] + } + }, + { + "input_1_index": { + "type": "file", + "description": "BAM/CRAM/SAM index file", + "pattern": "*.{bai,crai}", + "ontologies": [] + } + }, + { + "input_2": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}", + "ontologies": [] + } + }, + { + "input_2_index": { + "type": "file", + "description": "BAM/CRAM/SAM index file", + "pattern": "*.{bai,crai}", + "ontologies": [] + } + }, + { + "target_bed": { + "type": "file", + "description": "Optional - Limit analysis to targets listed in this BED-format FILE.", + "pattern": "*.bed", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test_reference' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "reference fasta file", + "pattern": ".{fa,fa.gz,fasta,fasta.gz}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test_reference' ]\n" + } + }, + { + "fasta_fai": { + "type": "file", + "description": "reference fasta file index", + "pattern": "*.{fa,fasta}.fai", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing meta information for the samples file.\ne.g. [ id:'test_samples' ]\n" + } + }, + { + "samples": { + "type": "file", + "description": "Optional - Limit analysis to samples listed (one per line) in the FILE.", + "pattern": "*.txt", + "ontologies": [] + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing meta information for the populations file.\ne.g. [ id:'test_populations' ]\n" + } + }, + { + "populations": { + "type": "file", + "description": "Optional - Each line of FILE should list a sample and a population which it is part of.", + "pattern": "*.txt", + "ontologies": [] + } + } + ], + [ + { + "meta6": { + "type": "map", + "description": "Groovy Map containing meta information for the cnv file.\ne.g. [ id:'test_cnv' ]\n" + } + }, + { + "cnv": { + "type": "file", + "description": "A copy number map BED file, which has either a sample-level ploidy:\nsample_name copy_number\nor a region-specific format:\nseq_name start end sample_name copy_number\n", + "pattern": "*.bed", + "ontologies": [] + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "Compressed VCF file", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "versions_freebayes": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "freebayes": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "freebayes --version 2>&1 | sed \"s/version:\\s*v//g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "freebayes": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "freebayes --version 2>&1 | sed \"s/version:\\s*v//g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@maxibor", "@FriederikeHanssen", "@maxulysse"], + "maintainers": ["@maxibor", "@FriederikeHanssen", "@maxulysse"] }, - { - "fasta": { - "type": "file", - "description": "FASTA file", - "pattern": "*.{fasta,fa,fna}", - "ontologies": [] - } - } - ] - ], - "output": { - "elfasta": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n", - "pattern": "*.elfasta" - } - }, - { - "*.elfasta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n", - "pattern": "*.elfasta" - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n", - "pattern": "*.elfasta" - } - }, - { - "logs/elprep/elprep*": { - "type": "file", - "description": "ELFasta log file", - "pattern": "*.log", - "ontologies": [] - } - } - ] - ], - "versions_elprep": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "elprep": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "elprep 2>&1 | sed -n '2s/^.*version //;s/ compiled.*$//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "elprep": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "elprep 2>&1 | sed -n '2s/^.*version //;s/ compiled.*$//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "mag", + "version": "5.4.2" + }, + { + "name": "radseq", + "version": "dev" + }, + { + "name": "sarek", + "version": "3.8.1" + } ] - ] - }, - "authors": [ - "@nvnieuwk" - ], - "maintainers": [ - "@nvnieuwk" - ] - } - }, - { - "name": "elprep_filter", - "path": "modules/nf-core/elprep/filter/meta.yml", - "type": "module", - "meta": { - "name": "elprep_filter", - "description": "Filter, sort and markdup sam/bam files, with optional BQSR and variant calling.", - "keywords": [ - "sort", - "bam", - "sam", - "filter", - "variant calling" - ], - "tools": [ - { - "elprep": { - "description": "elPrep is a high-performance tool for preparing .sam/.bam files for variant calling in sequencing pipelines. It can be used as a drop-in replacement for SAMtools/Picard/GATK4.", - "homepage": "https://github.com/ExaScience/elprep", - "documentation": "https://github.com/ExaScience/elprep", - "tool_dev_url": "https://github.com/ExaScience/elprep", - "doi": "10.1371/journal.pone.0244471", - "licence": [ - "AGPL v3" - ], - "identifier": "biotools:elprep" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "Input SAM/BAM file", - "pattern": "*.{bam,sam}", - "ontologies": [] - } - }, - { - "bai": { - "type": "file", - "description": "Input BAM file index", - "pattern": "*.bai", - "ontologies": [] - } - }, - { - "target_regions_bed": { - "type": "file", - "description": "Optional BED file containing target regions for BQSR and variant calling.", - "pattern": "*.bed", - "ontologies": [] - } - }, - { - "filter_regions_bed": { - "type": "file", - "description": "Optional BED file containing regions to filter.", - "pattern": "*.bed", - "ontologies": [] - } - }, - { - "intermediate_bqsr_tables": { - "type": "file", - "description": "Optional list of BQSR tables, used when parsing files created by `elprep split`", - "pattern": "*.table", - "ontologies": [] - } - }, - { - "recall_file": { - "type": "file", - "description": "Recall file with intermediate results for bqsr", - "pattern": "*.recall", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reference_sequences": { - "type": "file", - "description": "Optional SAM header to replace existing header.", - "pattern": "*.sam", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reference_elfasta": { - "type": "file", - "description": "Elfasta file, required for BQSR and variant calling.", - "pattern": "*.elfasta", - "ontologies": [] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + }, + { + "name": "freyja_boot", + "path": "modules/nf-core/freyja/boot/meta.yml", + "type": "module", + "meta": { + "name": "freyja_boot", + "description": "Bootstrap sample demixing by resampling each site based on a multinomial distribution of read depth across all sites, where the event probabilities were determined by the fraction of the total sample reads found at each site, followed by a secondary resampling at each site according to a multinomial distribution (that is, binomial when there was only one SNV at a site), where event probabilities were determined by the frequencies of each base at the site, and the number of trials is given by the sequencing depth.", + "keywords": ["variants", "fasta", "deconvolution", "wastewater", "bootstrapping"], + "tools": [ + { + "freyja": { + "description": "Freyja recovers relative lineage abundances from mixed SARS-CoV-2 samples and provides functionality to analyze lineage dynamics.", + "homepage": "https://github.com/andersen-lab/Freyja", + "documentation": "https://github.com/andersen-lab/Freyja/wiki", + "tool_dev_url": "https://github.com/andersen-lab/Freyja", + "doi": "10.1038/s41586-022-05049-6", + "licence": ["BSD-2-Clause"], + "identifier": "biotools:freyja" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "variants": { + "type": "file", + "description": "File containing identified variants in a gff-like format", + "pattern": "*.variants.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, + { + "depths": { + "type": "file", + "description": "File containing depth of the variants", + "pattern": "*.depth.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + { + "repeats": { + "type": "integer", + "description": "Number of bootstrap repeats to perform" + } + }, + { + "barcodes": { + "type": "file", + "description": "File containing lineage defining barcodes", + "pattern": "*barcodes.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + }, + { + "lineages_meta": { + "type": "file", + "description": "Optional file containing lineage metadata that correspond to barcodes", + "pattern": "*lineages.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + }, + { + "lineages_topology": { + "type": "file", + "description": "Optional file containing lineage topology information that correspond to barcodes", + "pattern": "*lineages.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ], + "output": { + "lineages": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*lineages.csv": { + "type": "file", + "description": "a csv file that includes the lineages present and their corresponding abundances", + "pattern": "*lineages.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "summarized": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*summarized.csv": { + "type": "file", + "description": "a csv file that includes the lineages present but summarized by constellation and their corresponding abundances", + "pattern": "*summarized.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "versions_freyja": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "freyja": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "freyja --version | sed 's/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "freyja": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "freyja --version | sed 's/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@Joon-Klaps"], + "maintainers": ["@Joon-Klaps"] }, - { - "known_sites_elsites": { - "type": "file", - "description": "Optional elsites file containing known SNPs for BQSR.", - "pattern": "*.elsites", - "ontologies": [] - } - } - ], - { - "run_haplotypecaller": { - "type": "boolean", - "description": "Run variant calling on the input files. Needed to generate gvcf output." - } - }, - { - "run_bqsr": { - "type": "boolean", - "description": "Run BQSR on the input files. Needed to generate recall metrics." - } - }, - { - "bqsr_tables_only": { - "type": "boolean", - "description": "Write intermediate BQSR tables, used when parsing files created by `elprep split`." - } - }, - { - "get_activity_profile": { - "type": "boolean", - "description": "Get the activity profile calculated by the haplotypecaller to the given file in IGV format." - } - }, - { - "get_assembly_regions": { - "type": "boolean", - "description": "Get the assembly regions calculated by haplotypecaller to the specified file in IGV format." - } - } - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.{bam,sam}": { - "type": "file", - "description": "BAM/SAM file", - "pattern": "*.{bam,sam}", - "ontologies": [] - } - } - ] - ], - "logs": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.log": { - "type": "file", - "description": "Log file", - "pattern": "elprep-*.log", - "ontologies": [] - } - } - ] - ], - "metrics": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.metrics.txt": { - "type": "file", - "description": "Metrics file", - "pattern": "*.{metrics.txt}", - "ontologies": [] - } - } - ] - ], - "recall": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.recall": { - "type": "file", - "description": "Recall file", - "pattern": "*.{recall}", - "ontologies": [] - } - } - ] - ], - "gvcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.vcf.gz": { - "type": "file", - "description": "VCF file", - "pattern": "*.{vcf.gz}", - "ontologies": [] - } - } - ] - ], - "table": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.table": { - "type": "file", - "description": "Table", - "pattern": "*.{table}", - "ontologies": [] - } - } - ] - ], - "activity_profile": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.activity_profile.igv": { - "type": "file", - "description": "Activity profile", - "pattern": "*.{activity_profile.igv}", - "ontologies": [] - } - } - ] - ], - "assembly_regions": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.assembly_regions.igv": { - "type": "file", - "description": "Assembly regions", - "pattern": "*.{assembly_regions.igv}", - "ontologies": [] - } - } - ] - ], - "versions_elprep": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "elprep": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "elprep 2>&1 | sed -n '2s/^.*version //;s/ compiled.*$//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "elprep": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "elprep 2>&1 | sed -n '2s/^.*version //;s/ compiled.*$//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "viralrecon", + "version": "3.0.0" + } ] - ] - }, - "authors": [ - "@matthdsm" - ], - "maintainers": [ - "@matthdsm" - ] - } - }, - { - "name": "elprep_merge", - "path": "modules/nf-core/elprep/merge/meta.yml", - "type": "module", - "meta": { - "name": "elprep_merge", - "description": "Merge split bam/sam chunks in one file", - "keywords": [ - "bam", - "sam", - "merge" - ], - "tools": [ - { - "elprep": { - "description": "elPrep is a high-performance tool for preparing .sam/.bam files for variant calling in sequencing pipelines. It can be used as a drop-in replacement for SAMtools/Picard/GATK4.", - "homepage": "https://github.com/ExaScience/elprep", - "documentation": "https://github.com/ExaScience/elprep", - "tool_dev_url": "https://github.com/ExaScience/elprep", - "doi": "10.1371/journal.pone.0244471", - "licence": [ - "AGPL v3" - ], - "identifier": "biotools:elprep" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + }, + { + "name": "freyja_demix", + "path": "modules/nf-core/freyja/demix/meta.yml", + "type": "module", + "meta": { + "name": "freyja_demix", + "description": "specify the relative abundance of each known haplotype", + "keywords": ["variants", "fasta", "deconvolution", "wastewater"], + "tools": [ + { + "freyja": { + "description": "Freyja recovers relative lineage abundances from mixed SARS-CoV-2 samples and provides functionality to analyze lineage dynamics.", + "homepage": "https://github.com/andersen-lab/Freyja", + "documentation": "https://github.com/andersen-lab/Freyja/wiki", + "tool_dev_url": "https://github.com/andersen-lab/Freyja", + "doi": "10.1038/s41586-022-05049-6", + "licence": ["BSD-2-Clause"], + "identifier": "biotools:freyja" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "variants": { + "type": "file", + "description": "File containing identified variants in a gff-like format", + "pattern": "*.variants.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, + { + "depths": { + "type": "file", + "description": "File containing depth of the variants", + "pattern": "*.depth.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + { + "barcodes": { + "type": "file", + "description": "File containing lineage defining barcodes", + "pattern": "*barcodes.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + }, + { + "lineages_meta": { + "type": "file", + "description": "Optional file containing lineage metadata that correspond to barcodes", + "pattern": "*lineages.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + }, + { + "lineages_topology": { + "type": "file", + "description": "Optional file containing lineage topology information that correspond to barcodes", + "pattern": "*lineages.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ], + "output": { + "demix": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "a tsv file that includes the lineages present, their corresponding abundances, and summarization by constellation", + "pattern": "*.demix.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_freyja": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "freyja": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "freyja --version | sed 's/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "freyja": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "freyja --version | sed 's/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@Joon-Klaps"], + "maintainers": ["@Joon-Klaps"] }, - { - "bam": { - "type": "file", - "description": "List of BAM/SAM chunks to merge", - "pattern": "*.{bam,sam}", - "ontologies": [] - } - } - ] - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "output/**.{bam,sam}": { - "type": "file", - "description": "Merged BAM/SAM file", - "pattern": "*.{bam,sam}", - "ontologies": [] - } - } - ] - ], - "versions_elprep": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "elprep": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "elprep 2>&1 | sed -n '2s/^.*version //;s/ compiled.*$//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "elprep": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "elprep 2>&1 | sed -n '2s/^.*version //;s/ compiled.*$//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "viralrecon", + "version": "3.0.0" + } ] - ] - }, - "authors": [ - "@matthdsm" - ], - "maintainers": [ - "@matthdsm" - ] - } - }, - { - "name": "elprep_split", - "path": "modules/nf-core/elprep/split/meta.yml", - "type": "module", - "meta": { - "name": "elprep_split", - "description": "Split bam file into manageable chunks", - "keywords": [ - "bam", - "split by chromosome", - "chunk" - ], - "tools": [ - { - "elprep": { - "description": "elPrep is a high-performance tool for preparing .sam/.bam files for variant calling in sequencing pipelines. It can be used as a drop-in replacement for SAMtools/Picard/GATK4.", - "homepage": "https://github.com/ExaScience/elprep", - "documentation": "https://github.com/ExaScience/elprep", - "tool_dev_url": "https://github.com/ExaScience/elprep", - "doi": "10.1371/journal.pone.0244471", - "licence": [ - "AGPL v3" - ], - "identifier": "biotools:elprep" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "List of BAM/SAM files", - "pattern": "*.{bam,sam}", - "ontologies": [] - } - } - ] - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "output/**.{bam,sam}": { - "type": "file", - "description": "List of split BAM/SAM files", - "pattern": "*.{bam,sam}", - "ontologies": [] - } - } - ] - ], - "versions_elprep": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "elprep": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "elprep 2>&1 | sed -n '2s/^.*version //;s/ compiled.*$//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "elprep": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "elprep 2>&1 | sed -n '2s/^.*version //;s/ compiled.*$//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@matthdsm" - ], - "maintainers": [ - "@matthdsm" - ] - } - }, - { - "name": "emboss_cons", - "path": "modules/nf-core/emboss/cons/meta.yml", - "type": "module", - "meta": { - "name": "emboss_cons", - "description": "cons calculates a consensus sequence from a multiple sequence alignment. To obtain the consensus, the sequence weights and a scoring matrix are used to calculate a score for each amino acid residue or nucleotide at each position in the alignment.", - "keywords": [ - "emboss", - "consensus", - "fasta", - "multiple sequence alignment", - "MSA" - ], - "tools": [ - { - "emboss": { - "description": "The European Molecular Biology Open Software Suite", - "homepage": "https://www.ebi.ac.uk/Tools/sfc/emboss_seqret/", - "documentation": "https://emboss.bioinformatics.nl/cgi-bin/emboss/help/seqret", - "tool_dev_url": "http://emboss.open-bio.org/", - "doi": "10.1016/s0168-9525(00)02024-2 ", - "licence": [ - "GPL" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Multiple sequence alignment (unzipped)", - "pattern": "*.{fasta,fa,fas,fsa,seq,mpfa,aln,clustal,clw,msf,phy,phylip,stockholm,sto,msf,afa,afa,a}", - "ontologies": [] - } - } - ] - ], - "output": { - "consensus": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.fa": { - "type": "file", - "description": "Consensus sequence calculated from multiple sequence alignment", - "pattern": "*.fa", - "ontologies": [] - } - } - ] - ], - "versions_emboss": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "emboss": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cons -version 2>&1 | sed \"s/EMBOSS://\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "emboss": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cons -version 2>&1 | sed \"s/EMBOSS://\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@Joon-Klaps" - ], - "maintainers": [ - "@Joon-Klaps" - ] - } - }, - { - "name": "emboss_revseq", - "path": "modules/nf-core/emboss/revseq/meta.yml", - "type": "module", - "meta": { - "name": "emboss_revseq", - "description": "the revseq program from emboss reverse complements a nucleotide sequence", - "keywords": [ - "nucleotides", - "reverse complement", - "sequences" - ], - "tools": [ - { - "emboss": { - "description": "The European Molecular Biology Open Software Suite", - "homepage": "https://www.ebi.ac.uk/Tools/sfc/emboss_seqret/", - "documentation": "https://emboss.bioinformatics.nl/cgi-bin/emboss/help/seqret", - "tool_dev_url": "http://emboss.open-bio.org/", - "doi": "10.1016/s0168-9525(00)02024-2 ", - "licence": [ - "GPL" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "sequences": { - "type": "file", - "description": "Input sequences", - "pattern": "*.{fasta,fna,fa,fst,aln,phy}", - "ontologies": [] - } - } - ] - ], - "output": { - "revseq": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*.${sequences.name - ~/.*\\./}": { - "type": "file", - "description": "File with reverse complemented sequences", - "pattern": "*.{fasta,fna,fa,fst,aln,phy}", - "ontologies": [] - } - } - ] - ], - "versions_emboss": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "emboss": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "revseq -version 2>&1 | sed 's/EMBOSS://'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "emboss": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "revseq -version 2>&1 | sed 's/EMBOSS://'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@erikrikarddaniel" - ], - "maintainers": [ - "@erikrikarddaniel" - ] - } - }, - { - "name": "emboss_seqret", - "path": "modules/nf-core/emboss/seqret/meta.yml", - "type": "module", - "meta": { - "name": "emboss_seqret", - "description": "Reads in one or more sequences, converts, filters, or transforms them and writes them out again", - "keywords": [ - "emboss", - "gff", - "embl", - "genbank", - "fasta", - "convert", - "swissprot" - ], - "tools": [ - { - "emboss": { - "description": "The European Molecular Biology Open Software Suite", - "homepage": "https://www.ebi.ac.uk/Tools/sfc/emboss_seqret/", - "documentation": "https://emboss.bioinformatics.nl/cgi-bin/emboss/help/seqret", - "tool_dev_url": "http://emboss.open-bio.org/", - "doi": "10.1016/s0168-9525(00)02024-2 ", - "licence": [ - "GPL" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "sequence": { - "type": "file", - "description": "Input sequence query", - "pattern": "*.{gff,em,gb,refseq,pir,swiss,sw,txt}", - "ontologies": [] - } - } - ], - { - "out_ext": { - "type": "string", - "description": "File extension of the output file. Unless otherwise set by a flag in `ext.args`, the extension dictates the output file format." - } - } - ], - "output": { - "outseq": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.${out_ext}": { - "type": "file", - "description": "Converted sequence file", - "pattern": "*", - "ontologies": [] - } - } - ] - ], - "versions_emboss": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "emboss": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "revseq -version 2>&1 | sed 's/EMBOSS://'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "emboss": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "revseq -version 2>&1 | sed 's/EMBOSS://'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@MillironX" - ], - "maintainers": [ - "@MillironX" - ] - } - }, - { - "name": "emmtyper", - "path": "modules/nf-core/emmtyper/meta.yml", - "type": "module", - "meta": { - "name": "emmtyper", - "description": "EMM typing of Streptococcus pyogenes assemblies", - "keywords": [ - "fasta", - "Streptococcus pyogenes", - "typing" - ], - "tools": [ - { - "emmtyper": { - "description": "Streptococcus pyogenes in silico EMM typer", - "homepage": "https://github.com/MDU-PHL/emmtyper", - "documentation": "https://github.com/MDU-PHL/emmtyper", - "tool_dev_url": "https://github.com/MDU-PHL/emmtyper", - "licence": [ - "GNU General Public v3 (GPL v3)" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA assembly file", - "pattern": "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}", - "ontologies": [] - } - } - ] - ], - "output": { - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "Tab-delimited result file", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_emmtyper": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "emmtyper": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python -c \"import emmtyper; 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"type": "module", + "meta": { + "name": "freyja_update", + "description": "downloads new versions of the curated SARS-CoV-2 lineage file and barcodes", + "keywords": ["database", "variants", "UShER"], + "tools": [ + { + "freyja": { + "description": "Freyja recovers relative lineage abundances from mixed SARS-CoV-2 samples and provides functionality to analyze lineage dynamics.", + "homepage": "https://github.com/andersen-lab/Freyja", + "documentation": "https://github.com/andersen-lab/Freyja/wiki", + "tool_dev_url": "https://github.com/andersen-lab/Freyja", + "doi": "10.1038/s41586-022-05049-6", + "licence": ["BSD-2-Clause"], + "identifier": "biotools:freyja" + } + } + ], + "input": [ + { + "db_name": { + "type": "string", + "description": "The name of the database directory" + } + } + ], + "output": { + "barcodes": [ + { + "${db_name}/*barcodes.*": { + "type": "file", + "description": "File containing lineage defining barcodes", + "pattern": "*barcodes.csv", + "ontologies": [ + { + 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- "@maxulysse" - ] - }, - "pipelines": [ { - "name": "pacsomatic", - "version": "dev" + "name": "freyja_variants", + "path": "modules/nf-core/freyja/variants/meta.yml", + "type": "module", + "meta": { + "name": "freyja_variants", + "description": "call variant and sequencing depth information of the variant", + "keywords": ["variants", "fasta", "wastewater"], + "tools": [ + { + "freyja": { + "description": "Freyja recovers relative lineage abundances from mixed SARS-CoV-2 samples and provides functionality to analyze lineage dynamics.", + "homepage": "https://github.com/andersen-lab/Freyja", + "documentation": "https://github.com/andersen-lab/Freyja/wiki", + "tool_dev_url": "https://github.com/andersen-lab/Freyja", + "doi": "10.1038/s41586-022-05049-6", + "licence": ["BSD-2-Clause"], + "identifier": "biotools:freyja" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "Sorted BAM file", + "pattern": "*.bam", + "ontologies": [] + } + } + ], + { + "fasta": { + "type": "file", + "description": "The reference sequence used for mapping and generating the BAM file", + "pattern": "*.fa", + "ontologies": [] + } + } + ], + "output": { + "variants": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.variants.tsv": { + "type": "file", + "description": "File containing identified variants in a gff-like format", + "pattern": "*.variants.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, + { + "*.depth.tsv": { + "type": "file", + "description": "File containing depth of the variants", + "pattern": "*.depth.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_freyja": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "freyja": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "freyja --version | sed 's/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "freyja": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "freyja --version | sed 's/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@Joon-Klaps"], + "maintainers": ["@Joon-Klaps"] + }, + "pipelines": [ + { + "name": "viralrecon", + "version": "3.0.0" + } + ] }, { - "name": "rnadnavar", - "version": "dev" + "name": "fusioncatcher_build", + "path": "modules/nf-core/fusioncatcher/build/meta.yml", + "type": "module", + "meta": { + "name": "fusioncatcher_build", + "description": "Build references for fusioncatcher", + "keywords": ["references", "fusions", "rna"], + "tools": [ + { + "fusioncatcher": { + "description": "Build genome for fusioncatcher", + "homepage": "https://github.com/ndaniel/fusioncatcher/", + "documentation": "https://github.com/ndaniel/fusioncatcher/blob/master/doc/manual.md", + "tool_dev_url": "https://github.com/ndaniel/fusioncatcher/", + "doi": "10.1101/011650", + "licence": ["GPL v3"], + "identifier": "biotools:fusioncatcher" + } + } + ], + "input": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + } + ], + "output": { + "reference": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}": { + "type": "file", + "description": "Diretory containing the fusioncatcher reference files", + "ontologies": [] + } + } + ] + ], + "versions_fusioncatcher": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "fusioncatcher": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "fusioncatcher --version |& sed 's/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "fusioncatcher": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "fusioncatcher --version |& sed 's/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@nvnieuwk"], + "maintainers": ["@nvnieuwk"] + } }, { - "name": "rnavar", - "version": "1.2.3" + "name": "fusioncatcher_fusioncatcher", + "path": "modules/nf-core/fusioncatcher/fusioncatcher/meta.yml", + "type": 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"*.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "json": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\n" + } + }, + { + "*.json": { + "type": "file", + "description": "Report in JSON format\n", + "pattern": "*.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "versions_fusionreport": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "fusion_report": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "fusion_report --version |& sed 's/fusion-report //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "fusion_report": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "fusion_report --version |& sed 's/fusion-report //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@praveenraj2018", "@rannick"] }, - { - "input": { - "type": "file", - "description": "VCF/TAB file annotated with vep", - "pattern": "*.{vcf,tab,tsv,txt}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - { - "feature_file": { - "type": "file", - "description": "File containing features on separate lines. 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{ - "fasta": { - "type": "file", - "description": "reference FASTA file (optional)\n", - "pattern": "*.{fasta,fa}", - "ontologies": [] - } - } - ], - { - "extra_files": { - "type": "file", - "description": "path to file(s) needed for plugins (optional)\n", - "ontologies": [] - } - } - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Map with sample information\n" - } - }, - { - "${prefix}.vcf.gz": { - "type": "file", - "description": "annotated vcf (optional)\n", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Map with sample information\n" - } - }, - { - "${prefix}.vcf.gz.tbi": { - "type": "file", - "description": "annotated vcf index (optional)\n", - "pattern": "*.vcf.gz.tbi", - "ontologies": [] - } - } - ] - ], - "tab": [ - [ - { - "meta": { - "type": "map", - "description": "Map with sample information\n" - } - }, - { - "${prefix}.tab.gz": { - "type": "file", - "description": "tab file with annotated variants (optional)\n", - "pattern": "*.ann.tab.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "json": [ - [ - { - "meta": { - "type": "map", - "description": "Map with sample information\n" - } - }, - { - "${prefix}.json.gz": { - "type": "file", - "description": "json file with annotated variants (optional)\n", - "pattern": "*.ann.json.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "report": [ - [ - { - "meta": { - "type": "map", - "description": "Map with sample information\n" - } - }, - { - "${task.process}": { - "type": "string", - "description": "The process" - } - }, - { - "ensemblvep": { - "type": "string", - "description": "The tool name" - } - }, - { - "*.html": { - "type": "file", - "description": "VEP report file", - "pattern": "*.html", - "ontologies": [] - } - } - ] - ], - "versions_ensemblvep": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process" - } - }, - { - "ensemblvep": { - "type": "string", - "description": "The tool name" - } - }, - { - "vep --help | sed -n '/ensembl-vep/s/.*: //p'": { - "type": "eval", - "description": "The command used to generate the version of the tool" - } - } - ] - ], - "versions_tabix": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process" - } - }, - { - "tabix": { - "type": "string", - "description": "The tool name" - } - }, - { - "tabix -h 2>&1 | grep -oP 'Version:\\s*\\K[^\\s]+'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_perlmathcdf": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process" - } - }, - { - "perl-math-cdf": { - "type": "string", - "description": "The tool name" - } - }, - { - "perl -MMath::CDF -e 'print \\\\$Math::CDF::VERSION'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "multiqc_files": [ - [ - { - "meta": { - "type": "string", - "description": "Map with sample information\n" - } - }, - { - "${task.process}": { - "type": "string", - "description": "The process" - } - }, - { - "ensemblvep": { - "type": "string", - "description": "The tool name" - } - }, - { - "*.html": { - "type": "file", - "description": "VEP report file", - "pattern": "*.html", - "ontologies": [] - } - } - ] - ], - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process" - } - }, - { - "ensemblvep": { - "type": "string", - "description": "The tool name" - } - }, - { - "vep --help | sed -n '/ensembl-vep/s/.*: //p'": { - "type": "eval", - "description": "The command used to generate the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The process" - } - }, - { - "tabix": { - "type": "string", - "description": "The tool name" - } - }, - { - "tabix -h 2>&1 | grep -oP 'Version:\\s*\\K[^\\s]+'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The process" - } - }, - { - "perl-math-cdf": { - "type": "string", - "description": "The tool name" - } - }, - { - "perl -MMath::CDF -e 'print \\\\$Math::CDF::VERSION'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "rnafusion", + "version": "4.1.2" + } ] - ] }, - "authors": [ - "@maxulysse", - "@matthdsm", - "@nvnieuwk" - ], - "maintainers": [ - "@maxulysse", - "@matthdsm", - "@nvnieuwk" - ] - }, - "pipelines": [ { - "name": "pacsomatic", - "version": "dev" + "name": "galah", + "path": "modules/nf-core/galah/meta.yml", + "type": "module", + "meta": { + "name": "galah", + "description": "Cluster genome FASTA files by average nucleotide identity", + "keywords": ["genomics", "cluster", "genome", "metagenomics"], + "tools": [ + { + "galah": { + "description": "Galah aims to be a more scalable metagenome assembled genome (MAG) dereplication method.", + "homepage": "https://github.com/wwood/galah", + "documentation": "https://github.com/wwood/galah", + "tool_dev_url": "https://github.com/wwood/galah", + "doi": "10.1111/NODOI", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "bins": { + "type": "file", + "description": "A list of fasta-formatted genomes for dereplication", + "pattern": "*.{fa,fna,fa.gz, etc}", + "ontologies": [] + } + }, + { + "qc_table": { + "type": "file", + "description": "(optional) A summary TSV from either CheckM [https://nf-co.re/modules/checkm_lineagewf],\nCheckM2 [https://nf-co.re/modules/checkm2_predict/], or a CSV\nin drep-style format [https://github.com/MrOlm/drep] with three columnns,\n`genome,completeness,contamination`. In both cases the first column should contain the\nnames of the input genome files, minus the last file extension\n(i.e. if the genome is gzipped, the genome name should\nretain the .fasta extension).\n", + "pattern": "*.{csv,tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + }, + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, + { + "qc_format": { + "type": "string", + "description": "Defines the type if input table in `qc_table`, if specified.", + "pattern": "checkm|checkm2|genome_info" + } + } + ] + ], + "output": { + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "TSV file in the format `representative_genome` \\t `member_genome`", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "dereplicated_bins": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "${prefix}/*": { + "type": "file", + "description": "The representative genomes following dereplication by galah.", + "pattern": "*", + "ontologies": [] + } + } + ] + ], + "versions_galah": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "galah": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "galah --version | sed \"s/galah //\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "galah": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "galah --version | sed \"s/galah //\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@prototaxites"], + "maintainers": ["@prototaxites"] + } }, { - "name": "raredisease", - "version": "3.0.0" + "name": "gamma_gamma", + "path": "modules/nf-core/gamma/gamma/meta.yml", + "type": "module", + "meta": { + "name": "gamma_gamma", + "description": "Gene Allele Mutation Microbial Assessment", + "keywords": ["gamma", "gene-calling", "microbial", "allele"], + "tools": [ + { + "gamma": { + "description": "Tool for Gene Allele Mutation Microbial Assessment", + "homepage": "https://github.com/rastanton/GAMMA", + "documentation": "https://github.com/rastanton/GAMMA", + "tool_dev_url": "https://github.com/rastanton/GAMMA", + "doi": "10.1093/bioinformatics/btab607", + "licence": ["Apache License 2.0"], + "identifier": "biotools:gamma" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA file", + "pattern": "*.{fa,fasta}", + "ontologies": [] + } + } + ], + { + "db": { + "type": "file", + "description": "Database in FASTA format", + "pattern": "*.{fa,fasta}", + "ontologies": [] + } + } + ], + "output": { + "gamma": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.gamma": { + "type": "file", + "description": "GAMMA file with annotated gene matches", + "pattern": "*.{gamma}", + "ontologies": [] + } + } + ] + ], + "psl": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.psl": { + "type": "file", + "description": "PSL file with all gene matches found", + "pattern": "*.{psl}", + "ontologies": [] + } + } + ] + ], + "gff": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.gff": { + "type": "file", + "description": "GFF file", + "pattern": "*.{gff}", + "ontologies": [] + } + } + ] + ], + "fasta": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fasta": { + "type": "file", + "description": "multifasta file of the gene matches", + "pattern": "*.{fasta}", + "ontologies": [] + } + } + ] + ], + "versions_gamma": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gamma": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "2.1": { + "type": "string", + "description": "The hard-coded version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gamma": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "2.1": { + "type": "string", + "description": "The hard-coded version of the tool" + } + } + ] + ] + }, + "authors": ["@sateeshperi", "@rastanton", "@jvhagey"], + "maintainers": ["@sateeshperi", "@rastanton", "@jvhagey"] + } }, { - "name": "rnadnavar", - "version": "dev" + "name": "gangstr", + "path": "modules/nf-core/gangstr/meta.yml", + "type": "module", + "meta": { + "name": "gangstr", + "description": "GangSTR is a tool for genome-wide profiling tandem repeats from short reads.", + "keywords": ["gangstr", "STR", "bam", "cram", "vcf"], + "tools": [ + { + "gangstr": { + "description": "GangSTR is a tool for genome-wide profiling tandem repeats from short reads.", + "homepage": "https://github.com/gymreklab/GangSTR", + "documentation": "https://github.com/gymreklab/GangSTR", + "tool_dev_url": "https://github.com/gymreklab/GangSTR", + "doi": "10.1093/nar/gkz501", + "licence": ["GPL v3-or-later"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "alignment_files": { + "type": "file", + "description": "Alignment files", + "ontologies": [] + } + }, + { + "alignment_indices": { + "type": "file", + "description": "The index/indices of the BAM/CRAM file(s)", + "pattern": "*.{bai,crai}", + "ontologies": [] + } + }, + { + "ref_regions": { + "type": "file", + "description": "A reference set of regions to genotype in a BED-like format. The file should have following columns:\n1. The name of the chromosome on which the STR is located\n2. The start position of the STR on its chromosome\n3. The end position of the STR on its chromosome\n4. The motif length\n5. The repeat motif\n", + "pattern": "*.bed", + "ontologies": [] + } + } + ], + { + "fasta": { + "type": "file", + "description": "The reference FASTA file", + "pattern": "*.{fasta,fa}", + "ontologies": [] + } + }, + { + "fasta_fai": { + "type": "file", + "description": "The index of the reference FASTA file", + "pattern": "*.fai", + "ontologies": [] + } + } + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "The resulting VCF file containing the genotypes", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "index": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz.tbi": { + "type": "file", + "description": "The resulting index of the VCF file containing the genotypes", + "pattern": "*.vcf.gz.tbi", + "ontologies": [] + } + } + ] + ], + "samplestats": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.samplestats.tab": { + "type": "file", + "description": "A tab-delimited file containing statistics for each sample", + "pattern": "*.tab", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_gangstr": [ + [ + { + "${task.process}": { + "type": "string", + "description": "Task process name" + } + }, + { + "gangstr": { + "type": "string", + "description": "Software name" + } + }, + { + "GangSTR --version 2>&1": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "Task process name" + } + }, + { + "gangstr": { + "type": "string", + "description": "Software name" + } + }, + { + "GangSTR --version 2>&1": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@nvnieuwk"], + "maintainers": ["@nvnieuwk"] + } }, { - "name": "rnavar", - "version": "1.2.3" + "name": "ganon_buildcustom", + "path": "modules/nf-core/ganon/buildcustom/meta.yml", + "type": "module", + "meta": { + "name": "ganon_buildcustom", + "description": "Build ganon database using custom reference sequences.", + "keywords": ["ganon", "metagenomics", "profiling", "taxonomy", "k-mer", "database"], + "tools": [ + { + "ganon": { + "description": "ganon classifies short DNA sequences against large sets of genomic reference sequences efficiently", + "homepage": "https://github.com/pirovc/ganon", + "documentation": "https://github.com/pirovc/ganon", + "tool_dev_url": "https://github.com/pirovc/ganon", + "doi": "10.1093/bioinformatics/btaa458", + "licence": ["MIT"], + "identifier": "biotools:ganon" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "List of input FASTA files, or a directory containing input FASTA files.\nNote you must supply --input-extension via ext.args if FASTA extensions do not end in the default `fna.gz`.\n", + "pattern": "*.{fasta,fna,fa,fa,fasta.gz,fna.gz,fa.gz,fa.gz}", + "ontologies": [] + } + } + ], + { + "input_tsv": { + "type": "string", + "description": "(Optional) Specify an TSV file containing the paths, and relevant metadata to the input FASTA files to use the `--input-file` option.\nThe 'file' column should be just the file name of each FASTA file (so that it's local to the working directory of the process).\nSee ganon documentation for more more information on the other columns.\n", + "pattern": "*tsv" + } + }, + { + "taxonomy_files": { + "type": "file", + "description": "Pre-downloaded taxonomy files of input sequences. See ganon docs for formats", + "ontologies": [] + } + }, + { + "genome_size_files": { + "type": "file", + "description": "Pre-downloaded NCBI or GTDB genome size files of input sequences. See ganon docs for formats", + "pattern": "{species_genome_size.txt.gz,*_metadata.tar.gz}", + "ontologies": [] + } + } + ], + "output": { + "db": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{hibf,ibf,tax}": { + "type": "file", + "description": "ganon database files", + "pattern": "*.{ibf,tax}", + "ontologies": [] + } + } + ] + ], + "info": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.info.tsv": { + "type": "file", + "description": "Copy of target info generated. Can be used for updating database.", + "pattern": "*info.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_ganon": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "ganon": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "ganon --version 2>1 | sed 's/.*ganon //g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "ganon": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "ganon --version 2>1 | sed 's/.*ganon //g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@jfy133"], + "maintainers": ["@jfy133"] + }, + "pipelines": [ + { + "name": "createtaxdb", + "version": "3.0.0" + } + ] }, { - "name": "sarek", - "version": "3.8.1" + "name": "ganon_classify", + "path": "modules/nf-core/ganon/classify/meta.yml", + "type": "module", + "meta": { + "name": "ganon_classify", + "description": "Classify FASTQ files against ganon database", + "keywords": ["ganon", "metagenomics", "profiling", "taxonomy", "k-mer", "classification", "classify"], + "tools": [ + { + "ganon": { + "description": "ganon classifies short DNA sequences against large sets of genomic reference sequences efficiently", + "homepage": "https://github.com/pirovc/ganon", + "documentation": "https://github.com/pirovc/ganon", + "tool_dev_url": "https://github.com/pirovc/ganon", + "doi": "10.1093/bioinformatics/btaa458", + "licence": ["MIT"], + "identifier": "biotools:ganon" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fastqs": { + "type": "file", + "description": "Single or paired FASTQ files, optionally gzipped", + "pattern": "*.{fq,fq.gz,fastq,fastq.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ], + { + "db": { + "type": "file", + "description": "Ganon database files from build or build-custom", + "pattern": "*.{ibf,tax}", + "ontologies": [] + } + } + ], + "output": { + "tre": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tre": { + "type": "file", + "description": "Full ganon report file", + "pattern": "*.tre", + "ontologies": [] + } + } + ] + ], + "report": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.rep": { + "type": "file", + "description": "Plain ganon report file with only targets with match", + "pattern": "*.rep", + "ontologies": [] + } + } + ] + ], + "one": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.one": { + "type": "file", + "description": "Information about a single (best) match of a given read after EM or LCA algorithms", + "pattern": "*.one", + "ontologies": [] + } + } + ] + ], + "all": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.all": { + "type": "file", + "description": "Information of all matches to a given read", + "pattern": "*.all", + "ontologies": [] + } + } + ] + ], + "unc": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.unc": { + "type": "file", + "description": "List of all reads without a hit", + "pattern": "*.unc", + "ontologies": [] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "Text file containing console output from ganon classify", + "pattern": "*.log", + "ontologies": [] + } + } + ] + ], + "versions_ganon": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "ganon": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "ganon --version 2>1 | sed 's/.*ganon //g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "ganon": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "ganon --version 2>1 | sed 's/.*ganon //g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@jfy133"], + "maintainers": ["@jfy133"] + }, + "pipelines": [ + { + "name": "taxprofiler", + "version": "2.0.0" + } + ] }, { - "name": "tumourevo", - "version": "dev" + "name": "ganon_report", + "path": "modules/nf-core/ganon/report/meta.yml", + "type": "module", + "meta": { + "name": "ganon_report", + "description": "Generate a ganon report file from the output of ganon classify", + "keywords": ["ganon", "metagenomics", "profiling", "taxonomy", "k-mer", "classification", "report"], + "tools": [ + { + "ganon": { + "description": "ganon classifies short DNA sequences against large sets of genomic reference sequences efficiently", + "homepage": "https://github.com/pirovc/ganon", + "documentation": "https://github.com/pirovc/ganon", + "tool_dev_url": "https://github.com/pirovc/ganon", + "doi": "10.1093/bioinformatics/btaa458", + "licence": ["MIT"], + "identifier": "biotools:ganon" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "rep": { + "type": "file", + "description": "Input 'repo' files from ganon classify", + "pattern": "*.rep", + "ontologies": [] + } + } + ], + { + "db": { + "type": "file", + "description": "Ganon database files from build or build-custom", + "pattern": "*.{ibf,tax}", + "ontologies": [] + } + } + ], + "output": { + "tre": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tre": { + "type": "file", + "description": "Output ganon report containing taxonomic profile information. Formatting of contents depends on --output-format.", + "pattern": "*.tre", + "ontologies": [] + } + } + ] + ], + "versions_ganon": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "ganon": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "ganon --version 2>1 | sed 's/.*ganon //g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "ganon": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "ganon --version 2>1 | sed 's/.*ganon //g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@jfy133"], + "maintainers": ["@jfy133"] + }, + "pipelines": [ + { + "name": "taxprofiler", + "version": "2.0.0" + } + ] }, { - "name": "variantcatalogue", - "version": "dev" - } - ] - }, - { - "name": "entrezdirect_esearch", - "path": "modules/nf-core/entrezdirect/esearch/meta.yml", - "type": "module", - "meta": { - "name": "entrezdirect_esearch", - "description": "Searches a term in a public NCBI database", - "keywords": [ - "public datasets", - "entrez", - "search", - "ncbi", - "database" - ], - "tools": [ - { - "entrezdirect": { - "description": "Entrez Direct (EDirect) is a method for accessing the NCBI's set of\ninterconnected databases (publication, sequence, structure, gene,\nvariation, expression, etc.) from a UNIX terminal window. Functions\ntake search terms from command line arguments. Individual operations\nare combined to build multi-step queries. Record retrieval and\nformatting normally complete the process.\n", - "homepage": "https://www.ncbi.nlm.nih.gov/books/NBK179288/", - "documentation": "https://www.ncbi.nlm.nih.gov/books/NBK25501/", - "tool_dev_url": "https://www.ncbi.nlm.nih.gov/books/NBK25498/", - "doi": "10.1016/S0076-6879(96)66012-1", - "licence": [ - "PUBLIC DOMAIN" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } + "name": "ganon_table", + "path": "modules/nf-core/ganon/table/meta.yml", + "type": "module", + "meta": { + "name": "ganon_table", + "description": "Generate a multi-sample report file from the output of ganon report runs", + "keywords": [ + "ganon", + "metagenomics", + "profiling", + "taxonomy", + "k-mer", + "classification", + "report", + "table" + ], + "tools": [ + { + "ganon": { + "description": "ganon classifies short DNA sequences against large sets of genomic reference sequences efficiently", + "homepage": "https://github.com/pirovc/ganon", + "documentation": "https://github.com/pirovc/ganon", + "tool_dev_url": "https://github.com/pirovc/ganon", + "doi": "10.1093/bioinformatics/btaa458", + "licence": ["MIT"], + "identifier": "biotools:ganon" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "tre": { + "type": "file", + "description": "A list of 'tre' files from ganon report", + "pattern": "*.tre", + "ontologies": [] + } + } + ] + ], + "output": { + "txt": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "Output ganon table containing taxonomic profile information of multiple samples. Formatting of contents depends on --output-format.", + "pattern": "*.txt", + "ontologies": [] + } + } + ] + ], + "versions_ganon": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "ganon": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "ganon --version 2>1 | sed 's/.*ganon //g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "ganon": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "ganon --version 2>1 | sed 's/.*ganon //g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@jfy133"], + "maintainers": ["@jfy133"] }, - { - "term": { - "type": "string", - "description": "Entrez text query. All special characters must be URL encoded.\nSpaces may be replaced by '+' signs.\n" - } - } - ], - { - "database": { - "type": "string", - "description": "Value must be a valid Entrez database name." - } - } - ], - "output": { - "xml": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.xml": { - "type": "file", - "description": "XML file containing search results", - "pattern": "*.xml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2332" - } - ] - } - } - ] - ], - "versions_esearch": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "ENTREZDIRECT": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "esearch -version 2>&1": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "ENTREZDIRECT": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "esearch -version 2>&1": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "taxprofiler", + "version": "2.0.0" + } ] - ] - }, - "authors": [ - "@alxndrdiaz" - ], - "maintainers": [ - "@alxndrdiaz" - ] - } - }, - { - "name": "entrezdirect_esummary", - "path": "modules/nf-core/entrezdirect/esummary/meta.yml", - "type": "module", - "meta": { - "name": "entrezdirect_esummary", - "description": "Queries an NCBI database using Unique Identifier(s)", - "keywords": [ - "public datasets", - "ncbi", - "entrez", - "metadata", - "query", - "database" - ], - "tools": [ - { - "entrezdirect": { - "description": "Entrez Direct (EDirect) is a method for accessing the NCBI's set of\ninterconnected databases (publication, sequence, structure, gene,\nvariation, expression, etc.) from a UNIX terminal window. Functions\ntake search terms from command line arguments. Individual operations\nare combined to build multi-step queries. Record retrieval and\nformatting normally complete the process.\n", - "homepage": "https://www.ncbi.nlm.nih.gov/books/NBK179288/", - "documentation": "https://www.ncbi.nlm.nih.gov/books/NBK25501/", - "tool_dev_url": "https://www.ncbi.nlm.nih.gov/books/NBK25498/", - "doi": "10.1016/S0076-6879(96)66012-1", - "licence": [ - "PUBLIC DOMAIN" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "uid": { - "type": "string", - "description": "Unique Identifier (UID) of record in NCBI database. Cannot be used at the same time as uids_file" - } + }, + { + "name": "gappa_examineassign", + "path": "modules/nf-core/gappa/examineassign/meta.yml", + "type": "module", + "meta": { + "name": "gappa_examineassign", + "description": "assigns taxonomy to query sequences in phylogenetic placement output", + "keywords": ["phylogeny", "phylogenetic placement", "classification", "taxonomy"], + "tools": [ + { + "gappa": { + "description": "Genesis Applications for Phylogenetic Placement Analysis", + "homepage": "https://github.com/lczech/gappa", + "documentation": "https://github.com/lczech/gappa/wiki", + "tool_dev_url": "https://github.com/lczech/gappa", + "doi": "10.1093/bioinformatics/btaa070", + "licence": ["GPL v3"], + "identifier": "biotools:GAPPA" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "jplace": { + "type": "file", + "description": "jplace file output from phylogenetic placement, e.g. EPA-NG, gzipped or not", + "pattern": "*.{jplace,jplace.gz}", + "ontologies": [] + } + }, + { + "taxonomy": { + "type": "file", + "description": "taxonomy file", + "ontologies": [] + } + } + ] + ], + "output": { + "profile": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*profile.tsv": { + "type": "file", + "description": "profile tsv file", + "pattern": "*profile.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "labelled_tree": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*labelled_tree.newick": { + "type": "file", + "description": "labelled tree in newick format", + "pattern": "*labelled_tree.newick", + "ontologies": [] + } + } + ] + ], + "per_query": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*per_query.tsv": { + "type": "file", + "description": "per query taxonomy assignments in tsv format", + "pattern": "*per_query.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "krona": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*krona.profile": { + "type": "file", + "description": "krona profile file", + "pattern": "*krona.profile", + "ontologies": [] + } + } + ] + ], + "sativa": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*sativa.tsv": { + "type": "file", + "description": "sativa output file", + "pattern": "*sativa.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_gappa": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gappa": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gappa --version 2>&1 | sed 's/v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gappa": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gappa --version 2>&1 | sed 's/v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@erikrikarddaniel"], + "maintainers": ["@erikrikarddaniel"] }, - { - "uids_file": { - "type": "file", - "description": "Text file containing multiple UIDs. Cannot be used at the same time as uid.", - "ontologies": [] - } - } - ], - { - "database": { - "type": "string", - "description": "Value must be a valid Entrez database name ('assembly', etc)." - } - } - ], - "output": { - "xml": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.xml": { - "type": "file", - "description": "Query result in XML format", - "pattern": "*.xml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2332" - } - ] - } - } - ] - ], - "versions_esummary": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "ENTREZDIRECT": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "esummary -version 2>&1": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "ENTREZDIRECT": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "esummary -version 2>&1": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "ampliseq", + "version": "2.17.0" + }, + { + "name": "phyloplace", + "version": "2.0.0" + } ] - ] - }, - "authors": [ - "@alxndrdiaz" - ], - "maintainers": [ - "@alxndrdiaz" - ] - } - }, - { - "name": "entrezdirect_xtract", - "path": "modules/nf-core/entrezdirect/xtract/meta.yml", - "type": "module", - "meta": { - "name": "entrezdirect_xtract", - "description": "Queries an NCBI database using an UID", - "keywords": [ - "public datasets", - "entrez", - "search", - "ncbi", - "database" - ], - "tools": [ - { - "entrezdirect": { - "description": "Entrez Direct (EDirect) is a method for accessing the NCBI's set of\ninterconnected databases (publication, sequence, structure, gene,\nvariation, expression, etc.) from a UNIX terminal window. Functions\ntake search terms from command line arguments. Individual operations\nare combined to build multi-step queries. 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Its powerful processing engine\nand high-performance computing features make it capable of taking on projects of any size.\n", + "homepage": "https://gatk.broadinstitute.org/hc/en-us", + "documentation": "https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s", + "doi": "10.1158/1538-7445.AM2017-3590", + "licence": ["Apache-2.0"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "intervals": { + "type": "file", + "description": "One or more interval files to annotate", + "pattern": "*.{interval_list,list,bed}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The reference FASTA file", + "pattern": "*.{fasta,fa}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta_fai": { + "type": "file", + "description": "The index of the reference FASTA file", + "pattern": "*.fai", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "dict": { + "type": "file", + "description": "The sequence dictionary reference FASTA file", + "pattern": "*.dict", + "ontologies": [] + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "mappable_regions": { + "type": "file", + "description": "Optional - Umap single-read mappability track\nThe track should correspond to the appropriate read length and overlapping intervals must be merged\n", + "pattern": "*.bed(.gz)?", + "ontologies": [] + } + } + ], + [ + { + "meta6": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "mappable_regions_tbi": { + "type": "file", + "description": "Optional - The index of the gzipped umap single-read mappability track", + "pattern": "*.bed.gz.tbi", + "ontologies": [] + } + } + ], + [ + { + "meta7": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "segmental_duplication_regions": { + "type": "file", + "description": "Optional - Segmental-duplication track", + "pattern": "*.bed(.gz)?", + "ontologies": [] + } + } + ], + [ + { + "meta8": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "segmental_duplication_regions_tbi": { + "type": "file", + "description": "Optional - The index of the gzipped segmental-duplication track", + "pattern": "*.bed.gz.tbi", + "ontologies": [] + } + } + ] + ], + "output": { + "annotated_intervals": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "The output TSV file with a SAM-style header containing the annotated intervals", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_gatk4": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@nvnieuwk"], + "maintainers": ["@nvnieuwk"] + }, + "pipelines": [ + { + "name": "createpanelrefs", + "version": "dev" + } + ] }, { - "name": "phyloplace", - "version": "2.0.0" - } - ] - }, - { - "name": "epic2_epic2", - "path": "modules/nf-core/epic2/epic2/meta.yml", - "type": "module", - "meta": { - "name": "epic2_epic2", - "description": "Domain calling of broad enriched genomic regions of ChIP-seq, Cut&Run or Cut&Tag", - "keywords": [ - "alignment", - "chip-seq", - "cut&run", - "cut&tag", - "domain-calling" - ], - "tools": [ - { - "epic2": { - "description": "Ultraperformant Chip-Seq broad domain finder based on SICER.", - "homepage": "https://github.com/biocore-ntnu/epic2", - "documentation": "https://github.com/biocore-ntnu/epic2", - "tool_dev_url": "https://github.com/biocore-ntnu/epic2", - "doi": "10.1093/bioinformatics/btz232", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "ipbam": { - "type": "file", - "description": "Sorted BAM file for IP sample", - "pattern": "*.bam", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } + "name": "gatk4_applybqsr", + "path": "modules/nf-core/gatk4/applybqsr/meta.yml", + "type": "module", + "meta": { + "name": "gatk4_applybqsr", + "description": "Apply base quality score recalibration (BQSR) to a bam file", + "keywords": ["bam", "base quality score recalibration", "bqsr", "cram", "gatk4"], + "tools": [ + { + "gatk4": { + "description": "Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools\nwith a primary focus on variant discovery and genotyping. Its powerful processing engine\nand high-performance computing features make it capable of taking on projects of any size.\n", + "homepage": "https://gatk.broadinstitute.org/hc/en-us", + "documentation": "https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s", + "doi": "10.1158/1538-7445.AM2017-3590", + "licence": ["Apache-2.0"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM file from alignment", + "pattern": "*.{bam,cram}", + "ontologies": [] + } + }, + { + "input_index": { + "type": "file", + "description": "BAI/CRAI file from alignment", + "pattern": "*.{bai,crai}", + "ontologies": [] + } + }, + { + "bqsr_table": { + "type": "file", + "description": "Recalibration table from gatk4_baserecalibrator", + "ontologies": [] + } + }, + { + "intervals": { + "type": "file", + "description": "Bed file with the genomic regions included in the library (optional)", + "ontologies": [] + } + } + ], + { + "fasta": { + "type": "file", + "description": "The reference fasta file", + "pattern": "*.fasta", + "ontologies": [] + } + }, + { + "fai": { + "type": "file", + "description": "Index of reference fasta file", + "pattern": "*.fasta.fai", + "ontologies": [] + } + }, + { + "dict": { + "type": "file", + "description": "GATK sequence dictionary", + "pattern": "*.dict", + "ontologies": [] + } + } + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.bam": { + "type": "file", + "description": "Recalibrated BAM file", + "pattern": "${prefix}.bam", + "ontologies": [] + } + } + ] + ], + "bai": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}*bai": { + "type": "file", + "description": "Recalibrated BAM index file", + "pattern": "${prefix}*bai", + "ontologies": [] + } + } + ] + ], + "cram": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.cram": { + "type": "file", + "description": "Recalibrated CRAM file", + "pattern": "${prefix}.cram", + "ontologies": [] + } + } + ] + ], + "versions_gatk4": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@yocra3", "@FriederikeHanssen"], + "maintainers": ["@yocra3", "@FriederikeHanssen"] }, - { - "controlbam": { - "type": "file", - "description": "Sorted BAM file for control sample", - "pattern": "*.bam", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - } - ] - ], - "output": { - "bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.bed": { - "type": "file", - "description": "BED file containing the called domains", - "pattern": "*.bed", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3003" - } - ] - } - } + "pipelines": [ + { + "name": "genomicrelatedness", + "version": "dev" + }, + { + "name": "rnadnavar", + "version": "dev" + }, + { + "name": "rnavar", + "version": "1.2.3" + }, + { + "name": "sarek", + "version": "3.8.1" + }, + { + "name": "tbanalyzer", + "version": "dev" + } ] - ], - "versions_epic2": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "epic2": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "epic2 --version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_python": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "python": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python --version | sed 's/Python //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_setuptools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "setuptools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python -c 'import setuptools; print(setuptools.__version__)'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "epic2": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "epic2 --version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "python": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python --version | sed 's/Python //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "setuptools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python -c 'import setuptools; print(setuptools.__version__)'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@Kevin-Brockers" - ], - "maintainers": [ - "@Kevin-Brockers" - ] - } - }, - { - "name": "estsfs", - "path": "modules/nf-core/estsfs/meta.yml", - "type": "module", - "meta": { - "name": "estsfs", - "description": "estimation of the unfolded site frequency spectrum", - "keywords": [ - "site frequency spectrum", - "ancestral alleles", - "derived alleles" - ], - "tools": [ - { - "estsfs": { - "description": "est-sfs ( Keightley and Jackson, 2018) is a stand-alone implementation of a method to infer the unfolded site frequency spectrum (the uSFS) and ancestral state probabilities by maximum likelihood (ML).", - "homepage": "https://sourceforge.net/projects/est-usfs/", - "documentation": "https://sourceforge.net/projects/est-usfs/", - "tool_dev_url": "https://sourceforge.net/projects/est-usfs/files/est-sfs-release-2.04.tar.gz", - "doi": "10.1534/genetics.118.301120", - "licence": [ - "Free for Academic Use" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" - } - }, - { - "e_config": { - "type": "file", - "description": "config file for est-sfs", - "pattern": "*.txt", - "ontologies": [] - } - }, - { - "data": { - "type": "file", - "description": "input data file for est-sfs", - "pattern": "*.txt", - "ontologies": [] - } - }, - { - "seed": { - "type": "file", - "description": "text file containing random number seed", - "pattern": "*.txt", - "ontologies": [] - } - } - ] - ], - "output": { - "sfs_out": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" - } - }, - { - "${prefix}_sfs.txt": { - "type": "file", - "description": "output file consists of the comma-separated estimated uSFS vector", - "pattern": "*.txt", - "ontologies": [] - } - } - ] - ], - "pvalues_out": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" - } - }, - { - "${prefix}_pvalues.txt": { - "type": "file", - "description": "this file contains the estimated ancestral state probabilities for each site", - "pattern": "*.txt", - "ontologies": [] - } - } - ] - ], - "versions_estsfs": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "est-sfs": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "2.04": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "est-sfs": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "2.04": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@BioInf2305" - ] - } - }, - { - "name": "evigene_tr2aacds", - "path": "modules/nf-core/evigene/tr2aacds/meta.yml", - "type": "module", - "meta": { - "name": "evigene_tr2aacds", - "description": "Uses evigene/scripts/prot/tr2aacds.pl to filter a transcript assembly", - "keywords": [ - "genomics", - "transcript", - "assembly", - "clean", - "polish", - "filter", - "redundant", - "duplicate" - ], - "tools": [ - { - "evigene": { - "description": "EvidentialGene is a genome informatics project for \"Evidence Directed Gene Construction\nfor Eukaryotes\", for constructing high quality, accurate gene sets for animals and\nplants (any eukaryotes), being developed by Don Gilbert at Indiana University, gilbertd at indiana edu.\n", - "homepage": "http://arthropods.eugenes.org/EvidentialGene/evigene/", - "documentation": "http://arthropods.eugenes.org/EvidentialGene/evigene/", - "tool_dev_url": "http://arthropods.eugenes.org/EvidentialGene/evigene/", - "doi": "10.7490/f1000research.1112594.1 ", - "licence": [ - "Don Gilbert, gilbertd At indiana edu, 2018" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Transcript assembly in fasta format", - "pattern": "*.{fsa,fa,fasta,fsa.gz,fa.gz,fasta.gz}", - "ontologies": [] - } - } - ] - ], - "output": { - "dropset": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "dropset": { - "type": "directory", - "description": "Directory containing dropped transcripts and associated files", - "pattern": "dropset" - } - } - ] - ], - "okayset": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "okayset": { - "type": "directory", - "description": "Directory containing included transcripts and associated files", - "pattern": "okayset" - } - } - ] - ], - "versions_tr2aacds": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "tr2aacds": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "\\$EVIGENEHOME/scripts/prot/tr2aacds.pl 2>&1 | sed '1!d;s/.*VERSION //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "tr2aacds": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "\\$EVIGENEHOME/scripts/prot/tr2aacds.pl 2>&1 | sed '1!d;s/.*VERSION //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@GallVp" - ], - "maintainers": [ - "@GallVp" - ] - }, - "pipelines": [ - { - "name": "denovotranscript", - "version": "1.2.1" - } - ] - }, - { - "name": "expansionhunter", - "path": "modules/nf-core/expansionhunter/meta.yml", - "type": "module", - "meta": { - "name": "expansionhunter", - "description": "Estimate repeat sizes using NGS data", - "keywords": [ - "STR", - "repeat_expansions", - "bam", - "cram", - "vcf", - "json" - ], - "tools": [ - { - "expansionhunter": { - "description": "A tool for estimating repeat sizes", - "homepage": "https://github.com/Illumina/ExpansionHunter", - "documentation": "https://github.com/Illumina/ExpansionHunter/blob/master/docs/01_Introduction.md", - "doi": "10.1093/bioinformatics/btz431", - "licence": [ - "Apache-2.0" - ], - "identifier": "biotools:ExpansionHunter" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM file", - "pattern": "*.{bam,cram}", - "ontologies": [] - } - }, - { - "bai": { - "type": "file", - "description": "Index of BAM/CRAM file", - "pattern": "*.{bai,crai}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome", - "pattern": "*.{fna,fa,fasta}", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "fasta_fai": { - "type": "file", - "description": "Reference genome index", - "pattern": "*.fai", - "ontologies": [] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "variant_catalog": { - "type": "file", - "description": "JSON file with repeat expansion sites to genotype", - "pattern": "*.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', gender:'female' ]\n" - } - }, - { - "*.vcf.gz": { - "type": "file", - "description": "VCF with repeat expansions", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "json": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', gender:'female' ]\n" - } - }, - { - "*.json.gz": { - "type": "file", - "description": "JSON with repeat expansions", - "pattern": "*.json.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', gender:'female' ]\n" - } - }, - { - "*_realigned.bam": { - "type": "file", - "description": "BAM/CRAM file", - "pattern": "*.{bam,cram}", - "ontologies": [] - } - } - ] - ], - "versions_expansionhunter": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "expansionhunter": { - "type": "string", - "description": "The tool name" - } - }, - { - "ExpansionHunter --version | head -1 | sed -n 's/^.*ExpansionHunter v//; s/]//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_bgzip": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bgzip": { - "type": "string", - "description": "The tool name" - } - }, - { - "bgzip --version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "expansionhunter": { - "type": "string", - "description": "The tool name" - } - }, - { - "ExpansionHunter --version | head -1 | sed -n 's/^.*ExpansionHunter v//; s/]//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bgzip": { - "type": "string", - "description": "The tool name" - } - }, - { - "bgzip --version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@jemten" - ], - "maintainers": [ - "@jemten" - ] - }, - "pipelines": [ - { - "name": "raredisease", - "version": "3.0.0" - } - ] - }, - { - "name": "expansionhunterdenovo_merge", - "path": "modules/nf-core/expansionhunterdenovo/merge/meta.yml", - "type": "module", - "meta": { - "name": "expansionhunterdenovo_merge", - "description": "Merge STR profiles into a multi-sample STR profile", - "keywords": [ - "expansionhunterdenovo", - "merge", - "str" - ], - "tools": [ - { - "expansionhunterdenovo": { - "description": "ExpansionHunter Denovo (EHdn) is a suite of tools for detecting novel expansions of short tandem repeats (STRs).", - "homepage": "https://github.com/Illumina/ExpansionHunterDenovo", - "documentation": "https://github.com/Illumina/ExpansionHunterDenovo/blob/master/documentation/00_Introduction.md", - "tool_dev_url": "https://github.com/Illumina/ExpansionHunterDenovo", - "licence": [ - "Apache License 2.0" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "manifest": { - "type": "file", - "description": "A tab-delimited file containing the sample name, whether it's case or control\nand the paths to the corresponding STR profiles.\nSee here for an example: https://github.com/Illumina/ExpansionHunterDenovo/blob/master/documentation/06_Merging_profiles.md#manifest-files\n", - "pattern": "*.{tsv,txt}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference FASTA file", - "pattern": "*.{fasta,fa}", - "ontologies": [] - } - }, - { - "fasta_fai": { - "type": "file", - "description": "The index of the reference FASTA file", - "pattern": "*.fai", - "ontologies": [] - } - } - ] - ], - "output": { - "merged_profiles": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.multisample_profile.json": { - "type": "file", - "description": "The merged STR profiles", - "pattern": "*.multisample_profile.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "versions_expansionhunterdenovo": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "expansionhunterdenovo": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "ExpansionHunterDenovo --help |& sed '1!d;s/ExpansionHunter Denovo v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "expansionhunterdenovo": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "ExpansionHunterDenovo --help |& sed '1!d;s/ExpansionHunter Denovo v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@nvnieuwk" - ], - "maintainers": [ - "@nvnieuwk" - ] - } - }, - { - "name": "expansionhunterdenovo_profile", - "path": "modules/nf-core/expansionhunterdenovo/profile/meta.yml", - "type": "module", - "meta": { - "name": "expansionhunterdenovo_profile", - "description": "Compute genome-wide STR profile", - "keywords": [ - "expansionhunterdenovo", - "profile", - "STR", - "genome", - "bam", - "cram" - ], - "tools": [ - { - "expansionhunterdenovo": { - "description": "ExpansionHunter Denovo (EHdn) is a suite of tools for detecting novel expansions of short tandem repeats (STRs).", - "homepage": "https://github.com/Illumina/ExpansionHunterDenovo", - "documentation": "https://github.com/Illumina/ExpansionHunterDenovo/blob/master/documentation/00_Introduction.md", - "tool_dev_url": "https://github.com/Illumina/ExpansionHunterDenovo", - "licence": [ - "Apache License 2.0" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "alignment_file": { - "type": "file", - "description": "BAM/CRAM file", - "pattern": "*.{bam,cram}", - "ontologies": [] - } - }, - { - "alignment_index": { - "type": "file", - "description": "Index of the BAM/CRAM file", - "pattern": "*.{bai,crai}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "The FASTA reference file", - "pattern": "*.{fasta,fa}", - "ontologies": [] - } + }, + { + "name": "gatk4_applyvqsr", + "path": "modules/nf-core/gatk4/applyvqsr/meta.yml", + "type": "module", + "meta": { + "name": "gatk4_applyvqsr", + "description": "Apply a score cutoff to filter variants based on a recalibration table.\nAplyVQSR performs the second pass in a two-stage process called Variant Quality Score Recalibration (VQSR).\nSpecifically, it applies filtering to the input variants based on the recalibration table produced\nin the first step by VariantRecalibrator and a target sensitivity value.\n", + "keywords": ["gatk4", "variant quality score recalibration", "vcf", "vqsr"], + "tools": [ + { + "gatk4": { + "description": "Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools\nwith a primary focus on variant discovery and genotyping. Its powerful processing engine\nand high-performance computing features make it capable of taking on projects of any size.\n", + "homepage": "https://gatk.broadinstitute.org/hc/en-us", + "documentation": "https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s", + "doi": "10.1158/1538-7445.AM2017-3590", + "licence": ["Apache-2.0"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF file to be recalibrated, this should be the same file as used for the first stage VariantRecalibrator.", + "pattern": "*.vcf", + "ontologies": [] + } + }, + { + "vcf_tbi": { + "type": "file", + "description": "tabix index for the input vcf file.", + "pattern": "*.vcf.tbi", + "ontologies": [] + } + }, + { + "recal": { + "type": "file", + "description": "Recalibration file produced when the input vcf was run through VariantRecalibrator in stage 1.", + "pattern": "*.recal", + "ontologies": [] + } + }, + { + "recal_index": { + "type": "file", + "description": "Index file for the recalibration file.", + "pattern": ".recal.idx", + "ontologies": [] + } + }, + { + "tranches": { + "type": "file", + "description": "Tranches file produced when the input vcf was run through VariantRecalibrator in stage 1.", + "pattern": ".tranches", + "ontologies": [] + } + } + ], + { + "fasta": { + "type": "file", + "description": "The reference fasta file", + "pattern": "*.fasta", + "ontologies": [] + } + }, + { + "fai": { + "type": "file", + "description": "Index of reference fasta file", + "pattern": "*.fasta.fai", + "ontologies": [] + } + }, + { + "dict": { + "type": "file", + "description": "GATK sequence dictionary", + "pattern": "*.dict", + "ontologies": [] + } + } + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "file", + "description": "compressed vcf file containing the recalibrated variants.", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "compressed vcf file containing the recalibrated variants.", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "tbi": [ + [ + { + "meta": { + "type": "file", + "description": "compressed vcf file containing the recalibrated variants.", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + }, + { + "*.tbi": { + "type": "file", + "description": "Index of recalibrated vcf file.", + "pattern": "*vcf.gz.tbi", + "ontologies": [] + } + } + ] + ], + "versions_gatk4": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@GCJMackenzie"], + "maintainers": ["@GCJMackenzie"] }, - { - "fasta_fai": { - "type": "file", - "description": "The index of the FASTA reference file", - "pattern": "*.fai", - "ontologies": [] - } - } - ] - ], - "output": { - "locus_tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.locus.tsv": { - "type": "file", - "description": "The locus TSV file", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "motif_tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.motif.tsv": { - "type": "file", - "description": "The motif TSV file", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "str_profile": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.str_profile.json": { - "type": "file", - "description": "The JSON file containing the STR profile", - "pattern": "*.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "versions_expansionhunterdenovo": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "expansionhunterdenovo": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "ExpansionHunterDenovo --help |& sed '1!d;s/ExpansionHunter Denovo v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "expansionhunterdenovo": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "ExpansionHunterDenovo --help |& sed '1!d;s/ExpansionHunter Denovo v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "sarek", + "version": "3.8.1" + }, + { + "name": "tbanalyzer", + "version": "dev" + } ] - ] - }, - "authors": [ - "@nvnieuwk" - ], - "maintainers": [ - "@nvnieuwk" - ] - } - }, - { - "name": "fairy_coverage", - "path": "modules/nf-core/fairy/coverage/meta.yml", - "type": "module", - "meta": { - "name": "fairy_coverage", - "description": "Computes coverage depth statistics for assembled contigs from one or more\nfairy sketch files, producing a MetaBAT2-compatible TSV with per-contig\nmean depth and variance columns.\n", - "keywords": [ - "metagenomics", - "coverage", - "binning", - "alignment-free", - "contig" - ], - "tools": [ - { - "fairy": { - "description": "fairy is a fast, alignment-free, k-mer-based tool for computing\ncoverage depth statistics for metagenomic samples. 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Its powerful processing engine\nand high-performance computing features make it capable of taking on projects of any size.\n", + "homepage": "https://gatk.broadinstitute.org/hc/en-us", + "documentation": "https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s", + "doi": "10.1158/1538-7445.AM2017-3590", + "licence": ["Apache-2.0"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file", + "pattern": "*.{bam}", + "ontologies": [] + } + }, + { + "bai": { + "type": "file", + "description": "index file for BAM file", + "pattern": "*.{bai}", + "ontologies": [] + } + }, + { + "vcf": { + "type": "file", + "description": "VCF file", + "pattern": "*.{vcf.gz}", + "ontologies": [] + } + }, + { + "tbi": { + "type": "file", + "description": "index file for VCF file", + "pattern": "*.{vcf.gz.tbi}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. `[ id:'reference' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "fasta file", + "pattern": "*.{fasta,fa}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. `[ id:'reference' ]`\n" + } + }, + { + "fai": { + "type": "file", + "description": "fasta index file", + "pattern": "*.{fai}", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. `[ id:'reference' ]`\n" + } + }, + { + "dict": { + "type": "file", + "description": "dictionary file", + "pattern": "*.{dict}", + "ontologies": [] + } + } + ], + { + "intervals": { + "type": "file", + "description": "interval file", + "ontologies": [] + } + } + ], + "output": { + "csv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + } + ], + "versions_gatk4": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@Lucpen"], + "maintainers": ["@Lucpen"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "sketches": { - "type": "file", - "description": "One or more fairy sketch files (.bcsp) produced by `fairy sketch`", - "pattern": "*.bcsp", - "ontologies": [] - } + }, + { + "name": "gatk4_baserecalibrator", + "path": "modules/nf-core/gatk4/baserecalibrator/meta.yml", + "type": "module", + "meta": { + "name": "gatk4_baserecalibrator", + "description": "Generate recalibration table for Base Quality Score Recalibration (BQSR)", + "keywords": ["base quality score recalibration", "table", "bqsr", "gatk4", "sort"], + "tools": [ + { + "gatk4": { + "description": "Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools\nwith a primary focus on variant discovery and genotyping. 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(optional)", + "pattern": "*.hd5", + "ontologies": [] + } } - ] - } - } - ] - ], - "versions_famsa": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "famsa": { - "type": "string", - "description": "The tool name" - } - }, - { - "famsa -help 2>&1 | sed '2!d;s/.*version //;s/ .*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "famsa": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "famsa -help 2>&1 | sed '2!d;s/.*version //;s/ .*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@luisas", - "@JoseEspinosa" - ], - "maintainers": [ - "@luisas", - "@JoseEspinosa", - "@vagkaratzas" - ] - }, - "pipelines": [ - { - "name": "multiplesequencealign", - "version": "1.1.1" - }, - { - "name": "proteinfamilies", - "version": "2.3.0" - } - ] - }, - { - "name": "famsa_guidetree", - "path": "modules/nf-core/famsa/guidetree/meta.yml", - "type": "module", - "meta": { - "name": "famsa_guidetree", - "description": "Renders a guidetree in famsa", - "keywords": [ - "guide tree", - "msa", - "newick" - ], - "tools": [ - { - "famsa": { - "description": "Algorithm for large-scale multiple sequence alignments", - "homepage": "https://github.com/refresh-bio/FAMSA", - "documentation": "https://github.com/refresh-bio/FAMSA", - "tool_dev_url": "https://github.com/refresh-bio/FAMSA", - "doi": "10.1038/srep33964", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:famsa" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input sequences in FASTA format", - "pattern": "*.{fa,fasta}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1919" - }, - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ], - "output": { - "tree": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" - } - }, - { - "*.dnd": { - "type": "file", - "description": "Guide tree file in Newick format", - "pattern": "*.{dnd}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2006" - } - ] - } - } - ] - ], - "versions_famsa": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "famsa": { - "type": "string", - "description": "The tool name" - } - }, - { - "famsa -help 2>&1 | sed '2!d;s/.*version //;s/ .*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "famsa": { - "type": "string", - "description": "The tool name" - } - }, - { - "famsa -help 2>&1 | sed '2!d;s/.*version //;s/ .*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@luisas", - "@JoseEspinosa" - ], - "maintainers": [ - "@luisas", - "@JoseEspinosa" - ] - }, - "pipelines": [ - { - "name": "multiplesequencealign", - "version": "1.1.1" - } - ] - }, - { - "name": "faqcs", - "path": "modules/nf-core/faqcs/meta.yml", - "type": "module", - "meta": { - "name": "faqcs", - "description": "Perform adapter and quality trimming on sequencing reads with reporting", - "keywords": [ - "trimming", - "quality control", - "fastq", - "faqcs" - ], - "tools": [ - { - "faqcs": { - "description": "FaQCs combines several features of currently available applications into a single, user-friendly process, and includes additional unique capabilities such as filtering the PhiX control sequences, conversion of FASTQ formats, and multi-threading. 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} - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.log": { - "type": "file", - "description": "fastq log file", - "pattern": "*.log", - "ontologies": [] - } - } - ] - ], - "versions_faqcs": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "faqcs": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "FaQCs --version 2>&1 | sed 's/^.*Version: //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "faqcs": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "FaQCs --version 2>&1 | sed 's/^.*Version: //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@mjcipriano", - "@sateeshperi", - "@hseabolt" - ], - "maintainers": [ - "@mjcipriano", - "@sateeshperi", - "@hseabolt" - ] - } - }, - { - "name": "fargene", - "path": "modules/nf-core/fargene/meta.yml", - "type": "module", - "meta": { - "name": "fargene", - "description": "tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output.", - "keywords": [ - "antibiotic resistance genes", - "ARGs", - "identifier", - "metagenomic", - "contigs" - ], - "tools": [ - { - "fargene": { - "description": "Fragmented Antibiotic Resistance Gene Identifier takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output", - "homepage": "https://github.com/fannyhb/fargene", - "documentation": "https://github.com/fannyhb/fargene", - "tool_dev_url": "https://github.com/fannyhb/fargene", - "licence": [ - "MIT" - ], - "identifier": "biotools:fargene" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "uncompressed fasta file or paired-end fastq files containing either genomes or longer contigs as nucleotide or protein sequences (fasta) or fragmented metagenomic reads (fastq)", - "pattern": "*.{fasta}", - "ontologies": [] - } - } - ], - { - "hmm_model": { - "type": "string", - "description": "name of custom hidden markov model to be used [pre-defined class_a, class_b_1_2, class_b_3, class_c, class_d_1, class_d_2, qnr, tet_efflux, tet_rpg, tet_enzyme]" - } - } - ], - "output": { - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.log": { - "type": "file", - "description": "log file", - "pattern": "*.{log}", - "ontologies": [] - } - } - ] - ], - "txt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/results_summary.txt": { - "type": "file", - "description": "analysis summary text file", - "pattern": "*.{txt}", - "ontologies": [] - } - } - ] - ], - "hmm": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/hmmsearchresults/*.out": { - "type": "file", - "description": "output from hmmsearch (both single gene annotations + contigs)", - "pattern": "*.{out}", - "ontologies": [] - } - } - ] - ], - "hmm_genes": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/hmmsearchresults/retrieved-*.out": { - "type": "file", - "description": "output from hmmsearch (single gene annotations only)", - "pattern": "retrieved-*.{out}", - "ontologies": [] - } - } - ] - ], - "orfs": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/predictedGenes/predicted-orfs.fasta": { - "type": "file", - "description": "open reading frames (ORFs)", - "pattern": "*.{fasta}", - "ontologies": [] - } - } - ] - ], - "orfs_amino": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/predictedGenes/predicted-orfs-amino.fasta": { - "type": "file", - "description": "protein translation of open reading frames (ORFs)", - "pattern": "*.{fasta}", - "ontologies": [] - } - } - ] - ], - "contigs": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/predictedGenes/retrieved-contigs.fasta": { - "type": "file", - "description": "(complete) contigs that passed the final full-length classification", - "pattern": "*.{fasta}", - "ontologies": [] - } - } - ] - ], - "contigs_pept": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/predictedGenes/retrieved-contigs-peptides.fasta": { - "type": "file", - "description": "parts of the contigs that passed the final classification step that aligned with the HMM, as amino acid sequences", - "pattern": "*.{fasta}", - "ontologies": [] - } - } - ] - ], - "filtered": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/predictedGenes/*filtered.fasta": { - "type": "file", - "description": "sequences that passed the final classification step, but only the parts that where predicted by the HMM to be part of the gene", - "pattern": "*.{fasta}", - "ontologies": [] - } - } - ] - ], - "filtered_pept": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/predictedGenes/*filtered-peptides.fasta": { - "type": "file", - "description": "sequences from filtered.fasta, translated in the same frame as the gene is predicted to be located", - "pattern": "*.{fasta}", - "ontologies": [] - } - } - ] - ], - "fragments": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/retrievedFragments/all_retrieved_*.fastq": { - "type": "file", - "description": "All quality controlled retrieved fragments that were classified as positive, together with its read-pair, gathered in two files", - "pattern": "*.{fastq}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "trimmed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/retrievedFragments/trimmedReads/*.fasta": { - "type": "file", - "description": "The quality controlled retrieved fragments from each input file.", - "pattern": "*.{fasta}", - "ontologies": [] - } - } - ] - ], - "spades": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/spades_assembly/*": { - "type": "directory", - "description": "The output from the SPAdes assembly", - "pattern": "spades_assembly" - } - } - ] - ], - "metagenome": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/tmpdir/*.fasta": { - "type": "file", - "description": "The FASTQ to FASTA converted input files from metagenomic reads.", - "pattern": "*.{fasta}", - "ontologies": [] - } - } - ] - ], - "tmp": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/tmpdir/*.out": { - "type": "file", - "description": "The from FASTQ to FASTA converted input files and their translated input sequences. Are only saved if option --store-peptides is used.", - "pattern": "*.{fasta}", - "ontologies": [] - } - } - ] - ], - "versions_fargene": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "fargene": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "0.1": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "fargene": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "0.1": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@louperelo" - ], - "maintainers": [ - "@louperelo" - ] - }, - "pipelines": [ - { - "name": "funcscan", - "version": "3.0.0" - } - ] - }, - { - "name": "fast2q", - "path": "modules/nf-core/fast2q/meta.yml", - "type": "module", - "meta": { - "name": "fast2q", - "description": "A program that counts sequence occurrences in FASTQ files.", - "keywords": [ - "CRISPRi", - "FASTQ", - "genomics" - ], - "tools": [ - { - "2FAST2Q": { - "description": "2FAST2Q is ideal for CRISPRi-Seq, and for extracting and counting any kind of information from reads in the fastq format, such as barcodes in Bar-seq experiments.\n2FAST2Q can work with sequence mismatches, Phred-score, and be used to find and extract unknown sequences delimited by known sequences.\n2FAST2Q can extract multiple features per read using either fixed positions or delimiting search sequences.\n", - "homepage": "https://github.com/afombravo/2FAST2Q", - "doi": "10.7717/peerj.14041", - "licence": [ - "GPL-3.0-or-later" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing output name.\ne.g. [ id:'test']\n" - } - }, - { - "fastq": { - "type": "directory", - "description": "Folder with FASTQ file(s). 2FAST2Q automatically picks up all the FASTQ files inside the provided folder.", - "pattern": "*.{fastq,gz}" - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'library_name', multiple_features_per_read:false ]\n" - } + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*cnn.vcf.gz": { + "type": "file", + "description": "Annotated VCF file", + "pattern": "*.vcf", + "ontologies": [] + } + } + ] + ], + "tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*cnn.vcf.gz.tbi": { + "type": "file", + "description": "VCF index file", + "pattern": "*.vcf.gz.tbi", + "ontologies": [] + } + } + ] + ], + "versions_gatk4": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@FriederikeHanssen"], + "maintainers": ["@FriederikeHanssen"] }, - { - "library": { - "type": "file", - "description": ".csv library file following the ´Feature_name,sequence´ or ´Feature_name,sequence1:sequence2´ format. See 2FAST2Q instructions for more information.", - "pattern": "*.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "output": { - "count_matrix": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing output name.\ne.g. [ id:'test' ]\n" - } - }, - { - "${prefix}.csv": { - "type": "file", - "description": "Count matrix csv file\n", - "ontologies": [] - } - } - ] - ], - "stats": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing output name.\ne.g. [ id:'test' ]\n" - } - }, - { - "${prefix}_stats.csv": { - "type": "file", - "description": "File containing all the relevant statistics such as quality passing reads, aligned reads, total reads, and sample run times.\n", - "ontologies": [] - } - } - ] - ], - "distribution_plot": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing output name.\ne.g. [ id:'test' ]\n" - } - }, - { - "${prefix}_distribution_plot.png": { - "type": "file", - "description": "Violin plot of the distribution of reads per feature across all samples.\n", - "ontologies": [] - } - } - ] - ], - "reads_plot": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing output name.\ne.g. [ id:'test' ]\n" - } - }, - { - "${prefix}_reads_plot.png": { - "type": "file", - "description": "Bar plot with the distribution of reads, in absolute numbers, binned to the different quality metrics indicated in the statistics.csv\n", - "ontologies": [] - } - } - ] - ], - "reads_plot_percentage": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing output name.\ne.g. [ id:'test' ]\n" - } - }, - { - "${prefix}_reads_plot_percentage.png": { - "type": "file", - "description": "Bar plot with the distribution of reads, in percentage, binned to the different quality metrics indicated in the statistics.csv\n", - "ontologies": [] - } - } - ] - ], - "versions_fast2q": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "fast2q": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "2fast2q -v | sed -n \"s/Version: //p\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "fast2q": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "2fast2q -v | sed -n \"s/Version: //p\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "sarek", + "version": "3.8.1" + } ] - ] - }, - "authors": [ - "@afombravo" - ], - "maintainers": [ - "@afombravo" - ] - } - }, - { - "name": "fastani", - "path": "modules/nf-core/fastani/meta.yml", - "type": "module", - "meta": { - "name": "fastani", - "description": "Alignment-free computation of Average Nucleotide Identity (ANI)", - "keywords": [ - "genome", - "fasta", - "ANI" - ], - "tools": [ - { - "fastani": { - "description": "FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI).", - "homepage": "https://github.com/ParBLiSS/FastANI", - "documentation": "https://github.com/ParBLiSS/FastANI", - "tool_dev_url": "https://github.com/ParBLiSS/FastANI", - "doi": "10.1038/s41467-018-07641-9", - "licence": [ - "Apache-2.0" - ], - "identifier": "biotools:fastani" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "query": { - "type": "file", - "description": "Fasta file to be used as the query. If provided, ql will be ignored.", - "pattern": "*.{fasta,fna,fa}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information for the reference" - } + }, + { + "name": "gatk4_collectreadcounts", + "path": "modules/nf-core/gatk4/collectreadcounts/meta.yml", + "type": "module", + "meta": { + "name": "gatk4_collectreadcounts", + "description": "Collects read counts at specified intervals. The count for each interval is calculated by counting the number of read starts that lie in the interval.", + "keywords": ["collectreadcounts", "bam", "cram", "gatk4"], + "tools": [ + { + "gatk4": { + "description": "Genome Analysis Toolkit (GATK4). Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.", + "homepage": "https://gatk.broadinstitute.org/hc/en-us", + "documentation": "https://gatk.broadinstitute.org/hc/en-us/articles/360037593911-CombineGVCFs", + "tool_dev_url": "https://github.com/broadinstitute/gatk", + "doi": "10.1158/1538-7445.AM2017-3590", + "licence": ["Apache-2.0"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}", + "ontologies": [] + } + }, + { + "input_index": { + "type": "file", + "description": "BAM/CRAM/SAM index file", + "pattern": "*.{bai,crai,sai}", + "ontologies": [] + } + }, + { + "intervals": { + "type": "file", + "description": "A file containing the specified intervals", + "pattern": "*.{bed,intervals}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Optional - Reference FASTA", + "pattern": "*.{fasta,fa}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Optional - Index of the reference FASTA file", + "pattern": "*.fai", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "dict": { + "type": "file", + "description": "Optional - Sequence dictionary of the reference FASTA file", + "pattern": "*.dict", + "ontologies": [] + } + } + ] + ], + "output": { + "hdf5": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.hdf5": { + "type": "file", + "description": "The read counts in hdf5 format", + "pattern": "*.hdf5", + "ontologies": [] + } + } + ] + ], + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "The read counts in TSV format", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_gatk4": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@nvnieuwk"], + "maintainers": ["@nvnieuwk"] }, - { - "reference": { - "type": "file", - "description": "Fasta file to be used as the reference. If provided, rl will be ignored.", - "pattern": "*.{fasta,fna,fa}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - { - "ql": { - "type": "file", - "description": "File containing a list of query fasta paths. query input takes precedence over this list if both are provided.", - "pattern": "*.txt", - "ontologies": [ + "pipelines": [ { - "edam": "http://edamontology.org/format_2330" - } - ] - } - }, - { - "rl": { - "type": "file", - "description": "File containing a list of reference fasta paths. reference input takes precedence over this list if both are provided.", - "pattern": "*.txt", - "ontologies": [ + "name": "createpanelrefs", + "version": "dev" + }, { - "edam": "http://edamontology.org/format_2330" + "name": "raredisease", + "version": "3.0.0" } - ] - } - } - ], - "output": { - "ani": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.txt": { - "type": "file", - "description": "ANI results file", - "pattern": "*.txt", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2330" - } - ] - } - } - ] - ], - "visual": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.visual": { - "type": "file", - "optional": true, - "description": "FastANI visualization output", - "pattern": "*.visual", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "matrix": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.matrix": { - "type": "file", - "optional": true, - "description": "ANI matrix output", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3033" - } - ] - } - } - ] - ], - "versions_fastani": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "fastani": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "fastANI --version 2>&1 | head -1 | sed \"s/version\\ //\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "fastani": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "fastANI --version 2>&1 | head -1 | sed \"s/version\\ //\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@abhi18av", - "@Ethan-Hetrick" - ], - "maintainers": [ - "@abhi18av", - "@Ethan-Hetrick" - ] - } - }, - { - "name": "fastavalidator", - "path": "modules/nf-core/fastavalidator/meta.yml", - "type": "module", - "meta": { - "name": "fastavalidator", - "description": "\"Python C-extension for a simple validator for fasta files. The module emits the validated file or an\nerror log upon validation failure.\"\n", - "deprecated": true, - "keywords": [ - "fasta", - "validation", - "genome" - ], - "tools": [ - { - "fasta_validate": { - "description": "\"Python C-extension for a simple C code to validate a fasta file. It only checks a few things,\nand by default only sets its response via the return code,\nso you will need to check that!\"\n", - "homepage": "https://github.com/linsalrob/py_fasta_validator", - "documentation": "https://github.com/linsalrob/py_fasta_validator", - "tool_dev_url": "https://github.com/linsalrob/py_fasta_validator", - "doi": "10.5281/zenodo.5002710", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing file information\ne.g. [ id:'test' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input fasta file", - "pattern": "*.fasta", - "ontologies": [] - } - } - ] - ], - "output": { - "success_log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing file information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.success.log": { - "type": "file", - "description": "Log file for successful validation", - "pattern": "*.success.log", - "ontologies": [] - } - } - ] - ], - "error_log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing file information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.error.log": { - "type": "file", - "description": "Log file for failed validation", - "pattern": "*.error.log", - "ontologies": [] - } - } - ] - ], - "versions_py_fasta_validator": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "py_fasta_validator": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "py_fasta_validator --version | cut -d\" \" -f3": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "py_fasta_validator": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "py_fasta_validator --version | cut -d\" \" -f3": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@gallvp" - ], - "maintainers": [ - "@gallvp" - ] - }, - "pipelines": [ - { - "name": "multiplesequencealign", - "version": "1.1.1" - } - ] - }, - { - "name": "fastawindows", - "path": "modules/nf-core/fastawindows/meta.yml", - "type": "module", - "meta": { - "name": "fastawindows", - "description": "Quickly compute statistics over a fasta file in windows.", - "keywords": [ - "genome", - "fasta", - "tsv", - "bed" - ], - "tools": [ - { - "fastawindows": { - "description": "fasta_windows is a tool written for Darwin Tree of Life chromosomal level genome assemblies. The executable takes a fasta formatted file and calculates some statistics of interest in windows", - "homepage": "https://github.com/tolkit/fasta_windows", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA file", - "pattern": "*.{fa,fasta,fna}", - "ontologies": [] - } - } - ] - ], - "output": { - "freq": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fw_out/*_freq_windows.tsv": { - "type": "file", - "description": "TSV file with frequencies and statistics", - "pattern": "*.{tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "mononuc": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fw_out/*_mononuc_windows.tsv": { - "type": "file", - "description": "TSV file with mononucleotide counts", - "pattern": "*.{tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "dinuc": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fw_out/*_dinuc_windows.tsv": { - "type": "file", - "description": "TSV file with dinucleotide counts", - "pattern": "*.{tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "trinuc": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fw_out/*_trinuc_windows.tsv": { - "type": "file", - "description": "TSV file with trinucleotide counts", - "pattern": "*.{tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "tetranuc": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fw_out/*_tetranuc_windows.tsv": { - "type": "file", - "description": "TSV file with tetranucleotide counts", - "pattern": "*.{tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_fasta_windows": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "fasta_windows": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "fasta_windows --version | cut -d\" \" -f3": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "fasta_windows": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "fasta_windows --version | cut -d\" \" -f3": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } ] - ] - }, - "authors": [ - "@muffato" - ], - "maintainers": [ - "@muffato" - ] - } - }, - { - "name": "fastcov", - "path": "modules/nf-core/fastcov/meta.yml", - "type": "module", - "meta": { - "name": "fastcov", - "description": "Generate a coverage plot from one or more bam files", - "keywords": [ - "coverage", - "bam", - "map" - ], - "tools": [ - { - "fastcov": { - "description": "Generate a coverage plot from one or more bam files", - "homepage": "https://github.com/RaverJay/fastcov/", - "documentation": "https://github.com/RaverJay/fastcov/blob/main/README.md", - "tool_dev_url": "https://github.com/RaverJay/fastcov/tree/main", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file", - "pattern": "*.bam", - "ontologies": [] - } - }, - { - "index": { - "type": "file", - "description": "BAM index file", - "pattern": "*.bai", - "ontologies": [] - } - } - ], - { - "file_ext": { - "type": "string", - "description": "output plot file extension string, e.g. `png` or `pdf`" - } - } - ], - "output": { - "coverage_plot": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n", - "pattern": "*.{png,svg,pdf}" - } - }, - { - "${prefix}.${file_ext}": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n", - "pattern": "*.{png,svg,pdf}" - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "log.txt": { - "type": "file", - "description": "Log output redirected to a text file", - "pattern": "log.txt", - "ontologies": [ + }, + { + "name": "gatk4_collectsvevidence", + "path": "modules/nf-core/gatk4/collectsvevidence/meta.yml", + "type": "module", + "meta": { + "name": "gatk4_collectsvevidence", + "description": "Gathers paired-end and split read evidence files for use in the GATK-SV pipeline. Output files are a file containing the location of and orientation of read pairs marked as discordant, and a file containing the clipping location of all soft clipped reads and the orientation of the clipping.", + "keywords": ["gatk4", "collectsvevidence", "structural variants", "metrics"], + "tools": [ + { + "gatk4": { + "description": "Genome Analysis Toolkit (GATK4)", + "homepage": "https://gatk.broadinstitute.org/hc/en-us", + "tool_dev_url": "https://github.com/broadinstitute/gatk", + "doi": "10.1158/1538-7445.AM2017-3590", + "licence": ["BSD-3-clause"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}", + "ontologies": [] + } + }, + { + "input_index": { + "type": "file", + "description": "Index of the BAM/CRAM/SAM file", + "pattern": "*.{bai,crai,sai}", + "ontologies": [] + } + }, + { + "site_depth_vcf": { + "type": "file", + "description": "Optional - input VCF of SNPs marking loci for site depths, needed for the site depths output", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + }, + { + "site_depth_vcf_tbi": { + "type": "file", + "description": "Optional - input VCF TBI of SNPs marking loci for site depths, needed for the site depths output", + "pattern": "*.vcf.gz.tbi", + "ontologies": [] + } + } + ], + { + "fasta": { + "type": "file", + "description": "Optional - reference FASTA file needed when the input is a CRAM file", + "pattern": "*.{fasta,fa}", + "ontologies": [] + } + }, { - "edam": "http://edamontology.org/data_1678" + "fasta_fai": { + "type": "file", + "description": "Optional - index of the reference FASTA file needed when the input is a CRAM file", + "pattern": "*.fai", + "ontologies": [] + } }, { - "edam": "http://edamontology.org/format_2330" + "dict": { + "type": "file", + "description": "Optional - sequence dictionary of the reference FASTA file needed when the input is a CRAM file", + "pattern": "*.dict", + "ontologies": [] + } } - ] - } - } - ] - ], - "versions_fastcov": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "fastcov": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "0.1.3": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "fastcov": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "0.1.3": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@davidfischer" - ], - "maintainers": [ - "@davidfischer" - ] - } - }, - { - "name": "fastk_fastk", - "path": "modules/nf-core/fastk/fastk/meta.yml", - "type": "module", - "meta": { - "name": "fastk_fastk", - "description": "A fast K-mer counter for high-fidelity shotgun datasets", - "keywords": [ - "k-mer", - "count", - "histogram" - ], - "tools": [ - { - "fastk": { - "description": "A fast K-mer counter for high-fidelity shotgun datasets", - "homepage": "https://github.com/thegenemyers/FASTK", - "tool_dev_url": "https://github.com/thegenemyers/FASTK", - "license": [ - "https://github.com/thegenemyers/FASTK/blob/master/LICENSE" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FASTA, FASTQ, SAM, BAM or CRAM files. All must be of the same type.\n", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - }, - { - "edam": "http://edamontology.org/format_2545" - }, - { - "edam": "http://edamontology.org/format_2573" - }, - { - "edam": "http://edamontology.org/format_2572" - }, - { - "edam": "http://edamontology.org/format_3462" - } - ] - } - } - ] - ], - "output": { - "hist": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.hist": { - "type": "file", - "description": "Histogram of k-mers", - "pattern": "*.hist", - "ontologies": [] - } - } - ] - ], - "ktab": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.ktab*": { - "type": "file", - "description": "A sorted table of all canonical k‑mers along with their counts.", - "pattern": "*.ktab*", - "ontologies": [] - } - } - ] - ], - "prof": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.{prof,pidx}*": { - "type": "file", - "description": "A k‑mer count profile of each sequence in the input data set.", - "pattern": "*.{prof,pidx}*", - "ontologies": [] - } - } - ] - ], - "versions_fastk": [ - [ - { - "${task.process}": { - "type": "string", - "description": "Name of the process" - } - }, - { - "fastk": { - "type": "string", - "description": "Name of the tool" - } - }, - { - "1.2": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.log": { - "type": "file", - "description": "FastK command stdout/stderr log file", - "pattern": "*.log", - "ontologies": [] - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "Name of the process" - } - }, - { - "fastk": { - "type": "string", - "description": "Name of the tool" - } - }, - { - "1.2": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@mahesh-panchal" - ], - "maintainers": [ - "@mahesh-panchal", - "@gallvp" - ] - } - }, - { - "name": "fastk_histex", - "path": "modules/nf-core/fastk/histex/meta.yml", - "type": "module", - "meta": { - "name": "fastk_histex", - "description": "A fast K-mer counter for high-fidelity shotgun datasets", - "keywords": [ - "k-mer", - "histogram", - "fastk" - ], - "tools": [ - { - "fastk": { - "description": "A fast K-mer counter for high-fidelity shotgun datasets", - "homepage": "https://github.com/thegenemyers/FASTK", - "tool_dev_url": "https://github.com/thegenemyers/FASTK", - "license": [ - "https://github.com/thegenemyers/FASTK/blob/master/LICENSE" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "histogram": { - "type": "file", - "description": "A FastK histogram file", - "pattern": "*.hist", - "ontologies": [] - } - } - ] - ], - "output": { - "hist": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.hist.txt": { - "type": "file", - "description": "A formatted histogram file", - "pattern": "*.hist", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_fastk": [ - [ - { - "${task.process}": { - "type": "string", - "description": "Name of the process" - } - }, - { - "fastk": { - "type": "string", - "description": "Name of the tool" - } - }, - { - "1.2": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "Name of the process" - } - }, - { - "fastk": { - "type": "string", - "description": "Name of the tool" - } - }, - { - "1.2": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@mahesh-panchal" - ], - "maintainers": [ - "@mahesh-panchal" - ] - } - }, - { - "name": "fastk_merge", - "path": "modules/nf-core/fastk/merge/meta.yml", - "type": "module", - "meta": { - "name": "fastk_merge", - "description": "A tool to merge FastK histograms", - "keywords": [ - "merge", - "k-mer", - "histogram", - "fastk" - ], - "tools": [ - { - "fastk": { - "description": "A fast K-mer counter for high-fidelity shotgun datasets", - "homepage": "https://github.com/thegenemyers/FASTK", - "tool_dev_url": "https://github.com/thegenemyers/FASTK", - "license": [ - "https://github.com/thegenemyers/FASTK/blob/master/LICENSE" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "hist": { - "type": "file", - "description": "FastK histogram file", - "ontologies": [] - } - }, - { - "ktab": { - "type": "file", - "description": "FastK ktab file", - "ontologies": [] - } - }, - { - "prof": { - "type": "file", - "description": "FastK prof file", - "ontologies": [] - } - } - ] - ], - "output": { - "hist": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.hist": { - "type": "file", - "description": "FastK histogram file", - "pattern": "*.hist", - "ontologies": [] - } - } - ] - ], - "ktab": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.ktab*": { - "type": "file", - "description": "FastK ktab file", - "pattern": "*.ktab" - } - } - ] - ], - "prof": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.{prof,pidx}*": { - "type": "file", - "description": "FastK prof file", - "pattern": "*.{prof,pidx}" - } - } - ] - ], - "versions_fastk": [ - [ - { - "${task.process}": { - "type": "string", - "description": "Name of the process" - } - }, - { - "fastk": { - "type": "string", - "description": "Name of the tool" - } - }, - { - "1.2": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "Name of the process" - } - }, - { - "fastk": { - "type": "string", - "description": "Name of the tool" - } - }, - { - "1.2": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@mahesh-panchal" - ], - "maintainers": [ - "@mahesh-panchal" - ] - } - }, - { - "name": "fastme", - "path": "modules/nf-core/fastme/meta.yml", - "type": "module", - "meta": { - "name": "fastme", - "description": "Distance-based phylogeny with FastME", - "keywords": [ - "phylogenetics", - "newick", - "minimum_evolution", - "distance-based" - ], - "tools": [ - { - "fastme": { - "description": "A comprehensive, accurate and fast distance-based phylogeny inference program.", - "homepage": "http://www.atgc-montpellier.fr/fastme", - "documentation": "http://www.atgc-montpellier.fr/fastme/usersguide.php", - "tool_dev_url": "https://gite.lirmm.fr/atgc/FastME/", - "doi": "10.1093/molbev/msv150", - "licence": [ - "GPL v3" - ], - "args_id": "$args", - "identifier": "biotools:fastme" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "A Groovy map containing sample information,\ne.g. [ id: \"test\" ]\n" - } - }, - { - "infile": { - "type": "file", - "description": "MSA or distance matrix in Phylip format", - "pattern": "*", - "ontologies": [] - } - }, - { - "initial_tree": { - "type": "file", - "description": "Initial tree", - "ontologies": [] - } - } - ] - ], - "output": { - "nwk": [ - [ - { - "meta": { - "type": "map", - "description": "A Groovy map containing sample information" - } - }, - { - "*.nwk": { - "type": "file", - "description": "Final phylogeny in Newick format", - "pattern": "*.nwk", - "ontologies": [] - } - } - ] - ], - "stats": [ - [ - { - "meta": { - "type": "map", - "description": "A Groovy map containing sample information" - } - }, - { - "*_stat.txt": { - "type": "file", - "description": "A text file with the statistics of the phylogeny", - "pattern": "*_stat.txt", - "ontologies": [] - } - } - ] - ], - "matrix": [ - [ - { - "meta": { - "type": "map", - "description": "A Groovy map containing sample information" - } - }, - { - "*.matrix.phy": { - "type": "file", - "description": "Optional; the distance matrix in Phylip matrix format; it is generated if the -O option is passed in ext.args, although the provided file name will be overwritten", - "pattern": "*.matrix.phy", - "ontologies": [] - } - } - ] - ], - "bootstrap": [ - [ - { - "meta": { - "type": "map", - "description": "A Groovy map containing sample information" - } - }, - { - "*.bootstrap": { - "type": "file", - "description": "A file containing all bootstrap trees in Newick format; it is generated if the -B option is passed in ext.args (and bootstrap is used), although the provided file name will be overwritten", - "pattern": "*.bootstrap", - "ontologies": [] - } - } - ] - ], - "versions_fastme": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "fastme": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "fastme --version |& sed '1!d ; s/FastME //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "fastme": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "fastme --version |& sed '1!d ; s/FastME //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@itrujnara" - ], - "maintainers": [ - "@itrujnara" - ] - } - }, - { - "name": "fastp", - "path": "modules/nf-core/fastp/meta.yml", - "type": "module", - "meta": { - "name": "fastp", - "description": "Perform adapter/quality trimming on sequencing reads", - "keywords": [ - "trimming", - "quality control", - "fastq" - ], - "tools": [ - { - "fastp": { - "description": "A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.\n", - "documentation": "https://github.com/OpenGene/fastp", - "doi": "10.1093/bioinformatics/bty560", - "licence": [ - "MIT" - ], - "identifier": "biotools:fastp" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information. Use 'single_end: true' to specify single ended or interleaved FASTQs. Use 'single_end: false' for paired-end reads.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively. If you wish to run interleaved paired-end data, supply as single-end data\nbut with `--interleaved_in` in your `modules.conf`'s `ext.args` for the module.\n", - "ontologies": [] - } - }, - { - "adapter_fasta": { - "type": "file", - "description": "File in FASTA format containing possible adapters to remove.", - "pattern": "*.{fasta,fna,fas,fa}", - "ontologies": [] - } - } - ], - { - "discard_trimmed_pass": { - "type": "boolean", - "description": "Specify true to not write any reads that pass trimming thresholds.\nThis can be used to use fastp for the output report only.\n" - } - }, - { - "save_trimmed_fail": { - "type": "boolean", - "description": "Specify true to save files that failed to pass trimming thresholds ending in `*.fail.fastq.gz`" - } - }, - { - "save_merged": { - "type": "boolean", - "description": "Specify true to save all merged reads to a file ending in `*.merged.fastq.gz`" + ], + "output": { + "split_read_evidence": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.sr.txt.gz": { + "type": "file", + "description": "Output file for split read evidence", + "pattern": "*.sr.txt.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "split_read_evidence_index": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.sr.txt.gz.tbi": { + "type": "file", + "description": "Index of the output file for split read evidence", + "pattern": "*.sr.txt.gz.tbi", + "ontologies": [] + } + } + ] + ], + "paired_end_evidence": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.pe.txt.gz": { + "type": "file", + "description": "Output file for paired end evidence", + "pattern": "*.pe.txt.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "paired_end_evidence_index": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.pe.txt.gz.tbi": { + "type": "file", + "description": "Index of the output file for paired end evidence", + "pattern": "*.pe.txt.gz.tbi", + "ontologies": [] + } + } + ] + ], + "site_depths": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.sd.txt.gz": { + "type": "file", + "description": "Output file for site depths", + "pattern": "*.sd.txt.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "site_depths_index": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.sd.txt.gz.tbi": { + "type": "file", + "description": "Index of the output file for site depths", + "pattern": "*.sd.txt.gz.tbi", + "ontologies": [] + } + } + ] + ], + "versions_gatk4": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@nvnieuwk"], + "maintainers": ["@nvnieuwk"] } - } - ], - "output": { - "reads": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.fastp.fastq.gz": { - "type": "file", - "description": "The trimmed/modified/unmerged fastq reads", - "pattern": "*fastp.fastq.gz", - "ontologies": [ + }, + { + "name": "gatk4_combinegvcfs", + "path": "modules/nf-core/gatk4/combinegvcfs/meta.yml", + "type": "module", + "meta": { + "name": "gatk4_combinegvcfs", + "description": "Combine per-sample gVCF files produced by HaplotypeCaller into a multi-sample gVCF file", + "keywords": ["gvcf", "gatk4", "vcf", "combinegvcfs", "short variant discovery"], + "tools": [ + { + "gatk4": { + "description": "Genome Analysis Toolkit (GATK4). Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.", + "homepage": "https://gatk.broadinstitute.org/hc/en-us", + "documentation": "https://gatk.broadinstitute.org/hc/en-us/articles/360037593911-CombineGVCFs", + "tool_dev_url": "https://github.com/broadinstitute/gatk", + "doi": "10.1158/1538-7445.AM2017-3590", + "licence": ["Apache-2.0"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "Compressed VCF files", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + }, + { + "vcf_idx": { + "type": "file", + "description": "VCF Index file", + "pattern": "*.vcf.gz.idx", + "ontologies": [] + } + } + ], { - "edam": "http://edamontology.org/format_1930" + "fasta": { + "type": "file", + "description": "The reference fasta file", + "pattern": "*.fasta", + "ontologies": [] + } + }, + { + "fai": { + "type": "file", + "description": "FASTA index file", + "pattern": "*.fasta.fai", + "ontologies": [] + } }, { - "edam": "http://edamontology.org/format_3989" + "dict": { + "type": "file", + "description": "FASTA dictionary file", + "pattern": "*.dict", + "ontologies": [] + } } - ] + ], + "output": { + "combined_gvcf": [ + [ + { + "meta": { + "type": "file", + "description": "Compressed Combined GVCF file", + "pattern": "*.combined.g.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + }, + { + "*.combined.g.vcf.gz": { + "type": "file", + "description": "Compressed Combined GVCF file", + "pattern": "*.combined.g.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "versions_gatk4": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@sateeshperi", "@mjcipriano", "@hseabolt", "@maxulysse"], + "maintainers": ["@sateeshperi", "@mjcipriano", "@hseabolt", "@maxulysse"] + }, + "pipelines": [ + { + "name": "rnavar", + "version": "1.2.3" } - } - ] - ], - "json": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.json": { - "type": "file", - "description": "Results in JSON format", - "pattern": "*.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "html": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.html": { - "type": "file", - "description": "Results in HTML format", - "pattern": "*.html", - "ontologies": [] - } - } ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.log": { - "type": "file", - "description": "fastq log file", - "pattern": "*.log", - "ontologies": [] - } - } - ] - ], - "reads_fail": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.fail.fastq.gz": { - "type": "file", - "description": "Reads the failed the preprocessing", - "pattern": "*fail.fastq.gz", - "ontologies": [ + }, + { + "name": "gatk4_composestrtablefile", + "path": "modules/nf-core/gatk4/composestrtablefile/meta.yml", + "type": "module", + "meta": { + "name": "gatk4_composestrtablefile", + "description": "This tool looks for low-complexity STR sequences along the reference that are later used to estimate the Dragstr model during single sample auto calibration CalibrateDragstrModel.", + "keywords": ["composestrtablefile", "dragstr", "gatk4"], + "tools": [ + { + "gatk4": { + "description": "Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools\nwith a primary focus on variant discovery and genotyping. Its powerful processing engine\nand high-performance computing features make it capable of taking on projects of any size.\n", + "homepage": "https://gatk.broadinstitute.org/hc/en-us", + "documentation": "https://gatk.broadinstitute.org/hc/en-us/articles/4405451249819-ComposeSTRTableFile", + "doi": "10.1158/1538-7445.AM2017-3590", + "licence": ["Apache-2.0"], + "identifier": "" + } + } + ], + "input": [ { - "edam": "http://edamontology.org/format_1930" + "fasta": { + "type": "file", + "description": "FASTA reference file", + "pattern": "*.{fasta,fa}", + "ontologies": [] + } + }, + { + "fasta_fai": { + "type": "file", + "description": "index of the FASTA reference file", + "pattern": "*.fai", + "ontologies": [] + } }, { - "edam": "http://edamontology.org/format_3989" + "dict": { + "type": "file", + "description": "Sequence dictionary of the FASTA reference file", + "pattern": "*.dict", + "ontologies": [] + } } - ] - } - } - ] - ], - "reads_merged": [ - [ - { - "meta": { - "type": "map", 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Its powerful processing engine\nand high-performance computing features make it capable of taking on projects of any size.\n", + "homepage": "https://gatk.broadinstitute.org/hc/en-us", + "documentation": "https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s", + "doi": "10.1158/1538-7445.AM2017-3590", + "tool_dev_url": "https://github.com/broadinstitute/gatk", + "licence": ["Apache-2.0"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "counts": { + "type": "file", + "description": "Read counts in hdf5 or tsv format.", + "pattern": "*.{hdf5,tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "pon": { + "type": "file", + "description": "Panel of normals file hdf5 or tsv format.", + "pattern": "*.{hdf5}", + "ontologies": [] + } + } + ] + ], + "output": { + "standardized": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*_standardizedCR.tsv": { + "type": "file", + "description": "Standardized copy ratios file.", + "pattern": "*.{tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "denoised": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*_denoisedCR.tsv": { + "type": "file", + "description": "Denoised copy ratios file", + "pattern": "*.{tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_gatk4": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@ramprasadn"], + "maintainers": ["@ramprasadn"] + }, + "pipelines": [ + { + "name": "raredisease", + "version": "3.0.0" + } + ] }, { - "name": "sarek", - "version": "3.8.1" + "name": "gatk4_determinegermlinecontigploidy", + "path": "modules/nf-core/gatk4/determinegermlinecontigploidy/meta.yml", + "type": "module", + "meta": { + "name": "gatk4_determinegermlinecontigploidy", + "description": "Determines the baseline contig ploidy for germline samples given counts data", + "keywords": ["copy number", "counts", "determinegermlinecontigploidy", "gatk4"], + "tools": [ + { + "gatk4": { + "description": "Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools\nwith a primary focus on variant discovery and genotyping. Its powerful processing engine\nand high-performance computing features make it capable of taking on projects of any size.\n", + "homepage": "https://gatk.broadinstitute.org/hc/en-us", + "documentation": "https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s", + "doi": "10.1158/1538-7445.AM2017-3590", + "licence": ["Apache-2.0"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "counts": { + "type": "file", + "description": "One or more count TSV files created with gatk/collectreadcounts", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, + { + "bed": { + "type": "file", + "description": "Optional - A bed file containing the intervals to include in the process", + "pattern": "*.bed", + "ontologies": [] + } + }, + { + "exclude_beds": { + "type": "file", + "description": "Optional - One or more bed files containing intervals to exclude from the process", + "pattern": "*.bed", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "ploidy_model": { + "type": "directory", + "description": "Optional - A folder containing the ploidy model.\nWhen a model is supplied to tool will run in CASE mode.\npattern: '*-model/'\n" + } + } + ], + { + "contig_ploidy_table": { + "type": "file", + "description": "The contig ploidy priors table", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + "output": { + "calls": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}-calls": { + "type": "directory", + "description": "A folder containing the calls from the input files", + "pattern": "*-calls/" + } + } + ] + ], + "model": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}-model": { + "type": "directory", + "description": "A folder containing the model from the input files.\nThis will only be created in COHORT mode (when no model is supplied to the process).\n", + "pattern": "*-model/" + } + } + ] + ], + "versions_gatk4": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@nvnieuwk"], + "maintainers": ["@nvnieuwk"] + }, + "pipelines": [ + { + "name": "createpanelrefs", + "version": "dev" + }, + { + "name": "raredisease", + "version": "3.0.0" + } + ] }, { - "name": "smrnaseq", - "version": "2.4.1" + "name": "gatk4_estimatelibrarycomplexity", + "path": "modules/nf-core/gatk4/estimatelibrarycomplexity/meta.yml", + "type": "module", + "meta": { + "name": "gatk4_estimatelibrarycomplexity", + "description": "Estimates the numbers of unique molecules in a sequencing library.", + "keywords": ["duplication metrics", "estimatelibrarycomplexity", "gatk4", "reporting"], + "tools": [ + { + "gatk4": { + "description": "Genome Analysis Toolkit (GATK4)", + "homepage": "https://gatk.broadinstitute.org/hc/en-us", + "documentation": "https://gatk.broadinstitute.org/hc/en-us", + "tool_dev_url": "https://github.com/broadinstitute/gatk", + "doi": "10.1158/1538-7445.AM2017-3590", + "licence": ["Apache-2.0"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}", + "ontologies": [] + } + } + ], + { + "fasta": { + "type": "file", + "description": "The reference fasta file", + "pattern": "*.fasta", + "ontologies": [] + } + }, + { + "fai": { + "type": "file", + "description": "Index of reference fasta file", + "pattern": "fasta.fai", + "ontologies": [] + } + }, + { + "dict": { + "type": "file", + "description": "GATK sequence dictionary", + "pattern": "*.dict", + "ontologies": [] + } + } + ], + "output": { + "metrics": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.metrics": { + "type": "file", + "description": "File containing metrics on the input files", + "pattern": "*.{metrics}", + "ontologies": [] + } + } + ] + ], + "versions_gatk4": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@FriederikeHanssen", "@maxulysse"], + "maintainers": ["@FriederikeHanssen", "@maxulysse"] + }, + "pipelines": [ + { + "name": "sarek", + "version": "3.8.1" + } + ] }, { - "name": "taxprofiler", - "version": "2.0.0" + "name": "gatk4_fastqtosam", + "path": "modules/nf-core/gatk4/fastqtosam/meta.yml", + "type": "module", + "meta": { + "name": "gatk4_fastqtosam", + "description": "Converts FastQ file to SAM/BAM format", + "keywords": ["bam", "convert", "fastq", "gatk4"], + "tools": [ + { + "gatk4": { + "description": "Genome Analysis Toolkit (GATK4) Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.", + "homepage": "https://gatk.broadinstitute.org/hc/en-us", + "documentation": "https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s", + "tool_dev_url": "https://github.com/broadinstitute/gatk", + "doi": "10.1158/1538-7445.AM2017-3590", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively.", + "pattern": "*.fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Converted BAM file", + "pattern": "*.bam", + "ontologies": [] + } + } + ] + ], + "versions_gatk4": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@ntoda03"], + "maintainers": ["@ntoda03"] + } }, { - "name": "viralmetagenome", - "version": "1.1.1" + "name": "gatk4_filterintervals", + "path": "modules/nf-core/gatk4/filterintervals/meta.yml", + "type": "module", + "meta": { + "name": "gatk4_filterintervals", + "description": "Filters intervals based on annotations and/or count statistics.", + "keywords": ["filterintervals", "gatk4", "interval_list"], + "tools": [ + { + "gatk4": { + "description": "Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.", + "homepage": "https://gatk.broadinstitute.org/hc/en-us", + "documentation": "https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s", + "doi": "10.1158/1538-7445.AM2017-3590", + "licence": ["Apache-2.0"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "intervals": { + "type": "file", + "description": "Processed interval list file (processed_intervals.interval_list)", + "pattern": "*.interval_list", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "read_counts": { + "type": "file", + "description": "Read counts input file", + "pattern": "*.{tsv, hdf5}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "annotated_intervals": { + "type": "file", + "description": "Annotated intervals TSV file (annotated_intervals.tsv).", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "output": { + "interval_list": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.interval_list": { + "type": "file", + "description": "Filtered interval list file", + "pattern": "*.interval_list", + "ontologies": [] + } + } + ] + ], + "versions_gatk4": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@ryanjameskennedy", "@ViktorHy"], + "maintainers": ["@ryanjameskennedy", "@ViktorHy"] + }, + "pipelines": [ + { + "name": "createpanelrefs", + "version": "dev" + } + ] }, { - "name": "viralrecon", - "version": "3.0.0" - } - ] - }, - { - "name": "fastplong", - "path": "modules/nf-core/fastplong/meta.yml", - "type": "module", - "meta": { - "name": "fastplong", - "description": "Perform adapter/quality trimming and QC on long sequencing reads (ONT, PacBio, etc.)", - "keywords": [ - "trimming", - "quality control", - "fastq", - "long reads" - ], - "tools": [ - { - "fastplong": { - "description": "Ultra-fast preprocessing and quality control for long-read sequencing data.", - "homepage": "https://github.com/OpenGene/fastplong/blob/v0.4.1/README.md", - "documentation": "https://github.com/OpenGene/fastplong/blob/v0.4.1/README.md", - "tool_dev_url": "https://github.com/OpenGene/fastplong", - "doi": "10.1002/imt2.107", - "licence": [ - "MIT" - ], - "identifier": "biotools:fastplong" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information. Use 'single_end: true' for single-end reads.\ne.g. [ id:'test', single_end:true ]\n" - } + "name": "gatk4_filtermutectcalls", + "path": "modules/nf-core/gatk4/filtermutectcalls/meta.yml", + "type": "module", + "meta": { + "name": "gatk4_filtermutectcalls", + "description": "Filters the raw output of mutect2, can optionally use outputs of calculatecontamination and learnreadorientationmodel to improve filtering.\n", + "keywords": ["filtermutectcalls", "filter", "gatk4", "mutect2", "vcf"], + "tools": [ + { + "gatk4": { + "description": "Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools\nwith a primary focus on variant discovery and genotyping. Its powerful processing engine\nand high-performance computing features make it capable of taking on projects of any size.\n", + "homepage": "https://gatk.broadinstitute.org/hc/en-us", + "documentation": "https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s", + "doi": "10.1158/1538-7445.AM2017-3590", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "compressed vcf file of mutect2calls", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + }, + { + "vcf_tbi": { + "type": "file", + "description": "Tabix index of vcf file", + "pattern": "*vcf.gz.tbi", + "ontologies": [] + } + }, + { + "stats": { + "type": "file", + "description": "Stats file that pairs with output vcf file", + "pattern": "*vcf.gz.stats", + "ontologies": [] + } + }, + { + "orientationbias": { + "type": "file", + "description": "files containing artifact priors for input vcf. Optional input.", + "pattern": "*.artifact-prior.tar.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + }, + { + "segmentation": { + "type": "file", + "description": "tables containing segmentation information for input vcf. Optional input.", + "pattern": "*.segmentation.table", + "ontologies": [] + } + }, + { + "table": { + "type": "file", + "description": "table(s) containing contamination data for input vcf. Optional input, takes priority over estimate.", + "pattern": "*.contamination.table", + "ontologies": [] + } + }, + { + "estimate": { + "type": "float", + "description": "estimation of contamination value as a double. Optional input, will only be used if table is not specified." + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The reference fasta file", + "pattern": "*.fasta", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Index of reference fasta file", + "pattern": "*.fasta.fai", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "dict": { + "type": "file", + "description": "GATK sequence dictionary", + "pattern": "*.dict", + "ontologies": [] + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "file", + "description": "file containing filtered mutect2 calls.", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "file containing filtered mutect2 calls.", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "tbi": [ + [ + { + "meta": { + "type": "file", + "description": "file containing filtered mutect2 calls.", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + }, + { + "*.vcf.gz.tbi": { + "type": "file", + "description": "tbi file that pairs with vcf.", + "pattern": "*.vcf.gz.tbi", + "ontologies": [] + } + } + ] + ], + "stats": [ + [ + { + "meta": { + "type": "file", + "description": "file containing filtered mutect2 calls.", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + }, + { + "*.filteringStats.tsv": { + "type": "file", + "description": "file containing statistics of the filtermutectcalls run.", + "pattern": "*.filteringStats.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_gatk4": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@GCJMackenzie", "@maxulysse", "@ramprasadn"], + "maintainers": ["@GCJMackenzie", "@maxulysse", "@ramprasadn"] }, - { - "reads": { - "type": "file", - "description": "Input FASTQ file. Gzip-compressed files are supported.\n", - "pattern": "*.{fastq.gz,fastq}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ], - { - "adapter_fasta": { - "type": "file", - "description": "Optional FASTA file containing adapter sequences to trim.\n", - "pattern": "*.{fasta,fa,fna}", - "ontologies": [] - } - }, - { - "discard_trimmed_pass": { - "type": "boolean", - "description": "If true, no reads that pass trimming thresholds will be written. Only reports will be generated.\n" - } - }, - { - "save_trimmed_fail": { - "type": "boolean", - "description": "If true, reads that fail filtering will be saved to a file ending in `*.fail.fastq.gz`.\n" - } - } - ], - "output": { - "reads": [ - [ - { - "meta": { - "type": "map", - "description": "Sample information map" + "pipelines": [ + { + "name": "raredisease", + "version": "3.0.0" + }, + { + "name": "rnadnavar", + "version": "dev" + }, + { + "name": "sarek", + "version": "3.8.1" + }, + { + "name": "variantcatalogue", + "version": "dev" } - }, - { - "*.fastplong.fastq.gz": { - "type": "file", - "description": "Trimmed and filtered reads", - "pattern": "*fastplong.fastq.gz", - "ontologies": [ + ] + }, + { + "name": "gatk4_filtervarianttranches", + "path": "modules/nf-core/gatk4/filtervarianttranches/meta.yml", + "type": "module", + "meta": { + "name": "gatk4_filtervarianttranches", + "description": "Apply tranche filtering", + "keywords": ["filtervarianttranches", "gatk4", "tranche filtering"], + "tools": [ + { + "gatk4": { + "description": "Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools\nwith a primary focus on variant discovery and genotyping. Its powerful processing engine\nand high-performance computing features make it capable of taking on projects of any size.\n", + "homepage": "https://gatk.broadinstitute.org/hc/en-us", + "documentation": "https://gatk.broadinstitute.org/hc/en-us/articles/360051308071-FilterVariantTranches", + "doi": "10.1158/1538-7445.AM2017-3590", + "licence": ["Apache-2.0"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "a VCF file containing variants, must have info key:CNN_2D", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + }, + { + "tbi": { + "type": "file", + "description": "tbi file matching with -vcf", + "pattern": "*.vcf.gz.tbi", + "ontologies": [] + } + }, + { + "intervals": { + "type": "file", + "description": "Intervals", + "ontologies": [] + } + } + ], { - "edam": "http://edamontology.org/format_1930" + "resources": { + "type": "list", + "description": "resource A VCF containing known SNP and or INDEL sites. Can be supplied as many times as necessary", + "pattern": "*.vcf.gz" + } }, { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "json": [ - [ - { - "meta": { - "type": "map", - "description": "Sample information map" - } - }, - { - "*.json": { - "type": "file", - "description": "QC report in JSON format", - "pattern": "*.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "html": [ - [ - { - "meta": { - "type": "map", - "description": "Sample information map" - } - }, - { - "*.html": { - "type": "file", - "description": "QC report in HTML format", - "pattern": "*.html", - "ontologies": [] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Sample information map" - } - }, - { - "*.log": { - "type": "file", - "description": "Log file generated during trimming", - "pattern": "*.log", - "ontologies": [] - } - } - ] - ], - "reads_fail": [ - [ - { - "meta": { - "type": "map", - "description": "Sample information map" - } - }, - { - "*.fail.fastq.gz": { - "type": "file", - "description": "Reads that failed quality/trimming filters", - "pattern": "*fail.fastq.gz", - "ontologies": [ + "resources_index": { + "type": "list", + "description": "Index of resource VCF containing known SNP and or INDEL sites. Can be supplied as many times as necessary", + "pattern": "*.vcf.gz" + } + }, + { + "fasta": { + "type": "file", + "description": "The reference fasta file", + "pattern": "*.fasta", + "ontologies": [] + } + }, { - "edam": "http://edamontology.org/format_1930" + "fai": { + "type": "file", + "description": "Index of reference fasta file", + "pattern": "fasta.fai", + "ontologies": [] + } }, { - "edam": "http://edamontology.org/format_3989" + "dict": { + "type": "file", + "description": "GATK sequence dictionary", + "pattern": ".dict", + "ontologies": [] + } } - ] - } - } - ] - ], - "versions_fastplong": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "fastplong": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "fastplong --version 2>&1 | sed -e \"s/fastplong //g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "fastplong": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "fastplong --version 2>&1 | sed -e \"s/fastplong //g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@Lupphes", - "@eit-maxlcummins" - ], - "maintainers": [ - "@Lupphes" - ] - } - }, - { - "name": "fastqc", - "path": "modules/nf-core/fastqc/meta.yml", - "type": "module", - "meta": { - "name": "fastqc", - "description": "Run FastQC on sequenced reads", - "keywords": [ - "quality control", - "qc", - "adapters", - "fastq" - ], - "tools": [ - { - "fastqc": { - "description": "FastQC gives general quality metrics about your reads.\nIt provides information about the quality score distribution\nacross your reads, the per base sequence content (%A/C/G/T).\n\nYou get information about adapter contamination and other\noverrepresented sequences.\n", - "homepage": "https://www.bioinformatics.babraham.ac.uk/projects/fastqc/", - "documentation": "https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/", - "licence": [ - "GPL-2.0-only" - ], - "identifier": "biotools:fastqc" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "VCF file", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz.tbi": { + "type": "file", + "description": "VCF index file", + "pattern": "*.vcf.gz.tbi", + "ontologies": [] + } + } + ] + ], + "versions_gatk4": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@FriederikeHanssen"], + "maintainers": ["@FriederikeHanssen"] }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", - "ontologies": [] - } - } - ] - ], - "output": { - "html": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.html": { - "type": "file", - "description": "FastQC report", - "pattern": "*_{fastqc.html}", - "ontologies": [] - } - } - ] - ], - "zip": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.zip": { - "type": "file", - "description": "FastQC report archive", - "pattern": "*_{fastqc.zip}", - "ontologies": [] - } - } - ] - ], - "versions_fastqc": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "fastqc": { - "type": "string", - "description": "The tool name" - } - }, - { - "fastqc --version | sed \"/FastQC v/!d; s/.*v//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "fastqc": { - "type": "string", - "description": "The tool name" - } - }, - { - "fastqc --version | sed \"/FastQC v/!d; s/.*v//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "sarek", + "version": "3.8.1" + } ] - ] - }, - "authors": [ - "@drpatelh", - "@grst", - "@ewels", - "@FelixKrueger" - ], - "maintainers": [ - "@drpatelh", - "@grst", - "@ewels", - "@FelixKrueger" - ], - "containers": { - "docker": { - "linux/arm64": { - "name": "community.wave.seqera.io/library/fastqc:0.12.1--e455e32f745abe68", - "build_id": "bd-e455e32f745abe68_1", - "scan_id": "sc-f102f736465af88c_1" - 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} - } - } - }, - "pipelines": [ - { - "name": "abotyper", - "version": "dev" - }, - { - "name": "airrflow", - "version": "5.0.0" - }, - { - "name": "alleleexpression", - "version": "dev" - }, - { - "name": "ampliseq", - "version": "2.17.0" - }, - { - "name": "atacseq", - "version": "2.1.2" - }, - { - "name": "bacass", - "version": "2.6.0" - }, - { - "name": "bamtofastq", - "version": "2.2.1" - }, - { - "name": "callingcards", - "version": "1.0.0" - }, - { - "name": "chipseq", - "version": "2.1.0" - }, - { - "name": "circdna", - "version": "1.1.0" - }, - { - "name": "circrna", - "version": "dev" - }, - { - "name": "coproid", - "version": "2.0.1" - }, - { - "name": "crisprseq", - "version": "2.3.0" }, { - "name": "cutandrun", - "version": "3.2.2" - }, - { - "name": "dartseq", - "version": "dev" - }, - { - "name": "deepmutscan", - "version": "dev" - }, - { - "name": "demo", - "version": "1.1.0" + "name": "gatk4_gatherbqsrreports", + "path": "modules/nf-core/gatk4/gatherbqsrreports/meta.yml", + "type": "module", + "meta": { + "name": "gatk4_gatherbqsrreports", + "description": "Gathers scattered BQSR recalibration reports into a single file", + "keywords": ["base quality score recalibration", "bqsr", "gatherbqsrreports", "gatk4"], + "tools": [ + { + "gatk4": { + "description": "Genome Analysis Toolkit (GATK4)", + "homepage": "https://gatk.broadinstitute.org/hc/en-us", + "documentation": "https://gatk.broadinstitute.org/hc/en-us", + "tool_dev_url": "https://github.com/broadinstitute/gatk", + "doi": "10.1158/1538-7445.AM2017-3590", + "licence": ["BSD-3-clause"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "table": { + "type": "file", + "description": "File(s) containing BQSR table(s)", + "pattern": "*.table", + "ontologies": [] + } + } + ] + ], + "output": { + "table": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.table": { + "type": "file", + "description": "File containing joined BQSR table", + "pattern": "*.table", + "ontologies": [] + } + } + ] + ], + "versions_gatk4": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@FriederikeHanssen"], + "maintainers": ["@FriederikeHanssen"] + }, + "pipelines": [ + { + "name": "genomicrelatedness", + "version": "dev" + }, + { + "name": "rnadnavar", + "version": "dev" + }, + { + "name": "sarek", + "version": "3.8.1" + } + ] }, { - "name": "demultiplex", - "version": "1.7.1" + "name": "gatk4_gatherpileupsummaries", + "path": "modules/nf-core/gatk4/gatherpileupsummaries/meta.yml", + "type": "module", + "meta": { + "name": "gatk4_gatherpileupsummaries", + "description": "write your description here", + "keywords": ["gatk4", "mpileup", "sort"], + "tools": [ + { + "gatk4": { + "description": "Genome Analysis Toolkit (GATK4)", + "homepage": "https://gatk.broadinstitute.org/hc/en-us", + "documentation": "https://gatk.broadinstitute.org/hc/en-us", + "tool_dev_url": "https://github.com/broadinstitute/gatk", + "doi": "10.1158/1538-7445.AM2017-3590", + "licence": ["BSD-3-clause"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "pileup": { + "type": "file", + "description": "Pileup files from gatk4/getpileupsummaries", + "pattern": "*.pileups.table", + "ontologies": [] + } + } + ], + { + "dict": { + "type": "file", + "description": "dictionary", + "ontologies": [] + } + } + ], + "output": { + "table": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.pileups.table": { + "type": "file", + "description": "pileup summaries table file", + "pattern": "*.pileups.table", + "ontologies": [] + } + } + ] + ], + "versions_gatk4": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@FriederikeHanssen", "@maxulysse"], + "maintainers": ["@FriederikeHanssen", "@maxulysse"] + }, + "pipelines": [ + { + "name": "rnadnavar", + "version": "dev" + }, + { + "name": "sarek", + "version": "3.8.1" + } + ] }, { - "name": "denovotranscript", - "version": "1.2.1" + "name": "gatk4_genomicsdbimport", + "path": "modules/nf-core/gatk4/genomicsdbimport/meta.yml", + "type": "module", + "meta": { + "name": "gatk4_genomicsdbimport", + "description": "merge GVCFs from multiple samples. For use in joint genotyping or somatic panel of normal creation.", + "keywords": ["gatk4", "genomicsdb", "genomicsdbimport", "jointgenotyping", "panelofnormalscreation"], + "tools": [ + { + "gatk4": { + "description": "Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools\nwith a primary focus on variant discovery and genotyping. Its powerful processing engine\nand high-performance computing features make it capable of taking on projects of any size.\n", + "homepage": "https://gatk.broadinstitute.org/hc/en-us", + "documentation": "https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s", + "doi": "10.1158/1538-7445.AM2017-3590", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "vcf": { + "type": "list", + "description": "either a list of vcf files to be used to create or update a genomicsdb, or a file that contains a map to vcf files to be used.", + "pattern": "*.vcf.gz" + } + }, + { + "tbi": { + "type": "list", + "description": "list of tbi files that match with the input vcf files", + "pattern": "*.vcf.gz_tbi" + } + }, + { + "interval_file": { + "type": "file", + "description": "file containing the intervals to be used when creating the genomicsdb", + "pattern": "*.interval_list", + "ontologies": [] + } + }, + { + "interval_value": { + "type": "string", + "description": "if an intervals file has not been specified, the value entered here will be used as an interval via the \"-L\" argument", + "pattern": "example: chr1:1000-10000" + } + }, + { + "wspace": { + "type": "file", + "description": "path to an existing genomicsdb to be used in update db mode or get intervals mode. This WILL NOT specify name of a new genomicsdb in create db mode.", + "pattern": "/path/to/existing/gendb", + "ontologies": [] + } + } + ], + { + "run_intlist": { + "type": "boolean", + "description": "Specify whether to run get interval list mode, this option cannot be specified at the same time as run_updatewspace.", + "pattern": "true/false" + } + }, + { + "run_updatewspace": { + "type": "boolean", + "description": "Specify whether to run update genomicsdb mode, this option takes priority over run_intlist.", + "pattern": "true/false" + } + }, + { + "input_map": { + "type": "boolean", + "description": "Specify whether the vcf input is providing a list of vcf file(s) or a single file containing a map of paths to vcf files to be used to create or update a genomicsdb.", + "pattern": "*.sample_map" + } + } + ], + "output": { + "genomicsdb": [ + [ + { + "meta": { + "type": "map", + "description": "A Groovy map containing sample information" + } + }, + { + "${prefix}": { + "type": "file", + "description": "genomicsdb", + "ontologies": [] + } + } + ] + ], + "updatedb": [ + [ + { + "meta": { + "type": "map", + "description": "A Groovy map containing sample information" + } + }, + { + "${updated_db}": { + "type": "file", + "description": "updated genomicsdb", + "ontologies": [] + } + } + ] + ], + "intervallist": [ + [ + { + "meta": { + "type": "map", + "description": "A Groovy map containing sample information" + } + }, + { + "*.interval_list": { + "type": "file", + "description": "File containing the intervals used to generate the genomicsdb, only created by get intervals mode.", + "pattern": "*.interval_list", + "ontologies": [] + } + } + ] + ], + "versions_gatk4": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@GCJMackenzie"], + "maintainers": ["@GCJMackenzie"] + }, + "pipelines": [ + { + "name": "createpanelrefs", + "version": "dev" + }, + { + "name": "genomicrelatedness", + "version": "dev" + }, + { + "name": "sarek", + "version": "3.8.1" + } + ] }, { - "name": "detaxizer", - "version": "1.3.0" + "name": "gatk4_genotypegvcfs", + "path": "modules/nf-core/gatk4/genotypegvcfs/meta.yml", + "type": "module", + "meta": { + "name": "gatk4_genotypegvcfs", + "description": "Perform joint genotyping on one or more samples pre-called with HaplotypeCaller.\n", + "keywords": ["gatk4", "genotype", "gvcf", "joint genotyping"], + "tools": [ + { + "gatk4": { + "description": "Genome Analysis Toolkit (GATK4)", + "homepage": "https://gatk.broadinstitute.org/hc/en-us", + "documentation": "https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s", + "tool_dev_url": "https://github.com/broadinstitute/gatk", + "doi": "10.1158/1538-7445.AM2017-3590", + "licence": ["BSD-3-clause"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "gVCF(.gz) file or a GenomicsDB\n", + "pattern": "*.{vcf,vcf.gz}", + "ontologies": [] + } + }, + { + "gvcf_index": { + "type": "file", + "description": "index of gvcf file, or empty when providing GenomicsDB\n", + "pattern": "*.{idx,tbi}", + "ontologies": [] + } + }, + { + "intervals": { + "type": "file", + "description": "Interval file with the genomic regions included in the library (optional)", + "ontologies": [] + } + }, + { + "intervals_index": { + "type": "file", + "description": "Interval index file (optional)", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing fasta information\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference fasta file", + "pattern": "*.fasta", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing fai information\ne.g. [ id:'test' ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Reference fasta index file", + "pattern": "*.fai", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing dict information\ne.g. [ id:'test' ]\n" + } + }, + { + "dict": { + "type": "file", + "description": "Reference fasta sequence dict file", + "pattern": "*.dict", + "ontologies": [] + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing dbsnp information\ne.g. [ id:'test' ]\n" + } + }, + { + "dbsnp": { + "type": "file", + "description": "dbSNP VCF file", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ], + [ + { + "meta6": { + "type": "map", + "description": "Groovy Map containing dbsnp tbi information\ne.g. [ id:'test' ]\n" + } + }, + { + "dbsnp_tbi": { + "type": "file", + "description": "dbSNP VCF index file", + "pattern": "*.tbi", + "ontologies": [] + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "Genotyped VCF file", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tbi": { + "type": "file", + "description": "Tbi index for VCF file", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "versions_gatk4": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@santiagorevale", "@maxulysse"], + "maintainers": ["@santiagorevale", "@maxulysse"] + }, + "pipelines": [ + { + "name": "genomicrelatedness", + "version": "dev" + }, + { + "name": "sarek", + "version": "3.8.1" + } + ] }, { - "name": "evexplorer", - "version": "dev" + "name": "gatk4_germlinecnvcaller", + "path": "modules/nf-core/gatk4/germlinecnvcaller/meta.yml", + "type": "module", + "meta": { + "name": "gatk4_germlinecnvcaller", + "description": "Calls copy-number variants in germline samples given their counts and the output of DetermineGermlineContigPloidy.", + "keywords": ["gatk", "germline contig ploidy", "germlinecnvcaller"], + "tools": [ + { + "gatk4": { + "description": "Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.", + "homepage": "https://gatk.broadinstitute.org/hc/en-us", + "documentation": "https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s", + "doi": "10.1158/1538-7445.AM2017-3590", + "licence": ["Apache-2.0"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "tsv": { + "type": "file", + "description": "One or more count TSV files created with gatk/collectreadcounts", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, + { + "intervals": { + "type": "file", + "description": "Optional - A bed file containing the intervals to include in the process", + "pattern": "*.bed", + "ontologies": [] + } + }, + { + "ploidy": { + "type": "directory", + "description": "Directory containing ploidy calls produced by determinegermlinecontigploidy case or cohort mode", + "pattern": "*-calls" + } + }, + { + "model": { + "type": "directory", + "description": "Optional - directory containing the model produced by germlinecnvcaller cohort mode", + "pattern": "*-cnv-model/*-model" + } + } + ] + ], + "output": { + "cohortcalls": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*-cnv-model/*-calls": { + "type": "directory", + "description": "Tar gzipped directory containing calls produced by germlinecnvcaller case mode", + "pattern": "*-cnv-model/*-calls" + } + } + ] + ], + "cohortmodel": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*-cnv-model/*-model": { + "type": "directory", + "description": "Optional - Tar gzipped directory containing the model produced by germlinecnvcaller cohort mode", + "pattern": "*-cnv-model/*-model" + } + } + ] + ], + "casecalls": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*-cnv-calls/*-calls": { + "type": "directory", + "description": "Tar gzipped directory containing calls produced by germlinecnvcaller case mode", + "pattern": "*-cnv-calls/*-calls" + } + } + ] + ], + "versions_gatk4": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@ryanjameskennedy", "@ViktorHy"], + "maintainers": ["@ryanjameskennedy", "@ViktorHy"] + }, + "pipelines": [ + { + "name": "createpanelrefs", + "version": "dev" + }, + { + "name": "raredisease", + "version": "3.0.0" + } + ] }, { - "name": "fastqrepair", - "version": "1.0.0" + "name": "gatk4_getpileupsummaries", + "path": "modules/nf-core/gatk4/getpileupsummaries/meta.yml", + "type": "module", + "meta": { + "name": "gatk4_getpileupsummaries", + "description": "Summarizes counts of reads that support reference, alternate and other alleles for given sites. Results can be used with CalculateContamination. Requires a common germline variant sites file, such as from gnomAD.\n", + "keywords": ["gatk4", "germlinevariantsites", "getpileupsumaries", "readcountssummary"], + "tools": [ + { + "gatk4": { + "description": "Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools\nwith a primary focus on variant discovery and genotyping. Its powerful processing engine\nand high-performance computing features make it capable of taking on projects of any size.\n", + "homepage": "https://gatk.broadinstitute.org/hc/en-us", + "documentation": "https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s", + "doi": "10.1158/1538-7445.AM2017-3590", + "licence": ["Apache-2.0"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM file to be summarised.", + "pattern": "*.{bam,cram}", + "ontologies": [] + } + }, + { + "index": { + "type": "file", + "description": "Index file for the input BAM/CRAM file.", + "pattern": "*.{bam.bai,cram.crai}", + "ontologies": [] + } + }, + { + "intervals": { + "type": "file", + "description": "File containing specified sites to be used for the summary. If this option is not specified, variants file is used instead automatically.", + "pattern": "*.interval_list", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The reference fasta file", + "pattern": "*.fasta", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Index of reference fasta file", + "pattern": "*.fasta.fai", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "dict": { + "type": "file", + "description": "GATK sequence dictionary", + "pattern": "*.dict", + "ontologies": [] + } + } + ], + { + "variants": { + "type": "file", + "description": "Population vcf of germline sequencing, containing allele fractions. Is also used as sites file if no separate sites file is specified.", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + }, + { + "variants_tbi": { + "type": "file", + "description": "Index file for the germline resource.", + "pattern": "*.vcf.gz.tbi", + "ontologies": [] + } + } + ], + "output": { + "table": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.pileups.table": { + "type": "file", + "description": "Table containing read counts for each site.", + "pattern": "*.pileups.table", + "ontologies": [] + } + } + ] + ], + "versions_gatk4": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@GCJMackenzie"], + "maintainers": ["@GCJMackenzie"] + }, + "pipelines": [ + { + "name": "rnadnavar", + "version": "dev" + }, + { + "name": "sarek", + "version": "3.8.1" + } + ] }, { - "name": "fastquorum", - "version": "1.2.0" - }, - { - "name": "funcprofiler", - "version": "dev" + "name": "gatk4_haplotypecaller", + "path": "modules/nf-core/gatk4/haplotypecaller/meta.yml", + "type": "module", + "meta": { + "name": "gatk4_haplotypecaller", + "description": "Call germline SNPs and indels via local re-assembly of haplotypes", + "keywords": ["gatk4", "haplotype", "haplotypecaller"], + "tools": [ + { + "gatk4": { + "description": "Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools\nwith a primary focus on variant discovery and genotyping. Its powerful processing engine\nand high-performance computing features make it capable of taking on projects of any size.\n", + "homepage": "https://gatk.broadinstitute.org/hc/en-us", + "documentation": "https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s", + "doi": "10.1158/1538-7445.AM2017-3590", + "licence": ["Apache-2.0"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM file from alignment", + "pattern": "*.{bam,cram}", + "ontologies": [] + } + }, + { + "input_index": { + "type": "file", + "description": "BAI/CRAI file from alignment", + "pattern": "*.{bai,crai}", + "ontologies": [] + } + }, + { + "intervals": { + "type": "file", + "description": "Bed file with the genomic regions included in the library (optional)", + "ontologies": [] + } + }, + { + "dragstr_model": { + "type": "file", + "description": "Text file containing the DragSTR model of the used BAM/CRAM file (optional)", + "pattern": "*.txt", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test_reference' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The reference fasta file", + "pattern": "*.fasta", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test_reference' ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Index of reference fasta file", + "pattern": "fasta.fai", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test_reference' ]\n" + } + }, + { + "dict": { + "type": "file", + "description": "GATK sequence dictionary", + "pattern": "*.dict", + "ontologies": [] + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing dbsnp information\ne.g. [ id:'test_dbsnp' ]\n" + } + }, + { + "dbsnp": { + "type": "file", + "description": "VCF file containing known sites (optional)", + "ontologies": [] + } + } + ], + [ + { + "meta6": { + "type": "map", + "description": "Groovy Map containing dbsnp information\ne.g. [ id:'test_dbsnp' ]\n" + } + }, + { + "dbsnp_tbi": { + "type": "file", + "description": "VCF index of dbsnp (optional)", + "ontologies": [] + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "Compressed VCF file", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tbi": { + "type": "file", + "description": "Index of VCF file", + "pattern": "*.vcf.gz.tbi", + "ontologies": [] + } + } + ] + ], + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.realigned.bam": { + "type": "file", + "description": "Assembled haplotypes and locally realigned reads", + "pattern": "*.realigned.bam", + "ontologies": [] + } + } + ] + ], + "versions_gatk4": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@suzannejin", "@FriederikeHanssen"], + "maintainers": ["@suzannejin", "@FriederikeHanssen"] + }, + "pipelines": [ + { + "name": "genomicrelatedness", + "version": "dev" + }, + { + "name": "pacvar", + "version": "1.0.1" + }, + { + "name": "rnavar", + "version": "1.2.3" + }, + { + "name": "sarek", + "version": "3.8.1" + } + ] }, { - 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GermlineCNVCaller and generates VCFs and denoised copy ratios", + "keywords": ["copy number", "gatk4", "postprocessgermlinecnvcalls"], + "tools": [ + { + "gatk4": { + "description": "Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools\nwith a primary focus on variant discovery and genotyping. Its powerful processing engine\nand high-performance computing features make it capable of taking on projects of any size.\n", + "homepage": "https://gatk.broadinstitute.org/hc/en-us", + "documentation": "https://gatk.broadinstitute.org/hc/en-us/articles/360037593411-PostprocessGermlineCNVCalls", + "doi": "10.1158/1538-7445.AM2017-3590", + "licence": ["Apache-2.0"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "calls": { + "type": "directory", + "description": "A folder containing the calls from the input files", + "pattern": "*-cnv-calls/*-calls" + } + }, + { + "model": { + "type": "directory", + "description": "A folder containing the model from the input files.\nThis will only be created in COHORT mode (when no model is supplied to the process).\n", + "pattern": "*-cnv-model/*-model" + } + }, + { + "ploidy": { + "type": "directory", + "description": "Optional - A folder containing the ploidy model.\nWhen a model is supplied to tool will run in CASE mode.\n", + "pattern": "*-calls/" + } + } + ] + ], + "output": { + "intervals": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_genotyped_intervals.vcf.gz": { + "type": "file", + "description": "Intervals VCF file", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "segments": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_genotyped_segments.vcf.gz": { + "type": "file", + "description": "Segments VCF file", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "denoised": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_denoised.vcf.gz": { + "type": "file", + "description": "Denoised copy ratio file", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "versions_gatk4": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@ryanjameskennedy"], + "maintainers": ["@ryanjameskennedy"] + }, + "pipelines": [ + { + "name": "raredisease", + "version": "3.0.0" + } + ] }, { - "name": "marsseq", - "version": "1.0.3" + "name": "gatk4_preprocessintervals", + "path": "modules/nf-core/gatk4/preprocessintervals/meta.yml", + "type": "module", + "meta": { + "name": "gatk4_preprocessintervals", + "description": "Prepares bins for coverage collection.", + "keywords": ["bed", "gatk4", "interval", "preprocessintervals"], + "tools": [ + { + "gatk4": { + "description": "Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.", + "homepage": "https://gatk.broadinstitute.org/hc/en-us", + "documentation": "https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s", + "doi": "10.1158/1538-7445.AM2017-3590", + "licence": ["Apache-2.0"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The reference fasta file", + "pattern": "*.fasta", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Index of reference fasta file", + "pattern": "*.fasta.fai", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "dict": { + "type": "file", + "description": "GATK sequence dictionary", + "pattern": "*.dict", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "intervals": { + "type": "file", + "description": "Interval file (bed or interval_list) with the genomic regions to be included from the analysis (optional)", + "pattern": "*.{bed,interval_list}", + "ontologies": [] + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "exclude_intervals": { + "type": "file", + "description": "Interval file (bed or interval_list) with the genomic regions to be excluded from the analysis (optional)", + "pattern": "*.{bed,interval_list}", + "ontologies": [] + } + } + ] + ], + "output": { + "interval_list": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "${prefix}.interval_list": { + "type": "file", + "description": "Processed interval list file", + "pattern": "*.interval_list", + "ontologies": [] + } + } + ] + ], + "versions_gatk4": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@ryanjameskennedy", "@ViktorHy", "@ramprasadn"], + "maintainers": ["@ryanjameskennedy", "@ViktorHy", "@ramprasadn"] + }, + "pipelines": [ + { + "name": "createpanelrefs", + "version": "dev" + } + ] }, { - "name": "metaboigniter", - "version": "2.0.1" + "name": "gatk4_printreads", + "path": "modules/nf-core/gatk4/printreads/meta.yml", + "type": "module", + "meta": { + "name": "gatk4_printreads", + "description": "Print reads in the SAM/BAM/CRAM file", + "keywords": ["bam", "cram", "gatk4", "printreads", "sam"], + "tools": [ + { + "gatk4": { + "description": "Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools\nwith a primary focus on variant discovery and genotyping. Its powerful processing engine\nand high-performance computing features make it capable of taking on projects of any size.\n", + "homepage": "https://gatk.broadinstitute.org/hc/en-us", + "documentation": "https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s", + "doi": "10.1158/1538-7445.AM2017-3590", + "licence": ["Apache-2.0"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}", + "ontologies": [] + } + }, + { + "index": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bai,crai,sai}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "reference fasta file", + "pattern": "*.{fa,fasta}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "reference fasta index file", + "pattern": "*.{fai}", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "dict": { + "type": "file", + "description": "reference fasta dictionary file", + "pattern": "*.{dict}", + "ontologies": [] + } + } + ] + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.bam": { + "type": "file", + "description": "Sorted BAM file", + "pattern": "*.{bam}", + "ontologies": [] + } + } + ] + ], + "cram": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.cram": { + "type": "file", + "description": "Sorted CRAM file", + "pattern": "*.{cram}", + "ontologies": [] + } + } + ] + ], + "sam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.sam": { + "type": "file", + "description": "Sorted SAM file", + "pattern": "*.{sam}", + "ontologies": [] + } + } + ] + ], + "versions_gatk4": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@ramprasadn"], + "maintainers": ["@ramprasadn"] + }, + "pipelines": [ + { + "name": "raredisease", + "version": "3.0.0" + }, + { + "name": "variantcatalogue", + "version": "dev" + } + ] }, { - "name": "metatdenovo", - "version": "1.3.0" + "name": "gatk4_printsvevidence", + "path": "modules/nf-core/gatk4/printsvevidence/meta.yml", + "type": "module", + "meta": { + "name": "gatk4_printsvevidence", + "description": "WARNING - this tool is still experimental and shouldn't be used in a production setting. Gathers paired-end and split read evidence files for use in the GATK-SV pipeline. Output files are a file containing the location of and orientation of read pairs marked as discordant, and a file containing the clipping location of all soft clipped reads and the orientation of the clipping.", + "keywords": ["gatk4", "printsvevidence", "structural variants"], + "tools": [ + { + "gatk4": { + "description": "Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools\nwith a primary focus on variant discovery and genotyping. Its powerful processing engine\nand high-performance computing features make it capable of taking on projects of any size.\n", + "homepage": "https://gatk.broadinstitute.org/hc/en-us", + "documentation": "https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s", + "doi": "10.1158/1538-7445.AM2017-3590", + "licence": ["Apache-2.0"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "evidence_files": { + "type": "file", + "description": "The evidence files created by CollectSVEvidence. They all need to be of the same type to print the SV evidence.", + "pattern": "*.{pe,sr,baf,rd}.txt(.gz)", + "ontologies": [] + } + }, + { + "evidence_indices": { + "type": "file", + "description": "The indices of the evidence files created by CollectSVEvidence", + "pattern": "*.{pe,sr,baf,rd}.txt(.gz).tbi", + "ontologies": [] + } + } + ], + { + "bed": { + "type": "file", + "description": "An optional BED file", + "pattern": "*.bed", + "ontologies": [] + } + }, + { + "fasta": { + "type": "file", + "description": "An optional reference FASTA file", + "pattern": "*.{fa,fasta}", + "ontologies": [] + } + }, + { + "fasta_fai": { + "type": "file", + "description": "An optional reference FASTA file index", + "pattern": "*.fai", + "ontologies": [] + } + }, + { + "dict": { + "type": "file", + "description": "The mandatory sequence dictionary file", + "pattern": "*.dict", + "ontologies": [] + } + } + ], + "output": { + "printed_evidence": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt.gz": { + "type": "file", + "description": "The output file containing the discordant read pairs or the soft clipped reads", + "pattern": "*.{pe,sr,baf,rd}.txt.gz", + "ontologies": [] + } + } + ] + ], + "printed_evidence_index": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt.gz.tbi": { + "type": "file", + "description": "The index file of the output compressed text file containing the discordant read pairs or the soft clipped reads", + "pattern": "*.{pe,sr,baf,rd}.txt.gz.tbi", + "ontologies": [] + } + } + ] + ], + "versions_gatk4": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@nvnieuwk"], + "maintainers": ["@nvnieuwk"] + } }, { - "name": "methylarray", - "version": "dev" + "name": "gatk4_reblockgvcf", + "path": "modules/nf-core/gatk4/reblockgvcf/meta.yml", + "type": "module", + "meta": { + "name": "gatk4_reblockgvcf", + "description": "Condenses homRef blocks in a single-sample GVCF", + "keywords": ["gatk4", "gvcf", "reblockgvcf"], + "tools": [ + { + "gatk4": { + "description": "Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools\nwith a primary focus on variant discovery and genotyping. 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Its powerful processing engine\nand high-performance computing features make it capable of taking on projects of any size.\n", + "homepage": "https://gatk.broadinstitute.org/hc/en-us", + "documentation": "https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s", + "doi": "10.1158/1538-7445.AM2017-3590", + "licence": ["Apache-2.0"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "bam": { + "type": "file", + "description": "The input bam/sam file", + "pattern": "*.{bam,sam}", + "ontologies": [] + } + } + ] + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "file", + "description": "The reverted bam/sam file", + "pattern": "*.reverted.bam", + "ontologies": [] + } + }, + { + "*.bam": { + "type": "file", + "description": "The reverted bam/sam file", + "pattern": "*.reverted.bam", + "ontologies": [] + } + } + ] + ], + "versions_gatk4": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@kevinmenden"], + "maintainers": ["@kevinmenden"] + }, + "pipelines": [ + { + "name": "raredisease", + "version": "3.0.0" + } + ] }, { - "name": "methylseq", - "version": "4.2.0" + "name": "gatk4_samtofastq", + "path": "modules/nf-core/gatk4/samtofastq/meta.yml", + "type": "module", + "meta": { + "name": "gatk4_samtofastq", + "description": "Converts BAM/SAM file to FastQ format", + "keywords": ["bed", "gatk4", "interval_list"], + "tools": [ + { + "gatk4": { + "description": "Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools\nwith a primary focus on variant discovery and genotyping. 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Output file is an annotated SV VCF.", + "keywords": ["annotate", "gatk4", "structural variants", "svannotate", "vcf"], + "tools": [ + { + "gatk4": { + "description": "Genome Analysis Toolkit (GATK4)", + "homepage": "https://gatk.broadinstitute.org/hc/en-us", + "documentation": "https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s", + "tool_dev_url": "https://github.com/broadinstitute/gatk", + "doi": "10.1158/1538-7445.AM2017-3590", + "licence": ["BSD-3-clause"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "A VCF file created with a structural variant caller", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + }, + { + "tbi": { + "type": "file", + "description": "The index file of the VCF", + "pattern": "*.vcf.gz.tbi", + "ontologies": [] + } + }, + { + "bed": { + "type": "file", + "description": "Regions to limit the analysis to", + "pattern": "*.bed", + "ontologies": [] + } + }, + { + "non_coding_bed": { + "type": "file", + "description": "File containing noncoding regions", + "pattern": "*.bed", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing FASTA information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Optional - reference FASTA file needed when the input is a CRAM file", + "pattern": "*.{fasta,fa}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing FAI information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta_fai": { + "type": "file", + "description": "Optional - index of the reference FASTA file needed when the input is a CRAM file", + "pattern": "*.fai", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing DICT information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "dict": { + "type": "file", + "description": "Optional - sequence dictionary of the reference FASTA file needed when the input is a CRAM file", + "pattern": "*.dict", + "ontologies": [] + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing GTF information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "gtf": { + "type": "file", + "description": "Optional - GTF file containing transcript information", + "pattern": "*.gtf", + "ontologies": [] + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "The annotated structural variant VCF", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz.tbi": { + "type": "file", + "description": "The index of the VCF", + "pattern": "*.vcf.gz.tbi", + "ontologies": [] + } + } + ] + ], + "versions_gatk4": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@nvnieuwk"], + "maintainers": ["@nvnieuwk"] + } }, { - "name": "readsimulator", - "version": "1.0.1" + "name": "gatk4_svcluster", + "path": "modules/nf-core/gatk4/svcluster/meta.yml", + "type": "module", + "meta": { + "name": "gatk4_svcluster", + "description": "Clusters structural variants based on coordinates, event type, and supporting algorithms", + "keywords": ["gatk4", "structural variants", "svcluster", "vcf"], + "tools": [ + { + "gatk4": { + "description": "Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools\nwith a primary focus on variant discovery and genotyping. Its powerful processing engine\nand high-performance computing features make it capable of taking on projects of any size.\n", + "homepage": "https://gatk.broadinstitute.org/hc/en-us", + "documentation": "https://github.com/broadinstitute/gatk", + "doi": "10.1158/1538-7445.AM2017-3590", + "licence": ["Apache-2.0"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcfs": { + "type": "file", + "description": "One or more VCF files created with a structural variant caller", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + }, + { + "indices": { + "type": "file", + "description": "Index files for the VCFs", + "pattern": "*.vcf.gz.tbi", + "ontologies": [] + } + } + ], + { + "ploidy_table": { + "type": "file", + "description": "The sample ploidy table", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, + { + "fasta": { + "type": "file", + "description": "Reference FASTA file needed when the input is a CRAM file", + "pattern": "*.{fasta,fa}", + "ontologies": [] + } + }, + { + "fasta_fai": { + "type": "file", + "description": "Index of the reference FASTA file needed when the input is a CRAM file", + "pattern": "*.fai", + "ontologies": [] + } + }, + { + "dict": { + "type": "file", + "description": "Sequence dictionary of the reference FASTA file needed when the input is a CRAM file", + "pattern": "*.dict", + "ontologies": [] + } + } + ], + "output": { + "clustered_vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "The VCF containing the clustered VCFs", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "clustered_vcf_index": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz.tbi": { + "type": "file", + "description": "The index of the VCF containing the clustered VCFs", + "pattern": "*.vcf.gz.tbi", + "ontologies": [] + } + } + ] + ], + "versions_gatk4": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@nvnieuwk"], + "maintainers": ["@nvnieuwk"] + } }, { - "name": "riboseq", - "version": "1.2.0" + "name": "gatk4_unmarkduplicates", + "path": "modules/nf-core/gatk4/unmarkduplicates/meta.yml", + "type": "module", + "meta": { + "name": "gatk4_unmarkduplicates", + "description": "This tool locates and unmark the marked duplicate reads in a BAM or SAM file, where duplicate reads are defined as originating from a single fragment of DNA.", + "keywords": ["bam", "gatk4", "unmarkduplicates"], + "tools": [ + { + "gatk4": { + "description": "Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.", + "homepage": "https://gatk.broadinstitute.org/hc/en-us", + "documentation": "https://gatk.broadinstitute.org/hc/en-us/articles/360036367192-UnmarkDuplicates", + "tool_dev_url": "https://github.com/broadinstitute/gatk", + "doi": "10.1158/1538-7445.AM2017-3590", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "Marked duplicates BAM file", + "pattern": "*.{bam}", + "ontologies": [] + } + } + ] + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*_UnmarkDuplicates.{bam}" + } + }, + { + "${prefix}.bam": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*_UnmarkDuplicates.{bam}" + } + } + ] + ], + "bai": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*_UnmarkDuplicates.{bam}" + } + }, + { + "${prefix}.bai": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*_UnmarkDuplicates.{bam.bai}" + } + } + ] + ], + "versions_gatk4": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@nikhil", "@anoronh4", "@mikefeixu", "@ajodeh-juma", "@FriederikeHanssen", "@maxulysse"], + "maintainers": ["@mikefeixu"] + } }, { - "name": "rnadnavar", - "version": "dev" + "name": "gatk4_variantfiltration", + "path": "modules/nf-core/gatk4/variantfiltration/meta.yml", + "type": "module", + "meta": { + "name": "gatk4_variantfiltration", + "description": "Filter variants", + "keywords": ["filter", "gatk4", "variantfiltration", "vcf"], + "tools": [ + { + "gatk4": { + "description": "Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools\nwith a primary focus on variant discovery and genotyping. Its powerful processing engine\nand high-performance computing features make it capable of taking on projects of any size.\n", + "homepage": "https://gatk.broadinstitute.org/hc/en-us", + "documentation": "https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s", + "doi": "10.1158/1538-7445.AM2017-3590", + "licence": ["Apache-2.0"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "vcf": { + "type": "list", + "description": "List of VCF(.gz) files", + "pattern": "*.{vcf,vcf.gz}" + } + }, + { + "tbi": { + "type": "list", + "description": "List of VCF file indexes", + "pattern": "*.{tbi}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Fasta file of reference genome", + "pattern": "*.fasta", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Index of fasta file", + "pattern": "*.fasta.fai", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "dict": { + "type": "file", + "description": "Sequence dictionary of fastea file", + "pattern": "*.dict", + "ontologies": [] + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "gzi": { + "type": "file", + "description": "Genome index file only needed when the genome file was compressed with the BGZF algorithm.", + "pattern": "*.gzi", + "ontologies": [] + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "file", + "description": "Compressed VCF file", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "Compressed VCF file", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "tbi": [ + [ + { + "meta": { + "type": "file", + "description": "Compressed VCF file", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + }, + { + "*.tbi": { + "type": "file", + "description": "Index of VCF file", + "pattern": "*.vcf.gz.tbi", + "ontologies": [] + } + } + ] + ], + "versions_gatk4": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@kevinmenden", "@ramprasadn"], + "maintainers": ["@kevinmenden", "@ramprasadn"] + }, + "pipelines": [ + { + "name": "genomicrelatedness", + "version": "dev" + }, + { + "name": "pathogensurveillance", + "version": "1.1.0" + }, + { + "name": "raredisease", + "version": "3.0.0" + }, + { + "name": "rnadnavar", + "version": "dev" + }, + { + "name": "rnavar", + "version": "1.2.3" + }, + { + "name": "variantcatalogue", + "version": "dev" + } + ] }, { - "name": "rnafusion", - "version": "4.1.2" + "name": "gatk4_variantrecalibrator", + "path": "modules/nf-core/gatk4/variantrecalibrator/meta.yml", + "type": "module", + "meta": { + "name": "gatk4_variantrecalibrator", + "description": "Build a recalibration model to score variant quality for filtering purposes.\nIt is highly recommended to follow GATK best practices when using this module,\nthe gaussian mixture model requires a large number of samples to be used for the\ntool to produce optimal results. For example, 30 samples for exome data. For more details see\nhttps://gatk.broadinstitute.org/hc/en-us/articles/4402736812443-Which-training-sets-arguments-should-I-use-for-running-VQSR-\n", + "keywords": ["gatk4", "recalibration model", "variantrecalibrator"], + "tools": [ + { + "gatk4": { + "description": "Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools\nwith a primary focus on variant discovery and genotyping. Its powerful processing engine\nand high-performance computing features make it capable of taking on projects of any size.\n", + "homepage": "https://gatk.broadinstitute.org/hc/en-us", + "documentation": "https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s", + "doi": "10.1158/1538-7445.AM2017-3590", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "input vcf file containing the variants to be recalibrated", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + }, + { + "tbi": { + "type": "file", + "description": "tbi file matching with -vcf", + "pattern": "*.vcf.gz.tbi", + "ontologies": [] + } + } + ], + { + "resource_vcf": { + "type": "file", + "description": "all resource vcf files that are used with the corresponding '--resource' label", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + }, + { + "resource_tbi": { + "type": "file", + "description": "all resource tbi files that are used with the corresponding '--resource' label", + "pattern": "*.vcf.gz.tbi", + "ontologies": [] + } + }, + { + "labels": { + "type": "string", + "description": "necessary arguments for GATK VariantRecalibrator. Specified to directly match the resources provided. More information can be found at https://gatk.broadinstitute.org/hc/en-us/articles/5358906115227-VariantRecalibrator" + } + }, + { + "fasta": { + "type": "file", + "description": "The reference fasta file", + "pattern": "*.fasta", + "ontologies": [] + } + }, + { + "fai": { + "type": "file", + "description": "Index of reference fasta file", + "pattern": "fasta.fai", + "ontologies": [] + } + }, + { + "dict": { + "type": "file", + "description": "GATK sequence dictionary", + "pattern": "*.dict", + "ontologies": [] + } + } + ], + "output": { + "recal": [ + [ + { + "meta": { + "type": "file", + "description": "Output recal file used by ApplyVQSR", + "pattern": "*.recal", + "ontologies": [] + } + }, + { + "*.recal": { + "type": "file", + "description": "Output recal file used by ApplyVQSR", + "pattern": "*.recal", + "ontologies": [] + } + } + ] + ], + "idx": [ + [ + { + "meta": { + "type": "file", + "description": "Output recal file used by ApplyVQSR", + "pattern": "*.recal", + "ontologies": [] + } + }, + { + "*.idx": { + "type": "file", + "description": "Index file for the recal output file", + "pattern": "*.idx", + "ontologies": [] + } + } + ] + ], + "tranches": [ + [ + { + "meta": { + "type": "file", + "description": "Output recal file used by ApplyVQSR", + "pattern": "*.recal", + "ontologies": [] + } + }, + { + "*.tranches": { + "type": "file", + "description": "Output tranches file used by ApplyVQSR", + "pattern": "*.tranches", + "ontologies": [] + } + } + ] + ], + "plots": [ + [ + { + "meta": { + "type": "file", + "description": "Output recal file used by ApplyVQSR", + "pattern": "*.recal", + "ontologies": [] + } + }, + { + "*plots.R": { + "type": "file", + "description": "Optional output rscript file to aid in visualization of the input data and learned model.", + "pattern": "*plots.R", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3999" + } + ] + } + } + ] + ], + "versions_gatk4": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@GCJMackenzie", "@nickhsmith"], + "maintainers": ["@GCJMackenzie", "@nickhsmith"] + }, + "pipelines": [ + { + "name": "rnadnavar", + "version": "dev" + }, + { + "name": "sarek", + "version": "3.8.1" + }, + { + "name": "tbanalyzer", + "version": "dev" + } + ] }, { - "name": "rnaseq", - "version": "3.26.0" + "name": "gatk4_variantstotable", + "path": "modules/nf-core/gatk4/variantstotable/meta.yml", + "type": "module", + "meta": { + "name": "gatk4_variantstotable", + "description": "Extract fields from a VCF file to a tab-delimited table", + "keywords": ["filter", "gatk4", "table", "vcf"], + "tools": [ + { + "gatk4": { + "description": "Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools\nwith a primary focus on variant discovery and genotyping. Its powerful processing engine\nand high-performance computing features make it capable of taking on projects of any size.\n", + "homepage": "https://gatk.broadinstitute.org/hc/en-us", + "documentation": "https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s", + "doi": "10.1158/1538-7445.AM2017-3590", + "licence": ["Apache-2.0"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing VCF information. Attribute `gatk_args` can be used to add arguments to gatk.\ne.g. [ id:'test', gatk_args:'-F CHROM -F POS -F TYPE -GF AD']\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF file", + "pattern": "*.{vcf,vcf.gz}", + "ontologies": [] + } + }, + { + "tbi": { + "type": "file", + "description": "Index of VCF file.", + "pattern": "*.{idx,tbi}", + "ontologies": [] + } + }, + { + "arguments_file": { + "type": "file", + "description": "optional GATK arguments file", + "pattern": "*.{txt,list,args,arguments}", + "ontologies": [] + } + }, + { + "include_intervals": { + "type": "file", + "description": "optional GATK region file", + "pattern": "*.{bed,bed.gz,interval,interval_list}", + "ontologies": [] + } + }, + { + "exclude_intervals": { + "type": "file", + "description": "optional GATK exclude region file", + "pattern": "*.{bed,bed.gz,interval,interval_list}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Fasta file of reference genome", + "pattern": "*.fasta", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Index of fasta file", + "pattern": "*.fasta.fai", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "dict": { + "type": "file", + "description": "Sequence dictionary of fastea file", + "pattern": "*.dict", + "ontologies": [] + } + } + ] + ], + "output": { + "table": [ + [ + { + "meta": { + "type": "file", + "description": "GATK output", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, + { + "*.tsv": { + "type": "file", + "description": "GATK output", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_gatk4": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@lindenb"], + "maintainers": ["@lindenb"] + }, + "pipelines": [ + { + "name": "tbanalyzer", + "version": "dev" + } + ] }, { - "name": "rnasplice", - "version": "1.0.4" + "name": "gatk4spark_applybqsr", + "path": "modules/nf-core/gatk4spark/applybqsr/meta.yml", + "type": "module", + "meta": { + "name": "gatk4spark_applybqsr", + "description": "Apply base quality score recalibration (BQSR) to a bam file", + "keywords": ["bam", "base quality score recalibration", "bqsr", "cram", "gatk4spark"], + "tools": [ + { + "gatk4": { + "description": "Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools\nwith a primary focus on variant discovery and genotyping. Its powerful processing engine\nand high-performance computing features make it capable of taking on projects of any size.\n", + "homepage": "https://gatk.broadinstitute.org/hc/en-us", + "documentation": "https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s", + "doi": "10.1158/1538-7445.AM2017-3590", + "licence": ["Apache-2.0"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM file from alignment", + "pattern": "*.{bam,cram}", + "ontologies": [] + } + }, + { + "input_index": { + "type": "file", + "description": "BAI/CRAI file from alignment", + "pattern": "*.{bai,crai}", + "ontologies": [] + } + }, + { + "bqsr_table": { + "type": "file", + "description": "Recalibration table from gatk4_baserecalibrator", + "ontologies": [] + } + }, + { + "intervals": { + "type": "file", + "description": "Bed file with the genomic regions included in the library (optional)", + "ontologies": [] + } + } + ], + { + "fasta": { + "type": "file", + "description": "The reference fasta file", + "pattern": "*.fasta", + "ontologies": [] + } + }, + { + "fai": { + "type": "file", + "description": "Index of reference fasta file", + "pattern": "*.fasta.fai", + "ontologies": [] + } + }, + { + "dict": { + "type": "file", + "description": "GATK sequence dictionary", + "pattern": "*.dict", + "ontologies": [] + } + } + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.bam": { + "type": "file", + "description": "Recalibrated BAM file", + "pattern": "${prefix}.bam", + "ontologies": [] + } + } + ] + ], + "bai": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}*bai": { + "type": "file", + "description": "Recalibrated BAM index file", + "pattern": "${prefix}*bai", + "ontologies": [] + } + } + ] + ], + "cram": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.cram": { + "type": "file", + "description": "Recalibrated CRAM file", + "pattern": "${prefix}.cram", + "ontologies": [] + } + } + ] + ], + "versions_gatk4": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@yocra3", "@FriederikeHanssen", "@maxulysse"], + "maintainers": ["@yocra3", "@FriederikeHanssen", "@maxulysse"] + }, + "pipelines": [ + { + "name": "sarek", + "version": "3.8.1" + } + ] }, { - "name": "rnavar", - "version": "1.2.3" + "name": "gatk4spark_baserecalibrator", + "path": "modules/nf-core/gatk4spark/baserecalibrator/meta.yml", + "type": "module", + "meta": { + "name": "gatk4spark_baserecalibrator", + "description": "Generate recalibration table for Base Quality Score Recalibration (BQSR)", + "keywords": ["base quality score recalibration", "table", "bqsr", "gatk4spark", "sort"], + "tools": [ + { + "gatk4": { + "description": "Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools\nwith a primary focus on variant discovery and genotyping. Its powerful processing engine\nand high-performance computing features make it capable of taking on projects of any size.\n", + "homepage": "https://gatk.broadinstitute.org/hc/en-us", + "documentation": "https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s", + "doi": "10.1158/1538-7445.AM2017-3590", + "licence": ["Apache-2.0"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM file from alignment", + "pattern": "*.{bam,cram}", + "ontologies": [] + } + }, + { + "input_index": { + "type": "file", + "description": "BAI/CRAI file from alignment", + "pattern": "*.{bai,crai}", + "ontologies": [] + } + }, + { + "intervals": { + "type": "file", + "description": "Bed file with the genomic regions included in the library (optional)", + "ontologies": [] + } + } + ], + { + "fasta": { + "type": "file", + "description": "The reference fasta file", + "pattern": "*.fasta", + "ontologies": [] + } + }, + { + "fai": { + "type": "file", + "description": "Index of reference fasta file", + "pattern": "*.fasta.fai", + "ontologies": [] + } + }, + { + "dict": { + "type": "file", + "description": "GATK sequence dictionary", + "pattern": "*.dict", + "ontologies": [] + } + }, + { + "known_sites": { + "type": "file", + "description": "VCF files with known sites for indels / snps (optional)", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + }, + { + "known_sites_tbi": { + "type": "file", + "description": "Tabix index of the known_sites (optional)", + "pattern": "*.vcf.gz.tbi", + "ontologies": [] + } + } + ], + "output": { + "table": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.table": { + "type": "file", + "description": "Recalibration table from BaseRecalibrator", + "pattern": "*.{table}", + "ontologies": [] + } + } + ] + ], + "versions_gatk4": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@yocra3", "@FriederikeHanssen", "@maxulysse"], + "maintainers": ["@yocra3", "@FriederikeHanssen", "@maxulysse"] + }, + "pipelines": [ + { + "name": "sarek", + "version": "3.8.1" + } + ] }, { - "name": "sammyseq", - "version": "dev" + "name": "gatk4spark_markduplicates", + "path": "modules/nf-core/gatk4spark/markduplicates/meta.yml", + "type": "module", + "meta": { + "name": "gatk4spark_markduplicates", + "description": "This tool locates and tags duplicate reads in a BAM or SAM file, where duplicate reads are defined as originating from a single fragment of DNA.", + "keywords": ["bam", "gatk4spark", "markduplicates", "sort"], + "tools": [ + { + "gatk4": { + "description": "Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.", + "homepage": "https://gatk.broadinstitute.org/hc/en-us", + "documentation": "https://gatk.broadinstitute.org/hc/en-us/articles/360037052812-MarkDuplicates-Picard-", + "tool_dev_url": "https://github.com/broadinstitute/gatk", + "doi": "10.1158/1538-7445.AM2017-3590", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "Sorted BAM file", + "pattern": "*.{bam}", + "ontologies": [] + } + } + ], + { + "fasta": { + "type": "file", + "description": "The reference fasta file", + "pattern": "*.fasta", + "ontologies": [] + } + }, + { + "fasta_fai": { + "type": "file", + "description": "Index of reference fasta file", + "pattern": "*.fai", + "ontologies": [] + } + }, + { + "dict": { + "type": "file", + "description": "GATK sequence dictionary", + "pattern": "*.dict", + "ontologies": [] + } + } + ], + "output": { + "output": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}": { + "type": "file", + "description": "Marked duplicates BAM/CRAM file", + "pattern": "*.{bam,cram}", + "ontologies": [] + } + } + ] + ], + "bam_index": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.bai": { + "type": "file", + "description": "Optional BAM index file", + "pattern": "*.bai", + "ontologies": [] + } + } + ] + ], + "metrics": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.metrics": { + "type": "file", + "description": "Metrics file", + "pattern": "*.metrics", + "ontologies": [] + } + } + ] + ], + "versions_gatk4": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@ajodeh-juma", "@FriederikeHanssen", "@maxulysse", "@SusiJo"], + "maintainers": ["@ajodeh-juma", "@FriederikeHanssen", "@maxulysse", "@SusiJo"] + }, + "pipelines": [ + { + "name": "sarek", + "version": "3.8.1" + } + ] }, { - "name": "sarek", - "version": "3.8.1" + "name": "gatk_indelrealigner", + "path": "modules/nf-core/gatk/indelrealigner/meta.yml", + "type": "module", + "meta": { + "name": "gatk_indelrealigner", + "description": "Performs local realignment around indels to correct for mapping errors", + "keywords": ["bam", "vcf", "variant calling", "indel", "realignment"], + "tools": [ + { + "gatk": { + "description": "The full Genome Analysis Toolkit (GATK) framework, license restricted.", + "homepage": "https://gatk.broadinstitute.org/hc/en-us", + "documentation": "https://github.com/broadinstitute/gatk-docs", + "licence": [ + "https://software.broadinstitute.org/gatk/download/licensing", + "BSD", + "https://www.broadinstitute.org/gatk/about/#licensing" + ], + "identifier": "biotools:gatk" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "Sorted and indexed BAM file", + "pattern": "*.bam", + "ontologies": [] + } + }, + { + "bai": { + "type": "file", + "description": "BAM index file", + "pattern": "*.bai", + "ontologies": [] + } + }, + { + "intervals": { + "type": "file", + "description": "Intervals file created by gatk3 RealignerTargetCreator", + "pattern": "*.{intervals,list}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference file used to generate BAM file", + "pattern": ".{fasta,fa,fna}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Index of reference file used to generate BAM file", + "pattern": ".fai", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "dict": { + "type": "file", + "description": "GATK dict file for reference", + "pattern": ".dict", + "ontologies": [] + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing file meta-information for known_vcf.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "known_vcf": { + "type": "file", + "description": "Optional input VCF file(s) with known indels", + "pattern": ".vcf", + "ontologies": [] + } + } + ] + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Sorted and indexed BAM file with local realignment around variants", + "pattern": "*.bam", + "ontologies": [] + } + }, + { + "*.bai": { + "type": "file", + "description": "Sorted and indexed BAM file with local realignment around variants", + "pattern": "*.bam", + "ontologies": [] + } + } + ] + ], + "versions_gatk": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk3 --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk3 --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@jfy133"], + "maintainers": ["@jfy133"] + } }, { - "name": "scnanoseq", - "version": "1.2.2" + "name": "gatk_realignertargetcreator", + "path": "modules/nf-core/gatk/realignertargetcreator/meta.yml", + "type": "module", + "meta": { + "name": "gatk_realignertargetcreator", + "description": "Generates a list of locations that should be considered for local realignment prior genotyping.", + "keywords": ["bam", "vcf", "variant calling", "indel", "realignment", "targets"], + "tools": [ + { + "gatk": { + "description": "The full Genome Analysis Toolkit (GATK) framework, license restricted.", + "homepage": "https://gatk.broadinstitute.org/hc/en-us", + "documentation": "https://github.com/broadinstitute/gatk-docs", + "licence": [ + "https://software.broadinstitute.org/gatk/download/licensing", + "BSD", + "https://www.broadinstitute.org/gatk/about/#licensing" + ], + "identifier": "biotools:gatk" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "Sorted and indexed BAM/CRAM/SAM file", + "pattern": "*.bam", + "ontologies": [] + } + }, + { + "bai": { + "type": "file", + "description": "BAM index file", + "pattern": "*.bai", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference file used to generate BAM file", + "pattern": ".{fasta,fa,fna}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Index of reference file used to generate BAM file", + "pattern": ".fai", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "dict": { + "type": "file", + "description": "GATK dict file for reference", + "pattern": ".dict", + "ontologies": [] + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing file meta-information for known_vcf.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "known_vcf": { + "type": "file", + "description": "Optional input VCF file(s) with known indels", + "pattern": ".vcf", + "ontologies": [] + } + } + ] + ], + "output": { + "intervals": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.intervals": { + "type": "file", + "description": "File containing intervals that represent sites of extant and potential indels.", + "pattern": "*.intervals", + "ontologies": [] + } + } + ] + ], + "versions_gatk": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk3 --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk3 --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@jfy133"], + "maintainers": ["@jfy133"] + } }, { - "name": "scrnaseq", - "version": "4.1.0" + "name": "gatk_unifiedgenotyper", + "path": "modules/nf-core/gatk/unifiedgenotyper/meta.yml", + "type": "module", + "meta": { + "name": "gatk_unifiedgenotyper", + "description": "SNP and Indel variant caller on a per-locus basis", + "keywords": ["bam", "vcf", "variant calling"], + "tools": [ + { + "gatk": { + "description": "The full Genome Analysis Toolkit (GATK) framework, license restricted.", + "homepage": "https://gatk.broadinstitute.org/hc/en-us", + "documentation": "https://github.com/broadinstitute/gatk-docs", + "licence": [ + "https://software.broadinstitute.org/gatk/download/licensing", + "BSD", + "https://www.broadinstitute.org/gatk/about/#licensing" + ], + "identifier": "biotools:gatk" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "Sorted and indexed BAM/CRAM/SAM file", + "pattern": "*.bam", + "ontologies": [] + } + }, + { + "bai": { + "type": "file", + "description": "BAM index file", + "pattern": "*.bai", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference file used to generate BAM file", + "pattern": ".{fasta,fa,fna}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Index of reference file used to generate BAM file", + "pattern": ".fai", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "dict": { + "type": "file", + "description": "GATK dict file for reference", + "pattern": ".dict", + "ontologies": [] + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "intervals": { + "type": "file", + "description": "Bed file with the genomic regions included in the library (optional)", + "pattern": "*.intervals", + "ontologies": [] + } + } + ], + [ + { + "meta6": { + "type": "map", + "description": "Groovy Map containing file meta-information for the contamination file.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "contamination": { + "type": "file", + "description": "Tab-separated file containing fraction of contamination in sequencing data (per sample) to aggressively remove", + "pattern": "*", + "ontologies": [] + } + } + ], + [ + { + "meta7": { + "type": "map", + "description": "Groovy Map containing file meta-information for the dbsnps file.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "dbsnp": { + "type": "file", + "description": "VCF file containing known sites (optional)", + "pattern": "*", + "ontologies": [] + } + } + ], + [ + { + "meta8": { + "type": "map", + "description": "Groovy Map containing file meta-information for the VCF comparison file.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "comp": { + "type": "file", + "description": "Comparison VCF file (optional)", + "pattern": "*", + "ontologies": [] + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "VCF file containing called variants", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "versions_gatk": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk3 --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gatk": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gatk3 --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@ilight1542", "@jfy133"], + "maintainers": ["@ilight1542", "@jfy133"] + } }, { - "name": "seqinspector", - "version": "1.0.1" + "name": "gawk", + "path": "modules/nf-core/gawk/meta.yml", + "type": "module", + "meta": { + "name": "gawk", + "description": "If you are like many computer users, you would frequently like to make changes in various text files\nwherever certain patterns appear, or extract data from parts of certain lines while discarding the rest.\nThe job is easy with awk, especially the GNU implementation gawk.\n", + "keywords": ["gawk", "awk", "txt", "text", "file parsing"], + "tools": [ + { + "gawk": { + "description": "GNU awk", + "homepage": "https://www.gnu.org/software/gawk/", + "documentation": "https://www.gnu.org/software/gawk/manual/", + "tool_dev_url": "https://www.gnu.org/prep/ftp.html", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "The input file - Specify the logic that needs to be executed on this file on the `ext.args2` or in the program file. If the files have a `.gz` extension, they will be unzipped using `zcat`.", + "pattern": "*", + "ontologies": [] + } + } + ], + { + "program_file": { + "type": "file", + "description": "Optional file containing logic for awk to execute. If you don't wish to use a file, you can use `ext.args2` to specify the logic.", + "pattern": "*", + "ontologies": [] + } + }, + { + "disable_redirect_output": { + "type": "boolean", + "description": "Disable the redirection of awk output to a given file. This is useful if you want to use awk's built-in redirect to write files instead of the shell's redirect." + } + } + ], + "output": { + "output": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.${suffix}": { + "type": "file", + "description": "The output file - if using shell redirection, specify the name of this file using `ext.prefix` and the extension using `ext.suffix`. Otherwise, ensure the awk program produces files with the extension in `ext.suffix`.", + "pattern": "*", + "ontologies": [] + } + } + ] + ], + "versions_gawk": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gawk": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "awk -Wversion | sed '1!d; s/.*Awk //; s/,.*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gawk": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "awk -Wversion | sed '1!d; s/.*Awk //; s/,.*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@nvnieuwk"], + "maintainers": ["@nvnieuwk"] + }, + "pipelines": [ + { + "name": "circrna", + "version": "dev" + }, + { + "name": "createpanelrefs", + "version": "dev" + }, + { + "name": "deepmodeloptim", + "version": "dev" + }, + { + "name": "denovotranscript", + "version": "1.2.1" + }, + { + "name": "genomeqc", + "version": "dev" + }, + { + "name": "genomicrelatedness", + "version": "dev" + }, + { + "name": "methylong", + "version": "2.0.0" + }, + { + "name": "phaseimpute", + "version": "1.1.0" + }, + { + "name": "raredisease", + "version": "3.0.0" + }, + { + "name": "references", + "version": "0.1" + }, + { + "name": "reportho", + "version": "1.1.0" + }, + { + "name": "sarek", + "version": "3.8.1" + }, + { + "name": "smrnaseq", + "version": "2.4.1" + }, + { + "name": "tfactivity", + "version": "dev" + }, + { + "name": "variantbenchmarking", + "version": "1.5.0" + } + ] }, { - "name": "smrnaseq", - "version": "2.4.1" + "name": "gcta_makegrm", + "path": "modules/nf-core/gcta/makegrm/meta.yml", + "type": "module", + "meta": { + "name": "gcta_makegrm", + "description": "Compute a whole dense GRM with GCTA", + "keywords": [ + "gcta", + "genome-wide complex trait analysis", + "grm", + "genetic relationship matrix", + "genetics" + ], + "tools": [ + { + "gcta": { + "description": "GCTA is a tool for genome-wide complex trait analysis.", + "homepage": "https://yanglab.westlake.edu.cn/software/gcta/", + "documentation": "https://yanglab.westlake.edu.cn/software/gcta/static/gcta_doc_latest.pdf", + "tool_dev_url": "https://github.com/jianyangqt/gcta", + "licence": ["GPL-3.0-only"], + "identifier": "biotools:gcta" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing GRM sample metadata\ne.g. `[ id:'gcta_grm' ]`\n" + } + }, + { + "mfile": { + "type": "file", + "description": "GCTA multi-input manifest consumed by `--mbfile` or `--mpfile`", + "pattern": "*.{mbfile,mpfile,txt}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + }, + { + "bed_pgen": { + "type": "file", + "description": "Collection of PLINK primary genotype files referenced by the multi-input manifest", + "pattern": "*.{bed,pgen}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3003" + } + ] + } + }, + { + "bim_pvar": { + "type": "file", + "description": "Collection of PLINK variant metadata files referenced by the multi-input manifest", + "pattern": "*.{bim,pvar}", + "ontologies": [] + } + }, + { + "fam_psam": { + "type": "file", + "description": "Collection of PLINK sample metadata files referenced by the multi-input manifest", + "pattern": "*.{fam,psam}", + "ontologies": [] + } + } + ] + ], + "output": { + "grm_files": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing GRM sample metadata\ne.g. `[ id:'gcta_grm' ]`\n" + } + }, + { + "*.grm.*": { + "type": "file", + "description": "Dense GRM sidecar files", + "pattern": "*.grm.{id,bin,N.bin}", + "ontologies": [] + } + } + ] + ], + "versions_gcta": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the version was collected from" + } + }, + { + "gcta": { + "type": "string", + "description": "The tool name" + } + }, + { + "gcta --version | sed -En 's/^[*] version v([0-9.]*).*/\\1/p'": { + "type": "eval", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "gcta": { + "type": "string", + "description": "The tool name" + } + }, + { + "gcta --version | sed -En 's/^[*] version v([0-9.]*).*/\\1/p'": { + "type": "eval", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@lyh970817"], + "maintainers": ["@lyh970817"] + } }, { - "name": "spatialvi", - "version": "dev" + "name": "gcta_makegrmpart", + "path": "modules/nf-core/gcta/makegrmpart/meta.yml", + "type": "module", + "meta": { + "name": "gcta_makegrmpart", + "description": "Compute one partition of a GCTA genetic relationship matrix", + "keywords": [ + "gcta", + "genome-wide complex trait analysis", + "grm", + "genetic relationship matrix", + "genetics" + ], + "tools": [ + { + "gcta": { + "description": "GCTA is a tool for genome-wide complex trait analysis.", + "homepage": "https://yanglab.westlake.edu.cn/software/gcta/", + "documentation": "https://yanglab.westlake.edu.cn/software/gcta/static/gcta_doc_latest.pdf", + "tool_dev_url": "https://github.com/jianyangqt/gcta", + "licence": ["GPL-3.0-only"], + "identifier": "biotools:gcta" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing GRM-partition sample metadata\ne.g. `[ id:'gcta_grm' ]`\n" + } + }, + { + "nparts_gcta": { + "type": "integer", + "description": "Total number of GRM partitions requested via `--make-grm-part`; defaults to `1` when `null`", + "default": 1 + } + }, + { + "part_gcta_job": { + "type": "integer", + "description": "One-based index of the GRM partition to compute via `--make-grm-part`; defaults to `1` when `null`", + "default": 1 + } + }, + { + "mfile": { + "type": "file", + "description": "GCTA multi-input manifest consumed by `--mbfile` or `--mpfile`", + "pattern": "*.{mbfile,mpfile,txt}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + }, + { + "bed_pgen": { + "type": "file", + "description": "Collection of PLINK primary genotype files referenced by the multi-input manifest", + "pattern": "*.{bed,pgen}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3003" + } + ] + } + }, + { + "bim_pvar": { + "type": "file", + "description": "Collection of PLINK variant metadata files referenced by the multi-input manifest", + "pattern": "*.{bim,pvar}", + "ontologies": [] + } + }, + { + "fam_psam": { + "type": "file", + "description": "Collection of PLINK sample metadata files referenced by the multi-input manifest", + "pattern": "*.{fam,psam}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing SNP-selection metadata\ne.g. `[ id:'snp_group1' ]`\n" + } + }, + { + "snp_group_file": { + "type": "file", + "description": "Optional SNP extraction file passed to `--extract`; provide `[]` when absent", + "pattern": "*.{txt,list}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + } + ] + ], + "output": { + "grm_files": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing GRM-partition sample metadata\ne.g. `[ id:'gcta_grm' ]`\n" + } + }, + { + "*.part_${nparts}_${part}.grm.*": { + "type": "file", + "description": "Partitioned GRM output files, including ID, binary matrix, and sample-count matrix files", + "pattern": "*.part_${nparts}_${part}.grm.*", + "ontologies": [] + } + }, + { + "nparts_gcta": { + "type": "integer", + "description": "Total number of GRM partitions requested via `--make-grm-part`" + } + }, + { + "part_gcta_job": { + "type": "integer", + "description": "One-based index of the GRM partition computed via `--make-grm-part`" + } + } + ] + ], + "versions_gcta": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "gcta": { + "type": "string", + "description": "The tool name" + } + }, + { + "gcta --version | sed -En 's/^[*] version v([0-9.]*).*/\\1/p'": { + "type": "eval", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "gcta": { + "type": "string", + "description": "The tool name" + } + }, + { + "gcta --version | sed -En 's/^[*] version v([0-9.]*).*/\\1/p'": { + "type": "eval", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@lyh970817"], + "maintainers": ["@lyh970817"] + } }, { - "name": "ssds", - "version": "dev" + "name": "gecco_convert", + "path": "modules/nf-core/gecco/convert/meta.yml", + "type": "module", + "meta": { + "name": "gecco_convert", + "description": "This command helps transforming the output files created by\nGECCO into helpful format, should you want to use the results in\ncombination with other tools.\n", + "keywords": ["bgc", "reformatting", "clusters", "gbk", "gff", "bigslice", "faa", "fna"], + "tools": [ + { + "gecco": { + "description": "Biosynthetic Gene Cluster prediction with Conditional Random Fields.", + "homepage": "https://gecco.embl.de", + "documentation": "https://gecco.embl.de", + "tool_dev_url": "https://github.com/zellerlab/GECCO", + "doi": "10.1101/2021.05.03.442509", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "clusters": { + "type": "file", + "description": "TSV file containing coordinates of gecco predicted clusters and BGC types.\n", + "pattern": "*.clusters.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, + { + "gbk": { + "type": "file", + "description": "Per cluster GenBank file containing sequence with annotations\n", + "pattern": "*.gbk", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1936" + } + ] + } + } + ], + { + "mode": { + "type": "string", + "description": "Either clusters or gbk folder output, depending on what is reformatted", + "enum": ["clusters", "gbk"] + } + }, + { + "format": { + "type": "string", + "description": "Format for the output file", + "enum": ["gff", "bigslice", "faa", "fna"] + } + } + ], + "output": { + "gff": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}/*.gff": { + "type": "file", + "description": "GFF3 converted cluster tables containing the position\nand metadata for all the predicted clusters\n", + "pattern": "*.gff", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1975" + } + ] + } + } + ] + ], + "bigslice": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}/*.region*.gbk": { + "type": "file", + "description": "Converted and aliased GenBank files so that they can be loaded by BiG-SLiCE\n", + "pattern": "*.region*.gbk", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1936" + } + ] + } + } + ] + ], + "faa": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}/*.faa": { + "type": "file", + "description": "Amino-acid FASTA converted GenBank files of all the proteins in a cluster\n", + "pattern": "*.faa", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ] + ], + "fna": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}/*.fna": { + "type": "file", + "description": "Nucleotide sequence FASTA converted GenBank files from the cluster\n", + "pattern": "*.fna", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ] + ], + "versions_gecco": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gecco": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gecco -V |& sed 's/gecco //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gecco": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gecco -V |& sed 's/gecco //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@vagkaratzas"], + "maintainers": ["@vagkaratzas"] + } }, { - "name": "taxprofiler", - "version": "2.0.0" + "name": "gecco_run", + "path": "modules/nf-core/gecco/run/meta.yml", + "type": "module", + "meta": { + "name": "gecco_run", + "description": "GECCO is a fast and scalable method for identifying putative novel Biosynthetic Gene Clusters (BGCs) in genomic and metagenomic data using Conditional Random Fields (CRFs).", + "keywords": ["bgc", "detection", "metagenomics", "contigs"], + "tools": [ + { + "gecco": { + "description": "Biosynthetic Gene Cluster prediction with Conditional Random Fields.", + "homepage": "https://gecco.embl.de", + "documentation": "https://gecco.embl.de", + "tool_dev_url": "https://github.com/zellerlab/GECCO", + "doi": "10.1101/2021.05.03.442509", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "A genomic file containing one or more sequences as input. Input type is any supported by Biopython (fasta, gbk, etc.)", + "pattern": "*", + "ontologies": [] + } + }, + { + "hmm": { + "type": "file", + "description": "Alternative HMM file(s) to use in HMMER format", + "pattern": "*.hmm", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1370" + } + ] + } + } + ], + { + "model_dir": { + "type": "directory", + "description": "Path to an alternative CRF (Conditional Random Fields) module to use" + } + } + ], + "output": { + "genes": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.genes.tsv": { + "type": "file", + "description": "TSV file containing detected/predicted genes with BGC probability scores. Will not be generated if no hits are found.", + "pattern": "*.genes.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "features": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.features.tsv": { + "type": "file", + "description": "TSV file containing identified domains", + "pattern": "*.features.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "clusters": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.clusters.tsv": { + "type": "file", + "description": "TSV file containing coordinates of predicted clusters and BGC types. Will not be generated if no hits are found.", + "pattern": "*.clusters.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "gbk": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_cluster_*.gbk": { + "type": "file", + "description": "Per cluster GenBank file (if found) containing sequence with annotations. Will not be generated if no hits are found.", + "pattern": "*.gbk", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1936" + } + ] + } + } + ] + ], + "json": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.json": { + "type": "file", + "description": "AntiSMASH v6 sideload JSON file (if --antismash-sideload) supplied. Will not be generated if no hits are found.", + "pattern": "*.gbk", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1936" + } + ] + } + } + ] + ], + "versions_gecco": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gecco": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gecco -V |& sed 's/gecco //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gecco": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gecco -V |& sed 's/gecco //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@jfy133"], + "maintainers": ["@jfy133"] + }, + "pipelines": [ + { + "name": "funcscan", + "version": "3.0.0" + } + ] }, { - "name": "tbanalyzer", - "version": "dev" + "name": "gedi_indexgenome", + "path": "modules/nf-core/gedi/indexgenome/meta.yml", + "type": "module", + "meta": { + "name": "gedi_indexgenome", + "description": "Build a GEDI genome index from a FASTA and GTF for downstream PRICE ORF prediction", + "keywords": ["riboseq", "index", "genome", "gedi", "price", "orf"], + "tools": [ + { + "gedi": { + "description": "Gedi is a Java software platform for working with genomic data (sequencing reads, sequences, per-base numeric values, annotations). It provides the PRICE algorithm for ribosome profiling ORF discovery.", + "homepage": "https://github.com/erhard-lab/gedi", + "documentation": "https://github.com/erhard-lab/gedi/wiki", + "tool_dev_url": "https://github.com/erhard-lab/gedi", + "doi": "10.1038/nmeth.4631", + "licence": ["GPL-3.0"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. `[ id:'homo_sapiens' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Genome FASTA file", + "pattern": "*.{fa,fasta,fna}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + }, + { + "gtf": { + "type": "file", + "description": "GTF annotation file", + "pattern": "*.{gtf}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2306" + } + ] + } + } + ] + ], + "output": { + "index": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. `[ id:'homo_sapiens' ]`\n" + } + }, + { + "${prefix}": { + "type": "directory", + "description": "GEDI genome index directory containing the `.oml` index file and\nits sidecar resources. Consumed as `-genomic` by PRICE. Directory\nname defaults to `meta.id` and can be overridden via `task.ext.prefix`.\n", + "pattern": "*" + } + } + ] + ], + "versions_gedi": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gedi": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gedi -e Version 2>&1 | sed -n 's/.*Gedi version \\([^ ]*\\).*/\\1/p' | head -n 1": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gedi": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gedi -e Version 2>&1 | sed -n 's/.*Gedi version \\([^ ]*\\).*/\\1/p' | head -n 1": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@pinin4fjords"], + "maintainers": ["@pinin4fjords"] + } }, { - "name": "troughgraph", - "version": "dev" + "name": "gedi_price", + "path": "modules/nf-core/gedi/price/meta.yml", + "type": "module", + "meta": { + "name": "gedi_price", + "description": "Identify translated ORFs from Ribo-seq BAMs using the PRICE algorithm", + "keywords": ["riboseq", "orf", "price", "gedi", "translation"], + "tools": [ + { + "gedi": { + "description": "Gedi is a Java software platform for working with genomic data (sequencing reads, sequences, per-base numeric values, annotations). It provides the PRICE algorithm (Probabilistic Inference of Codon Activities by an EM algorithm) for ribosome profiling ORF discovery with near-cognate start codon detection.", + "homepage": "https://github.com/erhard-lab/gedi", + "documentation": "https://github.com/erhard-lab/gedi/wiki", + "tool_dev_url": "https://github.com/erhard-lab/gedi", + "doi": "10.1038/nmeth.4631", + "licence": ["GPL-3.0"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map identifying the cohort of Ribo-seq BAMs analysed together.\nPRICE is run jointly across all BAMs in this tuple.\ne.g. `[ id:'all_samples' ]`\n" + } + }, + { + "bams": { + "type": "file", + "description": "One or more sorted Ribo-seq BAM files. Staged under `bams/` so PRICE\ndiscovers them via a generated bamlist.\n", + "pattern": "*.{bam}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + }, + { + "bais": { + "type": "file", + "description": "Index files matching the input BAMs.", + "pattern": "*.{bai}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information. `meta2.id` must match the\nbase name used when the index was built (`.oml` lives inside the\nindex directory).\ne.g. `[ id:'homo_sapiens' ]`\n" + } + }, + { + "index": { + "type": "directory", + "description": "GEDI genome index directory produced by GEDI_INDEXGENOME.", + "pattern": "price_index" + } + } + ] + ], + "output": { + "orfs_tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map identifying the analysed cohort.\n" + } + }, + { + "${prefix}.orfs.tsv": { + "type": "file", + "description": "Tab-delimited table of predicted translated ORFs with start codon,\nlocation, p-value and supporting read counts.\n", + "pattern": "*.orfs.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "orfs_cit": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map identifying the analysed cohort.\n" + } + }, + { + "${prefix}.orfs.cit": { + "type": "file", + "description": "GEDI binary CIT file of called ORFs.", + "pattern": "*.orfs.cit", + "ontologies": [] + } + } + ] + ], + "orfs_metadata": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map identifying the analysed cohort.\n" + } + }, + { + "${prefix}.orfs.cit.metadata.json": { + "type": "file", + "description": "JSON metadata accompanying the ORF CIT file.", + "pattern": "*.orfs.cit.metadata.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "codons_cit": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map identifying the analysed cohort.\n" + } + }, + { + "${prefix}.codons.cit": { + "type": "file", + "description": "GEDI binary CIT file of per-codon signal.", + "pattern": "*.codons.cit", + "ontologies": [] + } + } + ] + ], + "model": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map identifying the analysed cohort.\n" + } + }, + { + "${prefix}.model": { + "type": "file", + "description": "PRICE model parameters fit during the run.", + "pattern": "*.model", + "ontologies": [] + } + } + ] + ], + "signal": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map identifying the analysed cohort.\n" + } + }, + { + "${prefix}.signal.tsv": { + "type": "file", + "description": "Tab-delimited per-position signal summary.", + "pattern": "*.signal.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "param": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map identifying the analysed cohort.\n" + } + }, + { + "${prefix}.param": { + "type": "file", + "description": "PRICE run parameters file.", + "pattern": "*.param", + "ontologies": [] + } + } + ] + ], + "versions_gedi": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gedi": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gedi -e Version 2>&1 | sed -n 's/.*Gedi version \\([^ ]*\\).*/\\1/p' | head -n 1": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gedi": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gedi -e Version 2>&1 | sed -n 's/.*Gedi version \\([^ ]*\\).*/\\1/p' | head -n 1": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@pinin4fjords"], + "maintainers": ["@pinin4fjords"] + } }, { - "name": "variantcatalogue", - "version": "dev" + "name": "gem2_gem2bedmappability", + "path": "modules/nf-core/gem2/gem2bedmappability/meta.yml", + "type": "module", + "meta": { + "name": "gem2_gem2bedmappability", + "description": "Convert a mappability file to bedgraph format", + "keywords": ["mappability", "bedgraph", "index", "gem"], + "tools": [ + { + "gem2": { + "description": "GEM2 is a high-performance mapping tool. It also provide a unique tool to evaluate mappability.", + "homepage": "https://paoloribeca.science/gem", + "licence": ["Custom"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "map": { + "type": "file", + "description": "The mappability file created from the index", + "pattern": "*.mappability", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing index information\n" + } + }, + { + "index": { + "type": "file", + "description": "The index of the reference FASTA", + "pattern": "*.gem", + "ontologies": [] + } + } + ] + ], + "output": { + "bedgraph": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bg": { + "type": "file", + "description": "The resulting bedgraph file", + "pattern": "*.bg", + "ontologies": [] + } + } + ] + ], + "sizes": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.sizes": { + "type": "file", + "description": "The chromosome sizes", + "pattern": "*.sizes", + "ontologies": [] + } + } + ] + ], + "versions_gem2": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gem2": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "20200110": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gem2": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "20200110": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@nvnieuwk"], + "maintainers": ["@nvnieuwk"] + } }, { - "name": "viralintegration", - "version": "0.1.1" + "name": "gem2_gemindexer", + "path": "modules/nf-core/gem2/gemindexer/meta.yml", + "type": "module", + "meta": { + "name": "gem2_gemindexer", + "description": "Create a GEM index from a FASTA file", + "keywords": ["fasta", "index", "reference", "mappability"], + "tools": [ + { + "gem2": { + "description": "GEM2 is a high-performance mapping tool. It also provide a unique tool to evaluate mappability.", + "homepage": "https://paoloribeca.science/gem", + "licence": ["Custom"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "A reference FASTA file to index", + "pattern": "*.{fasta,fa,fna}", + "ontologies": [] + } + } + ] + ], + "output": { + "index": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.gem": { + "type": "file", + "description": "The GEM index file", + "pattern": "*.gem", + "ontologies": [] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "The execution log", + "pattern": "*.log", + "ontologies": [] + } + } + ] + ], + "versions_gem2": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gem2": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "20200110": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gem2": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "20200110": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@nvnieuwk"], + "maintainers": ["@nvnieuwk"] + } }, { - "name": "viralmetagenome", - "version": "1.1.1" + "name": "gem2_gemmappability", + "path": "modules/nf-core/gem2/gemmappability/meta.yml", + "type": "module", + "meta": { + "name": "gem2_gemmappability", + "description": "Define the mappability of a reference", + "keywords": ["mappability", "gem", "index", "reference"], + "tools": [ + { + "gem2": { + "description": "GEM2 is a high-performance mapping tool. It also provide a unique tool to evaluate mappability.", + "homepage": "https://paoloribeca.science/gem", + "licence": ["Custom"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "index": { + "type": "file", + "description": "The index created with gem-indexer from the reference FASTA", + "pattern": "*.gem", + "ontologies": [] + } + } + ], + { + "read_length": { + "type": "integer", + "description": "The read length to define the mappability of" + } + } + ], + "output": { + "map": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.mappability": { + "type": "file", + "description": "The resulting mappability file", + "pattern": "*.mappability", + "ontologies": [] + } + } + ] + ], + "versions_gem2": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gem2": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "20200110": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gem2": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "20200110": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@nvnieuwk"], + "maintainers": ["@nvnieuwk"] + } }, { - 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"type": "module", - "meta": { - "name": "fastqe", - "description": "fastqe is a bioinformatics command line tool that uses emojis to represent and analyze genomic data.", - "keywords": [ - "quality control", - "fastq", - "emoji", - "visualization" - ], - "tools": [ - { - "fastqe": { - "description": "A tool for visualizing FASTQ file quality using emoji", - "homepage": "https://github.com/fastqe/fastqe", - "documentation": "https://github.com/fastqe/fastqe#readme", - "tool_dev_url": "https://github.com/fastqe/fastqe", - "doi": "10.21105/joss.02400", - "licence": [ - "MIT" - ], - "identifier": "biotools:fastqe" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "fastq": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", - "ontologies": [] - } - } - ] - ], - "output": { - "tsv": [ - 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} - } - ] - ] - }, - "authors": [ - "@adamrtalbot" - ], - "maintainers": [ - "@adamrtalbot" - ] - } - }, - { - "name": "fastqscan", - "path": "modules/nf-core/fastqscan/meta.yml", - "type": "module", - "meta": { - "name": "fastqscan", - "description": "FASTQ summary statistics in JSON format", - "keywords": [ - "fastq", - "summary", - "statistics" - ], - "tools": [ - { - "fastqscan": { - "description": "FASTQ summary statistics in JSON format", - "homepage": "https://github.com/rpetit3/fastq-scan", - "documentation": "https://github.com/rpetit3/fastq-scan", - "tool_dev_url": "https://github.com/rpetit3/fastq-scan", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "FASTQ file", - "pattern": "*.{fastq.gz,fq.gz}", - "ontologies": [] - } - } - ] - ], - "output": { - "json": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.json": { - "type": "file", - "description": "JSON formatted file of summary statistics", - "pattern": "*.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "versions_fastqscan": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "fastqscan": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "fastq-scan -v 2>&1 | sed 's/^.*fastq-scan //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "fastqscan": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "fastq-scan -v 2>&1 | sed 's/^.*fastq-scan //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@rpetit3" - ], - "maintainers": [ - "@rpetit3" - ] - } - }, - { - "name": "fastqscreen_buildfromindex", - "path": "modules/nf-core/fastqscreen/buildfromindex/meta.yml", - "type": "module", - "meta": { - "name": "fastqscreen_buildfromindex", - "description": "Build fastq screen config file from bowtie index files", - "keywords": [ - "build", - "index", - "genome", - "reference" - ], - "tools": [ - { - "fastqscreen": { - "description": "FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect.", - "homepage": "https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/", - "documentation": "https://stevenwingett.github.io/FastQ-Screen/", - "tool_dev_url": "https://github.com/StevenWingett/FastQ-Screen/archive/refs/tags/v0.15.3.zip", - "doi": "10.5281/zenodo.5838377", - "licence": [ - "GPL-3.0-or-later" - ], - "identifier": "" - } - } - ], - "input": [ - { - "genome_names": { - "type": "string", - "description": "List of names for each index" - } - }, - { - "indexes": { - "type": "directory", - "description": "Bowtie2 genome directories containing index files" - } - } - ], - "output": { - "database": [ - { - "FastQ_Screen_Genomes": { - "type": "directory", - "description": "fastq screen database folder containing config file and index folders", - "pattern": "FastQ_Screen_Genomes" - } - } - ], - "versions_fastqscreen": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "fastqscreen": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "fastq_screen --version 2>&1 | sed \"s/^.*FastQ Screen v//;\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - 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}, - { - "0.5.0": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "fcsadaptor": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "0.5.0": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "raredisease", + "version": "3.0.0" + } ] - ] - }, - "authors": [ - "@d4straub" - ], - "maintainers": [ - "@d4straub", - "@gallvp" - ] - }, - "pipelines": [ - { - "name": "genomeqc", - "version": "dev" - } - ] - }, - { - "name": "fcs_fcsgx", - "path": "modules/nf-core/fcs/fcsgx/meta.yml", - "type": "module", - "meta": { - "name": "fcs_fcsgx", - "description": "Run FCS-GX on assembled genomes. The contigs of the assembly are searched against a reference database excluding the given taxid.", - "deprecated": true, - "keywords": [ - "assembly", - "genomics", - "quality control", - "contamination", - "NCBI" - ], - "tools": [ - { - "fcs": { - "description": "\"The Foreign Contamination Screening (FCS) tool rapidly detects contaminants from foreign\norganisms in genome assemblies to prepare your data for submission. Therefore, the\nsubmission process to NCBI is faster and fewer contaminated genomes are submitted.\nThis reduces errors in analyses and conclusions, not just for the original data submitter\nbut for all subsequent users of the assembly.\"\n", - "homepage": "https://www.ncbi.nlm.nih.gov/data-hub/cgr/data-quality-tools/", - "documentation": "https://github.com/ncbi/fcs/wiki/FCS-GX", - "tool_dev_url": "https://github.com/ncbi/fcs", - "license": [ - "United States Government Work" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "assembly": { - "type": "file", - "description": "assembly fasta file", - "ontologies": [] - } + }, + { + "name": "genmod_compound", + "path": "modules/nf-core/genmod/compound/meta.yml", + "type": "module", + "meta": { + "name": "genmod_compound", + "description": "Score compounds", + "keywords": ["compound", "genmod", "ranking"], + "tools": [ + { + "genmod": { + "description": "Annotate genetic inheritance models in variant files", + "homepage": "https://github.com/Clinical-Genomics/genmod", + "documentation": "https://github.com/Clinical-Genomics/genmod", + "tool_dev_url": "https://github.com/moonso", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input_vcf": { + "type": "file", + "description": "VCF file", + "pattern": "*.{vcf}", + "ontologies": [] + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ] #\n" + } + }, + { + "*_compound.vcf": { + "type": "file", + "description": "Output VCF file", + "pattern": "*.{vcf}", + "ontologies": [] + } + } + ] + ], + "versions_genmod": [ + [ + { + "${task.process}": { + "type": "string", + "description": "Name of the process" + } + }, + { + "genmod": { + "type": "string", + "description": "Name of the tool" + } + }, + { + "genmod --version | sed 's/^.*genmod version: //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "Name of the process" + } + }, + { + "genmod": { + "type": "string", + "description": "Name of the tool" + } + }, + { + "genmod --version | sed 's/^.*genmod version: //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@ramprasadn"], + "maintainers": ["@ramprasadn"] }, - { - "taxid": { - "type": "string", - "description": "Taxonomic id (e.g. \"6973\")" - } - } - ], - { - "gxdb": { - "type": "file", - "description": "The NCBI GenBank database to search against.", - "ontologies": [] - } - } - ], - "output": { - "fcs_gx_report": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "out/*.fcs_gx_report.txt": { - "type": "file", - "description": "Report containing the contig identifier and recommended action (EXCLUDE, TRIM, FIX, REVIEW)", - "pattern": "*.fcs_gx_report.txt", - "ontologies": [] - } - } - ] - ], - "taxonomy_report": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "out/*.taxonomy.rpt": { - "type": "file", - "description": "Report containing the contig identifier and mapped contaminant species", - "pattern": "*.taxonomy.rpt", - "ontologies": [] - } - } - ] - ], - "versions_fcsadaptor": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "fcsadaptor": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "0.4.0": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_python": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "python": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python3 --version |& sed 's/Python //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "fcsadaptor": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "0.4.0": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "python": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python3 --version |& sed 's/Python //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "raredisease", + "version": "3.0.0" + } ] - ] - }, - "authors": [ - "@tillenglert" - ], - "maintainers": [ - "@tillenglert" - ] - } - }, - { - "name": "fcsgx_cleangenome", - "path": "modules/nf-core/fcsgx/cleangenome/meta.yml", - "type": "module", - "meta": { - "name": "fcsgx_cleangenome", - "description": "Runs FCS-GX (Foreign Contamination Screen - Genome eXtractor) to remove foreign contamination from genome assemblies", - "keywords": [ - "genome", - "assembly", - "contamination", - "screening", - "cleaning", - "fcs-gx" - ], - "tools": [ - { - "fcsgx": { - "description": "The NCBI Foreign Contamination Screen. Genomic cross-species aligner, for contamination detection.", - "homepage": "https://github.com/ncbi/fcs-gx", - "documentation": "https://github.com/ncbi/fcs/wiki/", - "tool_dev_url": "https://github.com/ncbi/fcs-gx", - "doi": "10.1186/s13059-024-03198-7", - "licence": [ - "NCBI-PD" - ], - "identifier": "biotools:ncbi_fcs" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input genome assembly file in FASTA format", - "pattern": "*.{fa,fasta,fna}", - "ontologies": [] - } + }, + { + "name": "genmod_models", + "path": "modules/nf-core/genmod/models/meta.yml", + "type": "module", + "meta": { + "name": "genmod_models", + "description": "annotate models of inheritance", + "keywords": ["models", "genmod", "ranking"], + "tools": [ + { + "genmod": { + "description": "Annotate genetic inheritance models in variant files", + "homepage": "https://github.com/Clinical-Genomics/genmod", + "documentation": "https://github.com/Clinical-Genomics/genmod", + "tool_dev_url": "https://github.com/moonso", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input_vcf": { + "type": "file", + "description": "vcf file", + "pattern": "*.{vcf}", + "ontologies": [] + } + }, + { + "fam": { + "type": "file", + "description": "PED file with family information", + "ontologies": [] + } + } + ], + { + "reduced_penetrance": { + "type": "file", + "description": "file with gene ids that have reduced penetrance", + "pattern": "*.{tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_models.vcf": { + "type": "file", + "description": "Output VCF file", + "pattern": "*.{vcf}", + "ontologies": [] + } + } + ] + ], + "versions_genmod": [ + [ + { + "${task.process}": { + "type": "string", + "description": "Name of the process" + } + }, + { + "genmod": { + "type": "string", + "description": "Name of the tool" + } + }, + { + "genmod --version | sed 's/^.*genmod version: //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "Name of the process" + } + }, + { + "genmod": { + "type": "string", + "description": "Name of the tool" + } + }, + { + "genmod --version | sed 's/^.*genmod version: //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@ramprasadn"], + "maintainers": ["@ramprasadn"] }, - { - "fcsgx_report": { - "type": "file", - "description": "Final contamination report with contaminant cleaning actions. Generated using FCSGX_RUNGX", - "ontologies": [] - } - } - ] - ], - "output": { - "cleaned": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.cleaned.fasta": { - "type": "file", - "description": "The fasta file after cleaning, where sequences annotated as ACTION_EXCLUDE or ACTION_TRIM are excluded", - "ontologies": [] - } - } - ] - ], - "contaminants": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.contaminants.fasta": { - "type": "file", - "description": "Sequences annotated as ACTION_EXCLUDE which are marked as contaminants.", - "ontologies": [] - } - } - ] - ], - "versions_fcsgx": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "fcsgx": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gx --help | sed '/build/!d; s/.*:v//; s/-.*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "fcsgx": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gx --help | sed '/build/!d; s/.*:v//; s/-.*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@mahesh-panchal", - "@LaurenHuet" - ], - "maintainers": [ - "@mahesh-panchal" - ] - }, - "pipelines": [ - { - "name": "genomeqc", - "version": "dev" - } - ] - }, - { - "name": "fcsgx_fetchdb", - "path": "modules/nf-core/fcsgx/fetchdb/meta.yml", - "type": "module", - "meta": { - "name": "fcsgx_fetchdb", - "description": "Fetches the NCBI FCS-GX database using a provided manifest URL", - "keywords": [ - "fcs-gx", - "database", - "fetch", - "ncbi" - ], - "tools": [ - { - "fcsgx": { - "description": "The NCBI Foreign Contamination Screen. Genomic cross-species aligner, for contamination detection.", - "homepage": "https://github.com/ncbi/fcs-gx", - "documentation": "https://github.com/ncbi/fcs/wiki/", - "tool_dev_url": "https://github.com/ncbi/fcs-gx", - "doi": "10.1186/s13059-024-03198-7", - "licence": [ - "NCBI-PD" - ], - "identifier": "biotools:ncbi_fcs" - } - } - ], - "input": [ - { - "manifest": { - "type": "file", - "description": "URL to a FCXGX database", - "pattern": "https://ftp*.manifest", - "ontologies": [] - } - } - ], - "output": { - "database": [ - { - "$prefix": { - "type": "directory", - "description": "A directory containing an FCSGX database" - } - } - ], - "versions_fcsgx": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "fcsgx": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gx --help | sed '/build/!d; s/.*:v//; s/-.*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "fcsgx": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gx --help | sed '/build/!d; s/.*:v//; s/-.*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "raredisease", + "version": "3.0.0" + } ] - ] - }, - "authors": [ - "@mahesh-panchal" - ], - "maintainers": [ - "@mahesh-panchal" - ] - }, - "pipelines": [ - { - "name": "genomeqc", - "version": "dev" - } - ] - }, - { - "name": "fcsgx_rungx", - "path": "modules/nf-core/fcsgx/rungx/meta.yml", - "type": "module", - "meta": { - "name": "fcsgx_rungx", - "description": "Runs FCS-GX (Foreign Contamination Screen - Genome eXtractor) to screen and remove foreign contamination from genome assemblies", - "keywords": [ - "genome", - "assembly", - "contamination", - "screening", - "cleaning", - "fcs-gx" - ], - "tools": [ - { - "fcsgx": { - "description": "The NCBI Foreign Contamination Screen. Genomic cross-species aligner, for contamination detection.", - "homepage": "https://github.com/ncbi/fcs-gx", - "documentation": "https://github.com/ncbi/fcs/wiki/", - "tool_dev_url": "https://github.com/ncbi/fcs-gx", - "doi": "10.1186/s13059-024-03198-7", - "licence": [ - "NCBI-PD" - ], - "identifier": "biotools:ncbi_fcs" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "taxid": { - "type": "string", - "description": "Taxonomy ID of the expected organism" - } + }, + { + "name": "genmod_score", + "path": "modules/nf-core/genmod/score/meta.yml", + "type": "module", + "meta": { + "name": "genmod_score", + "description": "Score the variants of a vcf based on their annotation", + "keywords": ["score", "ranking", "genmod"], + "tools": [ + { + "genmod": { + "description": "Annotate genetic inheritance models in variant files", + "homepage": "https://github.com/Clinical-Genomics/genmod", + "documentation": "https://github.com/Clinical-Genomics/genmod", + "tool_dev_url": "https://github.com/moonso", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input_vcf": { + "type": "file", + "description": "vcf file", + "pattern": "*.{vcf}", + "ontologies": [] + } + }, + { + "fam": { + "type": "file", + "description": "PED file with family information", + "ontologies": [] + } + }, + { + "score_config": { + "type": "file", + "description": "rank model config file", + "pattern": "*.{ini}", + "ontologies": [] + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_score.vcf": { + "type": "file", + "description": "Output VCF file", + "pattern": "*.{vcf}", + "ontologies": [] + } + } + ] + ], + "versions_genmod": [ + [ + { + "${task.process}": { + "type": "string", + "description": "Name of the process" + } + }, + { + "genmod": { + "type": "string", + "description": "Name of the tool" + } + }, + { + "genmod --version | sed 's/^.*genmod version: //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "Name of the process" + } + }, + { + "genmod": { + "type": "string", + "description": "Name of the tool" + } + }, + { + "genmod --version | sed 's/^.*genmod version: //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@ramprasadn"], + "maintainers": ["@ramprasadn"] }, - { - "fasta": { - "type": "file", - "description": "Input genome assembly file in FASTA format", - "pattern": "*.{fa,fasta,fna}", - "ontologies": [] - } - } - ], - { - "gxdb": { - "type": "directory", - "description": "Directory containing the FCS-GX database" - } - }, - { - "ramdisk_path": { - "type": "string", - "description": "Path to RAM disk for improved performance (optional)" - } - } - ], - "output": { - "fcsgx_report": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.fcs_gx_report.txt": { - "type": "file", - "description": "Final contamination report with contaminant cleaning actions. Interpreted by gx clean genome to separate cleaned sequences from contaminants.", - "ontologies": [] - } - } - ] - ], - "taxonomy_report": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.taxonomy.rpt": { - "type": "file", - "description": "Intermediate report with assigned taxonomies to individual sequences.", - "pattern": "*.taxonomy.rpt", - "ontologies": [] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.summary.txt": { - "type": "file", - "description": "FCSGX log file", - "pattern": "*.summary.txt", - "ontologies": [] - } - } - ] - ], - "hits": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.hits.tsv.gz": { - "type": "file", - "description": "Save intermediate alignments", - "pattern": "*.hits.tsv.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "versions_fcsgx": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "fcsgx": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gx --help | sed '/build/!d; s/.*:v//; s/-.*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "fcsgx": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gx --help | sed '/build/!d; s/.*:v//; s/-.*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@tillenglert", - "@mahesh-panchal" - ], - "maintainers": [ - "@tillenglert", - "@mahesh-panchal" - ] - }, - "pipelines": [ - { - "name": "genomeqc", - "version": "dev" - } - ] - }, - { - "name": "ffq", - "path": "modules/nf-core/ffq/meta.yml", - "type": "module", - "meta": { - "name": "ffq", - "description": "A command line tool that makes it easier to find sequencing data from the SRA / GEO / ENA.", - "keywords": [ - "SRA", - "ENA", - "GEO", - "metadata", - "fetch", - "public", - "databases" - ], - "tools": [ - { - "ffq": { - "description": "A command line tool that makes it easier to find sequencing data from the SRA / GEO / ENA.", - "homepage": "https://github.com/pachterlab/ffq", - "documentation": "https://github.com/pachterlab/ffq#usage", - "tool_dev_url": "https://github.com/pachterlab/ffq", - "doi": "10.1101/2022.05.18.492548", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - { - "ids": { - "type": "list", - "description": "List of supported database ids e.g. SRA / GEO / ENA" - } - } - ], - "output": { - "json": [ - { - "*.json": { - "type": "file", - "description": "JSON file containing metadata for ids", - "pattern": "*.{json}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ], - "versions_ffq": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "ffq": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "ffq --help 2>&1 | sed 's/^.*ffq //; 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"description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_summary/*_plasmid_genes.tsv": { + "type": "file", + "description": "TSV file containing predicted plasmid genes and their annotations", + "pattern": "*_plasmid_genes.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "plasmid_proteins": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_summary/*_plasmid_proteins.faa.gz": { + "type": "file", + "description": "FASTA file containing predicted plasmid protein sequences", + "pattern": "*_plasmid_proteins.faa", + "ontologies": [] + } + } + ] + ], + "plasmid_summary": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_summary/*_plasmid_summary.tsv": { + "type": "file", + "description": "TSV file containing a summary of geNomad's plasmid predictions", + "pattern": "*_plasmid_summary.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "virus_fasta": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_summary/*_virus.fna.gz": { + "type": "file", + "description": "FASTA file containing predicted virus sequences", + "pattern": "*_virus.fna", + "ontologies": [] + } + } + ] + ], + "virus_genes": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_summary/*_virus_genes.tsv": { + "type": "file", + "description": "TSV file containing predicted virus genes and their annotations", + "pattern": "*_virus_genes.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + 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"ontologies": [] + } + } + ] + ], + "transformed_linear_plot_png": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}_transformed_linear_plot.png": { + "type": "file", + "description": "A genomescope2 transformed linear plot in PNG format", + "pattern": "*_transformed_linear_plot.png", + "ontologies": [] + } + } + ] + ], + "log_plot_png": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}_log_plot.png": { + "type": "file", + "description": "A genomescope2 log plot in PNG format", + "pattern": "*_log_plot.png", + "ontologies": [] + } + } + ] + ], + "transformed_log_plot_png": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}_transformed_log_plot.png": { + "type": "file", + "description": "A genomescope2 transformed log plot in PNG format", + "pattern": "*_transformed_log_plot.png", + "ontologies": [] + } + } + ] + ], + "model": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}_model.txt": { + "type": "file", + "description": "Genomescope2 model fit summary", + "pattern": "*_model.txt", + "ontologies": [] + } + } + ] + ], + "summary": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}_summary.txt": { + "type": "file", + "description": "Genomescope2 histogram summary", + "pattern": "*_summary.txt", + "ontologies": [] + } + } + ] + ], + "lookup_table": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}_lookup_table.txt": { + "type": "file", + "description": "Fitted histogram lookup table", + "pattern": "*_lookup_table.txt", + "ontologies": [] + } + } + ] + ], + "fitted_histogram_png": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}_fitted_hist.png": { + "type": "file", + "description": "A genomescope2 fitted histogram plot in PNG format", + "pattern": "*_fitted_hist.png", + "ontologies": [] + } + } + ] + ], + "json_report": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.json": { + "type": "file", + "description": "A JSON format report of the genomescope2 model", + "pattern": "*.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "versions_genomescope2": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "genomescope2": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "genomescope2 -v | sed \"s/GenomeScope //\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "genomescope2": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "genomescope2 -v | sed \"s/GenomeScope //\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@mahesh-panchal"], + "maintainers": ["@mahesh-panchal"] + } }, { - "name": "sarek", - "version": "3.8.1" - } - ] - }, - { - "name": "fgbio_collectduplexseqmetrics", - "path": "modules/nf-core/fgbio/collectduplexseqmetrics/meta.yml", - "type": "module", - "meta": { - "name": "fgbio_collectduplexseqmetrics", - "description": "Collects a suite of metrics to QC duplex sequencing data.", - "keywords": [ - "UMIs", - "QC", - "bam", - "duplex" - ], - "tools": [ - { - "fgbio": { - "description": "A set of tools for working with genomic and high throughput sequencing data, including UMIs", - "homepage": "http://fulcrumgenomics.github.io/fgbio/", - "documentation": "http://fulcrumgenomics.github.io/fgbio/", - "tool_dev_url": "https://github.com/fulcrumgenomics/fgbio", - "licence": [ - "MIT" - ], - "identifier": "biotools:fgbio" - } - }, - { - "r-ggplot2": { - "description": "ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics. ", - "homepage": "https://ggplot2.tidyverse.org/", - "documentation": "https://ggplot2.tidyverse.org/", - "tool_dev_url": "https://github.com/tidyverse/ggplot2", - "licence": [ - "MIT" - ], - "identifier": "biotools:fgbio" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "grouped_bam": { - "type": "file", - "description": "It has to be either 1)The exact BAM output by the GroupReadsByUmi tool (in the sort-order it was produced in) 2)A BAM file that has MI tags present on all reads (usually set by GroupReadsByUmi and has been sorted with SortBam into TemplateCoordinate order.", - "pattern": "*.bam", - "ontologies": [] - } - }, - { - "interval_list": { - "type": "file", - "description": "Calculation of metrics may be restricted to a set of regions using the --intervals parameter. The file format is descripted here https://samtools.github.io/htsjdk/javadoc/htsjdk/index.html?htsjdk/samtools/util/Interval.html", - "pattern": "*.{tsv|txt|interval_list}", - "ontologies": [] - } - } - ] - ], - "output": { - "family_sizes": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "**.family_sizes.txt": { - "type": "file", - "description": "Metrics on the frequency of different types of families of different sizes", - "pattern": "*.txt", - "ontologies": [] - } - } - ] - ], - "duplex_family_sizes": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "**.duplex_family_sizes.txt": { - "type": "file", - "description": "Metrics on the frequency of duplex tag families by the number of observations from each strand", - "pattern": "*.txt", - "ontologies": [] - } - } - ] - ], - "duplex_yield_metrics": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "**.duplex_yield_metrics.txt": { - "type": "file", - "description": "Summary QC metrics produced using 5%, 10%, 15%...100% of the data", - "pattern": "*.txt", - "ontologies": [] - } - } - ] - ], - "umi_counts": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "**.umi_counts.txt": { - "type": "file", - "description": "Metrics on the frequency of observations of UMIs within reads and tag families", - "pattern": "*.txt", - "ontologies": [] - } - } - ] - ], - "duplex_qc": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "**.duplex_qc.pdf": { - "type": "file", - "description": "A series of plots generated from the preceding metrics files for visualization", - "pattern": "*.pdf", - "ontologies": [] - } - } - ] - ], - "duplex_umi_counts": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "**.duplex_umi_counts.txt": { - "type": "file", - "description": "Metrics on the frequency of observations of duplex UMIs within reads and tag families.", - "pattern": "*.txt", - "ontologies": [] - } - } - ] - ], - "versions_fgbio": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "fgbio": { - "type": "string", - "description": "The tool name" - } - }, - { - "fgbio --version 2>&1 | tr -d \"[:cntrl:]\" | sed -e \"s/^.*Version: //;s/\\[.*$//\"": { - "type": "eval", - "description": "The command used to generate the version of the tool" - } - } - ] - ], - "versions_ggplot2": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "ggplot2": { - "type": "string", - "description": "The tool name" - } - }, - { - "Rscript -e \"cat(as.character(packageVersion('ggplot2')))\"": { - "type": "eval", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "fgbio": { - "type": "string", - "description": "The tool name" - } - }, - { - "fgbio --version 2>&1 | tr -d \"[:cntrl:]\" | sed -e \"s/^.*Version: //;s/\\[.*$//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "ggplot2": { - "type": "string", - "description": "The tool name" - } - }, - { - "Rscript -e \"cat(as.character(packageVersion('ggplot2')))\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@georgiakes" - ], - "maintainers": [ - "@georgiakes" - ] - } - }, - { - "name": "fgbio_copyumifromreadname", - "path": "modules/nf-core/fgbio/copyumifromreadname/meta.yml", - "type": "module", - "meta": { - "name": "fgbio_copyumifromreadname", - "description": "Copies the UMI at the end of a bam files read name to the RX tag.", - "keywords": [ - "fgbio", - "copy", - "umi", - "readname" - ], - "tools": [ - { - "fgbio": { - "description": "A set of tools for working with genomic and high throughput sequencing data, including UMIs", - "homepage": "http://fulcrumgenomics.github.io/fgbio/", - "documentation": "http://fulcrumgenomics.github.io/fgbio/tools/latest/CallDuplexConsensusReads.html", - "tool_dev_url": "https://github.com/fulcrumgenomics/fgbio", - "licence": [ - "MIT" - ], - "identifier": "biotools:fgbio" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - }, - { - "edam": "http://edamontology.org/format_2573" - }, - { - "edam": "http://edamontology.org/format_3462" - } - ] - } - }, - { - "bai": { - "type": "file", - "description": "Index for bam file", - "pattern": "*.{bai}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - }, - { - "edam": "http://edamontology.org/format_2573" - }, - { - "edam": "http://edamontology.org/format_3462" - } - ] - } - } - ] - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "Sorted BAM file", - "pattern": "*.{bam}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - } - ] - ], - "bai": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.bai": { - "type": "file", - "description": "Index for bam file", - "pattern": "*.{bai}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3327" - } - ] - } - } - ] - ], - "versions_fgbio": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "fgbio": { - "type": "string", - "description": "The tool name" - } - }, - { - "fgbio --version 2>&1 | tr -d \"[:cntrl:]\" | sed -e \"s/^.*Version: //;s/\\[.*$//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "fgbio": { - "type": "string", - "description": "The tool name" - } - }, - { - "fgbio --version 2>&1 | tr -d \"[:cntrl:]\" | sed -e \"s/^.*Version: //;s/\\[.*$//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@sppearce" - ], - "maintainers": [ - "@sppearce" - ] - }, - "pipelines": [ - { - "name": "sarek", - "version": "3.8.1" - } - ] - }, - { - "name": "fgbio_fastqtobam", - "path": "modules/nf-core/fgbio/fastqtobam/meta.yml", - "type": "module", - "meta": { - "name": "fgbio_fastqtobam", - "description": "Using the fgbio tools, converts FASTQ files sequenced into unaligned BAM or CRAM files possibly moving the UMI barcode into the RX field of the reads\n", - "keywords": [ - "unaligned", - "bam", - "cram" - ], - "tools": [ - { - "fgbio": { - "description": "A set of tools for working with genomic and high throughput sequencing data, including UMIs", - "homepage": "http://fulcrumgenomics.github.io/fgbio/", - "documentation": "http://fulcrumgenomics.github.io/fgbio/tools/latest/", - "tool_dev_url": "https://github.com/fulcrumgenomics/fgbio", - "licence": [ - "MIT" - ], - "identifier": "biotools:fgbio" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "pair of reads to be converted into BAM file", - "pattern": "*.{fastq.gz}", - "ontologies": [] - } - } - ] - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.{bam,cram}": { - "type": "file", - "description": "Unaligned, unsorted BAM or CRAM file", - "pattern": "*.{bam,cram}", - "ontologies": [] - } - } - ] - ], - "versions_fgbio": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "fgbio": { - "type": "string", - "description": "The tool name" - } - }, - { - "fgbio --version 2>&1 | tr -d \"[:cntrl:]\" | sed -e \"s/^.*Version: //;s/\\[.*$//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "fgbio": { - "type": "string", - "description": "The tool name" - } - }, - { - "fgbio --version 2>&1 | tr -d \"[:cntrl:]\" | sed -e \"s/^.*Version: //;s/\\[.*$//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@lescai", - "@matthdsm", - "@nvnieuwk" - ], - "maintainers": [ - "@lescai", - "@matthdsm", - "@nvnieuwk" - ] - }, - "pipelines": [ - { - "name": "radseq", - "version": "dev" - }, - { - "name": "sarek", - "version": "3.8.1" - } - ] - }, - { - "name": "fgbio_filterconsensusreads", - "path": "modules/nf-core/fgbio/filterconsensusreads/meta.yml", - "type": "module", - "meta": { - "name": "fgbio_filterconsensusreads", - "description": "Uses FGBIO FilterConsensusReads to filter consensus reads generated by CallMolecularConsensusReads or CallDuplexConsensusReads.", - "keywords": [ - "fgbio", - "filter", - "consensus", - "umi", - "duplexumi" - ], - "tools": [ - { - "fgbio": { - "description": "A set of tools for working with genomic and high throughput sequencing data, including UMIs", - "homepage": "http://fulcrumgenomics.github.io/fgbio/", - "documentation": "http://fulcrumgenomics.github.io/fgbio/tools/latest/FilterConsensusReads.html", - "tool_dev_url": "https://github.com/fulcrumgenomics/fgbio", - "licence": [ - "MIT" - ], - "identifier": "biotools:fgbio" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file", - "pattern": "*.bam", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing genome information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Fasta file containing genomic sequence information", - "pattern": "*.{fa,fasta,fna}", - "ontologies": [] - } - }, - { - "index": { - "type": "file", - "description": "Fasta index file", - "pattern": "*.fai", - "ontologies": [] - } - }, - { - "dict": { - "type": "file", - "description": "Fasta dictionary file", - "pattern": "*.dict", - "ontologies": [] - } - } - ], - { - "min_reads": { - "type": "integer", - "description": "Minimum number of reads required to keep a consensus read" - } - }, - { - "min_baseq": { - "type": "file", - "description": "Minimum base quality to consider", - "ontologies": [] - } - }, - { - "max_base_error_rate": { - "type": "file", - "description": "Maximum base error rate for a position before it is replaced with an N.", - "ontologies": [] + "name": "genotyphi_parse", + "path": "modules/nf-core/genotyphi/parse/meta.yml", + "type": "module", + "meta": { + "name": "genotyphi_parse", + "description": "Genotype Salmonella Typhi from Mykrobe results", + "keywords": ["genotype", "Salmonella Typhi", "Mykrobe"], + "tools": [ + { + "genotyphi": { + "description": "Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)", + "homepage": "https://github.com/katholt/genotyphi", + "documentation": "https://github.com/katholt/genotyphi", + "tool_dev_url": "https://github.com/katholt/genotyphi", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "json": { + "type": "file", + "description": "JSON formatted file of Mykrobe results", + "pattern": "*.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "output": { + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "A tab-delimited file of predicted genotypes", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_genotyphi": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "genotyphi": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "genotyphi --version |& sed 's/^.*GenoTyphi v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "genotyphi": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "genotyphi --version |& sed 's/^.*GenoTyphi v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@rpetit3"], + "maintainers": ["@rpetit3"] } - } - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.bam": { - "type": "file", - "description": "Filtered consensus BAM file", - "pattern": "*.bam", - "ontologies": [] - } - } - ] - ], - "versions_fgbio": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "fgbio": { - "type": "string", - "description": "The tool name" - } - }, - { - "fgbio --version 2>&1 | tr -d \"[:cntrl:]\" | sed -e \"s/^.*Version: //;s/\\[.*$//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "fgbio": { - "type": "string", - "description": "The tool name" - } - }, - { - "fgbio --version 2>&1 | tr -d \"[:cntrl:]\" | sed -e \"s/^.*Version: //;s/\\[.*$//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@lescai" - ], - "maintainers": [ - "@lescai" - ] - }, - "pipelines": [ - { - "name": "radseq", - "version": "dev" - } - ] - }, - { - "name": "fgbio_groupreadsbyumi", - "path": "modules/nf-core/fgbio/groupreadsbyumi/meta.yml", - "type": "module", - "meta": { - "name": "fgbio_groupreadsbyumi", - "description": "Groups reads together that appear to have come from the same original molecule.\nReads are grouped by template, and then templates are sorted by the 5’ mapping positions\nof the reads from the template, used from earliest mapping position to latest.\nReads that have the same end positions are then sub-grouped by UMI sequence.\n(!) Note: the MQ tag is required on reads with mapped mates (!)\nThis can be added using samblaster with the optional argument --addMateTags.\n", - "keywords": [ - "UMI", - "groupreads", - "fgbio" - ], - "tools": [ - { - "fgbio": { - "description": "A set of tools for working with genomic and high throughput sequencing data, including UMIs", - "homepage": "http://fulcrumgenomics.github.io/fgbio/", - "documentation": "http://fulcrumgenomics.github.io/fgbio/tools/latest/", - "tool_dev_url": "https://github.com/fulcrumgenomics/fgbio", - "licence": [ - "MIT" - ], - "identifier": "biotools:fgbio" + }, + { + "name": "genrich", + "path": "modules/nf-core/genrich/meta.yml", + "type": "module", + "meta": { + "name": "genrich", + "description": "Peak-calling for ChIP-seq and ATAC-seq enrichment experiments", + "keywords": ["peak-calling", "ChIP-seq", "ATAC-seq"], + "tools": [ + { + "genrich": { + "description": "Genrich is a peak-caller for genomic enrichment assays (e.g. ChIP-seq, ATAC-seq).\nIt analyzes alignment files generated following the assay and produces a file\ndetailing peaks of significant enrichment.\n", + "homepage": "https://github.com/jsh58/Genrich", + "documentation": "https://github.com/jsh58/Genrich#readme", + "tool_dev_url": "https://github.com/jsh58/Genrich", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "treatment_bam": { + "type": "file", + "description": "Coordinate sorted BAM/SAM file from treatment sample or list of BAM/SAM files from biological replicates", + "pattern": "*.{bam,sam}", + "ontologies": [] + } + }, + { + "control_bam": { + "type": "file", + "description": "Coordinate sorted BAM/SAM file from control sample or list of BAM/SAM files from control samples", + "pattern": "*.{bam,sam}", + "ontologies": [] + } + } + ], + { + "blacklist_bed": { + "type": "file", + "description": "Bed file containing genomic intervals to exclude from the analysis", + "pattern": "*.{bed}", + "ontologies": [] + } + } + ], + "output": { + "peak": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.narrowPeak": { + "type": "file", + "description": "Narrow peak file containing genomic intervals of significant enrichment", + "pattern": "*.{narrowPeak}", + "ontologies": [] + } + } + ] + ], + "versions_genrich": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "genrich": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "Genrich --version 2>&1 | head -n1 | sed 's/Genrich, version //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "bedgraph_pvalues": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.pvalues.bedGraph": { + "type": "file", + "description": "bedGraph file containing p/q values", + "pattern": "*.{pvalues.bedGraph}", + "ontologies": [] + } + } + ] + ], + "bedgraph_pileup": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.pileup.bedGraph": { + "type": "file", + "description": "bedGraph file containing pileups and p-values", + "pattern": "*.{pileup.bedGraph}", + "ontologies": [] + } + } + ] + ], + "bed_intervals": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.intervals.bed": { + "type": "file", + "description": "Bed file containing annotated intervals", + "pattern": "*.{intervals.bed}", + "ontologies": [] + } + } + ] + ], + "duplicates": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.duplicates.txt": { + "type": "file", + "description": "Text output file containing intervals corresponding to PCR duplicates", + "pattern": "*.{intervals.txt}", + "ontologies": [] + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "genrich": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "Genrich --version 2>&1 | head -n1 | sed 's/Genrich, version //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@JoseEspinosa", "@samuelruizperez"], + "maintainers": ["@JoseEspinosa", "@samuelruizperez"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + }, + { + "name": "gens_preparecovandbaf", + "path": "modules/nf-core/gens/preparecovandbaf/meta.yml", + "type": "module", + "meta": { + "name": "preparecovandbaf", + "description": "Tools for preparing inputs for visualization in Gens", + "keywords": ["gens", "preparecovandbaf", "preprocessing", "genomics", "CNV"], + "tools": [ + { + "gens": { + "description": "Scripts for preparing input data to Gens", + "homepage": "https://github.com/SMD-Bioinformatics-Lund/Prepare-Gens-input-data", + "documentation": "https://github.com/SMD-Bioinformatics-Lund/Prepare-Gens-input-data/README.md", + "tool_dev_url": "https://github.com/SMD-Bioinformatics-Lund/Prepare-Gens-input-data", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "read_counts": { + "type": "file", + "description": "Binned coverage calculations from GATK", + "pattern": "*.{tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, + { + "gvcf": { + "type": "file", + "description": "GVCF. It is used to calculate B-allele frequencies at the sites specified in baf_positions. It can be generated using any SNV-caller.", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + }, + { + "gvcf_tbi": { + "type": "file", + "description": "GVCF tabix index", + "pattern": "*.vcf.gz.tbi", + "ontologies": [] + } + } + ], + { + "baf_positions": { + "type": "file", + "description": "Sites to sample for BAF calculations", + "pattern": "*.{tsv,tsv.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + "output": { + "cov_gz": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\n" + } + }, + { + "*.cov.bed.gz": { + "type": "file", + "description": "Coverage bed (bgzipped)" + } + } + ] + ], + "cov_tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\n" + } + }, + { + "*.cov.bed.gz.tbi": { + "type": "file", + "description": "Tabix index for coverage bed" + } + } + ] + ], + "baf_gz": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\n" + } + }, + { + "*.baf.bed.gz": { + "type": "file", + "description": "BAF bed (bgzipped)" + } + } + ] + ], + "baf_tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\n" + } + }, + { + "*.baf.bed.gz.tbi": { + "type": "file", + "description": "Tabix index for BAF bed" + } + } + ] + ], + "versions_preparecovandbaf": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "preparecovandbaf": { + "type": "string", + "description": "The tool name" + } + }, + { + "generate_cov_and_baf --version": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "preparecovandbaf": { + "type": "string", + "description": "The tool name" + } + }, + { + "generate_cov_and_baf --version": { + "type": "eval", + "description": "The expression used to obtain the tool version" + } + } + ] + ] + }, + "authors": ["@jakob37"], + "maintainers": ["@jakob37"] }, - { - "bam": { - "type": "file", - "description": "BAM file. Note: the MQ tag is required on reads with mapped mates (!)\n", - "pattern": "*.bam", - "ontologies": [] - } - } - ], - { - "strategy": { - "type": "string", - "enum": [ - "Identity", - "Edit", - "Adjacency", - "Paired" - ], - "description": "Required argument: defines the UMI assignment strategy.\nMust be chosen among: Identity, Edit, Adjacency, Paired.\n" - } - } - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "UMI-grouped BAM", - "pattern": "*.bam", - "ontologies": [] - } - } - ] - ], - "histogram": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*histogram.txt": { - "type": "file", - "description": "A text file containing the tag family size counts", - "pattern": "*.txt", - "ontologies": [] - } - } - ] - ], - "read_metrics": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*read-metrics.txt": { - "type": "file", - "description": "A text file containing the read count metrics from grouping", - "pattern": "*.txt", - "ontologies": [] - } - } - ] - ], - "versions_fgbio": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "fgbio": { - "type": "string", - "description": "The tool name" - } - }, - { - "fgbio --version 2>&1 | tr -d \"[:cntrl:]\" | sed -e \"s/^.*Version: //;s/\\[.*$//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "fgbio": { - "type": "string", - "description": "The tool name" - } - }, - { - "fgbio --version 2>&1 | tr -d \"[:cntrl:]\" | sed -e \"s/^.*Version: //;s/\\[.*$//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "raredisease", + "version": "3.0.0" + } ] - ] }, - "authors": [ - "@lescai" - ], - "maintainers": [ - "@lescai" - ] - }, - "pipelines": [ { - "name": "radseq", - "version": "dev" + "name": "geofetch", + "path": "modules/nf-core/geofetch/meta.yml", + "type": "module", + "meta": { + "name": "geofetch", + "description": "geofetch is a command-line tool that downloads and organizes data and metadata from GEO and SRA", + "keywords": ["GEO", "expression", "microarray", "sequencing"], + "tools": [ + { + "geofetch": { + "description": "Downloads data and metadata from GEO and SRA and creates standard PEPs.", + "homepage": "http://geofetch.databio.org/", + "documentation": "http://geofetch.databio.org/", + "tool_dev_url": "https://github.com/pepkit/geofetch", + "licence": ["BSD-2-clause"], + "args_id": "$args", + "identifier": "" + } + } + ], + "input": [ + { + "geo_accession": { + "type": "string", + "description": "GEO accession ID" + } + } + ], + "output": { + "samples": [ + [ + { + "${geo_accession}": { + "type": "file", + "description": "List of sample files fetched", + "pattern": "${geo_accession}/*.CEL.gz", + "ontologies": [] + } + }, + { + "${geo_accession}/*.CEL.gz": { + "type": "file", + "description": "List of sample files fetched", + "pattern": "${geo_accession}/*.CEL.gz", + "ontologies": [] + } + } + ] + ], + "versions_geofetch": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "geofetch": { + "type": "string", + "description": "The tool name" + } + }, + { + "geofetch --version 2>&1 | sed '1!d; s/^geofetch //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "geofetch": { + "type": "string", + "description": "The tool name" + } + }, + { + "geofetch --version 2>&1 | sed '1!d; s/^geofetch //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@mribeirodantas"], + "maintainers": ["@mribeirodantas"] + } }, { - "name": "sarek", - "version": "3.8.1" - } - ] - }, - { - "name": "fgbio_sortbam", - "path": "modules/nf-core/fgbio/sortbam/meta.yml", - "type": "module", - "meta": { - "name": "fgbio_sortbam", - "description": "Sorts a SAM or BAM file. Several sort orders are available, including coordinate, queryname, random, and randomquery.", - "keywords": [ - "sort", - "bam", - "sam" - ], - "tools": [ - { - "fgbio": { - "description": "Tools for working with genomic and high throughput sequencing data.", - "homepage": "https://github.com/fulcrumgenomics/fgbio", - "documentation": "http://fulcrumgenomics.github.io/fgbio/", - "licence": [ - "MIT" - ], - "identifier": "biotools:fgbio" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false, collapse:false ]\n" - } + "name": "geoquery_getgeo", + "path": "modules/nf-core/geoquery/getgeo/meta.yml", + "type": "module", + "meta": { + "name": "geoquery_getgeo", + "description": "Retrieves GEO data from the Gene Expression Omnibus (GEO)", + "keywords": ["geo", "expression", "microarray"], + "tools": [ + { + "geoquery": { + "description": "Get data from NCBI Gene Expression Omnibus (GEO)", + "homepage": "https://bioconductor.org/packages/release/bioc/html/GEOquery.html", + "documentation": "https://bioconductor.org/packages/release/bioc/vignettes/GEOquery/inst/doc/GEOquery.html", + "tool_dev_url": "https://github.com/seandavi/GEOquery", + "doi": "10.1093/bioinformatics/btm254", + "licence": ["MIT"], + "identifier": "biotools:geoquery" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing metadata about the GEO dataset, minimally 'id'.\n" + } + }, + { + "querygse": { + "type": "string", + "description": "GSE identifier to pass to getGEO()\n" + } + } + ] + ], + "output": { + "rds": [ + [ + { + "meta": { + "type": "map", + "description": "A Groovy map containing sample information" + } + }, + { + "*.rds": { + "type": "file", + "description": "R object containing GEO data", + "pattern": "*.rds", + "ontologies": [] + } + } + ] + ], + "expression": [ + [ + { + "meta": { + "type": "map", + "description": "A Groovy map containing sample information" + } + }, + { + "*matrix.tsv": { + "type": "file", + "description": "TSV-format expression matrix", + "pattern": "*matrix.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "annotation": [ + [ + { + "meta": { + "type": "map", + "description": "A Groovy map containing sample information" + } + }, + { + "*annotation.tsv": { + "type": "file", + "description": "TSV-format annotation file", + "pattern": "*annotation.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "topics": { + "versions": [ + { + "versions.yml": { + "type": "string", + "description": "The name of the process" + } + } + ] + }, + "authors": ["@azedinez", "@pinin4fjords"], + "maintainers": ["@azedinez", "@pinin4fjords"] }, - { - "bam": { - "type": "file", - "description": "The input SAM or BAM file to be sorted.\n", - "pattern": "*.{bam,sam}", - "ontologies": [] - } - } - ] - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "Output SAM or BAM file.\n", - "pattern": "*.{bam,sam}", - "ontologies": [] - } - } - ] - ], - "versions_fgbio": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "fgbio": { - "type": "string", - "description": "The tool name" - } - }, - { - "fgbio --version 2>&1 | tr -d \"[:cntrl:]\" | sed -e \"s/^.*Version: //;s/\\[.*$//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "fgbio": { - "type": "string", - "description": "The tool name" - } - }, - { - "fgbio --version 2>&1 | tr -d \"[:cntrl:]\" | sed -e \"s/^.*Version: //;s/\\[.*$//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "differentialabundance", + "version": "1.5.0" + } ] - ] - }, - "authors": [ - "@sruthipsuresh" - ], - "maintainers": [ - "@sruthipsuresh" - ] - } - }, - { - "name": "fgbio_zipperbams", - "path": "modules/nf-core/fgbio/zipperbams/meta.yml", - "type": "module", - "meta": { - "name": "fgbio_zipperbams", - "description": "FGBIO tool to zip together an unmapped and mapped BAM to transfer metadata into the output BAM", - "keywords": [ - "fgbio", - "umi", - "unmapped", - "ubam", - "zipperbams" - ], - "tools": [ - { - "fgbio": { - "description": "A set of tools for working with genomic and high throughput sequencing data, including UMIs", - "homepage": "http://fulcrumgenomics.github.io/fgbio/", - "documentation": "http://fulcrumgenomics.github.io/fgbio/tools/latest/", - "tool_dev_url": "https://github.com/fulcrumgenomics/fgbio", - "licence": [ - "MIT" - ], - "identifier": "biotools:fgbio" + }, + { + "name": "getorganelle_config", + "path": "modules/nf-core/getorganelle/config/meta.yml", + "type": "module", + "meta": { + "name": "getorganelle_config", + "description": "Downloads databases needed for running getorganelle", + "keywords": ["assembly", "organelle", "mitochondria", "download", "database"], + "tools": [ + { + "getorganelle": { + "description": "Get organelle genomes from genome skimming data", + "homepage": "https://github.com/Kinggerm/GetOrganelle", + "documentation": "https://github.com/Kinggerm/GetOrganelle", + "tool_dev_url": "https://github.com/Kinggerm/GetOrganelle", + "doi": "10.1186/s13059-020-02154-5", + "licence": ["GPL v3"], + "identifier": "biotools:getorganelle" + } + } + ], + "input": [ + { + "organelle_type": { + "type": "string", + "description": "Type of database, esp. embplant_pt (embryophyta plant plastome), other_pt (non-embryophyta plant plastome), embplant_mt (plant mitochondrion), embplant_nr (plant nuclear ribosomal RNA), animal_mt (animal mitochondrion), and fungus_mt (fungus mitochondrion), fungus_nr (fungus nuclear ribosomal RNA)\n" + } + } + ], + "output": { + "db": [ + [ + { + "organelle_type": { + "type": "string", + "description": "Type of database, esp. embplant_pt (embryophyta plant plastome), other_pt (non-embryophyta plant plastome), embplant_mt (plant mitochondrion), embplant_nr (plant nuclear ribosomal RNA), animal_mt (animal mitochondrion), and fungus_mt (fungus mitochondrion), fungus_nr (fungus nuclear ribosomal RNA)\n" + } + }, + { + "getorganelle": { + "type": "directory", + "description": "Downloaded database for GetOrganelle" + } + } + ] + ], + "versions_getorganelle": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "getorganelle": { + "type": "string", + "description": "Downloaded database for GetOrganelle" + } + }, + { + "get_organelle_config.py --version |& sed 's/^GetOrganelle v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "getorganelle": { + "type": "string", + "description": "Downloaded database for GetOrganelle" + } + }, + { + "get_organelle_config.py --version |& sed 's/^GetOrganelle v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@erinyoung"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "mapped_bam": { - "type": "file", - "description": "mapped BAM/SAM file", - "pattern": "*.{bam,sam}", - "ontologies": [] - } - }, - { - "unmapped_bam": { - "type": "file", - "description": "unmapped BAM file", - "pattern": "*.bam", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'GRCh38' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "fasta file containing genomic sequence information", - "pattern": "*.{fasta,fna,fa}", - "ontologies": [] - } - }, - { - "index": { - "type": "file", - "description": "fasta index file", - "pattern": "*.fai", - "ontologies": [] - } - }, - { - "dict": { - "type": "file", - "description": "dict file containing a sequence dictionary for the fasta file", - "pattern": "*.dict", - "ontologies": [] - } - } - ] - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.bam": { - "type": "file", - "description": "Zipped BAM file", - "pattern": "*.bam", - "ontologies": [] - } - } - ] - ], - "versions_fgbio": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "fgbio": { - "type": "string", - "description": "The tool name" - } - }, - { - "fgbio --version 2>&1 | tr -d \"[:cntrl:]\" | sed -e \"s/^.*Version: //;s/\\[.*$//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "fgbio": { - "type": "string", - "description": "The tool name" - } - }, - { - "fgbio --version 2>&1 | tr -d \"[:cntrl:]\" | sed -e \"s/^.*Version: //;s/\\[.*$//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@lescai" - ], - "maintainers": [ - "@lescai" - ] - }, - "pipelines": [ - { - "name": "radseq", - "version": "dev" - } - ] - }, - { - "name": "fgumi_extract", - "path": "modules/nf-core/fgumi/extract/meta.yml", - "type": "module", - "meta": { - "name": "fgumi_extract", - "description": "Extract unique molecular indices (UMIs) from FASTQ files and write an unaligned BAM file.", - "keywords": [ - "umi", - "extract", - "fastq", - "bam" - ], - "tools": [ - { - "fgumi": { - "description": "High-performance tools for working with UMI-tagged sequencing data.", - "homepage": "https://github.com/fulcrumgenomics/fgumi", - "documentation": "https://docs.rs/fgumi", - "tool_dev_url": "https://github.com/fulcrumgenomics/fgumi", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "Input FASTQ files used for UMI extraction.", - "pattern": "*.fastq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - }, - { - "library": { - "type": "string", - "description": "Library name to store in the output BAM read group." - } - } - ] - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "Unaligned BAM with extracted UMIs in SAM tags.", - "pattern": "*.bam", - "ontologies": [] - } - } - ] - ], - "versions_fgumi": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "fgumi": { - "type": "string", - "description": "The tool name" - } - }, - { - "fgumi --version | sed \"s/^fgumi //\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "fgumi": { - "type": "string", - "description": "The tool name" - } - }, - { - "fgumi --version | sed \"s/^fgumi //\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@atrigila" - ], - "maintainers": [ - "@atrigila" - ] - } - }, - { - "name": "fibertoolsrs_addnucleosomes", - "path": "modules/nf-core/fibertoolsrs/addnucleosomes/meta.yml", - "type": "module", - "meta": { - "name": "fibertoolsrs_addnucleosomes", - "description": "Add nucleosomes positions and MSP position to ONT BAM files", - "keywords": [ - "methylation", - "genomics", - "bam", - "m6A", - "nucleosome", - "fiberseq" - ], - "tools": [ - { - "fibertoolsrs": { - "description": "Mitchell Vollger's rust tools for fiberseq data.", - "homepage": "https://fiberseq.github.io/fibertools/fibertools.html", - "documentation": "https://fiberseq.github.io/fibertools/fibertools.html", - "tool_dev_url": "https://github.com/fiberseq/fibertools-rs", - "doi": "10.5281/zenodo.14782951", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM/CRAM file", - "pattern": "*.{bam,cram}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - }, - { - "edam": "http://edamontology.org/format_2573" - } - ] - } - } - ] - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "bam file with nucleosome calls", - "pattern": "*.bam", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - } - ] - ], - "versions_fibertoolsrs": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "fibertools-rs": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "ft --version | sed 's/fibertools-rs v//;s/\\t.*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "fibertools-rs": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "ft --version | sed 's/fibertools-rs v//;s/\\t.*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@YiJin-Xiong" - ], - "maintainers": [ - "@YiJin-Xiong" - ] - }, - "pipelines": [ - { - "name": "methylong", - "version": "2.0.0" - } - ] - }, - { - "name": "fibertoolsrs_extract", - "path": "modules/nf-core/fibertoolsrs/extract/meta.yml", - "type": "module", - "meta": { - "name": "fibertoolsrs_extract", - "description": "Extract Fiber-seq information (such as m6A, CpG, nucleosomes, and MSPs) from BAM file into BED file", - "keywords": [ - "methylation", - "genomics", - "bam", - "m6A", - "fiberseq" - ], - "tools": [ - { - "fibertoolsrs": { - "description": "Mitchell Vollger's rust tools for fiberseq data.", - "homepage": "https://fiberseq.github.io/fibertools/fibertools.html", - "documentation": "https://fiberseq.github.io/fibertools/fibertools.html", - "tool_dev_url": "https://github.com/fiberseq/fibertools-rs", - "doi": "10.5281/zenodo.14782951", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM/CRAM file", - "pattern": "*.{bam,cram}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - }, - { - "edam": "http://edamontology.org/format_2573" - } - ] - } - } - ], - { - "extract_type": { - "type": "string", - "description": "Type of fiberseq information to extract\ne.g. `m6a`, `cpg`, `msp`, `nuc`, `all`\n" - } - } - ], - "output": { - "bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.bed.gz": { - "type": "file", - "description": "Gzipped BED file with fiber-seq information", - "pattern": "*.bed.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "versions_fibertoolsrs": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "fibertools-rs": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "ft --version | sed 's/fibertools-rs v//;s/\\t.*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "fibertools-rs": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "ft --version | sed 's/fibertools-rs v//;s/\\t.*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@YiJin-Xiong" - ], - "maintainers": [ - "@YiJin-Xiong" - ] - }, - "pipelines": [ - { - "name": "methylong", - "version": "2.0.0" - } - ] - }, - { - "name": "fibertoolsrs_predictm6a", - "path": "modules/nf-core/fibertoolsrs/predictm6a/meta.yml", - "type": "module", - "meta": { - "name": "fibertoolsrs_predictm6a", - "description": "Predict m6A positions using HiFi kinetics data and encode the results in the MM and ML bam tags. Also adds nucleosome (nl, ns) and MTase sensitive patches (al, as)", - "keywords": [ - "methylation", - "genomics", - "bam", - "m6A", - "nucleosome", - "fiberseq" - ], - "tools": [ - { - "fibertoolsrs": { - "description": "Mitchell Vollger's rust tools for fiberseq data.", - "homepage": "https://fiberseq.github.io/fibertools/fibertools.html", - "documentation": "https://fiberseq.github.io/fibertools/fibertools.html", - "tool_dev_url": "https://github.com/fiberseq/fibertools-rs", - "doi": "10.5281/zenodo.14782951", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM/CRAM file", - "pattern": "*.{bam,cram}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - }, - { - "edam": "http://edamontology.org/format_2573" - } - ] - } - } - ] - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "bam file with m6A calls in new/extended MM and ML bam tags", - "pattern": "*.bam", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - } - ] - ], - "versions_fibertoolsrs": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "fibertools-rs": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "ft --version | sed 's/fibertools-rs v//;s/\\t.*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "fibertools-rs": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "ft --version | sed 's/fibertools-rs v//;s/\\t.*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@YiJin-Xiong" - ], - "maintainers": [ - "@YiJin-Xiong" - ] - }, - "pipelines": [ - { - "name": "methylong", - "version": "2.0.0" - } - ] - }, - { - "name": "filtlong", - "path": "modules/nf-core/filtlong/meta.yml", - "type": "module", - "meta": { - "name": "filtlong", - "description": "Filtlong filters long reads based on quality measures or short read data.", - "keywords": [ - "nanopore", - "quality control", - "QC", - "filtering", - "long reads", - "short reads" - ], - "tools": [ - { - "filtlong": { - "description": "Filtlong is a tool for filtering long reads. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.", - "homepage": "https://anaconda.org/bioconda/filtlong", - "tool_dev_url": "https://github.com/rrwick/Filtlong", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:filtlong" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "shortreads": { - "type": "file", - "description": "fastq file", - "pattern": "*.{fq,fastq,fq.gz,fastq.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - }, - { - "longreads": { - "type": "file", - "description": "fastq file", - "pattern": "*.{fq,fastq,fq.gz,fastq.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "output": { - "reads": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.fastq.gz": { - "type": "file", - "description": "Filtered (compressed) fastq file", - "pattern": "*.fastq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.log": { - "type": "file", - "description": "Standard error logging file containing summary statistics", - "pattern": "*.log", - "ontologies": [] - } - } - ] - ], - "versions_filtlong": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "filtlong": { - "type": "string", - "description": "The tool name" - } - }, - { - "filtlong --version | sed -e \"s/Filtlong v//g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "filtlong": { - "type": "string", - "description": "The tool name" - } - }, - { - "filtlong --version | sed -e \"s/Filtlong v//g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@d4straub", - "@sofstam" - ], - "maintainers": [ - "@d4straub", - "@sofstam" - ] - }, - "pipelines": [ - { - "name": "bacass", - "version": "2.6.0" }, { - "name": "circrna", - "version": "dev" - }, - { - "name": "mag", - "version": "5.4.2" + "name": "getorganelle_fromreads", + "path": "modules/nf-core/getorganelle/fromreads/meta.yml", + "type": "module", + "meta": { + "name": "getorganelle_fromreads", + "description": "Assembles organelle genomes from genomic data", + "keywords": ["assembly", "organelle", "mitochondria", "illumina"], + "tools": [ + { + "getorganelle": { + "description": "Get organelle genomes from genome skimming data", + "homepage": "https://github.com/Kinggerm/GetOrganelle", + "documentation": "https://github.com/Kinggerm/GetOrganelle", + "tool_dev_url": "https://github.com/Kinggerm/GetOrganelle", + "doi": "10.1186/s13059-020-02154-5", + "licence": ["GPL v3"], + "identifier": "biotools:getorganelle" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "fastq": { + "type": "file", + "description": "Input fastq files", + "pattern": "*.{fastq.gz}", + "ontologies": [] + } + } + ], + [ + { + "organelle_type": { + "type": "string", + "description": "Type of database, esp. embplant_pt (embryophyta plant plastome), other_pt (non-embryophyta plant plastome), embplant_mt (plant mitochondrion), embplant_nr (plant nuclear ribosomal RNA), animal_mt (animal mitochondrion), and fungus_mt (fungus mitochondrion), fungus_nr (fungus nuclear ribosomal RNA)\n" + } + }, + { + "db": { + "type": "directory", + "description": "GetOrganelle database" + } + } + ] + ], + "output": { + "fasta": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "results/${prefix}.${organelle_type}.fasta.gz": { + "type": "file", + "description": "Complete or partial organelle sequences", + "pattern": "*.fasta.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "etc": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "results/*": { + "type": "file", + "description": "Other output files", + "ontologies": [] + } + } + ] + ], + "versions_getorganelle": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "getorganelle": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "get_organelle_from_reads.py --version |& sed 's/^GetOrganelle v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "getorganelle": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "get_organelle_from_reads.py --version |& sed 's/^GetOrganelle v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@erinyoung"] + } }, { - "name": "taxprofiler", - "version": "2.0.0" - } - ] - }, - { - "name": "finaletoolkit_delfi", - "path": "modules/nf-core/finaletoolkit/delfi/meta.yml", - "type": "module", - "meta": { - "name": "finaletoolkit_delfi", - "description": "Calculate the DELFI scores (Cristiano et al., 2019) from a BAM file.\n", - "keywords": [ - "delfi_score", - "genomics", - "fragmentomics" - ], - "tools": [ - { - "finaletoolkit": { - "description": "Extract cfDNA fragmentation features from sequencing data.", - "homepage": "https://epifluidlab.github.io/FinaleToolkit/", - "documentation": "https://epifluidlab.github.io/FinaleToolkit/documentation/index.html", - "tool_dev_url": "https://github.com/epifluidlab/FinaleToolkit", - "doi": "10.1093/bioadv/vbaf236", - "licence": [ - "MIT" - ], - "identifier": "biotools:finaletoolkit" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM file", - "pattern": "*.bam", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - }, - { - "bai": { - "type": "file", - "description": "BAM file index", - "pattern": "*.bai", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3327" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "genome_2bit": { - "type": "file", - "description": "2bit compressed genome file (must be the same as the one used for the\nBAM file)\n", - "pattern": "*.2bit", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3009" - } - ] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "chromosome_sizes": { - "type": "file", - "pattern": "*.sizes", - "description": "Two-column file containing the size for each chromosome\n", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "bins": { - "type": "file", - "description": "BED containing binned genomic coordinates\n", - "pattern": "*.bed", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3003" - } - ] - } - } - ] - ], - "output": { - "bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.bed": { - "type": "file", - "pattern": "*.bed", - "description": "BED file containing DELFI scores\n", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3003" - } - ] - } - } - ] - ], - "versions_finaletoolkit": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "finaletoolkit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "finaletoolkit --version | sed 's/FinaleToolkit //g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "finaletoolkit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "finaletoolkit --version | sed 's/FinaleToolkit //g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@lbeltrame" - ], - "maintainers": [ - "@lbeltrame" - ] - } - }, - { - "name": "finaletoolkit_fraglengthbins", - "path": "modules/nf-core/finaletoolkit/fraglengthbins/meta.yml", - "type": "module", - "meta": { - "name": "finaletoolkit_fraglengthbins", - "description": "Generate a binned fragment profile and a fragment distribution histogram", - "keywords": [ - "sort", - "genomics", - "fragmentomics" - ], - "tools": [ - { - "finaletoolkit": { - "description": "Extract cfDNA fragmentation features from sequencing data.", - "homepage": "https://epifluidlab.github.io/FinaleToolkit/", - "documentation": "https://epifluidlab.github.io/FinaleToolkit/documentation/index.html", - "tool_dev_url": "https://github.com/epifluidlab/FinaleToolkit", - "doi": "10.1093/bioadv/vbaf236", - "licence": [ - "MIT" - ], - "identifier": "biotools:finaletoolkit" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM file", - "pattern": "*.bam", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - }, - { - "bai": { - "type": "file", - "description": "BAM file index", - "pattern": "*.bai", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3327" - } - ] - } - } - ] - ], - "output": { - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.frag_len.tsv": { - "type": "file", - "pattern": "*.frag_len.tsv", - "description": "Binned fragment length counts for the sample\n", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "png": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*_hist.png": { - "type": "file", - "pattern": "*_hist.png", - "description": "Histogram of fragment length distributions", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3603" - } - ] - } - } - ] - ], - "versions_finaletoolkit": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "finaletoolkit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "finaletoolkit --version | sed 's/FinaleToolkit //g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "finaletoolkit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "finaletoolkit --version | sed 's/FinaleToolkit //g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@lbeltrame" - ], - "maintainers": [ - "@lbeltrame" - ] - } - }, - { - "name": "finaletoolkit_wps", - "path": "modules/nf-core/finaletoolkit/wps/meta.yml", - "type": "module", - "meta": { - "name": "finaletoolkit_wps", - "description": "Calculate the windowed protection score (WPS; Snyder et al., 2016)\nfrom a BAM file and a list of transcription start sites.\n", - "keywords": [ - "windowed_protection-score", - "genomics", - "fragmentomics" - ], - "tools": [ - { - "finaletoolkit": { - "description": "Extract cfDNA fragmentation features from sequencing data.", - "homepage": "https://epifluidlab.github.io/FinaleToolkit/", - "documentation": "https://epifluidlab.github.io/FinaleToolkit/documentation/index.html", - "tool_dev_url": "https://github.com/epifluidlab/FinaleToolkit", - "doi": "10.1093/bioadv/vbaf236", - "licence": [ - "MIT" - ], - "identifier": "biotools:finaletoolkit" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM file", - "pattern": "*.bam", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - }, - { - "bai": { - "type": "file", - "description": "BAM file index", - "pattern": "*.bai", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3327" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "site_bed": { - "type": "file", - "pattern": "*.bed", - "description": "BED file containing transcription start sites (TSS)\n", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3003" - } - ] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "chromosome_sizes": { - "type": "file", - "pattern": "*.sizes", - "description": "Two-column file containing the size for each chromosome\n", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "output": { - "bigwig": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}.bw": { - "type": "file", - "pattern": "*.bw", - "description": "BigWig file containing WPS scores for the observed sites\n", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3006" - } - ] - } - } - ] - ], - "versions_finaletoolkit": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "finaletoolkit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "finaletoolkit --version | sed 's/FinaleToolkit //g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "finaletoolkit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "finaletoolkit --version | sed 's/FinaleToolkit //g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@lbeltrame" - ], - "maintainers": [ - "@lbeltrame" - ] - } - }, - { - "name": "find_concatenate", - "path": "modules/nf-core/find/concatenate/meta.yml", - "type": "module", - "meta": { - "name": "find_concatenate", - "description": "A module for concatenation of gzipped or uncompressed files getting around UNIX terminal argument size", - "keywords": [ - "concatenate", - "gzip", - "cat", - "find", - "pigz" - ], - "tools": [ - { - "find": { - "description": "GNU find searches the directory tree rooted at each given starting-point by evaluating the given expression", - "documentation": "https://man7.org/linux/man-pages/man1/find.1.html", - "licence": [ - "GPL-3.0-or-later" - ], - "identifier": "" - } - }, - { - "pigz": { - "description": "pigz, which stands for Parallel Implementation of GZip, is a fully functional replacement for gzip that exploits multiple processors and multiple cores to the hilt when compressing data.", - "documentation": "https://zlib.net/pigz/pigz.pdf", - "licence": [ - "other" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } + "name": "gfaffix", + "path": "modules/nf-core/gfaffix/meta.yml", + "type": "module", + "meta": { + "name": "gfaffix", + "description": "Collapse walk-preserving shared affixes in variation graphs in GFA format", + "keywords": ["gfa", "graph", "pangenome", "variation graph"], + "tools": [ + { + "gfaffix": { + "description": "GFAffix identifies walk-preserving shared affixes in variation graphs and\ncollapses them into a non-redundant graph structure.\n", + "homepage": "https://github.com/marschall-lab/GFAffix", + "documentation": "https://github.com/marschall-lab/GFAffix", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "gfa": { + "type": "file", + "description": "Variation graph in GFA format", + "pattern": "*.{gfa}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3975" + } + ] + } + } + ] + ], + "output": { + "gfa": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.gfa": { + "type": "file", + "description": "Non-redundant variation graph in GFA 1.0 format", + "pattern": "*.{gfa}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3975" + } + ] + } + } + ] + ], + "affixes": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "Shared affixes in tab-separated values (TSV) text format", + "pattern": "*.{txt}", + "ontologies": [] + } + } + ] + ], + "versions_gfaffix": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gfaffix": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gfaffix --version | cut -d\" \" -f2": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gfaffix": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gfaffix --version | cut -d\" \" -f2": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@heuermh"], + "maintainers": ["@heuermh"] }, - { - "files_in": { - "type": "file", - "description": "List of either compressed or uncompressed files", - "pattern": "*", - "ontologies": [] - } - } - ] - ], - "output": { - "file_out": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "${prefix}": { - "type": "file", - "description": "Concatenated file. Will be gzipped if ${prefix} ends with \".gz\" or inputs are gzipped, will be uncompressed otherwise.", - "pattern": "${file_out}", - "ontologies": [] - } - } - ] - ], - "versions_find": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "find": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "find --version | sed '1!d; s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_pigz": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pigz": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pigz --version 2>&1 | sed 's/pigz //g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_coreutils": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "coreutils": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cat --version | sed '1!d; s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "find": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "find --version | sed '1!d; s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pigz": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pigz --version 2>&1 | sed 's/pigz //g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "coreutils": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "cat --version | sed '1!d; s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "pangenome", + "version": "1.1.3" + } ] - ] }, - "authors": [ - "@BioWilko" - ], - "maintainers": [ - "@BioWilko" - ] - }, - "pipelines": [ { - "name": "createpanelrefs", - "version": "dev" + "name": "gfastats", + "path": "modules/nf-core/gfastats/meta.yml", + "type": "module", + "meta": { + "name": "gfastats", + "description": "A single fast and exhaustive tool for summary statistics and simultaneous *fa*\n(fasta, fastq, gfa [.gz]) genome assembly file manipulation.\n", + "keywords": [ + "gfastats", + "fasta", + "genome assembly", + "genome summary", + "genome manipulation", + "genome statistics" + ], + "tools": [ + { + "gfastats": { + "description": "The swiss army knife for genome assembly.", + "homepage": "https://github.com/vgl-hub/gfastats", + "documentation": "https://github.com/vgl-hub/gfastats/tree/main/instructions", + "tool_dev_url": "https://github.com/vgl-hub/gfastats", + "doi": "10.1093/bioinformatics/btac460", + "licence": ["MIT"], + "identifier": "biotools:gfastats" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "assembly": { + "type": "file", + "description": "Draft assembly file", + "pattern": "*.{fasta,fastq,gfa}(.gz)?", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + }, + { + "edam": "http://edamontology.org/format_3975" + } + ] + } + } + ], + { + "out_fmt": { + "type": "string", + "description": "Output format (fasta, fastq, gfa)" + } + }, + { + "genome_size": { + "type": "integer", + "description": "estimated genome size (bp) for NG* statistics (optional)." + } + }, + { + "target": { + "type": "string", + "description": "target specific sequence by header, optionally with coordinates (optional)." + } + }, + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "agpfile": { + "type": "file", + "description": "converts input agp to path and replaces existing paths.", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "include_bed": { + "type": "file", + "description": "generates output on a subset list of headers or coordinates in 0-based bed format.", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "exclude_bed": { + "type": "file", + "description": "opposite of --include-bed. They can be combined (no coordinates).", + "ontologies": [] + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "instructions": { + "type": "file", + "description": "set of instructions provided as an ordered list.", + "ontologies": [] + } + } + ] + ], + "output": { + "assembly_summary": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.assembly_summary": { + "type": "file", + "description": "Assembly summary statistics file", + "pattern": "*.assembly_summary", + "ontologies": [] + } + } + ] + ], + "assembly": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.${out_fmt}.gz": { + "type": "file", + "description": "The assembly as modified by gfastats", + "pattern": "*.{fasta,fastq,gfa}.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + }, + { + "edam": "http://edamontology.org/format_3975" + } + ] + } + } + ] + ], + "versions_gfastats": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gfastats": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gfastats -v | sed '1!d;s/.*v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gfastats": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gfastats -v | sed '1!d;s/.*v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@mahesh-panchal"], + "maintainers": ["@mahesh-panchal"] + } }, { - "name": "createtaxdb", - "version": "3.0.0" + "name": "gfatools_gfa2fa", + "path": "modules/nf-core/gfatools/gfa2fa/meta.yml", + "type": "module", + "meta": { + "name": "gfatools_gfa2fa", + "description": "Converts GFA or rGFA files to FASTA", + "keywords": ["gfa", "rgfa", "fasta", "assembly", "genome graph", "genomics"], + "tools": [ + { + "gfatools": { + "description": "Tools for manipulating sequence graphs in the GFA and rGFA formats", + "homepage": "https://github.com/lh3/gfatools", + "documentation": "https://github.com/lh3/gfatools", + "tool_dev_url": "https://github.com/lh3/gfatools", + "doi": "no DOI available", + "licence": ["Unknown"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "gfa": { + "type": "file", + "description": "GFA or rGFA file", + "pattern": "*.gfa", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3975" + } + ] + } + } + ] + ], + "output": { + "fasta": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.fasta.gz": { + "type": "file", + "description": "FASTA file", + "pattern": "*.fasta", + "ontologies": [] + } + } + ] + ], + "versions_gfatools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gfatools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gfatools version | sed '1!d; s/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gfatools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gfatools version | sed '1!d; s/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@mahesh-panchal"], + "maintainers": ["@mahesh-panchal"] + } }, { - "name": "proteinfamilies", - "version": "2.3.0" + "name": "gfatools_stat", + "path": "modules/nf-core/gfatools/stat/meta.yml", + "type": "module", + "meta": { + "name": "gfatools_stat", + "description": "Summary statistics for GFA files", + "keywords": ["summary", "statistics", "gfa", "rgfa", "graph", "genomics"], + "tools": [ + { + "gfatools": { + "description": "Tools for manipulating sequence graphs in the GFA and rGFA formats", + "homepage": "https://github.com/lh3/gfatools", + "documentation": "https://github.com/lh3/gfatools", + "tool_dev_url": "https://github.com/lh3/gfatools", + "doi": "no DOI available", + "licence": ["Unknown"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "gfa": { + "type": "file", + "description": "GFA or rGFA file", + "pattern": "*.gfa", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3975" + } + ] + } + } + ] + ], + "output": { + "stats": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.stats": { + "type": "file", + "description": "Summary statistics of the GFA file", + "pattern": "*.stats", + "ontologies": [] + } + } + ] + ], + "versions_gfatools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gfatools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gfatools version | sed '1!d; s/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gfatools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gfatools version | sed '1!d; s/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@mahesh-panchal"], + "maintainers": ["@mahesh-panchal"] + } }, { - "name": "seqsubmit", - "version": "dev" - } - ] - }, - { - "name": "find_unpigz", - "path": "modules/nf-core/find/unpigz/meta.yml", - "type": "module", - "meta": { - "name": "find_unpigz", - "description": "A module for decompressing a large number of gzipped files, getting around the UNIX terminal argument limit", - "keywords": [ - "gzip", - "find", - "pigz" - ], - "tools": [ - { - "find": { - "description": "GNU find searches the directory tree rooted at each given starting-point by evaluating the given expression", - "documentation": "https://man7.org/linux/man-pages/man1/find.1.html", - "licence": [ - "GPL-3.0-or-later" - ], - "identifier": "" - } - }, - { - "pigz": { - "description": "pigz, which stands for Parallel Implementation of GZip, is a fully functional replacement for gzip that exploits multiple processors and multiple cores to the hilt when compressing data.", - "documentation": "https://zlib.net/pigz/pigz.pdf", - "licence": [ - "other" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "files_in": { - "type": "file", - "description": "List of gzipped files to decompress", - "pattern": "*.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "output": { - "file_out": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n", - "pattern": "*" - } - }, - { - "ungzipped/*": { - "type": "file", - "description": "Files that have been decompressed\n", - "pattern": "*", - "ontologies": [] - } - } - ] - ], - "versions_find": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "find": { - "type": "string", - "description": "The tool name" - } - }, - { - "find --version | sed '1!d; s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_pigz": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "pigz": { - "type": "string", - "description": "The tool name" - } - }, - { - "pigz --version 2>&1 | sed \"s/^.*pigz[[:space:]]*//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "find": { - "type": "string", - "description": "The tool name" - } - }, - { - "find --version | sed '1!d; s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "pigz": { - "type": "string", - "description": "The tool name" - } - }, - { - "pigz --version 2>&1 | sed \"s/^.*pigz[[:space:]]*//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@Biowilko" - ], - "maintainers": [ - "@Biowilko" - ] - }, - "pipelines": [ - { - "name": "createtaxdb", - "version": "3.0.0" - } - ] - }, - { - "name": "flash", - "path": "modules/nf-core/flash/meta.yml", - "type": "module", - "meta": { - "name": "flash", - "description": "Perform merging of mate paired-end sequencing reads", - "keywords": [ - "sort", - "reads merging", - "merge mate pairs" - ], - "tools": [ - { - "flash": { - "description": "Merge mates from fragments that are shorter than twice the read length\n", - "homepage": "https://ccb.jhu.edu/software/FLASH/", - "doi": "10.1093/bioinformatics/btr507", - "licence": [ - "GPL v3+" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 2; i.e., paired-end data.\n", - "pattern": "*fastq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "output": { - "merged": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.extendedFrags.fastq.gz": { - "type": "file", - "description": "The merged fastq reads", - "pattern": ".extendedFrags.fastq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "notcombined": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.notCombined_*.fastq.gz": { - "type": "file", - "description": "Not combined reads from flash", - "pattern": ".notCombined_*.fastq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "histogram": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.hist": { - "type": "file", - "description": "HistogramNumeric histogram of merged read lengths.", - "pattern": ".hist", - "ontologies": [] - } - } - ] - ], - "versions_flash": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "flash": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "flash --version |& sed '1!d;s/^.*FLASH v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "flash": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "flash --version |& sed '1!d;s/^.*FLASH v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@Erkison" - ], - "maintainers": [ - "@Erkison" - ] - } - }, - { - "name": "flye", - "path": "modules/nf-core/flye/meta.yml", - "type": "module", - "meta": { - "name": "flye", - "description": "De novo assembler for single molecule sequencing reads", - "keywords": [ - "assembly", - "genome", - "de novo", - "genome assembler", - "single molecule" - ], - "tools": [ - { - "flye": { - "description": "Fast and accurate de novo assembler for single molecule sequencing reads", - "homepage": "https://github.com/fenderglass/Flye", - "documentation": "https://github.com/fenderglass/Flye/blob/flye/docs/USAGE.md", - "tool_dev_url": "https://github.com/fenderglass/Flye", - "doi": "10.1038/s41592-020-00971-x", - "licence": [ - "BSD-3-clause" - ], - "identifier": "biotools:Flye" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } + "name": "gffcompare", + "path": "modules/nf-core/gffcompare/meta.yml", + "type": "module", + "meta": { + "name": "gffcompare", + "description": "Compare, merge, annotate and estimate accuracy of generated gtf files", + "keywords": ["transcripts", "gtf", "merge", "compare"], + "tools": [ + { + "gffcompare": { + "description": "GffCompare by Geo Pertea", + "homepage": "http://ccb.jhu.edu/software/stringtie/gffcompare.shtml", + "documentation": "http://ccb.jhu.edu/software/stringtie/gffcompare.shtml", + "tool_dev_url": "https://github.com/gpertea/gffcompare", + "doi": "10.12688/f1000research.23297.1", + "licence": ["MIT"], + "identifier": "biotools:gffcompare" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing meta data\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "gtfs": { + "type": "file", + "description": "GTF/GFF files\ne.g. [ 'file_1.gtf', 'file_2.gtf' ]\n", + "pattern": "*.{gtf,gff}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing meta data\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Genome reference fasta file (optional)", + "pattern": "*.{fasta,fa}", + "ontologies": [] + } + }, + { + "fai": { + "type": "file", + "description": "Index for fasta file", + "pattern": "*.fai", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing meta data\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reference_gtf": { + "type": "file", + "description": "Reference annotation in gtf/gff format (optional)", + "pattern": "*.{gtf,gff}", + "ontologies": [] + } + } + ] + ], + "output": { + "annotated_gtf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing meta data\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.annotated.gtf": { + "type": "file", + "description": "Annotated gtf file when reference gtf is provided (optional)\n", + "pattern": "*.annotated.gtf", + "ontologies": [] + } + } + ] + ], + "combined_gtf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing meta data\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.combined.gtf": { + "type": "file", + "description": "Combined gtf file when multiple input files are\nprovided (optional)\n", + "pattern": "*.annotated.gtf", + "ontologies": [] + } + } + ] + ], + "tmap": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing meta data\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tmap": { + "type": "file", + "description": "File listing the most closely matching reference transcript\nfor each query transcript (optional)\n", + "pattern": "*.tmap", + "ontologies": [] + } + } + ] + ], + "refmap": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing meta data\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.refmap": { + "type": "file", + "description": "File listing the reference transcripts with overlapping\nquery transcripts (optional)\n", + "pattern": "*.refmap", + "ontologies": [] + } + } + ] + ], + "loci": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing meta data\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.loci": { + "type": "file", + "description": "File with loci", + "pattern": "*.loci", + "ontologies": [] + } + } + ] + ], + "stats": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing meta data\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.stats": { + "type": "file", + "description": "File with stats for input transcripts as compared to\nreference alternatively stats for the combined gtf\n", + "pattern": "*.stats", + "ontologies": [] + } + } + ] + ], + "tracking": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing meta data\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tracking": { + "type": "file", + "description": "This file matches transcripts up between samples\n", + "pattern": "*.tracking", + "ontologies": [] + } + } + ] + ], + "versions_gffcompare": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gffcompare": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gffcompare --version 2>&1 | sed \"s/gffcompare v//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gffcompare": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gffcompare --version 2>&1 | sed \"s/gffcompare v//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@jemten"], + "maintainers": ["@jemten", "@gallvp"] }, - { - "reads": { - "type": "file", - "description": "Input reads from Oxford Nanopore or PacBio data in FASTA/FASTQ format.", - "pattern": "*.{fasta,fastq,fasta.gz,fastq.gz,fa,fq,fa.gz,fq.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ], - { - "mode": { - "type": "string", - "description": "Flye mode depending on the input data (source and error rate)", - "pattern": "--pacbio-raw|--pacbio-corr|--pacbio-hifi|--nano-raw|--nano-corr|--nano-hq" - } - } - ], - "output": { - "fasta": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.fasta.gz": { - "type": "file", - "description": "Assembled FASTA file", - "pattern": "*.fasta.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "gfa": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.gfa.gz": { - "type": "file", - "description": "Repeat graph in gfa format", - "pattern": "*.gfa.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "gv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.gv.gz": { - "type": "file", - "description": "Repeat graph in gv format", - "pattern": "*.gv.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "txt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.txt": { - "type": "file", - "description": "Extra information and statistics about resulting contigs", - "pattern": "*.txt", - "ontologies": [] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.log": { - "type": "file", - "description": "Flye log file", - "pattern": "*.log", - "ontologies": [] - } - } - ] - ], - "json": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.json": { - "type": "file", - "description": "Flye parameters", - "pattern": "*.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "versions_flye": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "flye": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "flye --version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "flye": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "flye --version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "lncpipe", + "version": "dev" + } ] - ] }, - "authors": [ - "@mirpedrol" - ], - "maintainers": [ - "@mirpedrol" - ] - }, - "pipelines": [ { - "name": "bacass", - "version": "2.6.0" + "name": "gffread", + "path": "modules/nf-core/gffread/meta.yml", + "type": "module", + "meta": { + "name": "gffread", + "description": "Validate, filter, convert and perform various other operations on GFF files", + "keywords": ["gff", "conversion", "validation"], + "tools": [ + { + "gffread": { + "description": "GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more.", + "homepage": "http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread", + "documentation": "http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread", + "tool_dev_url": "https://github.com/gpertea/gffread", + "doi": "10.12688/f1000research.23297.1", + "licence": ["MIT"], + "identifier": "biotools:gffread" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing meta data\ne.g. [ id:'test' ]\n" + } + }, + { + "gff": { + "type": "file", + "description": "A reference file in either the GFF3, GFF2 or GTF format.", + "pattern": "*.{gff, gtf}", + "ontologies": [] + } + } + ], + { + "fasta": { + "type": "file", + "description": "A multi-fasta file with the genomic sequences", + "pattern": "*.{fasta,fa,faa,fas,fsa}", + "ontologies": [] + } + } + ], + "output": { + "gtf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing meta data\ne.g. [ id:'test' ]\n" + } + }, + { + "*.gtf": { + "type": "file", + "description": "GTF file resulting from the conversion of the GFF input file if '-T' argument is present", + "pattern": "*.{gtf}", + "ontologies": [] + } + } + ] + ], + "gffread_gff": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing meta data\ne.g. [ id:'test' ]\n" + } + }, + { + "*.gff3": { + "type": "file", + "description": "GFF3 file resulting from the conversion of the GFF input file if '-T' argument is absent", + "pattern": "*.gff3", + "ontologies": [] + } + } + ] + ], + "gffread_fasta": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing meta data\ne.g. [ id:'test' ]\n" + } + }, + { + "*.fasta": { + "type": "file", + "description": "Fasta file produced when either of '-w', '-x', '-y' parameters is present", + "pattern": "*.fasta", + "ontologies": [] + } + } + ] + ], + "bed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing meta data\ne.g. [ id:'test' ]\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "BED file resulting from the conversion of the GFF input file when the '--bed' argument is present", + "pattern": "*.bed", + "ontologies": [] + } + } + ] + ], + "versions_gffread": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "gffread": { + "type": "string", + "description": "The tool name" + } + }, + { + "gffread --version 2>&1": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "gffread": { + "type": "string", + "description": "The tool name" + } + }, + { + "gffread --version 2>&1": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@edmundmiller"], + "maintainers": ["@edmundmiller", "@gallvp"] + }, + "pipelines": [ + { + "name": "atacseq", + "version": "2.1.2" + }, + { + "name": "chipseq", + "version": "2.1.0" + }, + { + "name": "circrna", + "version": "dev" + }, + { + "name": "genomeqc", + "version": "dev" + }, + { + "name": "hicar", + "version": "1.0.0" + }, + { + "name": "lncpipe", + "version": "dev" + }, + { + "name": "nascent", + "version": "2.3.0" + }, + { + "name": "references", + "version": "0.1" + }, + { + "name": "riboseq", + "version": "1.2.0" + }, + { + "name": "rnadnavar", + "version": "dev" + }, + { + "name": "rnafusion", + "version": "4.1.2" + }, + { + "name": "rnaseq", + "version": "3.26.0" + }, + { + "name": "rnasplice", + "version": "1.0.4" + }, + { + "name": "rnavar", + "version": "1.2.3" + }, + { + "name": "sammyseq", + "version": "dev" + }, + { + "name": "scrnaseq", + "version": "4.1.0" + } + ] }, { - "name": "genomeassembler", - "version": "1.1.0" + "name": "gget_gget", + "path": "modules/nf-core/gget/gget/meta.yml", + "type": "module", + "meta": { + "name": "gget_gget", + "description": "gget is a free, open-source command-line tool and Python package that enables efficient querying of genomic databases. gget consists of a collection of separate but interoperable modules, each designed to facilitate one type of database querying in a single line of code.", + "keywords": ["gget", "reference", "database", "databases", "download"], + "tools": [ + { + "gget": { + "description": "gget enables efficient querying of genomic databases", + "homepage": "https://github.com/pachterlab/gget", + "documentation": "https://pachterlab.github.io/gget/", + "tool_dev_url": "https://github.com/pachterlab/gget", + "doi": "10.1093/bioinformatics/btac836", + "licence": ["BSD-2-clause"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "files": { + "type": "file", + "description": "Optional input files which can be specified for certain tools. This is mostly used to supply a FASTA file for gget muscle.\n", + "ontologies": [] + } + } + ] + ], + "output": { + "files": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*[!${prefix}.${extension}]*": { + "type": "file", + "description": "File containing output of gget command.", + "ontologies": [] + } + } + ] + ], + "output": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.${extension}": { + "type": "file", + "description": "File containing output of gget command (-o for most gget tools).", + "pattern": "*.{json,csv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + }, + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "versions_gget": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gget": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gget --version |& sed 's/gget version: //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gget": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gget --version |& sed 's/gget version: //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@adamrtalbot"], + "maintainers": ["@adamrtalbot"] + } }, { - "name": "mag", - "version": "5.4.2" + "name": "glimpse2_chunk", + "path": "modules/nf-core/glimpse2/chunk/meta.yml", + "type": "module", + "meta": { + "name": "glimpse2_chunk", + "description": "Defines chunks where to run imputation", + "keywords": ["chunk", "low-coverage", "imputation", "glimpse"], + "tools": [ + { + "glimpse2": { + "description": "GLIMPSE2 is a phasing and imputation method for large-scale low-coverage sequencing studies.", + "homepage": "https://odelaneau.github.io/GLIMPSE", + "documentation": "https://odelaneau.github.io/GLIMPSE/commands.html", + "tool_dev_url": "https://github.com/odelaneau/GLIMPSE", + "doi": "10.1038/s41588-020-00756-0", + "licence": ["MIT"], + "identifier": "biotools:glimpse2" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "Target dataset in VCF/BCF format defined at all variable positions.\nThe file could possibly be without GT field (for efficiency reasons a file containing only the positions is recommended).\n", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", + "ontologies": [] + } + }, + { + "input_index": { + "type": "file", + "description": "Index file of the input VCF/BCF file containing genotype likelihoods.", + "pattern": "*.{vcf.gz.csi,bcf.gz.csi}", + "ontologies": [] + } + }, + { + "region": { + "type": "string", + "description": "Target region, usually a full chromosome (e.g. chr20:1000000-2000000 or chr20).\nFor chrX, please treat PAR and non-PAR regions as different choromosome in order to avoid mixing ploidy.\n" + } + }, + { + "map": { + "type": "file", + "description": "File containing the genetic map.", + "pattern": "*.gmap", + "ontologies": [] + } + } + ], + { + "model": { + "type": "string", + "description": "Algorithm model to use:\n\"recursive\": Recursive algorithm\n\"sequential\": Sequential algorithm (Recommended)\n\"uniform-number-variants\": Experimental. Uniform the number of variants in the sequential algorithm\n", + "pattern": "{recursive,sequential,uniform-number-variants}" + } + } + ], + "output": { + "chunk_chr": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "Tab delimited output txt file containing buffer and imputation regions.", + "pattern": "*.{txt}", + "ontologies": [] + } + } + ] + ], + "versions_glimpse2": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "glimpse2": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "GLIMPSE2_chunk --help | grep -oE 'v[0-9.]+' | cut -c2-": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "glimpse2": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "GLIMPSE2_chunk --help | grep -oE 'v[0-9.]+' | cut -c2-": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@louislenezet"], + "maintainers": ["@louislenezet"], + "requirements": ["AVX2"] + }, + "pipelines": [ + { + "name": "phaseimpute", + "version": "1.1.0" + } + ] }, { - "name": "pathogensurveillance", - "version": "1.1.0" - } - ] - }, - { - "name": "foldcomp_compress", - "path": "modules/nf-core/foldcomp/compress/meta.yml", - "type": "module", - "meta": { - "name": "foldcomp_compress", - "description": "Efficient compression tool for protein structures", - "keywords": [ - "protein", - "structure", - "compression" - ], - "tools": [ - { - "foldcomp": { - "description": "Foldcomp: a library and format for compressing and indexing large protein structure sets", - "homepage": "https://github.com/steineggerlab/foldcomp", - "documentation": "https://github.com/steineggerlab/foldcomp", - "tool_dev_url": "https://github.com/steineggerlab/foldcomp", - "doi": "10.1093/bioinformatics/btad153", - "licence": [ - "GPL v3-or-later" - ], - "identifier": "biotools:foldcomp" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } + "name": "glimpse2_concordance", + "path": "modules/nf-core/glimpse2/concordance/meta.yml", + "type": "module", + "meta": { + "name": "glimpse2_concordance", + "description": "Program to compute the genotyping error rate at the sample or marker level.", + "keywords": ["concordance", "low-coverage", "glimpse", "imputation"], + "tools": [ + { + "glimpse2": { + "description": "GLIMPSE2 is a phasing and imputation method for large-scale low-coverage sequencing studies.", + "homepage": "https://odelaneau.github.io/GLIMPSE", + "documentation": "https://odelaneau.github.io/GLIMPSE/commands.html", + "tool_dev_url": "https://github.com/odelaneau/GLIMPSE", + "doi": "10.1038/s41588-020-00756-0", + "licence": ["MIT"], + "identifier": "biotools:glimpse2" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "estimate": { + "type": "file", + "description": "Imputed dataset file obtain after phasing.", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", + "ontologies": [] + } + }, + { + "estimate_index": { + "type": "file", + "description": "Index file for the imputed dataset file.", + "ontologies": [] + } + }, + { + "truth": { + "type": "file", + "description": "Validation dataset called at the same positions as the imputed file.", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", + "ontologies": [] + } + }, + { + "truth_index": { + "type": "file", + "description": "Index file for the truth file.", + "ontologies": [] + } + }, + { + "freq": { + "type": "file", + "description": "File containing allele frequencies at each site.", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", + "ontologies": [] + } + }, + { + "freq_index": { + "type": "file", + "description": "Index file for the allele frequencies file.", + "ontologies": [] + } + }, + { + "samples": { + "type": "file", + "description": "List of samples to process, one sample ID per line.", + "pattern": "*.{txt,tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, + { + "region": { + "type": "string", + "description": "Target region used for imputation, including left and right buffers (e.g. chr20:1000000-2000000). Can also be a list of such regions.", + "pattern": "chrXX:leftBufferPosition-rightBufferPosition" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "groups": { + "type": "file", + "description": "Alternative to frequency bins, group bins are user defined, provided in a file.", + "pattern": "*.{txt,tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, + { + "bins": { + "type": "string", + "description": "Allele frequency bins used for rsquared computations.\nBy default they should as MAF bins [0-0.5], while\nthey should take the full range [0-1] if --use-ref-alt is used.\n", + "pattern": "0 0.01 0.05 ... 0.5" + } + }, + { + "ac_bins": { + "type": "string", + "description": "User-defined allele count bins used for rsquared computations.", + "pattern": "1 2 5 10 20 ... 100000" + } + }, + { + "allele_counts": { + "type": "string", + "description": "Default allele count bins used for rsquared computations.\nAN field must be defined in the frequency file.\n" + } + }, + { + "min_val_gl": { + "type": "float", + "description": "Minimum genotype likelihood probability P(G|R) in validation data.\nSet to zero to have no filter of if using –gt-validation\n" + } + }, + { + "min_val_dp": { + "type": "integer", + "description": "Minimum coverage in validation data.\nIf FORMAT/DP is missing and –min_val_dp > 0, the program exits with an error.\nSet to zero to have no filter of if using –gt-validation\n" + } + } + ] + ], + "output": { + "errors_cal": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.error.cal.txt.gz": { + "type": "file", + "description": "Calibration correlation errors between imputed dosages (in MAF bins) and highly-confident genotype.", + "pattern": "*.errors.cal.txt.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "errors_grp": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.error.grp.txt.gz": { + "type": "file", + "description": "Groups correlation errors between imputed dosages (in MAF bins) and highly-confident genotype.", + "pattern": "*.errors.grp.txt.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "errors_spl": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.error.spl.txt.gz": { + "type": "file", + "description": "Samples correlation errors between imputed dosages (in MAF bins) and highly-confident genotype.", + "pattern": "*.errors.spl.txt.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "rsquare_grp": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.rsquare.grp.txt.gz": { + "type": "file", + "description": "Groups r-squared correlation between imputed dosages (in MAF bins) and highly-confident genotype.", + "pattern": "*.rsquare.grp.txt.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "rsquare_spl": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.rsquare.spl.txt.gz": { + "type": "file", + "description": "Samples r-squared correlation between imputed dosages (in MAF bins) and highly-confident genotype.", + "pattern": "*.rsquare.spl.txt.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "rsquare_per_site": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_r2_sites.txt.gz": { + "type": "file", + "description": "Variant r-squared correlation between imputed dosages (in MAF bins) and highly-confident genotype.", + "pattern": "_r2_sites.txt.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "versions_glimpse2": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "glimpse2": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "GLIMPSE2_concordance --help | grep -oE 'v[0-9.]+' | cut -c2-": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "glimpse2": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "GLIMPSE2_concordance --help | grep -oE 'v[0-9.]+' | cut -c2-": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@louislenezet"], + "maintainers": ["@louislenezet"] }, - { - "pdb": { - "type": "file", - "description": "Protein structure(s) in PDB or CIF format to compress (also works with folder input)", - "pattern": "*.{pdb,cif}", - "ontologies": [] - } - } - ] - ], - "output": { - "fcz": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*fcz": { - "type": "file", - "description": "Either single compressed protein structure (if input was file) or folder with all compressed protein structures (if input was directory)\n", - "pattern": "{*_fcz,*.fcz}", - "ontologies": [] - } - } - ] - ], - "versions_foldcomp": [ - [ - { - "${task.process}": { - "type": "string", - "description": "Task process name" - } - }, - { - "foldcomp": { - "type": "string", - "description": "Software name" - } - }, - { - "foldcomp --version | cut -d' ' -f2": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "Task process name" - } - }, - { - "foldcomp": { - "type": "string", - "description": "Software name" - } - }, - { - "foldcomp --version | cut -d' ' -f2": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "phaseimpute", + "version": "1.1.0" + } ] - ] - }, - "authors": [ - "@vagkaratzas" - ], - "maintainers": [ - "@vagkaratzas" - ] - } - }, - { - "name": "foldcomp_decompress", - "path": "modules/nf-core/foldcomp/decompress/meta.yml", - "type": "module", - "meta": { - "name": "foldcomp_decompress", - "description": "Decompression tool for foldcomp compressed structures", - "keywords": [ - "protein", - "structure", - "compression" - ], - "tools": [ - { - "foldcomp": { - "description": "Foldcomp: a library and format for compressing and indexing large protein structure sets", - "homepage": "https://github.com/steineggerlab/foldcomp", - "documentation": "https://github.com/steineggerlab/foldcomp", - "tool_dev_url": "https://github.com/steineggerlab/foldcomp", - "doi": "10.1093/bioinformatics/btad153", - "licence": [ - "GPL v3-or-later" - ], - "identifier": "biotools:foldcomp" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } + }, + { + "name": "glimpse2_ligate", + "path": "modules/nf-core/glimpse2/ligate/meta.yml", + "type": "module", + "meta": { + "name": "glimpse2_ligate", + "description": "Ligatation of multiple phased BCF/VCF files into a single whole chromosome file.\nGLIMPSE2 is run in chunks that are ligated into chromosome-wide files maintaining the phasing.\n", + "keywords": ["ligate", "low-coverage", "glimpse", "imputation"], + "tools": [ + { + "glimpse2": { + "description": "GLIMPSE2 is a phasing and imputation method for large-scale low-coverage sequencing studies.", + "homepage": "https://odelaneau.github.io/GLIMPSE", + "documentation": "https://odelaneau.github.io/GLIMPSE/commands.html", + "tool_dev_url": "https://github.com/odelaneau/GLIMPSE", + "doi": "10.1038/s41588-020-00756-0", + "licence": ["MIT"], + "identifier": "biotools:glimpse2" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input_list": { + "type": "file", + "description": "VCF/BCF file containing genotype probabilities (GP field).", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", + "ontologies": [] + } + }, + { + "input_index": { + "type": "file", + "description": "Index file of the input VCF/BCF file containing genotype likelihoods.", + "pattern": "*.{csi,tbi}", + "ontologies": [] + } + } + ] + ], + "output": { + "merged_variants": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{vcf,bcf,vcf.gz,bcf.gz}": { + "type": "file", + "description": "Output ligated (phased) file in VCF/BCF format.", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", + "ontologies": [] + } + } + ] + ], + "versions_glimpse2": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "glimpse2": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "GLIMPSE2_ligate --help | grep -oE 'v[0-9.]+' | cut -c2-": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "glimpse2": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "GLIMPSE2_ligate --help | grep -oE 'v[0-9.]+' | cut -c2-": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@louislenezet"], + "maintainers": ["@louislenezet"] }, - { - "fcz": { - "type": "file", - "description": "Foldcomp compressed protein structure(s) (also works with folder input)", - "pattern": "*{*,*.fcz}", - "ontologies": [] - } - } - ] - ], - "output": { - "pdb": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "{*pdb,*.cif}": { - "type": "file", - "description": "Either single protein structure (if input was file) or folder with all decompressed protein structures (if input was directory)\n", - "pattern": "{*_pdb,*.pdb,*.cif}", - "ontologies": [] - } - } - ] - ], - "versions_foldcomp": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "foldcomp": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "foldcomp --version | cut -d' ' -f2": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "foldcomp": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "foldcomp --version | cut -d' ' -f2": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "phaseimpute", + "version": "1.1.0" + } ] - ] - }, - "authors": [ - "@vagkaratzas" - ] - } - }, - { - "name": "foldmason_createdb", - "path": "modules/nf-core/foldmason/createdb/meta.yml", - "type": "module", - "meta": { - "name": "foldmason_createdb", - "description": "Creates a database for Foldmason.", - "keywords": [ - "alignment", - "MSA", - "genomics", - "structure" - ], - "tools": [ - { - "foldmason": { - "description": "Multiple Protein Structure Alignment at Scale with FoldMason", - "homepage": "https://github.com/steineggerlab/foldmason", - "documentation": "https://github.com/steineggerlab/foldmason", - "tool_dev_url": "https://github.com/steineggerlab/foldmason", - "doi": "10.1101/2024.08.01.606130", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:foldmason" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } + }, + { + "name": "glimpse2_phase", + "path": "modules/nf-core/glimpse2/phase/meta.yml", + "type": "module", + "meta": { + "name": "glimpse2_phase", + "description": "Tool for imputation and phasing from vcf file or directly from bam files.", + "keywords": ["phasing", "low-coverage", "imputation", "glimpse"], + "tools": [ + { + "glimpse2": { + "description": "GLIMPSE2 is a phasing and imputation method for large-scale low-coverage sequencing studies.", + "homepage": "https://odelaneau.github.io/GLIMPSE", + "documentation": "https://odelaneau.github.io/GLIMPSE/commands.html", + "tool_dev_url": "https://github.com/odelaneau/GLIMPSE", + "doi": "10.1038/s41588-020-00756-0", + "licence": ["MIT"], + "identifier": "biotools:glimpse2" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "input": { + "type": "file", + "description": "Either one or multiple BAM/CRAM files in an array containing low-coverage sequencing reads or one VCF/BCF file containing the genotype likelihoods.\nWhen using BAM/CRAM the name of the file is used as samples name.\n", + "pattern": "*.{bam,cram,vcf,vcf.gz,bcf,bcf.gz}", + "ontologies": [] + } + }, + { + "input_index": { + "type": "file", + "description": "Index file of the input BAM/CRAM/VCF/BCF file.", + "pattern": "*.{bam.bai,cram.crai,vcf.gz.csi,bcf.gz.csi}", + "ontologies": [] + } + }, + { + "bamlist": { + "type": "file", + "description": "File containing the list of BAM/CRAM files to be phased.\nOne file per line and a second column can be added to indicate the sample name.\n", + "pattern": "*.{txt,tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, + { + "samples_file": { + "type": "file", + "description": "File with sample names and ploidy information.\nOne sample per line with a mandatory second column indicating ploidy (1 or 2).\nSample names that are not present are assumed to have ploidy 2 (diploids).\nGLIMPSE does NOT handle the use of sex (M/F) instead of ploidy.\n", + "pattern": "*.{txt,tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, + { + "input_region": { + "type": "string", + "description": "Target region used for imputation, including left and right buffers (e.g. chr20:1000000-2000000).\nOptional if reference panel is in bin format.\n", + "pattern": "chrXX:leftBufferPosition-rightBufferPosition" + } + }, + { + "output_region": { + "type": "string", + "description": "Target imputed region, excluding left and right buffers (e.g. chr20:1000000-2000000).\nOptional if reference panel is in bin format.\n", + "pattern": "chrXX:leftBufferPosition-rightBufferPosition" + } + }, + { + "reference": { + "type": "file", + "description": "Reference panel of haplotypes in VCF/BCF format.", + "pattern": "*.{vcf.gz,bcf.gz}", + "ontologies": [] + } + }, + { + "reference_index": { + "type": "file", + "description": "Index file of the Reference panel file.", + "pattern": "*.{vcf.gz.csi,bcf.gz.csi}", + "ontologies": [] + } + }, + { + "map": { + "type": "file", + "description": "File containing the genetic map.\nOptional if reference panel is in bin format.\n", + "pattern": "*.gmap", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing genomic map information\ne.g. `[ map:'GRCh38' ]`\n" + } + }, + { + "fasta_reference": { + "type": "file", + "description": "Faidx-indexed reference sequence file in the appropriate genome build.\nNecessary for CRAM files.\n", + "pattern": "*.fasta", + "ontologies": [] + } + }, + { + "fasta_reference_index": { + "type": "file", + "description": "Faidx index of the reference sequence file in the appropriate genome build.\nNecessary for CRAM files.\n", + "pattern": "*.fai", + "ontologies": [] + } + } + ], + { + "output_suffix": { + "type": "string", + "description": "Output file suffix used to choose the GLIMPSE2 output format. Defaults to `vcf.gz` when empty. Supported values: `vcf`, `vcf.gz`, `bcf`, `bgen`.\n", + "pattern": "vcf|vcf.gz|bcf|bgen" + } + } + ], + "output": { + "phased_variants": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.{vcf,vcf.gz,bcf,bgen}": { + "type": "file", + "description": "Output VCF/BCF/BGEN file containing genotype probabilities (GP field), imputed dosages (DS field), best guess genotypes (GT field), sampled haplotypes in the last (max 16) main iterations (HS field) and info-score.\n", + "pattern": "*.{vcf,vcf.gz,bcf,bgen}", + "ontologies": [] + } + } + ] + ], + "stats_coverage": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.txt.gz": { + "type": "file", + "description": "Optional coverage statistic file created when BAM/CRAM files are used as inputs.", + "pattern": "*.txt.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "versions_glimpse2": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "glimpse2": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "GLIMPSE2_phase --help | grep -oE 'v[0-9.]+' | cut -c2-": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "glimpse2": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "GLIMPSE2_phase --help | grep -oE 'v[0-9.]+' | cut -c2-": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@LouisLeNezet"], + "maintainers": ["@LouisLeNezet"] }, - { - "structures": { - "type": "file", - "description": "Input protein structures in `PDB` or `mmCIF` format.", - "pattern": "*.{pdb,mmcif}", - "ontologies": [] - } - } - ] - ], - "output": { - "db": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "${prefix}*": { - "type": "file", - "description": "All database files created by Foldmason", - "pattern": "*", - "ontologies": [] - } - } - ] - ], - "versions_foldmason": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "foldmason": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "foldmason version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "foldmason": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "foldmason version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "phaseimpute", + "version": "1.1.0" + } ] - ] - }, - "authors": [ - "@luisas" - ], - "maintainers": [ - "@luisas" - ] - }, - "pipelines": [ - { - "name": "multiplesequencealign", - "version": "1.1.1" - } - ] - }, - { - "name": "foldmason_easymsa", - "path": "modules/nf-core/foldmason/easymsa/meta.yml", - "type": "module", - "meta": { - "name": "foldmason_easymsa", - "description": "Aligns protein structures using foldmason", - "keywords": [ - "alignment", - "MSA", - "genomics", - "structure" - ], - "tools": [ - { - "foldmason": { - "description": "Multiple Protein Structure Alignment at Scale with FoldMason", - "homepage": "https://github.com/steineggerlab/foldmason", - "documentation": "https://github.com/steineggerlab/foldmason", - "tool_dev_url": "https://github.com/steineggerlab/foldmason", - "doi": "10.1101/2024.08.01.606130", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:foldmason" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "pdbs": { - "type": "file", - "description": "Input protein structures in PDB format.", - "pattern": "*.{pdb,mmcif}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1476" - }, - { - "edam": "http://edamontology.org/format_1477" - } - ] - } + }, + { + "name": "glimpse2_splitreference", + "path": "modules/nf-core/glimpse2/splitreference/meta.yml", + "type": "module", + "meta": { + "name": "glimpse2_splitreference", + "description": "Tool to create a binary reference panel for quick reading time.", + "keywords": ["split", "reference", "phasing", "imputation"], + "tools": [ + { + "glimpse2": { + "description": "GLIMPSE2 is a phasing and imputation method for large-scale low-coverage sequencing studies.", + "homepage": "https://odelaneau.github.io/GLIMPSE", + "documentation": "https://odelaneau.github.io/GLIMPSE/commands.html", + "tool_dev_url": "https://github.com/odelaneau/GLIMPSE", + "doi": "10.1038/s41588-020-00756-0", + "licence": ["MIT"], + "identifier": "biotools:glimpse2" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reference": { + "type": "file", + "description": "Reference panel of haplotypes in VCF/BCF format.", + "pattern": "*.{vcf.gz,bcf.gz}", + "ontologies": [] + } + }, + { + "reference_index": { + "type": "file", + "description": "Index file of the Reference panel file.", + "pattern": "*.{vcf.gz.csi,bcf.gz.csi}", + "ontologies": [] + } + }, + { + "input_region": { + "type": "string", + "description": "Target region used for imputation, including left and right buffers (e.g. chr20:1000000-2000000).", + "pattern": "chrXX:leftBufferPosition-rightBufferPosition" + } + }, + { + "output_region": { + "type": "string", + "description": "Target imputed region, excluding left and right buffers (e.g. chr20:1000000-2000000).", + "pattern": "chrXX:leftBufferPosition-rightBufferPosition" + } + }, + { + "map": { + "type": "file", + "description": "File containing the genetic map.", + "pattern": "*.gmap", + "ontologies": [] + } + } + ] + ], + "output": { + "bin_ref": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bin": { + "type": "file", + "description": "binary reference panel", + "pattern": "*.bin", + "ontologies": [] + } + } + ] + ], + "versions_glimpse2": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "glimpse2": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "GLIMPSE2_split_reference --help | grep -oE 'v[0-9.]+' | cut -c2-": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "glimpse2": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "GLIMPSE2_split_reference --help | grep -oE 'v[0-9.]+' | cut -c2-": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@LouisLeNezet"], + "maintainers": ["@LouisLeNezet"], + "requirements": ["AVX2"] } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } + }, + { + "name": "glimpse_chunk", + "path": "modules/nf-core/glimpse/chunk/meta.yml", + "type": "module", + "meta": { + "name": "glimpse_chunk", + "description": "Defines chunks where to run imputation", + "keywords": ["chunk", "imputation", "low coverage"], + "tools": [ + { + "glimpse": { + "description": "GLIMPSE is a phasing and imputation method for large-scale low-coverage sequencing studies.", + "homepage": "https://odelaneau.github.io/GLIMPSE", + "documentation": "https://odelaneau.github.io/GLIMPSE/commands.html", + "tool_dev_url": "https://github.com/odelaneau/GLIMPSE", + "doi": "10.1038/s41588-020-00756-0", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "Target dataset in VCF/BCF format defined at all variable positions.\nThe file could possibly be without GT field (for efficiency reasons a file containing only the positions is recommended).\n", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", + "ontologies": [] + } + }, + { + "input_index": { + "type": "file", + "description": "Index file for the input VCF/BCF file.", + "ontologies": [] + } + }, + { + "region": { + "type": "string", + "description": "Target region, usually a full chromosome (e.g. chr20:1000000-2000000 or chr20).\nFor chrX, please treat PAR and non-PAR regions as different choromosome in order to avoid mixing ploidy.\n" + } + } + ] + ], + "output": { + "chunk_chr": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "Tab delimited output txt file containing buffer and imputation regions.", + "pattern": "*.txt", + "ontologies": [] + } + } + ] + ], + "versions_glimpse": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "glimpse": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "GLIMPSE_chunk --help | sed -n '/Version/s/.*: //p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "glimpse": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "GLIMPSE_chunk --help | sed -n '/Version/s/.*: //p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@louislenezet"], + "maintainers": ["@louislenezet"] }, - { - "tree": { - "type": "file", - "description": "Input guide tree in Newick format.", - "pattern": "*.{dnd,nwk}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2006" - }, - { - "edam": "http://edamontology.org/format_1910" - } - ] - } - } - ], - { - "compress": { - "type": "boolean", - "description": "Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded." - } - } - ], - "output": { - "msa_3di": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + "pipelines": [ + { + "name": "phaseimpute", + "version": "1.1.0" } - }, - { - "${prefix}_3di.fa${compress ? '.gz' : ''}": { - "type": "file", - "description": "Fasta file containing the multiple sequence alignment with 3Di alphabet", - "pattern": "*.{fa}", - "ontologies": [ + ] + }, + { + "name": "glimpse_concordance", + "path": "modules/nf-core/glimpse/concordance/meta.yml", + "type": "module", + "meta": { + "name": "glimpse_concordance", + "description": "Compute the r2 correlation between imputed dosages (in MAF bins) and highly-confident genotype calls from the high-coverage dataset.", + "keywords": ["concordance", "low-coverage", "glimpse", "imputation"], + "tools": [ + { + "glimpse": { + "description": "GLIMPSE is a phasing and imputation method for large-scale low-coverage sequencing studies.", + "homepage": "https://odelaneau.github.io/GLIMPSE", + "documentation": "https://odelaneau.github.io/GLIMPSE/commands.html", + "tool_dev_url": "https://github.com/odelaneau/GLIMPSE", + "doi": "10.1038/s41588-020-00756-0", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "estimate": { + "type": "file", + "description": "Imputed data.", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", + "ontologies": [] + } + }, + { + "estimate_index": { + "type": "file", + "description": "Index file for the imputed data.", + "ontologies": [] + } + }, + { + "freq": { + "type": "file", + "description": "File containing allele frequencies at each site.", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", + "ontologies": [] + } + }, + { + "freq_index": { + "type": "file", + "description": "Index file for the allele frequencies file.", + "ontologies": [] + } + }, + { + "truth": { + "type": "file", + "description": "Validation dataset called at the same positions as the imputed file.", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", + "ontologies": [] + } + }, + { + "truth_index": { + "type": "file", + "description": "Index file for the truth file.", + "ontologies": [] + } + }, + { + "region": { + "type": "string", + "description": "Target region used for imputation, including left and right buffers (e.g. chr20:1000000-2000000).", + "pattern": "chrXX:leftBufferPosition-rightBufferPosition" + } + } + ], { - "edam": "http://edamontology.org/format_2554" + "min_prob": { + "type": "float", + "description": "Minimum posterior probability P(G|R) in validation data" + } }, { - "edam": "http://edamontology.org/format_1921" + "min_dp": { + "type": "integer", + "description": "Minimum coverage in validation data.\nIf FORMAT/DP is missing and --minDP > 0, the program exits with an error.\n" + } }, { - "edam": "http://edamontology.org/format_1984" + "bins": { + "type": "string", + "description": "Allele frequency bins used for rsquared computations.\nBy default they should as MAF bins [0-0.5], while\nthey should take the full range [0-1] if --use-ref-alt is used.\n" + } + } + ], + "output": { + "errors_cal": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.error.cal.txt.gz": { + "type": "file", + "description": "Calibration correlation errors between imputed dosages (in MAF bins) and highly-confident genotype.", + "pattern": "*.errors.cal.txt.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "errors_grp": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.error.grp.txt.gz": { + "type": "file", + "description": "Groups correlation errors between imputed dosages (in MAF bins) and highly-confident genotype.", + "pattern": "*.errors.grp.txt.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "errors_spl": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.error.spl.txt.gz": { + "type": "file", + "description": "Samples correlation errors between imputed dosages (in MAF bins) and highly-confident genotype.", + "pattern": "*.errors.spl.txt.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "rsquare_grp": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.rsquare.grp.txt.gz": { + "type": "file", + "description": "Groups r-squared correlation between imputed dosages (in MAF bins) and highly-confident genotype.", + "pattern": "*.rsquare.grp.txt.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "rsquare_spl": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.rsquare.spl.txt.gz": { + "type": "file", + "description": "Samples r-squared correlation between imputed dosages (in MAF bins) and highly-confident genotype.", + "pattern": "*.rsquare.spl.txt.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "versions_glimpse": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "glimpse": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "GLIMPSE_concordance --help | sed -n '/Version/s/.*: //p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "glimpse": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "GLIMPSE_concordance --help | sed -n '/Version/s/.*: //p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@louislenezet"], + "maintainers": ["@louislenezet"] + } + }, + { + "name": "glimpse_ligate", + "path": "modules/nf-core/glimpse/ligate/meta.yml", + "type": "module", + "meta": { + "name": "glimpse_ligate", + "description": "Concatenates imputation chunks in a single VCF/BCF file ligating phased information.", + "keywords": ["ligate", "low-coverage", "glimpse", "imputation"], + "tools": [ + { + "glimpse": { + "description": "GLIMPSE is a phasing and imputation method for large-scale low-coverage sequencing studies.", + "homepage": "https://odelaneau.github.io/GLIMPSE", + "documentation": "https://odelaneau.github.io/GLIMPSE/commands.html", + "tool_dev_url": "https://github.com/odelaneau/GLIMPSE", + "doi": "10.1038/s41588-020-00756-0", + "licence": ["MIT"], + "identifier": "" + } } - ] + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input_list": { + "type": "file", + "description": "VCF/BCF file containing genotype probabilities (GP field).", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", + "ontologies": [] + } + }, + { + "input_index": { + "type": "file", + "description": "Index file of the input VCF/BCF file containing genotype likelihoods.", + "pattern": "*.{vcf.gz.csi,bcf.gz.csi}", + "ontologies": [] + } + } + ] + ], + "output": { + "merged_variants": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{vcf,bcf,vcf.gz,bcf.gz}": { + "type": "file", + "description": "Output VCF/BCF file for the merged regions.\nPhased information (HS field) is updated accordingly for the full region.\n", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", + "ontologies": [] + } + } + ] + ], + "versions_glimpse": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "glimpse": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "GLIMPSE_ligate --help | sed -n '/Version/s/.*: //p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "glimpse": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "GLIMPSE_ligate --help | sed -n '/Version/s/.*: //p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@louislenezet"], + "maintainers": ["@louislenezet"] + }, + "pipelines": [ + { + "name": "phaseimpute", + "version": "1.1.0" } - } ] - ], - "msa_aa": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "${prefix}_aa.fa${compress ? '.gz' : ''}": { - "type": "file", - "description": "Fasta file containing the multiple sequence alignment with Amino Acid alphabet", - "pattern": "*.{fa}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2554" - }, - { - "edam": "http://edamontology.org/format_1921" - }, - { - "edam": "http://edamontology.org/format_1984" + }, + { + "name": "glimpse_phase", + "path": "modules/nf-core/glimpse/phase/meta.yml", + "type": "module", + "meta": { + "name": "glimpse_phase", + "description": "main GLIMPSE algorithm, performs phasing and imputation refining genotype likelihoods", + "keywords": ["phase", "imputation", "low-coverage", "glimpse"], + "tools": [ + { + "glimpse": { + "description": "GLIMPSE is a phasing and imputation method for large-scale low-coverage sequencing studies.", + "homepage": "https://odelaneau.github.io/GLIMPSE", + "documentation": "https://odelaneau.github.io/GLIMPSE/commands.html", + "tool_dev_url": "https://github.com/odelaneau/GLIMPSE", + "doi": "10.1038/s41588-020-00756-0", + "licence": ["MIT"], + "identifier": "" + } } - ] + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "Input VCF/BCF file containing genotype likelihoods.", + "pattern": "*.{vcf.gz,bcf.gz}", + "ontologies": [] + } + }, + { + "input_index": { + "type": "file", + "description": "Index file of the input VCF/BCF file containing genotype likelihoods.", + "pattern": "*.{vcf.gz.csi,bcf.gz.csi}", + "ontologies": [] + } + }, + { + "samples_file": { + "type": "file", + "description": "File with sample names and ploidy information.\nOne sample per line with a mandatory second column indicating ploidy (1 or 2).\nSample names that are not present are assumed to have ploidy 2 (diploids).\nGLIMPSE does NOT handle the use of sex (M/F) instead of ploidy.\n", + "pattern": "*.{txt,tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, + { + "input_region": { + "type": "string", + "description": "Target region used for imputation, including left and right buffers (e.g. chr20:1000000-2000000).", + "pattern": "chrXX:leftBufferPosition-rightBufferPosition" + } + }, + { + "output_region": { + "type": "string", + "description": "Target imputed region, excluding left and right buffers (e.g. chr20:1000000-2000000).", + "pattern": "chrXX:leftBufferPosition-rightBufferPosition" + } + }, + { + "reference": { + "type": "file", + "description": "Reference panel of haplotypes in VCF/BCF format.", + "pattern": "*.{vcf.gz,bcf.gz}", + "ontologies": [] + } + }, + { + "reference_index": { + "type": "file", + "description": "Index file of the Reference panel file.", + "pattern": "*.{vcf.gz.csi,bcf.gz.csi}", + "ontologies": [] + } + }, + { + "map": { + "type": "file", + "description": "File containing the genetic map.", + "pattern": "*.gmap", + "ontologies": [] + } + } + ] + ], + "output": { + "phased_variants": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{vcf,bcf,vcf.gz,bcf.gz}": { + "type": "file", + "description": "Output VCF/BCF file containing genotype probabilities (GP field),\nimputed dosages (DS field), best guess genotypes (GT field),\nsampled haplotypes in the last (max 16) main iterations (HS field) and info-score.\n", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", + "ontologies": [] + } + } + ] + ], + "versions_glimpse": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "glimpse": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "GLIMPSE_phase --help | sed -n '/Version/s/.*: //p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "glimpse": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "GLIMPSE_phase --help | sed -n '/Version/s/.*: //p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@louislenezet"], + "maintainers": ["@louislenezet"] + }, + "pipelines": [ + { + "name": "phaseimpute", + "version": "1.1.0" } - } ] - ], - "versions_foldmason": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "foldmason": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "foldmason version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_pigz": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pigz": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pigz --version 2>&1 | sed \"s/^.*pigz[[:space:]]*//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "foldmason": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "foldmason version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pigz": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pigz --version 2>&1 | sed \"s/^.*pigz[[:space:]]*//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@luisas" - ], - "maintainers": [ - "@luisas" - ] - }, - "pipelines": [ - { - "name": "multiplesequencealign", - "version": "1.1.1" - } - ] - }, - { - "name": "foldmason_msa2lddtreport", - "path": "modules/nf-core/foldmason/msa2lddtreport/meta.yml", - "type": "module", - "meta": { - "name": "foldmason_msa2lddtreport", - "description": "Renders a visualization report using foldmason", - "keywords": [ - "alignment", - "MSA", - "genomics", - "structure" - ], - "tools": [ - { - "foldmason": { - "description": "Multiple Protein Structure Alignment at Scale with FoldMason", - "homepage": "https://github.com/steineggerlab/foldmason", - "documentation": "https://github.com/steineggerlab/foldmason", - "tool_dev_url": "https://github.com/steineggerlab/foldmason", - "doi": "10.1101/2024.08.01.606130", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:foldmason" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "msa": { - "type": "file", - "description": "Input alignment file.", - "pattern": "*.{fa,fasta,aln}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "db": { - "type": "file", - "description": "Input foldmason database.", - "pattern": "*", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "pdbs": { - "type": "file", - "description": "Protein structures used for the visualization.", - "pattern": "*.{pdb}", - "ontologies": [] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "tree": { - "type": "file", - "description": "Guide tree used for the visualization .", - "pattern": "*.{nwk,dnd}", - "ontologies": [] - } - } - ] - ], - "output": { - "html": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "${prefix}.html": { - "type": "file", - "description": "HTML file with the foldmason visualization", - "pattern": "*.{html}", - "ontologies": [] - } - } - ] - ], - "versions_foldmason": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "foldmason": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "foldmason version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "foldmason": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "foldmason version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@luisas" - ], - "maintainers": [ - "@luisas" - ] - }, - "pipelines": [ - { - "name": "multiplesequencealign", - "version": "1.1.1" - } - ] - }, - { - "name": "foldseek_createdb", - "path": "modules/nf-core/foldseek/createdb/meta.yml", - "type": "module", - "meta": { - "name": "foldseek_createdb", - "description": "Create a database from protein structures", - "keywords": [ - "protein", - "structure", - "comparisons" - ], - "tools": [ - { - "foldseek": { - "description": "Foldseek: fast and accurate protein structure search", - "homepage": "https://search.foldseek.com/search", - "documentation": "https://github.com/steineggerlab/foldseek", - "tool_dev_url": "https://github.com/steineggerlab/foldseek", - "doi": "10.1038/s41587-023-01773-0", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:foldseek" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "pdb": { - "type": "file", - "description": "Protein structure(s) in PDB, mmCIF or mmJSON format (also works with folder input)", - "pattern": "*.{pdb,mmcif,mmjson}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1476" - }, - { - "edam": "http://edamontology.org/format_1477" - } - ] - } - } - ] - ], - "output": { - "db": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "${prefix}": { - "type": "directory", - "description": "Directory containing pdb database files", - "pattern": "*" - } - } - ] - ], - "versions_foldseek": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "foldseek": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "foldseek --help |& sed -n 's/.*Version: //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "foldseek": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "foldseek --help |& sed -n 's/.*Version: //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@vagkaratzas" - ] - } - }, - { - "name": "foldseek_easysearch", - "path": "modules/nf-core/foldseek/easysearch/meta.yml", - "type": "module", - "meta": { - "name": "foldseek_easysearch", - "description": "Search for protein structural hits against a foldseek database of protein structures", - "keywords": [ - "protein", - "structure", - "comparisons" - ], - "tools": [ - { - "foldseek": { - "description": "Foldseek: fast and accurate protein structure search", - "homepage": "https://search.foldseek.com/search", - "documentation": "https://github.com/steineggerlab/foldseek", - "tool_dev_url": "https://github.com/steineggerlab/foldseek", - "doi": "10.1038/s41587-023-01773-0", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:foldseek" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "pdb": { - "type": "file", - "description": "Protein structure(s) in PDB, mmCIF or mmJSON format to compare against a foldseek database (also works with folder input)", - "pattern": "*.{pdb,mmcif,mmjson}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1476" - }, - { - "edam": "http://edamontology.org/format_1477" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information for the foldseek db\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "db": { - "type": "directory", - "description": "foldseek database from protein structures", - "pattern": "*" - } - } - ] - ], - "output": { - "aln": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "${prefix}.m8": { - "type": "file", - "description": "Structural comparisons file output\nQuery, Target, Identity, Alignment length, Mismatches, Gap openings,\nQuery start, Query end, Target start, Target end, E-value, Bit score\n", - "pattern": "*.{m8}", - "ontologies": [] - } - } - ] - ], - "versions_foldseek": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "foldseek": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "foldseek --help |& sed -n 's/.*Version: //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "foldseek": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "foldseek --help |& sed -n 's/.*Version: //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] }, - "authors": [ - "@vagkaratzas" - ] - }, - "pipelines": [ { - "name": "proteinfold", - "version": "2.0.0" - } - ] - }, - { - "name": "force_cube", - "path": "modules/nf-core/force/cube/meta.yml", - "type": "module", - "meta": { - "name": "force_cube", - "description": "Generate processing masks for a give datacube definition and area of interest.\nThese files can be used to spatially restrict downstream analysis tasks.\n", - "keywords": [ - "satellite data", - "processing masks", - "binary masks", - "area of interest", - "datacube", - "mask" - ], - "tools": [ - { - "force": { - "description": "A all-in-one tool for processing satellite data.\nSpecialized on medium resolution data such as Landsat or Sentinel imagery.\n", - "homepage": "https://davidfrantz.github.io/code/force/", - "documentation": "https://force-eo.readthedocs.io/en/latest/index.html", - "tool_dev_url": "https://github.com/davidfrantz/force", - "doi": "10.3390/rs11091124", - "licence": [ - "GPL-3.0" - ], - "identifier": "" - } - } - ], - "input": [ - { - "aoi": { - "type": "file", - "description": "Vector file (either shapefile geometry or geopackage) defining the area of interest.", - "pattern": "*.{shp,gpkg}", - "ontologies": [] - } - }, - { - "mask/datacube-definition.prj": { - "type": "file", - "description": "Datacube file in FORCE format defining the properties of the targeted datacube", - "pattern": "*.{prj}", - "ontologies": [] - } - }, - { - "shapefile_dbf": { - "type": "file", - "description": "Optional attribute table for shapefiles. Required if aoi is a shapefile.", - "pattern": "*.{dbf}", - "ontologies": [] - } - }, - { - "shapefile_prj": { - "type": "file", - "description": "Optional projection for shapefiles. Required if aoi is a shapefile.", - "pattern": "*.{prj}", - "ontologies": [] - } - }, - { - "shapefile_shx": { - "type": "file", - "description": "Optional shape index for shapefiles. Required if aoi is a shapefile.", - "pattern": "*.{shx}", - "ontologies": [] - } - } - ], - "output": { - "masks": [ - { - "mask/*/*.tif": { - "type": "file", - "description": "Binary analysis masks for every tile. Directory names indicate corresponding datacube tile. Pixel values indicate usable pixels in downstream analysis.", - "pattern": "*.tif", - "ontologies": [] - } - } - ], - "versions_force": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "force": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "force-cube -v": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "force": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "force-cube -v": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@Felix-Kummer" - ], - "maintainers": [ - "@Felix-Kummer" - ] - } - }, - { - "name": "force_tileextent", - "path": "modules/nf-core/force/tileextent/meta.yml", - "type": "module", - "meta": { - "name": "force_tileextent", - "description": "Compute valid tiles for a given datacube definition and area of interest.\nThis list can be used by downstream analysis tasks to limit processing to the area of interest when satellite data covers a larger region.\n", - "keywords": [ - "satellite data", - "extent", - "tile", - "datacube" - ], - "tools": [ - { - "force": { - "description": "A all-in-one tool for processing satellite data.\nSpecialized on medium resolution data such as Landsat or Sentinel imagery.\n", - "homepage": "https://davidfrantz.github.io/code/force/", - "documentation": "https://force-eo.readthedocs.io/en/latest/index.html", - "tool_dev_url": "https://github.com/davidfrantz/force", - "doi": "10.3390/rs11091124", - "licence": [ - "GPL-3.0" - ], - "identifier": "" - } - } - ], - "input": [ - { - "aoi": { - "type": "file", - "description": "Vector file (either shapefile geometry or geopackage) defining the area of interest.", - "pattern": "*.{shp,gpkg}", - "ontologies": [] - } - }, - { - "datacube_definition": { - "type": "file", - "description": "Datacube file in FORCE format defining the properties of the targeted datacube.", - "pattern": "*.{prj}", - "ontologies": [] - } - }, - { - "shapefile_dbf": { - "type": "file", - "description": "Optional attribute table for shapefiles. Required if aoi is a shapefile.", - "pattern": "*.{dbf}", - "ontologies": [] - } - }, - { - "shapefile_prj": { - "type": "file", - "description": "Optional projection for shapefiles. Required if aoi is a shapefile.", - "pattern": "*.{prj}", - "ontologies": [] - } - }, - { - "shapefile_shx": { - "type": "file", - "description": "Optional shape index for shapefiles. Required if aoi is a shapefile.", - "pattern": "*.{shx}", - "ontologies": [] - } - } - ], - "output": { - "tile_allow": [ - { - "tile_allow.txt": { - "type": "file", - "description": "List of allowed datacube tiles. Each line contains an tile identifier.", - "pattern": "tile_allow.txt", - "ontologies": [] - } - } - ], - "versions_force": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "force": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "force-tile-extent -v": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "force": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "force-tile-extent -v": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@Felix-Kummer" - ], - "maintainers": [ - "@Felix-Kummer" - ] - } - }, - { - "name": "fq_generate", - "path": "modules/nf-core/fq/generate/meta.yml", - "type": "module", - "meta": { - "name": "fq_generate", - "description": "fq generate is a FASTQ file pair generator. It creates two reads, formatting names as described by Illumina. While generate creates \"valid\" FASTQ reads, the content of the files are completely random. The sequences do not align to any genome. This requires a seed (--seed) to be supplied in ext.args.\n", - "keywords": [ - "generate", - "fastq", - "random", - "sequence" - ], - "tools": [ - { - "fq": { - "description": "fq is a library to generate and validate FASTQ file pairs.", - "homepage": "https://github.com/stjude-rust-labs/fq", - "documentation": "https://github.com/stjude-rust-labs/fq", - "tool_dev_url": "https://github.com/stjude-rust-labs/fq", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - { + "name": "glimpse_sample", + "path": "modules/nf-core/glimpse/sample/meta.yml", + "type": "module", "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - } - ], - "output": { - "fastq": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.fastq.gz": { - "type": "file", - "description": "Random generated FASTQ files.", - "pattern": "*_R[12].fastq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "versions_fq": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "fq": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "fq generate --version | sed 's/fq-generate //;s/ .*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "fq": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "fq generate --version | sed 's/fq-generate //;s/ .*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@adamrtalbot" - ], - "maintainers": [ - "@adamrtalbot" - ] - } - }, - { - "name": "fq_lint", - "path": "modules/nf-core/fq/lint/meta.yml", - "type": "module", - "meta": { - "name": "fq_lint", - "description": "fq lint is a FASTQ file pair validator.", - "keywords": [ - "lint", - "fastq", - "validate" - ], - "tools": [ - { - "fq": { - "description": "fq is a library to generate and validate FASTQ file pairs.", - "homepage": "https://github.com/stjude-rust-labs/fq", - "documentation": "https://github.com/stjude-rust-labs/fq", - "tool_dev_url": "https://github.com/stjude-rust-labs/fq", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fastq": { - "type": "file", - "description": "FASTQ file list", - "pattern": "*.fastq{,.gz}", - "ontologies": [] - } + "name": "glimpse_sample", + "description": "Generates haplotype calls by sampling haplotype estimates", + "keywords": ["Sample", "Haplotypes", "Imputation"], + "tools": [ + { + "glimpse": { + "description": "GLIMPSE is a phasing and imputation method for large-scale low-coverage sequencing studies.", + "homepage": "https://odelaneau.github.io/GLIMPSE", + "documentation": "https://odelaneau.github.io/GLIMPSE/commands.html", + "tool_dev_url": "https://github.com/odelaneau/GLIMPSE", + "doi": "10.1038/s41588-020-00756-0", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "Imputed VCF/BCF file", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", + "ontologies": [] + } + }, + { + "index": { + "type": "file", + "description": "Index file of the input VCF/BCF file.", + "pattern": "*.{vcf.gz.csi,bcf.gz.csi}", + "ontologies": [] + } + } + ] + ], + "output": { + "haplo_sampled": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{vcf,bcf,vcf.gz,bcf.gz}": { + "type": "file", + "description": "Output VCF/BCF file containing phased genotypes.", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", + "ontologies": [] + } + } + ] + ], + "versions_glimpse": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "glimpse": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "GLIMPSE_sample --help | sed -n '/Version/s/.*: //p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "glimpse": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "GLIMPSE_sample --help | sed -n '/Version/s/.*: //p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@louislenezet"], + "maintainers": ["@louislenezet"] } - ] - ], - "output": { - "lint": [ - [ - { - "meta": { - "type": "file", - "description": "Lint output", - "pattern": "*.fq_lint.txt", - "ontologies": [] - } - }, - { - "*.fq_lint.txt": { - "type": "file", - "description": "Lint output", - "pattern": "*.fq_lint.txt", - "ontologies": [] - } - } - ] - ], - "versions_fq": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "fq": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "fq lint --version | sed 's/fq-lint //; s/ .*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "fq": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "fq lint --version | sed 's/fq-lint //; s/ .*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] }, - "authors": [ - "@adamrtalbot" - ], - "maintainers": [ - "@adamrtalbot" - ] - }, - "pipelines": [ { - "name": "lncpipe", - "version": "dev" - }, - { - "name": "riboseq", - "version": "1.2.0" - }, - { - "name": "rnaseq", - "version": "3.26.0" - } - ] - }, - { - "name": "fq_subsample", - "path": "modules/nf-core/fq/subsample/meta.yml", - "type": "module", - "meta": { - "name": "fq_subsample", - "description": "fq subsample outputs a subset of records from single or paired FASTQ files. This requires a seed (--seed) to be set in ext.args.", - "keywords": [ - "fastq", - "fq", - "subsample" - ], - "tools": [ - { - "fq": { - "description": "fq is a library to generate and validate FASTQ file pairs.", - "homepage": "https://github.com/stjude-rust-labs/fq", - "documentation": "https://github.com/stjude-rust-labs/fq", - "tool_dev_url": "https://github.com/stjude-rust-labs/fq", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + "name": "glnexus", + "path": "modules/nf-core/glnexus/meta.yml", + "type": "module", + "meta": { + "name": "glnexus", + "description": "merge gVCF files and perform joint variant calling", + "keywords": ["merge", "gvcf", "joint-variant-calling"], + "tools": [ + { + "glnexus": { + "description": "scalable gVCF merging and joint variant calling for population sequencing projects.", + "homepage": "https://github.com/dnanexus-rnd/GLnexus", + "documentation": "https://github.com/dnanexus-rnd/GLnexus/wiki/Getting-Started", + "doi": "10.1101/343970", + "licence": ["Apache-2.0"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "gvcfs": { + "type": "list", + "description": "Input genomic vcf files", + "pattern": "*.{gvcf,gvcf.gz,g.vcf,g.vcf.gz}" + } + }, + { + "custom_config": { + "type": "file", + "description": "Custom YML config for additional profiles", + "pattern": "*.{yml,yaml}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing regions information\ne.g. [ id:'test' ]\n" + } + }, + { + "bed": { + "type": "list", + "description": "Input BED file", + "pattern": "*.bed" + } + } + ] + ], + "output": { + "bcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.bcf": { + "type": "file", + "description": "merged BCF file", + "pattern": "*.bcf", + "ontologies": [] + } + } + ] + ], + "versions_glnexus": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "glnexus": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "glnexus_cli 2>&1 | grep -oE '[0-9]+\\.[0-9]+\\.[0-9]+'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "glnexus": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "glnexus_cli 2>&1 | grep -oE '[0-9]+\\.[0-9]+\\.[0-9]+'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@ramprasadn"], + "maintainers": ["@ramprasadn"] }, - { - "fastq": { - "type": "file", - "description": "FASTQ file", - "pattern": "*.{fq,fastq}{,.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "output": { - "fastq": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.fastq.gz": { - "type": "file", - "description": "Randomly sampled FASTQ files.", - "pattern": "*_R[12].fastq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "versions_fq": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "fq": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "fq subsample --version | sed 's/fq-subsample //; s/ .*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "fq": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "fq subsample --version | sed 's/fq-subsample //; s/ .*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "raredisease", + "version": "3.0.0" + }, + { + "name": "variantcatalogue", + "version": "dev" + } ] - ] }, - "authors": [ - "@adamrtalbot" - ], - "maintainers": [ - "@adamrtalbot" - ] - }, - "pipelines": [ { - "name": "lncpipe", - "version": "dev" - }, - { - "name": "riboseq", - "version": "1.2.0" + "name": "gmmdemux", + "path": "modules/nf-core/gmmdemux/meta.yml", + "type": "module", + "meta": { + "name": "gmmdemux", + "description": "GMM-Demux is a Gaussian-Mixture-Model-based software for processing sample barcoding data (cell hashing and MULTI-seq).", + "keywords": ["demultiplexing", "hashing-based deconvolution", "single-cell"], + "tools": [ + { + "gmmdemux": { + "description": "GMM-Demux is a Gaussian-Mixture-Model-based software for processing sample barcoding data (cell hashing and MULTI-seq).", + "homepage": "https://pypi.org/project/GMM-Demux/", + "documentation": "https://github.com/CHPGenetics/GMM-Demux", + "tool_dev_url": "https://github.com/CHPGenetics/GMM-demux", + "doi": "10.1186/s13059-020-02084-2", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "hto_matrix": { + "type": "file", + "description": "path to matrix from cell hashing data, the tool receives either CSV files or TSV, type must be specified using parameters", + "ontologies": [] + } + }, + { + "hto_names": { + "type": "string", + "description": "Comma separated list of HTO names, without whitespace\n" + } + } + ], + { + "type_report": { + "type": "boolean", + "description": "If true, full classification report is generated, otherwise the simplified classification report.\n" + } + }, + { + "summary_report": { + "type": "boolean", + "description": "If true, summary report is generated.\n" + } + }, + { + "skip": { + "type": "file", + "description": "Load a full classification report and skip the mtx folder as input. Require a path argument.\n", + "ontologies": [] + } + }, + { + "examine": { + "type": "file", + "description": "Provide the cell list. Requires a file argument. Only executes if -u is set.\n", + "ontologies": [] + } + } + ], + "output": { + "barcodes": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "barcodes.tsv.gz": { + "type": "file", + "description": "barcodes tsv file with removed cell-hashing-identifiable multiplets\n", + "pattern": "barcodes.tsv.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "matrix": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "matrix.mtx.gz": { + "type": "file", + "description": "matrix mtx.tsv file with removed cell-hashing-identifiable multiplets\n", + "pattern": "matrix.mtx.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "features": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "features.tsv.gz": { + "type": "file", + "description": "features tsv file with removed cell-hashing-identifiable multiplets\n", + "pattern": "features.tsv.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "classification_report": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "GMM_*.csv": { + "type": "file", + "description": "full or simplified classification report\n", + "pattern": "GMM_*.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "config_report": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "GMM_*.config": { + "type": "file", + "description": "Configuration report mapping the results obtained by the tool to the respective names of the HTOs in the classification report.\n", + "pattern": "GMM_*.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "summary_report": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "summary_report_*.txt": { + "type": "file", + "description": "summary report, optional output\n", + "pattern": "test/summary_report_*.txt", + "ontologies": [] + } + } + ] + ], + "versions_gmmdemux": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "GMM-Demux": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "0.2.2.3": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "GMM-Demux": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "0.2.2.3": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@mari-ga", "@maxozo", "@wxicu", "@Zethson"], + "maintainers": ["@mari-ga", "@maxozo", "@wxicu", "@Zethson"] + } }, { - "name": "rnaseq", - "version": "3.26.0" - } - ] - }, - { - "name": "fqtk", - "path": "modules/nf-core/fqtk/meta.yml", - "type": "module", - "meta": { - "name": "fqtk", - "description": "Demultiplex fastq files", - "keywords": [ - "demultiplex", - "fastq", - "rust" - ], - "tools": [ - { - "fqtk": { - "description": "A toolkit for working with FASTQ files, written in Rust.", - "homepage": "https://github.com/fulcrumgenomics/fqtk", - "documentation": "https://github.com/fulcrumgenomics/fqtk", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "sample_sheet": { - "type": "file", - "description": "Tsv file, with two columns sample_id and barcode", - "pattern": "*.{tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - }, - { - "fastq_folder": { - "type": "file", - "description": "Directory containing fastq files that will be staged as 'input' folder", - "pattern": "*", - "ontologies": [] - } - }, - { - "fastq_readstructure_pairs": { - "type": "map", - "description": "List of lists i.e. [[, ],...]" - } - } - ] - ], - "output": { - "sample_fastq": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "output/*.fq.gz": { - "type": "file", - "description": "Demultiplexed per-sample FASTQ files", - "pattern": "output/*R*.fastq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "metrics": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "output/demux-metrics.txt": { - "type": "file", - "description": "Demultiplexing summary stats; sample_id, barcode templates, frac_templates, ratio_to_mean, ratio_to_best\n", - "pattern": "output/demux-metrics.txt", - "ontologies": [] - } - } - ] - ], - "most_frequent_unmatched": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "output/unmatched*.fq.gz": { - "type": "file", - "description": "File containing unmatched fastq records\n", - "pattern": "output/unmatched*.fq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "versions_fqtk": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "fqtk": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "fqtk --version 2>&1 | cut -d \" \" -f2": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "fqtk": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "fqtk --version 2>&1 | cut -d \" \" -f2": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@nh13", - "@sam-white04" - ], - "maintainers": [ - "@nh13", - "@sam-white04" - ] - }, - "pipelines": [ - { - "name": "demultiplex", - "version": "1.7.1" - } - ] - }, - { - "name": "freebayes", - "path": "modules/nf-core/freebayes/meta.yml", - "type": "module", - "meta": { - "name": "freebayes", - "description": "A haplotype-based variant detector", - "keywords": [ - "variant caller", - "SNP", - "genotyping", - "somatic variant calling", - "germline variant calling", - "bacterial variant calling", - "bayesian" - ], - "tools": [ - { - "freebayes": { - "description": "Bayesian haplotype-based polymorphism discovery and genotyping", - "homepage": "https://github.com/freebayes/freebayes", - "documentation": "https://github.com/freebayes/freebayes", - "tool_dev_url": "https://github.com/freebayes/freebayes", - "doi": "10.48550/arXiv.1207.3907", - "licence": [ - "MIT" - ], - "identifier": "biotools:freebayes" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input_1": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } - }, - { - "input_1_index": { - "type": "file", - "description": "BAM/CRAM/SAM index file", - "pattern": "*.{bai,crai}", - "ontologies": [] - } - }, - { - "input_2": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } - }, - { - "input_2_index": { - "type": "file", - "description": "BAM/CRAM/SAM index file", - "pattern": "*.{bai,crai}", - "ontologies": [] - } - }, - { - "target_bed": { - "type": "file", - "description": "Optional - Limit analysis to targets listed in this BED-format FILE.", - "pattern": "*.bed", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test_reference' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "reference fasta file", - "pattern": ".{fa,fa.gz,fasta,fasta.gz}", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test_reference' ]\n" - } - }, - { - "fasta_fai": { - "type": "file", - "description": "reference fasta file index", - "pattern": "*.{fa,fasta}.fai", - "ontologies": [] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing meta information for the samples file.\ne.g. [ id:'test_samples' ]\n" - } - }, - { - "samples": { - "type": "file", - "description": "Optional - Limit analysis to samples listed (one per line) in the FILE.", - "pattern": "*.txt", - "ontologies": [] - } - } - ], - [ - { - "meta5": { - "type": "map", - "description": "Groovy Map containing meta information for the populations file.\ne.g. [ id:'test_populations' ]\n" - } - }, - { - "populations": { - "type": "file", - "description": "Optional - Each line of FILE should list a sample and a population which it is part of.", - "pattern": "*.txt", - "ontologies": [] - } - } - ], - [ - { - "meta6": { - "type": "map", - "description": "Groovy Map containing meta information for the cnv file.\ne.g. [ id:'test_cnv' ]\n" - } + "name": "gnu_sort", + "path": "modules/nf-core/gnu/sort/meta.yml", + "type": "module", + "meta": { + "name": "gnu_sort", + "description": "Writes a sorted concatenation of file/s\n", + "keywords": ["GNU", "coreutils", "sort", "merge compare"], + "tools": [ + { + "gnu": { + "description": "The GNU Core Utilities are the basic file, shell and text manipulation utilities of the GNU operating system. These are the core utilities which are expected to exist on every operating system.", + "homepage": "https://www.gnu.org/software/coreutils/", + "documentation": "https://www.gnu.org/software/coreutils/manual/html_node/index.html", + "tool_dev_url": "https://git.savannah.gnu.org/cgit/coreutils.git", + "doi": "10.5281/zenodo.581670", + "licence": ["GPL"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "Draft assembly file", + "pattern": "*.{txt,bed,interval,genome,bins}", + "ontologies": [] + } + }, + { + "suffix": { + "type": "string", + "description": "Output suffix" + } + } + ] + ], + "output": { + "sorted": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "${output_file}" + } + }, + { + "${output_file}": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "${output_file}" + } + } + ] + ], + "versions_coreutils": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "coreutils": { + "type": "string", + "description": "The tool name" + } + }, + { + "sort --version |& sed '1!d ; s/sort (GNU coreutils) //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "coreutils": { + "type": "string", + "description": "The tool name" + } + }, + { + "sort --version |& sed '1!d ; s/sort (GNU coreutils) //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@DLBPointon"], + "maintainers": ["@DLBPointon"] }, - { - "cnv": { - "type": "file", - "description": "A copy number map BED file, which has either a sample-level ploidy:\nsample_name copy_number\nor a region-specific format:\nseq_name start end sample_name copy_number\n", - "pattern": "*.bed", - "ontologies": [] - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.vcf.gz": { - "type": "file", - "description": "Compressed VCF file", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "versions_freebayes": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "freebayes": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "freebayes --version 2>&1 | sed \"s/version:\\s*v//g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "freebayes": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "freebayes --version 2>&1 | sed \"s/version:\\s*v//g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "circrna", + "version": "dev" + }, + { + "name": "isoseq", + "version": "2.0.0" + }, + { + "name": "tfactivity", + "version": "dev" + }, + { + "name": "variantbenchmarking", + "version": "1.5.0" + } ] - ] }, - "authors": [ - "@maxibor", - "@FriederikeHanssen", - "@maxulysse" - ], - "maintainers": [ - "@maxibor", - "@FriederikeHanssen", - "@maxulysse" - ] - }, - "pipelines": [ { - "name": "mag", - "version": "5.4.2" + "name": "gnu_split", + "path": "modules/nf-core/gnu/split/meta.yml", + "type": "module", + "meta": { + "name": "gnu_split", + "description": "Split a file into consecutive or interleaved sections", + "keywords": ["gnu", "split", "coreutils", "generic"], + "tools": [ + { + "gnu": { + "description": "The GNU Core Utilities are the basic file, shell and text manipulation utilities of the GNU operating system. These are the core utilities which are expected to exist on every operating system.", + "homepage": "https://www.gnu.org/software/coreutils/", + "documentation": "https://www.gnu.org/software/coreutils/manual/html_node/index.html", + "tool_dev_url": "https://git.savannah.gnu.org/cgit/coreutils.git", + "doi": "10.5281/zenodo.581670", + "licence": ["GPL"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "input": { + "type": "file", + "description": "Text file, possibly gzip file", + "ontologies": [] + } + } + ] + ], + "output": { + "split": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}.*": { + "type": "file", + "description": "Split files", + "pattern": "${prefix}.*", + "ontologies": [] + } + } + ] + ], + "versions_coreutils": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "coreutils": { + "type": "string", + "description": "The tool name" + } + }, + { + "sort --version |& sed '1!d ; s/sort (GNU coreutils) //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "coreutils": { + "type": "string", + "description": "The tool name" + } + }, + { + "sort --version |& sed '1!d ; s/sort (GNU coreutils) //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@k1sauce"], + "maintainers": ["@k1sauce"] + } }, { - "name": "radseq", - "version": "dev" + "name": "goat_taxonsearch", + "path": "modules/nf-core/goat/taxonsearch/meta.yml", + "type": "module", + "meta": { + "name": "goat_taxonsearch", + "description": "Query metadata for any taxon across the tree of life.", + "keywords": ["public datasets", "ncbi", "genomes on a tree"], + "tools": [ + { + "goat": { + "description": "goat-cli is a command line interface to query the\nGenomes on a Tree Open API.\n", + "homepage": "https://github.com/genomehubs/goat-cli", + "documentation": "https://github.com/genomehubs/goat-cli/wiki", + "tool_dev_url": "https://genomehubs.github.io/goat-cli/goat_cli/", + "licence": ["MIT"], + "identifier": "biotools:goat" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "taxon": { + "type": "string", + "description": "The taxon to search. An NCBI taxon ID, or the name of a taxon at any rank.\n" + } + }, + { + "taxa_file": { + "type": "file", + "description": "A file of NCBI taxonomy ID's (tips) and/or binomial names. Each line\nshould contain a single entry.File size is limited to 500 entries.\n", + "pattern": "*.txt", + "ontologies": [] + } + } + ] + ], + "output": { + "taxonsearch": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "TSV file containing search results.", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_goat": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "goat": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "goat-cli --version | cut -d' ' -f2": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "goat": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "goat-cli --version | cut -d' ' -f2": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@alxndrdiaz"], + "maintainers": ["@alxndrdiaz", "@muffato"] + } }, { - 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A bam index has 16KB resolution so that's what this gives, but it provides what appears to be a high-quality coverage estimate in seconds per genome.", + "keywords": ["coverage", "cnv", "genomics", "depth"], + "tools": [ + { + "goleft": { + "description": "goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary", + "homepage": "https://github.com/brentp/goleft", + "documentation": "https://github.com/brentp/goleft", + "tool_dev_url": "https://github.com/brentp/goleft", + "doi": "10.1093/gigascience/gix090", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false]\n" + } + }, + { + "bams": { + "type": "file", + "description": "Sorted BAM/CRAM/SAM files", + "pattern": "*.{bam,cram,sam}", + "ontologies": [] + } + }, + { + "indexes": { + "type": "file", + "description": "BAI/CRAI files", + "pattern": "*.{bai,crai}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false]\n" + } + }, + { + "fai": { + "type": "file", + "description": "FASTA index", + "pattern": "*.{fai}", + "ontologies": [] + } + } + ] + ], + "output": { + "output": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/*": { + "type": "file", + "description": "Files generated by indexcov", + "ontologies": [] + } + } + ] + ], + "ped": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/*ped": { + "type": "file", + "description": "ped files", + "pattern": "*ped", + "ontologies": [] + } + } + ] + ], + "bed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/*bed.gz": { + "type": "file", + "description": "bed files", + "pattern": "*bed.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "bed_index": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/*bed.gz.tbi": { + "type": "file", + "description": "bed index files", + "pattern": "*bed.gz.tbi", + "ontologies": [] + } + } + ] + ], + "roc": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/*roc": { + "type": "file", + "description": "roc files", + "pattern": "*roc", + "ontologies": [] + } + } + ] + ], + "html": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/*html": { + "type": "file", + "description": "html files", + "pattern": "*html", + "ontologies": [] + } + } + ] + ], + "png": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/*png": { + "type": "file", + "description": "png files", + "pattern": "*png", + "ontologies": [] + } + } + ] + ], + "versions_goleft": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "goleft": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "goleft --version |& sed '1!d;s/^.*goleft Version: //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_tabix": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "tabix": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "tabix -h |& sed -n 's/^.*Version: //p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "goleft": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "goleft --version |& sed '1!d;s/^.*goleft Version: //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "tabix": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "tabix -h |& sed -n 's/^.*Version: //p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@lindenb"], + "maintainers": ["@lindenb"] }, - { - "depths": { - "type": "file", - "description": "File containing depth of the variants", - "pattern": "*.depth.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - { - "repeats": { - "type": "integer", - "description": "Number of bootstrap repeats to perform" - } - }, - { - "barcodes": { - "type": "file", - "description": "File containing lineage defining barcodes", - "pattern": "*barcodes.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - }, - { - "lineages_meta": { - "type": "file", - "description": "Optional file containing lineage metadata that correspond to barcodes", - "pattern": "*lineages.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - }, - { - "lineages_topology": { - "type": "file", - "description": "Optional file containing lineage topology information that correspond to barcodes", - "pattern": "*lineages.yml", - "ontologies": [ + "pipelines": [ { - "edam": "http://edamontology.org/format_3750" + "name": "sarek", + "version": "3.8.1" } - ] - } - } - ], - "output": { - "lineages": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*lineages.csv": { - "type": "file", - "description": "a csv file that includes the lineages present and their corresponding abundances", - "pattern": "*lineages.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "summarized": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*summarized.csv": { - "type": "file", - "description": "a csv file that includes the lineages present but summarized by constellation and their corresponding abundances", - "pattern": "*summarized.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "versions_freyja": [ - 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This can be an expression matrix (see also background_column parameter); if so, will only consider those genes with an expression value > 0 in at least one sample. Alternatively, this can be a TXT file containing only a list of gene IDs.\n", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + }, + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "output": { + "all_enrich": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ]\n" + } + }, + { + "*.gprofiler2.all_enriched_pathways.tsv": { + "type": "file", + "description": "TSV file; table listing all enriched pathways that were found. This table will always be created (empty if no enrichment was found), the other output files are only created if enriched pathways were found\n", + "pattern": "*gprofiler2.*all_enriched_pathways.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "rds": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ]\n" + } + }, + { + "*.gprofiler2.gost_results.rds": { + "type": "file", + "description": "RDS file; R object containing the results of the gost query\n", + "pattern": "*gprofiler2.*gost_results.rds", + "ontologies": [] + } + } + ] + ], + "plot_png": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ]\n" + } + }, + { + "*.gprofiler2.gostplot.png": { + "type": "file", + "description": "PNG file; Manhattan plot of all enriched pathways\n", + "pattern": "*gprofiler2.*gostplot.png", + "ontologies": [] + } + } + ] + ], + "plot_html": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ]\n" + } + }, + { + "*.gprofiler2.gostplot.html": { + "type": "file", + "description": "HTML file; interactive Manhattan plot of all enriched pathways\n", + "pattern": "*gprofiler2.*gostplot.html", + "ontologies": [] + } + } + ] + ], + "sub_enrich": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ]\n" + } + }, + { + "*.gprofiler2.*.sub_enriched_pathways.tsv": { + "type": "file", + "description": "TSV file; table listing enriched pathways that were found from one particular source\n", + "pattern": "*gprofiler2.*sub_enriched_pathways.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "sub_plot": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ]\n" + } + }, + { + "*.gprofiler2.*.sub_enriched_pathways.png": { + "type": "file", + "description": "PNG file; bar plot showing the fraction of genes that were found enriched in each pathway\n", + "pattern": "*gprofiler2.*sub_enriched_pathways.png", + "ontologies": [] + } + } + ] + ], + "filtered_gmt": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ]\n" + } + }, + { + "*ENSG_filtered.gmt": { + "type": "file", + "description": "GMT file that was provided as input or that was downloaded from g:profiler if no input GMT file was given; filtered for the selected datasources\n", + "pattern": "*ENSG_filtered.gmt", + "ontologies": [] + } + } + ] + ], + "session_info": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ]\n" + } + }, + { + "*R_sessionInfo.log": { + "type": "file", + "description": "Log file containing information about the R session that was run for this module\n", + "pattern": "*R_sessionInfo.log", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "YAML file containing versions of tools used in the module", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "topics": { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "YAML file containing versions of tools used in the module", + "ontologies": [] + } + } + ] + }, + "authors": ["@WackerO"] }, - { - "depths": { - "type": "file", - "description": "File containing depth of the variants", - "pattern": "*.depth.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - { - "barcodes": { - "type": "file", - "description": "File containing lineage defining barcodes", - "pattern": "*barcodes.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - }, - { - "lineages_meta": { - "type": "file", - "description": "Optional file containing lineage metadata that correspond to barcodes", - "pattern": "*lineages.json", - "ontologies": [ + "pipelines": [ { - "edam": "http://edamontology.org/format_3464" - } - ] - } - }, - { - "lineages_topology": { - "type": "file", - "description": "Optional file containing lineage topology information that correspond to barcodes", - "pattern": "*lineages.yml", - "ontologies": [ + "name": "differentialabundance", + "version": "1.5.0" + }, { - "edam": "http://edamontology.org/format_3750" + "name": "diseasemodulediscovery", + "version": "dev" } - ] - } - } - ], - "output": { - "demix": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "a tsv file that includes the lineages present, their corresponding abundances, and summarization by constellation", - "pattern": "*.demix.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_freyja": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "freyja": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "freyja --version | sed 's/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "freyja": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "freyja --version | sed 's/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@Joon-Klaps" - ], - "maintainers": [ - "@Joon-Klaps" - ] - }, - "pipelines": [ - { - "name": "viralrecon", - "version": "3.0.0" - } - ] - }, - { - "name": "freyja_update", - "path": "modules/nf-core/freyja/update/meta.yml", - "type": "module", - "meta": { - "name": "freyja_update", - "description": "downloads new versions of the curated SARS-CoV-2 lineage file and barcodes", - "keywords": [ - "database", - "variants", - "UShER" - ], - "tools": [ - { - "freyja": { - "description": "Freyja recovers relative lineage abundances from mixed SARS-CoV-2 samples and provides functionality to analyze lineage dynamics.", - "homepage": "https://github.com/andersen-lab/Freyja", - "documentation": "https://github.com/andersen-lab/Freyja/wiki", - "tool_dev_url": "https://github.com/andersen-lab/Freyja", - "doi": "10.1038/s41586-022-05049-6", - "licence": [ - "BSD-2-Clause" - ], - "identifier": "biotools:freyja" - } - } - ], - "input": [ - { - "db_name": { - "type": "string", - "description": "The name of the database directory" - } - } - ], - "output": { - "barcodes": [ - { - "${db_name}/*barcodes.*": { - "type": "file", - "description": "File containing lineage defining barcodes", - "pattern": "*barcodes.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ], - "lineages_topology": [ - { - "${db_name}/*lineages.yml": { - "type": "file", - "description": "File containing lineage topology information that correspond to barcodes", - "pattern": "*lineages.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ], - "lineages_meta": [ - { - "${db_name}/*curated_lineages.json": { - "type": "file", - "description": "File containing lineage metadata that correspond to barcodes", - "pattern": "*curated_lineages.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ], - "config": [ - { - "${db_name}/*pathogen_config.yml": { - "type": "file", - "description": "File containing pathogen configuration information for Freyja", - "pattern": "*pathogen_config.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ], - "versions_freyja": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "freyja": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "freyja --version | sed 's/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "freyja": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "freyja --version | sed 's/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@Joon-Klaps" - ], - "maintainers": [ - "@Joon-Klaps" - ] - }, - "pipelines": [ - { - "name": "viralrecon", - "version": "3.0.0" - } - ] - }, - { - "name": "freyja_variants", - "path": "modules/nf-core/freyja/variants/meta.yml", - "type": "module", - "meta": { - "name": "freyja_variants", - "description": "call variant and sequencing depth information of the variant", - "keywords": [ - "variants", - "fasta", - "wastewater" - ], - "tools": [ - { - "freyja": { - "description": "Freyja recovers relative lineage abundances from mixed SARS-CoV-2 samples and provides functionality to analyze lineage dynamics.", - "homepage": "https://github.com/andersen-lab/Freyja", - "documentation": "https://github.com/andersen-lab/Freyja/wiki", - "tool_dev_url": "https://github.com/andersen-lab/Freyja", - "doi": "10.1038/s41586-022-05049-6", - "licence": [ - "BSD-2-Clause" - ], - "identifier": "biotools:freyja" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM file", - "pattern": "*.bam", - "ontologies": [] - } - } - ], - { - "fasta": { - "type": "file", - "description": "The reference sequence used for mapping and generating the BAM file", - "pattern": "*.fa", - "ontologies": [] - } - } - ], - "output": { - "variants": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.variants.tsv": { - "type": "file", - "description": "File containing identified variants in a gff-like format", - "pattern": "*.variants.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - }, - { - "*.depth.tsv": { - "type": "file", - "description": "File containing depth of the variants", - "pattern": "*.depth.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_freyja": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "freyja": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "freyja --version | sed 's/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "freyja": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "freyja --version | sed 's/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@Joon-Klaps" - ], - "maintainers": [ - "@Joon-Klaps" - ] - }, - "pipelines": [ - { - "name": "viralrecon", - "version": "3.0.0" - } - ] - }, - { - "name": "fusioncatcher_build", - "path": "modules/nf-core/fusioncatcher/build/meta.yml", - "type": "module", - 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} - }, - { - "${prefix}": { - "type": "file", - "description": "Diretory containing the fusioncatcher reference files", - "ontologies": [] - } - } - ] - ], - "versions_fusioncatcher": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "fusioncatcher": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "fusioncatcher --version |& sed 's/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "fusioncatcher": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "fusioncatcher --version |& sed 's/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@nvnieuwk" - ], - "maintainers": [ - "@nvnieuwk" - ] - 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"pattern": "*.log", - "ontologies": [ + }, + { + "name": "graphmap2_align", + "path": "modules/nf-core/graphmap2/align/meta.yml", + "type": "module", + "meta": { + "name": "graphmap2_align", + "description": "A versatile pairwise aligner for genomic and spliced nucleotide sequences", + "keywords": ["align", "fasta", "fastq", "genome", "reference"], + "tools": [ + { + "graphmap2": { + "description": "A versatile pairwise aligner for genomic and spliced nucleotide sequences.\n", + "homepage": "https://github.com/lbcb-sci/graphmap2", + "documentation": "https://github.com/lbcb-sci/graphmap2#graphmap2---a-highly-sensitive-and-accurate-mapper-for-long-error-prone-reads", + "licence": ["MIT"], + "identifier": "biotools:Graphmap2" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "file containing reads to be aligned.", + "ontologies": [] + } + } + ], { - 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} - ] - } - } - ] - ], - "igv_inputs": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "IGV_inputs": { - "type": "directory", - "description": "IGV inputs directory", - "pattern": "IGV_inputs" - } - } - ] - ], - "fi_workdir": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fi_workdir": { - "type": "directory", - "description": "FusionInspector work directory", - "pattern": "fi_workdir" - } - } - ] - ], - "chckpts_dir": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "chckpts_dir": { - "type": "directory", - "description": "Checkpoints directory", - "pattern": "chckpts_dir" - } - } - ] - ], - "versions_fusioninspector": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "fusion-inspector": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "FusionInspector --version |& sed -n 's/.*version: //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "fusion-inspector": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "FusionInspector --version |& sed -n 's/.*version: //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@rannick", - "@delfiterradas", - "@sofiromano", - "@alanmmobbs93", - "@martings" - ] - }, - "pipelines": [ - { - "name": "rnafusion", - "version": "4.1.2" - } - ] - }, - { - "name": "fusionreport_detect", - "path": "modules/nf-core/fusionreport/detect/meta.yml", - 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"edam": "http://edamontology.org/format_3475" - } - ] - } - }, - { - "fusioncatcher_fusions": { - "type": "file", - "description": "File containing fusions from fusioncatcher", - "pattern": "*.fusions.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\n" - } - }, - { - "fusionreport_ref": { - "type": "directory", - "description": "directory containing the genome resource files required for fusioncatcher", - "pattern": "fusion_report_db" - } - } - ], - { - "tools_cutoff": { - "type": "integer", - "description": "Discard fusions detected by less than $tools_cutoff tools both for display in fusionreport html index and to consider in fusioninspector." + ], + "output": { + "sam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.sam": { + "type": "file", + "description": "Alignment in SAM format", + "pattern": "*.sam", + "ontologies": [] + } + } + ] + ], + "versions_graphmap2": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "graphmap2": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "graphmap2 2>&1 | sed -n 's/Version: v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "graphmap2": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "graphmap2 2>&1 | sed -n 's/Version: v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@yuukiiwa", "@drpatelh"], + "maintainers": ["@yuukiiwa", "@drpatelh"] } - 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"meta": { - "name": "fusionreport_download", - "description": "Build DB for fusionreport", - "keywords": [ - "sort", - "RNA-seq", - "fusion_report", - "download" - ], - "tools": [ - { - "fusionreport": { - "description": "Generate an interactive summary report from fusion detection tools.", - "homepage": "https://github.com/Clinical-Genomics/fusion-report", - "documentation": "https://github.com/Clinical-Genomics/fusion-report/blob/master/README.md", - "tool_dev_url": "https://github.com/Clinical-Genomics/fusion-report", - "licence": [ - "GPL v3" - ], - "identifier": "" - } - } - ], - "input": [ - { + "name": "graphmap2_index", + "path": "modules/nf-core/graphmap2/index/meta.yml", + "type": "module", "meta": { - "type": "map", - "description": "Groovy Map containing database information\n" + "name": "graphmap2_index", + "description": "A versatile pairwise aligner for genomic and spliced nucleotide sequences", + "keywords": ["index", "fasta", "reference"], + "tools": [ + { + "graphmap2": { + "description": "A versatile pairwise aligner for genomic and spliced nucleotide sequences.\n", + "homepage": "https://github.com/lbcb-sci/graphmap2", + "documentation": "https://github.com/lbcb-sci/graphmap2#graphmap2---a-highly-sensitive-and-accurate-mapper-for-long-error-prone-reads", + "licence": ["MIT"], + "identifier": "biotools:Graphmap2" + } + } + ], + "input": [ + { + "fasta": { + "type": "file", + "description": "Reference database in FASTA format.\n", + "ontologies": [] + } + } + ], + "output": { + "index": [ + { + "*.gmidx": { + "type": "file", + "description": "Index file in gmidx format", + "pattern": "*.gmidx", + "ontologies": [] + } + } + ], + "versions_graphmap2": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "graphmap2": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "graphmap2 2>&1 | sed -n 's/Version: v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "graphmap2": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "graphmap2 2>&1 | sed -n 's/Version: v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@yuukiiwa", "@drpatelh"], + "maintainers": ["@yuukiiwa", "@drpatelh"] } - } - ], - "output": { - "fusionreport_ref": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing database information\n" - } - }, - { - "${prefix}": { - "type": "directory", - "description": "directory containing the genome resource files required for fusioncatcher", - "pattern": "${prefix}" - } - } - ] - ], - "versions_fusionreport": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "fusion_report": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "fusion_report --version |& sed 's/fusion-report //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "fusion_report": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "fusion_report --version |& sed 's/fusion-report //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] }, - "authors": [ - "@praveenraj2018" - ] - }, - "pipelines": [ { - "name": "rnafusion", - "version": "4.1.2" - } - ] - }, - { - "name": "galah", - "path": "modules/nf-core/galah/meta.yml", - "type": "module", - "meta": { - "name": "galah", - "description": "Cluster genome FASTA files by average nucleotide identity", - "keywords": [ - "genomics", - "cluster", - "genome", - "metagenomics" - ], - "tools": [ - { - "galah": { - "description": "Galah aims to be a more scalable metagenome assembled genome (MAG) dereplication method.", - "homepage": "https://github.com/wwood/galah", - "documentation": "https://github.com/wwood/galah", - "tool_dev_url": "https://github.com/wwood/galah", - "doi": "10.1111/NODOI", - "licence": [ - "GPL v3" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "bins": { - "type": "file", - "description": "A list of fasta-formatted genomes for dereplication", - "pattern": "*.{fa,fna,fa.gz, etc}", - "ontologies": [] - } - }, - { - "qc_table": { - "type": "file", - "description": "(optional) A summary TSV from either CheckM [https://nf-co.re/modules/checkm_lineagewf],\nCheckM2 [https://nf-co.re/modules/checkm2_predict/], or a CSV\nin drep-style format [https://github.com/MrOlm/drep] with three columnns,\n`genome,completeness,contamination`. In both cases the first column should contain the\nnames of the input genome files, minus the last file extension\n(i.e. if the genome is gzipped, the genome name should\nretain the .fasta extension).\n", - "pattern": "*.{csv,tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - }, - { - "edam": "http://edamontology.org/format_3475" - } - ] - } + "name": "graphtyper_genotype", + "path": "modules/nf-core/graphtyper/genotype/meta.yml", + "type": "module", + "meta": { + "name": "graphtyper_genotype", + "description": "Tools for population-scale genotyping using pangenome graphs.", + "keywords": ["variant", "vcf", "bam", "cram", "pangenome"], + "tools": [ + { + "graphtyper": { + "description": "A graph-based variant caller capable of genotyping population-scale short read data sets while incorporating previously discovered variants.", + "homepage": "https://github.com/DecodeGenetics/graphtyper", + "documentation": "https://github.com/DecodeGenetics/graphtyper/wiki/User-guide", + "tool_dev_url": "https://github.com/DecodeGenetics/graphtyper", + "doi": "10.1038/ng.3964", + "licence": ["MIT"], + "identifier": "biotools:Graphtyper" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM file", + "pattern": "*.{bam,cram}", + "ontologies": [] + } + }, + { + "bai": { + "type": "file", + "description": "BAM index file. This is automatically found base on BAM input file name", + "pattern": "*.{bai}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "ref": { + "type": "file", + "description": "Reference fasta file", + "pattern": "*.{fa, fasta, fas}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "ref_fai": { + "type": "file", + "description": "Reference index file. This is automatically found based on reference input file name.", + "pattern": "*.{.fai}", + "ontologies": [] + } + } + ], + { + "region_file": { + "type": "file", + "description": "File with a list of chromosome/locations in reference genome to genotype. One region per line in the format :-. This or `--region` (in ext.args) must be specified.", + "pattern": "*", + "ontologies": [] + } + } + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "results/*/*.vcf.gz": { + "type": "file", + "description": "VCF file with genotyped variants", + "pattern": "*.{vcf.gz}", + "ontologies": [] + } + } + ] + ], + "tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "results/*/*.vcf.gz.tbi": { + "type": "file", + "description": "VCF index file", + "pattern": "*.{vcf.gz.tbi}", + "ontologies": [] + } + } + ] + ], + "versions_graphtyper": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "graphtyper": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "graphtyper --help | tail -1 | sed 's/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "graphtyper": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "graphtyper --help | tail -1 | sed 's/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@zachary-foster"], + "maintainers": ["@zachary-foster"] }, - { - "qc_format": { - "type": "string", - "description": "Defines the type if input table in `qc_table`, if specified.", - "pattern": "checkm|checkm2|genome_info" - } - } - ] - ], - "output": { - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "TSV file in the format `representative_genome` \\t `member_genome`", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "dereplicated_bins": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "${prefix}/*": { - "type": "file", - "description": "The representative genomes following dereplication by galah.", - "pattern": "*", - "ontologies": [] - } - } - ] - ], - "versions_galah": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "galah": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "galah --version | sed \"s/galah //\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "galah": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "galah --version | sed \"s/galah //\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "pathogensurveillance", + "version": "1.1.0" + } ] - ] - }, - "authors": [ - "@prototaxites" - ], - "maintainers": [ - "@prototaxites" - ] - } - }, - { - "name": "gamma_gamma", - "path": "modules/nf-core/gamma/gamma/meta.yml", - "type": "module", - "meta": { - "name": "gamma_gamma", - "description": "Gene Allele Mutation Microbial Assessment", - "keywords": [ - "gamma", - "gene-calling", - "microbial", - "allele" - ], - "tools": [ - { - "gamma": { - "description": "Tool for Gene Allele Mutation Microbial Assessment", - "homepage": "https://github.com/rastanton/GAMMA", - "documentation": "https://github.com/rastanton/GAMMA", - "tool_dev_url": "https://github.com/rastanton/GAMMA", - "doi": "10.1093/bioinformatics/btab607", - "licence": [ - "Apache License 2.0" - ], - "identifier": "biotools:gamma" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + }, + { + "name": "graphtyper_vcfconcatenate", + "path": "modules/nf-core/graphtyper/vcfconcatenate/meta.yml", + "type": "module", + "meta": { + "name": "graphtyper_vcfconcatenate", + "description": "Tools for population-scale genotyping using pangenome graphs.", + "keywords": ["combine", "concatenate", "variant", "vcf"], + "tools": [ + { + "graphtyper": { + "description": "A graph-based variant caller capable of genotyping population-scale short read data sets while incorporating previously discovered variants.", + "homepage": "https://github.com/DecodeGenetics/graphtyper", + "documentation": "https://github.com/DecodeGenetics/graphtyper/wiki/User-guide", + "tool_dev_url": "https://github.com/DecodeGenetics/graphtyper", + "doi": "10.1038/ng.3964", + "licence": ["MIT"], + "identifier": "biotools:Graphtyper" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF files", + "pattern": "*.{vcf,vcf.gz}", + "ontologies": [] + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "${prefix}.vcf.gz": { + "type": "file", + "description": "Concatenated VCF file", + "pattern": "*.{vcf.gz}", + "ontologies": [] + } + } + ] + ], + "tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "${prefix}.vcf.gz.tbi": { + "type": "file", + "description": "Concatenated VCF file index", + "pattern": "*.{tbi}", + "ontologies": [] + } + } + ] + ], + "versions_graphtyper": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "graphtyper": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "graphtyper --help | tail -1 | sed 's/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "graphtyper": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "graphtyper --help | tail -1 | sed 's/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@zachary-foster"], + "maintainers": ["@zachary-foster"] }, - { - "fasta": { - "type": "file", - "description": "FASTA file", - "pattern": "*.{fa,fasta}", - "ontologies": [] - } - } - ], - { - "db": { - "type": "file", - "description": "Database in FASTA format", - "pattern": "*.{fa,fasta}", - "ontologies": [] - } - } - ], - "output": { - "gamma": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.gamma": { - "type": "file", - "description": "GAMMA file with annotated gene matches", - "pattern": "*.{gamma}", - "ontologies": [] - } - } - ] - ], - "psl": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.psl": { - "type": "file", - "description": "PSL file with all gene matches found", - "pattern": "*.{psl}", - "ontologies": [] - } - } - ] - ], - "gff": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.gff": { - "type": "file", - "description": "GFF file", - "pattern": "*.{gff}", - "ontologies": [] - } - } - ] - ], - "fasta": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.fasta": { - "type": "file", - "description": "multifasta file of the gene matches", - "pattern": "*.{fasta}", - "ontologies": [] - } - } - ] - ], - "versions_gamma": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gamma": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "2.1": { - "type": "string", - "description": "The hard-coded version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gamma": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "2.1": { - "type": "string", - "description": "The hard-coded version of the tool" - } - } + "pipelines": [ + { + "name": "pathogensurveillance", + "version": "1.1.0" + } ] - ] - }, - "authors": [ - "@sateeshperi", - "@rastanton", - "@jvhagey" - ], - "maintainers": [ - "@sateeshperi", - "@rastanton", - "@jvhagey" - ] - } - }, - { - "name": "gangstr", - "path": "modules/nf-core/gangstr/meta.yml", - "type": "module", - "meta": { - "name": "gangstr", - "description": "GangSTR is a tool for genome-wide profiling tandem repeats from short reads.", - "keywords": [ - "gangstr", - "STR", - "bam", - "cram", - "vcf" - ], - "tools": [ - { - "gangstr": { - "description": "GangSTR is a tool for genome-wide profiling tandem repeats from short reads.", - "homepage": "https://github.com/gymreklab/GangSTR", - "documentation": "https://github.com/gymreklab/GangSTR", - "tool_dev_url": "https://github.com/gymreklab/GangSTR", - "doi": "10.1093/nar/gkz501", - "licence": [ - "GPL v3-or-later" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "alignment_files": { - "type": "file", - "description": "Alignment files", - "ontologies": [] - } - }, - { - "alignment_indices": { - "type": "file", - "description": "The index/indices of the BAM/CRAM file(s)", - "pattern": "*.{bai,crai}", - "ontologies": [] - } - }, - { - "ref_regions": { - "type": "file", - "description": "A reference set of regions to genotype in a BED-like format. The file should have following columns:\n1. The name of the chromosome on which the STR is located\n2. The start position of the STR on its chromosome\n3. The end position of the STR on its chromosome\n4. The motif length\n5. The repeat motif\n", - "pattern": "*.bed", - "ontologies": [] - } - } - ], - { - "fasta": { - "type": "file", - "description": "The reference FASTA file", - "pattern": "*.{fasta,fa}", - "ontologies": [] - } - }, - { - "fasta_fai": { - "type": "file", - "description": "The index of the reference FASTA file", - "pattern": "*.fai", - "ontologies": [] + }, + { + "name": "gridss_annotate", + "path": "modules/nf-core/gridss/annotate/meta.yml", + "type": "module", + "meta": { + "name": "gridss_annotate", + "description": "Annotates single breakends in a GRIDSS VCF with RepeatMasker annotations using gridss_annotate_vcf_repeatmasker.", + "keywords": ["gridss", "structural variants", "annotation", "repeatmasker", "vcf"], + "tools": [ + { + "gridss": { + "description": "GRIDSS: the Genomic Rearrangement IDentification Software Suite", + "documentation": "https://github.com/PapenfussLab/gridss/wiki/GRIDSS-Documentation", + "tool_dev_url": "https://github.com/PapenfussLab/gridss", + "doi": "10.1186/s13059-021-02423-x", + "licence": ["GPL v3"], + "identifier": "biotools:gridss" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "vcf": { + "type": "file", + "description": "Input VCF file generated with GRIDSS", + "pattern": "*.{vcf,vcf.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + } + ] + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "Annotated VCF file compressed with bgzip", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "versions_gridss": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process" + } + }, + { + "gridss": { + "type": "string", + "description": "The tool name" + } + }, + { + "GeneratePonBedpe --version 2>&1 | sed 's/-gridss//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process" + } + }, + { + "gridss": { + "type": "string", + "description": "The tool name" + } + }, + { + "GeneratePonBedpe --version 2>&1 | sed 's/-gridss//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@emmcauley"], + "maintainers": ["@emmcauley"] } - } - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.vcf.gz": { - "type": "file", - "description": "The resulting VCF file containing the genotypes", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "index": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.vcf.gz.tbi": { - "type": "file", - "description": "The resulting index of the VCF file containing the genotypes", - "pattern": "*.vcf.gz.tbi", - "ontologies": [] - } - } - ] - ], - "samplestats": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.samplestats.tab": { - "type": "file", - "description": "A tab-delimited file containing statistics for each sample", - "pattern": "*.tab", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_gangstr": [ - [ - { - "${task.process}": { - "type": "string", - "description": "Task process name" - } - }, - { - "gangstr": { - "type": "string", - "description": "Software name" - } - }, - { - "GangSTR --version 2>&1": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "Task process name" - } - }, - { - "gangstr": { - "type": "string", - "description": "Software name" - } - }, - { - "GangSTR --version 2>&1": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@nvnieuwk" - ], - "maintainers": [ - "@nvnieuwk" - ] - } - }, - { - "name": "ganon_buildcustom", - "path": "modules/nf-core/ganon/buildcustom/meta.yml", - "type": "module", - "meta": { - "name": "ganon_buildcustom", - "description": "Build ganon database using custom reference sequences.", - "keywords": [ - "ganon", - "metagenomics", - "profiling", - "taxonomy", - "k-mer", - "database" - ], - "tools": [ - { - "ganon": { - "description": "ganon classifies short DNA sequences against large sets of genomic reference sequences efficiently", - "homepage": "https://github.com/pirovc/ganon", - "documentation": "https://github.com/pirovc/ganon", - "tool_dev_url": "https://github.com/pirovc/ganon", - "doi": "10.1093/bioinformatics/btaa458", - "licence": [ - "MIT" - ], - "identifier": "biotools:ganon" + }, + { + "name": "gridss_generateponbedpe", + "path": "modules/nf-core/gridss/generateponbedpe/meta.yml", + "type": "module", + "meta": { + "name": "gridss_generateponbedpe", + "description": "GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements.", + "keywords": ["gridss", "structural variants", "bedpe", "bed", "vcf"], + "tools": [ + { + "gridss": { + "description": "GRIDSS: the Genomic Rearrangement IDentification Software Suite", + "documentation": "https://github.com/PapenfussLab/gridss/wiki/GRIDSS-Documentation", + "tool_dev_url": "https://github.com/PapenfussLab/gridss", + "doi": "10.1186/s13059-021-02423-x", + "licence": ["GPL v3"], + "identifier": "biotools:gridss" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "vcf": { + "type": "file", + "description": "GRIDSS generated vcf file", + "pattern": "*.vcf", + "ontologies": [] + } + }, + { + "bedpe": { + "type": "file", + "description": "GRIDSS generated bedpe file", + "pattern": "*.bedpe", + "ontologies": [] + } + }, + { + "bed": { + "type": "file", + "description": "GRIDSS generated bed file", + "pattern": "*.bed", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test']\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The reference fasta", + "pattern": "*.{fa,fna,fasta}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference fai information\ne.g. [ id:'test']\n" + } + }, + { + "fai": { + "type": "file", + "description": "The index of the reference fasta", + "pattern": "*.fai", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing bwa generated index information\ne.g. [ id:'test']\n" + } + }, + { + "bwa_index": { + "type": "directory", + "description": "OPTIONAL - The BWA index created from the reference fasta, will be generated by Gridss in the setupreference step" + } + } + ] + ], + "output": { + "bedpe": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.bedpe": { + "type": "file", + "description": "GRIDSS generated breakpoint pon bedpe file", + "pattern": "*.bedpe", + "ontologies": [] + } + } + ] + ], + "bed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "GRIDSS generated breakpoint pon bed file", + "pattern": "*.bed", + "ontologies": [] + } + } + ] + ], + "versions_gridss": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process" + } + }, + { + "gridss": { + "type": "string", + "description": "The tool name" + } + }, + { + "GeneratePonBedpe --version 2>&1 | sed 's/-gridss//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process" + } + }, + { + "gridss": { + "type": "string", + "description": "The tool name" + } + }, + { + "GeneratePonBedpe --version 2>&1 | sed 's/-gridss//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@kubranarci"], + "maintainers": ["@famosab"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "List of input FASTA files, or a directory containing input FASTA files.\nNote you must supply --input-extension via ext.args if FASTA extensions do not end in the default `fna.gz`.\n", - "pattern": "*.{fasta,fna,fa,fa,fasta.gz,fna.gz,fa.gz,fa.gz}", - "ontologies": [] - } - } - ], - { - "input_tsv": { - "type": "string", - "description": "(Optional) Specify an TSV file containing the paths, and relevant metadata to the input FASTA files to use the `--input-file` option.\nThe 'file' column should be just the file name of each FASTA file (so that it's local to the working directory of the process).\nSee ganon documentation for more more information on the other columns.\n", - "pattern": "*tsv" - } - }, - { - "taxonomy_files": { - "type": "file", - "description": "Pre-downloaded taxonomy files of input sequences. See ganon docs for formats", - "ontologies": [] - } - }, - { - "genome_size_files": { - "type": "file", - "description": "Pre-downloaded NCBI or GTDB genome size files of input sequences. See ganon docs for formats", - "pattern": "{species_genome_size.txt.gz,*_metadata.tar.gz}", - "ontologies": [] - } - } - ], - "output": { - "db": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.{hibf,ibf,tax}": { - "type": "file", - "description": "ganon database files", - "pattern": "*.{ibf,tax}", - "ontologies": [] - } - } - ] - ], - "info": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.info.tsv": { - "type": "file", - "description": "Copy of target info generated. Can be used for updating database.", - "pattern": "*info.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_ganon": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "ganon": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "ganon --version 2>1 | sed 's/.*ganon //g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "ganon": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "ganon --version 2>1 | sed 's/.*ganon //g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@jfy133" - ], - "maintainers": [ - "@jfy133" - ] - }, - "pipelines": [ - { - "name": "createtaxdb", - "version": "3.0.0" - } - ] - }, - { - "name": "ganon_classify", - "path": "modules/nf-core/ganon/classify/meta.yml", - "type": "module", - "meta": { - "name": "ganon_classify", - "description": "Classify FASTQ files against ganon database", - "keywords": [ - "ganon", - "metagenomics", - "profiling", - "taxonomy", - "k-mer", - "classification", - "classify" - ], - "tools": [ - { - "ganon": { - "description": "ganon classifies short DNA sequences against large sets of genomic reference sequences efficiently", - "homepage": "https://github.com/pirovc/ganon", - "documentation": "https://github.com/pirovc/ganon", - "tool_dev_url": "https://github.com/pirovc/ganon", - "doi": "10.1093/bioinformatics/btaa458", - "licence": [ - "MIT" - ], - "identifier": "biotools:ganon" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fastqs": { - "type": "file", - "description": "Single or paired FASTQ files, optionally gzipped", - "pattern": "*.{fq,fq.gz,fastq,fastq.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ], - { - "db": { - "type": "file", - "description": "Ganon database files from build or build-custom", - "pattern": "*.{ibf,tax}", - "ontologies": [] - } - } - ], - "output": { - "tre": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tre": { - "type": "file", - "description": "Full ganon report file", - "pattern": "*.tre", - "ontologies": [] - } - } - ] - ], - "report": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.rep": { - "type": "file", - "description": "Plain ganon report file with only targets with match", - "pattern": "*.rep", - "ontologies": [] - } - } - ] - ], - "one": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.one": { - "type": "file", - "description": "Information about a single (best) match of a given read after EM or LCA algorithms", - "pattern": "*.one", - "ontologies": [] - } - } - ] - ], - "all": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.all": { - "type": "file", - "description": "Information of all matches to a given read", - "pattern": "*.all", - "ontologies": [] - } - } - ] - ], - "unc": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.unc": { - "type": "file", - "description": "List of all reads without a hit", - "pattern": "*.unc", - "ontologies": [] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.log": { - "type": "file", - "description": "Text file containing console output from ganon classify", - "pattern": "*.log", - "ontologies": [] - } - } - ] - ], - "versions_ganon": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "ganon": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "ganon --version 2>1 | sed 's/.*ganon //g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "ganon": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "ganon --version 2>1 | sed 's/.*ganon //g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@jfy133" - ], - "maintainers": [ - "@jfy133" - ] - }, - "pipelines": [ - { - "name": "taxprofiler", - "version": "2.0.0" - } - ] - }, - { - "name": "ganon_report", - "path": "modules/nf-core/ganon/report/meta.yml", - "type": "module", - "meta": { - "name": "ganon_report", - "description": "Generate a ganon report file from the output of ganon classify", - "keywords": [ - "ganon", - "metagenomics", - "profiling", - "taxonomy", - "k-mer", - "classification", - "report" - ], - "tools": [ - { - "ganon": { - "description": "ganon classifies short DNA sequences against large sets of genomic reference sequences efficiently", - "homepage": "https://github.com/pirovc/ganon", - "documentation": "https://github.com/pirovc/ganon", - "tool_dev_url": "https://github.com/pirovc/ganon", - "doi": "10.1093/bioinformatics/btaa458", - "licence": [ - "MIT" - ], - "identifier": "biotools:ganon" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "rep": { - "type": "file", - "description": "Input 'repo' files from ganon classify", - "pattern": "*.rep", - "ontologies": [] - } - } - ], - { - "db": { - "type": "file", - "description": "Ganon database files from build or build-custom", - "pattern": "*.{ibf,tax}", - "ontologies": [] - } - } - ], - "output": { - "tre": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tre": { - "type": "file", - "description": "Output ganon report containing taxonomic profile information. Formatting of contents depends on --output-format.", - "pattern": "*.tre", - "ontologies": [] - } - } - ] - ], - "versions_ganon": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "ganon": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "ganon --version 2>1 | sed 's/.*ganon //g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "ganon": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "ganon --version 2>1 | sed 's/.*ganon //g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@jfy133" - ], - "maintainers": [ - "@jfy133" - ] - }, - "pipelines": [ - { - "name": "taxprofiler", - "version": "2.0.0" - } - ] - }, - { - "name": "ganon_table", - "path": "modules/nf-core/ganon/table/meta.yml", - "type": "module", - "meta": { - "name": "ganon_table", - "description": "Generate a multi-sample report file from the output of ganon report runs", - "keywords": [ - "ganon", - "metagenomics", - "profiling", - "taxonomy", - "k-mer", - "classification", - "report", - "table" - ], - "tools": [ - { - "ganon": { - "description": "ganon classifies short DNA sequences against large sets of genomic reference sequences efficiently", - "homepage": "https://github.com/pirovc/ganon", - "documentation": "https://github.com/pirovc/ganon", - "tool_dev_url": "https://github.com/pirovc/ganon", - "doi": "10.1093/bioinformatics/btaa458", - "licence": [ - "MIT" - ], - "identifier": "biotools:ganon" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "tre": { - "type": "file", - "description": "A list of 'tre' files from ganon report", - "pattern": "*.tre", - "ontologies": [] - } - } - ] - ], - "output": { - "txt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.txt": { - "type": "file", - "description": "Output ganon table containing taxonomic profile information of multiple samples. Formatting of contents depends on --output-format.", - "pattern": "*.txt", - "ontologies": [] - } - } - ] - ], - "versions_ganon": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "ganon": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "ganon --version 2>1 | sed 's/.*ganon //g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "ganon": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "ganon --version 2>1 | sed 's/.*ganon //g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@jfy133" - ], - "maintainers": [ - "@jfy133" - ] - }, - "pipelines": [ - { - "name": "taxprofiler", - "version": "2.0.0" - } - ] - }, - { - "name": "gappa_examineassign", - "path": "modules/nf-core/gappa/examineassign/meta.yml", - "type": "module", - "meta": { - "name": "gappa_examineassign", - "description": "assigns taxonomy to query sequences in phylogenetic placement output", - "keywords": [ - "phylogeny", - "phylogenetic placement", - "classification", - "taxonomy" - ], - "tools": [ - { - "gappa": { - "description": "Genesis Applications for Phylogenetic Placement Analysis", - "homepage": "https://github.com/lczech/gappa", - "documentation": "https://github.com/lczech/gappa/wiki", - "tool_dev_url": "https://github.com/lczech/gappa", - "doi": "10.1093/bioinformatics/btaa070", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:GAPPA" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "jplace": { - "type": "file", - "description": "jplace file output from phylogenetic placement, e.g. EPA-NG, gzipped or not", - "pattern": "*.{jplace,jplace.gz}", - "ontologies": [] - } - }, - { - "taxonomy": { - "type": "file", - "description": "taxonomy file", - "ontologies": [] - } - } - ] - ], - "output": { - "profile": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*profile.tsv": { - "type": "file", - "description": "profile tsv file", - "pattern": "*profile.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "labelled_tree": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*labelled_tree.newick": { - "type": "file", - "description": "labelled tree in newick format", - "pattern": "*labelled_tree.newick", - "ontologies": [] - } - } - ] - ], - "per_query": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*per_query.tsv": { - "type": "file", - "description": "per query taxonomy assignments in tsv format", - "pattern": "*per_query.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "krona": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*krona.profile": { - "type": "file", - "description": "krona profile file", - "pattern": "*krona.profile", - "ontologies": [] - } - } - ] - ], - "sativa": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*sativa.tsv": { - "type": "file", - "description": "sativa output file", - "pattern": "*sativa.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_gappa": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gappa": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gappa --version 2>&1 | sed 's/v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gappa": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gappa --version 2>&1 | sed 's/v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@erikrikarddaniel" - ], - "maintainers": [ - "@erikrikarddaniel" - ] - }, - "pipelines": [ - { - "name": "ampliseq", - "version": "2.17.0" }, { - "name": "phyloplace", - "version": "2.0.0" - } - ] - }, - { - "name": "gappa_examinegraft", - "path": "modules/nf-core/gappa/examinegraft/meta.yml", - "type": "module", - "meta": { - "name": "gappa_examinegraft", - "description": "Grafts query sequences from phylogenetic placement on the reference tree", - 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["@pinin4fjords"], + "maintainers": ["@pinin4fjords", "@nschcolnicov"] }, - { - "jplace": { - "type": "file", - "description": "jplace file output from phylogenetic placement, e.g. EPA-NG, gzipped or not", - "pattern": "*.{jplace,jplace.gz}", - "ontologies": [] - } - } - ] - ], - "output": { - "newick": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.newick": { - "type": "file", - "description": "phylogenetic tree file in newick format", - "pattern": "*.newick", - "ontologies": [] - } - } - ] - ], - "nexus": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.nexus": { - "type": "file", - "description": "coloured phylogenetic tree file in nexus format", - "pattern": "*.nexus", - "ontologies": [] - } - } - ] - ], - "phyloxml": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample 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"log file from the run", - "pattern": "*.log", - "ontologies": [] - } - } - ] - ], - "versions_gappa": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gappa": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gappa --version 2>&1 | sed 's/v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gappa": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gappa --version 2>&1 | sed 's/v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "differentialabundance", + "version": "1.5.0" + } ] - ] - }, - "authors": [ - "@erikrikarddaniel" - ], - "maintainers": [ - "@erikrikarddaniel" - ] - }, - "pipelines": [ - { - "name": "ampliseq", - "version": "2.17.0" }, { - "name": "phyloplace", - "version": "2.0.0" - } - ] - }, - { - "name": "gatk4_addorreplacereadgroups", - "path": "modules/nf-core/gatk4/addorreplacereadgroups/meta.yml", - "type": "module", - "meta": { - "name": "gatk4_addorreplacereadgroups", - "description": "Assigns all the reads in a file to a single new read-group", - "keywords": [ - "add", - "replace", - "read-group", - "picard", - "gatk" - ], - "tools": [ - { - "gatk4": { - "description": "Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools\nwith a primary focus on variant discovery and genotyping. Its powerful processing engine\nand high-performance computing features make it capable of taking on projects of any size.\n", - "homepage": "https://gatk.broadinstitute.org/hc/en-us", - "documentation": "https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s", - "doi": "10.1158/1538-7445.AM2017-3590", - "licence": [ - "Apache-2.0" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "Input BAM file", - "pattern": "*.{bam}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome file", - "pattern": "*.{fasta,fa,fasta.gz,fa.gz}", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta_index": { - "type": "file", - "description": "Reference genome index file", - "pattern": "*.{fai,fasta.fai,fa.fai,fasta.gz.fai,fa.gz.fai}", - "ontologies": [] - } - } - ] - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "Output BAM file", - "pattern": "*.{bam}", - "ontologies": [] - } - } - ] - ], - "bai": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bai": { - "type": "file", - "description": "An optional BAM index file", - "pattern": "*.{bai}", - "ontologies": [] - } - } - ] - ], - "cram": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.cram": { - "type": "file", - "description": "Output CRAM file", - "pattern": "*.{cram}", - "ontologies": [] - } - } - ] - ], - "versions_gatk4": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gatk4": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gatk4": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@sateeshperi", - "@mjcipriano", - "@hseabolt", - "@cmatKhan", - "@muffato" - ], - "maintainers": [ - "@sateeshperi", - "@mjcipriano", - "@hseabolt", - "@cmatKhan", - "@muffato" - ] - }, - "pipelines": [ - { - "name": "genomicrelatedness", - "version": "dev" - } - ] - }, - { - "name": "gatk4_analyzecovariates", - "path": "modules/nf-core/gatk4/analyzecovariates/meta.yml", - "type": "module", - "meta": { - "name": "gatk4_analyzecovariates", - "description": "Evaluate and compare base quality score recalibration (BQSR) tables", - "keywords": [ - "bqsr", - "gatk4", - "genomics" - ], - "tools": [ - { - "gatk4": { - "description": "Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools\nwith a primary focus on variant discovery and genotyping. Its powerful processing engine\nand high-performance computing features make it capable of taking on projects of any size.\n", - "homepage": "https://gatk.broadinstitute.org/hc/en-us", - "documentation": "https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s", - "doi": "10.1158/1538-7445.AM2017-3590", - "licence": [ - "Apache-2.0" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "before_table": { - "type": "file", - "description": "Base quality score recalibration (BQSR) table before recalibration", - "pattern": "*.table", - "ontologies": [] - } - }, - { - "after_table": { - "type": "file", - "description": "Base quality score recalibration (BQSR) table after recalibration", - "pattern": "*.table", - "ontologies": [] - } - }, - { - "additional_table": { - "type": "file", - "description": "An additional base quality score recalibration (BQSR) table to be included in the comparison (optional)", - "pattern": "*.table", - "ontologies": [] - } - } - ] - ], - "output": { - "plots": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "*.pdf": { - "type": "file", - "description": "PDF file containing the plots generated by AnalyzeCovariates", - "pattern": "*.pdf", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3508" - } - ] - } - } - ] - ], - "data": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "*.csv": { - "type": "file", - "description": "CSV file containing the data generated by AnalyzeCovariates", - "pattern": "*.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "versions_gatk4": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gatk4": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gatk4": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@thomasisensee" - ], - "maintainers": [ - "@thomasisensee" - ] - }, - "pipelines": [ - { - "name": "genomicrelatedness", - "version": "dev" - } - ] - }, - { - "name": "gatk4_annotateintervals", - "path": "modules/nf-core/gatk4/annotateintervals/meta.yml", - "type": "module", - "meta": { - "name": "gatk4_annotateintervals", - "description": "Annotates intervals with GC content, mappability, and segmental-duplication content", - "keywords": [ - "annotateintervals", - "annotation", - "bed", - "gatk4", - "intervals" - ], - "tools": [ - { - "gatk4": { - "description": "Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools\nwith a primary focus on variant discovery and genotyping. Its powerful processing engine\nand high-performance computing features make it capable of taking on projects of any size.\n", - "homepage": "https://gatk.broadinstitute.org/hc/en-us", - "documentation": "https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s", - "doi": "10.1158/1538-7445.AM2017-3590", - "licence": [ - "Apache-2.0" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "intervals": { - "type": "file", - "description": "One or more interval files to annotate", - "pattern": "*.{interval_list,list,bed}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference FASTA file", - "pattern": "*.{fasta,fa}", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "fasta_fai": { - "type": "file", - "description": "The index of the reference FASTA file", - "pattern": "*.fai", - "ontologies": [] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "dict": { - "type": "file", - "description": "The sequence dictionary reference FASTA file", - "pattern": "*.dict", - "ontologies": [] - } - } - ], - [ - { - "meta5": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "mappable_regions": { - "type": "file", - "description": "Optional - Umap single-read mappability track\nThe track should correspond to the appropriate read length and overlapping intervals must be merged\n", - "pattern": "*.bed(.gz)?", - "ontologies": [] - } - } - ], - [ - { - "meta6": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "mappable_regions_tbi": { - "type": "file", - "description": "Optional - The index of the gzipped umap single-read mappability track", - "pattern": "*.bed.gz.tbi", - "ontologies": [] - } - } - ], - [ - { - "meta7": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "segmental_duplication_regions": { - "type": "file", - "description": "Optional - Segmental-duplication track", - "pattern": "*.bed(.gz)?", - "ontologies": [] - } - } - ], - [ - { - "meta8": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "segmental_duplication_regions_tbi": { - "type": "file", - "description": "Optional - The index of the gzipped segmental-duplication track", - "pattern": "*.bed.gz.tbi", - "ontologies": [] - } - } - ] - ], - "output": { - "annotated_intervals": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "The output TSV file with a SAM-style header containing the annotated intervals", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_gatk4": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gatk4": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gatk4": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@nvnieuwk" - ], - "maintainers": [ - "@nvnieuwk" - ] - }, - "pipelines": [ - { - "name": "createpanelrefs", - "version": "dev" - } - ] - }, - { - "name": "gatk4_applybqsr", - "path": "modules/nf-core/gatk4/applybqsr/meta.yml", - "type": "module", - "meta": { - "name": "gatk4_applybqsr", - "description": "Apply base quality score recalibration (BQSR) to a bam file", - "keywords": [ - "bam", - "base quality score recalibration", - "bqsr", - "cram", - "gatk4" - ], - "tools": [ - { - "gatk4": { - "description": "Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools\nwith a primary focus on variant discovery and genotyping. Its powerful processing engine\nand high-performance computing features make it capable of taking on projects of any size.\n", - "homepage": "https://gatk.broadinstitute.org/hc/en-us", - "documentation": "https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s", - "doi": "10.1158/1538-7445.AM2017-3590", - "licence": [ - "Apache-2.0" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM file from alignment", - "pattern": "*.{bam,cram}", - "ontologies": [] - } - }, - { - "input_index": { - "type": "file", - "description": "BAI/CRAI file from alignment", - "pattern": "*.{bai,crai}", - "ontologies": [] - } - }, - { - "bqsr_table": { - "type": "file", - "description": "Recalibration table from gatk4_baserecalibrator", - "ontologies": [] - } + "name": "gstama_collapse", + "path": "modules/nf-core/gstama/collapse/meta.yml", + "type": "module", + "meta": { + "name": "gstama_collapse", + "description": "Collapse redundant transcript models in Iso-Seq data.", + "keywords": [ + "tama_collapse.py", + "isoseq", + "nanopore", + "long-read", + "transcriptome", + "gene model", + "TAMA" + ], + "tools": [ + { + "tama_collapse.py": { + "description": "Collapse similar gene model", + "homepage": "https://github.com/sguizard/gs-tama", + "documentation": "https://github.com/GenomeRIK/tama/wiki", + "tool_dev_url": "https://github.com/sguizard/gs-tama", + "doi": "10.1186/s12864-020-07123-7", + "licence": ["GNU GPL3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "A sorted BAM or sam file of aligned reads", + "pattern": "*.{bam,sam}", + "ontologies": [] + } + } + ], + { + "fasta": { + "type": "file", + "description": "A fasta file of the genome used for the mapping", + "pattern": "*.{fasta,fa}", + "ontologies": [] + } + } + ], + "output": { + "bed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*_collapsed.bed": { + "type": "file", + "description": "a bed12 format file containing the final collapsed version of your transcriptome", + "pattern": "*.bed", + "ontologies": [] + } + } + ] + ], + "bed_trans_reads": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*_trans_read.bed": { + "type": "file", + "description": "This file uses bed12 format to show the transcript model for each read based on the mapping prior to collapsing. This only contains the reads which were accepted according to the defined thresholds. You can use this file to see if there were any strange occurrences during collapsing. It also contains the relationships between reads and collapsed transcript models. The 1st subfield in the 4th column shows the final transcript ID and the 2nd subfield in the 4th column shows the read ID. If you used no_cap mode for collapsing there may be multiple lines for a single read. This happens when a 5' degraded read can match to multiple 5' longer transcript models.", + "pattern": "*_trans_read.bed", + "ontologies": [] + } + } + ] + ], + "local_density_error": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*_local_density_error.txt": { + "type": "file", + "description": "This file contains the log of filtering for local density error around the splice junctions (\"-lde\")", + "pattern": "*_local_density_error.txt", + "ontologies": [] + } + } + ] + ], + "polya": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*_polya.txt": { + "type": "file", + "description": "This file contains the reads with potential poly A truncation.", + "pattern": "*_polya.txt", + "ontologies": [] + } + } + ] + ], + "read": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*_read.txt": { + "type": "file", + "description": "This file contains information for all mapped reads from the input SAM/BAM file. It shows both accepted and discarded reads and should match the number of mapped reads in your SAM/BAM file", + "pattern": "*_read.txt", + "ontologies": [] + } + } + ] + ], + "strand_check": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*_strand_check.txt": { + "type": "file", + "description": "This file shows instances where the sam flag strand information contrasted the GMAP strand information.", + "pattern": "*_strand_check.txt", + "ontologies": [] + } + } + ] + ], + "trans_report": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*_trans_report.txt": { + "type": "file", + "description": "This file contains collapsing information for each transcript.", + "pattern": "*_trans_report.txt", + "ontologies": [] + } + } + ] + ], + "varcov": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*_varcov.txt": { + "type": "file", + "description": "This file contains the coverage information for each variant detected.", + "pattern": "*_varcov.txt", + "ontologies": [] + } + } + ] + ], + "variants": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*_variants.txt": { + "type": "file", + "description": "This file contains the variants called. Variants are only called if 5 or more reads show the variant at a specific locus. If you would like to change the threshold, please make an issue about this in the Github repo.", + "pattern": "*_variants.txt", + "ontologies": [] + } + } + ] + ], + "versions_gstama": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gstama": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "tama_collapse.py -version | sed -n 's/tc_version_date_//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gstama": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "tama_collapse.py -version | sed -n 's/tc_version_date_//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@sguizard"], + "maintainers": ["@sguizard"] }, - { - "intervals": { - "type": "file", - "description": "Bed file with the genomic regions included in the library (optional)", - "ontologies": [] - } - } - ], - { - "fasta": { - "type": "file", - "description": "The reference fasta file", - "pattern": "*.fasta", - "ontologies": [] - } - }, - { - "fai": { - "type": "file", - "description": "Index of reference fasta file", - "pattern": "*.fasta.fai", - "ontologies": [] - } - }, - { - "dict": { - "type": "file", - "description": "GATK sequence dictionary", - "pattern": "*.dict", - "ontologies": [] - } - } - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.bam": { - "type": "file", - "description": "Recalibrated BAM file", - "pattern": "${prefix}.bam", - "ontologies": [] - } - } - ] - ], - "bai": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}*bai": { - "type": "file", - "description": "Recalibrated BAM index file", - "pattern": "${prefix}*bai", - "ontologies": [] - } - } - ] - ], - "cram": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.cram": { - "type": "file", - "description": "Recalibrated CRAM file", - "pattern": "${prefix}.cram", - "ontologies": [] - } - } - ] - ], - "versions_gatk4": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gatk4": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gatk4": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "isoseq", + "version": "2.0.0" + } ] - ] - }, - "authors": [ - "@yocra3", - "@FriederikeHanssen" - ], - "maintainers": [ - "@yocra3", - "@FriederikeHanssen" - ] - }, - "pipelines": [ - { - "name": "genomicrelatedness", - "version": "dev" - }, - { - "name": "rnadnavar", - "version": "dev" }, { - "name": "rnavar", - "version": "1.2.3" - }, - { - "name": "sarek", - "version": "3.8.1" + "name": "gstama_merge", + "path": "modules/nf-core/gstama/merge/meta.yml", + "type": "module", + "meta": { + "name": "gstama_merge", + "description": "Merge multiple transcriptomes while maintaining source information.", + "keywords": [ + "gstama", + "gstama/merge", + "long-read", + "isoseq", + "nanopore", + "tama", + "trancriptome", + "annotation" + ], + "tools": [ + { + "gstama": { + "description": "Gene-Switch Transcriptome Annotation by Modular Algorithms", + "homepage": "https://github.com/sguizard/gs-tama", + "documentation": "https://github.com/GenomeRIK/tama/wiki", + "tool_dev_url": "https://github.com/sguizard/gs-tama", + "doi": "10.1186/s12864-020-07123-7", + "licence": ["GPL v3 License"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bed": { + "type": "file", + "description": "bed12 file generated by TAMA collapse", + "pattern": "*.bed", + "ontologies": [] + } + } + ], + { + "filelist": { + "type": "file", + "description": "list of files", + "ontologies": [] + } + } + ], + "output": { + "bed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "This is the main merged annotation file. Transcripts are coloured according to the source support for each model. Sources are numbered based on the order supplied in the input filelist file. For example the first file named in the filelist file would have its transcripts coloured in red. If a transcript has multiple sources the colour is shown as magenta.", + "pattern": "*.bed", + "ontologies": [] + } + } + ] + ], + "gene_report": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*_gene_report.txt": { + "type": "file", + "description": "This contains a report of the genes from the merged file. \"num_clusters\" refers to the number of source transcripts that were used to make this gene model. \"num_final_trans\" refers to the number of transcripts in the final gene model.", + "pattern": "*_gene_report.txt", + "ontologies": [] + } + } + ] + ], + "merge": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*_merge.txt": { + "type": "file", + "description": "This contains a bed12 format file which shows the coordinates of each input transcript matched to the merged transcript ID. I used the \"txt\" extension even though it is a bed file just to avoid confusion with the main bed file. You can use this file to map the final merged transcript models to their pre-merged supporting transcripts. The 1st subfield in the 4th column shows the final merged transcript ID while the 2nd subfield shows the pre-merged transcript ID with source prefix.", + "pattern": "*_merge.txt", + "ontologies": [] + } + } + ] + ], + "trans_report": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*_trans_report.txt": { + "type": "file", + "description": "This contains the source information for each merged transcript.", + "pattern": "*_trans_report.txt", + "ontologies": [] + } + } + ] + ], + "versions_gstama": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gstama": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "tama_merge.py -version | sed '1!d'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gstama": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "tama_merge.py -version | sed '1!d'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@sguizard"], + "maintainers": ["@sguizard"] + }, + "pipelines": [ + { + "name": "isoseq", + "version": "2.0.0" + } + ] }, { - "name": "tbanalyzer", - "version": "dev" - } - ] - }, - { - "name": "gatk4_applyvqsr", - "path": "modules/nf-core/gatk4/applyvqsr/meta.yml", - "type": "module", - "meta": { - "name": "gatk4_applyvqsr", - "description": "Apply a score cutoff to filter variants based on a recalibration table.\nAplyVQSR performs the second pass in a two-stage process called Variant Quality Score Recalibration (VQSR).\nSpecifically, it applies filtering to the input variants based on the recalibration table produced\nin the first step by VariantRecalibrator and a target sensitivity value.\n", - "keywords": [ - "gatk4", - "variant quality score recalibration", - "vcf", - "vqsr" - ], - "tools": [ - { - "gatk4": { - "description": "Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools\nwith a primary focus on variant discovery and genotyping. Its powerful processing engine\nand high-performance computing features make it capable of taking on projects of any size.\n", - "homepage": "https://gatk.broadinstitute.org/hc/en-us", - "documentation": "https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s", - "doi": "10.1158/1538-7445.AM2017-3590", - "licence": [ - "Apache-2.0" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF file to be recalibrated, this should be the same file as used for the first stage VariantRecalibrator.", - "pattern": "*.vcf", - "ontologies": [] - } - }, - { - "vcf_tbi": { - "type": "file", - "description": "tabix index for the input vcf file.", - "pattern": "*.vcf.tbi", - "ontologies": [] - } - }, - { - "recal": { - "type": "file", - "description": "Recalibration file produced when the input vcf was run through VariantRecalibrator in stage 1.", - "pattern": "*.recal", - "ontologies": [] - } - }, - { - "recal_index": { - "type": "file", - "description": "Index file for the recalibration file.", - "pattern": ".recal.idx", - "ontologies": [] - } + "name": "gstama_polyacleanup", + "path": "modules/nf-core/gstama/polyacleanup/meta.yml", + "type": "module", + "meta": { + "name": "gstama_polyacleanup", + "description": "Helper script, remove remaining polyA sequences from Full Length Non Chimeric reads (Pacbio isoseq3)", + "keywords": [ + "gstama", + "gstama/polyacleanup", + "long-read", + "isoseq", + "tama", + "trancriptome", + "annotation" + ], + "tools": [ + { + "gstama": { + "description": "Gene-Switch Transcriptome Annotation by Modular Algorithms", + "homepage": "https://github.com/sguizard/gs-tama", + "documentation": "https://github.com/GenomeRIK/tama/wiki", + "tool_dev_url": "https://github.com/sguizard/gs-tama", + "doi": "10.1186/s12864-020-07123-7", + "licence": ["GPL v3 License"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Full Length Non Chimeric reads in fasta format", + "pattern": "*.{fa,fasta}", + "ontologies": [] + } + } + ] + ], + "output": { + "fasta": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fa.gz": { + "type": "file", + "description": "The Full Length Non Chimeric reads cleaned from remaining polyA tails. The sequences are in FASTA format compressed with gzip.", + "pattern": "*.fa.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "report": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_polya_flnc_report.txt.gz": { + "type": "file", + "description": "A text file describing the number of polyA tails removed and their length. Compressed with gzip.", + "pattern": "*_polya_flnc_report.txt.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "tails": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_tails.fa.gz": { + "type": "file", + "description": "A gzip compressed FASTA file of trimmed polyA tails.", + "pattern": "*_tails.fa.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "versions_gstama": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gstama": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "tama_collapse.py -version | sed -n 's/tc_version_date_//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gstama": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "tama_collapse.py -version | sed -n 's/tc_version_date_//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@sguizard"], + "maintainers": ["@sguizard"] }, - { - "tranches": { - "type": "file", - "description": "Tranches file produced when the input vcf was run through VariantRecalibrator in stage 1.", - "pattern": ".tranches", - "ontologies": [] - } - } - ], - { - "fasta": { - "type": "file", - "description": "The reference fasta file", - "pattern": "*.fasta", - "ontologies": [] - } - }, - { - "fai": { - "type": "file", - "description": "Index of reference fasta file", - "pattern": "*.fasta.fai", - "ontologies": [] - } - }, - { - "dict": { - "type": "file", - "description": "GATK sequence dictionary", - "pattern": "*.dict", - "ontologies": [] - } - } - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "file", - "description": "compressed vcf file containing the recalibrated variants.", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - }, - { - "*.vcf.gz": { - "type": "file", - "description": "compressed vcf file containing the recalibrated variants.", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "tbi": [ - [ - { - "meta": { - "type": "file", - "description": "compressed vcf file containing the recalibrated variants.", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - }, - { - "*.tbi": { - "type": "file", - "description": "Index of recalibrated vcf file.", - "pattern": "*vcf.gz.tbi", - "ontologies": [] - } - } - ] - ], - "versions_gatk4": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gatk4": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gatk4": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "isoseq", + "version": "2.0.0" + } ] - ] }, - "authors": [ - "@GCJMackenzie" - ], - "maintainers": [ - "@GCJMackenzie" - ] - }, - "pipelines": [ { - "name": "sarek", - "version": "3.8.1" + "name": "gt_gff3", + "path": "modules/nf-core/gt/gff3/meta.yml", + "type": "module", + "meta": { + "name": "gt_gff3", + "description": "GenomeTools gt-gff3 utility to parse, possibly transform, and output GFF3 files", + "keywords": ["genome", "gff3", "annotation"], + "tools": [ + { + "gt": { + "description": "The GenomeTools genome analysis system", + "homepage": "https://genometools.org/index.html", + "documentation": "https://genometools.org/documentation.html", + "tool_dev_url": "https://github.com/genometools/genometools", + "doi": "10.1109/TCBB.2013.68", + "licence": ["ISC"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "gff3": { + "type": "file", + "description": "Input gff3 file", + "pattern": "*.{gff,gff3}", + "ontologies": [] + } + } + ] + ], + "output": { + "gt_gff3": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "*.gt.gff3": { + "type": "file", + "description": "Parsed gff3 file produced only if there is no parsing error", + "pattern": "*.gt.gff3", + "ontologies": [] + } + } + ] + ], + "error_log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "*.error.log": { + "type": "file", + "description": "Error log if gt-gff3 failed to parse the input gff3 file", + "pattern": "*.error.log", + "ontologies": [] + } + } + ] + ], + "versions_gt": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "genometools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gt --version | sed '1!d;s/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "genometools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gt --version | sed '1!d;s/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@gallvp"], + "maintainers": ["@gallvp"] + } }, { - "name": "tbanalyzer", - "version": "dev" - } - ] - }, - { - "name": "gatk4_asereadcounter", - "path": "modules/nf-core/gatk4/asereadcounter/meta.yml", - "type": "module", - "meta": { - "name": "gatk4_asereadcounter", - "description": "Calculates the allele-specific read counts for allele-specific expression analysis of RNAseq data", - "keywords": [ - "allele-specific", - "asereadcounter", - "gatk4", - "vcf" - ], - "tools": [ - { - "gatk4": { - "description": "Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools\nwith a primary focus on variant discovery and genotyping. 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"name": "rnadnavar", - "version": "dev" + "name": "gt_stat", + "path": "modules/nf-core/gt/stat/meta.yml", + "type": "module", + "meta": { + "name": "gt_stat", + "description": "GenomeTools gt-stat utility to show statistics about features contained in GFF3 files", + "keywords": ["genome", "gff3", "annotation", "statistics", "stats"], + "tools": [ + { + "gt": { + "description": "The GenomeTools genome analysis system", + "homepage": "https://genometools.org/index.html", + "documentation": "https://genometools.org/documentation.html", + "tool_dev_url": "https://github.com/genometools/genometools", + "doi": "10.1109/TCBB.2013.68", + "licence": ["ISC"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "gff3": { + "type": "file", + "description": "Input gff3 file", + "pattern": "*.{gff,gff3}", + "ontologies": [] + } + } + ] + ], + "output": { + "stats": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "${prefix}.yml": { + "type": "file", + "description": "Stats file in yaml format", + "pattern": "*.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + ], + "versions_gt": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "genometools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gt --version | sed '1!d;s/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "genometools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gt --version | sed '1!d;s/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@GallVp"], + "maintainers": ["@GallVp"] + } }, { - 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taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB.", + "keywords": [ + "GTDB taxonomy", + "taxonomic classification", + "metagenomics", + "classification", + "genome taxonomy database", + "bacteria", + "archaea" + ], + "tools": [ + { + "gtdbtk": { + "description": "GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB.", + "homepage": "https://ecogenomics.github.io/GTDBTk/", + "documentation": "https://ecogenomics.github.io/GTDBTk/", + "tool_dev_url": "https://github.com/Ecogenomics/GTDBTk", + "doi": "10.1093/bioinformatics/btz848", + "licence": ["GNU General Public v3 (GPL v3)"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false, assembler:'spades' ]\n" + } + }, + { + "bins/*": { + "type": "file", + "description": "A list of one or more bins in FASTA format for classification", + "pattern": "*.{fasta,fna,fas,fa}{,.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + [ + { + "db_name": { + "type": "string", + "description": "The name of the GTDB database to use." + } + }, + { + "db": { + "type": "file", + "description": "Path to a directory containing a GDTB database, as uncompressed from from the 'full package' gtdbdtk_data.tar.gz file.\nYou can give the 'release' directory here.\nMust contain the 'metadata' subdirectory\n", + "pattern": "release[0-9]+/", + "ontologies": [] + } + } + ], + { + "use_pplacer_scratch_dir": { + "type": "boolean", + "description": "Set to true to reduce pplacer memory usage by writing to disk (slower)" + } + } + ], + "output": { + "gtdb_outdir": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false, assembler:'spades' ]\n", + "pattern": "*" + } + }, + { + "${prefix}": { + "type": "directory", + "description": "All files output by GTDB-Tk", + "pattern": "*" + } + } + ] + ], + "summary": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false, assembler:'spades' ]\n", + "pattern": "*" + } + }, + { + "${prefix}/classify/*.summary.tsv": { + "type": "file", + "description": "A TSV summary file for the classification", + "pattern": "*.{summary.tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "tree": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false, assembler:'spades' ]\n", + "pattern": "*" + } + }, + { + "${prefix}/classify/*.classify.tree": { + "type": "file", + "description": "Groovy Map NJ or UPGMA trees in Newick format produced from a multiple sequence\nalignment\n", + "pattern": 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\\$GTDBTK_DATA_PATH/metadata/metadata.txt | sed \"s/VERSION_DATA=//\"": { + "type": "eval", + "description": "The expression to obtain the version of the database" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gtdbtk": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gtdbtk --version 2>&1 | grep -Eo '[0-9]+(\\.[0-9]+)+' | head -1": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gtdb_db": { + "type": "string", + "description": "The name of the database" + } + }, + { + "grep VERSION_DATA \\$GTDBTK_DATA_PATH/metadata/metadata.txt | sed \"s/VERSION_DATA=//\"": { + "type": "eval", + "description": "The expression to obtain the version of the database" + } + } + ] + ] + }, + "authors": 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} - }, - { - "gatk4": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gatk4": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@FriederikeHanssen", - "@maxulysse" - ], - "maintainers": [ - "@FriederikeHanssen", - "@maxulysse" - ] - }, - "pipelines": [ - { - "name": "sarek", - "version": "3.8.1" - } - ] - }, - { - "name": "gatk4_fastqtosam", - "path": "modules/nf-core/gatk4/fastqtosam/meta.yml", - "type": "module", - "meta": { - "name": "gatk4_fastqtosam", - "description": "Converts FastQ file to SAM/BAM format", - 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Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.", - "homepage": "https://gatk.broadinstitute.org/hc/en-us", - "documentation": "https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s", - "doi": "10.1158/1538-7445.AM2017-3590", - "licence": [ - "Apache-2.0" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "intervals": { - "type": "file", - "description": "Processed interval list file (processed_intervals.interval_list)", - "pattern": "*.interval_list", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "read_counts": { - "type": "file", - "description": "Read counts input file", - "pattern": "*.{tsv, hdf5}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "annotated_intervals": { - "type": "file", - "description": "Annotated intervals TSV file (annotated_intervals.tsv).", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "output": { - "interval_list": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.interval_list": { - "type": "file", - "description": "Filtered interval list file", - "pattern": "*.interval_list", - "ontologies": [] - } - } - ] - ], - "versions_gatk4": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gatk4": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gatk4": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@ryanjameskennedy", - "@ViktorHy" - ], - "maintainers": [ - "@ryanjameskennedy", - "@ViktorHy" - ] - }, - "pipelines": [ - { - "name": "createpanelrefs", - "version": "dev" - } - ] - }, - { - "name": "gatk4_filtermutectcalls", - "path": "modules/nf-core/gatk4/filtermutectcalls/meta.yml", - "type": "module", - "meta": { - "name": "gatk4_filtermutectcalls", - "description": "Filters the raw output of mutect2, can optionally use outputs of calculatecontamination and learnreadorientationmodel to improve filtering.\n", - "keywords": [ - "filtermutectcalls", - "filter", - "gatk4", - "mutect2", - "vcf" - ], - "tools": [ - { - "gatk4": { - "description": "Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools\nwith a primary focus on variant discovery and genotyping. Its powerful processing engine\nand high-performance computing features make it capable of taking on projects of any size.\n", - "homepage": "https://gatk.broadinstitute.org/hc/en-us", - "documentation": "https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s", - "doi": "10.1158/1538-7445.AM2017-3590", - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "compressed vcf file of mutect2calls", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - }, - { - "vcf_tbi": { - "type": "file", - "description": "Tabix index of vcf file", - "pattern": "*vcf.gz.tbi", - "ontologies": [] - } - }, - { - "stats": { - "type": "file", - "description": "Stats file that pairs with output vcf file", - "pattern": "*vcf.gz.stats", - "ontologies": [] - } - }, - { - "orientationbias": { - "type": "file", - "description": "files containing artifact priors for input vcf. Optional input.", - "pattern": "*.artifact-prior.tar.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - }, - { - "segmentation": { - "type": "file", - "description": "tables containing segmentation information for input vcf. Optional input.", - "pattern": "*.segmentation.table", - "ontologies": [] - } - }, - { - "table": { - "type": "file", - "description": "table(s) containing contamination data for input vcf. Optional input, takes priority over estimate.", - "pattern": "*.contamination.table", - "ontologies": [] - } - }, - { - "estimate": { - "type": "float", - "description": "estimation of contamination value as a double. 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"pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - }, - { - "*.vcf.gz": { - "type": "file", - "description": "file containing filtered mutect2 calls.", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "tbi": [ - [ - { - "meta": { - "type": "file", - "description": "file containing filtered mutect2 calls.", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - }, - { - "*.vcf.gz.tbi": { - "type": "file", - "description": "tbi file that pairs with vcf.", - "pattern": "*.vcf.gz.tbi", - "ontologies": [] - } - } - ] - ], - "stats": [ - [ - { - "meta": { - "type": "file", - "description": "file containing filtered mutect2 calls.", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" + "name": "hamronization_abricate", + "path": "modules/nf-core/hamronization/abricate/meta.yml", + "type": "module", + "meta": { + "name": "hamronization_abricate", + "description": "Tool to convert and summarize ABRicate outputs using the hAMRonization specification", + "keywords": ["amr", "antimicrobial resistance", "reporting", "abricate"], + "tools": [ + { + "hamronization": { + "description": "Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification", + "homepage": "https://github.com/pha4ge/hAMRonization/", + "documentation": "https://github.com/pha4ge/hAMRonization/", + "tool_dev_url": "https://github.com/pha4ge/hAMRonization", + "licence": ["GNU Lesser General Public v3 (LGPL v3)"], + "identifier": "biotools:hamronization" + } } - ] - } - }, - { - "*.filteringStats.tsv": { - "type": "file", - "description": "file containing statistics of the filtermutectcalls run.", - "pattern": "*.filteringStats.tsv", - "ontologies": [ + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "report": { + "type": "file", + "description": "Output TSV or CSV file from ABRicate", + "pattern": "*.{csv,tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + }, + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + { + "format": { + "type": "string", + "description": "Type of report file to be produced", + "pattern": "tsv|json" + } + }, + { + "software_version": { + "type": "string", + "description": "Version of ABRicate used", + "pattern": "[0-9].[0-9].[0-9]" + } + }, { - "edam": "http://edamontology.org/format_3475" + "reference_db_version": { + "type": "string", + "description": "Database version of ABRicate used", + "pattern": "[0-9][0-9][0-9][0-9]-[A-Z][a-z][a-z]-[0-9][0-9]" + } } - ] + ], + "output": { + "json": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.json": { + "type": "file", + "description": "hAMRonised report in JSON format", + "pattern": "*.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "hAMRonised report in TSV format", + "pattern": "*.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "versions_hamronization": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "hamronization": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "hamronize --version 2>&1 | sed 's/hamronize //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "hamronization": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "hamronize --version 2>&1 | sed 's/hamronize //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@jasmezz"], + "maintainers": ["@jasmezz"] + }, + "pipelines": [ + { + "name": "funcscan", + "version": "3.0.0" } - } ] - ], - "versions_gatk4": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gatk4": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gatk4": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@GCJMackenzie", - "@maxulysse", - "@ramprasadn" - ], - "maintainers": [ - "@GCJMackenzie", - "@maxulysse", - "@ramprasadn" - ] - }, - "pipelines": [ - { - "name": "raredisease", - "version": "3.0.0" }, { - "name": "rnadnavar", - "version": "dev" + "name": "hamronization_amrfinderplus", + "path": "modules/nf-core/hamronization/amrfinderplus/meta.yml", + "type": "module", + "meta": { + "name": "hamronization_amrfinderplus", + "description": "Tool to convert and summarize AMRfinderPlus outputs using the hAMRonization specification.", + "keywords": [ + "amr", + "antimicrobial resistance", + "arg", + "antimicrobial resistance genes", + "reporting", + "amrfinderplus" + ], + "tools": [ + { + "hamronization": { + "description": "Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification", + "homepage": "https://github.com/pha4ge/hAMRonization/", + "documentation": "https://github.com/pha4ge/hAMRonization/", + "tool_dev_url": "https://github.com/pha4ge/hAMRonization", + "licence": ["GNU Lesser General Public v3 (LGPL v3)"], + "identifier": "biotools:hamronization" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "report": { + "type": "file", + "description": "Output .tsv file from AMRfinderPlus", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + { + "format": { + "type": "string", + "description": "Type of report file to be produced", + "pattern": "tsv|json" + } + }, + { + "software_version": { + "type": "string", + "description": "Version of AMRfinder used", + "pattern": "[0-9].[0-9].[0-9]" + } + }, + { + "reference_db_version": { + "type": "string", + "description": "Database version of ncbi_AMRfinder used", + "pattern": "[0-9]-[0-9]-[0-9].[0-9]" + } + } + ], + "output": { + "json": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.json": { + "type": "file", + "description": "hAMRonised report in JSON format", + "pattern": "*.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "hAMRonised report in TSV format", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_hamronization": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "hamronization": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "hamronize --version 2>&1 | sed 's/hamronize //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "hamronization": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "hamronize --version 2>&1 | sed 's/hamronize //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@louperelo"], + "maintainers": ["@louperelo"] + }, + "pipelines": [ + { + "name": "funcscan", + "version": "3.0.0" + } + ] }, { - "name": "sarek", - "version": "3.8.1" + "name": "hamronization_deeparg", + "path": "modules/nf-core/hamronization/deeparg/meta.yml", + "type": "module", + "meta": { + "name": "hamronization_deeparg", + "description": "Tool to convert and summarize DeepARG outputs using the hAMRonization specification", + "keywords": ["amr", "antimicrobial resistance", "reporting", "deeparg"], + "tools": [ + { + "hamronization": { + "description": "Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification", + "homepage": "https://github.com/pha4ge/hAMRonization/", + "documentation": "https://github.com/pha4ge/hAMRonization/", + "tool_dev_url": "https://github.com/pha4ge/hAMRonization", + "licence": ["GNU Lesser General Public v3 (LGPL v3)"], + "identifier": "biotools:hamronization" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "report": { + "type": "file", + "description": "Output .mapping.ARG file from DeepARG", + "pattern": "*.mapping.ARG", + "ontologies": [] + } + } + ], + { + "format": { + "type": "string", + "description": "Type of report file to be produced", + "pattern": "tsv|json" + } + }, + { + "software_version": { + "type": "string", + "description": "Version of DeepARG used", + "pattern": "[0-9].[0-9].[0-9]" + } + }, + { + "reference_db_version": { + "type": "integer", + "description": "Database version of DeepARG used", + "pattern": "[0-9]" + } + } + ], + "output": { + "json": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.json": { + "type": "file", + "description": "hAMRonised report in JSON format", + "pattern": "*.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "hAMRonised report in TSV format", + "pattern": "*.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "versions_hamronization": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "hamronization": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "hamronize --version 2>&1 | sed 's/hamronize //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "hamronization": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "hamronize --version 2>&1 | sed 's/hamronize //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@jfy133"], + "maintainers": ["@jfy133"] + }, + "pipelines": [ + { + "name": "funcscan", + "version": "3.0.0" + } + ] }, { - 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Its powerful processing engine\nand high-performance computing features make it capable of taking on projects of any size.\n", - "homepage": "https://gatk.broadinstitute.org/hc/en-us", - "documentation": "https://gatk.broadinstitute.org/hc/en-us/articles/360051308071-FilterVariantTranches", - "doi": "10.1158/1538-7445.AM2017-3590", - "licence": [ - "Apache-2.0" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "a VCF file containing variants, must have info key:CNN_2D", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - }, - { - "tbi": { - "type": "file", - "description": "tbi file matching with -vcf", - "pattern": "*.vcf.gz.tbi", - "ontologies": [] - } + "name": "hamronization_fargene", + "path": "modules/nf-core/hamronization/fargene/meta.yml", + "type": "module", + "meta": { + "name": "hamronization_fargene", + "description": "Tool to convert and summarize fARGene outputs using the hAMRonization specification", + "keywords": [ + "amr", + "antimicrobial resistance", + "arg", + "antimicrobial resistance genes", + "reporting", + "fARGene" + ], + "tools": [ + { + "hamronization": { + "description": "Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification", + "homepage": "https://github.com/pha4ge/hAMRonization/", + "documentation": "https://github.com/pha4ge/hAMRonization/", + "tool_dev_url": "https://github.com/pha4ge/hAMRonization", + "licence": ["GNU Lesser General Public v3 (LGPL v3)"], + "identifier": "biotools:hamronization" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "report": { + "type": "file", + "description": "Output .txt file from fARGene", + "pattern": "*.txt", + "ontologies": [] + } + } + ], + { + "format": { + "type": "string", + "description": "Type of report file to be produced", + "pattern": "tsv|json" + } + }, + { + "software_version": { + "type": "string", + "description": "Version of fARGene used", + "pattern": "[0-9].[0-9].[0-9]" + } + }, + { + "reference_db_version": { + "type": "string", + "description": "Database version of fARGene used", + "pattern": "[0-9].[0-9].[0-9]" + } + } + ], + "output": { + "json": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.json": { + "type": "file", + "description": "hAMRonised report in JSON format", + "pattern": "*.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "hAMRonised report in TSV format", + "pattern": "*.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "versions_hamronization": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "hamronization": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "hamronize --version 2>&1 | sed 's/hamronize //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "hamronization": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "hamronize --version 2>&1 | sed 's/hamronize //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@jfy133"], + "maintainers": ["@jfy133"] }, - { - "intervals": { - "type": "file", - "description": "Intervals", - "ontologies": [] - } - } - ], - { - "resources": { - "type": "list", - "description": "resource A VCF containing known SNP and or INDEL sites. Can be supplied as many times as necessary", - "pattern": "*.vcf.gz" - } - }, - { - "resources_index": { - "type": "list", - "description": "Index of resource VCF containing known SNP and or INDEL sites. Can be supplied as many times as necessary", - "pattern": "*.vcf.gz" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference fasta file", - "pattern": "*.fasta", - "ontologies": [] - } - }, - { - "fai": { - "type": "file", - "description": "Index of reference fasta file", - "pattern": "fasta.fai", - "ontologies": [] - } - }, - { - "dict": { - "type": "file", - "description": "GATK sequence dictionary", - "pattern": ".dict", - "ontologies": [] - } - } - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.vcf.gz": { - "type": "file", - "description": "VCF file", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.vcf.gz.tbi": { - "type": "file", - "description": "VCF index file", - "pattern": "*.vcf.gz.tbi", - "ontologies": [] - } - } - ] - ], - "versions_gatk4": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gatk4": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gatk4": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "funcscan", + "version": "3.0.0" + } ] - ] - }, - "authors": [ - "@FriederikeHanssen" - ], - "maintainers": [ - "@FriederikeHanssen" - ] - }, - "pipelines": [ - { - "name": "sarek", - "version": "3.8.1" - } - ] - }, - { - "name": "gatk4_gatherbqsrreports", - "path": "modules/nf-core/gatk4/gatherbqsrreports/meta.yml", - "type": "module", - "meta": { - "name": "gatk4_gatherbqsrreports", - "description": "Gathers scattered BQSR recalibration reports into a single file", - "keywords": [ - "base quality score recalibration", - "bqsr", - "gatherbqsrreports", - "gatk4" - ], - "tools": [ - { - "gatk4": { - "description": "Genome Analysis Toolkit (GATK4)", - "homepage": "https://gatk.broadinstitute.org/hc/en-us", - "documentation": "https://gatk.broadinstitute.org/hc/en-us", - "tool_dev_url": "https://github.com/broadinstitute/gatk", - "doi": "10.1158/1538-7445.AM2017-3590", - "licence": [ - "BSD-3-clause" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + }, + { + "name": "hamronization_rgi", + "path": "modules/nf-core/hamronization/rgi/meta.yml", + "type": "module", + "meta": { + "name": "hamronization_rgi", + "description": "Tool to convert and summarize RGI outputs using the hAMRonization specification.", + "keywords": [ + "amr", + "antimicrobial resistance", + "arg", + "antimicrobial resistance genes", + "reporting", + "rgi" + ], + "tools": [ + { + "hamronization": { + "description": "Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification", + "homepage": "https://github.com/pha4ge/hAMRonization/", + "documentation": "https://github.com/pha4ge/hAMRonization/", + "tool_dev_url": "https://github.com/pha4ge/hAMRonization", + "licence": ["GNU Lesser General Public v3 (LGPL v3)"], + "identifier": "biotools:hamronization" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "report": { + "type": "file", + "description": "Output .txt file from RGI", + "pattern": "*.txt", + "ontologies": [] + } + } + ], + { + "format": { + "type": "string", + "description": "Type of report file to be produced", + "pattern": "tsv|json" + } + }, + { + "software_version": { + "type": "string", + "description": "Version of DeepARG used", + "pattern": "[0-9].[0-9].[0-9]" + } + }, + { + "reference_db_version": { + "type": "string", + "description": "Database version of DeepARG used", + "pattern": "[0-9].[0-9].[0-9]" + } + } + ], + "output": { + "json": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.json": { + "type": "file", + "description": "hAMRonised report in JSON format", + "pattern": "*.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "hAMRonised report in TSV format", + "pattern": "*.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "versions_hamronization": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "hamronization": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "hamronize --version 2>&1 | sed 's/hamronize //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "hamronization": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "hamronize --version 2>&1 | sed 's/hamronize //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@louperelo"], + "maintainers": ["@louperelo"] }, - { - "table": { - "type": "file", - "description": "File(s) containing BQSR table(s)", - "pattern": "*.table", - "ontologies": [] - } - } - ] - ], - "output": { - "table": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.table": { - "type": "file", - "description": "File containing joined BQSR table", - "pattern": "*.table", - "ontologies": [] - } - } - ] - ], - "versions_gatk4": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gatk4": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gatk4": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "funcscan", + "version": "3.0.0" + } ] - ] }, - "authors": [ - "@FriederikeHanssen" - ], - "maintainers": [ - "@FriederikeHanssen" - ] - }, - "pipelines": [ { - "name": "genomicrelatedness", - "version": "dev" + "name": "hamronization_summarize", + "path": "modules/nf-core/hamronization/summarize/meta.yml", + "type": "module", + "meta": { + "name": "hamronization_summarize", + "description": "Tool to summarize and combine all hAMRonization reports into a single file", + "keywords": ["amr", "antimicrobial resistance", "reporting"], + "tools": [ + { + "hamronization": { + "description": "Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification", + "homepage": "https://github.com/pha4ge/hAMRonization/", + "documentation": "https://github.com/pha4ge/hAMRonization/", + "tool_dev_url": "https://github.com/pha4ge/hAMRonization", + "licence": ["GNU Lesser General Public v3 (LGPL v3)"], + "identifier": "biotools:hamronization" + } + } + ], + "input": [ + { + "reports": { + "type": "file", + "description": "List of multiple hAMRonization reports in either JSON or TSV format", + "pattern": "*.{json,tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + }, + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, + { + "format": { + "type": "string", + "description": "Type of final combined report file to be produced", + "pattern": "tsv|json|interactive" + } + } + ], + "output": { + "json": [ + { + "hamronization_combined_report.json": { + "type": "file", + "description": "hAMRonised summary in JSON format", + "pattern": "*.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ], + "tsv": [ + { + "hamronization_combined_report.tsv": { + "type": "file", + "description": "hAMRonised summary in TSV format", + "pattern": "*.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ], + "html": [ + { + "hamronization_combined_report.html": { + "type": "file", + "description": "hAMRonised summary in HTML format", + "pattern": "*.html", + "ontologies": [] + } + } + ], + "versions_hamronization": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "hamronization": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "hamronize --version 2>&1 | sed 's/hamronize //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "hamronization": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "hamronize --version 2>&1 | sed 's/hamronize //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@jfy133"], + "maintainers": ["@jfy133"] + }, + "pipelines": [ + { + "name": "funcscan", + "version": "3.0.0" + } + ] }, { - "name": "rnadnavar", - "version": "dev" + "name": "hapibd", + "path": "modules/nf-core/hapibd/meta.yml", + "type": "module", + "meta": { + "name": "hapibd", + "description": "The hap-ibd program detects identity-by-descent (IBD) segments and homozygosity-by-descent (HBD) segments in phased genotype data. The hap-ibd program can analyze data sets with hundreds of thousands of samples.", + "keywords": ["ibd", "hbd", "beagle"], + "tools": [ + { + "hapibd": { + "description": "Hap-ibd Detects identity-by-descent (IBD) segments and homozygosity-by-descent (HBD) segments in phased genotype data.", + "homepage": "https://github.com/browning-lab/hap-ibd/blob/master/README.md", + "documentation": "https://github.com/browning-lab/hap-ibd/blob/master/README.md", + "doi": "10.1016/j.ajhg.2020.02.010", + "licence": ["Apache-2.0"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing cohort information\ne.g. [ id:'test' ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "phased VCF file with a GT FORMAT subfield with no missing alleles", + "pattern": "*.{vcf,vcf.gz}", + "ontologies": [] + } + } + ], + { + "map": { + "type": "file", + "description": "genetic map with cM units in PLINK format", + "pattern": "*.{map,map.gz,map.zip}", + "ontologies": [] + } + }, + { + "exclude": { + "type": "file", + "description": "text file containing samples one sample per line to be excluded from the analysis", + "pattern": "*.*", + "ontologies": [] + } + } + ], + "output": { + "hbd": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing cohort information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.hbd.gz": { + "type": "file", + "description": "contains HBD segments within individuals", + "pattern": "*.hbd.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "ibd": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing cohort information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.ibd.gz": { + "type": "file", + "description": "contains IBD segments shared between individuals", + "pattern": "*.ibd.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing cohort information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "contains a summary of the analysis which includes the analysis parameters the number of markers the number of samples the number of output HBD and IBD segments and the mean number of HBD and IBD segments per sample", + "pattern": "*.log", + "ontologies": [] + } + } + ] + ], + "versions_hapibd": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "hapibd": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "hap-ibd 2>&1 | sed '1!d;s/^.* version //;s/,.*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "hapibd": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "hap-ibd 2>&1 | sed '1!d;s/^.* version //;s/,.*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@ashotmarg"], + "maintainers": ["@ashotmarg"] + } }, { - "name": "sarek", - "version": "3.8.1" - } - ] - }, - { - "name": "gatk4_gatherpileupsummaries", - "path": "modules/nf-core/gatk4/gatherpileupsummaries/meta.yml", - "type": "module", - "meta": { - "name": "gatk4_gatherpileupsummaries", - "description": "write your description here", - "keywords": [ - "gatk4", - "mpileup", - "sort" - ], - "tools": [ - { - "gatk4": { - "description": "Genome Analysis Toolkit (GATK4)", - "homepage": "https://gatk.broadinstitute.org/hc/en-us", - "documentation": "https://gatk.broadinstitute.org/hc/en-us", - "tool_dev_url": "https://github.com/broadinstitute/gatk", - "doi": "10.1158/1538-7445.AM2017-3590", - "licence": [ - "BSD-3-clause" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + "name": "haplocheck", + "path": "modules/nf-core/haplocheck/meta.yml", + "type": "module", + "meta": { + "name": "haplocheck", + "description": "Haplocheck detects contamination patterns in mtDNA AND WGS sequencing studies by analyzing\nthe mitochondrial DNA. Haplocheck also works as a proxy tool for nDNA studies and provides\nusers a graphical report to investigate the contamination further. Internally, it uses the\nHaplogrep tool, that supports rCRS and RSRS mitochondrial versions.\n", + "keywords": ["mitochondrial", "mtDNA", "contamination"], + "tools": [ + { + "haplocheck": { + "description": "Detects in-sample contamination in mtDNA or WGS sequencing studies by analyzing the mitochondrial content.", + "homepage": "https://github.com/genepi/haplocheck", + "documentation": "https://github.com/genepi/haplocheck", + "tool_dev_url": "https://github.com/genepi/haplocheck", + "doi": "10.1101/gr.256545.119", + "licence": ["MIT"], + "identifier": "biotools:haplocheck" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF file", + "pattern": "*.{vcf.gz}", + "ontologies": [] + } + } + ] + ], + "output": { + "txt": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "Raw report in txt format", + "pattern": "*.{txt}", + "ontologies": [] + } + } + ] + ], + "html": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.html": { + "type": "file", + "description": "Haplocheck HTML report", + "pattern": "*.{html}", + "ontologies": [] + } + } + ] + ], + "versions_haplocheck": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "haplocheck": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "haplocheck --version 2>&1 | sed -n 's/^haplocheck //p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "haplocheck": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "haplocheck --version 2>&1 | sed -n 's/^haplocheck //p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@lmtani"], + "maintainers": ["@lmtani"] }, - { - "pileup": { - "type": "file", - "description": "Pileup files from gatk4/getpileupsummaries", - "pattern": "*.pileups.table", - "ontologies": [] - } - } - ], - { - "dict": { - "type": "file", - "description": "dictionary", - "ontologies": [] - } - } - ], - "output": { - "table": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.pileups.table": { - "type": "file", - "description": "pileup summaries table file", - "pattern": "*.pileups.table", - "ontologies": [] - } - } - ] - ], - "versions_gatk4": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gatk4": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gatk4": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "variantcatalogue", + "version": "dev" + } ] - ] - }, - "authors": [ - "@FriederikeHanssen", - "@maxulysse" - ], - "maintainers": [ - "@FriederikeHanssen", - "@maxulysse" - ] - }, - "pipelines": [ - { - "name": "rnadnavar", - "version": "dev" }, { - "name": "sarek", - "version": "3.8.1" - } - ] - }, - { - "name": "gatk4_genomicsdbimport", - "path": "modules/nf-core/gatk4/genomicsdbimport/meta.yml", - "type": "module", - "meta": { - "name": "gatk4_genomicsdbimport", - "description": "merge GVCFs from multiple samples. For use in joint genotyping or somatic panel of normal creation.", - "keywords": [ - "gatk4", - "genomicsdb", - "genomicsdbimport", - "jointgenotyping", - "panelofnormalscreation" - ], - "tools": [ - { - "gatk4": { - "description": "Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools\nwith a primary focus on variant discovery and genotyping. Its powerful processing engine\nand high-performance computing features make it capable of taking on projects of any size.\n", - "homepage": "https://gatk.broadinstitute.org/hc/en-us", - "documentation": "https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s", - "doi": "10.1158/1538-7445.AM2017-3590", - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "vcf": { - "type": "list", - "description": "either a list of vcf files to be used to create or update a genomicsdb, or a file that contains a map to vcf files to be used.", - "pattern": "*.vcf.gz" - } - }, - { - "tbi": { - "type": "list", - "description": "list of tbi files that match with the input vcf files", - "pattern": "*.vcf.gz_tbi" - } - }, - { - "interval_file": { - "type": "file", - "description": "file containing the intervals to be used when creating the genomicsdb", - "pattern": "*.interval_list", - "ontologies": [] - } - }, - { - "interval_value": { - "type": "string", - "description": "if an intervals file has not been specified, the value entered here will be used as an interval via the \"-L\" argument", - "pattern": "example: chr1:1000-10000" - } - }, - { - "wspace": { - "type": "file", - "description": "path to an existing genomicsdb to be used in update db mode or get intervals mode. This WILL NOT specify name of a new genomicsdb in create db mode.", - "pattern": "/path/to/existing/gendb", - "ontologies": [] - } - } - ], - { - "run_intlist": { - "type": "boolean", - "description": "Specify whether to run get interval list mode, this option cannot be specified at the same time as run_updatewspace.", - "pattern": "true/false" - } - }, - { - "run_updatewspace": { - "type": "boolean", - "description": "Specify whether to run update genomicsdb mode, this option takes priority over run_intlist.", - "pattern": "true/false" - } - }, - { - "input_map": { - "type": "boolean", - "description": "Specify whether the vcf input is providing a list of vcf file(s) or a single file containing a map of paths to vcf files to be used to create or update a genomicsdb.", - "pattern": "*.sample_map" + "name": "haplogrep2_classify", + "path": "modules/nf-core/haplogrep2/classify/meta.yml", + "type": "module", + "meta": { + "name": "haplogrep2_classify", + "description": "classification into haplogroups", + "keywords": ["haplogroups", "classify", "mtDNA"], + "tools": [ + { + "haplogrep2": { + "description": "A tool for mtDNA haplogroup classification.", + "homepage": "https://github.com/seppinho/haplogrep-cmd", + "documentation": "https://github.com/seppinho/haplogrep-cmd", + "tool_dev_url": "https://github.com/seppinho/haplogrep-cmd", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "inputfile": { + "type": "file", + "description": "valid options are hsd, vcf, or fasta files", + "pattern": "*.{vcf,vcf.gz,fasta,hsd}", + "ontologies": [] + } + } + ], + { + "format": { + "type": "string", + "description": "either \"vcf\", \"fasta\" or \"hsd\"" + } + } + ], + "output": { + "txt": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "text file with classification information", + "pattern": "*.{txt}", + "ontologies": [] + } + } + ] + ], + "versions_haplogrep2": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "haplogrep2": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "haplogrep --version 2>&1 | sed '2!d;s/.*v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "haplogrep2": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "haplogrep --version 2>&1 | sed '2!d;s/.*v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@lucpen"], + "maintainers": ["@lucpen"] } - } - ], - "output": { - "genomicsdb": [ - [ - { - "meta": { - "type": "map", - "description": "A Groovy map containing sample information" - } - }, - { - "${prefix}": { - "type": "file", - "description": "genomicsdb", - "ontologies": [] - } - } - ] - ], - "updatedb": [ - [ - { - "meta": { - "type": "map", - "description": "A Groovy map containing sample information" - } - }, - { - "${updated_db}": { - "type": "file", - "description": "updated genomicsdb", - "ontologies": [] - } - } - ] - ], - "intervallist": [ - [ - { - "meta": { - "type": "map", - "description": "A Groovy map containing sample information" - } - }, - { - "*.interval_list": { - "type": "file", - "description": "File containing the intervals used to generate the genomicsdb, only created by get intervals mode.", - "pattern": "*.interval_list", - "ontologies": [] - } - } - ] - ], - "versions_gatk4": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gatk4": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gatk4": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] }, - "authors": [ - "@GCJMackenzie" - ], - "maintainers": [ - "@GCJMackenzie" - ] - }, - "pipelines": [ { - "name": "createpanelrefs", - "version": "dev" + "name": "haplogrep3_classify", + "path": "modules/nf-core/haplogrep3/classify/meta.yml", + "type": "module", + "meta": { + "name": "haplogrep3_classify", + "description": "classification into haplogroups", + "keywords": ["haplogroups", "classify", "mtDNA"], + "tools": [ + { + "haplogrep3": { + "description": "A tool for mtDNA haplogroup classification.", + "homepage": "https://github.com/genepi/haplogrep3", + "documentation": "https://github.com/genepi/haplogrep3", + "tool_dev_url": "https://github.com/genepi/haplogrep3", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "inputfile": { + "type": "file", + "description": "valid options are hsd, vcf, or fasta files", + "pattern": "*.{vcf,vcf.gz,fasta,hsd}", + "ontologies": [] + } + } + ] + ], + "output": { + "txt": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "text file with classification information", + "pattern": "*.{txt}", + "ontologies": [] + } + } + ] + ], + "versions_haplogrep3": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "haplogrep3": { + "type": "string", + "description": "The tool name" + } + }, + { + "haplogrep3 | sed -n 's/.*Haplogrep 3 \\([0-9.]\\+\\).*/\\1/p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "haplogrep3": { + "type": "string", + "description": "The tool name" + } + }, + { + "haplogrep3 | sed -n 's/.*Haplogrep 3 \\([0-9.]\\+\\).*/\\1/p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@lucpen"], + "maintainers": ["@lucpen", "@ramprasadn"] + } }, { - "name": "genomicrelatedness", - "version": "dev" + "name": "happy_ftxpy", + "path": "modules/nf-core/happy/ftxpy/meta.yml", + "type": "module", + "meta": { + "name": "happy_ftxpy", + "description": "Somatic VCF Feature Extraction tool from hap.y.", + "keywords": ["happy", "featuretable", "somatic", "extraction"], + "tools": [ + { + "happy": { + "description": "Haplotype VCF comparison tools", + "homepage": "https://www.illumina.com/products/by-type/informatics-products/basespace-sequence-hub/apps/hap-py-benchmarking.html", + "documentation": "https://github.com/Illumina/hap.py", + "tool_dev_url": "https://github.com/Illumina/hap.py", + "licence": ["BSD-2-clause"], + "identifier": "biotools:happy" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF file to process", + "pattern": "*.{vcf,vcf.gz}", + "ontologies": [] + } + }, + { + "regions_bed": { + "type": "file", + "description": "BED file. Restrict analysis to given (sparse) regions.", + "pattern": "*.bed", + "ontologies": [] + } + }, + { + "targets_bed": { + "type": "file", + "description": "Restrict analysis to given (dense) regions.", + "pattern": "*.bed", + "ontologies": [] + } + }, + { + "bam": { + "type": "file", + "description": "Pass one or more BAM files for feature table extraction", + "pattern": "*.bam", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information for reference fasta\ne.g. [ id:'test2']\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA file of the reference genome", + "pattern": "*.{fa,fasta}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information for reference fai\ne.g. [ id:'test3' ]\n" + } + }, + { + "fasta_fai": { + "type": "file", + "description": "The index of the reference FASTA", + "pattern": "*.fai", + "ontologies": [] + } + } + ] + ], + "output": { + "features": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.csv": { + "type": "file", + "description": "Fuature table", + "pattern": "*.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "versions_happy": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "happy": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "0.3.15": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "happy": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "0.3.15": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@kubranarci"], + "maintainers": ["@kubranarci"] + } }, { - "name": "sarek", - "version": "3.8.1" - } - ] - }, - { - "name": "gatk4_genotypegvcfs", - "path": "modules/nf-core/gatk4/genotypegvcfs/meta.yml", - "type": "module", - "meta": { - "name": "gatk4_genotypegvcfs", - "description": "Perform joint genotyping on one or more samples pre-called with HaplotypeCaller.\n", - "keywords": [ - "gatk4", - "genotype", - "gvcf", - "joint genotyping" - ], - "tools": [ - { - "gatk4": { - "description": "Genome Analysis Toolkit (GATK4)", - "homepage": "https://gatk.broadinstitute.org/hc/en-us", - "documentation": "https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s", - "tool_dev_url": "https://github.com/broadinstitute/gatk", - "doi": "10.1158/1538-7445.AM2017-3590", - "licence": [ - "BSD-3-clause" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "gVCF(.gz) file or a GenomicsDB\n", - "pattern": "*.{vcf,vcf.gz}", - "ontologies": [] - } - }, - { - "gvcf_index": { - "type": "file", - "description": "index of gvcf file, or empty when providing GenomicsDB\n", - "pattern": "*.{idx,tbi}", - "ontologies": [] - } - }, - { - "intervals": { - "type": "file", - "description": "Interval file with the genomic regions included in the library (optional)", - "ontologies": [] - } - }, - { - "intervals_index": { - "type": "file", - "description": "Interval index file (optional)", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing fasta information\ne.g. [ id:'test' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference fasta file", - "pattern": "*.fasta", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing fai information\ne.g. [ id:'test' ]\n" - } - }, - { - "fai": { - "type": "file", - "description": "Reference fasta index file", - "pattern": "*.fai", - "ontologies": [] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing dict information\ne.g. [ id:'test' ]\n" - } - }, - { - "dict": { - "type": "file", - "description": "Reference fasta sequence dict file", - "pattern": "*.dict", - "ontologies": [] - } - } - ], - [ - { - "meta5": { - "type": "map", - "description": "Groovy Map containing dbsnp information\ne.g. [ id:'test' ]\n" - } - }, - { - "dbsnp": { - "type": "file", - "description": "dbSNP VCF file", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ], - [ - { - "meta6": { - "type": "map", - "description": "Groovy Map containing dbsnp tbi information\ne.g. [ id:'test' ]\n" - } + "name": "happy_happy", + "path": "modules/nf-core/happy/happy/meta.yml", + "type": "module", + "meta": { + "name": "happy_happy", + "description": "Hap.py is a tool to compare diploid genotypes at haplotype level. Rather than comparing VCF records row by row, hap.py will generate and match alternate sequences in a superlocus. A superlocus is a small region of the genome (sized between 1 and around 1000 bp) that contains one or more variants.", + "keywords": ["happy", "benchmark", "haplotype", "validation"], + "tools": [ + { + "happy": { + "description": "Haplotype VCF comparison tools", + "homepage": "https://www.illumina.com/products/by-type/informatics-products/basespace-sequence-hub/apps/hap-py-benchmarking.html", + "documentation": "https://github.com/Illumina/hap.py", + "tool_dev_url": "https://github.com/Illumina/hap.py", + "licence": ["BSD-2-clause"], + "identifier": "biotools:happy" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "query_vcf": { + "type": "file", + "description": "VCF/GVCF file to query", + "pattern": "*.{gvcf,vcf}.gz", + "ontologies": [] + } + }, + { + "truth_vcf": { + "type": "file", + "description": "gold standard VCF file", + "pattern": "*.{gvcf,vcf}.gz", + "ontologies": [] + } + }, + { + "regions_bed": { + "type": "file", + "description": "Sparse regions to restrict the analysis to", + "pattern": "*.bed", + "ontologies": [] + } + }, + { + "targets_bed": { + "type": "file", + "description": "Dense regions to restrict the analysis to", + "pattern": "*.bed", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing fasta file information\ne.g. [ id:'test2']\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA file of the reference genome", + "pattern": "*.{fa,fasta}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing fai file information\ne.g. [ id:'test3']\n" + } + }, + { + "fasta_fai": { + "type": "file", + "description": "The index of the reference FASTA", + "pattern": "*.fai", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing false_positives_bed file information\ne.g. [ id:'test4']\n" + } + }, + { + "false_positives_bed": { + "type": "file", + "description": "False positive / confident call regions. Calls outside these regions will be labelled as UNK.", + "pattern": "*.{bed,bed.gz}", + "ontologies": [] + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing stratification_tsv file information\ne.g. [ id:'test5']\n" + } + }, + { + "stratification_tsv": { + "type": "file", + "description": "Stratification file list in TSV format", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + [ + { + "meta6": { + "type": "map", + "description": "Groovy Map containing stratification_beds file information\ne.g. [ id:'test6']\n" + } + }, + { + "stratification_beds": { + "type": "file", + "description": "One or more BED files used for stratification (these should be referenced in the stratification TSV)", + "pattern": "*.bed", + "ontologies": [] + } + } + ] + ], + "output": { + "summary_csv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.summary.csv": { + "type": "file", + "description": "A CSV file containing the summary of the benchmarking", + "pattern": "*.summary.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "roc_all_csv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.roc.all.csv.gz": { + "type": "file", + "description": "A CSV file containing ROC values for all variants", + "pattern": "*.roc.all.csv.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "roc_indel_locations_csv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.roc.Locations.INDEL.csv.gz": { + "type": "file", + "description": "A CSV file containing ROC values for all indels", + "pattern": "*.roc.Locations.INDEL.csv.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "roc_indel_locations_pass_csv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.roc.Locations.INDEL.PASS.csv.gz": { + "type": "file", + "description": "A CSV file containing ROC values for all indels that passed all filters", + "pattern": "*.roc.Locations.INDEL.PASS.csv.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "roc_snp_locations_csv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.roc.Locations.SNP.csv.gz": { + "type": "file", + "description": "A CSV file containing ROC values for all SNPs", + "pattern": "*.roc.Locations.SNP.csv.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "roc_snp_locations_pass_csv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.roc.Locations.SNP.PASS.csv.gz": { + "type": "file", + "description": "A CSV file containing ROC values for all SNPs that passed all filters", + "pattern": "*.roc.Locations.SNP.PASS.csv.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "extended_csv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.extended.csv": { + "type": "file", + "description": "A CSV file containing extended info of the benchmarking", + "pattern": "*.extended.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "runinfo": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.runinfo.json": { + "type": "file", + "description": "A JSON file containing the benchmarking metrics", + "pattern": "*.metrics.json.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "metrics_json": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.metrics.json.gz": { + "type": "file", + "description": "A JSON file containing the run info", + "pattern": "*.runinfo.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "An annotated VCF", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tbi": { + "type": "file", + "description": "The index of the annotated VCF", + "pattern": "*.tbi", + "ontologies": [] + } + } + ] + ], + "versions_happy": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "happy": { + "type": "string", + "description": "The tool name" + } + }, + { + "0.3.15": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "happy": { + "type": "string", + "description": "The tool name" + } + }, + { + "0.3.15": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@nvnieuwk"], + "maintainers": ["@nvnieuwk"] }, - { - "dbsnp_tbi": { - "type": "file", - "description": "dbSNP VCF index file", - "pattern": "*.tbi", - "ontologies": [] - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.vcf.gz": { - "type": "file", - "description": "Genotyped VCF file", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tbi": { - "type": "file", - "description": "Tbi index for VCF file", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "versions_gatk4": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gatk4": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gatk4": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "variantbenchmarking", + "version": "1.5.0" + } ] - ] }, - "authors": [ - "@santiagorevale", - "@maxulysse" - ], - "maintainers": [ - "@santiagorevale", - "@maxulysse" - ] - }, - "pipelines": [ { - "name": "genomicrelatedness", - "version": "dev" - }, - { - "name": "sarek", - "version": "3.8.1" - } - ] - }, - { - "name": "gatk4_germlinecnvcaller", - "path": "modules/nf-core/gatk4/germlinecnvcaller/meta.yml", - "type": "module", - "meta": { - "name": "gatk4_germlinecnvcaller", - "description": "Calls copy-number variants in germline samples given their counts and the output of DetermineGermlineContigPloidy.", - "keywords": [ - "gatk", - "germline contig ploidy", - "germlinecnvcaller" - ], - "tools": [ - { - "gatk4": { - "description": "Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.", - "homepage": "https://gatk.broadinstitute.org/hc/en-us", - "documentation": "https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s", - "doi": "10.1158/1538-7445.AM2017-3590", - "licence": [ - "Apache-2.0" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "tsv": { - "type": "file", - "description": "One or more count TSV files created with gatk/collectreadcounts", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - }, - { - "intervals": { - "type": "file", - "description": "Optional - A bed file containing the intervals to include in the process", - "pattern": "*.bed", - "ontologies": [] - } - }, - { - "ploidy": { - "type": "directory", - "description": "Directory containing ploidy calls produced by determinegermlinecontigploidy case or cohort mode", - "pattern": "*-calls" - } + "name": "happy_prepy", + "path": "modules/nf-core/happy/prepy/meta.yml", + "type": "module", + "meta": { + "name": "happy_prepy", + "description": "Pre.py is a preprocessing tool made to preprocess VCF files for Hap.py", + "keywords": ["happy", "benchmark", "haplotype"], + "tools": [ + { + "happy": { + "description": "Haplotype VCF comparison tools", + "homepage": "https://www.illumina.com/products/by-type/informatics-products/basespace-sequence-hub/apps/hap-py-benchmarking.html", + "documentation": "https://github.com/Illumina/hap.py", + "tool_dev_url": "https://github.com/Illumina/hap.py", + "licence": ["BSD-2-clause"], + "identifier": "biotools:happy" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF file to preprocess", + "pattern": "*.{vcf,vcf.gz}", + "ontologies": [] + } + }, + { + "bed": { + "type": "file", + "description": "BED file", + "pattern": "*.bed", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information for reference fasta\ne.g. [ id:'test2']\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA file of the reference genome", + "pattern": "*.{fa,fasta}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information for reference fai\ne.g. [ id:'test3' ]\n" + } + }, + { + "fasta_fai": { + "type": "file", + "description": "The index of the reference FASTA", + "pattern": "*.fai", + "ontologies": [] + } + } + ] + ], + "output": { + "preprocessed_vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "Preprocessed VCF file", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "versions_happy": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "happy": { + "type": "string", + "description": "The tool name" + } + }, + { + "0.3.15": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "happy": { + "type": "string", + "description": "The tool name" + } + }, + { + "0.3.15": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@nvnieuwk"], + "maintainers": ["@nvnieuwk"] }, - { - "model": { - "type": "directory", - "description": "Optional - directory containing the model produced by germlinecnvcaller cohort mode", - "pattern": "*-cnv-model/*-model" - } - } - ] - ], - "output": { - "cohortcalls": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*-cnv-model/*-calls": { - "type": "directory", - "description": "Tar gzipped directory containing calls produced by germlinecnvcaller case mode", - "pattern": "*-cnv-model/*-calls" - } - } - ] - ], - "cohortmodel": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*-cnv-model/*-model": { - "type": "directory", - "description": "Optional - Tar gzipped directory containing the model produced by germlinecnvcaller cohort mode", - "pattern": "*-cnv-model/*-model" - } - } - ] - ], - "casecalls": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*-cnv-calls/*-calls": { - "type": "directory", - "description": "Tar gzipped directory containing calls produced by germlinecnvcaller case mode", - "pattern": "*-cnv-calls/*-calls" - } - } - ] - ], - "versions_gatk4": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gatk4": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gatk4": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "variantbenchmarking", + "version": "1.5.0" + } ] - ] }, - "authors": [ - "@ryanjameskennedy", - "@ViktorHy" - ], - "maintainers": [ - "@ryanjameskennedy", - "@ViktorHy" - ] - }, - "pipelines": [ { - "name": "createpanelrefs", - "version": "dev" - }, - { - "name": "raredisease", - "version": "3.0.0" - } - ] - }, - { - "name": "gatk4_getpileupsummaries", - "path": "modules/nf-core/gatk4/getpileupsummaries/meta.yml", - "type": "module", - "meta": { - "name": "gatk4_getpileupsummaries", - "description": "Summarizes counts of reads that support reference, alternate and other alleles for given sites. Results can be used with CalculateContamination. Requires a common germline variant sites file, such as from gnomAD.\n", - "keywords": [ - "gatk4", - "germlinevariantsites", - "getpileupsumaries", - "readcountssummary" - ], - "tools": [ - { - "gatk4": { - "description": "Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools\nwith a primary focus on variant discovery and genotyping. Its powerful processing engine\nand high-performance computing features make it capable of taking on projects of any size.\n", - "homepage": "https://gatk.broadinstitute.org/hc/en-us", - "documentation": "https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s", - "doi": "10.1158/1538-7445.AM2017-3590", - "licence": [ - "Apache-2.0" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM file to be summarised.", - "pattern": "*.{bam,cram}", - "ontologies": [] - } - }, - { - "index": { - "type": "file", - "description": "Index file for the input BAM/CRAM file.", - "pattern": "*.{bam.bai,cram.crai}", - "ontologies": [] - } - }, - { - "intervals": { - "type": "file", - "description": "File containing specified sites to be used for the summary. If this option is not specified, variants file is used instead automatically.", - "pattern": "*.interval_list", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference fasta file", - "pattern": "*.fasta", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fai": { - "type": "file", - "description": "Index of reference fasta file", - "pattern": "*.fasta.fai", - "ontologies": [] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } + "name": "happy_sompy", + "path": "modules/nf-core/happy/sompy/meta.yml", + "type": "module", + "meta": { + "name": "happy_sompy", + "description": "Hap.py is a tool to compare diploid genotypes at haplotype level. som.py is a part of hap.py compares somatic variations.", + "keywords": ["happy", "sompy", "benchmark", "haplotype", "validation", "somatic variants"], + "tools": [ + { + "sompy": { + "description": "Haplotype VCF comparison tools somatic variant comparison", + "homepage": "https://www.illumina.com/products/by-type/informatics-products/basespace-sequence-hub/apps/hap-py-benchmarking.html", + "documentation": "https://github.com/Illumina/hap.py/blob/master/doc/sompy.md", + "tool_dev_url": "https://github.com/Illumina/hap.py", + "licence": ["BSD-2-clause"], + "identifier": "biotools:happy" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "query_vcf": { + "type": "file", + "description": "VCF/GVCF file to query", + "pattern": "*.{gvcf,vcf}.gz", + "ontologies": [] + } + }, + { + "truth_vcf": { + "type": "file", + "description": "gold standard VCF file", + "pattern": "*.{gvcf,vcf}.gz", + "ontologies": [] + } + }, + { + "regions_bed": { + "type": "file", + "description": "Sparse regions to restrict the analysis to", + "pattern": "*.bed", + "ontologies": [] + } + }, + { + "targets_bed": { + "type": "file", + "description": "Dense regions to restrict the analysis to", + "pattern": "*.bed", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing fasta file information\ne.g. [ id:'test2']\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA file of the reference genome", + "pattern": "*.{fa,fasta}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing fai file information\ne.g. [ id:'test3']\n" + } + }, + { + "fasta_fai": { + "type": "file", + "description": "The index of the reference FASTA", + "pattern": "*.fai", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing false_positives_bed file information\ne.g. [ id:'test4']\n" + } + }, + { + "false_positives_bed": { + "type": "file", + "description": "False positive / confident call regions. Calls outside these regions will be labelled as UNK.", + "pattern": "*.{bed,bed.gz}", + "ontologies": [] + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing ambiguous_beds file information\ne.g. [ id:'test5']\n" + } + }, + { + "ambiguous_beds": { + "type": "file", + "description": "Ambiguous regions", + "pattern": "*.{bed,bed.gz}", + "ontologies": [] + } + } + ], + [ + { + "meta6": { + "type": "map", + "description": "Groovy Map containing bam file information\ne.g. [ id:'test6']\n" + } + }, + { + "bams": { + "type": "file", + "description": "one or more BAM files for feature table extraction", + "pattern": "*.bam", + "ontologies": [] + } + } + ] + ], + "output": { + "features": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.features.csv": { + "type": "file", + "description": "One or more than one (if AF count is on ) CSV file containing feature information", + "pattern": "*.features.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "metrics": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.metrics.json": { + "type": "file", + "description": "One or more than one (if AF count is on ) JSON file with metrics", + "pattern": "*.metrics.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "stats": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.stats.csv": { + "type": "file", + "description": "One or more than one (if AF count is on ) CSV file with benchmark stats", + "pattern": "*.stats.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "versions_happy": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "happy": { + "type": "string", + "description": "The tool name" + } + }, + { + "0.3.15": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "happy": { + "type": "string", + "description": "The tool name" + } + }, + { + "0.3.15": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@kubranarci"] }, - { - "dict": { - "type": "file", - "description": "GATK sequence dictionary", - "pattern": "*.dict", - "ontologies": [] - } - } - ], - { - "variants": { - "type": "file", - "description": "Population vcf of germline sequencing, containing allele fractions. Is also used as sites file if no separate sites file is specified.", - "pattern": "*.vcf.gz", - "ontologies": [ + "pipelines": [ { - "edam": "http://edamontology.org/format_3989" + "name": "variantbenchmarking", + "version": "1.5.0" } - ] - } - }, - { - "variants_tbi": { - "type": "file", - "description": "Index file for the germline resource.", - "pattern": "*.vcf.gz.tbi", - "ontologies": [] - } - } - ], - "output": { - "table": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.pileups.table": { - "type": "file", - "description": "Table containing read counts for each site.", - "pattern": "*.pileups.table", - "ontologies": [] - } - } - ] - ], - "versions_gatk4": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gatk4": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gatk4": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] }, - "authors": [ - "@GCJMackenzie" - ], - "maintainers": [ - "@GCJMackenzie" - ] - }, - "pipelines": [ { - "name": "rnadnavar", - "version": "dev" + "name": "hasheddrops", + "path": "modules/nf-core/hasheddrops/meta.yml", + "type": "module", + "meta": { + "name": "hasheddrops", + "description": "Generating cell hashing calls from a matrix of count data.", + "keywords": ["demultiplexing", "hashing-based deconvolution", "single-cell"], + "tools": [ + { + "hasheddrops": { + "description": "Demultiplex cell barcodes into their samples of origin based on the most abundant hash tag oligo (HTO). Also identify potential doublets based on the presence of multiple significant HTOs.", + "homepage": "https://rdrr.io/github/MarioniLab/DropletUtils/man/hashedDrops.html", + "documentation": "https://rdrr.io/github/MarioniLab/DropletUtils/man/hashedDrops.html", + "tool_dev_url": "https://github.com/MarioniLab/DropletUtils", + "doi": "10.18129/B9.bioc.DropletUtils", + "licence": ["GPL-3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "hto_matrix": { + "type": "file", + "description": "Directory that contains the HTO matrix in a 10X format.\n", + "ontologies": [ + { + "edam": "http://edamontology.org/data_3917" + } + ] + } + }, + { + "runEmptyDrops": { + "type": "boolean", + "description": "Run EmptyDrops() before hashedDrops() (\"TRUE\") or not (\"FALSE\").\n" + } + }, + { + "rna_matrix": { + "type": "file", + "description": "Path to RNA count matrix, which is only uses if runEmptyDrops == \"TRUE\".\n", + "ontologies": [ + { + "edam": "http://edamontology.org/data_3917" + } + ] + } + } + ] + ], + "output": { + "empty_drops_plot": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_emptyDrops.png": { + "type": "file", + "description": "EmptyDrops results plot\n", + "pattern": "_emptyDrops.png", + "ontologies": [] + } + } + ] + ], + "empty_drops_csv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_emptyDrops.csv": { + "type": "file", + "description": "EmptyDrops results in CSV format\n", + "pattern": "_emptyDrops.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "empty_drops_rds": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_emptyDrops.rds": { + "type": "file", + "description": "EmptyDrops results in RDS format\n", + "pattern": "_emptyDrops.rds", + "ontologies": [] + } + } + ] + ], + "results": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_results_hasheddrops.csv": { + "type": "file", + "description": "HashedDrops results\n", + "pattern": "_results_hasheddrops.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "id_to_hash": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_id_to_hash.csv": { + "type": "file", + "description": "A table mapping integer indices used by hashedDrops results (e.g. the column `Best` or `Second`) to HTO names (or combinations of HTO names joined with `+` if `combinations` is speficied in `ext.args`).\n", + "pattern": "_id_to_hash.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "rds": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_hasheddrops.rds": { + "type": "file", + "description": "HashedDrops results in RDS format\n", + "pattern": "_hasheddrops.rds", + "ontologies": [] + } + } + ] + ], + "plot": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_plot_hasheddrops.png": { + "type": "file", + "description": "HashedDrops plot\n", + "pattern": "_plot_hasheddrops.png", + "ontologies": [] + } + } + ] + ], + "params": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_params_hasheddrops.csv": { + "type": "file", + "description": "The used parameters to call hashedDrops() in the R-Script.\n", + "pattern": "_params_hasheddrops.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "topics": { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@LuisHeinzlmeier"], + "maintainers": ["@LuisHeinzlmeier"] + } }, { - "name": "sarek", - "version": "3.8.1" - } - ] - }, - { - "name": "gatk4_haplotypecaller", - "path": "modules/nf-core/gatk4/haplotypecaller/meta.yml", - "type": "module", - "meta": { - "name": "gatk4_haplotypecaller", - "description": "Call germline SNPs and indels via local re-assembly of haplotypes", - "keywords": [ - "gatk4", - "haplotype", - "haplotypecaller" - ], - "tools": [ - { - "gatk4": { - "description": "Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools\nwith a primary focus on variant discovery and genotyping. Its powerful processing engine\nand high-performance computing features make it capable of taking on projects of any size.\n", - "homepage": "https://gatk.broadinstitute.org/hc/en-us", - "documentation": "https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s", - "doi": "10.1158/1538-7445.AM2017-3590", - "licence": [ - "Apache-2.0" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM file from alignment", - "pattern": "*.{bam,cram}", - "ontologies": [] - } - }, - { - "input_index": { - "type": "file", - "description": "BAI/CRAI file from alignment", - "pattern": "*.{bai,crai}", - "ontologies": [] - } - }, - { - "intervals": { - "type": "file", - "description": "Bed file with the genomic regions included in the library (optional)", - "ontologies": [] - } - }, - { - "dragstr_model": { - "type": "file", - "description": "Text file containing the DragSTR model of the used BAM/CRAM file (optional)", - "pattern": "*.txt", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test_reference' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference fasta file", - "pattern": "*.fasta", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test_reference' ]\n" - } - }, - { - "fai": { - "type": "file", - "description": "Index of reference fasta file", - "pattern": "fasta.fai", - "ontologies": [] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test_reference' ]\n" - } - }, - { - "dict": { - "type": "file", - "description": "GATK sequence dictionary", - "pattern": "*.dict", - "ontologies": [] - } - } - ], - [ - { - "meta5": { - "type": "map", - "description": "Groovy Map containing dbsnp information\ne.g. [ id:'test_dbsnp' ]\n" - } - }, - { - "dbsnp": { - "type": "file", - "description": "VCF file containing known sites (optional)", - "ontologies": [] - } - } - ], - [ - { - "meta6": { - "type": "map", - "description": "Groovy Map containing dbsnp information\ne.g. [ id:'test_dbsnp' ]\n" - } - }, - { - "dbsnp_tbi": { - "type": "file", - "description": "VCF index of dbsnp (optional)", - "ontologies": [] - } + "name": "helitronscanner_draw", + "path": "modules/nf-core/helitronscanner/draw/meta.yml", + "type": "module", + "meta": { + "name": "helitronscanner_draw", + "description": "HelitronScanner draw tool for Helitron transposons in genomes", + "keywords": ["genomics", "helitron", "scanner"], + "tools": [ + { + "helitronscanner": { + "description": "HelitronScanner uncovers a large overlooked cache of Helitron transposons in many genomes", + "homepage": "https://sourceforge.net/projects/helitronscanner", + "documentation": "https://sourceforge.net/projects/helitronscanner", + "tool_dev_url": "https://sourceforge.net/projects/helitronscanner", + "doi": "10.1073/pnas.1410068111", + "licence": ["GPL v3-or-later"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Genome data to scan for Helitrons", + "pattern": "*.{fa,fsa,fasta}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "head": { + "type": "file", + "description": "Output of the HelitronScanner head command", + "pattern": "*.{head}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "tail": { + "type": "file", + "description": "Output of the HelitronScanner tail command", + "pattern": "*.{tail}", + "ontologies": [] + } + } + ] + ], + "output": { + "draw": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n", + "pattern": "*.{draw}" + } + }, + { + "*.draw": { + "type": "map", + "description": "The draw output from HelitronScanner\n", + "pattern": "*.{draw}" + } + } + ] + ], + "versions_helitronscanner": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "helitronscanner": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "HelitronScanner |& sed -n 's/HelitronScanner V//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "helitronscanner": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "HelitronScanner |& sed -n 's/HelitronScanner V//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@GallVp", "@jguhlin"], + "maintainers": ["@GallVp"] } - 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] - ], - "versions_gatk4": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gatk4": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gatk4": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] }, - "authors": [ - "@suzannejin", - "@FriederikeHanssen" - ], - "maintainers": [ - "@suzannejin", - "@FriederikeHanssen" - ] - }, - "pipelines": [ { - "name": "genomicrelatedness", - "version": "dev" + "name": "helitronscanner_scan", + "path": "modules/nf-core/helitronscanner/scan/meta.yml", + "type": "module", + "meta": { + "name": "helitronscanner_scan", + "description": "HelitronScanner scanHead and scanTail tools for Helitron transposons in genomes", + "keywords": ["genomics", "helitron", "scanner"], + "tools": [ + { + "helitronscanner": { + "description": "HelitronScanner uncovers a large overlooked cache of Helitron transposons in many genomes", + "homepage": "https://sourceforge.net/projects/helitronscanner", + "documentation": "https://sourceforge.net/projects/helitronscanner", + "tool_dev_url": "https://sourceforge.net/projects/helitronscanner", + "doi": "10.1073/pnas.1410068111", + "licence": ["GPL v3-or-later"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Genome data to scan for Helitrons", + "pattern": "*.{fa,fsa,fasta}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + { + "command": { + "type": "string", + "description": "Command to execute. 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"name": "tbanalyzer", - "version": "dev" - } - ] - }, - { - "name": "gatk4_intervallisttobed", - "path": "modules/nf-core/gatk4/intervallisttobed/meta.yml", - "type": "module", - "meta": { - "name": "gatk4_intervallisttobed", - "description": "Converts an Picard IntervalList file to a BED file.", - "keywords": [ - "bed", - "conversion", - "gatk4", - "interval" - ], - "tools": [ - { - "gatk4": { - "description": "Genome Analysis Toolkit (GATK4)", - "homepage": "https://gatk.broadinstitute.org/hc/en-us", - "documentation": "https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s", - "tool_dev_url": "https://github.com/broadinstitute/gatk", - "doi": "10.1158/1538-7445.AM2017-3590", - "licence": [ - "BSD-3-clause" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "intervals": { - "type": "file", - "description": "IntervalList file", - "ontologies": [] - } + "name": "hifiadapterfilt_downloaddb", + "path": "modules/nf-core/hifiadapterfilt/downloaddb/meta.yml", + "type": "module", + "meta": { + "name": "hifiadapterfilt_downloaddb", + "description": "Downloads the pre-built PacBio adapter BLAST database from the HiFiAdapterFilt\nGitHub repository. The database contains two adapter sequences: NGB00972.1\n(Pacific Biosciences Blunt Adapter, 45 bp) and NGB00973.1 (C2 Primer, 35 bp).\nThis module is consumed by hifiadapterfilt/hifiadapterfilt as a prerequisite to\nprovide the BLAST database for adapter detection.\n", + "keywords": ["pacbio", "hifi", "adapter", "blast", "database", "download"], + "tools": [ + { + "hifiadapterfilt": { + "description": "HiFiAdapterFilt uses BLAST to identify and remove adapter sequences\nfrom PacBio HiFi reads, producing adapter-filtered FASTQ output along\nwith detailed statistics.\n", + "homepage": "https://github.com/sheinasim/HiFiAdapterFilt", + "documentation": "https://github.com/sheinasim/HiFiAdapterFilt", + "tool_dev_url": "https://github.com/sheinasim/HiFiAdapterFilt", + "licence": ["MIT"], + "identifier": "biotools:HiFiAdapterFilt" + } + } + ], + "input": [], + "output": { + "db": [ + { + "DB": { + "type": "directory", + "description": "Directory containing the pre-built BLAST nucleotide database for PacBio\nadapter sequences. Contains pacbio_vectors_db.* files (NGB00972.1 Blunt\nAdapter and NGB00973.1 C2 Primer).\n", + "pattern": "DB" + } + } + ], + "versions_hifiadapterfilt": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "hifiadapterfilt": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "hifiadapterfilt.sh --version 2>&1 | head -1": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "hifiadapterfilt": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "hifiadapterfilt.sh --version 2>&1 | head -1": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@vagkaratzas"], + "maintainers": ["@vagkaratzas"] } - ] - ], - "output": { - "bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.bed": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", - "pattern": "${prefix}.bed" - } - } - ] - ], - "versions_gatk4": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gatk4": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gatk4": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] }, - "authors": [ - "@FriederikeHanssen" - ], - "maintainers": [ - "@FriederikeHanssen" - ] - }, - "pipelines": [ { - "name": "rnadnavar", - "version": "dev" + "name": "hifiadapterfilt_hifiadapterfilt", + "path": "modules/nf-core/hifiadapterfilt/hifiadapterfilt/meta.yml", + "type": "module", + "meta": { + "name": "hifiadapterfilt_hifiadapterfilt", + "description": "Remove adapter sequences from PacBio HiFi (CCS) reads using BLAST-based\ndetection. Produces filtered FASTQ output, filtering statistics, BLAST hits,\nand a list of blocked read IDs.\n", + "keywords": ["pacbio", "hifi", "adapter", "filtering", "long reads", "ccs"], + "tools": [ + { + "hifiadapterfilt": { + "description": "HiFiAdapterFilt uses BLAST to identify and remove adapter sequences\nfrom PacBio HiFi reads, producing adapter-filtered FASTQ output along\nwith detailed statistics.\n", + "homepage": "https://github.com/sheinasim/HiFiAdapterFilt", + "documentation": "https://github.com/sheinasim/HiFiAdapterFilt", + "tool_dev_url": "https://github.com/sheinasim/HiFiAdapterFilt", + "licence": ["MIT"], + "identifier": "biotools:HiFiAdapterFilt" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "reads": { + "type": "file", + "description": "PacBio HiFi reads in BAM or FASTQ (compressed or uncompressed) format", + "pattern": "*.{bam,fastq|fq(.gz)}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + }, + { + "edam": "http://edamontology.org/format_1930" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + }, + { + "db": { + "type": "directory", + "description": "Directory containing the pre-built BLAST nucleotide database for PacBio\nadapter sequences, as produced by the hifiadapterfilt/downloaddb module.\nMust contain pacbio_vectors_db.* files.\n", + "pattern": "DB" + } + } + ] + ], + "output": { + "fastq": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}.filt.fastq.gz": { + "type": "file", + "description": "Adapter-filtered reads in gzipped FASTQ format", + "pattern": "*.filt.fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "stats": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}.stats": { + "type": "file", + "description": "Filtering statistics file", + "pattern": "*.stats", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3671" + } + ] + } + } + ] + ], + "blastout": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}.contaminant.blastout": { + "type": "file", + "description": "BLAST tabular output for reads containing adapter sequences", + "pattern": "*.contaminant.blastout", + "ontologies": [] + } + } + ] + ], + "blocklist": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}.blocklist": { + "type": "file", + "description": "List of read IDs blocked due to adapter contamination", + "pattern": "*.blocklist", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3671" + } + ] + } + } + ] + ], + "versions_hifiadapterfilt": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "hifiadapterfilt": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "hifiadapterfilt.sh --version 2>&1 | head -1": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "hifiadapterfilt": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "hifiadapterfilt.sh --version 2>&1 | head -1": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@vagkaratzas"], + "maintainers": ["@vagkaratzas"] + } }, { - "name": "sarek", - "version": "3.8.1" - } - ] - }, - { - "name": "gatk4_intervallisttools", - "path": "modules/nf-core/gatk4/intervallisttools/meta.yml", - "type": "module", - "meta": { - "name": "gatk4_intervallisttools", - "description": "Splits the interval list file into unique, equally-sized interval files and place it under a directory", - "keywords": [ - "bed", - "gatk4", - "interval_list", - "sort" - ], - "tools": [ - { - "gatk4": { - "description": "Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools\nwith a primary focus on variant discovery and genotyping. Its powerful processing engine\nand high-performance computing features make it capable of taking on projects of any size.\n", - "homepage": "https://gatk.broadinstitute.org/hc/en-us", - "documentation": "https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s", - "doi": "10.1158/1538-7445.AM2017-3590", - "licence": [ - "Apache-2.0" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + "name": "hifiasm", + "path": "modules/nf-core/hifiasm/meta.yml", + "type": "module", + "meta": { + "name": "hifiasm", + "description": "Whole-genome assembly using PacBio HiFi reads", + "keywords": ["genome assembly", "haplotype resolution", "phasing", "PacBio", "HiFi", "long reads"], + "tools": [ + { + "hifiasm": { + "description": "Haplotype-resolved assembler for accurate HiFi reads", + "homepage": "https://github.com/chhylp123/hifiasm", + "documentation": "https://github.com/chhylp123/hifiasm", + "tool_dev_url": "https://github.com/chhylp123/hifiasm", + "doi": "10.1038/s41592-020-01056-5", + "licence": ["MIT"], + "identifier": "biotools:hifiasm" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "long_reads": { + "type": "file", + "description": "Long reads PacBio HiFi reads or ONT reads (requires ext.arg '--ont').", + "ontologies": [] + } + }, + { + "ul_reads": { + "type": "file", + "description": "ONT long reads to use with --ul.", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing information about parental kmers.\n" + } + }, + { + "paternal_kmer_dump": { + "type": "file", + "description": "Yak kmer dump file for paternal reads (can be used for haplotype resolution). It can have an arbitrary extension.", + "ontologies": [] + } + }, + { + "maternal_kmer_dump": { + "type": "file", + "description": "Yak kmer dump file for maternal reads (can be used for haplotype resolution). It can have an arbitrary extension.", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing information about Hi-C reads\n" + } + }, + { + "hic_read1": { + "type": "file", + "description": "Hi-C data Forward reads.", + "ontologies": [] + } + }, + { + "hic_read2": { + "type": "file", + "description": "Hi-C data Reverse reads.", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing information about the input bin files\n" + } + }, + { + "bin_files": { + "type": "file", + "description": "bin files produced during a previous Hifiasm run", + "ontologies": [] + } + } + ] + ], + "output": { + "raw_unitigs": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.r_utg.gfa": { + "type": "file", + "description": "Raw unitigs", + "pattern": "*.r_utg.gfa", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3975" + } + ] + } + } + ] + ], + "bin_files": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bin": { + "type": "file", + "description": "Binary files containing processed data for hifiasm, including\nerror-corrected reads, read overlaps, and Hi-C alignments. Can\nbe re-used as an input for subsequent re-runs of hifiasm with new\ninputs or modified parameters in order to save recomputation of\ninitial results, which are the most computationally-expensive\nsteps.\n", + "pattern": "*.bin", + "ontologies": [] + } + } + ] + ], + "processed_unitigs": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.p_utg.gfa": { + "type": "file", + "description": "Processed unitigs", + "pattern": "*.p_utg.gfa", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3975" + } + ] + } + } + ] + ], + "primary_contigs": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.{p_ctg,bp.p_ctg,hic.p_ctg}.gfa": { + "type": "file", + "description": "Contigs representing the primary assembly", + "pattern": "${prefix}.{p_ctg,bp.p_ctg,hic.p_ctg}.gfa", + "ontologies": [] + } + } + ] + ], + "alternate_contigs": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.{a_ctg,hic.a_ctg}.gfa": { + "type": "file", + "description": "Contigs representing the alternative assembly", + "pattern": "${prefix}.{a_ctg,hic.a_ctg}.gfa", + "ontologies": [] + } + } + ] + ], + "hap1_contigs": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.*.hap1.p_ctg.gfa": { + "type": "file", + "description": "Contigs for the first haplotype. How the haplotypes are represented\ndepends on the input mode; in standard HiFi-only mode, these\nare partially-phased parental contigs. In Hi-C mode, they\nare fully phased parental contigs, but the phasing is not maintained\nbetween contigs. In trio mode, they are fully phased paternal contigs\nall originating from a single parental haplotype.\n", + "pattern": "${prefix}.*.hap1.p_ctg.gfa", + "ontologies": [] + } + } + ] + ], + "hap2_contigs": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.*.hap2.p_ctg.gfa": { + "type": "file", + "description": "Contigs for the second haplotype. How the haplotypes are represented\ndepends on the input mode; in standard HiFi-only mode, these\nare partially-phased parental contigs. In Hi-C mode, they\nare fully phased parental contigs, but the phasing is not maintained\nbetween contigs. In trio mode, they are fully phased paternal contigs\nall originating from a single parental haplotype.\n", + "pattern": "${prefix}.*.hap2.p_ctg.gfa", + "ontologies": [] + } + } + ] + ], + "corrected_reads": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.ec.fa.gz": { + "type": "file", + "description": "If option --write-ec specified, a gzipped fasta file containing the error corrected\nreads produced by the hifiasm error correction module\n", + "pattern": "*.ec.fa.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "read_overlaps": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.ovlp.paf.gz": { + "type": "file", + "description": "If option --write-paf specified, a gzipped paf file describing the overlaps\namong all error-corrected reads\n", + "pattern": "*.ovlp.paf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.stderr.log": { + "type": "file", + "description": "Stderr log", + "pattern": "*.stderr.log", + "ontologies": [] + } + } + ] + ], + "versions_hifiasm": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "hifiasm": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "hifiasm --version 2>&1": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "hifiasm": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "hifiasm --version 2>&1": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@sidorov-si", "@scorreard", "@mbeavitt", "@schmytzi", "@prototaxites"], + "maintainers": ["@sidorov-si", "@scorreard"] }, - { - "intervals": { - "type": "file", - "description": "Interval file", - "ontologies": [] - } - } - ] - ], - "output": { - "interval_list": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_split/*/*.interval_list": { - "type": "file", - "description": "Interval list files", - "pattern": "*.interval_list", - "ontologies": [] - } - } - ] - ], - "versions_gatk4": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gatk4": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gatk4": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "genomeassembler", + "version": "1.1.0" + } ] - ] - }, - "authors": [ - "@praveenraj2018" - ], - "maintainers": [ - "@praveenraj2018" - ] - }, - "pipelines": [ - { - "name": "createpanelrefs", - "version": "dev" }, { - "name": "raredisease", - "version": "3.0.0" + "name": "hificnv", + "path": "modules/nf-core/hificnv/meta.yml", + "type": "module", + "meta": { + "name": "hificnv", + "description": "Copy number variant calling from PacBio HiFi reads", + "keywords": ["copy number variation", "cnv", "PacBio", "HiFi", "long reads", "structural variation"], + "tools": [ + { + "hificnv": { + "description": "Copy number variant caller designed for PacBio HiFi reads", + "homepage": "https://github.com/PacificBiosciences/HiFiCNV", + "documentation": "https://github.com/PacificBiosciences/HiFiCNV", + "tool_dev_url": "https://github.com/PacificBiosciences/HiFiCNV", + "doi": "10.1093/bioinformatics/btac808", + "licence": ["Pacific Biosciences Software License Agreement"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "bam": { + "type": "file", + "description": "Sorted BAM or CRAM file from PacBio HiFi reads", + "pattern": "*.{bam,cram}", + "ontologies": [] + } + }, + { + "bai": { + "type": "file", + "description": "BAM index file (CSI, CRAI, or BAI format)", + "pattern": "*.{bai,csi,crai}", + "ontologies": [] + } + }, + { + "maf": { + "type": "file", + "description": "Minor allele frequency file (VCF format)", + "pattern": "*.{vcf,vcf.gz}", + "optional": true, + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference genome information\ne.g. `[ id:'GATK.GRCh38' ]`\n" + } + }, + { + "ref": { + "type": "file", + "description": "Reference genome FASTA file", + "pattern": "*.{fa,fasta,fa.gz,fasta.gz}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing exclude regions information\ne.g. `[ id:'excluded_regions' ]`\n" + } + }, + { + "exclude": { + "type": "file", + "description": "BED file containing regions to exclude from CNV calling", + "pattern": "*.{bed,bed.gz}", + "optional": true, + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing expected copy number information\ne.g. `[ id:'male_expected_cn' ]`\n" + } + }, + { + "expected_cn": { + "type": "file", + "description": "BED file containing expected copy number regions", + "pattern": "*.{bed,bed.gz}", + "optional": true, + "ontologies": [] + } + } + ] + ], + "output": { + "copynum": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.copynum.bedgraph": { + "type": "file", + "description": "Copy number bedGraph file", + "pattern": "*.copynum.bedgraph", + "ontologies": [] + } + } + ] + ], + "depth": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.depth.bw": { + "type": "file", + "description": "Depth coverage bigWig file", + "pattern": "*.depth.bw", + "ontologies": [] + } + } + ] + ], + "maf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.maf.bw": { + "type": "file", + "description": "Minor allele frequency bigWig file", + "pattern": "*.maf.bw", + "optional": true, + "ontologies": [] + } + } + ] + ], + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "Copy number variants in VCF format", + "pattern": "*.{vcf.gz}", + "ontologies": [] + } + } + ] + ], + "versions_hificnv": [ + [ + { + "${task.process}": { + "type": "string", + "description": "Name of the process" + } + }, + { + "hificnv": { + "type": "string", + "description": "Name of the tool" + } + }, + { + "hificnv --version | sed 's/.* //g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "Name of the process" + } + }, + { + "hificnv": { + "type": "string", + "description": "Name of the tool" + } + }, + { + "hificnv --version | sed 's/.* //g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@chaochaowong"], + "maintainers": ["@chaochaowong"] + } }, { - "name": "rnavar", - "version": "1.2.3" - } - ] - }, - { - "name": "gatk4_learnreadorientationmodel", - "path": "modules/nf-core/gatk4/learnreadorientationmodel/meta.yml", - "type": "module", - "meta": { - "name": "gatk4_learnreadorientationmodel", - "description": "Uses f1r2 counts collected during mutect2 to Learn the prior probability of read orientation artifacts\n", - "keywords": [ - "gatk4", - "learnreadorientationmodel", - "mutect2", - "readorientationartifacts" - ], - "tools": [ - { - "gatk4": { - "description": "Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools\nwith a primary focus on variant discovery and genotyping. Its powerful processing engine\nand high-performance computing features make it capable of taking on projects of any size.\n", - "homepage": "https://gatk.broadinstitute.org/hc/en-us", - "documentation": "https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s", - "doi": "10.1158/1538-7445.AM2017-3590", - "licence": [ - "Apache-2.0" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "f1r2": { - "type": "list", - "description": "list of f1r2 files to be used as input.", - "pattern": "*.f1r2.tar.gz" - } + "name": "hifitrimmer_filterbam", + "path": "modules/nf-core/hifitrimmer/filterbam/meta.yml", + "type": "module", + "meta": { + "name": "hifitrimmer_filterbam", + "description": "Run hifi_trimmer filter_bam to filter and trim adapter hits from PacBio HiFi reads (BAM/FASTA/FASTQ) using BLAST against\nadapter sequences. Primary output is filtered FASTA/FASTQ.\n", + "keywords": [ + "pacbio", + "bam", + "fasta", + "hifi_trimmer", + "filtering", + "trimming", + "quality control", + "adapter removal" + ], + "tools": [ + { + "hifi_trimmer": { + "description": "hifi_trimmer: tools for processing HiFi read BLAST results and filtering/trimming\nread files to output processed FASTA/FASTQ and accompanying summary and hit (optional) files.\n", + "homepage": "https://github.com/sanger-tol/hifi-trimmer", + "documentation": "https://github.com/sanger-tol/hifi-trimmer", + "licence": ["MIT"] + } + }, + { + "samtools": { + "description": "SAMtools is a set of utilities for interacting with and post-processing\nshort DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.\nThese files are generated as output by short read aligners like BWA.\n", + "homepage": "http://www.htslib.org/", + "documentation": "http://www.htslib.org/doc/samtools.html", + "doi": "10.1093/bioinformatics/btp352", + "licence": ["MIT"], + "identifier": "biotools:samtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "input": { + "type": "file", + "description": "Input BAM/FASTA/FASTQ file to filter", + "pattern": "*.{bam,fa,fasta,fa.gz,fasta.gz,fastq,fq,fastq.gz,fq.gz}" + } + }, + { + "bed": { + "type": "file", + "description": "Input gzipped bed file contains regions to filter/trim", + "pattern": "*.bed.gz" + } + } + ] + ], + "output": { + "filtered": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.fast{q,a}.gz": { + "type": "file", + "description": "Gzipped FASTA/FASTQ produced by hifi_trimmer", + "pattern": "*.fast{q,a}.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + }, + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ] + ], + "versions_hifitrimmer": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "hifi_trimmer": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "hifi_trimmer --version | cut -d' ' -f3": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_samtools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "Name of the process" + } + }, + { + "samtools": { + "type": "string", + "description": "Name of the tool" + } + }, + { + "samtools --version | head -1 | sed -e \"s/samtools //\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "hifi_trimmer": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "hifi_trimmer --version | cut -d' ' -f3": { + "type": "eval", + "description": "The expression to obtain the version" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "Name of the process" + } + }, + { + "samtools": { + "type": "string", + "description": "Name of the tool" + } + }, + { + "samtools --version | head -1 | sed -e \"s/samtools //\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@sainsachiko"], + "maintainers": ["@sainsachiko"] } - ] - ], - "output": { - "artifactprior": [ - [ - { - "meta": { - "type": "file", - "description": "file containing artifact-priors to be used by filtermutectcalls", - "pattern": "*.tar.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - }, - { - "*.tar.gz": { - "type": "file", - "description": "file containing artifact-priors to be used by filtermutectcalls", - "pattern": "*.tar.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "versions_gatk4": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gatk4": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gatk4": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] }, - "authors": [ - "@GCJMackenzie" - ], - "maintainers": [ - "@GCJMackenzie" - ] - }, - "pipelines": [ { - "name": "rnadnavar", - "version": "dev" + "name": "hifitrimmer_processblast", + "path": "modules/nf-core/hifitrimmer/processblast/meta.yml", + "type": "module", + "meta": { + "name": "hifitrimmer_processblast", + "description": "Run hifi_trimmer process_blast to process a BLAST search of adapter sequences against PacBio HiFi reads.\nPrimary output is a BED describing regions to exclude, a json of summary information, and an optional hits file.\n", + "keywords": ["pacbio", "bam", "hifi_trimmer", "processblast", "quality control", "adapter removal"], + "tools": [ + { + "hifi_trimmer": { + "description": "hifi_trimmer: tools for processing HiFi read BLAST results and filtering/trimming\nBAM files to output processed FASTA/FASTQ and accompanying summary and hit (optional) files.\n", + "homepage": "https://github.com/sanger-tol/hifi-trimmer", + "documentation": "https://github.com/sanger-tol/hifi-trimmer", + "licence": ["MIT"] + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "blast": { + "type": "file", + "description": "BLAST TSV output file used by hifi_trimmer (e.g. .blast, .out). Must be generated using \"blastn -query -db -outfmt '6 std qlen'\".", + "pattern": "*.blast" + } + } + ], + [ + { + "meta1": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "yaml": { + "type": "file", + "description": "YAML file contain trimming/filtering configuration for `hifi_trimmer`", + "pattern": "*.{yaml,yml}" + } + } + ] + ], + "output": { + "bed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.bed.gz": { + "type": "file", + "description": "Gzipped BED file of selected reads", + "pattern": "*.bed.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3003" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "summary": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.summary.json": { + "type": "file", + "description": "JSON summary including trimming and filtering information", + "pattern": "*.summary.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "hits": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.hits": { + "type": "file", + "description": "Optional hits file produced by hifi_trimmer (may be absent when no hits found or '-hf' is not specified)", + "pattern": "*.hits", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_hifitrimmer": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "hifi_trimmer": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "hifi_trimmer --version | cut -d' ' -f3": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "hifi_trimmer": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "hifi_trimmer --version | cut -d' ' -f3": { + "type": "eval", + "description": "The expression to obtain the version" + } + } + ] + ] + }, + "authors": ["@sainsachiko"], + "maintainers": ["@sainsachiko"] + } }, { - "name": "sarek", - "version": "3.8.1" - } - ] - }, - { - "name": "gatk4_leftalignandtrimvariants", - "path": "modules/nf-core/gatk4/leftalignandtrimvariants/meta.yml", - "type": "module", - "meta": { - "name": "gatk4_leftalignandtrimvariants", - "description": "Left align and trim variants using GATK4 LeftAlignAndTrimVariants.", - "keywords": [ - "gatk4", - "leftalignandtrimvariants", - "norm", - "normalize", - "vcf" - ], - "tools": [ - { - "gatk4": { - "description": "Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools\nwith a primary focus on variant discovery and genotyping. Its powerful processing engine\nand high-performance computing features make it capable of taking on projects of any size.\n", - "homepage": "https://gatk.broadinstitute.org/hc/en-us", - "documentation": "https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s", - "doi": "10.1158/1538-7445.AM2017-3590", - "licence": [ - "Apache-2.0" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "The vcf file to be normalized\ne.g. 'file1.vcf.gz'\n", - "ontologies": [] - } - }, - { - "tbi": { - "type": "file", - "description": "Index of the vcf file to be normalized\ne.g. 'file1.vcf.gz.tbi'\n", - "ontologies": [] - } + "name": "hiphase", + "path": "modules/nf-core/hiphase/meta.yml", + "type": "module", + "meta": { + "name": "hiphase", + "description": "Small and structural variant phasing tool for PacBio HiFi reads, supporting co-phasing of SNVs and SVs across multiple BAM files and samples", + "keywords": ["pacbio", "structural variant", "phasing", "pacbio hifi", "snv", "haplotagging"], + "tools": [ + { + "hiphase": { + "description": "Small and structural variant phasing tool for PacBio HiFi reads", + "homepage": "https://github.com/PacificBiosciences/HiPhase", + "documentation": "https://github.com/PacificBiosciences/HiPhase", + "tool_dev_url": "https://github.com/PacificBiosciences/HiPhase", + "licence": ["Pacific Biosciences Software License Agreement"], + "identifier": "biotools:hiphase" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "bams": { + "type": "file", + "description": "One or more sorted BAM/CRAM files", + "pattern": "*.{bam,cram}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + }, + { + "bais": { + "type": "file", + "description": "Index files associated with the BAM/CRAM files", + "pattern": "*.{bai,crai,csi}", + "ontologies": [] + } + }, + { + "snv": { + "type": "file", + "description": "Compressed VCF file containing SNV/small variants to phase (optional)", + "pattern": "*.{vcf.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + } + ] + } + }, + { + "snv_index": { + "type": "file", + "description": "Index file for the SNV VCF (optional)", + "pattern": "*.{tbi,csi}", + "ontologies": [] + } + }, + { + "sv": { + "type": "file", + "description": "Compressed VCF file containing structural variants to co-phase (optional)", + "pattern": "*.{vcf.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + } + ] + } + }, + { + "sv_index": { + "type": "file", + "description": "Index file for the SV VCF (optional)", + "pattern": "*.{tbi,csi}", + "ontologies": [] + } + }, + { + "samples": { + "type": "list", + "description": "List of sample names to phase within the VCF, if empty only the first sample is phased." + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference genome information\ne.g. `[ id:'GRCh38' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference genome FASTA file used for the BAM alignment", + "pattern": "*.{fasta,fa}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + }, + { + "fai": { + "type": "file", + "description": "FASTA index file (.fai) for the reference genome", + "pattern": "*.fai", + "ontologies": [] + } + } + ], + { + "output_bam": { + "type": "boolean", + "description": "Whether to output haplotagged BAM files. Set to true to emit phased BAM files with haplotag information." + } + }, + { + "summary_file": { + "type": "boolean", + "description": "Whether to output a phasing summary file." + } + }, + { + "blocks_file": { + "type": "boolean", + "description": "Whether to output a phasing blocks file." + } + }, + { + "stats_file": { + "type": "boolean", + "description": "Whether to output a per-read phasing statistics file." + } + }, + { + "haplotag_file": { + "type": "boolean", + "description": "Whether to output a haplotag assignments file." + } + }, + { + "file_format": { + "type": "string", + "description": "Output file format for summary/blocks/stats/haplotag files, either 'tsv' or 'csv'." + } + } + ], + "output": { + "vcfs": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_snv_phased.vcf.gz": { + "type": "file", + "description": "Phased and compressed SNV VCF file (optional, only emitted when SNV VCF input is provided)", + "pattern": "*_snv_phased.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "sv_vcfs": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_sv_phased.vcf.gz": { + "type": "file", + "description": "Phased and compressed SV VCF file (optional, only emitted when SV VCF input is provided)", + "pattern": "*_sv_phased.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "vcfs_indexes": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_snv_phased.vcf.gz.{tbi,csi}": { + "type": "file", + "description": "Index file for the phased SNV VCF (optional)", + "pattern": "*_snv_phased.vcf.gz.{tbi,csi}", + "ontologies": [] + } + } + ] + ], + "sv_vcfs_indexes": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_sv_phased.vcf.gz.{tbi,csi}": { + "type": "file", + "description": "Index file for the phased SV VCF (optional)", + "pattern": "*_sv_phased.vcf.gz.{tbi,csi}", + "ontologies": [] + } + } + ] + ], + "summary_tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.summary.tsv": { + "type": "file", + "description": "TSV file containing phasing summary statistics (optional)", + "pattern": "*.summary.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "summary_csv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.summary.csv": { + "type": "file", + "description": "CSV file containing phasing summary statistics (optional)", + "pattern": "*.summary.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "blocks_tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.blocks.tsv": { + "type": "file", + "description": "TSV file containing phasing block information (optional)", + "pattern": "*.blocks.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "blocks_csv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.blocks.csv": { + "type": "file", + "description": "CSV file containing phasing block information (optional)", + "pattern": "*.blocks.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "stats_tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.stats.tsv": { + "type": "file", + "description": "TSV file containing per-read phasing statistics (optional)", + "pattern": "*.stats.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "stats_csv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.stats.csv": { + "type": "file", + "description": "CSV file containing per-read phasing statistics (optional)", + "pattern": "*.stats.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "haplotag_tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.haplotag.tsv": { + "type": "file", + "description": "TSV file containing haplotag assignments per read (optional)", + "pattern": "*.haplotag.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "haplotag_csv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.haplotag.csv": { + "type": "file", + "description": "CSV file containing haplotag assignments per read (optional)", + "pattern": "*.haplotag.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "bams": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Haplotagged BAM file(s) with haplotype information in the HP tag (optional, only emitted when output_bam is true)", + "pattern": "*.bam", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + } + ] + ], + "bams_indexes": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.bam.{bai,csi}": { + "type": "file", + "description": "Index file(s) for the haplotagged BAM file(s) (optional, only emitted when output_bam is true)", + "pattern": "*.bam.{bai,csi}", + "ontologies": [] + } + } + ] + ], + "versions_hiphase": [ + [ + { + "${task.process}": { + "type": "string", + "description": "Name of the process" + } + }, + { + "hiphase": { + "type": "string", + "description": "Name of the tool" + } + }, + { + "hiphase --version | sed 's/.* //g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "Name of the process" + } + }, + { + "hiphase": { + "type": "string", + "description": "Name of the tool" + } + }, + { + "hiphase --version | sed 's/.* //g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@tanyasarkjain", "@fellen31"], + "maintainers": ["@fellen31"] }, - { - "intervals": { - "type": "file", - "description": "Bed file with the genomic regions included in the library (optional)", - "ontologies": [] - } - } - ], - { - "fasta": { - "type": "file", - "description": "The reference fasta file", - "pattern": "*.fasta", - "ontologies": [] - } - }, - { - "fai": { - "type": "file", - "description": "Index of reference fasta file", - "pattern": "*.fasta.fai", - "ontologies": [] - } - }, - { - "dict": { - "type": "file", - "description": "GATK sequence dictionary", - "pattern": "*.dict", - "ontologies": [] - } - } - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.vcf.gz": { - "type": "file", - "description": "VCF normalized output file", - "pattern": "*.{vcf.gz}", - "ontologies": [] - } - } - ] - ], - "tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tbi": { - "type": "file", - "description": "Tbi index for VCF file", - "pattern": "*.tbi", - "ontologies": [] - } - } - ] - ], - "versions_gatk4": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gatk4": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gatk4": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "pacsomatic", + "version": "dev" + }, + { + "name": "pacvar", + "version": "1.0.1" + } ] - ] - }, - "authors": [ - "@adamrtalbot" - ], - "maintainers": [ - "@adamrtalbot" - ] - }, - "pipelines": [ - { - "name": "variantcatalogue", - "version": "dev" - } - ] - }, - { - "name": "gatk4_markduplicates", - "path": "modules/nf-core/gatk4/markduplicates/meta.yml", - "type": "module", - "meta": { - "name": "gatk4_markduplicates", - "description": "This tool locates and tags duplicate reads in a BAM or SAM file, where duplicate reads are defined as originating from a single fragment of DNA.", - "keywords": [ - "bam", - "gatk4", - "markduplicates", - "sort" - ], - "tools": [ - { - "gatk4": { - "description": "Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.", - "homepage": "https://gatk.broadinstitute.org/hc/en-us", - "documentation": "https://gatk.broadinstitute.org/hc/en-us/articles/360037052812-MarkDuplicates-Picard-", - "tool_dev_url": "https://github.com/broadinstitute/gatk", - "doi": "10.1158/1538-7445.AM2017-3590", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM file", - "pattern": "*.{bam}", - "ontologies": [] - } - } - ], - { - "fasta": { - "type": "file", - "description": "Fasta file", - "pattern": "*.{fasta}", - "ontologies": [] - } - }, - { - "fasta_fai": { - "type": "file", - "description": "Fasta index file", - "pattern": "*.{fai}", - "ontologies": [] - } - } - ], - "output": { - "cram": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*cram": { - "type": "file", - "description": "Marked duplicates CRAM file", - "pattern": "*.{cram}", - "ontologies": [] - } - } - ] - ], - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*bam": { - "type": "file", - "description": "Marked duplicates BAM file", - "pattern": "*.{bam}", - "ontologies": [] - } - } - ] - ], - "crai": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.crai": { - "type": "file", - "description": "CRAM index file", - "pattern": "*.{cram.crai}", - "ontologies": [] - } - } - ] - ], - "bai": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bai": { - "type": "file", - "description": "BAM index file", - "pattern": "*.{bam.bai}", - "ontologies": [] - } - } - ] - ], - "metrics": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.metrics": { - "type": "file", - "description": "Duplicate metrics file generated by GATK", - "pattern": "*.{metrics.txt}", - "ontologies": [] - } - } - ] - ], - "versions_gatk4": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gatk4": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_samtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gatk4": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] }, - "authors": [ - "@ajodeh-juma", - "@FriederikeHanssen", - "@maxulysse" - ], - "maintainers": [ - 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If none is specified, an index will be built.", + "pattern": "*.txt", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + }, + { + "index": { + "type": "file", + "description": "Index file from another run.", + "ontologies": [] + } + } + ], + "output": { + "hmm": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.hmm": { + "type": "file", + "description": "File with one or more HMM models", + "pattern": "selection.hmm", + "ontologies": [] + } + } + ] + ], + "index": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.ssi": { + "type": "file", + "description": "Index for HMM database. 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Its powerful processing engine\nand high-performance computing features make it capable of taking on projects of any size.\n", - "homepage": "https://gatk.broadinstitute.org/hc/en-us", - "documentation": "https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s", - "doi": "10.1158/1538-7445.AM2017-3590", - "licence": [ - "Apache-2.0" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "input": { - "type": "list", - "description": "list of BAM files, also able to take CRAM as an input", - "pattern": "*.{bam/cram}" - } - }, - { - "input_index": { - "type": "list", - "description": "list of BAM file indexes, also able to take CRAM indexes as an input", - "pattern": "*.{bam.bai/cram.crai}" - } - }, - { - "intervals": { - "type": "file", - "description": "Specify region the tools is run on.", - "pattern": ".{bed,interval_list}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference fasta file", - "pattern": "*.{fasta,fasta.gz}", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fai": { - "type": "file", - "description": "Index of reference fasta file", - "pattern": "*.{fasta.fai,fasta.fai.gz}", - "ontologies": [] - } - }, - { - "gzi": { - "type": "file", - "description": "Index of bgzipped reference fasta file", - "pattern": "*.fasta.gz.gzi", - "ontologies": [] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } + }, + { + "name": "hmmer_hmmsearch", + "path": "modules/nf-core/hmmer/hmmsearch/meta.yml", + "type": "module", + "meta": { + "name": "hmmer_hmmsearch", + "description": "search profile(s) against a sequence database", + "keywords": ["Hidden Markov Model", "HMM", "hmmer", "hmmsearch"], + "tools": [ + { + "hmmer": { + "description": "Biosequence analysis using profile hidden Markov models", + "homepage": "http://hmmer.org/", + "documentation": "http://hmmer.org/documentation.html", + "tool_dev_url": "https://github.com/EddyRivasLab/hmmer", + "doi": "10.1371/journal.pcbi.1002195", + "licence": ["BSD"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "hmmfile": { + "type": "file", + "description": "One or more HMM profiles created with hmmbuild", + "pattern": "*.{hmm,hmm.gz}", + "ontologies": [] + } + }, + { + "seqdb": { + "type": "file", + "description": "Database of sequences in FASTA format", + "pattern": "*.{fasta,fna,faa,fa,fasta.gz,fna.gz,faa.gz,fa.gz}", + "ontologies": [] + } + }, + { + "write_align": { + "type": "boolean", + "description": "Flag to save optional alignment output. Specify with 'true' to save." + } + }, + { + "write_target": { + "type": "boolean", + "description": "Flag to save optional per target summary. Specify with 'true' to save." + } + }, + { + "write_domain": { + "type": "boolean", + "description": "Flag to save optional per domain summary. Specify with 'true' to save." + } + } + ] + ], + "output": { + "output": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt.gz": { + "type": "file", + "description": "Human readable output summarizing hmmsearch results", + "pattern": "*.{txt.gz}", + "ontologies": [] + } + } + ] + ], + "alignments": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.sto.gz": { + "type": "file", + "description": "Optional multiple sequence alignment (MSA) in Stockholm format", + "pattern": "*.{sto.gz}", + "ontologies": [] + } + } + ] + ], + "target_summary": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tbl.gz": { + "type": "file", + "description": "Optional tabular (space-delimited) summary of per-target output", + "pattern": "*.{tbl.gz}", + "ontologies": [] + } + } + ] + ], + "domain_summary": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.domtbl.gz": { + "type": "file", + "description": "Optional tabular (space-delimited) summary of per-domain output", + "pattern": "*.{domtbl.gz}", + "ontologies": [] + } + } + ] + ], + "versions_hmmer": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "hmmer": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "hmmsearch -h | sed '2!d;s/^# HMMER *//;s/ .*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "hmmer": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "hmmsearch -h | sed '2!d;s/^# HMMER *//;s/ .*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@Midnighter"], + "maintainers": ["@Midnighter"] }, - { - "dict": { - "type": "file", - "description": "GATK sequence dictionary", - "pattern": "*.dict", - "ontologies": [] - } - } - ], - { - "alleles": { - "type": "file", - "description": "vcf file to be used to force-call alleles.", - "pattern": "*.vcf.gz", - "ontologies": [ + "pipelines": [ { - "edam": "http://edamontology.org/format_3989" - } - ] - } - }, - { - "alleles_tbi": { - "type": "file", - "description": "Index file for alleles to be force-called.", - "pattern": "*.vcf.gz.tbi", - "ontologies": [] - } - }, - { - "germline_resource": { - "type": "file", - "description": "Population vcf of germline sequencing, containing allele fractions.", - "pattern": "*.vcf.gz", - "ontologies": [ + "name": "ampliseq", + "version": "2.17.0" + }, { - "edam": "http://edamontology.org/format_3989" - } - ] - } - }, - { - "germline_resource_tbi": { - "type": "file", - "description": "Index file for the germline resource.", - "pattern": "*.vcf.gz.tbi", - "ontologies": [] - } - }, - { - "panel_of_normals": { - "type": "file", - "description": "vcf file to be used as a panel of normals.", - "pattern": "*.vcf.gz", - "ontologies": [ + "name": "funcscan", + "version": "3.0.0" + }, { - "edam": "http://edamontology.org/format_3989" + "name": "metatdenovo", + "version": "1.3.0" + }, + { + "name": "phyloplace", + "version": "2.0.0" + }, + { + "name": "proteinannotator", + "version": "1.1.0" + }, + { + "name": "proteinfamilies", + "version": "2.3.0" } - ] - } - }, - { - "panel_of_normals_tbi": { - "type": "file", - "description": "Index for the panel of normals.", - "pattern": "*.vcf.gz.tbi", - "ontologies": [] - } - } - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "A Groovy map containing sample information" - } - }, - { - "${prefix}.vcf.gz": { - "type": "file", - "description": "compressed vcf file", - "pattern": "${prefix}.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } ] - ], - "tbi": [ - [ - { - "meta": { - "type": "map", - "description": "A Groovy map containing sample information" - } - }, - { - "${prefix}.vcf.gz.tbi": { - "type": "file", - "description": "Index of vcf file", - "pattern": "${prefix}.vcf.gz.tbi", - "ontologies": [] - } - } - ] - ], - "stats": [ - [ - { - "meta": { - "type": "map", - "description": "A Groovy map containing sample information" - } - }, - { - "${prefix}.vcf.gz.stats": { - "type": "file", - "description": "Stats file that pairs with output vcf file", - "pattern": "${prefix}.vcf.gz.stats", - "ontologies": [] - } - } - ] - ], - "f1r2": [ - [ - { - "meta": { - "type": "map", - "description": "A Groovy map containing sample information" - } - }, - { - "${prefix}.f1r2.tar.gz": { - "type": "file", - "description": "file containing information to be passed to LearnReadOrientationModel (only outputted when tumor_normal_pair mode is run)", - "pattern": "${prefix}.f1r2.tar.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "versions_gatk4": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gatk4": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gatk4": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@GCJMackenzie", - "@ramprasadn" - ], - "maintainers": [ - "@GCJMackenzie", - "@ramprasadn" - ] - }, - "pipelines": [ - { - "name": "createpanelrefs", - "version": "dev" }, { - "name": "raredisease", - "version": "3.0.0" + "name": "hmmer_jackhmmer", + "path": "modules/nf-core/hmmer/jackhmmer/meta.yml", + "type": "module", + "meta": { + "name": "hmmer_jackhmmer", + "description": "iterative searches to detect distant homologs by refining an HMM profile from hits", + "keywords": ["HMM", "homologs", "iterative model refinement"], + "tools": [ + { + "hmmer": { + "description": "Biosequence analysis using profile hidden Markov models", + "homepage": "http://hmmer.org/", + "documentation": "http://hmmer.org/documentation.html", + "tool_dev_url": "https://github.com/EddyRivasLab/hmmer", + "doi": "10.1371/journal.pcbi.1002195", + "licence": ["BSD"], + "identifier": "biotools:hmmer3" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "One or multiple amino acid sequences from which to start building a model iteratively (one model per input sequence)", + "pattern": "*.{fasta,fna,faa,fa,fasta.gz,fna.gz,faa.gz,fa.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + }, + { + "seqdb": { + "type": "file", + "description": "Database of sequences in FASTA format", + "pattern": "*.{fasta,fna,faa,fa,fasta.gz,fna.gz,faa.gz,fa.gz}", + "ontologies": [] + } + }, + { + "write_align": { + "type": "boolean", + "description": "Flag to save optional alignment output. Specify with 'true' to save." + } + }, + { + "write_target": { + "type": "boolean", + "description": "Flag to save optional per target summary. Specify with 'true' to save." + } + }, + { + "write_domain": { + "type": "boolean", + "description": "Flag to save optional per domain summary. Specify with 'true' to save." + } + } + ] + ], + "output": { + "output": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt.gz": { + "type": "file", + "description": "Human readable output summarizing hmmsearch results", + "pattern": "*.{txt.gz}", + "ontologies": [] + } + } + ] + ], + "alignments": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.sto.gz": { + "type": "file", + "description": "Optional multiple sequence alignment (MSA) in Stockholm format", + "pattern": "*.{sto.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "target_summary": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tbl.gz": { + "type": "file", + "description": "Optional tabular (space-delimited) summary of per-target output", + "pattern": "*.{tbl.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "domain_summary": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.domtbl.gz": { + "type": "file", + "description": "Optional tabular (space-delimited) summary of per-domain output", + "pattern": "*.{domtbl.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "versions_hmmer": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "hmmer": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "jackhmmer -h | sed '2!d;s/^# HMMER *//;s/ .*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "hmmer": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "jackhmmer -h | sed '2!d;s/^# HMMER *//;s/ .*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@vagkaratzas"], + "maintainers": ["@vagkaratzas"] + } }, { - "name": "rnadnavar", - "version": "dev" + "name": "hmtnote_annotate", + "path": "modules/nf-core/hmtnote/annotate/meta.yml", + "type": "module", + "meta": { + "name": "hmtnote_annotate", + "description": "Human mitochondrial variants annotation using HmtVar. Contains .plk file with annotation, so can be run offline", + "deprecated": true, + "keywords": ["hmtnote", "mitochondria", "annotation"], + "tools": [ + { + "hmtnote": { + "description": "Human mitochondrial variants annotation using HmtVar.", + "homepage": "https://github.com/robertopreste/HmtNote", + "documentation": "https://hmtnote.readthedocs.io/en/latest/usage.html", + "doi": "10.1101/600619", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\n" + } + }, + { + "vcf": { + "type": "file", + "description": "vcf file", + "pattern": "*.vcf", + "ontologies": [] + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\n" + } + }, + { + "*_annotated.vcf": { + "type": "file", + "description": "annotated vcf", + "pattern": "*_annotated.vcf", + "ontologies": [] + } + } + ] + ], + "versions_hmtnote": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "hmtnote": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "hmtnote --version 2>&1 | sed 's/.*version //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "hmtnote": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "hmtnote --version 2>&1 | sed 's/.*version //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@sysbiocoder"], + "maintainers": ["@sysbiocoder"] + } }, { - "name": "sarek", - "version": "3.8.1" + "name": "homer_annotatepeaks", + "path": "modules/nf-core/homer/annotatepeaks/meta.yml", + "type": "module", + "meta": { + "name": "homer_annotatepeaks", + "description": "Annotate peaks with HOMER suite", + "keywords": ["annotations", "peaks", "bed"], + "tools": [ + { + "homer": { + "description": "HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.\n", + "documentation": "http://homer.ucsd.edu/homer/", + "doi": "10.1016/j.molcel.2010.05.004.", + "licence": ["GPL-3.0-or-later"], + "identifier": "biotools:homer" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "peak": { + "type": "file", + "description": "Peak file to annotate", + "ontologies": [] + } + } + ], + { + "fasta": { + "type": "file", + "description": "Fasta file of reference genome", + "pattern": "*.fasta", + "ontologies": [] + } + }, + { + "gtf": { + "type": "file", + "description": "GTF file of reference genome", + "pattern": "*.gtf", + "ontologies": [] + } + } + ], + "output": { + "txt": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*annotatePeaks.txt": { + "type": "file", + "description": "Annotated peaks in txt file", + "pattern": "*annotatePeaks.txt", + "ontologies": [] + } + } + ] + ], + "stats": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*annStats.txt": { + "type": "file", + "description": "Annotation statistics in txt file", + "pattern": "*annStats.txt", + "ontologies": [] + } + } + ] + ], + "versions_homer": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "homer": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "4.11": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "homer": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "4.11": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@drpatelh", "@kevinmenden"], + "maintainers": ["@drpatelh", "@kevinmenden"] + }, + "pipelines": [ + { + "name": "atacseq", + "version": "2.1.2" + }, + { + "name": "chipseq", + "version": "2.1.0" + } + ] }, { - "name": "variantcatalogue", - "version": "dev" - } - ] - }, - { - "name": "gatk4_postprocessgermlinecnvcalls", - "path": "modules/nf-core/gatk4/postprocessgermlinecnvcalls/meta.yml", - "type": "module", - "meta": { - "name": "gatk4_postprocessgermlinecnvcalls", - "description": "Postprocesses the output of GermlineCNVCaller and generates VCFs and denoised copy ratios", - "keywords": [ - "copy number", - "gatk4", - "postprocessgermlinecnvcalls" - ], - "tools": [ - { - "gatk4": { - "description": "Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools\nwith a primary focus on variant discovery and genotyping. Its powerful processing engine\nand high-performance computing features make it capable of taking on projects of any size.\n", - "homepage": "https://gatk.broadinstitute.org/hc/en-us", - "documentation": "https://gatk.broadinstitute.org/hc/en-us/articles/360037593411-PostprocessGermlineCNVCalls", - "doi": "10.1158/1538-7445.AM2017-3590", - "licence": [ - "Apache-2.0" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "calls": { - "type": "directory", - "description": "A folder containing the calls from the input files", - "pattern": "*-cnv-calls/*-calls" - } - }, - { - "model": { - "type": "directory", - "description": "A folder containing the model from the input files.\nThis will only be created in COHORT mode (when no model is supplied to the process).\n", - "pattern": "*-cnv-model/*-model" - } + "name": "homer_findpeaks", + "path": "modules/nf-core/homer/findpeaks/meta.yml", + "type": "module", + "meta": { + "name": "homer_findpeaks", + "description": "Find peaks with HOMER suite", + "keywords": ["annotation", "peaks", "enrichment"], + "tools": [ + { + "homer": { + "description": "HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.\n", + "homepage": "http://homer.ucsd.edu/homer/index.html", + "documentation": "http://homer.ucsd.edu/homer/", + "tool_dev_url": "http://homer.ucsd.edu/homer/ngs/peaks.html", + "doi": "10.1016/j.molcel.2010.05.004.", + "licence": ["GPL-3.0-or-later"], + "identifier": "biotools:homer" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "tagDir": { + "type": "directory", + "description": "The 'Tag Directory'", + "pattern": "tagDir" + } + } + ], + { + "uniqmap": { + "type": "directory", + "description": "(directory of binary files specifying uniquely mappable locations) Download from http://biowhat.ucsd.edu/homer/groseq/", + "pattern": "uniqmap/" + } + } + ], + "output": { + "txt": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.peaks.txt": { + "type": "file", + "description": "Peaks in txt file", + "pattern": "*.peaks.txt", + "ontologies": [] + } + } + ] + ], + "versions_homer": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "homer": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "4.11": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "homer": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "4.11": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@edmundmiller"], + "maintainers": ["@edmundmiller"] }, - { - "ploidy": { - "type": "directory", - "description": "Optional - A folder containing the ploidy model.\nWhen a model is supplied to tool will run in CASE mode.\n", - "pattern": "*-calls/" - } - } - ] - ], - "output": { - "intervals": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_genotyped_intervals.vcf.gz": { - "type": "file", - "description": "Intervals VCF file", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "segments": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_genotyped_segments.vcf.gz": { - "type": "file", - "description": "Segments VCF file", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "denoised": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_denoised.vcf.gz": { - "type": "file", - "description": "Denoised copy ratio file", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "versions_gatk4": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gatk4": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gatk4": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "nascent", + "version": "2.3.0" + } ] - ] - }, - "authors": [ - "@ryanjameskennedy" - ], - "maintainers": [ - "@ryanjameskennedy" - ] - }, - "pipelines": [ - { - "name": "raredisease", - "version": "3.0.0" - } - ] - }, - { - "name": "gatk4_preprocessintervals", - "path": "modules/nf-core/gatk4/preprocessintervals/meta.yml", - "type": "module", - "meta": { - "name": "gatk4_preprocessintervals", - "description": "Prepares bins for coverage collection.", - "keywords": [ - "bed", - "gatk4", - "interval", - "preprocessintervals" - ], - "tools": [ - { - "gatk4": { - "description": "Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.", - "homepage": "https://gatk.broadinstitute.org/hc/en-us", - "documentation": "https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s", - "doi": "10.1158/1538-7445.AM2017-3590", - "licence": [ - "Apache-2.0" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference fasta file", - "pattern": "*.fasta", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "fai": { - "type": "file", - "description": "Index of reference fasta file", - "pattern": "*.fasta.fai", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "dict": { - "type": "file", - "description": "GATK sequence dictionary", - "pattern": "*.dict", - "ontologies": [] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "intervals": { - "type": "file", - "description": "Interval file (bed or interval_list) with the genomic regions to be included from the analysis (optional)", - "pattern": "*.{bed,interval_list}", - "ontologies": [] - } - } - ], - [ - { - "meta5": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "exclude_intervals": { - "type": "file", - "description": "Interval file (bed or interval_list) with the genomic regions to be excluded from the analysis (optional)", - "pattern": "*.{bed,interval_list}", - "ontologies": [] - } - } - ] - ], - "output": { - "interval_list": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "${prefix}.interval_list": { - "type": "file", - "description": "Processed interval list file", - "pattern": "*.interval_list", - "ontologies": [] - } - } - ] - ], - "versions_gatk4": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gatk4": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gatk4": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@ryanjameskennedy", - "@ViktorHy", - "@ramprasadn" - ], - "maintainers": [ - "@ryanjameskennedy", - "@ViktorHy", - "@ramprasadn" - ] - }, - "pipelines": [ - { - "name": "createpanelrefs", - "version": "dev" - } - ] - }, - { - "name": "gatk4_printreads", - "path": "modules/nf-core/gatk4/printreads/meta.yml", - "type": "module", - "meta": { - "name": "gatk4_printreads", - "description": "Print reads in the SAM/BAM/CRAM file", - "keywords": [ - "bam", - "cram", - "gatk4", - "printreads", - "sam" - ], - "tools": [ - { - "gatk4": { - "description": "Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools\nwith a primary focus on variant discovery and genotyping. Its powerful processing engine\nand high-performance computing features make it capable of taking on projects of any size.\n", - "homepage": "https://gatk.broadinstitute.org/hc/en-us", - "documentation": "https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s", - "doi": "10.1158/1538-7445.AM2017-3590", - "licence": [ - "Apache-2.0" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } - }, - { - "index": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bai,crai,sai}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "reference fasta file", - "pattern": "*.{fa,fasta}", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fai": { - "type": "file", - "description": "reference fasta index file", - "pattern": "*.{fai}", - "ontologies": [] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "dict": { - "type": "file", - "description": "reference fasta dictionary file", - "pattern": "*.{dict}", - "ontologies": [] - } - } - ] - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.bam": { - "type": "file", - "description": "Sorted BAM file", - "pattern": "*.{bam}", - "ontologies": [] - } - } - ] - ], - "cram": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.cram": { - "type": "file", - "description": "Sorted CRAM file", - "pattern": "*.{cram}", - "ontologies": [] - } - } - ] - ], - "sam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.sam": { - "type": "file", - "description": "Sorted SAM file", - "pattern": "*.{sam}", - "ontologies": [] - } - } - ] - ], - "versions_gatk4": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gatk4": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gatk4": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@ramprasadn" - ], - "maintainers": [ - "@ramprasadn" - ] - }, - "pipelines": [ - { - "name": "raredisease", - "version": "3.0.0" }, { - "name": "variantcatalogue", - "version": "dev" - } - ] - }, - { - "name": "gatk4_printsvevidence", - "path": "modules/nf-core/gatk4/printsvevidence/meta.yml", - "type": "module", - "meta": { - "name": "gatk4_printsvevidence", - "description": "WARNING - this tool is still experimental and shouldn't be used in a production setting. Gathers paired-end and split read evidence files for use in the GATK-SV pipeline. Output files are a file containing the location of and orientation of read pairs marked as discordant, and a file containing the clipping location of all soft clipped reads and the orientation of the clipping.", - "keywords": [ - "gatk4", - "printsvevidence", - "structural variants" - ], - "tools": [ - { - "gatk4": { - "description": "Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools\nwith a primary focus on variant discovery and genotyping. Its powerful processing engine\nand high-performance computing features make it capable of taking on projects of any size.\n", - "homepage": "https://gatk.broadinstitute.org/hc/en-us", - "documentation": "https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s", - "doi": "10.1158/1538-7445.AM2017-3590", - "licence": [ - "Apache-2.0" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "evidence_files": { - "type": "file", - "description": "The evidence files created by CollectSVEvidence. They all need to be of the same type to print the SV evidence.", - "pattern": "*.{pe,sr,baf,rd}.txt(.gz)", - "ontologies": [] - } - }, - { - "evidence_indices": { - "type": "file", - "description": "The indices of the evidence files created by CollectSVEvidence", - "pattern": "*.{pe,sr,baf,rd}.txt(.gz).tbi", - "ontologies": [] - } - } - ], - { - "bed": { - "type": "file", - "description": "An optional BED file", - "pattern": "*.bed", - "ontologies": [] - } - }, - { - "fasta": { - "type": "file", - "description": "An optional reference FASTA file", - "pattern": "*.{fa,fasta}", - "ontologies": [] - } - }, - { - "fasta_fai": { - "type": "file", - "description": "An optional reference FASTA file index", - "pattern": "*.fai", - "ontologies": [] - } - }, - { - "dict": { - "type": "file", - "description": "The mandatory sequence dictionary file", - "pattern": "*.dict", - "ontologies": [] - } - } - ], - "output": { - "printed_evidence": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.txt.gz": { - "type": "file", - "description": "The output file containing the discordant read pairs or the soft clipped reads", - "pattern": "*.{pe,sr,baf,rd}.txt.gz", - "ontologies": [] - } - } - ] - ], - "printed_evidence_index": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.txt.gz.tbi": { - "type": "file", - "description": "The index file of the output compressed text file containing the discordant read pairs or the soft clipped reads", - "pattern": "*.{pe,sr,baf,rd}.txt.gz.tbi", - "ontologies": [] - } - } - ] - ], - "versions_gatk4": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gatk4": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gatk4": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@nvnieuwk" - ], - "maintainers": [ - "@nvnieuwk" - ] - } - }, - { - "name": "gatk4_reblockgvcf", - "path": "modules/nf-core/gatk4/reblockgvcf/meta.yml", - "type": "module", - "meta": { - "name": "gatk4_reblockgvcf", - "description": "Condenses homRef blocks in a single-sample GVCF", - "keywords": [ - "gatk4", - "gvcf", - "reblockgvcf" - ], - "tools": [ - { - "gatk4": { - "description": "Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools\nwith a primary focus on variant discovery and genotyping. Its powerful processing engine\nand high-performance computing features make it capable of taking on projects of any size.\n", - "homepage": "https://gatk.broadinstitute.org/hc/en-us", - "documentation": "https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s", - "doi": "10.1158/1538-7445.AM2017-3590", - "licence": [ - "Apache-2.0" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "gvcf": { - "type": "file", - "description": "GVCF file created using HaplotypeCaller using the '-ERC GVCF' or '-ERC BP_RESOLUTION' mode", - "pattern": "*.{vcf,gvcf}.gz", - "ontologies": [] - } - }, - { - "tbi": { - "type": "file", - "description": "Index of the GVCF file", - "pattern": "*.tbi", - "ontologies": [] - } + "name": "homer_maketagdirectory", + "path": "modules/nf-core/homer/maketagdirectory/meta.yml", + "type": "module", + "meta": { + "name": "homer_maketagdirectory", + "description": "Create a tag directory with the HOMER suite", + "keywords": ["peaks", "bed", "bam", "sam"], + "tools": [ + { + "homer": { + "description": "HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.\n", + "documentation": "http://homer.ucsd.edu/homer/", + "doi": "10.1016/j.molcel.2010.05.004.", + "licence": ["GPL-3.0-or-later"], + "identifier": "biotools:homer" + } + }, + { + "samtools": { + "description": "SAMtools is a set of utilities for interacting with and post-processing\nshort DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.\nThese files are generated as output by short read aligners like BWA.\n", + "homepage": "http://www.htslib.org/", + "documentation": "http://www.htslib.org/doc/samtools.html", + "doi": "10.1093/bioinformatics/btp352", + "licence": ["MIT"], + "identifier": "biotools:homer" + } + }, + { + "DESeq2": { + "description": "Differential gene expression analysis based on the negative binomial distribution\n", + "homepage": "https://bioconductor.org/packages/DESeq2", + "documentation": "https://bioconductor.org/packages/DESeq2", + "tool_dev_url": "https://github.com/mikelove/DESeq2", + "doi": "10.18129/B9.bioc.DESeq2", + "licence": ["LGPL-3.0-or-later"], + "identifier": "biotools:homer" + } + }, + { + "edgeR": { + "description": "Empirical Analysis of Digital Gene Expression Data in R\n", + "homepage": "https://bioinf.wehi.edu.au/edgeR", + "documentation": "https://bioconductor.org/packages/edgeR", + "tool_dev_url": "https://git.bioconductor.org/packages/edgeR", + "doi": "10.18129/B9.bioc.edgeR", + "licence": ["GPL >=2"], + "identifier": "biotools:homer" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/BED/SAM file", + "pattern": "*.{bam,bed,sam}", + "ontologies": [] + } + } + ], + { + "fasta": { + "type": "file", + "description": "Fasta file of reference genome", + "pattern": "*.fasta", + "ontologies": [] + } + } + ], + "output": { + "tagdir": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_tagdir": { + "type": "directory", + "description": "The \"Tag Directory\"", + "pattern": "*_tagdir" + } + } + ] + ], + "taginfo": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_tagdir/tagInfo.txt": { + "type": "directory", + "description": "The tagInfo.txt included to ensure there's proper output", + "pattern": "*_tagdir/tagInfo.txt" + } + } + ] + ], + "versions_homer": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "homer": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "4.11": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_samtools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "samtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "samtools --version 2>&1 | sed '1!d;s/^.*samtools //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_deseq2": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "deseq2": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "Rscript -e \"cat(as.character(packageVersion('DESeq2')))\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_edger": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "edger": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "Rscript -e \"cat(as.character(packageVersion('edgeR')))\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "homer": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "4.11": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "samtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "samtools --version 2>&1 | sed '1!d;s/^.*samtools //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "deseq2": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "Rscript -e \"cat(as.character(packageVersion('DESeq2')))\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "edger": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "Rscript -e \"cat(as.character(packageVersion('edgeR')))\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@edmundmiller"], + "maintainers": ["@edmundmiller"] }, - { - "intervals": { - "type": "file", - "description": "Bed file with the genomic regions included in the library (optional)", - "ontologies": [] - } - } - ], - { - "fasta": { - "type": "file", - "description": "The reference fasta file", - "pattern": "*.fasta", - "ontologies": [] - } - }, - { - "fai": { - "type": "file", - "description": "Index of reference fasta file", - "pattern": "fasta.fai", - "ontologies": [] - } - }, - { - "dict": { - "type": "file", - "description": "GATK sequence dictionary", - "pattern": "*.dict", - "ontologies": [] - } - }, - { - "dbsnp": { - "type": "file", - "description": "VCF file containing known sites (optional)", - "ontologies": [] - } - }, - { - "dbsnp_tbi": { - "type": "file", - "description": "VCF index of dbsnp (optional)", - "ontologies": [] - } - } - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.rb.g.vcf.gz": { - "type": "file", - "description": "The reblocked GVCF file", - "pattern": "*.rb.g.vcf.gz", - "ontologies": [ - { - "edam": 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"2.3.0" + } ] - ] - }, - "authors": [ - "@nvnieuwk" - ], - "maintainers": [ - "@nvnieuwk" - ] - } - }, - { - "name": "gatk4_revertsam", - "path": "modules/nf-core/gatk4/revertsam/meta.yml", - "type": "module", - "meta": { - "name": "gatk4_revertsam", - "description": "Reverts SAM or BAM files to a previous state.", - "keywords": [ - "gatk4", - "revert", - "sam" - ], - "tools": [ - { - "gatk4": { - "description": "Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools\nwith a primary focus on variant discovery and genotyping. 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Assumes that the hash tag oligo (HTO) data has been added and normalized.\n", + "ontologies": [] + } + }, + { + "assay": { + "type": "string", + "description": "Name of the Hashtag assay, usually called \"HTO\" by default. Use the custom name if the assay has been named differently.\n" + } + } + ] + ], + "output": { + "params": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_params_htodemux.csv": { + "type": "file", + "description": "The used parameters to call HTODemux in the R-Script.", + "pattern": "params_htodemux.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "assignment": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_assignment_htodemux.csv": { + "type": "file", + "description": "Assignment results.", + "pattern": "assignment_htodemux.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "classification": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_classification_htodemux.csv": { + "type": "file", + "description": "Classification results.", + "pattern": "classification_htodemux.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "rds": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_htodemux.rds": { + "type": "file", + "description": "SeuratObject saved as RDS.", + "pattern": "htodemux.rds", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@LuisHeinzlmeier"], + "maintainers": ["@LuisHeinzlmeier"] + } }, { - "name": "tbanalyzer", - "version": "dev" - } - ] - }, - { - "name": "gatk4_shiftfasta", - "path": "modules/nf-core/gatk4/shiftfasta/meta.yml", - "type": "module", - "meta": { - "name": "gatk4_shiftfasta", - "description": "Create a fasta with the bases shifted by offset", - "keywords": [ - "gatk4", - "mitochondria", - "shiftchain", - "shiftfasta", - "shiftintervals" - ], - "tools": [ - { - "gatk4": { - "description": "Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools\nwith a primary focus on variant discovery and genotyping. 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{ - "dict": { - "type": "file", - "description": "Reference sequence dictionary", - "pattern": "*.dict", - "ontologies": [] - } - } - ] - ], - "output": { - "split_intervals": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n", - "pattern": "*.interval_list" - } - }, - { - "**.interval_list": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n", - "pattern": "*.interval_list" - } - } - ] - ], - "versions_gatk4": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gatk4": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - 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Only used when creating an index for the output file.", + "pattern": "*.{bed,txt,tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + }, + { + "edam": "http://edamontology.org/format_3003" + } + ] + } + } + ], + { + "action": { + "type": "string", + "description": "Action to perform, either `compress` or `decompress`" + } + }, + { + "make_index": { + "type": "boolean", + "description": "Whether to create a tabix index for the output file; only used if `action` is `compress`" + } + }, + { + "out_ext": { + "type": "string", + "description": "Output file extension without `.gz` suffix (for example `vcf`)" + } + } + ], + "output": { + "output": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample1' ]\n" + } + }, + { + "${outfile}": { + "type": "file", + "description": "Compressed or decompressed output file", + "pattern": "*", + "ontologies": [] + } + } + ] + ], + "index": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample1' ]\n" + } + }, + { + "${outfile}.{tbi,csi}": { + "type": "file", + "description": "Tabix index file for the compressed output file", + "pattern": "*.{tbi,csi}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3616" + } + ] + } + } + ] + ], + "versions_htslib": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "htslib": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bgzip --version | sed '1! d; s/bgzip (htslib) //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_xz": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "xz": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "xz --version | sed '1! d; s/xz (XZ Utils) //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "htslib": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bgzip --version | sed '1! d; s/bgzip (htslib) //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "xz": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "xz --version | sed '1! d; s/xz (XZ Utils) //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@itrujnara"], + "maintainers": ["@itrujnara"] + } }, { - "name": "raredisease", - "version": "3.0.0" - } - ] - }, - { - "name": "gatk4_splitncigarreads", - "path": "modules/nf-core/gatk4/splitncigarreads/meta.yml", - "type": "module", - "meta": { - "name": "gatk4_splitncigarreads", - "description": "Splits reads that contain Ns in their cigar string", - "keywords": [ - "gatk4", - "merge", - "vcf" - ], - "tools": [ - { - "gatk4": { - "description": "Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools\nwith a primary focus on variant discovery and genotyping. 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The downloaded file is emitted\nwith this name in the task work directory.\n" + } + } + ] + ], + "output": { + "output": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "hf_file": { + "type": "file", + "description": "Downloaded file from the Hugging Face repository", + "ontologies": [] + } + } + ] + ], + "versions_huggingface_hub": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "huggingface_hub": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "hf --version 2>&1 | tail -n1 | awk '{print \\$NF}'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "huggingface_hub": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "hf --version 2>&1 | tail -n1 | awk '{print \\$NF}'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@toniher", "@lucacozzuto"], + "maintainers": ["@toniher", "@lucacozzuto"] + } }, { - "name": "rnavar", - "version": "1.2.3" - } - ] - }, - { - "name": "gatk4_svannotate", - "path": "modules/nf-core/gatk4/svannotate/meta.yml", - "type": "module", - "meta": { - "name": "gatk4_svannotate", - "description": "Adds predicted functional consequence, gene overlap, and noncoding element overlap annotations to SV VCF from GATK-SV pipeline. Input files are an SV VCF, a GTF file containing primary or canonical transcripts, and a BED file containing noncoding elements. 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Its powerful processing engine\nand high-performance computing features make it capable of taking on projects of any size.\n", - "homepage": "https://gatk.broadinstitute.org/hc/en-us", - "documentation": "https://github.com/broadinstitute/gatk", - "doi": "10.1158/1538-7445.AM2017-3590", - "licence": [ - "Apache-2.0" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcfs": { - "type": "file", - "description": "One or more VCF files created with a structural variant caller", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } + "name": "humann3_humann", + "path": "modules/nf-core/humann3/humann/meta.yml", + "type": "module", + "meta": { + "name": "humann3_humann", + "description": "Functional analysis of metagenome or metatranscriptome data", + "keywords": ["function", "metagenomics", "metatranscriptomics", "profiling", "community"], + "tools": [ + { + "humann": { + "description": "HUMAnN: The HMP Unified Metabolic Analysis Network", + "homepage": "http://huttenhower.sph.harvard.edu/humann", + "documentation": "https://github.com/biobakery/biobakery/wiki/humann3", + "tool_dev_url": "https://github.com/biobakery/humann", + "doi": "10.7554/eLife.65088", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "input": { + "type": "file", + "description": "A metagenome (DNA reads) or metatranscriptome (RNA reads) [fastq,fastq.gz,fasta,fasta.gz]\nOR pre-computed mappings [sam,bam,blastm8]\nOR pre-computed abundance tables [tsv,biom]\n", + "pattern": "*.{fastq,fastq.gz,fasta,fasta.gz,sam,bam,blastm8,tsv,biom}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + }, + { + "edam": "http://edamontology.org/format_3475" + }, + { + "edam": "http://edamontology.org/format_3746" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "profile": { + "type": "file", + "description": "Pre-computed MetaPhlAn taxonomic profile", + "pattern": "*.{txt}", + "ontologies": [] + } + } + ], + { + "nucleotide_db": { + "type": "directory", + "description": "ChocoPhlAn nucleotide database directory (v3: *.ffn.gz, v4: *.fna.gz)\n" + } + }, + { + "protein_db": { + "type": "directory", + "description": "UniRef protein database directory containing *.dmnd files\n" + } + }, + { + "utility_db": { + "type": "directory", + "description": "HUMAnN utility mapping database directory\n" + } + } + ], + "output": { + "genefamilies": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*_genefamilies.tsv.gz": { + "type": "file", + "description": "Compressed gene families abundance table", + "pattern": "*.{tsv.gz}", + "ontologies": [] + } + } + ] + ], + "pathabundance": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*_pathabundance.tsv.gz": { + "type": "file", + "description": "Compressed pathway abundance table", + "pattern": "*.{tsv.gz}", + "ontologies": [] + } + } + ] + ], + "pathcoverage": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*_pathcoverage.tsv.gz": { + "type": "file", + "description": "Compressed pathway coverage table", + "pattern": "*.{tsv.gz}", + "ontologies": [] + } + } + ] + ], + "reactions": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*_reactions.tsv.gz": { + "type": "file", + "description": "Compressed 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{ + "type": "string", + "description": "The name of the tool" + } + }, + { + "metaphlan --version 2>&1 | sed 's/MetaPhlAn version //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "Python": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python --version 2>&1 | sed 's/Python //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@nickp60", "@d4straub", "@vinisalazar"], + "maintainers": ["@nickp60", "@vinisalazar"] }, - { - "indices": { - "type": "file", - "description": "Index files for the VCFs", - "pattern": "*.vcf.gz.tbi", - "ontologies": [] - } - } - ], - { - "ploidy_table": { - "type": "file", - "description": "The sample ploidy table", - "pattern": "*.tsv", - "ontologies": [ + "pipelines": [ { - "edam": "http://edamontology.org/format_3475" + "name": "funcprofiler", + "version": "dev" } - ] - } - }, - { - "fasta": { - "type": "file", - "description": "Reference FASTA file needed when the input is a CRAM file", - "pattern": "*.{fasta,fa}", - "ontologies": [] - } - }, - { - "fasta_fai": { - "type": "file", - "description": "Index of the reference FASTA file needed when the input is a CRAM file", - "pattern": "*.fai", - "ontologies": [] - } - }, - { - "dict": { - "type": "file", - "description": "Sequence dictionary of the reference FASTA file needed when the input is a CRAM file", - "pattern": "*.dict", - "ontologies": [] - } - } - ], - "output": { - "clustered_vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.vcf.gz": { - "type": "file", - "description": "The VCF containing the clustered VCFs", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": 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"name": "variantcatalogue", - "version": "dev" - } - ] - }, - { - "name": "gatk4_variantrecalibrator", - "path": "modules/nf-core/gatk4/variantrecalibrator/meta.yml", - "type": "module", - "meta": { - "name": "gatk4_variantrecalibrator", - "description": "Build a recalibration model to score variant quality for filtering purposes.\nIt is highly recommended to follow GATK best practices when using this module,\nthe gaussian mixture model requires a large number of samples to be used for the\ntool to produce optimal results. For example, 30 samples for exome data. For more details see\nhttps://gatk.broadinstitute.org/hc/en-us/articles/4402736812443-Which-training-sets-arguments-should-I-use-for-running-VQSR-\n", - "keywords": [ - "gatk4", - "recalibration model", - "variantrecalibrator" - ], - "tools": [ - { - "gatk4": { - "description": "Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools\nwith a primary focus on variant discovery and genotyping. Its powerful processing engine\nand high-performance computing features make it capable of taking on projects of any size.\n", - "homepage": "https://gatk.broadinstitute.org/hc/en-us", - "documentation": "https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s", - "doi": "10.1158/1538-7445.AM2017-3590", - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "input vcf file containing the variants to be recalibrated", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } + "name": "humid", + "path": "modules/nf-core/humid/meta.yml", + "type": "module", + "meta": { + "name": "humid", + "description": "HUMID is a tool to quickly and easily remove duplicate reads from FastQ files, with or without UMIs.", + "keywords": ["umi", "fastq", "deduplication", "hamming-distance", "clustering"], + "tools": [ + { + "humid": { + "description": "HUMID -- High-performance UMI Deduplicator", + "homepage": "https://github.com/jfjlaros/HUMID", + "documentation": "https://humid.readthedocs.io/en/latest/", + "tool_dev_url": "https://github.com/jfjlaros/HUMID", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "reads": { + "type": "file", + "description": "Fastq file(s) to deduplicate", + "pattern": "*.{fastq,fq,fastq.gz,fq.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "umi_file": { + "type": "file", + "description": "UMI file", + "ontologies": [] + } + } + ] + ], + "output": { + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}.log": { + "type": "file", + "description": "Log file of humid, containing progress and errors", + "pattern": "*.log", + "ontologies": [] + } + } + ] + ], + "dedup": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*_dedup*.fastq.gz": { + "type": "file", + "description": "Deduplicated Fastq file(s)", + "pattern": "*.{fastq,fq,fastq.gz,fq.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ] + ], + "annotated": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*_annotated*.fastq.gz": { + "type": "file", + "description": "Annotated Fastq file(s)", + "pattern": "*.{fastq,fq,fastq.gz,fq.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ] + ], + "stats": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}": { + "type": "directory", + "description": "Directory containing statistics file, use for multiqc.", + "pattern": "${prefix}/" + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@Joon-Klaps"], + "maintainers": ["@Joon-Klaps"] }, - { - "tbi": { - "type": "file", - "description": "tbi file matching with -vcf", - "pattern": "*.vcf.gz.tbi", - "ontologies": [] - } - } - ], - { - "resource_vcf": { - "type": "file", - "description": "all resource vcf files that are used with the corresponding '--resource' label", - "pattern": "*.vcf.gz", - "ontologies": [ + "pipelines": [ { - "edam": "http://edamontology.org/format_3989" + "name": "viralmetagenome", + "version": "1.1.1" } - ] - } - }, - { - "resource_tbi": { - "type": "file", - "description": "all resource tbi files that are used with the corresponding '--resource' label", - "pattern": "*.vcf.gz.tbi", - "ontologies": [] - } - }, - { - "labels": { - "type": "string", - "description": "necessary arguments for GATK VariantRecalibrator. Specified to directly match the resources provided. More information can be found at https://gatk.broadinstitute.org/hc/en-us/articles/5358906115227-VariantRecalibrator" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference fasta file", - "pattern": "*.fasta", - "ontologies": [] - } - }, - { - "fai": { - "type": "file", - "description": "Index of reference fasta file", - "pattern": "fasta.fai", - "ontologies": [] - } - }, - { - "dict": { - "type": "file", - "description": "GATK sequence dictionary", - "pattern": "*.dict", - "ontologies": [] - } - } - ], - "output": { - "recal": [ - [ - { - "meta": { - "type": "file", - "description": "Output recal file used by ApplyVQSR", - "pattern": "*.recal", - "ontologies": [] - } - }, - { - "*.recal": { - "type": "file", - "description": "Output recal file used by ApplyVQSR", - "pattern": "*.recal", - "ontologies": [] - } - } - ] - ], - "idx": [ - [ - { - "meta": { - "type": "file", - "description": "Output recal file used by ApplyVQSR", - "pattern": "*.recal", - "ontologies": [] - } - }, - { - "*.idx": { - "type": "file", - "description": "Index file for the recal output file", - "pattern": "*.idx", - "ontologies": [] - } - } ] - ], - "tranches": [ - [ - { - "meta": { - "type": "file", - "description": "Output recal file used by ApplyVQSR", - "pattern": "*.recal", - "ontologies": [] - } - }, - { - "*.tranches": { - "type": "file", - "description": "Output tranches file used by ApplyVQSR", - "pattern": "*.tranches", - "ontologies": [] - } - } - ] - ], - "plots": [ - [ - { - "meta": { - "type": "file", - "description": "Output recal file used by ApplyVQSR", - "pattern": "*.recal", - "ontologies": [] - } - }, - { - "*plots.R": { - "type": "file", - "description": "Optional output rscript file to aid in visualization of the input data and learned model.", - "pattern": "*plots.R", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3999" - } - ] - } - } - ] - ], - "versions_gatk4": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gatk4": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gatk4": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] }, - "authors": [ - "@GCJMackenzie", - "@nickhsmith" - ], - "maintainers": [ - "@GCJMackenzie", - "@nickhsmith" - ] - }, - "pipelines": [ { - "name": "rnadnavar", - "version": "dev" + "name": "hypo", + "path": "modules/nf-core/hypo/meta.yml", + "type": "module", + "meta": { + "name": "hypo", + "description": "Assembly polisher using short (and long) reads", + "keywords": ["assembly", "polishing", "nanopore", "illumina"], + "tools": [ + { + "hypo": { + "description": "Super Fast and Accurate Polisher for Long Read Genome Assemblies.", + "homepage": "https://github.com/kensung-lab/hypo", + "documentation": "https://github.com/kensung-lab/hypo/blob/master/README.md", + "tool_dev_url": "https://github.com/kensung-lab/hypo", + "doi": "10.1101/2019.12.19.882506", + "licence": ["GPL v3"], + "identifier": "biotools:hypo" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "sr_bam": { + "type": "file", + "description": "Aligned short-read BAM/SAM file. Must have CIGAR information.", + "pattern": "*.{bam,sam}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "Short reads file(s). In fastq or fasta, compressed or uncompressed", + "ontologies": [] + } + } + ], + { + "draft": { + "type": "file", + "description": "Input (fasta) file containing draft contig assembly", + "ontologies": [] + } + }, + { + "genome_size": { + "type": "string", + "description": "Estimated size of the genome. Number or nts or use suffixes k/m/g, e.g. 5m, 3.2g" + } + }, + { + "reads_coverage": { + "type": "integer", + "description": "Appprimate depth of coverage of short reads." + } + } + ], + "output": { + "fasta": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fasta": { + "type": "file", + "description": "Polished assembly fasta file", + "pattern": "*.fasta", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@remiolsen"], + "maintainers": ["@remiolsen"] + } }, { - "name": "sarek", - "version": "3.8.1" + "name": "ichorcna_createpon", + "path": "modules/nf-core/ichorcna/createpon/meta.yml", + "type": "module", + "meta": { + "name": "ichorcna_createpon", + "description": "ichorCNA is an R package for calculating copy number alteration from (low-pass) whole genome sequencing, particularly for use in cell-free DNA. This module generates a panel of normals", + "keywords": ["ichorcna", "cnv", "cna", "cfDNA", "wgs", "panel_of_normals"], + "tools": [ + { + "ichorcna": { + "description": "Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.", + "homepage": "https://github.com/broadinstitute/ichorCNA", + "documentation": "https://github.com/broadinstitute/ichorCNA/wiki", + "tool_dev_url": "https://github.com/broadinstitute/ichorCNA", + "doi": "10.1038/s41467-017-00965-y", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + { + "wigs": { + "type": "file", + "description": "Any number of hmmcopy/readCounter processed .wig files giving the number of reads in the sample, in each genomic window. These will be averaged over to generate the panel of normals.", + "pattern": "*.{wig}", + "ontologies": [] + } + }, + { + "gc_wig": { + "type": "file", + "description": "hmmcopy/gcCounter processed .wig file giving the gc content in the reference fasta, in each genomic window", + "pattern": "*.{wig}", + "ontologies": [] + } + }, + { + "map_wig": { + "type": "file", + "description": "hmmcopy/mapCounter processed .wig file giving the mapability in the reference fasta, in each genomic window", + "pattern": "*.{wig}", + "ontologies": [] + } + }, + { + "centromere": { + "type": "file", + "description": "Text file giving centromere locations of each genome, to exclude these windows", + "pattern": "*.{txt}", + "ontologies": [] + } + }, + { + "rep_time_wig": { + "type": "file", + "description": "Replication/timing .wig file.", + "pattern": "*.{wig}", + "ontologies": [] + } + }, + { + "exons": { + "type": "file", + "description": "BED file for exon regions to annotate CNA regions.", + "pattern": "*.{bed}", + "ontologies": [] + } + } + ], + "output": { + "rds": [ + { + "${prefix}*.rds": { + "type": "file", + "description": "R data file (.rds) containing panel of normals data, medians of each bin.", + "pattern": "*.rds", + "ontologies": [] + } + } + ], + "txt": [ + { + "${prefix}*.txt": { + "type": "file", + "description": "Text file containing panel of normals data, medians of each bin.", + "pattern": "*.txt", + "ontologies": [] + } + } + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@sppearce"], + "maintainers": ["@sppearce"] + } }, { - "name": "tbanalyzer", - "version": "dev" - } - ] - }, - { - "name": "gatk4_variantstotable", - "path": "modules/nf-core/gatk4/variantstotable/meta.yml", - "type": "module", - "meta": { - "name": "gatk4_variantstotable", - "description": "Extract fields from a VCF file to a tab-delimited table", - "keywords": [ - "filter", - "gatk4", - "table", - "vcf" - ], - "tools": [ - { - "gatk4": { - "description": "Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools\nwith a primary focus on variant discovery and genotyping. Its powerful processing engine\nand high-performance computing features make it capable of taking on projects of any size.\n", - "homepage": "https://gatk.broadinstitute.org/hc/en-us", - "documentation": "https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s", - "doi": "10.1158/1538-7445.AM2017-3590", - "licence": [ - "Apache-2.0" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing VCF information. Attribute `gatk_args` can be used to add arguments to gatk.\ne.g. [ id:'test', gatk_args:'-F CHROM -F POS -F TYPE -GF AD']\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF file", - "pattern": "*.{vcf,vcf.gz}", - "ontologies": [] - } - }, - { - "tbi": { - "type": "file", - "description": "Index of VCF file.", - "pattern": "*.{idx,tbi}", - "ontologies": [] - } - }, - { - "arguments_file": { - "type": "file", - "description": "optional GATK arguments file", - "pattern": "*.{txt,list,args,arguments}", - "ontologies": [] - } - }, - { - "include_intervals": { - "type": "file", - "description": "optional GATK region file", - "pattern": "*.{bed,bed.gz,interval,interval_list}", - "ontologies": [] - } - }, - { - "exclude_intervals": { - "type": "file", - "description": "optional GATK exclude region file", - "pattern": "*.{bed,bed.gz,interval,interval_list}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Fasta file of reference genome", - "pattern": "*.fasta", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fai": { - "type": "file", - "description": "Index of fasta file", - "pattern": "*.fasta.fai", - "ontologies": [] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "dict": { - "type": "file", - "description": "Sequence dictionary of fastea file", - "pattern": "*.dict", - "ontologies": [] - } - } - ] - ], - "output": { - "table": [ - [ - { - "meta": { - "type": "file", - "description": "GATK output", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - }, - { - "*.tsv": { - "type": "file", - "description": "GATK output", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_gatk4": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gatk4": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gatk4": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@lindenb" - ], - "maintainers": [ - "@lindenb" - ] - }, - "pipelines": [ - { - "name": "tbanalyzer", - "version": "dev" - } - ] - }, - { - "name": "gatk4spark_applybqsr", - "path": "modules/nf-core/gatk4spark/applybqsr/meta.yml", - "type": "module", - "meta": { - "name": "gatk4spark_applybqsr", - "description": "Apply base quality score recalibration (BQSR) to a bam file", - "keywords": [ - "bam", - "base quality score recalibration", - "bqsr", - "cram", - "gatk4spark" - ], - "tools": [ - { - "gatk4": { - "description": "Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools\nwith a primary focus on variant discovery and genotyping. Its powerful processing engine\nand high-performance computing features make it capable of taking on projects of any size.\n", - "homepage": "https://gatk.broadinstitute.org/hc/en-us", - "documentation": "https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s", - "doi": "10.1158/1538-7445.AM2017-3590", - "licence": [ - "Apache-2.0" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM file from alignment", - "pattern": "*.{bam,cram}", - "ontologies": [] - } - }, - { - "input_index": { - "type": "file", - "description": "BAI/CRAI file from alignment", - "pattern": "*.{bai,crai}", - "ontologies": [] - } - }, - { - "bqsr_table": { - "type": "file", - "description": "Recalibration table from gatk4_baserecalibrator", - "ontologies": [] - } - }, - { - "intervals": { - "type": "file", - "description": "Bed file with the genomic regions included in the library (optional)", - "ontologies": [] - } - } - ], - { - "fasta": { - "type": "file", - "description": "The reference fasta file", - "pattern": "*.fasta", - "ontologies": [] - } - }, - { - "fai": { - "type": "file", - "description": "Index of reference fasta file", - "pattern": "*.fasta.fai", - "ontologies": [] - } - }, - { - "dict": { - "type": "file", - "description": "GATK sequence dictionary", - "pattern": "*.dict", - "ontologies": [] - } - } - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.bam": { - "type": "file", - "description": "Recalibrated BAM file", - "pattern": "${prefix}.bam", - "ontologies": [] - } - } - ] - ], - "bai": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}*bai": { - "type": "file", - "description": "Recalibrated BAM index file", - "pattern": "${prefix}*bai", - "ontologies": [] - } - } - ] - ], - "cram": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.cram": { - "type": "file", - "description": "Recalibrated CRAM file", - "pattern": "${prefix}.cram", - "ontologies": [] - } - } - ] - ], - "versions_gatk4": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gatk4": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gatk4": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@yocra3", - "@FriederikeHanssen", - "@maxulysse" - ], - "maintainers": [ - "@yocra3", - "@FriederikeHanssen", - "@maxulysse" - ] - }, - "pipelines": [ - { - "name": "sarek", - "version": "3.8.1" - } - ] - }, - { - "name": "gatk4spark_baserecalibrator", - "path": "modules/nf-core/gatk4spark/baserecalibrator/meta.yml", - "type": "module", - "meta": { - "name": "gatk4spark_baserecalibrator", - "description": "Generate recalibration table for Base Quality Score Recalibration (BQSR)", - "keywords": [ - "base quality score recalibration", - "table", - "bqsr", - "gatk4spark", - "sort" - ], - "tools": [ - { - "gatk4": { - "description": "Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools\nwith a primary focus on variant discovery and genotyping. Its powerful processing engine\nand high-performance computing features make it capable of taking on projects of any size.\n", - "homepage": "https://gatk.broadinstitute.org/hc/en-us", - "documentation": "https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s", - "doi": "10.1158/1538-7445.AM2017-3590", - "licence": [ - "Apache-2.0" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM file from alignment", - "pattern": "*.{bam,cram}", - "ontologies": [] - } - }, - { - "input_index": { - "type": "file", - "description": "BAI/CRAI file from alignment", - "pattern": "*.{bai,crai}", - "ontologies": [] - } - }, - { - "intervals": { - "type": "file", - "description": "Bed file with the genomic regions included in the library (optional)", - "ontologies": [] - } - } - ], - { - "fasta": { - "type": "file", - "description": "The reference fasta file", - "pattern": "*.fasta", - "ontologies": [] - } - }, - { - "fai": { - "type": "file", - "description": "Index of reference fasta file", - "pattern": "*.fasta.fai", - "ontologies": [] - } - }, - { - "dict": { - "type": "file", - "description": "GATK sequence dictionary", - "pattern": "*.dict", - "ontologies": [] - } - }, - { - "known_sites": { - "type": "file", - "description": "VCF files with known sites for indels / snps (optional)", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - }, - { - "known_sites_tbi": { - "type": "file", - "description": "Tabix index of the known_sites (optional)", - "pattern": "*.vcf.gz.tbi", - "ontologies": [] - } - } - ], - "output": { - "table": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.table": { - "type": "file", - "description": "Recalibration table from BaseRecalibrator", - "pattern": "*.{table}", - "ontologies": [] - } - } - ] - ], - "versions_gatk4": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gatk4": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gatk4": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@yocra3", - "@FriederikeHanssen", - "@maxulysse" - ], - "maintainers": [ - "@yocra3", - "@FriederikeHanssen", - "@maxulysse" - ] - }, - "pipelines": [ - { - "name": "sarek", - "version": "3.8.1" - } - ] - }, - { - "name": "gatk4spark_markduplicates", - "path": "modules/nf-core/gatk4spark/markduplicates/meta.yml", - "type": "module", - "meta": { - "name": "gatk4spark_markduplicates", - "description": "This tool locates and tags duplicate reads in a BAM or SAM file, where duplicate reads are defined as originating from a single fragment of DNA.", - "keywords": [ - "bam", - "gatk4spark", - "markduplicates", - "sort" - ], - "tools": [ - { - "gatk4": { - "description": "Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.", - "homepage": "https://gatk.broadinstitute.org/hc/en-us", - "documentation": "https://gatk.broadinstitute.org/hc/en-us/articles/360037052812-MarkDuplicates-Picard-", - "tool_dev_url": "https://github.com/broadinstitute/gatk", - "doi": "10.1158/1538-7445.AM2017-3590", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM file", - "pattern": "*.{bam}", - "ontologies": [] - } - } - ], - { - "fasta": { - "type": "file", - "description": "The reference fasta file", - "pattern": "*.fasta", - "ontologies": [] - } - }, - { - "fasta_fai": { - "type": "file", - "description": "Index of reference fasta file", - "pattern": "*.fai", - "ontologies": [] - } - }, - { - "dict": { - "type": "file", - "description": "GATK sequence dictionary", - "pattern": "*.dict", - "ontologies": [] - } - } - ], - "output": { - "output": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}": { - "type": "file", - "description": "Marked duplicates BAM/CRAM file", - "pattern": "*.{bam,cram}", - "ontologies": [] - } - } - ] - ], - "bam_index": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.bai": { - "type": "file", - "description": "Optional BAM index file", - "pattern": "*.bai", - "ontologies": [] - } - } - ] - ], - "metrics": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.metrics": { - "type": "file", - "description": "Metrics file", - "pattern": "*.metrics", - "ontologies": [] - } - } - ] - ], - "versions_gatk4": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gatk4": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gatk4": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gatk --version | sed -n '/GATK.*v/s/.*v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@ajodeh-juma", - "@FriederikeHanssen", - "@maxulysse", - "@SusiJo" - ], - "maintainers": [ - "@ajodeh-juma", - "@FriederikeHanssen", - "@maxulysse", - "@SusiJo" - ] - }, - "pipelines": [ - { - "name": "sarek", - "version": "3.8.1" - } - ] - }, - { - "name": "gatk_indelrealigner", - "path": "modules/nf-core/gatk/indelrealigner/meta.yml", - "type": "module", - "meta": { - "name": "gatk_indelrealigner", - "description": "Performs local realignment around indels to correct for mapping errors", - "keywords": [ - "bam", - "vcf", - "variant calling", - "indel", - "realignment" - ], - "tools": [ - { - "gatk": { - "description": "The full Genome Analysis Toolkit (GATK) framework, license restricted.", - "homepage": "https://gatk.broadinstitute.org/hc/en-us", - "documentation": "https://github.com/broadinstitute/gatk-docs", - "licence": [ - "https://software.broadinstitute.org/gatk/download/licensing", - "BSD", - "https://www.broadinstitute.org/gatk/about/#licensing" - ], - "identifier": "biotools:gatk" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted and indexed BAM file", - "pattern": "*.bam", - "ontologies": [] - } - }, - { - "bai": { - "type": "file", - "description": "BAM index file", - "pattern": "*.bai", - "ontologies": [] - } - }, - { - "intervals": { - "type": "file", - "description": "Intervals file created by gatk3 RealignerTargetCreator", - "pattern": "*.{intervals,list}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference file used to generate BAM file", - "pattern": ".{fasta,fa,fna}", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fai": { - "type": "file", - "description": "Index of reference file used to generate BAM file", - "pattern": ".fai", - "ontologies": [] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "dict": { - "type": "file", - "description": "GATK dict file for reference", - "pattern": ".dict", - "ontologies": [] - } - } - ], - [ - { - "meta5": { - "type": "map", - "description": "Groovy Map containing file meta-information for known_vcf.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "known_vcf": { - "type": "file", - "description": "Optional input VCF file(s) with known indels", - "pattern": ".vcf", - "ontologies": [] - } - } - ] - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "Sorted and indexed BAM file with local realignment around variants", - "pattern": "*.bam", - "ontologies": [] - } - }, - { - "*.bai": { - "type": "file", - "description": "Sorted and indexed BAM file with local realignment around variants", - "pattern": "*.bam", - "ontologies": [] - } - } - ] - ], - "versions_gatk": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gatk": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gatk3 --version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gatk": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gatk3 --version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@jfy133" - ], - "maintainers": [ - "@jfy133" - ] - } - }, - { - "name": "gatk_realignertargetcreator", - "path": "modules/nf-core/gatk/realignertargetcreator/meta.yml", - "type": "module", - "meta": { - "name": "gatk_realignertargetcreator", - "description": "Generates a list of locations that should be considered for local realignment prior genotyping.", - "keywords": [ - "bam", - "vcf", - "variant calling", - "indel", - "realignment", - "targets" - ], - "tools": [ - { - "gatk": { - "description": "The full Genome Analysis Toolkit (GATK) framework, license restricted.", - "homepage": "https://gatk.broadinstitute.org/hc/en-us", - "documentation": "https://github.com/broadinstitute/gatk-docs", - "licence": [ - "https://software.broadinstitute.org/gatk/download/licensing", - "BSD", - "https://www.broadinstitute.org/gatk/about/#licensing" - ], - "identifier": "biotools:gatk" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted and indexed BAM/CRAM/SAM file", - "pattern": "*.bam", - "ontologies": [] - } - }, - { - "bai": { - "type": "file", - "description": "BAM index file", - "pattern": "*.bai", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference file used to generate BAM file", - "pattern": ".{fasta,fa,fna}", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fai": { - "type": "file", - "description": "Index of reference file used to generate BAM file", - "pattern": ".fai", - "ontologies": [] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "dict": { - "type": "file", - "description": "GATK dict file for reference", - "pattern": ".dict", - "ontologies": [] - } - } - ], - [ - { - "meta5": { - "type": "map", - "description": "Groovy Map containing file meta-information for known_vcf.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "known_vcf": { - "type": "file", - "description": "Optional input VCF file(s) with known indels", - "pattern": ".vcf", - "ontologies": [] - } - } - ] - ], - "output": { - "intervals": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.intervals": { - "type": "file", - "description": "File containing intervals that represent sites of extant and potential indels.", - "pattern": "*.intervals", - "ontologies": [] - } - } - ] - ], - "versions_gatk": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gatk": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gatk3 --version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gatk": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gatk3 --version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@jfy133" - ], - "maintainers": [ - "@jfy133" - ] - } - }, - { - "name": "gatk_unifiedgenotyper", - "path": "modules/nf-core/gatk/unifiedgenotyper/meta.yml", - "type": "module", - "meta": { - "name": "gatk_unifiedgenotyper", - "description": "SNP and Indel variant caller on a per-locus basis", - "keywords": [ - "bam", - "vcf", - "variant calling" - ], - "tools": [ - { - "gatk": { - "description": "The full Genome Analysis Toolkit (GATK) framework, license restricted.", - "homepage": "https://gatk.broadinstitute.org/hc/en-us", - "documentation": "https://github.com/broadinstitute/gatk-docs", - 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} - }, - { - "fai": { - "type": "file", - "description": "Index of reference file used to generate BAM file", - "pattern": ".fai", - "ontologies": [] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "dict": { - "type": "file", - "description": "GATK dict file for reference", - "pattern": ".dict", - "ontologies": [] - } - } - ], - [ - { - "meta5": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "intervals": { - "type": "file", - "description": "Bed file with the genomic regions included in the library (optional)", - "pattern": "*.intervals", - "ontologies": [] - } - } - ], - [ - { - "meta6": { - "type": "map", - "description": "Groovy Map containing file meta-information for the contamination file.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "contamination": { - "type": "file", - "description": "Tab-separated file containing fraction of contamination in sequencing data (per sample) to aggressively remove", - "pattern": "*", - "ontologies": [] - } - } - ], - [ - { - "meta7": { - "type": "map", - "description": "Groovy Map containing file meta-information for the dbsnps file.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "dbsnp": { - "type": "file", - "description": "VCF file containing known sites (optional)", - "pattern": "*", - "ontologies": [] - } - } - ], - [ - { - "meta8": { - "type": "map", - "description": "Groovy Map containing file meta-information for the VCF comparison file.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "comp": { - "type": "file", - "description": "Comparison VCF file (optional)", - "pattern": "*", - "ontologies": [] - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.vcf.gz": { - 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If the files have a `.gz` extension, they will be unzipped using `zcat`.", - "pattern": "*", - "ontologies": [] - } - } - ], - { - "program_file": { - "type": "file", - "description": "Optional file containing logic for awk to execute. If you don't wish to use a file, you can use `ext.args2` to specify the logic.", - "pattern": "*", - "ontologies": [] - } - }, - { - "disable_redirect_output": { - "type": "boolean", - "description": "Disable the redirection of awk output to a given file. 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generated by calling ichorCNA on a set of normal samples with the same window size etc.", + "pattern": "*.{rds}", + "ontologies": [] + } + }, + { + "centromere": { + "type": "file", + "description": "Text file giving centromere locations of each genome, to exclude these windows", + "pattern": "*.{txt}", + "ontologies": [] + } + }, + { + "rep_time_wig": { + "type": "file", + "description": "Replication/timing .wig file.", + "pattern": "*.{wig}", + "ontologies": [] + } + }, + { + "exons": { + "type": "file", + "description": "BED file for exon regions to annotate CNA regions.", + "pattern": "*.{bed}", + "ontologies": [] + } + } + ], + "output": { + "rdata": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "${prefix}.RData": { + "type": "file", + "description": "RData file containing all the intermediate R objects", + "pattern": "*.{cng.seg}", + "ontologies": [] + } + } + ] + ], + "seg": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "${prefix}.seg": { + "type": "file", + "description": "Predicted copy number variation per segment", + "pattern": "*.{seg}", + "ontologies": [] + } + } + ] + ], + "cna_seg": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "${prefix}.cna.seg": { + "type": "file", + "description": "Predicted copy number variation per segment", + "pattern": "*.{cng.seg}", + "ontologies": [] + } + } + ] + ], + "seg_txt": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "${prefix}.seg.txt": { + "type": "file", + "description": "Predicted copy number variation per segment", + "pattern": "*.{seg.txt}", + "ontologies": [] + } + } + ] + ], + "corrected_depth": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "${prefix}.correctedDepth.txt": { + "type": "file", + "description": "A text file with corrected depth per bin", + "pattern": "*.{params.txt}", + "ontologies": [] + } + } + ] + ], + "ichorcna_params": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "${prefix}.params.txt": { + "type": "file", + "description": "A text file showing the values that ichorCNA has estimated for tumour fraction, ploidy etc", + "pattern": "*.{params.txt}", + "ontologies": [] + } + } + ] + ], + "plots": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "${prefix}/*.pdf": { + "type": "file", + "description": "Plots with e.g. individual chromosomes and different considered ploidy", + "pattern": "*.{pdf}", + "ontologies": [] + } + } + ] + ], + "genome_plot": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "**/${prefix}_genomeWide.pdf": { + "type": "file", + "description": "A plot with the best-fit genome-wide CNV data", + "pattern": "*.{genomeWide.pdf}", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@sppearce", "@adamrtalbot"], + "maintainers": ["@sppearce", "@adamrtalbot"] } - } - ], - "output": { - "output": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.${suffix}": { - "type": "file", - "description": "The output file - if using shell redirection, specify the name of this file using `ext.prefix` and the extension using `ext.suffix`. Otherwise, ensure the awk program produces files with the extension in `ext.suffix`.", - "pattern": "*", - "ontologies": [] - } - } - ] - ], - "versions_gawk": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gawk": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "awk -Wversion | sed '1!d; s/.*Awk //; s/,.*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gawk": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "awk -Wversion | sed '1!d; s/.*Awk //; s/,.*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] }, - "authors": [ - "@nvnieuwk" - ], - "maintainers": [ - "@nvnieuwk" - ] - }, - "pipelines": [ { - "name": "circrna", - "version": "dev" + "name": "icountmini_metagene", + "path": "modules/nf-core/icountmini/metagene/meta.yml", + "type": "module", + "meta": { + "name": "icountmini_metagene", + "description": "Plot a metagene of cross-link events/sites around various transcriptomic landmarks.", + "keywords": ["iCLIP", "gtf", "genomics"], + "tools": [ + { + "icount": { + "description": "Computational pipeline for analysis of iCLIP data", + "homepage": "https://icount.readthedocs.io/en/latest/", + "documentation": "https://icount.readthedocs.io/en/latest/", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bed": { + "type": "file", + "description": "BED file of crosslinks", + "ontologies": [] + } + } + ], + { + "segmentation": { + "type": "file", + "description": "A iCount segmentation file", + "pattern": "*.{gtf}", + "ontologies": [] + } + } + ], + "output": { + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "metagene_*/*plot_data.tsv": { + "type": "file", + "description": "Metagene table", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@marc-jones", "@chris-cheshire", "@charlotteanne"], + "maintainers": ["@marc-jones", "@chris-cheshire", "@charlotteanne"] + } }, { - "name": "createpanelrefs", - "version": "dev" + "name": "icountmini_peaks", + "path": "modules/nf-core/icountmini/peaks/meta.yml", + "type": "module", + "meta": { + "name": "icountmini_peaks", + "description": "Runs iCount peaks on a BED file of crosslinks", + "keywords": ["iCLIP", "bed", "genomics"], + "tools": [ + { + "icount": { + "description": "Computational pipeline for analysis of iCLIP data", + "homepage": "https://github.com/ulelab/iCount-Mini", + "documentation": "https://github.com/ulelab/iCount-Mini", + "tool_dev_url": "https://github.com/ulelab/iCount-Mini", + "doi": "10.1038/nsmb.1838", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bed": { + "type": "file", + "description": "BED file of crosslinks", + "pattern": "*.{bed}", + "ontologies": [] + } + }, + { + "sigxls": { + "type": "file", + "description": "TSV file of sigxls from iCount sigxls", + "pattern": "*.{tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "output": { + "peaks": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.peaks.bed.gz": { + "type": "file", + "description": "Crosslinks deemed significant by iCount", + "pattern": "*.{bed.gz}", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@marc-jones", "@chris-cheshire", "@charlotteanne"], + "maintainers": ["@marc-jones", "@chris-cheshire", "@charlotteanne"] + } }, { - 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Check the documentation at:\n https://github.com/igvteam/igv-webapp for an example and\n https://github.com/igvteam/igv.js/wiki/Data-Server-Requirements for server requirements\n", + "homepage": "https://github.com/igvteam/igv.js", + "documentation": "https://github.com/igvteam/igv.js/wiki", + "tool_dev_url": "https://github.com/igvteam/igv.js", + "doi": "10.1093/bioinformatics/btac830", + "licence": ["MIT"], + "identifier": "biotools:igv" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "alignment": { + "type": "file", + "description": "Sorted BAM/CRAM file", + "pattern": "*.{bam,cram}", + "ontologies": [] + } + }, + { + "index": { + "type": "file", + "description": "Index of sorted BAM/CRAM file", + "pattern": "*.{bai,crai}", + "ontologies": [] + } + } + ] + ], + "output": { + "browser": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_genome-browser.html": { + "type": "file", + "description": "Genome browser HTML file", + "pattern": "*.{html}", + "ontologies": [] + } + } + ] + ], + "align_files": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "alignment": { + "type": "file", + "description": "Copy of the input sorted BAM/CRAM file", + "pattern": "*.{bam,cram}", + "ontologies": [] + } + } + ] + ], + "index_files": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "index": { + "type": "file", + "description": "Copy of the input index of sorted BAM/CRAM file", + "pattern": "*.{bai,crai}", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@mirpedrol"], + "maintainers": ["@mirpedrol"] + } }, { - 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Ilastik contains a graphical user interface to interactively label pixels. 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Ilastik contains a graphical user interface to interactively label pixels. However, this nextflow module will implement the --headless mode, to apply pixel classification using a pre-trained .ilp file on an input image.", + "keywords": ["pixel_classification", "segmentation", "probability_maps"], + "tools": [ + { + "ilastik": { + "description": "Ilastik is a user friendly tool that enables pixel classification, segmentation and analysis.", + "homepage": "https://www.ilastik.org/", + "documentation": "https://www.ilastik.org/documentation/", + "tool_dev_url": "https://github.com/ilastik/ilastik", + "licence": ["GPL3"], + "identifier": "biotools:ilastik" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information for h5 file\ne.g. [ id:'test' ]\n" + } + }, + { + "input_img": { + "type": "file", + "description": "Input img file containing image stack to classify. Input format is specified within the .ilp project file.", + "ontologies": [] + } + }, + { + "output_format": { + "type": "string", + "description": "String specifying the output format passed as the file extension to the output file specified with the `output_filename_format` parameter." + } + }, + { + "export_source": { + "type": "string", + "description": "String passed to the `export_source` parameter - valid options are 'probabilities', '\"simple segmentation\"', 'uncertainty', 'features', 'labels']" + } + } + ], + { + "ilp": { + "type": "file", + "description": "Trained ilastik pixel classification .ilp project file", + "pattern": "*.{ilp}", + "ontologies": [] + } + } + ], + "output": { + "output": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.${output_format}": { + "type": "file", + "description": "Output file from ilastik pixel classification, as specified by the `output_format` parameter.", + "ontologies": [] + } + } + ] + ], + "versions_ilastik": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "ilastik": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "/opt/ilastik-1.4.0-Linux/run_ilastik.sh --headless --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "ilastik": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "/opt/ilastik-1.4.0-Linux/run_ilastik.sh --headless --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@FloWuenne"], + "maintainers": ["@FloWuenne"] + }, + "pipelines": [ + { + "name": "mcmicro", + "version": "dev" + }, + { + "name": "molkart", + "version": "1.2.0" + } + ] }, { - "name": "sarek", - "version": "3.8.1" + "name": "imc2mc", + "path": "modules/nf-core/imc2mc/meta.yml", + "type": "module", + "meta": { + "name": "imc2mc", + "description": "Staging module transforming Imaging Mass Cytometry .txt files to .tif files with OME-XML metadata. Includes optional hot pixel removal.", + "keywords": ["imaging", "ome-tif", "staging", "MCMICRO"], + "tools": [ + { + "imc2mc": { + "description": "Formatting Imaging Mass Cytrometry (IMC) output files to be compatible with the MCMICRO pipeline.", + "homepage": "https://github.com/SchapiroLabor/imc2mc", + "documentation": "https://github.com/SchapiroLabor/imc2mc/README.md", + "tool_dev_url": "https://github.com/SchapiroLabor/imc2mc", + "licence": ["GPL-3.0 license"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "txtfile": { + "type": "file", + "description": "Acquisition TXT file", + "pattern": "*.{txt}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1964" + } + ] + } + } + ] + ], + "output": { + "tif": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.tif": { + "type": "file", + "description": "One output .tif file containing acquisition and metadata", + "pattern": "*.{tif}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3591" + } + ] + } + } + ] + ], + "versions_imc2mc": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "imc2mc": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "imc2mc --version | sed 's/v//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "imc2mc": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "imc2mc --version | sed 's/v//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@MargotCh", "@kbestak"], + "maintainers": ["@MargotCh"] + } }, { - "name": "smrnaseq", - "version": "2.4.1" + "name": "immunedeconv", + "path": "modules/nf-core/immunedeconv/meta.yml", + "type": "module", + "meta": { + "name": "immunedeconv", + "description": "Perform immune cell deconvolution using RNA-seq data and various computational methods.", + "keywords": ["Immune Deconvolution", "RNA-seq", "Bioinformatics Tools", "Computational Immunology"], + "tools": [ + { + "immunedeconv": { + "description": "The immunedeconv R package provides functions for immune cell deconvolution\nfrom RNA-seq data. It supports multiple deconvolution methods and generates\nresults as well as visualizations.\n", + "homepage": "https://github.com/icbi-lab/immunedeconv", + "documentation": "https://icbi-lab.github.io/immunedeconv/", + "licence": ["GPL-2"], + "identifier": "biotools:immunedeconv" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "input_file": { + "type": "file", + "description": "Input matrix with genes in rows and samples in columns.", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, + { + "method": { + "type": "string", + "description": "The deconvolution method to use (e.g., 'CIBERSORT', 'EPIC', 'xCell')." + } + }, + { + "function": { + "type": "string", + "description": "The specific function from immunedeconv to execute for analysis." + } + } + ], + { + "gene_symbol_col": { + "type": "string", + "description": "Column name for gene symbols in the matrix input file." + } + } + ], + "output": { + "deconv_table": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.deconvolution_results.tsv": { + "type": "file", + "description": "Results table containing deconvolution data.", + "pattern": "*.deconvolution_results.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "deconv_plots": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.png": { + "type": "file", + "description": "Visualization plots generated during deconvolution.", + "pattern": "*.png", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@grst", "@nschcolnicov"], + "maintainers": ["@grst", "@nschcolnicov"] + } }, { - "name": "tfactivity", - "version": "dev" + "name": "infernal_cmsearch", + "path": "modules/nf-core/infernal/cmsearch/meta.yml", + "type": "module", + "meta": { + "name": "infernal_cmsearch", + "description": "Search covariance models against a sequence database", + "keywords": ["rrna", "covariance model", "sequence search"], + "tools": [ + { + "infernal": { + "description": "Infernal is for searching DNA sequence databases for RNA structure and sequence similarities.", + "homepage": "http://eddylab.org/infernal/Userguide.pdf", + "documentation": "http://eddylab.org/infernal/Userguide.pdf", + "tool_dev_url": "https://github.com/EddyRivasLab/infernal", + "doi": "10.1093/bioinformatics/btt509", + "licence": ["BSD-3-clause"], + "identifier": "biotools:infernal" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "cmfile": { + "type": "file", + "description": "A calibrated Infernal covariance model file\n", + "ontologies": [ + { + "edam": "http://edamontology.org/data_1364" + } + ] + } + }, + { + "seqdb": { + "type": "file", + "description": "A FASTA file of sequences to search the covariance models\nagainst. Can be gzipped.\n", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + { + "write_align": { + "type": "boolean", + "description": "Flag to save optional alignment output in Stockholm\nformat. Specify with 'true' to save.\n" + } + }, + { + "write_target": { + "type": "boolean", + "description": "Flag to save optional per target summary in a tabular\nformat. Specify with 'true' to save.\n" + } + } + ], + "output": { + "output": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.txt.gz": { + "type": "file", + "description": "Human readable output summarizing hmmsearch results", + "pattern": "*.{txt.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/data_3671" + } + ] + } + } + ] + ], + "alignments": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.sto.gz": { + "type": "file", + "description": "Optional multiple sequence alignment (MSA) in Stockholm format", + "pattern": "*.{sto.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1961" + } + ] + } + } + ] + ], + "target_summary": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.tbl.gz": { + "type": "file", + "description": "Optional tabular (space-delimited) summary of per-target output", + "pattern": "*.{tbl.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_infernal": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "infernal": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cmsearch -h | sed '2!d;s/.*INFERNAL //;s/ .*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_gzip": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gzip": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gzip --version |& sed '1!d;s/gzip //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "infernal": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "cmsearch -h | sed '2!d;s/.*INFERNAL //;s/ .*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gzip": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gzip --version |& sed '1!d;s/gzip //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@prototaxites"], + "maintainers": ["@prototaxites"] + } }, { - "name": "variantbenchmarking", - "version": "1.5.0" - } - ] - }, - { - "name": "gcta_makegrm", - "path": "modules/nf-core/gcta/makegrm/meta.yml", - "type": "module", - "meta": { - "name": "gcta_makegrm", - "description": "Compute a whole dense GRM with GCTA", - "keywords": [ - "gcta", - "genome-wide complex trait analysis", - "grm", - "genetic relationship matrix", - "genetics" - ], - "tools": [ - { - "gcta": { - "description": "GCTA is a tool for genome-wide complex trait analysis.", - "homepage": "https://yanglab.westlake.edu.cn/software/gcta/", - "documentation": "https://yanglab.westlake.edu.cn/software/gcta/static/gcta_doc_latest.pdf", - "tool_dev_url": "https://github.com/jianyangqt/gcta", - "licence": [ - "GPL-3.0-only" - ], - "identifier": "biotools:gcta" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing GRM sample metadata\ne.g. `[ id:'gcta_grm' ]`\n" - } - }, - { - "mfile": { - "type": "file", - "description": "GCTA multi-input manifest consumed by `--mbfile` or `--mpfile`", - "pattern": "*.{mbfile,mpfile,txt}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2330" - } - ] - } - }, - { - "bed_pgen": { - "type": "file", - "description": "Collection of PLINK primary genotype files referenced by the multi-input manifest", - "pattern": "*.{bed,pgen}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3003" - } - ] - } - }, - { - "bim_pvar": { - "type": "file", - "description": "Collection of PLINK variant metadata files referenced by the multi-input manifest", - "pattern": "*.{bim,pvar}", - "ontologies": [] - } - }, - { - "fam_psam": { - "type": "file", - "description": "Collection of PLINK sample metadata files referenced by the multi-input manifest", - "pattern": "*.{fam,psam}", - "ontologies": [] - } - } - ] - ], - "output": { - "grm_files": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing GRM sample metadata\ne.g. `[ id:'gcta_grm' ]`\n" - } - }, - { - "*.grm.*": { - "type": "file", - "description": "Dense GRM sidecar files", - "pattern": "*.grm.{id,bin,N.bin}", - "ontologies": [] - } - } - ] - ], - "versions_gcta": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the version was collected from" - } - }, - { - "gcta": { - "type": "string", - "description": "The tool name" - } - }, - { - "gcta --version | sed -En 's/^[*] version v([0-9.]*).*/\\1/p'": { - "type": "eval", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "gcta": { - "type": "string", - "description": "The tool name" - } - }, - { - "gcta --version | sed -En 's/^[*] version v([0-9.]*).*/\\1/p'": { - "type": "eval", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@lyh970817" - ], - "maintainers": [ - "@lyh970817" - ] - } - }, - { - "name": "gcta_makegrmpart", - "path": "modules/nf-core/gcta/makegrmpart/meta.yml", - "type": "module", - "meta": { - "name": "gcta_makegrmpart", - "description": "Compute one partition of a GCTA genetic relationship matrix", - "keywords": [ - "gcta", - "genome-wide complex trait analysis", - "grm", - "genetic relationship matrix", - "genetics" - ], - "tools": [ - { - "gcta": { - "description": "GCTA is a tool for genome-wide complex trait analysis.", - "homepage": "https://yanglab.westlake.edu.cn/software/gcta/", - "documentation": "https://yanglab.westlake.edu.cn/software/gcta/static/gcta_doc_latest.pdf", - "tool_dev_url": "https://github.com/jianyangqt/gcta", - "licence": [ - "GPL-3.0-only" - ], - "identifier": "biotools:gcta" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing GRM-partition sample metadata\ne.g. `[ id:'gcta_grm' ]`\n" - } - }, - { - "nparts_gcta": { - "type": "integer", - "description": "Total number of GRM partitions requested via `--make-grm-part`; defaults to `1` when `null`", - "default": 1 - } - }, - { - "part_gcta_job": { - "type": "integer", - "description": "One-based index of the GRM partition to compute via `--make-grm-part`; defaults to `1` when `null`", - "default": 1 - } - }, - { - "mfile": { - "type": "file", - "description": "GCTA multi-input manifest consumed by `--mbfile` or `--mpfile`", - "pattern": "*.{mbfile,mpfile,txt}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2330" - } - ] - } - }, - { - "bed_pgen": { - "type": "file", - "description": "Collection of PLINK primary genotype files referenced by the multi-input manifest", - "pattern": "*.{bed,pgen}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3003" - } - ] - } - }, - { - "bim_pvar": { - "type": "file", - "description": "Collection of PLINK variant metadata files referenced by the multi-input manifest", - "pattern": "*.{bim,pvar}", - "ontologies": [] - } - }, - { - "fam_psam": { - "type": "file", - "description": "Collection of PLINK sample metadata files referenced by the multi-input manifest", - "pattern": "*.{fam,psam}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing SNP-selection metadata\ne.g. `[ id:'snp_group1' ]`\n" - } + "name": "instrain_compare", + "path": "modules/nf-core/instrain/compare/meta.yml", + "type": "module", + "meta": { + "name": "instrain_compare", + "description": "Strain-level comparisons across multiple inStrain profiles", + "keywords": ["instrain", "compare", "align", "diversity", "coverage"], + "tools": [ + { + "instrain": { + "description": "Calculation of strain-level metrics", + "homepage": "https://github.com/MrOlm/instrain", + "documentation": "https://instrain.readthedocs.io/en/latest/", + "tool_dev_url": "https://github.com/MrOlm/instrain", + "doi": "10.1038/s41587-020-00797-0", + "licence": ["MIT"], + "identifier": "biotools:instrain" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "bams": { + "type": "file", + "description": "Path to .bam files that were profiled", + "pattern": "*.{bam,sam}", + "ontologies": [] + } + }, + { + "profiles": { + "type": "directory", + "description": "InStrain profile folders", + "pattern": "*.IS/" + } + } + ], + { + "stb_file": { + "type": "file", + "description": "Path to .stb (scaffold to bin) file that was profiled", + "pattern": "*.stb", + "ontologies": [] + } + } + ], + "output": { + "compare": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.IS_compare": { + "type": "directory", + "description": "inStrain compare folders", + "pattern": "*.IS_compare/" + } + } + ] + ], + "comparisons_table": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.IS_compare/output/*.IS_compare_comparisonsTable.tsv": { + "type": "file", + "description": "Comparisons table", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "pooled_snv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.IS_compare/output/*.IS_compare_pooled_SNV_data.tsv": { + "type": "file", + "description": "Pooled SNV", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "snv_keys": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.IS_compare/output/*.IS_compare_pooled_SNV_data_keys.tsv": { + "type": "file", + "description": "SNV keys", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "snv_info": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.IS_compare/output/*.IS_compare_pooled_SNV_info.tsv": { + "type": "file", + "description": "SNV information", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@margotl9", "@CarsonJM"], + "maintainers": ["@margotl9", "@CarsonJM"] }, - { - "snp_group_file": { - "type": "file", - "description": "Optional SNP extraction file passed to `--extract`; provide `[]` when absent", - "pattern": "*.{txt,list}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2330" - } - ] - } - } - ] - ], - "output": { - "grm_files": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing GRM-partition sample metadata\ne.g. `[ id:'gcta_grm' ]`\n" - } - }, - { - "*.part_${nparts}_${part}.grm.*": { - "type": "file", - "description": "Partitioned GRM output files, including ID, binary matrix, and sample-count matrix files", - "pattern": "*.part_${nparts}_${part}.grm.*", - "ontologies": [] - } - }, - { - "nparts_gcta": { - "type": "integer", - "description": "Total number of GRM partitions requested via `--make-grm-part`" - } - }, - { - "part_gcta_job": { - "type": "integer", - "description": "One-based index of the GRM partition computed via `--make-grm-part`" - } - } - ] - ], - "versions_gcta": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "gcta": { - "type": "string", - "description": "The tool name" - } - }, - { - "gcta --version | sed -En 's/^[*] version v([0-9.]*).*/\\1/p'": { - "type": "eval", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "gcta": { - "type": "string", - "description": "The tool name" - } - }, - { - "gcta --version | sed -En 's/^[*] version v([0-9.]*).*/\\1/p'": { - "type": "eval", - "description": "The command used to generate the version of the tool" - } - } + "pipelines": [ + { + "name": "phageannotator", + "version": "dev" + } ] - ] - }, - "authors": [ - "@lyh970817" - ], - "maintainers": [ - "@lyh970817" - ] - } - }, - { - "name": "gecco_convert", - "path": "modules/nf-core/gecco/convert/meta.yml", - "type": "module", - "meta": { - "name": "gecco_convert", - "description": "This command helps transforming the output files created by\nGECCO into helpful format, should you want to use the results in\ncombination with other tools.\n", - "keywords": [ - "bgc", - "reformatting", - "clusters", - "gbk", - "gff", - "bigslice", - "faa", - "fna" - ], - "tools": [ - { - "gecco": { - "description": "Biosynthetic Gene Cluster prediction with Conditional Random Fields.", - "homepage": "https://gecco.embl.de", - "documentation": "https://gecco.embl.de", - "tool_dev_url": "https://github.com/zellerlab/GECCO", - "doi": "10.1101/2021.05.03.442509", - "licence": [ - "GPL v3" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "clusters": { - "type": "file", - "description": "TSV file containing coordinates of gecco predicted clusters and BGC types.\n", - "pattern": "*.clusters.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } + }, + { + "name": "instrain_profile", + "path": "modules/nf-core/instrain/profile/meta.yml", + "type": "module", + "meta": { + "name": "instrain_profile", + "description": "inStrain is python program for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification", + "keywords": ["instrain", "metagenomics", "population genomics", "profile"], + "tools": [ + { + "instrain": { + "description": "Calculation of strain-level metrics", + "homepage": "https://github.com/MrOlm/instrain", + "documentation": "https://instrain.readthedocs.io/en/latest/", + "tool_dev_url": "https://github.com/MrOlm/instrain", + "doi": "10.1038/s41587-020-00797-0", + "licence": ["MIT"], + "identifier": "biotools:instrain" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'test']" + } + }, + { + "bam": { + "type": "file", + "description": "Path to .bam file to be profiled", + "pattern": "*.{bam,sam}", + "ontologies": [] + } + } + ], + { + "genome_fasta": { + "type": "file", + "description": "Path to .fasta file to be profiled; MUST be the .fasta file that was mapped to to create the .bam file", + "pattern": "*.{fasta,fna,fa}", + "ontologies": [] + } + }, + { + "genes_fasta": { + "type": "file", + "description": "Path to .fna file of genes to be profiled (OPTIONAL)", + "pattern": "*.{fasta,fna,fa}", + "ontologies": [] + } + }, + { + "stb_file": { + "type": "file", + "description": "Path to .stb (scaffold to bin) file to be profiled (OPTIONAL)", + "pattern": "*.stb", + "ontologies": [] + } + } + ], + "output": { + "profile": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.IS": { + "type": "directory", + "description": "InStrain profile folder", + "pattern": "*.IS/" + } + } + ] + ], + "snvs": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.IS/output/*.IS_SNVs.tsv": { + "type": "file", + "description": "SNVs", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "gene_info": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.IS/output/*.IS_gene_info.tsv": { + "type": "file", + "description": "Gene information", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "genome_info": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.IS/output/*.IS_genome_info.tsv": { + "type": "file", + "description": "Genome information", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "linkage": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.IS/output/*.IS_linkage.tsv": { + "type": "file", + "description": "Linkage information", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "mapping_info": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.IS/output/*.IS_mapping_info.tsv": { + "type": "file", + "description": "Mapping information", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "scaffold_info": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.IS/output/*.IS_scaffold_info.tsv": { + "type": "file", + "description": "Scaffold information", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@mrolm"], + "maintainers": ["@mrolm"] }, - { - "gbk": { - "type": "file", - "description": "Per cluster GenBank file containing sequence with annotations\n", - "pattern": "*.gbk", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1936" - } - ] - } - } - ], - { - "mode": { - "type": "string", - "description": "Either clusters or gbk folder output, depending on what is reformatted", - "enum": [ - "clusters", - "gbk" - ] - } - }, - { - "format": { - "type": "string", - "description": "Format for the output file", - "enum": [ - "gff", - "bigslice", - "faa", - "fna" - ] - } - } - ], - "output": { - "gff": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}/*.gff": { - "type": "file", - "description": "GFF3 converted cluster tables containing the position\nand metadata for all the predicted clusters\n", - "pattern": "*.gff", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1975" - } - ] - } - } - ] - ], - "bigslice": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}/*.region*.gbk": { - "type": "file", - "description": "Converted and aliased GenBank files so that they can be loaded by BiG-SLiCE\n", - "pattern": "*.region*.gbk", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1936" - } - ] - } - } - ] - ], - "faa": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}/*.faa": { - "type": "file", - "description": "Amino-acid FASTA converted GenBank files of all the proteins in a cluster\n", - "pattern": "*.faa", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ], - "fna": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}/*.fna": { - "type": "file", - "description": "Nucleotide sequence FASTA converted GenBank files from the cluster\n", - "pattern": "*.fna", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ], - "versions_gecco": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gecco": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gecco -V |& sed 's/gecco //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gecco": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gecco -V |& sed 's/gecco //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "phageannotator", + "version": "dev" + } ] - ] - }, - "authors": [ - "@vagkaratzas" - ], - "maintainers": [ - "@vagkaratzas" - ] - } - }, - { - "name": "gecco_run", - "path": "modules/nf-core/gecco/run/meta.yml", - "type": "module", - "meta": { - "name": "gecco_run", - "description": "GECCO is a fast and scalable method for identifying putative novel Biosynthetic Gene Clusters (BGCs) in genomic and metagenomic data using Conditional Random Fields (CRFs).", - "keywords": [ - "bgc", - "detection", - "metagenomics", - "contigs" - ], - "tools": [ - { - "gecco": { - "description": "Biosynthetic Gene Cluster prediction with Conditional Random Fields.", - "homepage": "https://gecco.embl.de", - "documentation": "https://gecco.embl.de", - "tool_dev_url": "https://github.com/zellerlab/GECCO", - "doi": "10.1101/2021.05.03.442509", - "licence": [ - "GPL v3" - ], - "identifier": "" + }, + { + "name": "integronfinder", + "path": "modules/nf-core/integronfinder/meta.yml", + "type": "module", + "meta": { + "name": "integronfinder", + "description": "Detect integrons in DNA sequences", + "keywords": ["bacteria", "fasta", "mobile genetic elements", "integron"], + "tools": [ + { + "integronfinder": { + "description": "Integron Finder aims at detecting independently integron integrase and attC recombination sites in DNA sequences", + "homepage": "https://integronfinder.readthedocs.io/en/latest/", + "documentation": "https://integronfinder.readthedocs.io/en/latest/", + "tool_dev_url": "https://github.com/gem-pasteur/Integron_Finder/", + "doi": "10.3390/microorganisms10040700", + "licence": ["GPL v3-or-later"], + "identifier": "biotools:integron_finder" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Nucleotide sequences in FASTA format", + "pattern": "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/data_2977" + }, + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ] + ], + "output": { + "gbk": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*/*.gbk": { + "type": "file", + "description": "Creates a Genbank files with all the annotations found (present in the .integrons file)", + "pattern": "*.gbk", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1936" + } + ] + } + } + ] + ], + "integrons": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*/*.integrons": { + "type": "file", + "description": "A file with all integrons and their elements detected in all sequences in the input file", + "pattern": "*.integrons", + "ontologies": [] + } + } + ] + ], + "summary": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*/*.summary": { + "type": "file", + "description": "A summary file with the number and type of integrons per sequence", + "pattern": "*.summary", + "ontologies": [] + } + } + ] + ], + "out": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*/integron_finder.out": { + "type": "file", + "description": "A copy standard output. The stdout can be silenced with the argument --mute", + "pattern": "integron_finder.out", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@nguyent-son", "@juke34", "@jhayer"], + "maintainers": ["@nguyent-son", "@juke34", "@jhayer"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "A genomic file containing one or more sequences as input. Input type is any supported by Biopython (fasta, gbk, etc.)", - "pattern": "*", - "ontologies": [] - } + }, + { + "name": "interproscan", + "path": "modules/nf-core/interproscan/meta.yml", + "type": "module", + "meta": { + "name": "interproscan", + "description": "Produces protein annotations and predictions from an amino acids FASTA file", + "keywords": ["annotation", "fasta", "protein", "dna", "interproscan"], + "tools": [ + { + "interproscan": { + "description": "InterPro integrates together predictive information about proteins function from a number of partner resources", + "homepage": "https://www.ebi.ac.uk/interpro/search/sequence/", + "documentation": "https://interproscan-docs.readthedocs.io", + "tool_dev_url": "https://github.com/ebi-pf-team/interproscan", + "doi": "10.1093/bioinformatics/btu031", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input fasta file containing the amino acid or dna query sequences", + "pattern": "*.{fa,fasta,fa.gz,fasta.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + { + "interproscan_database": { + "type": "directory", + "description": "Path to the interproscan database (untarred http://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/${version_major}-${version_minor}/interproscan-${version_major}-${version_minor}-64-bit.tar.gz)" + } + } + ], + "output": { + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.tsv": { + "type": "file", + "description": "Tab separated file containing with detailed hits", + "pattern": "*.{tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "xml": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.xml": { + "type": "file", + "description": "XML file containing with detailed hits", + "pattern": "*.{xml}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2332" + } + ] + } + } + ] + ], + "gff3": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.gff3": { + "type": "file", + "description": "GFF3 file containing with detailed hits", + "pattern": "*.{gff3}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1975" + } + ] + } + } + ] + ], + "json": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.json": { + "type": "file", + "description": "JSON file containing with detailed hits", + "pattern": "*.{json}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "versions_interproscan": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "interproscan": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "interproscan.sh --version | sed \"1!d; s/.*version //\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "interproscan": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "interproscan.sh --version | sed \"1!d; s/.*version //\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@toniher", "@mahesh-panchal"], + "maintainers": ["@toniher", "@vagkaratzas", "@mahesh-panchal"] }, - { - "hmm": { - "type": "file", - "description": "Alternative HMM file(s) to use in HMMER format", - "pattern": "*.hmm", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1370" - } - ] - } - } - ], - { - "model_dir": { - "type": "directory", - "description": "Path to an alternative CRF (Conditional Random Fields) module to use" - } - } - ], - "output": { - "genes": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.genes.tsv": { - "type": "file", - "description": "TSV file containing detected/predicted genes with BGC probability scores. Will not be generated if no hits are found.", - "pattern": "*.genes.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "features": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.features.tsv": { - "type": "file", - "description": "TSV file containing identified domains", - "pattern": "*.features.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "clusters": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.clusters.tsv": { - "type": "file", - "description": "TSV file containing coordinates of predicted clusters and BGC types. Will not be generated if no hits are found.", - "pattern": "*.clusters.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "gbk": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_cluster_*.gbk": { - "type": "file", - "description": "Per cluster GenBank file (if found) containing sequence with annotations. Will not be generated if no hits are found.", - "pattern": "*.gbk", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1936" - } - ] - } - } - ] - ], - "json": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.json": { - "type": "file", - "description": "AntiSMASH v6 sideload JSON file (if --antismash-sideload) supplied. Will not be generated if no hits are found.", - "pattern": "*.gbk", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1936" - } - ] - } - } - ] - ], - "versions_gecco": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gecco": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gecco -V |& sed 's/gecco //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gecco": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gecco -V |& sed 's/gecco //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "funcscan", + "version": "3.0.0" + }, + { + "name": "proteinannotator", + "version": "1.1.0" + } ] - ] - }, - "authors": [ - "@jfy133" - ], - "maintainers": [ - "@jfy133" - ] - }, - "pipelines": [ - { - "name": "funcscan", - "version": "3.0.0" - } - ] - }, - { - "name": "gedi_indexgenome", - "path": "modules/nf-core/gedi/indexgenome/meta.yml", - "type": "module", - "meta": { - "name": "gedi_indexgenome", - "description": "Build a GEDI genome index from a FASTA and GTF for downstream PRICE ORF prediction", - "keywords": [ - "riboseq", - "index", - "genome", - "gedi", - "price", - "orf" - ], - "tools": [ - { - "gedi": { - "description": "Gedi is a Java software platform for working with genomic data (sequencing reads, sequences, per-base numeric values, annotations). It provides the PRICE algorithm for ribosome profiling ORF discovery.", - "homepage": "https://github.com/erhard-lab/gedi", - "documentation": "https://github.com/erhard-lab/gedi/wiki", - "tool_dev_url": "https://github.com/erhard-lab/gedi", - "doi": "10.1038/nmeth.4631", - "licence": [ - "GPL-3.0" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. `[ id:'homo_sapiens' ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Genome FASTA file", - "pattern": "*.{fa,fasta,fna}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } + }, + { + "name": "iphop_download", + "path": "modules/nf-core/iphop/download/meta.yml", + "type": "module", + "meta": { + "name": "iphop_download", + "description": "Download, extract, and check md5 of iPHoP databases", + "keywords": ["metagenomics", "iphop", "database", "download", "phage", "bacteria", "host"], + "tools": [ + { + "iphop": { + "description": "Predict host genus from genomes of uncultivated phages.", + "homepage": "https://bitbucket.org/srouxjgi/iphop/src/main/", + "documentation": "https://bitbucket.org/srouxjgi/iphop/src/main/", + "tool_dev_url": "https://bitbucket.org/srouxjgi/iphop/src/main/", + "doi": "10.1371/journal.pbio.3002083", + "licence": ["Modified GPL v3"], + "identifier": "" + } + } + ], + "output": { + "iphop_db": [ + { + "iphop_db/": { + "type": "directory", + "description": "Directory containing downloaded and md5 checked iPHoP database", + "pattern": "iphop_db/" + } + } + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@CarsonJM"], + "maintainers": ["@CarsonJM"] }, - { - "gtf": { - "type": "file", - "description": "GTF annotation file", - "pattern": "*.{gtf}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2306" - } - ] - } - } - ] - ], - "output": { - "index": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. `[ id:'homo_sapiens' ]`\n" - } - }, - { - "${prefix}": { - "type": "directory", - "description": "GEDI genome index directory containing the `.oml` index file and\nits sidecar resources. Consumed as `-genomic` by PRICE. Directory\nname defaults to `meta.id` and can be overridden via `task.ext.prefix`.\n", - "pattern": "*" - } - } - ] - ], - "versions_gedi": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gedi": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gedi -e Version 2>&1 | sed -n 's/.*Gedi version \\([^ ]*\\).*/\\1/p' | head -n 1": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gedi": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gedi -e Version 2>&1 | sed -n 's/.*Gedi version \\([^ ]*\\).*/\\1/p' | head -n 1": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "phageannotator", + "version": "dev" + } ] - ] - }, - "authors": [ - "@pinin4fjords" - ], - "maintainers": [ - "@pinin4fjords" - ] - } - }, - { - "name": "gedi_price", - "path": "modules/nf-core/gedi/price/meta.yml", - "type": "module", - "meta": { - "name": "gedi_price", - "description": "Identify translated ORFs from Ribo-seq BAMs using the PRICE algorithm", - "keywords": [ - "riboseq", - "orf", - "price", - "gedi", - "translation" - ], - "tools": [ - { - "gedi": { - "description": "Gedi is a Java software platform for working with genomic data (sequencing reads, sequences, per-base numeric values, annotations). It provides the PRICE algorithm (Probabilistic Inference of Codon Activities by an EM algorithm) for ribosome profiling ORF discovery with near-cognate start codon detection.", - "homepage": "https://github.com/erhard-lab/gedi", - "documentation": "https://github.com/erhard-lab/gedi/wiki", - "tool_dev_url": "https://github.com/erhard-lab/gedi", - "doi": "10.1038/nmeth.4631", - "licence": [ - "GPL-3.0" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map identifying the cohort of Ribo-seq BAMs analysed together.\nPRICE is run jointly across all BAMs in this tuple.\ne.g. `[ id:'all_samples' ]`\n" - } - }, - { - "bams": { - "type": "file", - "description": "One or more sorted Ribo-seq BAM files. Staged under `bams/` so PRICE\ndiscovers them via a generated bamlist.\n", - "pattern": "*.{bam}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - }, - { - "bais": { - "type": "file", - "description": "Index files matching the input BAMs.", - "pattern": "*.{bai}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information. `meta2.id` must match the\nbase name used when the index was built (`.oml` lives inside the\nindex directory).\ne.g. `[ id:'homo_sapiens' ]`\n" - } - }, - { - "index": { - "type": "directory", - "description": "GEDI genome index directory produced by GEDI_INDEXGENOME.", - "pattern": "price_index" - } - } - ] - ], - "output": { - "orfs_tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map identifying the analysed cohort.\n" - } - }, - { - "${prefix}.orfs.tsv": { - "type": "file", - "description": "Tab-delimited table of predicted translated ORFs with start codon,\nlocation, p-value and supporting read counts.\n", - "pattern": "*.orfs.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "orfs_cit": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map identifying the analysed cohort.\n" - } - }, - { - "${prefix}.orfs.cit": { - "type": "file", - "description": "GEDI binary CIT file of called ORFs.", - "pattern": "*.orfs.cit", - "ontologies": [] - } - } - ] - ], - "orfs_metadata": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map identifying the analysed cohort.\n" - } - }, - { - "${prefix}.orfs.cit.metadata.json": { - "type": "file", - "description": "JSON metadata accompanying the ORF CIT file.", - "pattern": "*.orfs.cit.metadata.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "codons_cit": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map identifying the analysed cohort.\n" - } - }, - { - "${prefix}.codons.cit": { - "type": "file", - "description": "GEDI binary CIT file of per-codon signal.", - "pattern": "*.codons.cit", - "ontologies": [] - } - } - ] - ], - "model": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map identifying the analysed cohort.\n" - } - }, - { - "${prefix}.model": { - "type": "file", - "description": "PRICE model parameters fit during the run.", - "pattern": "*.model", - "ontologies": [] - } - } - ] - ], - "signal": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map identifying the analysed cohort.\n" - } - }, - { - "${prefix}.signal.tsv": { - "type": "file", - "description": "Tab-delimited per-position signal summary.", - "pattern": "*.signal.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "param": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map identifying the analysed cohort.\n" - } - }, - { - "${prefix}.param": { - "type": "file", - "description": "PRICE run parameters file.", - "pattern": "*.param", - "ontologies": [] - } - } - ] - ], - "versions_gedi": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gedi": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gedi -e Version 2>&1 | sed -n 's/.*Gedi version \\([^ ]*\\).*/\\1/p' | head -n 1": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gedi": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gedi -e Version 2>&1 | sed -n 's/.*Gedi version \\([^ ]*\\).*/\\1/p' | head -n 1": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@pinin4fjords" - ], - "maintainers": [ - "@pinin4fjords" - ] - } - }, - { - "name": "gem2_gem2bedmappability", - "path": "modules/nf-core/gem2/gem2bedmappability/meta.yml", - "type": "module", - "meta": { - "name": "gem2_gem2bedmappability", - "description": "Convert a mappability file to bedgraph format", - "keywords": [ - "mappability", - "bedgraph", - "index", - "gem" - ], - "tools": [ - { - "gem2": { - "description": "GEM2 is a high-performance mapping tool. It also provide a unique tool to evaluate mappability.", - "homepage": "https://paoloribeca.science/gem", - "licence": [ - "Custom" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "map": { - "type": "file", - "description": "The mappability file created from the index", - "pattern": "*.mappability", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing index information\n" - } - }, - { - "index": { - "type": "file", - "description": "The index of the reference FASTA", - "pattern": "*.gem", - "ontologies": [] - } - } - ] - ], - "output": { - "bedgraph": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bg": { - "type": "file", - "description": "The resulting bedgraph file", - "pattern": "*.bg", - "ontologies": [] - } - } - ] - ], - "sizes": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.sizes": { - "type": "file", - "description": "The chromosome sizes", - "pattern": "*.sizes", - "ontologies": [] - } - } - ] - ], - "versions_gem2": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gem2": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "20200110": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gem2": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "20200110": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@nvnieuwk" - ], - "maintainers": [ - "@nvnieuwk" - ] - } - }, - { - "name": "gem2_gemindexer", - "path": "modules/nf-core/gem2/gemindexer/meta.yml", - "type": "module", - "meta": { - "name": "gem2_gemindexer", - "description": "Create a GEM index from a FASTA file", - "keywords": [ - "fasta", - "index", - "reference", - "mappability" - ], - "tools": [ - { - "gem2": { - "description": "GEM2 is a high-performance mapping tool. It also provide a unique tool to evaluate mappability.", - "homepage": "https://paoloribeca.science/gem", - "licence": [ - "Custom" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "A reference FASTA file to index", - "pattern": "*.{fasta,fa,fna}", - "ontologies": [] - } - } - ] - ], - "output": { - "index": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.gem": { - "type": "file", - "description": "The GEM index file", - "pattern": "*.gem", - "ontologies": [] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.log": { - "type": "file", - "description": "The execution log", - "pattern": "*.log", - "ontologies": [] - } - } - ] - ], - "versions_gem2": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gem2": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "20200110": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gem2": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "20200110": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@nvnieuwk" - ], - "maintainers": [ - "@nvnieuwk" - ] - } - }, - { - "name": "gem2_gemmappability", - "path": "modules/nf-core/gem2/gemmappability/meta.yml", - "type": "module", - "meta": { - "name": "gem2_gemmappability", - "description": "Define the mappability of a reference", - "keywords": [ - "mappability", - "gem", - "index", - "reference" - ], - "tools": [ - { - "gem2": { - "description": "GEM2 is a high-performance mapping tool. It also provide a unique tool to evaluate mappability.", - "homepage": "https://paoloribeca.science/gem", - "licence": [ - "Custom" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "index": { - "type": "file", - "description": "The index created with gem-indexer from the reference FASTA", - "pattern": "*.gem", - "ontologies": [] - } - } - ], - { - "read_length": { - "type": "integer", - "description": "The read length to define the mappability of" - } - } - ], - "output": { - "map": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.mappability": { - "type": "file", - "description": "The resulting mappability file", - "pattern": "*.mappability", - "ontologies": [] - } - } - ] - ], - "versions_gem2": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gem2": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "20200110": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gem2": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "20200110": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@nvnieuwk" - ], - "maintainers": [ - "@nvnieuwk" - ] - } - }, - { - "name": "gem3_gem3indexer", - "path": "modules/nf-core/gem3/gem3indexer/meta.yml", - "type": "module", - "meta": { - "name": "gem3_gem3indexer", - "description": "Create a GEM index from a FASTA file", - "keywords": [ - "fastq", - "genomics", - "mappability" - ], - "tools": [ - { - "gem3": { - "description": "The GEM indexer (v3).", - "homepage": "https://github.com/miqalvarez/gem3/tree/gem3-indexer", - "licence": [ - "GPL v3" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing information about the fasta file\ne.g. [ id:'test' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "A reference FASTA file to index", - "pattern": "*.{fasta,fa,fna}", - "ontologies": [] - } - } - ] - ], - "output": { - "index": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.gem": { - "type": "file", - "description": "The GEM index file", - "pattern": "*.gem", - "ontologies": [] - } - } - ] - ], - "info": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.info": { - "type": "file", - "description": "The execution log", - "pattern": "*.info", - "ontologies": [] - } - } - ] - ], - "versions_gem3": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gem3-indexer": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gem-indexer --version 2>&1 | sed 's/v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gem3-indexer": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gem-indexer --version 2>&1 | sed 's/v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@miqalvarez" - ], - "maintainers": [ - "@miqalvarez" - ] - } - }, - { - "name": "gem3_gem3mapper", - "path": "modules/nf-core/gem3/gem3mapper/meta.yml", - "type": "module", - "meta": { - "name": "gem3_gem3mapper", - "description": "Performs fastq alignment to a fasta reference using using gem3-mapper", - "keywords": [ - "fastq", - "genomics", - "mappability" - ], - "tools": [ - { - "gem3": { - "description": "The GEM indexer (v3).", - "homepage": "https://github.com/smarco/gem3-mapper", - "licence": [ - "GPL v3" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference/index information\ne.g. [ id:'test' ]\n" - } - }, - { - "gem": { - "type": "file", - "description": "GEM3 genome index files", - "pattern": "*.{gem}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "fastq": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively.", - "pattern": "*.{fastq,fq,fastq.gz,fq.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ], - { - "sort_bam": { - "type": "boolean", - "description": "use samtools sort (true) or samtools view (false)", - "pattern": "true or false" - } - } - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "Sorted BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } - } - ] - ], - "versions_gem3": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gem3-mapper": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gem-mapper --version 2>&1 | sed 's/v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gem3-mapper": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gem-mapper --version 2>&1 | sed 's/v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@miqalvarez" - ] - } - }, - { - "name": "gemmi_cif2json", - "path": "modules/nf-core/gemmi/cif2json/meta.yml", - "type": "module", - "meta": { - "name": "gemmi_cif2json", - "description": "Convert macromolecular structure files from mmCIF format to JSON format using gemmi.", - "keywords": [ - "structure", - "mmcif", - "cif", - "json", - "structural-biology" - ], - "tools": [ - { - "gemmi": { - "description": "Gemmi is a library and command-line tool for parsing, manipulating,\nand converting macromolecular structural biology data formats such as\nmmCIF, PDB, and MTZ.\n", - "homepage": "https://gemmi.readthedocs.io/", - "documentation": "https://gemmi.readthedocs.io/en/latest/program.html", - "tool_dev_url": "https://github.com/project-gemmi/gemmi", - "doi": "10.5281/zenodo.3697983", - "licence": [ - "MPL-2.0" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "cif": { - "type": "file", - "description": "macromolecular structure file in mmCIF (.cif) format", - "pattern": "*.cif", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1477" - } - ] - } - } - ] - ], - "output": { - "json": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.json": { - "type": "file", - "description": "Structure file converted to JSON format", - "pattern": "*.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "versions_gemmi": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gemmi": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gemmi --version | sed -E 's/^gemmi ([^ ]+).*/\\1/'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gemmi": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gemmi --version | sed -E 's/^gemmi ([^ ]+).*/\\1/'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@vagkaratzas" - ], - "maintainers": [ - "@vagkaratzas" - ] - } - }, - { - "name": "genescopefk", - "path": "modules/nf-core/genescopefk/meta.yml", - "type": "module", - "meta": { - "name": "genescopefk", - "description": "A derivative of GenomeScope2.0 modified to work with FastK", - "keywords": [ - "k-mer", - "genome profile", - "histogram" - ], - "tools": [ - { - "genescopefk": { - "description": "A derivative of GenomeScope2.0 modified to work with FastK", - "homepage": "https://github.com/thegenemyers/GENESCOPE.FK", - "tool_dev_url": "https://github.com/thegenemyers/GENESCOPE.FK", - "license": [ - "https://github.com/thegenemyers/GENESCOPE.FK/blob/main/LICENSE" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fastk_histex_histogram": { - "type": "file", - "description": "A histogram formatted for GeneScope using the -G parameter from Fastk Histex", - "pattern": "*.hist", - "ontologies": [] - } - } - ] - ], - "output": { - "linear_plot": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_linear_plot.png": { - "type": "file", - "description": "A GeneScope linear plot in PNG format", - "pattern": "*_linear_plot.png", - "ontologies": [] - } - } - ] - ], - "log_plot": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_log_plot.png": { - "type": "file", - "description": "A GeneScope log plot in PNG format", - "pattern": "*_log_plot.png", - "ontologies": [] - } - } - ] - ], - "model": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_model.txt": { - "type": "file", - "description": "GeneScope model fit summary", - "pattern": "*_model.txt", - "ontologies": [] - } - } - ] - ], - "summary": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_summary.txt": { - "type": "file", - "description": "GeneScope histogram summary", - "pattern": "*_summary.txt", - "ontologies": [] - } - } - ] - ], - "transformed_linear_plot": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_transformed_linear_plot.png": { - "type": "file", - "description": "A GeneScope transformed linear plot in PNG format", - "pattern": "*_transformed_linear_plot.png", - "ontologies": [] - } - } - ] - ], - "transformed_log_plot": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_transformed_log_plot.png": { - "type": "file", - "description": "A GeneScope transformed log plot in PNG format", - "pattern": "*_transformed_log_plot.png", - "ontologies": [] - } - } - ] - ], - "kmer_cov": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "KMERCOV": { - "type": "float", - "description": "Average kmer coverage value extracted from summary file", - "pattern": "[0-9.]+" - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_genescopefk.log": { - "type": "file", - "description": "GeneScopeFK command stdout log", - "pattern": "*_genescopefk.log", - "ontologies": [] - } - } - ] - ], - "versions_genescopefk": [ - [ - { - "${task.process}": { - "type": "string", - "description": "Name of the process" - } - }, - { - "genescopefk": { - "type": "string", - "description": "Name of the tool" - } - }, - { - "R --version | sed '1!d; s/.*version //; s/ .*//'": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "Name of the process" - } - }, - { - "genescopefk": { - "type": "string", - "description": "Name of the tool" - } - }, - { - "R --version | sed '1!d; s/.*version //; s/ .*//'": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@mahesh-panchal" - ], - "maintainers": [ - "@mahesh-panchal" - ] - } - }, - { - "name": "genin2", - "path": "modules/nf-core/genin2/meta.yml", - "type": "module", - "meta": { - "name": "genin2", - "description": "Genin2 is a lightining-fast bioinformatic tool to predict genotypes for H5 viruses belonging to the European clade 2.3.4.4b.", - "keywords": [ - "genotype", - "avian influenza", - "H5", - "clade 2.3.4.4b", - "genin2", - "genomics" - ], - "tools": [ - { - "genin2": { - "description": "Genin2 is a lightining-fast bioinformatic tool to predict genotypes for H5 viruses belonging to the European clade 2.3.4.4b.", - "homepage": "https://izsvenezie-virology.github.io/genin2", - "documentation": "https://izsvenezie-virology.github.io/genin2", - "tool_dev_url": "https://github.com/izsvenezie-virology/genin2", - "licence": [ - "AGPL v3-or-later" - ], - "identifier": "biotools:genin2" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input sequence in FASTA format", - "pattern": "*.{fa,fna,fasta,fas}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ], - "output": { - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "Output TSV file with cluster IDs and genotypes", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_genin2": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "genin2": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "genin2 --version | grep -Eo '[0-9]+\\.[0-9]+\\.[0-9]+'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "genin2": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "genin2 --version | grep -Eo '[0-9]+\\.[0-9]+\\.[0-9]+'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@AlexSartori" - ], - "maintainers": [ - "@AlexSartori" - ] - } - }, - { - "name": "genmap_index", - "path": "modules/nf-core/genmap/index/meta.yml", - "type": "module", - "meta": { - "name": "genmap_index", - "description": "create index file for genmap", - "keywords": [ - "index", - "mappability", - "fasta" - ], - "tools": [ - { - "genmap": { - "description": "Ultra-fast computation of genome mappability.", - "homepage": "https://github.com/cpockrandt/genmap", - "documentation": "https://github.com/cpockrandt/genmap", - "tool_dev_url": "https://github.com/cpockrandt/genmap", - "doi": "10.1093/bioinformatics/btaa222", - "licence": [ - "BSD-3-Clause" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "fasta file to index", - "pattern": "*.{fasta,fa,fna}", - "ontologies": [] - } - } - ] - ], - "output": { - "index": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}": { - "type": "directory", - "description": "Genmap index directory" - } - } - ] - ], - "versions_genmap": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "genmap": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "genmap --version |& sed -n 's/GenMap version: //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "genmap": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "genmap --version |& sed -n 's/GenMap version: //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@jianhong", - "@nvnieuwk" - ], - "maintainers": [ - "@jianhong", - "@nvnieuwk" - ] - }, - "pipelines": [ - { - "name": "hicar", - "version": "1.0.0" - } - ] - }, - { - "name": "genmap_map", - "path": "modules/nf-core/genmap/map/meta.yml", - "type": "module", - "meta": { - "name": "genmap_map", - "description": "create mappability files for a genome", - "keywords": [ - "mappability", - "index", - "fasta", - "bedgraph", - "csv", - "wig" - ], - "tools": [ - { - "genmap": { - "description": "Ultra-fast computation of genome mappability.", - "homepage": "https://github.com/cpockrandt/genmap", - "documentation": "https://github.com/cpockrandt/genmap", - "tool_dev_url": "https://github.com/cpockrandt/genmap", - "doi": "10.1093/bioinformatics/btaa222", - "licence": [ - "BSD-3-Clause" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "index": { - "type": "directory", - "description": "index directory" - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing regions information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "regions": { - "type": "file", - "description": "optional - a bed file with regions to define the mappability off", - "pattern": "*.bed", - "ontologies": [] - } - } - ] - ], - "output": { - "wig": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.wig": { - "type": "file", - "description": "genmap wig mappability file", - "pattern": "*.wig", - "ontologies": [] - } - } - ] - ], - "bedgraph": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bedgraph": { - "type": "file", - "description": "genmap bedgraph mappability file", - "pattern": "*.bedgraph", - "ontologies": [] - } - } - ] - ], - "txt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.txt": { - "type": "file", - "description": "genmap text mappability file", - "pattern": "*.txt", - "ontologies": [] - } - } - ] - ], - "csv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.csv": { - "type": "file", - "description": "genmap csv mappability file", - "pattern": "*.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "versions_genmap": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "genmap": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "genmap --version |& sed -n 's/GenMap version: //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "genmap": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "genmap --version |& sed -n 's/GenMap version: //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@jianhong", - "@nvnieuwk" - ], - "maintainers": [ - "@jianhong", - "@nvnieuwk" - ] - } - }, - { - "name": "genmod_annotate", - "path": "modules/nf-core/genmod/annotate/meta.yml", - "type": "module", - "meta": { - "name": "genmod_annotate", - "description": "for annotating regions, frequencies, cadd scores", - "keywords": [ - "annotate", - "genmod", - "ranking" - ], - "tools": [ - { - "genmod": { - "description": "Annotate genetic inheritance models in variant files", - "homepage": "https://github.com/Clinical-Genomics/genmod", - "documentation": "https://github.com/Clinical-Genomics/genmod", - "tool_dev_url": "https://github.com/moonso", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input_vcf": { - "type": "file", - "description": "VCF file", - "pattern": "*.{vcf}", - "ontologies": [] - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_annotate.vcf": { - "type": "file", - "description": "Annotated VCF file", - "pattern": "*.{vcf}", - "ontologies": [] - } - } - ] - ], - "versions_genmod": [ - [ - { - "${task.process}": { - "type": "string", - "description": "Name of the process" - } - }, - { - "genmod": { - "type": "string", - "description": "Name of the tool" - } - }, - { - "genmod --version | sed 's/^.*genmod version: //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "Name of the process" - } - }, - { - "genmod": { - "type": "string", - "description": "Name of the tool" - } - }, - { - "genmod --version | sed 's/^.*genmod version: //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@ramprasadn" - ], - "maintainers": [ - "@ramprasadn" - ] - }, - "pipelines": [ - { - "name": "raredisease", - "version": "3.0.0" - } - ] - }, - { - "name": "genmod_compound", - "path": "modules/nf-core/genmod/compound/meta.yml", - "type": "module", - "meta": { - "name": "genmod_compound", - "description": "Score compounds", - "keywords": [ - "compound", - "genmod", - "ranking" - ], - "tools": [ - { - "genmod": { - "description": "Annotate genetic inheritance models in variant files", - "homepage": "https://github.com/Clinical-Genomics/genmod", - "documentation": "https://github.com/Clinical-Genomics/genmod", - "tool_dev_url": "https://github.com/moonso", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input_vcf": { - "type": "file", - "description": "VCF file", - "pattern": "*.{vcf}", - "ontologies": [] - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ] #\n" - } - }, - { - "*_compound.vcf": { - "type": "file", - "description": "Output VCF file", - "pattern": "*.{vcf}", - "ontologies": [] - } - } - ] - ], - "versions_genmod": [ - [ - { - "${task.process}": { - "type": "string", - "description": "Name of the process" - } - }, - { - "genmod": { - "type": "string", - "description": "Name of the tool" - } - }, - { - "genmod --version | sed 's/^.*genmod version: //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "Name of the process" - } - }, - { - "genmod": { - "type": "string", - "description": "Name of the tool" - } - }, - { - "genmod --version | sed 's/^.*genmod version: //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@ramprasadn" - ], - "maintainers": [ - "@ramprasadn" - ] - }, - "pipelines": [ - { - "name": "raredisease", - "version": "3.0.0" - } - ] - }, - { - "name": "genmod_models", - "path": "modules/nf-core/genmod/models/meta.yml", - "type": "module", - "meta": { - "name": "genmod_models", - "description": "annotate models of inheritance", - "keywords": [ - "models", - "genmod", - "ranking" - ], - "tools": [ - { - "genmod": { - "description": "Annotate genetic inheritance models in variant files", - "homepage": "https://github.com/Clinical-Genomics/genmod", - "documentation": "https://github.com/Clinical-Genomics/genmod", - "tool_dev_url": "https://github.com/moonso", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input_vcf": { - "type": "file", - "description": "vcf file", - "pattern": "*.{vcf}", - "ontologies": [] - } - }, - { - "fam": { - "type": "file", - "description": "PED file with family information", - 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"type": "file", - "description": "A genomescope2 fitted histogram plot in PNG format", - "pattern": "*_fitted_hist.png", - "ontologies": [] - } - } - ] - ], - "json_report": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.json": { - "type": "file", - "description": "A JSON format report of the genomescope2 model", - "pattern": "*.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "versions_genomescope2": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "genomescope2": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "genomescope2 -v | sed \"s/GenomeScope //\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "genomescope2": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "genomescope2 -v | sed \"s/GenomeScope //\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@mahesh-panchal" - ], - "maintainers": [ - "@mahesh-panchal" - ] - } - }, - { - "name": "genotyphi_parse", - "path": "modules/nf-core/genotyphi/parse/meta.yml", - "type": "module", - "meta": { - "name": "genotyphi_parse", - "description": "Genotype Salmonella Typhi from Mykrobe results", - "keywords": [ - "genotype", - "Salmonella Typhi", - "Mykrobe" - ], - "tools": [ - { - "genotyphi": { - "description": "Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)", - "homepage": "https://github.com/katholt/genotyphi", - "documentation": "https://github.com/katholt/genotyphi", - "tool_dev_url": "https://github.com/katholt/genotyphi", - "licence": [ - "GPL v3" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "json": { - "type": "file", - "description": "JSON formatted file of Mykrobe results", - "pattern": "*.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "output": { - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "A tab-delimited file of predicted genotypes", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_genotyphi": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "genotyphi": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "genotyphi --version |& sed 's/^.*GenoTyphi v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "genotyphi": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "genotyphi --version |& sed 's/^.*GenoTyphi v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@rpetit3" - ], - "maintainers": [ - "@rpetit3" - ] - } - }, - { - "name": "genrich", - "path": "modules/nf-core/genrich/meta.yml", - "type": "module", - "meta": { - "name": "genrich", - "description": "Peak-calling for ChIP-seq and ATAC-seq enrichment experiments", - "keywords": [ - "peak-calling", - "ChIP-seq", - "ATAC-seq" - ], - "tools": [ - { - "genrich": { - "description": "Genrich is a peak-caller for genomic enrichment assays (e.g. ChIP-seq, ATAC-seq).\nIt analyzes alignment files generated following the assay and produces a file\ndetailing peaks of significant enrichment.\n", - "homepage": "https://github.com/jsh58/Genrich", - "documentation": "https://github.com/jsh58/Genrich#readme", - "tool_dev_url": "https://github.com/jsh58/Genrich", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "treatment_bam": { - "type": "file", - "description": "Coordinate sorted BAM/SAM file from treatment sample or list of BAM/SAM files from biological replicates", - "pattern": "*.{bam,sam}", - "ontologies": [] - } - }, - { - "control_bam": { - "type": "file", - "description": "Coordinate sorted BAM/SAM file from control sample or list of BAM/SAM files from control samples", - "pattern": "*.{bam,sam}", - "ontologies": [] - } - } - ], - { - "blacklist_bed": { - "type": "file", - "description": "Bed file containing genomic intervals to exclude from the analysis", - "pattern": "*.{bed}", - "ontologies": [] - } - } - ], - "output": { - "peak": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.narrowPeak": { - "type": "file", - "description": "Narrow peak file containing genomic intervals of significant enrichment", - "pattern": "*.{narrowPeak}", - "ontologies": [] - } - } - ] - ], - "versions_genrich": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "genrich": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "Genrich --version 2>&1 | head -n1 | sed 's/Genrich, version //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "bedgraph_pvalues": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.pvalues.bedGraph": { - "type": "file", - "description": "bedGraph file containing p/q values", - "pattern": "*.{pvalues.bedGraph}", - "ontologies": [] - } - } - ] - ], - "bedgraph_pileup": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.pileup.bedGraph": { - "type": "file", - "description": "bedGraph file containing pileups and p-values", - "pattern": "*.{pileup.bedGraph}", - "ontologies": [] - } - } - ] - ], - "bed_intervals": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.intervals.bed": { - "type": "file", - "description": "Bed file containing annotated intervals", - "pattern": "*.{intervals.bed}", - "ontologies": [] - } - } - ] - ], - "duplicates": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.duplicates.txt": { - "type": "file", - "description": "Text output file containing intervals corresponding to PCR duplicates", - "pattern": "*.{intervals.txt}", - "ontologies": [] - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "genrich": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "Genrich --version 2>&1 | head -n1 | sed 's/Genrich, version //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@JoseEspinosa", - "@samuelruizperez" - ], - "maintainers": [ - "@JoseEspinosa", - "@samuelruizperez" - ] - } - }, - { - "name": "gens_preparecovandbaf", - "path": "modules/nf-core/gens/preparecovandbaf/meta.yml", - "type": "module", - "meta": { - "name": "preparecovandbaf", - "description": "Tools for preparing inputs for visualization in Gens", - "keywords": [ - "gens", - "preparecovandbaf", - "preprocessing", - "genomics", - "CNV" - ], - "tools": [ - { - "gens": { - "description": "Scripts for preparing input data to Gens", - "homepage": "https://github.com/SMD-Bioinformatics-Lund/Prepare-Gens-input-data", - "documentation": "https://github.com/SMD-Bioinformatics-Lund/Prepare-Gens-input-data/README.md", - "tool_dev_url": "https://github.com/SMD-Bioinformatics-Lund/Prepare-Gens-input-data", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "read_counts": { - "type": "file", - "description": "Binned coverage calculations from GATK", - "pattern": "*.{tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - }, - { - "gvcf": { - "type": "file", - "description": "GVCF. It is used to calculate B-allele frequencies at the sites specified in baf_positions. It can be generated using any SNV-caller.", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } + "name": "iqtree", + "path": "modules/nf-core/iqtree/meta.yml", + "type": "module", + "meta": { + "name": "iqtree", + "description": "Produces a Newick format phylogeny from a multiple sequence alignment using the maximum likelihood algorithm. Capable of bacterial genome size alignments.", + "keywords": ["phylogeny", "newick", "maximum likelihood"], + "tools": [ + { + "iqtree": { + "description": "Efficient phylogenomic software by maximum likelihood.", + "homepage": "http://www.iqtree.org", + "documentation": "http://www.iqtree.org/doc", + "tool_dev_url": "https://github.com/iqtree/iqtree2", + "doi": "10.1093/molbev/msaa015", + "licence": ["GPL v2-or-later"], + "identifier": "biotools:iqtree" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy map containing sample information for the\nalignment/tree file, e.g. [ id: 'test' ]\n" + } + }, + { + "alignment": { + "type": "file", + "description": "One or more input alignment file in PHYLIP, FASTA, NEXUS, CLUSTAL or MSF format or a directory of such files (-s)", + "pattern": "*.{fasta,fas,fa,mfa,phy,aln,nex,nexus,msf}", + "ontologies": [] + } + }, + { + "tree": { + "type": "file", + "description": "File containing one or multiple phylogenetic trees (-t): - Single tree used e.g. as starting tree for tree search - Set of trees used e.g. for distance computation, consensus tree construction", + "pattern": "*.{tre,tree,treefile,newick,nwk,nex,nexus}", + "ontologies": [] + } + } + ], + { + "tree_te": { + "type": "file", + "description": "File containing single phylogenetic tree (-te) Use cases: - fixed user tree to skip tree search - ancestral sequence reconstruction", + "pattern": "*.{tre,tree,treefile,newick,nwk,nex,nexus}", + "ontologies": [] + } + }, + { + "lmclust": { + "type": "file", + "description": "NEXUS file containing taxon clusters for quartet mapping analysis (-lmclust)", + "pattern": "*.nex{us}", + "ontologies": [] + } + }, + { + "mdef": { + "type": "file", + "description": "NEXUS model file defining new models (-mdef)", + "pattern": "*.nex{us}", + "ontologies": [] + } + }, + { + "partitions_equal": { + "type": "file", + "description": "Partition file for edge-equal partition model, all partitions share same set of branch lengths (-q)", + "pattern": "*.{nex,nexus,tre,tree,treefile}", + "ontologies": [] + } + }, + { + "partitions_proportional": { + "type": "file", + "description": "Partition file for edge-equal partition model, all partitions share same set of branch lengths (-spp)", + "pattern": "*.{nex,nexus,tre,tree,treefile}", + "ontologies": [] + } + }, + { + "partitions_unlinked": { + "type": "file", + "description": "Partition file for edge-equal partition model, all partitions share same set of branch lengths (-sp)", + "pattern": "*.{nex,nexus,tre,tree,treefile}", + "ontologies": [] + } + }, + { + "guide_tree": { + "type": "file", + "description": "File containing guide tree for inference of site frequency profiles (-ft)", + "pattern": "*.{nex,nexus,tre,tree,treefile}", + "ontologies": [] + } + }, + { + "sitefreq_in": { + "type": "file", + "description": "Site frequency file (-fs)", + "pattern": "*.sitefreq", + "ontologies": [] + } + }, + { + "constraint_tree": { + "type": "file", + "description": "File containing opological constraint tree in NEWICK format. The constraint tree can be a multifurcating tree and need not to include all taxa. (-g)", + "pattern": "*.{nwk,newick}", + "ontologies": [] + } + }, + { + "trees_z": { + "type": "file", + "description": "File containing a set of trees for which log-likelihoods should be computed (-z)", + "ontologies": [] + } + }, + { + "suptree": { + "type": "file", + "description": "File containing input “target” tree, support values are extracted from trees passed via -t, and mapped onto the target tree (-sup)", + "ontologies": [] + } + }, + { + "trees_rf": { + "type": "file", + "description": "File containing a second tree set (-rf). Used for computing the distance to the primary tree set (`tree`)", + "pattern": "*.{tre,tree,treefile,newick,nwk,nex,nexus}", + "ontologies": [] + } + } + ], + "output": { + "phylogeny": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.treefile": { + "type": "file", + "description": "A phylogeny in Newick format", + "pattern": "*.{treefile}", + "ontologies": [] + } + } + ] + ], + "report": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.iqtree": { + "type": "file", + "description": "Main report file containing computational\nresults as well as a textual visualization\nof the final tree\n", + "pattern": "*.{iqtree}", + "ontologies": [] + } + } + ] + ], + "mldist": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.mldist": { + "type": "file", + "description": "File containing the pairwise maximum\nlikelihood distances as a matrix\n", + "pattern": "*.{mldist}", + "ontologies": [] + } + } + ] + ], + "lmap_svg": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.lmap.svg": { + "type": "file", + "description": "File containing likelihood mapping analysis\nresults in .svg format (-lmap/-lmclust)\n", + "pattern": "*.lmap.svg", + "ontologies": [] + } + } + ] + ], + "lmap_eps": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.lmap.eps": { + "type": "file", + "description": "File containing likelihood mapping analysis\nresults in .eps format (-lmap/-lmclust)\n", + "pattern": "*.lmap.eps", + "ontologies": [] + } + } + ] + ], + "lmap_quartetlh": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.lmap.quartetlh": { + "type": "file", + "description": "File containing quartet log-likelihoods (-wql)\n", + "pattern": "*.lmap.quartetlh", + "ontologies": [] + } + } + ] + ], + "sitefreq_out": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.sitefreq": { + "type": "file", + "description": "File containing site frequency profiles (-ft)\n", + "pattern": "*.sitefreq", + "ontologies": [] + } + } + ] + ], + "bootstrap": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.ufboot": { + "type": "file", + "description": "File containing all bootstrap trees (-wbt/-wbtl)\n", + "pattern": "*.ufboot", + "ontologies": [] + } + } + ] + ], + "state": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.state": { + "type": "file", + "description": "File containing ancestral sequences for all\nnodes of the tree by empirical Bayesian method (-asr)\n", + "pattern": "*.{state}", + "ontologies": [] + } + } + ] + ], + "contree": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.contree": { + "type": "file", + "description": "File containing consensus tree (-con/-bb)\n", + "pattern": "*.{contree}", + "ontologies": [] + } + } + ] + ], + "nex": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.nex": { + "type": "file", + "description": "File containing consensus network (-net/-bb)\n", + "pattern": "*.{nex}", + "ontologies": [] + } + } + ] + ], + "splits": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.splits": { + "type": "file", + "description": "File containing consensus network in star-dot format (-wsplits)\n", + "pattern": "*.{splits}", + "ontologies": [] + } + } + ] + ], + "suptree": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.suptree": { + "type": "file", + "description": "File containing tree with assigned support\nvalues based on supplied \"target\" tree (-sup)\n", + "pattern": "*.{suptree}", + "ontologies": [] + } + } + ] + ], + "alninfo": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.alninfo": { + "type": "file", + "description": "File containing alignment site statistics (-alninfo)\n", + "pattern": "*.{alninfo}", + "ontologies": [] + } + } + ] + ], + "partlh": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.partlh": { + "type": "file", + "description": "File containing partition log-likelihoods (-wpl)\n", + "pattern": "*.{partlh}", + "ontologies": [] + } + } + ] + ], + "siteprob": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.siteprob": { + "type": "file", + "description": "File containing site posterior probabilities (-wspr/-wspm/-wspmr)\n", + "pattern": "*.{siteprob}", + "ontologies": [] + } + } + ] + ], + "sitelh": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.sitelh": { + "type": "file", + "description": "File containing site log-likelihoods (-wsl/-wslr/-wslm/-wslmr)\n", + "pattern": "*.{sitelh}", + "ontologies": [] + } + } + ] + ], + "treels": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.treels": { + "type": "file", + "description": "File containing all locally optimal trees (-wt)\n", + "pattern": "*.{treels}", + "ontologies": [] + } + } + ] + ], + "rate": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.rate ": { + "type": "file", + "description": "File containing inferred site-specific\nevolutionary rates (-wsr)\n", + "pattern": "*.{rate}", + "ontologies": [] + } + } + ] + ], + "mlrate": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.mlrate": { + "type": "file", + "description": "File containing site-specific substitution\nrates determined by maximum likelihood (--mlrate)\n", + "pattern": "*.{mlrate}", + "ontologies": [] + } + } + ] + ], + "exch_matrix": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "GTRPMIX.nex": { + "type": "file", + "description": "File containing the exchangeability matrix obtained from the optimization (--link-exchange-rates)", + "pattern": "GTRPMIX.nex", + "ontologies": [] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.log": { + "type": "file", + "description": "Log file of entire run", + "pattern": "*.{log}", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@avantonder", "@aunderwo"], + "maintainers": ["@avantonder", "@aunderwo"] }, - { - "gvcf_tbi": { - "type": "file", - "description": "GVCF tabix index", - "pattern": "*.vcf.gz.tbi", - "ontologies": [] - } - } - ], - { - "baf_positions": { - "type": "file", - "description": "Sites to sample for BAF calculations", - "pattern": "*.{tsv,tsv.gz}", - "ontologies": [ + "pipelines": [ + { + "name": "pathogensurveillance", + "version": "1.1.0" + }, { - "edam": "http://edamontology.org/format_3475" + "name": "tbanalyzer", + "version": "dev" } - ] - } - } - ], - "output": { - "cov_gz": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\n" - } - }, - { - "*.cov.bed.gz": { - "type": "file", - "description": "Coverage bed (bgzipped)" - } - } - ] - ], - "cov_tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\n" - } - }, - { - "*.cov.bed.gz.tbi": { - "type": "file", - "description": "Tabix index for coverage bed" - } - } - ] - ], - "baf_gz": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\n" - } - }, - { - "*.baf.bed.gz": { - "type": "file", - "description": "BAF bed (bgzipped)" - } - } - ] - ], - "baf_tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\n" - } - }, - { - "*.baf.bed.gz.tbi": { - "type": "file", - "description": "Tabix index for BAF bed" - } - } - ] - ], - "versions_preparecovandbaf": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "preparecovandbaf": { - "type": "string", - "description": "The tool name" - } - }, - { - "generate_cov_and_baf --version": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "preparecovandbaf": { - "type": "string", - "description": "The tool name" - } - }, - { - "generate_cov_and_baf --version": { - "type": "eval", - "description": "The expression used to obtain the tool version" - } - } - ] - ] - }, - "authors": [ - "@jakob37" - ], - "maintainers": [ - "@jakob37" - ] - }, - "pipelines": [ - { - "name": "raredisease", - "version": "3.0.0" - } - ] - }, - { - "name": "geofetch", - "path": "modules/nf-core/geofetch/meta.yml", - "type": "module", - "meta": { - "name": "geofetch", - "description": "geofetch is a command-line tool that downloads and organizes data and metadata from GEO and SRA", - "keywords": [ - "GEO", - "expression", - "microarray", - "sequencing" - ], - "tools": [ - { - "geofetch": { - "description": "Downloads data and metadata from GEO and SRA and creates standard PEPs.", - "homepage": "http://geofetch.databio.org/", - "documentation": "http://geofetch.databio.org/", - "tool_dev_url": "https://github.com/pepkit/geofetch", - "licence": [ - "BSD-2-clause" - ], - "args_id": "$args", - "identifier": "" - } - } - ], - "input": [ - { - "geo_accession": { - "type": "string", - "description": "GEO accession ID" - } - } - ], - "output": { - "samples": [ - [ - { - "${geo_accession}": { - "type": "file", - "description": "List of sample files fetched", - "pattern": "${geo_accession}/*.CEL.gz", - "ontologies": [] - } - }, - { - "${geo_accession}/*.CEL.gz": { - "type": "file", - "description": "List of sample files fetched", - "pattern": "${geo_accession}/*.CEL.gz", - "ontologies": [] - } - } - ] - ], - "versions_geofetch": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "geofetch": { - "type": "string", - "description": "The tool name" - } - }, - { - "geofetch --version 2>&1 | sed '1!d; s/^geofetch //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "geofetch": { - "type": "string", - "description": "The tool name" - } - }, - { - "geofetch --version 2>&1 | sed '1!d; s/^geofetch //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@mribeirodantas" - ], - "maintainers": [ - "@mribeirodantas" - ] - } - }, - { - "name": "geoquery_getgeo", - "path": "modules/nf-core/geoquery/getgeo/meta.yml", - "type": "module", - "meta": { - "name": "geoquery_getgeo", - "description": "Retrieves GEO data from the Gene Expression Omnibus (GEO)", - "keywords": [ - "geo", - "expression", - "microarray" - ], - "tools": [ - { - "geoquery": { - "description": "Get data from NCBI Gene Expression Omnibus (GEO)", - "homepage": "https://bioconductor.org/packages/release/bioc/html/GEOquery.html", - "documentation": "https://bioconductor.org/packages/release/bioc/vignettes/GEOquery/inst/doc/GEOquery.html", - "tool_dev_url": "https://github.com/seandavi/GEOquery", - "doi": "10.1093/bioinformatics/btm254", - "licence": [ - "MIT" - ], - "identifier": "biotools:geoquery" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing metadata about the GEO dataset, minimally 'id'.\n" - } - }, - { - "querygse": { - "type": "string", - "description": "GSE identifier to pass to getGEO()\n" - } - } - ] - ], - "output": { - "rds": [ - [ - { - "meta": { - "type": "map", - "description": "A Groovy map containing sample information" - } - }, - { - "*.rds": { - "type": "file", - "description": "R object containing GEO data", - "pattern": "*.rds", - "ontologies": [] - } - } - ] - ], - "expression": [ - [ - { - "meta": { - "type": "map", - "description": "A Groovy map containing sample information" - } - }, - { - "*matrix.tsv": { - "type": "file", - "description": "TSV-format expression matrix", - "pattern": "*matrix.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "annotation": [ - [ - { - "meta": { - "type": "map", - "description": "A Groovy map containing sample information" - } - }, - { - "*annotation.tsv": { - "type": "file", - "description": "TSV-format annotation file", - "pattern": "*annotation.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "topics": { - "versions": [ - { - "versions.yml": { - "type": "string", - "description": "The name of the process" - } - } - ] - }, - "authors": [ - "@azedinez", - "@pinin4fjords" - ], - "maintainers": [ - "@azedinez", - "@pinin4fjords" - ] - }, - "pipelines": [ - { - "name": "differentialabundance", - "version": "1.5.0" - } - ] - }, - { - "name": "getorganelle_config", - "path": "modules/nf-core/getorganelle/config/meta.yml", - "type": "module", - "meta": { - "name": "getorganelle_config", - "description": "Downloads databases needed for running getorganelle", - "keywords": [ - "assembly", - "organelle", - "mitochondria", - "download", - "database" - ], - "tools": [ - { - "getorganelle": { - "description": "Get organelle genomes from genome skimming data", - "homepage": "https://github.com/Kinggerm/GetOrganelle", - "documentation": "https://github.com/Kinggerm/GetOrganelle", - "tool_dev_url": "https://github.com/Kinggerm/GetOrganelle", - "doi": "10.1186/s13059-020-02154-5", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:getorganelle" - } - } - ], - "input": [ - { - "organelle_type": { - "type": "string", - "description": "Type of database, esp. embplant_pt (embryophyta plant plastome), other_pt (non-embryophyta plant plastome), embplant_mt (plant mitochondrion), embplant_nr (plant nuclear ribosomal RNA), animal_mt (animal mitochondrion), and fungus_mt (fungus mitochondrion), fungus_nr (fungus nuclear ribosomal RNA)\n" - } - } - ], - "output": { - "db": [ - [ - { - "organelle_type": { - "type": "string", - "description": "Type of database, esp. embplant_pt (embryophyta plant plastome), other_pt (non-embryophyta plant plastome), embplant_mt (plant mitochondrion), embplant_nr (plant nuclear ribosomal RNA), animal_mt (animal mitochondrion), and fungus_mt (fungus mitochondrion), fungus_nr (fungus nuclear ribosomal RNA)\n" - } - }, - { - "getorganelle": { - "type": "directory", - "description": "Downloaded database for GetOrganelle" - } - } - ] - ], - "versions_getorganelle": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "getorganelle": { - "type": "string", - "description": "Downloaded database for GetOrganelle" - } - }, - { - "get_organelle_config.py --version |& sed 's/^GetOrganelle v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "getorganelle": { - "type": "string", - "description": "Downloaded database for GetOrganelle" - } - }, - { - "get_organelle_config.py --version |& sed 's/^GetOrganelle v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@erinyoung" - ] - } - }, - { - "name": "getorganelle_fromreads", - "path": "modules/nf-core/getorganelle/fromreads/meta.yml", - "type": "module", - "meta": { - "name": "getorganelle_fromreads", - "description": "Assembles organelle genomes from genomic data", - "keywords": [ - "assembly", - "organelle", - "mitochondria", - "illumina" - ], - "tools": [ - { - "getorganelle": { - "description": "Get organelle genomes from genome skimming data", - "homepage": "https://github.com/Kinggerm/GetOrganelle", - "documentation": "https://github.com/Kinggerm/GetOrganelle", - "tool_dev_url": "https://github.com/Kinggerm/GetOrganelle", - "doi": "10.1186/s13059-020-02154-5", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:getorganelle" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "fastq": { - "type": "file", - "description": "Input fastq files", - "pattern": "*.{fastq.gz}", - "ontologies": [] - } - } - ], - [ - { - "organelle_type": { - "type": "string", - "description": "Type of database, esp. embplant_pt (embryophyta plant plastome), other_pt (non-embryophyta plant plastome), embplant_mt (plant mitochondrion), embplant_nr (plant nuclear ribosomal RNA), animal_mt (animal mitochondrion), and fungus_mt (fungus mitochondrion), fungus_nr (fungus nuclear ribosomal RNA)\n" - } - }, - { - "db": { - "type": "directory", - "description": "GetOrganelle database" - } - } - ] - ], - "output": { - "fasta": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "results/${prefix}.${organelle_type}.fasta.gz": { - "type": "file", - "description": "Complete or partial organelle sequences", - "pattern": "*.fasta.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "etc": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "results/*": { - "type": "file", - "description": "Other output files", - "ontologies": [] - } - } - ] - ], - "versions_getorganelle": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "getorganelle": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "get_organelle_from_reads.py --version |& sed 's/^GetOrganelle v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "getorganelle": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "get_organelle_from_reads.py --version |& sed 's/^GetOrganelle v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@erinyoung" - ] - } - }, - { - "name": "gfaffix", - "path": "modules/nf-core/gfaffix/meta.yml", - "type": "module", - "meta": { - "name": "gfaffix", - "description": "Collapse walk-preserving shared affixes in variation graphs in GFA format", - "keywords": [ - "gfa", - "graph", - "pangenome", - "variation graph" - ], - "tools": [ - { - "gfaffix": { - "description": "GFAffix identifies walk-preserving shared affixes in variation graphs and\ncollapses them into a non-redundant graph structure.\n", - "homepage": "https://github.com/marschall-lab/GFAffix", - "documentation": "https://github.com/marschall-lab/GFAffix", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "gfa": { - "type": "file", - "description": "Variation graph in GFA format", - "pattern": "*.{gfa}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3975" - } - ] - } - } - ] - ], - "output": { - "gfa": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.gfa": { - "type": "file", - "description": "Non-redundant variation graph in GFA 1.0 format", - "pattern": "*.{gfa}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3975" - } - ] - } - } - ] - ], - "affixes": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.txt": { - "type": "file", - "description": "Shared affixes in tab-separated values (TSV) text format", - "pattern": "*.{txt}", - "ontologies": [] - } - } - ] - ], - "versions_gfaffix": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gfaffix": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gfaffix --version | cut -d\" \" -f2": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gfaffix": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gfaffix --version | cut -d\" \" -f2": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@heuermh" - ], - "maintainers": [ - "@heuermh" - ] - }, - "pipelines": [ - { - "name": "pangenome", - "version": "1.1.3" - } - ] - }, - { - "name": "gfastats", - "path": "modules/nf-core/gfastats/meta.yml", - "type": "module", - "meta": { - "name": "gfastats", - "description": "A single fast and exhaustive tool for summary statistics and simultaneous *fa*\n(fasta, fastq, gfa [.gz]) genome assembly file manipulation.\n", - "keywords": [ - "gfastats", - "fasta", - "genome assembly", - "genome summary", - "genome manipulation", - "genome statistics" - ], - "tools": [ - { - "gfastats": { - "description": "The swiss army knife for genome assembly.", - "homepage": "https://github.com/vgl-hub/gfastats", - "documentation": "https://github.com/vgl-hub/gfastats/tree/main/instructions", - "tool_dev_url": "https://github.com/vgl-hub/gfastats", - "doi": "10.1093/bioinformatics/btac460", - "licence": [ - "MIT" - ], - "identifier": "biotools:gfastats" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "assembly": { - "type": "file", - "description": "Draft assembly file", - "pattern": "*.{fasta,fastq,gfa}(.gz)?", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - }, - { - "edam": "http://edamontology.org/format_3975" - } - ] - } - } - ], - { - "out_fmt": { - "type": "string", - "description": "Output format (fasta, fastq, gfa)" - } - }, - { - "genome_size": { - "type": "integer", - "description": "estimated genome size (bp) for NG* statistics (optional)." - } - }, - { - "target": { - "type": "string", - "description": "target specific sequence by header, optionally with coordinates (optional)." - } - }, - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "agpfile": { - "type": "file", - "description": "converts input agp to path and replaces existing paths.", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "include_bed": { - "type": "file", - "description": "generates output on a subset list of headers or coordinates in 0-based bed format.", - "ontologies": [] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "exclude_bed": { - "type": "file", - "description": "opposite of --include-bed. They can be combined (no coordinates).", - "ontologies": [] - } - } - ], - [ - { - "meta5": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "instructions": { - "type": "file", - "description": "set of instructions provided as an ordered list.", - "ontologies": [] - } - } - ] - ], - "output": { - "assembly_summary": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.assembly_summary": { - "type": "file", - "description": "Assembly summary statistics file", - "pattern": "*.assembly_summary", - "ontologies": [] - } - } ] - ], - "assembly": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.${out_fmt}.gz": { - "type": "file", - "description": "The assembly as modified by gfastats", - "pattern": "*.{fasta,fastq,gfa}.gz", - "ontologies": [ + }, + { + "name": "irescue", + "path": "modules/nf-core/irescue/meta.yml", + "type": "module", + "meta": { + "name": "irescue", + "description": "Quantification of transposable elements expression in scRNA-seq", + "keywords": ["scRNA-seq", "transposons", "repeats"], + "tools": [ + { + "irescue": { + "description": "IRescue is a tool for uncertainty-aware quantification of transposable elements expression in scRNA-seq", + "homepage": "https://pypi.org/project/IRescue", + "documentation": "https://pypi.org/project/IRescue", + "tool_dev_url": "https://github.com/bodegalab/irescue", + "doi": "10.1093/nar/gkae793", + "licence": ["MIT"], + "identifier": "biotools:irescue" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "bam": { + "type": "file", + "description": "Sorted BAM file", + "pattern": "*.bam", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + } + ], { - "edam": "http://edamontology.org/format_1930" + "genome": { + "type": "string", + "description": "Genome assembly symbol. Not used when bed file is provided.\nIn this case, it can be any value or an empty string.\n" + } }, { - "edam": "http://edamontology.org/format_3975" + "bed": { + "type": "file", + "description": "Bed file of repeats genomic coordinates (optional).", + "pattern": "*.bed", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3003" + } + ] + } } - ] - } - } - ] - ], - "versions_gfastats": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gfastats": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gfastats -v | sed '1!d;s/.*v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gfastats": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gfastats -v | sed '1!d;s/.*v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@mahesh-panchal" - ], - "maintainers": [ - "@mahesh-panchal" - ] - } - }, - { - "name": "gfatools_gfa2fa", - "path": "modules/nf-core/gfatools/gfa2fa/meta.yml", - "type": "module", - "meta": { - "name": "gfatools_gfa2fa", - "description": "Converts GFA or rGFA files to FASTA", - "keywords": [ - "gfa", - "rgfa", - "fasta", - "assembly", - "genome graph", - "genomics" - ], - "tools": [ - { - "gfatools": { - "description": "Tools for manipulating sequence graphs in the GFA and rGFA formats", - "homepage": "https://github.com/lh3/gfatools", - "documentation": "https://github.com/lh3/gfatools", - "tool_dev_url": "https://github.com/lh3/gfatools", - "doi": "no DOI available", - "licence": [ - "Unknown" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "gfa": { - "type": "file", - "description": "GFA or rGFA file", - "pattern": "*.gfa", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3975" - } - ] - } - } - ] - ], - "output": { - "fasta": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*.fasta.gz": { - "type": "file", - "description": "FASTA file", - "pattern": "*.fasta", - "ontologies": [] - } - } - ] - ], - "versions_gfatools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gfatools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gfatools version | sed '1!d; s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - 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Specifies which bases to use as cell/molecular barcodes.", + "pattern": "^(?:\\d{1,2}[UBGX]-)+T$|^(?:\\d{1,2}[UBGX]-)+T(?:-\\d{1,2}[UBGX])+$|^T(?:-\\d{1,2}[UBGX])+$" + } + } + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "*.flt.bam": { + "type": "file", + "description": "BAM file with full-length tagged reads", + "pattern": "*.flt.bam", + "ontologies": [] + } + } + ] + ], + "pbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "*.flt.bam.pbi": { + "type": "file", + "description": "Pacbio index file of full-length tagged reads", + "pattern": "*.flt.bam.pbi", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@skraettli"], + "maintainers": ["@skraettli"] + } }, { - "name": "sammyseq", - "version": "dev" + "name": "isoseq_cluster", + "path": "modules/nf-core/isoseq/cluster/meta.yml", + "type": "module", + "meta": { + "name": "isoseq_cluster", + "description": "IsoSeq - Cluster - Cluster trimmed consensus sequences", + "keywords": ["cluster", "HiFi", "isoseq", "Pacbio"], + "tools": [ + { + "isoseq": { + "description": "IsoSeq - Cluster - Cluster trimmed consensus sequences", + "homepage": "https://github.com/PacificBiosciences/IsoSeq/blob/master/isoseq-clustering.md", + "documentation": "https://github.com/PacificBiosciences/IsoSeq/blob/master/isoseq-clustering.md", + "tool_dev_url": "https://github.com/PacificBiosciences/IsoSeq/blob/master/isoseq-clustering.md", + "licence": ["BSD-3-Clause-Clear"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file generated by isoseq refine", + "pattern": "*.bam", + "ontologies": [] + } + } + ] + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.transcripts.bam": { + "type": "file", + "description": "BAM file of clustered consensus", + "pattern": "*.transcripts.bam", + "ontologies": [] + } + } + ] + ], + "pbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.transcripts.bam.pbi": { + "type": "file", + "description": "Pacbio Index of consensus reads generated by clustering", + "pattern": "*.transcripts.bam.pbi", + "ontologies": [] + } + } + ] + ], + "cluster": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.transcripts.cluster": { + "type": "file", + "description": "A two columns (from, to) file describing original read name to new read name", + "pattern": "*.transcripts.cluster", + "ontologies": [] + } + } + ] + ], + "cluster_report": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.transcripts.cluster_report.csv": { + "type": "file", + "description": "A table files clusters (transcripts) members (read)", + "pattern": "*.transcripts.cluster_report.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "transcriptset": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.transcripts.transcriptset.xml": { + "type": "file", + "description": "A metadata xml file which contains full paths to data files", + "pattern": "*.transcripts.transcriptset.xml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2332" + } + ] + } + } + ] + ], + "hq_bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.transcripts.hq.bam": { + "type": "file", + "description": "High quality reads (when --use-qvs is set)", + "pattern": "*.transcripts.hq.bam", + "ontologies": [] + } + } + ] + ], + "hq_pbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.transcripts.hq.bam.pbi": { + "type": "file", + "description": "Pacbio index of high quality reads (when --use-qvs is set)", + "pattern": "*.transcripts.hq.bam.pbi", + "ontologies": [] + } + } + ] + ], + "lq_bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.transcripts.lq.bam": { + "type": "file", + "description": "Low quality reads (when --use-qvs is set)", + "pattern": "*.transcripts.lq.bam", + "ontologies": [] + } + } + ] + ], + "lq_pbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.transcripts.lq.bam.pbi": { + "type": "file", + "description": "Pacbio index of low quality reads (when --use-qvs is set)", + "pattern": "*.transcripts.lq.bam.pbi", + "ontologies": [] + } + } + ] + ], + "singletons_bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.transcripts.singletons.bam": { + "type": "file", + "description": "Unclustered reads (when --singletons is set)", + "pattern": "*.transcripts.singletons.bam", + "ontologies": [] + } + } + ] + ], + "singletons_pbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.transcripts.singletons.bam.pbi": { + "type": "file", + "description": "Pacbio index of unclustered reads (when --singletons is set)", + "pattern": "*.transcripts.singletons.bam.pbi", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software version", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@sguizard"], + "maintainers": ["@sguizard"] + } }, { - "name": "scrnaseq", - "version": "4.1.0" - } - ] - }, - { - "name": "gget_gget", - "path": "modules/nf-core/gget/gget/meta.yml", - "type": "module", - "meta": { - "name": "gget_gget", - "description": "gget is a free, open-source command-line tool and Python package that enables efficient querying of genomic databases. gget consists of a collection of separate but interoperable modules, each designed to facilitate one type of database querying in a single line of code.", - "keywords": [ - "gget", - "reference", - "database", - "databases", - "download" - ], - "tools": [ - { - "gget": { - "description": "gget enables efficient querying of genomic databases", - "homepage": "https://github.com/pachterlab/gget", - "documentation": "https://pachterlab.github.io/gget/", - "tool_dev_url": "https://github.com/pachterlab/gget", - "doi": "10.1093/bioinformatics/btac836", - "licence": [ - "BSD-2-clause" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } + "name": "isoseq_refine", + "path": "modules/nf-core/isoseq/refine/meta.yml", + "type": "module", + "meta": { + "name": "isoseq_refine", + "description": "Remove polyA tail and artificial concatemers", + "keywords": ["isoseq", "refine", "ccs", "pacbio", "polyA_tail"], + "tools": [ + { + "isoseq": { + "description": "IsoSeq - Scalable De Novo Isoform Discovery", + "homepage": "https://github.com/PacificBiosciences/IsoSeq/blob/master/isoseq-clustering.md", + "documentation": "https://github.com/PacificBiosciences/IsoSeq/blob/master/isoseq-clustering.md", + "tool_dev_url": "https://github.com/PacificBiosciences/IsoSeq/blob/master/isoseq-clustering.md", + "licence": ["BSD-3-Clause-Clear"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file, cleaned ccs generated by lima", + "pattern": "*.bam", + "ontologies": [] + } + } + ], + { + "primers": { + "type": "file", + "description": "fasta file of primers", + "pattern": "*.fasta", + "ontologies": [] + } + } + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Set of complete reads (with polyA tail), where the polyA has been trimmed", + "pattern": "*.bam", + "ontologies": [] + } + } + ] + ], + "pbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.bam.pbi": { + "type": "file", + "description": "Pacbio index file from polyA trimmed reads", + "pattern": "*.pbi", + "ontologies": [] + } + } + ] + ], + "consensusreadset": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.consensusreadset.xml": { + "type": "file", + "description": "Metadata about read library", + "pattern": "*.xml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2332" + } + ] + } + } + ] + ], + "summary": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.filter_summary.report.json": { + "type": "file", + "description": "json file describing number of full length reads, full length non chimeric reads and full length non chimeric polyA reads", + "pattern": "*.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "report": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.report.csv": { + "type": "file", + "description": "Metadata about primer and polyA detection (primers/polyA/insert length, strand, primer name)", + "pattern": "*.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@sguizard"], + "maintainers": ["@sguizard"] }, - { - "files": { - "type": "file", - "description": "Optional input files which can be specified for certain tools. This is mostly used to supply a FASTA file for gget muscle.\n", - "ontologies": [] - } - } - ] - ], - "output": { - "files": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*[!${prefix}.${extension}]*": { - "type": "file", - "description": "File containing output of gget command.", - "ontologies": [] - } - } - ] - ], - "output": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + "pipelines": [ + { + "name": "isoseq", + "version": "2.0.0" } - }, - { - "${prefix}.${extension}": { - "type": "file", - "description": "File containing output of gget command (-o for most gget tools).", - "pattern": "*.{json,csv}", - "ontologies": [ + ] + }, + { + "name": "ivar_consensus", + "path": "modules/nf-core/ivar/consensus/meta.yml", + "type": "module", + "meta": { + "name": "ivar_consensus", + "description": "Generate a consensus sequence from a BAM file using iVar", + "keywords": ["amplicon sequencing", "consensus", "fasta"], + "tools": [ + { + "ivar": { + "description": "iVar - a computational package that contains functions broadly useful for viral amplicon-based sequencing.\n", + "homepage": "https://github.com/andersen-lab/ivar", + "documentation": "https://andersen-lab.github.io/ivar/html/manualpage.html", + "licence": ["GPL-3.0-or-later"], + "identifier": "biotools:andersen-lab_ivar" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "A sorted (with samtools sort) and trimmed (with iVar trim) bam file", + "pattern": "*.bam", + "ontologies": [] + } + } + ], { - "edam": "http://edamontology.org/format_3464" + "fasta": { + "type": "file", + "description": "The reference sequence used for mapping and generating the BAM file", + "pattern": "*.fa", + "ontologies": [] + } }, { - "edam": "http://edamontology.org/format_3752" + "save_mpileup": { + "type": "boolean", + "description": "Save mpileup file generated by ivar consensus", + "pattern": "*.mpileup" + } } - ] + ], + "output": { + "fasta": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fa": { + "type": "file", + "description": "iVar generated consensus sequence", + "pattern": "*.fa", + "ontologies": [] + } + } + ] + ], + "qual": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.qual.txt": { + "type": "file", + "description": "iVar generated quality file", + "pattern": "*.qual.txt", + "ontologies": [] + } + } + ] + ], + "mpileup": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.mpileup": { + "type": "file", + "description": "mpileup output from samtools mpileup [OPTIONAL]", + "pattern": "*.mpileup", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@andersgs", "@drpatelh"], + "maintainers": ["@andersgs", "@drpatelh"] + }, + "pipelines": [ + { + "name": "viralmetagenome", + "version": "1.1.1" + }, + { + "name": "viralrecon", + "version": "3.0.0" } - } - ] - ], - "versions_gget": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gget": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gget --version |& sed 's/gget version: //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gget": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gget --version |& sed 's/gget version: //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@adamrtalbot" - ], - "maintainers": [ - "@adamrtalbot" - ] - } - }, - { - "name": "glimpse2_chunk", - "path": "modules/nf-core/glimpse2/chunk/meta.yml", - "type": "module", - "meta": { - "name": "glimpse2_chunk", - "description": "Defines chunks where to run imputation", - "keywords": [ - "chunk", - "low-coverage", - "imputation", - "glimpse" - ], - "tools": [ - { - "glimpse2": { - "description": "GLIMPSE2 is a phasing and imputation method for large-scale low-coverage sequencing studies.", - "homepage": "https://odelaneau.github.io/GLIMPSE", - "documentation": "https://odelaneau.github.io/GLIMPSE/commands.html", - "tool_dev_url": "https://github.com/odelaneau/GLIMPSE", - "doi": "10.1038/s41588-020-00756-0", - "licence": [ - "MIT" - ], - "identifier": "biotools:glimpse2" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "Target dataset in VCF/BCF format defined at all variable positions.\nThe file could possibly be without GT field (for efficiency reasons a file containing only the positions is recommended).\n", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", - "ontologies": [] - } - }, - { - "input_index": { - "type": "file", - "description": "Index file of the input VCF/BCF file containing genotype likelihoods.", - "pattern": "*.{vcf.gz.csi,bcf.gz.csi}", - "ontologies": [] - } - }, - { - "region": { - "type": "string", - "description": "Target region, usually a full chromosome (e.g. chr20:1000000-2000000 or chr20).\nFor chrX, please treat PAR and non-PAR regions as different choromosome in order to avoid mixing ploidy.\n" - } - }, - { - "map": { - "type": "file", - "description": "File containing the genetic map.", - "pattern": "*.gmap", - "ontologies": [] - } - } - ], - { - "model": { - "type": "string", - "description": "Algorithm model to use:\n\"recursive\": Recursive algorithm\n\"sequential\": Sequential algorithm (Recommended)\n\"uniform-number-variants\": Experimental. Uniform the number of variants in the sequential algorithm\n", - "pattern": "{recursive,sequential,uniform-number-variants}" - } - } - ], - "output": { - "chunk_chr": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.txt": { - "type": "file", - "description": "Tab delimited output txt file containing buffer and imputation regions.", - "pattern": "*.{txt}", - "ontologies": [] - } - } - ] - ], - "versions_glimpse2": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "glimpse2": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "GLIMPSE2_chunk --help | grep -oE 'v[0-9.]+' | cut -c2-": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "glimpse2": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "GLIMPSE2_chunk --help | grep -oE 'v[0-9.]+' | cut -c2-": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@louislenezet" - ], - "maintainers": [ - "@louislenezet" - ], - "requirements": [ - "AVX2" - ] - }, - "pipelines": [ - { - "name": "phaseimpute", - "version": "1.1.0" - } - ] - }, - { - "name": "glimpse2_concordance", - "path": "modules/nf-core/glimpse2/concordance/meta.yml", - "type": "module", - "meta": { - "name": "glimpse2_concordance", - "description": "Program to compute the genotyping error rate at the sample or marker level.", - "keywords": [ - "concordance", - "low-coverage", - "glimpse", - "imputation" - ], - "tools": [ - { - "glimpse2": { - "description": "GLIMPSE2 is a phasing and imputation method for large-scale low-coverage sequencing studies.", - "homepage": "https://odelaneau.github.io/GLIMPSE", - "documentation": "https://odelaneau.github.io/GLIMPSE/commands.html", - "tool_dev_url": "https://github.com/odelaneau/GLIMPSE", - "doi": "10.1038/s41588-020-00756-0", - "licence": [ - "MIT" - ], - "identifier": "biotools:glimpse2" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "estimate": { - "type": "file", - "description": "Imputed dataset file obtain after phasing.", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", - "ontologies": [] - } - }, - { - "estimate_index": { - "type": "file", - "description": "Index file for the imputed dataset file.", - "ontologies": [] - } - }, - { - "truth": { - "type": "file", - "description": "Validation dataset called at the same positions as the imputed file.", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", - "ontologies": [] - } - }, - { - "truth_index": { - "type": "file", - "description": "Index file for the truth file.", - "ontologies": [] - } - }, - { - "freq": { - "type": "file", - "description": "File containing allele frequencies at each site.", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", - "ontologies": [] - } - }, - { - "freq_index": { - "type": "file", - "description": "Index file for the allele frequencies file.", - "ontologies": [] - } - }, - { - "samples": { - "type": "file", - "description": "List of samples to process, one sample ID per line.", - "pattern": "*.{txt,tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - }, - { - "region": { - "type": "string", - "description": "Target region used for imputation, including left and right buffers (e.g. chr20:1000000-2000000). Can also be a list of such regions.", - "pattern": "chrXX:leftBufferPosition-rightBufferPosition" - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "groups": { - "type": "file", - "description": "Alternative to frequency bins, group bins are user defined, provided in a file.", - "pattern": "*.{txt,tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - }, - { - "bins": { - "type": "string", - "description": "Allele frequency bins used for rsquared computations.\nBy default they should as MAF bins [0-0.5], while\nthey should take the full range [0-1] if --use-ref-alt is used.\n", - "pattern": "0 0.01 0.05 ... 0.5" - } - }, - { - "ac_bins": { - "type": "string", - "description": "User-defined allele count bins used for rsquared computations.", - "pattern": "1 2 5 10 20 ... 100000" - } - }, - { - "allele_counts": { - "type": "string", - "description": "Default allele count bins used for rsquared computations.\nAN field must be defined in the frequency file.\n" - } - }, - { - "min_val_gl": { - "type": "float", - "description": "Minimum genotype likelihood probability P(G|R) in validation data.\nSet to zero to have no filter of if using –gt-validation\n" - } - }, - { - "min_val_dp": { - "type": "integer", - "description": "Minimum coverage in validation data.\nIf FORMAT/DP is missing and –min_val_dp > 0, the program exits with an error.\nSet to zero to have no filter of if using –gt-validation\n" - } - } - ] - ], - "output": { - "errors_cal": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.error.cal.txt.gz": { - "type": "file", - "description": "Calibration correlation errors between imputed dosages (in MAF bins) and highly-confident genotype.", - "pattern": "*.errors.cal.txt.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "errors_grp": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.error.grp.txt.gz": { - "type": "file", - "description": "Groups correlation errors between imputed dosages (in MAF bins) and highly-confident genotype.", - "pattern": "*.errors.grp.txt.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "errors_spl": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.error.spl.txt.gz": { - "type": "file", - "description": "Samples correlation errors between imputed dosages (in MAF bins) and highly-confident genotype.", - "pattern": "*.errors.spl.txt.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "rsquare_grp": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.rsquare.grp.txt.gz": { - "type": "file", - "description": "Groups r-squared correlation between imputed dosages (in MAF bins) and highly-confident genotype.", - "pattern": "*.rsquare.grp.txt.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "rsquare_spl": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.rsquare.spl.txt.gz": { - "type": "file", - "description": "Samples r-squared correlation between imputed dosages (in MAF bins) and highly-confident genotype.", - "pattern": "*.rsquare.spl.txt.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "rsquare_per_site": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_r2_sites.txt.gz": { - "type": "file", - "description": "Variant r-squared correlation between imputed dosages (in MAF bins) and highly-confident genotype.", - "pattern": "_r2_sites.txt.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "versions_glimpse2": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "glimpse2": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "GLIMPSE2_concordance --help | grep -oE 'v[0-9.]+' | cut -c2-": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "glimpse2": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "GLIMPSE2_concordance --help | grep -oE 'v[0-9.]+' | cut -c2-": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@louislenezet" - ], - "maintainers": [ - "@louislenezet" - ] - }, - "pipelines": [ - { - "name": "phaseimpute", - "version": "1.1.0" - } - ] - }, - { - "name": "glimpse2_ligate", - "path": "modules/nf-core/glimpse2/ligate/meta.yml", - "type": "module", - "meta": { - "name": "glimpse2_ligate", - "description": "Ligatation of multiple phased BCF/VCF files into a single whole chromosome file.\nGLIMPSE2 is run in chunks that are ligated into chromosome-wide files maintaining the phasing.\n", - "keywords": [ - "ligate", - "low-coverage", - "glimpse", - "imputation" - ], - "tools": [ - { - "glimpse2": { - "description": "GLIMPSE2 is a phasing and imputation method for large-scale low-coverage sequencing studies.", - "homepage": "https://odelaneau.github.io/GLIMPSE", - "documentation": "https://odelaneau.github.io/GLIMPSE/commands.html", - "tool_dev_url": "https://github.com/odelaneau/GLIMPSE", - "doi": "10.1038/s41588-020-00756-0", - "licence": [ - "MIT" - ], - "identifier": "biotools:glimpse2" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input_list": { - "type": "file", - "description": "VCF/BCF file containing genotype probabilities (GP field).", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", - "ontologies": [] - } - }, - { - "input_index": { - "type": "file", - "description": "Index file of the input VCF/BCF file containing genotype likelihoods.", - "pattern": "*.{csi,tbi}", - "ontologies": [] - } - } - ] - ], - "output": { - "merged_variants": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.{vcf,bcf,vcf.gz,bcf.gz}": { - "type": "file", - "description": "Output ligated (phased) file in VCF/BCF format.", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", - "ontologies": [] - } - } - ] - ], - "versions_glimpse2": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "glimpse2": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "GLIMPSE2_ligate --help | grep -oE 'v[0-9.]+' | cut -c2-": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "glimpse2": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "GLIMPSE2_ligate --help | grep -oE 'v[0-9.]+' | cut -c2-": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@louislenezet" - ], - "maintainers": [ - "@louislenezet" - ] - }, - "pipelines": [ - { - "name": "phaseimpute", - "version": "1.1.0" - } - ] - }, - { - "name": "glimpse2_phase", - "path": "modules/nf-core/glimpse2/phase/meta.yml", - "type": "module", - "meta": { - "name": "glimpse2_phase", - "description": "Tool for imputation and phasing from vcf file or directly from bam files.", - "keywords": [ - "phasing", - "low-coverage", - "imputation", - "glimpse" - ], - "tools": [ - { - "glimpse2": { - "description": "GLIMPSE2 is a phasing and imputation method for large-scale low-coverage sequencing studies.", - "homepage": "https://odelaneau.github.io/GLIMPSE", - "documentation": "https://odelaneau.github.io/GLIMPSE/commands.html", - "tool_dev_url": "https://github.com/odelaneau/GLIMPSE", - "doi": "10.1038/s41588-020-00756-0", - "licence": [ - "MIT" - ], - "identifier": "biotools:glimpse2" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "input": { - "type": "file", - "description": "Either one or multiple BAM/CRAM files in an array containing low-coverage sequencing reads or one VCF/BCF file containing the genotype likelihoods.\nWhen using BAM/CRAM the name of the file is used as samples name.\n", - "pattern": "*.{bam,cram,vcf,vcf.gz,bcf,bcf.gz}", - "ontologies": [] - } - }, - { - "input_index": { - "type": "file", - "description": "Index file of the input BAM/CRAM/VCF/BCF file.", - "pattern": "*.{bam.bai,cram.crai,vcf.gz.csi,bcf.gz.csi}", - "ontologies": [] - } - }, - { - "bamlist": { - "type": "file", - "description": "File containing the list of BAM/CRAM files to be phased.\nOne file per line and a second column can be added to indicate the sample name.\n", - "pattern": "*.{txt,tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - }, - { - "samples_file": { - "type": "file", - "description": "File with sample names and ploidy information.\nOne sample per line with a mandatory second column indicating ploidy (1 or 2).\nSample names that are not present are assumed to have ploidy 2 (diploids).\nGLIMPSE does NOT handle the use of sex (M/F) instead of ploidy.\n", - "pattern": "*.{txt,tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - }, - { - "input_region": { - "type": "string", - "description": "Target region used for imputation, including left and right buffers (e.g. chr20:1000000-2000000).\nOptional if reference panel is in bin format.\n", - "pattern": "chrXX:leftBufferPosition-rightBufferPosition" - } - }, - { - "output_region": { - "type": "string", - "description": "Target imputed region, excluding left and right buffers (e.g. chr20:1000000-2000000).\nOptional if reference panel is in bin format.\n", - "pattern": "chrXX:leftBufferPosition-rightBufferPosition" - } - }, - { - "reference": { - "type": "file", - "description": "Reference panel of haplotypes in VCF/BCF format.", - "pattern": "*.{vcf.gz,bcf.gz}", - "ontologies": [] - } - }, - { - "reference_index": { - "type": "file", - "description": "Index file of the Reference panel file.", - "pattern": "*.{vcf.gz.csi,bcf.gz.csi}", - "ontologies": [] - } - }, - { - "map": { - "type": "file", - "description": "File containing the genetic map.\nOptional if reference panel is in bin format.\n", - "pattern": "*.gmap", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing genomic map information\ne.g. `[ map:'GRCh38' ]`\n" - } - }, - { - "fasta_reference": { - "type": "file", - "description": "Faidx-indexed reference sequence file in the appropriate genome build.\nNecessary for CRAM files.\n", - "pattern": "*.fasta", - "ontologies": [] - } - }, - { - "fasta_reference_index": { - "type": "file", - "description": "Faidx index of the reference sequence file in the appropriate genome build.\nNecessary for CRAM files.\n", - "pattern": "*.fai", - "ontologies": [] - } - } - ], - { - "output_suffix": { - "type": "string", - "description": "Output file suffix used to choose the GLIMPSE2 output format. Defaults to `vcf.gz` when empty. Supported values: `vcf`, `vcf.gz`, `bcf`, `bgen`.\n", - "pattern": "vcf|vcf.gz|bcf|bgen" - } - } - ], - "output": { - "phased_variants": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*.{vcf,vcf.gz,bcf,bgen}": { - "type": "file", - "description": "Output VCF/BCF/BGEN file containing genotype probabilities (GP field), imputed dosages (DS field), best guess genotypes (GT field), sampled haplotypes in the last (max 16) main iterations (HS field) and info-score.\n", - "pattern": "*.{vcf,vcf.gz,bcf,bgen}", - "ontologies": [] - } - } - ] - ], - "stats_coverage": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*.txt.gz": { - "type": "file", - "description": "Optional coverage statistic file created when BAM/CRAM files are used as inputs.", - "pattern": "*.txt.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "versions_glimpse2": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "glimpse2": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "GLIMPSE2_phase --help | grep -oE 'v[0-9.]+' | cut -c2-": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "glimpse2": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "GLIMPSE2_phase --help | grep -oE 'v[0-9.]+' | cut -c2-": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@LouisLeNezet" - ], - "maintainers": [ - "@LouisLeNezet" - ] - }, - "pipelines": [ - { - "name": "phaseimpute", - "version": "1.1.0" - } - ] - }, - { - "name": "glimpse2_splitreference", - "path": "modules/nf-core/glimpse2/splitreference/meta.yml", - "type": "module", - "meta": { - "name": "glimpse2_splitreference", - "description": "Tool to create a binary reference panel for quick reading time.", - "keywords": [ - "split", - "reference", - "phasing", - "imputation" - ], - "tools": [ - { - "glimpse2": { - "description": "GLIMPSE2 is a phasing and imputation method for large-scale low-coverage sequencing studies.", - "homepage": "https://odelaneau.github.io/GLIMPSE", - "documentation": "https://odelaneau.github.io/GLIMPSE/commands.html", - "tool_dev_url": "https://github.com/odelaneau/GLIMPSE", - "doi": "10.1038/s41588-020-00756-0", - "licence": [ - "MIT" - ], - "identifier": "biotools:glimpse2" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reference": { - "type": "file", - "description": "Reference panel of haplotypes in VCF/BCF format.", - "pattern": "*.{vcf.gz,bcf.gz}", - "ontologies": [] - } - }, - { - "reference_index": { - "type": "file", - "description": "Index file of the Reference panel file.", - "pattern": "*.{vcf.gz.csi,bcf.gz.csi}", - "ontologies": [] - } - }, - { - "input_region": { - "type": "string", - "description": "Target region used for imputation, including left and right buffers (e.g. chr20:1000000-2000000).", - "pattern": "chrXX:leftBufferPosition-rightBufferPosition" - } - }, - { - "output_region": { - "type": "string", - "description": "Target imputed region, excluding left and right buffers (e.g. chr20:1000000-2000000).", - "pattern": "chrXX:leftBufferPosition-rightBufferPosition" - } - }, - { - "map": { - "type": "file", - "description": "File containing the genetic map.", - "pattern": "*.gmap", - "ontologies": [] - } - } - ] - ], - "output": { - "bin_ref": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bin": { - "type": "file", - "description": "binary reference panel", - "pattern": "*.bin", - "ontologies": [] - } - } - ] - ], - "versions_glimpse2": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "glimpse2": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "GLIMPSE2_split_reference --help | grep -oE 'v[0-9.]+' | cut -c2-": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "glimpse2": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "GLIMPSE2_split_reference --help | grep -oE 'v[0-9.]+' | cut -c2-": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@LouisLeNezet" - ], - "maintainers": [ - "@LouisLeNezet" - ], - "requirements": [ - "AVX2" - ] - } - }, - { - "name": "glimpse_chunk", - "path": "modules/nf-core/glimpse/chunk/meta.yml", - "type": "module", - "meta": { - "name": "glimpse_chunk", - "description": "Defines chunks where to run imputation", - "keywords": [ - "chunk", - "imputation", - "low coverage" - ], - "tools": [ - { - "glimpse": { - "description": "GLIMPSE is a phasing and imputation method for large-scale low-coverage sequencing studies.", - "homepage": "https://odelaneau.github.io/GLIMPSE", - "documentation": "https://odelaneau.github.io/GLIMPSE/commands.html", - "tool_dev_url": "https://github.com/odelaneau/GLIMPSE", - "doi": "10.1038/s41588-020-00756-0", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "Target dataset in VCF/BCF format defined at all variable positions.\nThe file could possibly be without GT field (for efficiency reasons a file containing only the positions is recommended).\n", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", - "ontologies": [] - } - }, - { - "input_index": { - "type": "file", - "description": "Index file for the input VCF/BCF file.", - "ontologies": [] - } - }, - { - "region": { - "type": "string", - "description": "Target region, usually a full chromosome (e.g. chr20:1000000-2000000 or chr20).\nFor chrX, please treat PAR and non-PAR regions as different choromosome in order to avoid mixing ploidy.\n" - } - } - ] - ], - "output": { - "chunk_chr": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.txt": { - "type": "file", - "description": "Tab delimited output txt file containing buffer and imputation regions.", - "pattern": "*.txt", - "ontologies": [] - } - } - ] - ], - "versions_glimpse": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "glimpse": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "GLIMPSE_chunk --help | sed -n '/Version/s/.*: //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "glimpse": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "GLIMPSE_chunk --help | sed -n '/Version/s/.*: //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@louislenezet" - ], - "maintainers": [ - "@louislenezet" - ] - }, - "pipelines": [ - { - "name": "phaseimpute", - "version": "1.1.0" - } - ] - }, - { - "name": "glimpse_concordance", - "path": "modules/nf-core/glimpse/concordance/meta.yml", - "type": "module", - "meta": { - "name": "glimpse_concordance", - "description": "Compute the r2 correlation between imputed dosages (in MAF bins) and highly-confident genotype calls from the high-coverage dataset.", - "keywords": [ - "concordance", - "low-coverage", - "glimpse", - "imputation" - ], - "tools": [ - { - "glimpse": { - "description": "GLIMPSE is a phasing and imputation method for large-scale low-coverage sequencing studies.", - "homepage": "https://odelaneau.github.io/GLIMPSE", - "documentation": "https://odelaneau.github.io/GLIMPSE/commands.html", - "tool_dev_url": "https://github.com/odelaneau/GLIMPSE", - "doi": "10.1038/s41588-020-00756-0", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "estimate": { - "type": "file", - "description": "Imputed data.", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", - "ontologies": [] - } - }, - { - "estimate_index": { - "type": "file", - "description": "Index file for the imputed data.", - "ontologies": [] - } - }, - { - "freq": { - "type": "file", - "description": "File containing allele frequencies at each site.", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", - "ontologies": [] - } - }, - { - "freq_index": { - "type": "file", - "description": "Index file for the allele frequencies file.", - "ontologies": [] - } - }, - { - "truth": { - "type": "file", - "description": "Validation dataset called at the same positions as the imputed file.", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", - "ontologies": [] - } - }, - { - "truth_index": { - "type": "file", - "description": "Index file for the truth file.", - "ontologies": [] - } - }, - { - "region": { - "type": "string", - "description": "Target region used for imputation, including left and right buffers (e.g. chr20:1000000-2000000).", - "pattern": "chrXX:leftBufferPosition-rightBufferPosition" - } - } - ], - { - "min_prob": { - "type": "float", - "description": "Minimum posterior probability P(G|R) in validation data" - } - }, - { - "min_dp": { - "type": "integer", - "description": "Minimum coverage in validation data.\nIf FORMAT/DP is missing and --minDP > 0, the program exits with an error.\n" - } - }, - { - "bins": { - "type": "string", - "description": "Allele frequency bins used for rsquared computations.\nBy default they should as MAF bins [0-0.5], while\nthey should take the full range [0-1] if --use-ref-alt is used.\n" - } - } - ], - "output": { - "errors_cal": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.error.cal.txt.gz": { - "type": "file", - "description": "Calibration correlation errors between imputed dosages (in MAF bins) and highly-confident genotype.", - "pattern": "*.errors.cal.txt.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "errors_grp": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.error.grp.txt.gz": { - "type": "file", - "description": "Groups correlation errors between imputed dosages (in MAF bins) and highly-confident genotype.", - "pattern": "*.errors.grp.txt.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "errors_spl": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.error.spl.txt.gz": { - "type": "file", - "description": "Samples correlation errors between imputed dosages (in MAF bins) and highly-confident genotype.", - "pattern": "*.errors.spl.txt.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "rsquare_grp": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.rsquare.grp.txt.gz": { - "type": "file", - "description": "Groups r-squared correlation between imputed dosages (in MAF bins) and highly-confident genotype.", - "pattern": "*.rsquare.grp.txt.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "rsquare_spl": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.rsquare.spl.txt.gz": { - "type": "file", - "description": "Samples r-squared correlation between imputed dosages (in MAF bins) and highly-confident genotype.", - "pattern": "*.rsquare.spl.txt.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "versions_glimpse": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "glimpse": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "GLIMPSE_concordance --help | sed -n '/Version/s/.*: //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "glimpse": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "GLIMPSE_concordance --help | sed -n '/Version/s/.*: //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@louislenezet" - ], - "maintainers": [ - "@louislenezet" - ] - } - }, - { - "name": "glimpse_ligate", - "path": "modules/nf-core/glimpse/ligate/meta.yml", - "type": "module", - "meta": { - "name": "glimpse_ligate", - "description": "Concatenates imputation chunks in a single VCF/BCF file ligating phased information.", - "keywords": [ - "ligate", - "low-coverage", - "glimpse", - "imputation" - ], - "tools": [ - { - "glimpse": { - "description": "GLIMPSE is a phasing and imputation method for large-scale low-coverage sequencing studies.", - "homepage": "https://odelaneau.github.io/GLIMPSE", - "documentation": "https://odelaneau.github.io/GLIMPSE/commands.html", - "tool_dev_url": "https://github.com/odelaneau/GLIMPSE", - "doi": "10.1038/s41588-020-00756-0", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input_list": { - "type": "file", - "description": "VCF/BCF file containing genotype probabilities (GP field).", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", - "ontologies": [] - } - }, - { - "input_index": { - "type": "file", - "description": "Index file of the input VCF/BCF file containing genotype likelihoods.", - "pattern": "*.{vcf.gz.csi,bcf.gz.csi}", - "ontologies": [] - } - } - ] - ], - "output": { - "merged_variants": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.{vcf,bcf,vcf.gz,bcf.gz}": { - "type": "file", - "description": "Output VCF/BCF file for the merged regions.\nPhased information (HS field) is updated accordingly for the full region.\n", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", - "ontologies": [] - } - } - ] - ], - "versions_glimpse": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "glimpse": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "GLIMPSE_ligate --help | sed -n '/Version/s/.*: //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "glimpse": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "GLIMPSE_ligate --help | sed -n '/Version/s/.*: //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@louislenezet" - ], - "maintainers": [ - "@louislenezet" - ] - }, - "pipelines": [ - { - "name": "phaseimpute", - "version": "1.1.0" - } - ] - }, - { - "name": "glimpse_phase", - "path": "modules/nf-core/glimpse/phase/meta.yml", - "type": "module", - "meta": { - "name": "glimpse_phase", - "description": "main GLIMPSE algorithm, performs phasing and imputation refining genotype likelihoods", - "keywords": [ - "phase", - "imputation", - "low-coverage", - "glimpse" - ], - "tools": [ - { - "glimpse": { - "description": "GLIMPSE is a phasing and imputation method for large-scale low-coverage sequencing studies.", - "homepage": "https://odelaneau.github.io/GLIMPSE", - "documentation": "https://odelaneau.github.io/GLIMPSE/commands.html", - "tool_dev_url": "https://github.com/odelaneau/GLIMPSE", - "doi": "10.1038/s41588-020-00756-0", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "Input VCF/BCF file containing genotype likelihoods.", - "pattern": "*.{vcf.gz,bcf.gz}", - "ontologies": [] - } - }, - { - "input_index": { - "type": "file", - "description": "Index file of the input VCF/BCF file containing genotype likelihoods.", - "pattern": "*.{vcf.gz.csi,bcf.gz.csi}", - "ontologies": [] - } - }, - { - "samples_file": { - "type": "file", - "description": "File with sample names and ploidy information.\nOne sample per line with a mandatory second column indicating ploidy (1 or 2).\nSample names that are not present are assumed to have ploidy 2 (diploids).\nGLIMPSE does NOT handle the use of sex (M/F) instead of ploidy.\n", - "pattern": "*.{txt,tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - }, - { - "input_region": { - "type": "string", - "description": "Target region used for imputation, including left and right buffers (e.g. chr20:1000000-2000000).", - "pattern": "chrXX:leftBufferPosition-rightBufferPosition" - } - }, - { - "output_region": { - "type": "string", - "description": "Target imputed region, excluding left and right buffers (e.g. chr20:1000000-2000000).", - "pattern": "chrXX:leftBufferPosition-rightBufferPosition" - } - }, - { - "reference": { - "type": "file", - "description": "Reference panel of haplotypes in VCF/BCF format.", - "pattern": "*.{vcf.gz,bcf.gz}", - "ontologies": [] - } - }, - { - "reference_index": { - "type": "file", - "description": "Index file of the Reference panel file.", - "pattern": "*.{vcf.gz.csi,bcf.gz.csi}", - "ontologies": [] - } - }, - { - "map": { - "type": "file", - "description": "File containing the genetic map.", - "pattern": "*.gmap", - "ontologies": [] - } - } - ] - ], - "output": { - "phased_variants": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.{vcf,bcf,vcf.gz,bcf.gz}": { - "type": "file", - "description": "Output VCF/BCF file containing genotype probabilities (GP field),\nimputed dosages (DS field), best guess genotypes (GT field),\nsampled haplotypes in the last (max 16) main iterations (HS field) and info-score.\n", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", - "ontologies": [] - } - } - ] - ], - "versions_glimpse": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "glimpse": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "GLIMPSE_phase --help | sed -n '/Version/s/.*: //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "glimpse": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "GLIMPSE_phase --help | sed -n '/Version/s/.*: //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@louislenezet" - ], - "maintainers": [ - "@louislenezet" - ] - }, - "pipelines": [ - { - "name": "phaseimpute", - "version": "1.1.0" - } - ] - }, - { - "name": "glimpse_sample", - "path": "modules/nf-core/glimpse/sample/meta.yml", - "type": "module", - "meta": { - "name": "glimpse_sample", - "description": "Generates haplotype calls by sampling haplotype estimates", - "keywords": [ - "Sample", - "Haplotypes", - "Imputation" - ], - "tools": [ - { - "glimpse": { - "description": "GLIMPSE is a phasing and imputation method for large-scale low-coverage sequencing studies.", - "homepage": "https://odelaneau.github.io/GLIMPSE", - "documentation": "https://odelaneau.github.io/GLIMPSE/commands.html", - "tool_dev_url": "https://github.com/odelaneau/GLIMPSE", - "doi": "10.1038/s41588-020-00756-0", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "Imputed VCF/BCF file", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", - "ontologies": [] - } + }, + { + "name": "ivar_trim", + "path": "modules/nf-core/ivar/trim/meta.yml", + "type": "module", + "meta": { + "name": "ivar_trim", + "description": "Trim primer sequences rom a BAM file with iVar", + "keywords": ["amplicon sequencing", "trimming", "fasta"], + "tools": [ + { + "ivar": { + "description": "iVar - a computational package that contains functions broadly useful for viral amplicon-based sequencing.\n", + "homepage": "https://github.com/andersen-lab/ivar", + "documentation": "https://andersen-lab.github.io/ivar/html/manualpage.html", + "licence": ["GPL-3.0-or-later"], + "identifier": "biotools:andersen-lab_ivar" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "Co-ordinate sorted BAM file", + "pattern": "*.bam", + "ontologies": [] + } + }, + { + "bai": { + "type": "file", + "description": "Index file for co-ordinate sorted BAM file", + "pattern": "*.bai", + "ontologies": [] + } + } + ], + { + "bed": { + "type": "file", + "description": "BED file with primer labels and positions", + "pattern": "*.bed", + "ontologies": [] + } + } + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "iVar generated trimmed bam file (unsorted)", + "pattern": "*.bam", + "ontologies": [] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "Log file generated by iVar for use with MultiQC", + "pattern": "*.log", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@andersgs", "@drpatelh"], + "maintainers": ["@andersgs", "@drpatelh"] }, - { - "index": { - "type": "file", - "description": "Index file of the input VCF/BCF file.", - "pattern": "*.{vcf.gz.csi,bcf.gz.csi}", - "ontologies": [] - } - } - ] - ], - "output": { - "haplo_sampled": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.{vcf,bcf,vcf.gz,bcf.gz}": { - "type": "file", - "description": "Output VCF/BCF file containing phased genotypes.", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", - "ontologies": [] - } - } - ] - ], - "versions_glimpse": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "glimpse": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "GLIMPSE_sample --help | sed -n '/Version/s/.*: //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "glimpse": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "GLIMPSE_sample --help | sed -n '/Version/s/.*: //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "viralrecon", + "version": "3.0.0" + } ] - ] - }, - "authors": [ - "@louislenezet" - ], - "maintainers": [ - "@louislenezet" - ] - } - }, - { - "name": "glnexus", - "path": "modules/nf-core/glnexus/meta.yml", - "type": "module", - "meta": { - "name": "glnexus", - "description": "merge gVCF files and perform joint variant calling", - "keywords": [ - "merge", - "gvcf", - "joint-variant-calling" - ], - "tools": [ - { - "glnexus": { - "description": "scalable gVCF merging and joint variant calling for population sequencing projects.", - "homepage": "https://github.com/dnanexus-rnd/GLnexus", - "documentation": "https://github.com/dnanexus-rnd/GLnexus/wiki/Getting-Started", - "doi": "10.1101/343970", - "licence": [ - "Apache-2.0" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "gvcfs": { - "type": "list", - "description": "Input genomic vcf files", - "pattern": "*.{gvcf,gvcf.gz,g.vcf,g.vcf.gz}" - } - }, - { - "custom_config": { - "type": "file", - "description": "Custom YML config for additional profiles", - "pattern": "*.{yml,yaml}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing regions information\ne.g. [ id:'test' ]\n" - } + }, + { + "name": "ivar_variants", + "path": "modules/nf-core/ivar/variants/meta.yml", + "type": "module", + "meta": { + "name": "ivar_variants", + "description": "Call variants from a BAM file using iVar", + "keywords": ["amplicon sequencing", "variants", "fasta"], + "tools": [ + { + "ivar": { + "description": "iVar - a computational package that contains functions broadly useful for viral amplicon-based sequencing.\n", + "homepage": "https://github.com/andersen-lab/ivar", + "documentation": "https://andersen-lab.github.io/ivar/html/manualpage.html", + "licence": ["GPL-3.0-or-later"], + "identifier": "biotools:andersen-lab_ivar" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "A sorted (with samtools sort) and trimmed (with iVar trim) bam file", + "pattern": "*.bam", + "ontologies": [] + } + } + ], + { + "fasta": { + "type": "file", + "description": "The reference sequence used for mapping and generating the BAM file", + "pattern": "*.fa", + "ontologies": [] + } + }, + { + "fai": { + "type": "file", + "description": "The index for the reference sequence used for mapping and generating the BAM file", + "pattern": "*.fai", + "ontologies": [] + } + }, + { + "gff": { + "type": "file", + "description": "A GFF file in the GFF3 format can be supplied to specify coordinates of open reading frames (ORFs). In absence of GFF file, amino acid translation will not be done.", + "pattern": "*.gff", + "ontologies": [] + } + }, + { + "save_mpileup": { + "type": "boolean", + "description": "Save mpileup file generated by ivar variants", + "pattern": "*.mpileup" + } + } + ], + "output": { + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "iVar generated TSV file with the variants", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "mpileup": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.mpileup": { + "type": "file", + "description": "mpileup output from samtools mpileup [OPTIONAL]", + "pattern": "*.mpileup", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@andersgs", "@drpatelh"], + "maintainers": ["@andersgs", "@drpatelh"] }, - { - "bed": { - "type": "list", - "description": "Input BED file", - "pattern": "*.bed" - } - } - ] - ], - "output": { - "bcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.bcf": { - "type": "file", - "description": "merged BCF file", - "pattern": "*.bcf", - "ontologies": [] - } - } - ] - ], - "versions_glnexus": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "glnexus": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "glnexus_cli 2>&1 | grep -oE '[0-9]+\\.[0-9]+\\.[0-9]+'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "glnexus": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "glnexus_cli 2>&1 | grep -oE '[0-9]+\\.[0-9]+\\.[0-9]+'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "viralmetagenome", + "version": "1.1.1" + }, + { + "name": "viralrecon", + "version": "3.0.0" + } ] - ] }, - "authors": [ - "@ramprasadn" - ], - "maintainers": [ - "@ramprasadn" - ] - }, - "pipelines": [ { - "name": "raredisease", - "version": "3.0.0" + "name": "jasminesv", + "path": "modules/nf-core/jasminesv/meta.yml", + "type": "module", + "meta": { + "name": "jasminesv", + "description": "Jointly Accurate Sv Merging with Intersample Network Edges", + "keywords": ["jasminesv", "jasmine", "structural variants", "vcf", "bam"], + "tools": [ + { + "jasminesv": { + "description": "Software for merging structural variants between individuals", + "homepage": "https://github.com/mkirsche/Jasmine/wiki/Jasmine-User-Manual", + "documentation": "https://github.com/mkirsche/Jasmine/wiki/Jasmine-User-Manual", + "tool_dev_url": "https://github.com/mkirsche/Jasmine", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcfs": { + "type": "list", + "description": "The VCF files that need to be merged\n", + "pattern": "*.{vcf,vcf.gz}" + } + }, + { + "bams": { + "type": "list", + "description": "Optional - The BAM files from which the VCFs were created", + "pattern": "*.bam" + } + }, + { + "bais": { + "type": "list", + "description": "Optional - The BAM index files from which the VCFs were created", + "pattern": "*.bai" + } + }, + { + "sample_dists": { + "type": "file", + "description": "Optional - A txt file containing the distance thresholds for each sample", + "pattern": "*.txt", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing fasta information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Optional - The reference FASTA file used to create the VCFs", + "pattern": "*.{fasta,fa}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing fasta index information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta_fai": { + "type": "file", + "description": "Optional - The index of the reference FASTA file used to create the VCFs", + "pattern": "*.fai", + "ontologies": [] + } + } + ], + { + "chr_norm": { + "type": "file", + "description": "Optional - A txt file containing the chromosomes and their aliases for normalization", + "pattern": "*.txt", + "ontologies": [] + } + } + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "The merged VCF file", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "versions_jasminesv": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "jasminesv": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "jasmine 2>&1 | grep \"version\" | sed \"s/Jasmine version //\"": { + "type": "eval", + "description": "The version of the tool" + } + } + ] + ], + "versions_bgzip": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bgzip": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bgzip --version | head -1 | sed -e \"s/bgzip (htslib) //\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "jasminesv": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "jasmine 2>&1 | grep \"version\" | sed \"s/Jasmine version //\"": { + "type": "eval", + "description": "The version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bgzip": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "bgzip --version | head -1 | sed -e \"s/bgzip (htslib) //\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@nvnieuwk"], + "maintainers": ["@nvnieuwk"] + } }, { - "name": "variantcatalogue", - "version": "dev" - } - ] - }, - { - "name": "gmmdemux", - "path": "modules/nf-core/gmmdemux/meta.yml", - "type": "module", - "meta": { - "name": "gmmdemux", - "description": "GMM-Demux is a Gaussian-Mixture-Model-based software for processing sample barcoding data (cell hashing and MULTI-seq).", - "keywords": [ - "demultiplexing", - "hashing-based deconvolution", - "single-cell" - ], - "tools": [ - { - "gmmdemux": { - "description": "GMM-Demux is a Gaussian-Mixture-Model-based software for processing sample barcoding data (cell hashing and MULTI-seq).", - "homepage": "https://pypi.org/project/GMM-Demux/", - "documentation": "https://github.com/CHPGenetics/GMM-Demux", - "tool_dev_url": "https://github.com/CHPGenetics/GMM-demux", - "doi": "10.1186/s13059-020-02084-2", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } - }, - { - "hto_matrix": { - "type": "file", - "description": "path to matrix from cell hashing data, the tool receives either CSV files or TSV, type must be specified using parameters", - "ontologies": [] - } - }, - { - "hto_names": { - "type": "string", - "description": "Comma separated list of HTO names, without whitespace\n" - } - } - ], - { - "type_report": { - "type": "boolean", - "description": "If true, full classification report is generated, otherwise the simplified classification report.\n" + "name": "jellyfish_count", + "path": "modules/nf-core/jellyfish/count/meta.yml", + "type": "module", + "meta": { + "name": "jellyfish_count", + "description": "Efficiently counts k-mers from DNA sequencing reads using a fast, memory-efficient, parallelized algorithm", + "keywords": ["k-mer", "DNA", "substrings"], + "tools": [ + { + "jellyfish": { + "description": "Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence", + "homepage": "https://github.com/gmarcais/Jellyfish", + "documentation": "https://github.com/gmarcais/Jellyfish/blob/master/doc/Readme.md", + "tool_dev_url": "https://github.com/gmarcais/Jellyfish", + "doi": "10.1093/bioinformatics/btr011", + "licence": ["GPL v3"], + "identifier": "biotools:jellyfish" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Nucleotide sequences in FASTA format", + "pattern": "*.{fasta,fa,fna,faa}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + { + "kmer_length": { + "type": "integer", + "description": "k-mer size to use" + } + }, + { + "size": { + "type": "string", + "description": "Specifies the memory hash size (in bytes) to allocate for the k-mer counting hash table (e.g., '100M').\nA mean estimation could be carried with this formula: 'genome size + (genome size * coverage * kmer-length * error rate)'\n" + } + } + ], + "output": { + "jf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}.jf": { + "type": "file", + "description": "Jellyfish binary k-mer database", + "pattern": "*.jf", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@vagkaratzas"], + "maintainers": ["@vagkaratzas"] } - }, - { - "summary_report": { - "type": "boolean", - "description": "If true, summary report is generated.\n" + }, + { + "name": "jellyfish_dump", + "path": "modules/nf-core/jellyfish/dump/meta.yml", + "type": "module", + "meta": { + "name": "jellyfish_dump", + "description": "Dumps the results from a jellyfish binary file into a human readable format", + "keywords": ["k-mer", "DNA", "substrings"], + "tools": [ + { + "jellyfish": { + "description": "Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence", + "homepage": "https://github.com/gmarcais/Jellyfish", + "documentation": "https://github.com/gmarcais/Jellyfish/blob/master/doc/Readme.md", + "tool_dev_url": "https://github.com/gmarcais/Jellyfish", + "doi": "10.1093/bioinformatics/btr011", + "licence": ["GPL v3"], + "identifier": "biotools:jellyfish" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "jf": { + "type": "file", + "description": "Jellyfish binary k-mer database", + "pattern": "*.jf", + "ontologies": [] + } + } + ] + ], + "output": { + "output": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}.${extension}": { + "type": "file", + "description": "Human readable k-mer database in fasta format, or in 2-column space delimited format if the -c argument is provided", + "pattern": "*.{fa,txt}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + }, + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@vagkaratzas"], + "maintainers": ["@vagkaratzas"] } - }, - { - "skip": { - "type": "file", - "description": "Load a full classification report and skip the mtx folder as input. Require a path argument.\n", - "ontologies": [] + }, + { + "name": "juicertools_pre", + "path": "modules/nf-core/juicertools/pre/meta.yml", + "type": "module", + "meta": { + "name": "juicertools_pre", + "description": "Create a multi-resolution .hic contact matrix for analysis with Juicer", + "keywords": ["hic", "contact map", "genomics"], + "tools": [ + { + "juicertools": { + "description": "Visualization and analysis software for Hi-C data", + "homepage": "https://github.com/aidenlab/juicer", + "documentation": "https://github.com/aidenlab/juicer", + "tool_dev_url": "https://github.com/aidenlab/juicer", + "doi": "10.1016/j.cels.2016.07.002", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "pairs": { + "type": "file", + "description": "Optionally gzipped TSV file, in one of a number of formats,\nincluding pairs format. See https://github.com/aidenlab/juicer/wiki/Pre#file-format\nfor details.\n", + "pattern": "*.{pairs,tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "genome_id": { + "type": "string", + "description": "String of a supported genome ID, see https://github.com/aidenlab/juicer/wiki/Pre#usage\nfor details. Incompatible with chromsizes option.\n" + } + }, + { + "chromsizes": { + "type": "file", + "description": "Headerless TSV file describing chromosome sizes with format:\nchrom_name\\tlength\n\nIncompatible with genome_id option.\n", + "pattern": "*.{tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "output": { + "hic": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.hic": { + "type": "file", + "description": ".hic file for analysis and visualisation in Juicer", + "pattern": "*.{hic}", + "ontologies": [] + } + } + ] + ], + "versions_juicertools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "juicer_tools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "juicer_tools -V | grep \"Version\" | sed \"s/Juicer Tools Version //\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "juicer_tools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "juicer_tools -V | grep \"Version\" | sed \"s/Juicer Tools Version //\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@prototaxites"], + "maintainers": ["@prototaxites"] } - }, - { - "examine": { - "type": "file", - "description": "Provide the cell list. Requires a file argument. Only executes if -u is set.\n", - "ontologies": [] + }, + { + "name": "jupyternotebook", + "path": "modules/nf-core/jupyternotebook/meta.yml", + "type": "module", + "meta": { + "name": "jupyternotebook", + "description": "Render jupyter (or jupytext) notebooks to HTML reports. Supports parametrization\nthrough papermill.\n", + "keywords": ["Python", "Jupyter", "jupytext", "papermill", "notebook", "reports"], + "tools": [ + { + "jupytext": { + "description": "Jupyter notebooks as plain text scripts or markdown documents", + "homepage": "https://github.com/mwouts/jupytext/", + "documentation": "https://jupyter.org/documentation", + "tool_dev_url": "https://github.com/mwouts/jupytext/", + "license": ["MIT"], + "identifier": "" + } + }, + { + "papermill": { + "description": "Parameterize, execute, and analyze notebooks", + "homepage": "https://github.com/nteract/papermill", + "documentation": "http://papermill.readthedocs.io/en/latest/", + "tool_dev_url": "https://github.com/nteract/papermill", + "license": ["BSD 3-clause"], + "identifier": "" + } + }, + { + "nbconvert": { + "description": "Parameterize, execute, and analyze notebooks", + "homepage": "https://nbconvert.readthedocs.io/en/latest/", + "documentation": "https://nbconvert.readthedocs.io/en/latest/", + "tool_dev_url": "https://github.com/jupyter/nbconvert", + "license": ["BSD 3-clause"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "notebook": { + "type": "file", + "description": "Jupyter notebook or jupytext representation thereof", + "pattern": "*.{ipynb,py,md,Rmd,myst}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3996" + }, + { + "edam": "http://edamontology.org/format_4000" + } + ] + } + } + ], + { + "parameters": { + "type": "map", + "description": "Groovy map with notebook parameters which will be passed\nto papermill in order to create parametrized reports.\n" + } + }, + { + "input_files": { + "type": "file", + "description": "One or multiple files serving as input data for the notebook.", + "pattern": "*", + "ontologies": [] + } + }, + { + "kernel_": { + "type": "string", + "description": "Name of the kernel to use." + } + } + ], + "output": { + "report": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.html": { + "type": "file", + "description": "HTML report generated from Jupyter notebook", + "pattern": "*.html", + "ontologies": [] + } + } + ] + ], + "artifacts": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "artifacts/": { + "type": "directory", + "description": "Directory containing all artifacts generated by the notebook", + "pattern": "artifacts/" + } + } + ] + ], + "versions_jupytext": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "jupytext": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "jupytext --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_ipykernel": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "ipykernel": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python -c \"import ipykernel; print(ipykernel.__version__)\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_nbconvert": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "nbconvert": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "jupyter nbconvert --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_papermill": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "papermill": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "papermill --version | cut -f1 -d\" \"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "jupytext": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "jupytext --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "ipykernel": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python -c \"import ipykernel; print(ipykernel.__version__)\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "nbconvert": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "jupyter nbconvert --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "papermill": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "papermill --version | cut -f1 -d\" \"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@grst"], + "maintainers": ["@grst"] } - } - ], - "output": { - "barcodes": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "barcodes.tsv.gz": { - "type": "file", - "description": "barcodes tsv file with removed cell-hashing-identifiable multiplets\n", - "pattern": "barcodes.tsv.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "matrix": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "matrix.mtx.gz": { - "type": "file", - "description": "matrix mtx.tsv file with removed cell-hashing-identifiable multiplets\n", - "pattern": "matrix.mtx.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "features": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "features.tsv.gz": { - "type": "file", - "description": "features tsv file with removed cell-hashing-identifiable multiplets\n", - "pattern": "features.tsv.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "classification_report": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "GMM_*.csv": { - "type": "file", - "description": "full or simplified classification report\n", - "pattern": "GMM_*.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "config_report": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "GMM_*.config": { - "type": "file", - "description": "Configuration report mapping the results obtained by the tool to the respective names of the HTOs in the classification report.\n", - "pattern": "GMM_*.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "summary_report": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "summary_report_*.txt": { - "type": "file", - "description": "summary report, optional output\n", - "pattern": "test/summary_report_*.txt", - "ontologies": [] - } - } - ] - ], - "versions_gmmdemux": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "GMM-Demux": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "0.2.2.3": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "GMM-Demux": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "0.2.2.3": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@mari-ga", - "@maxozo", - "@wxicu", - "@Zethson" - ], - "maintainers": [ - "@mari-ga", - "@maxozo", - "@wxicu", - "@Zethson" - ] - } - }, - { - "name": "gnu_sort", - "path": "modules/nf-core/gnu/sort/meta.yml", - "type": "module", - "meta": { - "name": "gnu_sort", - "description": "Writes a sorted concatenation of file/s\n", - "keywords": [ - "GNU", - "coreutils", - "sort", - "merge compare" - ], - "tools": [ - { - "gnu": { - "description": "The GNU Core Utilities are the basic file, shell and text manipulation utilities of the GNU operating system. These are the core utilities which are expected to exist on every operating system.", - "homepage": "https://www.gnu.org/software/coreutils/", - "documentation": "https://www.gnu.org/software/coreutils/manual/html_node/index.html", - "tool_dev_url": "https://git.savannah.gnu.org/cgit/coreutils.git", - "doi": "10.5281/zenodo.581670", - "licence": [ - "GPL" - ], - "identifier": "" + }, + { + "name": "jvarkit_dict2bed", + "path": "modules/nf-core/jvarkit/dict2bed/meta.yml", + "type": "module", + "meta": { + "name": "jvarkit_dict2xml", + "description": "Extract BED file from hts files containing a dictionary (VCF,BAM, CRAM, DICT, etc...)", + "keywords": ["vcf", "bcf", "bed", "dict", "dictionary", "fasta", "fai"], + "tools": [ + { + "jvarkit": { + "description": "Java utilities for Bioinformatics.", + "homepage": "https://github.com/lindenb/jvarkit", + "documentation": "https://jvarkit.readthedocs.io/", + "tool_dev_url": "https://github.com/lindenb/jvarkit", + "doi": "10.6084/m9.figshare.1425030", + "licence": ["MIT License"], + "args_id": "$args", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing dict file information\ne.g. [ id:'test_reference' ]\n" + } + }, + { + "dict_files": { + "type": "file", + "description": "File(s) containing a dictionary VCF/BCF/BAM/DICT etc...", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz,dict,fai,bam,cram,interval_list}", + "ontologies": [] + } + } + ] + ], + "output": { + "bed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing VCF information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "BED output file", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@lindenb"], + "maintainers": ["@lindenb"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "Draft assembly file", - "pattern": "*.{txt,bed,interval,genome,bins}", - "ontologies": [] - } - }, - { - "suffix": { - "type": "string", - "description": "Output suffix" - } + }, + { + "name": "jvarkit_sam2tsv", + "path": "modules/nf-core/jvarkit/sam2tsv/meta.yml", + "type": "module", + "meta": { + "name": "jvarkit_sam2tsv", + "description": "Convert sam files to tsv files", + "keywords": ["sam", "tsv", "jvarkit"], + "tools": [ + { + "jvarkit": { + "description": "Java utilities for Bioinformatics.", + "homepage": "https://github.com/lindenb/jvarkit", + "documentation": "https://jvarkit.readthedocs.io/", + "tool_dev_url": "https://github.com/lindenb/jvarkit", + "doi": "10.6084/m9.figshare.1425030", + "licence": ["MIT License"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM file from alignment", + "pattern": "*.{bam,cram}", + "ontologies": [] + } + }, + { + "bai": { + "type": "file", + "description": "BAI/CRAI file from alignment", + "pattern": "*.{bai,crai}", + "ontologies": [] + } + }, + { + "regions_file": { + "type": "file", + "description": "Optional. Restrict to regions listed in a file", + "pattern": "*.{vcf,bed,gtf,gff,vcf.gz,bed.gz,gtf.gz,gff.gz}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [id: 'reference']\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference genome", + "pattern": "*.{fasta,fa}", + "ontologies": [] + } + }, + { + "fasta_index": { + "type": "file", + "description": "Reference genome information for fasta index", + "pattern": "*.{fasta.fai,fa.fai}", + "ontologies": [] + } + }, + { + "fasta_dict": { + "type": "file", + "description": "Reference genome information for fasta dict", + "pattern": "*.{.dict}", + "ontologies": [] + } + } + ] + ], + "output": { + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing TSV information e.g. [ id:'test' ]" + } + }, + { + "*.tsv": { + "type": "file", + "description": "Output file", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@lmfaber"], + "maintainers": ["@lmfaber"] } - ] - ], - "output": { - "sorted": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", - "pattern": "${output_file}" - } - }, - { - "${output_file}": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", - "pattern": "${output_file}" - } - } - ] - ], - "versions_coreutils": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "coreutils": { - "type": "string", - "description": "The tool name" - } - }, - { - "sort --version |& sed '1!d ; s/sort (GNU coreutils) //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "coreutils": { - "type": "string", - "description": "The tool name" - } - }, - { - "sort --version |& sed '1!d ; s/sort (GNU coreutils) //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] }, - "authors": [ - "@DLBPointon" - ], - "maintainers": [ - "@DLBPointon" - ] - }, - "pipelines": [ { - "name": "circrna", - "version": "dev" + "name": "jvarkit_vcf2table", + "path": "modules/nf-core/jvarkit/vcf2table/meta.yml", + "type": "module", + "meta": { + "name": "jvarkit_vcf2table", + "description": "Convert VCF to a user friendly table", + "keywords": ["vcf", "bcf", "text", "html", "visualization"], + "tools": [ + { + "jvarkit": { + "description": "Java utilities for Bioinformatics.", + "homepage": "https://github.com/lindenb/jvarkit", + "documentation": "https://jvarkit.readthedocs.io/", + "tool_dev_url": "https://github.com/lindenb/jvarkit", + "doi": "10.6084/m9.figshare.1425030", + "licence": ["MIT"], + "args_id": "$args2", + "identifier": "" + } + }, + { + "bcftools": { + "description": "View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF\n", + "homepage": "http://samtools.github.io/bcftools/bcftools.html", + "documentation": "http://www.htslib.org/doc/bcftools.html", + "doi": "10.1093/bioinformatics/btp352", + "licence": ["MIT"], + "args_id": "$args1", + "identifier": "biotools:samtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing VCF information\ne.g. [ id:'genome' ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "Input vcf/bcf file", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", + "ontologies": [] + } + }, + { + "tbi": { + "type": "file", + "description": "Optional index file for the VCF", + "pattern": "*.{tbi,csi}", + "ontologies": [] + } + }, + { + "regions_file": { + "type": "file", + "description": "Optional. Restrict to regions listed in a file", + "pattern": "*.{bed,bed.gz,txt,tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing pedigree information\n" + } + }, + { + "pedigree": { + "type": "file", + "description": "Optional pedigree for jvarkit", + "pattern": "*.{ped,pedigree}", + "ontologies": [] + } + } + ] + ], + "output": { + "output": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing VCF information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.${extension}": { + "type": "file", + "description": "Output file", + "pattern": "*.{txt,html}", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@lindenb"], + "maintainers": ["@lindenb"] + } }, { - "name": "isoseq", - "version": "2.0.0" + "name": "jvarkit_vcffilterjdk", + "path": "modules/nf-core/jvarkit/vcffilterjdk/meta.yml", + "type": "module", + "meta": { + "name": "jvarkit_vcffilterjdk", + "description": "Filtering VCF with dynamically-compiled java expressions", + "keywords": ["vcf", "bcf", "filter", "variant", "java", "script"], + "tools": [ + { + "jvarkit": { + "description": "Java utilities for Bioinformatics.", + "homepage": "https://github.com/lindenb/jvarkit", + "documentation": "https://jvarkit.readthedocs.io/", + "tool_dev_url": "https://github.com/lindenb/jvarkit", + "doi": "10.1093/bioinformatics/btx734 ", + "licence": ["MIT License"], + "args_id": "$args2", + "identifier": "" + } + }, + { + "bcftools": { + "description": "View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF\n", + "homepage": "http://samtools.github.io/bcftools/bcftools.html", + "documentation": "http://www.htslib.org/doc/bcftools.html", + "doi": "10.1093/bioinformatics/btp352", + "licence": ["MIT"], + "args_id": ["$args1", "$args3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing VCF information\ne.g. [ id:'test_reference' ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "Input VCF/BCF file", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", + "ontologies": [] + } + }, + { + "tbi": { + "type": "file", + "description": "Optional VCF/BCF index file", + "pattern": "*.{tbi,csi}", + "ontologies": [] + } + }, + { + "regions_file": { + "type": "file", + "description": "Optional. Restrict to regions listed in a file", + "pattern": "*.{bed,bed.gz,txt,tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing fasta information\ne.g. [ id:'test_reference' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Fasta reference file", + "pattern": "*.fasta", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing fasta.fai information\ne.g. [ id:'test_reference' ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Fasta file index", + "pattern": "*.fasta.fai", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing fasta.dict information\ne.g. [ id:'test_reference' ]\n" + } + }, + { + "dict": { + "type": "file", + "description": "GATK sequence dictionary", + "pattern": "*.dict", + "ontologies": [] + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing code information\ne.g. [ id:'test_reference' ]\n" + } + }, + { + "code": { + "type": "file", + "description": "File containing custom user code . May be empty if script if provided via `task.ext.args2`.", + "pattern": "*.{code,script,txt,tsv,java,js}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + [ + { + "meta6": { + "type": "map", + "description": "Groovy Map containing pedigree information\ne.g. [ id:'test_reference' ]\n" + } + }, + { + "pedigree": { + "type": "file", + "description": "Optional jvarkit pedigree.", + "pattern": "*.{tsv,ped,pedigree}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing VCF information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.${extension}": { + "type": "file", + "description": "VCF filtered output file", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", + "ontologies": [] + } + } + ] + ], + "tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing VCF information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tbi": { + "type": "file", + "description": "Alternative VCF file index", + "pattern": "*.tbi", + "ontologies": [] + } + } + ] + ], + "csi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing VCF information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.csi": { + "type": "file", + "description": "Default VCF file index", + "pattern": "*.csi", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@lindenb"], + "maintainers": ["@lindenb"] + } }, { - "name": "tfactivity", - "version": "dev" + "name": "jvarkit_vcfpolyx", + "path": "modules/nf-core/jvarkit/vcfpolyx/meta.yml", + "type": "module", + "meta": { + "name": "jvarkit_vcfpolyx", + "description": "annotate VCF files for poly repeats", + "keywords": ["vcf", "bcf", "annotation", "repeats"], + "tools": [ + { + "jvarkit": { + "description": "Java utilities for Bioinformatics.", + "homepage": "https://github.com/lindenb/jvarkit", + "documentation": "https://jvarkit.readthedocs.io/", + "tool_dev_url": "https://github.com/lindenb/jvarkit", + "doi": "10.6084/m9.figshare.1425030", + "licence": ["MIT License"], + "identifier": "" + } + }, + { + "bcftools": { + "description": "View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF\n", + "homepage": "http://samtools.github.io/bcftools/bcftools.html", + "documentation": "http://www.htslib.org/doc/bcftools.html", + "doi": "10.1093/bioinformatics/btp352", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing VCF information\n" + } + }, + { + "vcf": { + "type": "file", + "description": "Groovy Map containing reference genome information for vcf", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", + "ontologies": [] + } + }, + { + "tbi": { + "type": "file", + "description": "Alternative VCF file index", + "pattern": "*.tbi", + "ontologies": [] + } + }, + { + "regions_file": { + "type": "file", + "description": "Regions file", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing fasta information\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Groovy Map containing reference genome information for fai reference fasta file", + "pattern": "*.fasta", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing fasta.fai information\n" + } + }, + { + "fai": { + "type": "file", + "description": "Groovy Map containing reference genome information for fai", + "pattern": "*.fasta.fai", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing fasta.dict information\n" + } + }, + { + "dict": { + "type": "file", + "description": "Groovy Map containing reference genome information for GATK sequence dictionary", + "pattern": "*.dict", + "ontologies": [] + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing VCF information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.${extension}": { + "type": "file", + "description": "VCF filtered output file", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", + "ontologies": [] + } + } + ] + ], + "tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing VCF information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tbi": { + "type": "file", + "description": "Alternative VCF file index", + "pattern": "*.tbi", + "ontologies": [] + } + } + ] + ], + "csi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing VCF information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.csi": { + "type": "file", + "description": "Default VCF file index", + "pattern": "*.csi", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@lindenb"], + "maintainers": ["@lindenb"] + } }, { - "name": "variantbenchmarking", - "version": "1.5.0" - } - ] - }, - { - "name": "gnu_split", - "path": "modules/nf-core/gnu/split/meta.yml", - "type": "module", - "meta": { - "name": "gnu_split", - "description": "Split a file into consecutive or interleaved sections", - "keywords": [ - "gnu", - "split", - "coreutils", - "generic" - ], - "tools": [ - { - "gnu": { - "description": "The GNU Core Utilities are the basic file, shell and text manipulation utilities of the GNU operating system. These are the core utilities which are expected to exist on every operating system.", - "homepage": "https://www.gnu.org/software/coreutils/", - "documentation": "https://www.gnu.org/software/coreutils/manual/html_node/index.html", - "tool_dev_url": "https://git.savannah.gnu.org/cgit/coreutils.git", - "doi": "10.5281/zenodo.581670", - "licence": [ - "GPL" - ], - "identifier": "" + "name": "jvarkit_wgscoverageplotter", + "path": "modules/nf-core/jvarkit/wgscoverageplotter/meta.yml", + "type": "module", + "meta": { + "name": "jvarkit_wgscoverageplotter", + "description": "Plot whole genome coverage from BAM/CRAM file as SVG", + "keywords": ["bam", "cram", "depth", "coverage", "xml", "svg", "visualization"], + "tools": [ + { + "jvarkit": { + "description": "Java utilities for Bioinformatics.", + "homepage": "https://github.com/lindenb/jvarkit", + "documentation": "https://jvarkit.readthedocs.io/", + "tool_dev_url": "https://github.com/lindenb/jvarkit", + "doi": "10.6084/m9.figshare.1425030", + "licence": ["MIT License"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM file from alignment", + "pattern": "*.{bam,cram}", + "ontologies": [] + } + }, + { + "bai": { + "type": "file", + "description": "BAI/CRAI file from alignment", + "pattern": "*.{bai,crai}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test_reference' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The reference fasta file", + "pattern": "*.fasta", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference fai information\ne.g. [ id:'test_reference' ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Index of reference fasta file", + "pattern": "fasta.fai", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing reference dict information\ne.g. [ id:'test_reference' ]\n" + } + }, + { + "dict": { + "type": "file", + "description": "GATK sequence dictionary", + "pattern": "*.dict", + "ontologies": [] + } + } + ] + ], + "output": { + "output": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing Sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.svg": { + "type": "file", + "description": "Output SVG file", + "pattern": "*.svg", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@lindenb"], + "maintainers": ["@lindenb"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } + }, + { + "name": "kaiju_kaiju", + "path": "modules/nf-core/kaiju/kaiju/meta.yml", + "type": "module", + "meta": { + "name": "kaiju_kaiju", + "description": "Taxonomic classification of metagenomic sequence data using a protein reference database", + "keywords": ["classify", "metagenomics", "fastq", "taxonomic profiling"], + "tools": [ + { + "kaiju": { + "description": "Fast and sensitive taxonomic classification for metagenomics", + "homepage": "https://kaiju.binf.ku.dk/", + "documentation": "https://github.com/bioinformatics-centre/kaiju/blob/master/README.md", + "tool_dev_url": "https://github.com/bioinformatics-centre/kaiju", + "doi": "10.1038/ncomms11257", + "licence": ["GNU GPL v3"], + "identifier": "biotools:kaiju" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input fastq/fasta files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", + "pattern": "*.{fastq,fq,fasta,fa,fsa,fas,fna,fastq.gz,fq.gz,fasta.gz,fa.gz,fsa.gz,fas.gz,fna.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ], + { + "db": { + "type": "directory", + "description": "List or directory containing the database and NCBI taxonomy files (names and nodes) for Kaiju\ne.g. [ 'database.fmi', 'names.dmp', 'nodes.dmp' ]\n" + } + } + ], + "output": { + "results": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "Results with taxonomic classification of each read", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_kaiju": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "kaiju": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "kaiju -h 2>&1 | sed -n 1p | sed 's/^.*Kaiju //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "kaiju": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "kaiju -h 2>&1 | sed -n 1p | sed 's/^.*Kaiju //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@talnor", "@sofstam", "@jfy133"], + "maintainers": ["@talnor", "@sofstam", "@jfy133"] }, - { - "input": { - "type": "file", - "description": "Text file, possibly gzip file", - "ontologies": [] - } - } - ] - ], - "output": { - "split": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "${prefix}.*": { - "type": "file", - "description": "Split files", - "pattern": "${prefix}.*", - "ontologies": [] - } - } - ] - ], - "versions_coreutils": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "coreutils": { - "type": "string", - "description": "The tool name" - } - }, - { - "sort --version |& sed '1!d ; s/sort (GNU coreutils) //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "coreutils": { - "type": "string", - "description": "The tool name" - } - }, - { - "sort --version |& sed '1!d ; s/sort (GNU coreutils) //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } + "pipelines": [ + { + "name": "taxprofiler", + "version": "2.0.0" + }, + { + "name": "viralmetagenome", + "version": "1.1.1" + } ] - ] - }, - "authors": [ - "@k1sauce" - ], - "maintainers": [ - "@k1sauce" - ] - } - }, - { - "name": "goat_taxonsearch", - "path": "modules/nf-core/goat/taxonsearch/meta.yml", - "type": "module", - "meta": { - "name": "goat_taxonsearch", - "description": "Query metadata for any taxon across the tree of life.", - "keywords": [ - "public datasets", - "ncbi", - "genomes on a tree" - ], - "tools": [ - { - "goat": { - "description": "goat-cli is a command line interface to query the\nGenomes on a Tree Open API.\n", - "homepage": "https://github.com/genomehubs/goat-cli", - "documentation": "https://github.com/genomehubs/goat-cli/wiki", - "tool_dev_url": "https://genomehubs.github.io/goat-cli/goat_cli/", - "licence": [ - "MIT" - ], - "identifier": "biotools:goat" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "taxon": { - "type": "string", - "description": "The taxon to search. An NCBI taxon ID, or the name of a taxon at any rank.\n" - } + }, + { + "name": "kaiju_kaiju2krona", + "path": "modules/nf-core/kaiju/kaiju2krona/meta.yml", + "type": "module", + "meta": { + "name": "kaiju_kaiju2krona", + "description": "Convert Kaiju's tab-separated output file into a tab-separated text file which can be imported into Krona.", + "keywords": ["taxonomy", "visualisation", "krona chart", "metagenomics"], + "tools": [ + { + "kaiju": { + "description": "Fast and sensitive taxonomic classification for metagenomics", + "homepage": "https://kaiju.binf.ku.dk/", + "documentation": "https://github.com/bioinformatics-centre/kaiju/blob/master/README.md", + "tool_dev_url": "https://github.com/bioinformatics-centre/kaiju", + "doi": "10.1038/ncomms11257", + "licence": ["GNU GPL v3"], + "identifier": "biotools:kaiju" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "tsv": { + "type": "file", + "description": "Kaiju tab-separated output file", + "pattern": "*.{tsv,txt}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + { + "db": { + "type": "file", + "description": "Kaiju database file", + "ontologies": [] + } + } + ], + "output": { + "txt": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "Krona text-based input file converted from Kaiju report", + "pattern": "*.{txt,krona}", + "ontologies": [] + } + } + ] + ], + "versions_kaiju": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "kaiju": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "kaiju -h 2>&1 | sed -n 1p | sed 's/^.*Kaiju //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "kaiju": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "kaiju -h 2>&1 | sed -n 1p | sed 's/^.*Kaiju //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@MillironX"], + "maintainers": ["@MillironX"] }, - { - "taxa_file": { - "type": "file", - "description": "A file of NCBI taxonomy ID's (tips) and/or binomial names. Each line\nshould contain a single entry.File size is limited to 500 entries.\n", - "pattern": "*.txt", - "ontologies": [] - } - } - ] - ], - "output": { - "taxonsearch": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "TSV file containing search results.", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_goat": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "goat": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "goat-cli --version | cut -d' ' -f2": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "goat": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "goat-cli --version | cut -d' ' -f2": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "taxprofiler", + "version": "2.0.0" + }, + { + "name": "viralmetagenome", + "version": "1.1.1" + } ] - ] - }, - "authors": [ - "@alxndrdiaz" - ], - "maintainers": [ - "@alxndrdiaz", - "@muffato" - ] - } - }, - { - "name": "goatools_findenrichment", - "path": "modules/nf-core/goatools/findenrichment/meta.yml", - "type": "module", - "meta": { - "name": "goatools_findenrichment", - "description": "Find enriched GO terms in a list of genes", - "keywords": [ - "goatools", - "enrichment", - "ontology", - "geneontology", - "go", - "genomics" - ], - "tools": [ - { - "goatools": { - "description": "Python scripts to find enrichment of GO terms", - "homepage": "https://github.com/tanghaibao/goatools", - "documentation": "https://github.com/tanghaibao/goatools/blob/main/README.md", - "tool_dev_url": "https://github.com/tanghaibao/goatools", - "doi": "10.1038/s41598-018-28948-z", - "licence": [ - "BSD-2-clause" - ] - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "study_list": { - "type": "file", - "description": "Plain text file with one study gene identifier per line", - "pattern": "*.{txt,tsv,csv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2330" - } - ] - } - }, - { - "population_list": { - "type": "file", - "description": "Plain text file with one background population gene identifier per line", - "pattern": "*.{txt,tsv,csv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2330" - } - ] - } + }, + { + "name": "kaiju_kaiju2table", + "path": "modules/nf-core/kaiju/kaiju2table/meta.yml", + "type": "module", + "meta": { + "name": "kaiju_kaiju2table", + "description": "write your description here", + "keywords": ["classify", "metagenomics", "taxonomic profiling"], + "tools": [ + { + "kaiju": { + "description": "Fast and sensitive taxonomic classification for metagenomics", + "homepage": "https://kaiju.binf.ku.dk/", + "documentation": "https://github.com/bioinformatics-centre/kaiju/blob/master/README.md", + "tool_dev_url": "https://github.com/bioinformatics-centre/kaiju", + "doi": "10.1038/ncomms11257", + "licence": ["GNU GPL v3"], + "identifier": "biotools:kaiju" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "Kaiju input file", + "ontologies": [] + } + } + ], + { + "db": { + "type": "file", + "description": "Kaiju database", + "ontologies": [] + } + }, + { + "taxon_rank": { + "type": "string", + "description": "Taxonomic rank to display in report\npattern: \"phylum|class|order|family|genus|species\"\n" + } + } + ], + "output": { + "summary": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "Kaiju output file", + "pattern": "*.txt", + "ontologies": [] + } + } + ] + ], + "versions_kaiju": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "kaiju": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "kaiju -h 2>&1 | sed -n 1p | sed 's/^.*Kaiju //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "kaiju": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "kaiju -h 2>&1 | sed -n 1p | sed 's/^.*Kaiju //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@sofstam", "@talnor", "@jfy133"], + "maintainers": ["@sofstam", "@talnor", "@jfy133"] }, - { - "annotation": { - "type": "file", - "description": "Gene-to-GO association file used by GOATOOLS", - "pattern": "*" - } - } - ], - { - "obo": { - "type": "file", - "description": "Gene Ontology OBO file", - "pattern": "*.obo", - "ontologies": [ + "pipelines": [ { - "edam": "http://edamontology.org/format_2549" - } - ] - } - }, - { - "goslim": { - "type": "file", - "description": "GO slim mapping file used for slim-specific enrichment summaries", - "pattern": "*.obo", - "ontologies": [ + "name": "taxprofiler", + "version": "2.0.0" + }, { - "edam": "http://edamontology.org/format_2549" + "name": "viralmetagenome", + "version": "1.1.1" } - ] - } - } - ], - "output": { - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "GO enrichment analysis table generated by GOATOOLS find_enrichment", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_goatools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "goatools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "goatools --version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "goatools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "goatools --version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@itrujnara" - ], - "maintainers": [ - "@itrujnara" - ] - } - }, - { - "name": "goleft_indexcov", - "path": "modules/nf-core/goleft/indexcov/meta.yml", - "type": "module", - "meta": { - "name": "goleft_indexcov", - "description": "Quickly estimate coverage from a whole-genome bam or cram index. A bam index has 16KB resolution so that's what this gives, but it provides what appears to be a high-quality coverage estimate in seconds per genome.", - "keywords": [ - "coverage", - "cnv", - "genomics", - "depth" - ], - "tools": [ - { - "goleft": { - "description": "goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary", - "homepage": "https://github.com/brentp/goleft", - "documentation": "https://github.com/brentp/goleft", - "tool_dev_url": "https://github.com/brentp/goleft", - "doi": "10.1093/gigascience/gix090", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false]\n" - } - }, - { - "bams": { - "type": "file", - "description": "Sorted BAM/CRAM/SAM files", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } - }, - { - "indexes": { - "type": "file", - "description": "BAI/CRAI files", - "pattern": "*.{bai,crai}", - "ontologies": [] - } + }, + { + "name": "kaiju_mergeoutputs", + "path": "modules/nf-core/kaiju/mergeoutputs/meta.yml", + "type": "module", + "meta": { + "name": "kaiju_mergeoutputs", + "description": "Merge two tab-separated output files of Kaiju and Kraken in the column format", + "keywords": ["classify", "metagenomics", "fastq", "taxonomic profiling"], + "tools": [ + { + "kaiju": { + "description": "Fast and sensitive taxonomic classification for metagenomics", + "homepage": "https://kaiju.binf.ku.dk/", + "documentation": "https://github.com/bioinformatics-centre/kaiju/blob/master/README.md", + "tool_dev_url": "https://github.com/bioinformatics-centre/kaiju", + "doi": "10.1038/ncomms11257", + "licence": ["GNU GPL v3"], + "identifier": "biotools:kaiju" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "kaiju": { + "type": "file", + "description": "Results with taxonomic classification of each read from Kaiju\n", + "ontologies": [] + } + }, + { + "kraken": { + "type": "file", + "description": "Results with taxonomic classification of each read from Kraken\n", + "pattern": "*.{tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + { + "db": { + "type": "directory", + "description": "List containing the database and nodes files for Kaiju\ne.g. [ 'database.fmi', 'nodes.dmp' ]\n" + } + } + ], + "output": { + "merged": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "Results with merged taxonomic classification of each read based on the given strategy '1', '2', 'lca' [default] or 'lowest'", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_kaiju": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "kaiju": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "kaiju -h 2>&1 | sed -n 1p | sed 's/^.*Kaiju //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "kaiju": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "kaiju -h 2>&1 | sed -n 1p | sed 's/^.*Kaiju //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@Joon-Klaps"], + "maintainers": ["@Joon-Klaps"] } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false]\n" - } + }, + { + "name": "kaiju_mkfmi", + "path": "modules/nf-core/kaiju/mkfmi/meta.yml", + "type": "module", + "meta": { + "name": "kaiju_mkfmi", + "description": "Make Kaiju FMI-index file from a protein FASTA file", + "keywords": ["classify", "metagenomics", "fastq", "taxonomic profiling", "database", "index"], + "tools": [ + { + "kaiju": { + "description": "Fast and sensitive taxonomic classification for metagenomics", + "homepage": "https://bioinformatics-centre.github.io/kaiju/", + "documentation": "https://github.com/bioinformatics-centre/kaiju/blob/master/README.md", + "tool_dev_url": "https://github.com/bioinformatics-centre/kaiju", + "doi": "10.1038/ncomms11257", + "licence": ["GNU GPL v3"], + "identifier": "biotools:kaiju" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Uncompressed Protein FASTA file (mandatory)", + "pattern": "*.{fa,faa,fasta}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + { + "nodes_dmp": { + "type": "file", + "description": "NCBI nodes.dmp file (mandatory)", + "pattern": "nodes.dmp", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3751" + } + ] + } + }, + { + "names_dmp": { + "type": "file", + "description": "NCBI names.dmp file (mandatory)", + "pattern": "names.dmp", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3751" + } + ] + } + }, + { + "keep_intermediate": { + "type": "boolean", + "description": "Keep intermediate files", + "pattern": "true|false" + } + } + ], + "output": { + "fmi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.{fmi,dmp}": { + "type": "file", + "description": "Kaiju FM-index file, and input {names,nodes}.dmp NCBI taxonomy files required for downstream Kaiju commands", + "pattern": "*.{fmi,dmp}", + "ontologies": [] + } + } + ] + ], + "bwt": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.bwt": { + "type": "file", + "description": "Kaiju intermedite bwt-index file (not needed for classification)", + "pattern": "*.{bwt}", + "ontologies": [] + } + } + ] + ], + "sa": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.sa": { + "type": "file", + "description": "Kaiju intermedite bwt-index file (not needed for classification)", + "pattern": "*.{sa}", + "ontologies": [] + } + } + ] + ], + "versions_kaiju": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "kaiju": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "kaiju -h 2>&1 | sed -n 1p | sed 's/^.*Kaiju //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "kaiju": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "kaiju -h 2>&1 | sed -n 1p | sed 's/^.*Kaiju //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@alxndrdiaz", "@jfy133"] }, - { - "fai": { - "type": "file", - "description": "FASTA index", - "pattern": "*.{fai}", - "ontologies": [] - } - } - ] - ], - "output": { - "output": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/*": { - "type": "file", - "description": "Files generated by indexcov", - "ontologies": [] - } - } - ] - ], - "ped": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/*ped": { - "type": "file", - "description": "ped files", - "pattern": "*ped", - "ontologies": [] - } - } - ] - ], - "bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/*bed.gz": { - "type": "file", - "description": "bed files", - "pattern": "*bed.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "bed_index": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/*bed.gz.tbi": { - "type": "file", - "description": "bed index files", - "pattern": "*bed.gz.tbi", - "ontologies": [] - } - } - ] - ], - "roc": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/*roc": { - "type": "file", - "description": "roc files", - "pattern": "*roc", - "ontologies": [] - } - } - ] - ], - "html": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/*html": { - "type": "file", - "description": "html files", - "pattern": "*html", - "ontologies": [] - } - } - ] - ], - "png": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/*png": { - "type": "file", - "description": "png files", - "pattern": "*png", - "ontologies": [] - } - } - ] - ], - "versions_goleft": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "goleft": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "goleft --version |& sed '1!d;s/^.*goleft Version: //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_tabix": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "tabix": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "tabix -h |& sed -n 's/^.*Version: //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "goleft": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "goleft --version |& sed '1!d;s/^.*goleft Version: //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "tabix": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "tabix -h |& sed -n 's/^.*Version: //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "createtaxdb", + "version": "3.0.0" + } ] - ] - }, - "authors": [ - "@lindenb" - ], - "maintainers": [ - "@lindenb" - ] - }, - "pipelines": [ - { - "name": "sarek", - "version": "3.8.1" - } - ] - }, - { - "name": "goleft_indexsplit", - "path": "modules/nf-core/goleft/indexsplit/meta.yml", - "type": "module", - "meta": { - "name": "goleft_indexsplit", - "description": "Quickly generate evenly sized (by amount of data) regions across a number of bam/cram files", - "keywords": [ - "bam", - "bed", - "cram", - "index", - "split" - ], - "tools": [ - { - "goleft": { - "description": "goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary", - "homepage": "https://github.com/brentp/goleft", - "documentation": "https://github.com/brentp/goleft", - "tool_dev_url": "https://github.com/brentp/goleft", - "doi": "10.1093/gigascience/gix090", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bai": { - "type": "file", - "description": "BAI/CRAI file", - "pattern": "*.{bai,crai}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } + }, + { + "name": "kalign_align", + "path": "modules/nf-core/kalign/align/meta.yml", + "type": "module", + "meta": { + "name": "kalign_align", + "description": "Aligns sequences using kalign", + "keywords": ["alignment", "MSA", "genomics"], + "tools": [ + { + "kalign": { + "description": "Kalign is a fast and accurate multiple sequence alignment algorithm.", + "homepage": "https://msa.sbc.su.se/cgi-bin/msa.cgi", + "documentation": "https://github.com/TimoLassmann/kalign", + "tool_dev_url": "https://github.com/TimoLassmann/kalign", + "doi": "10.1093/bioinformatics/btz795", + "licence": ["GPL v3"], + "identifier": "biotools:kalign" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input sequences in FASTA format. May be gzipped or uncompressed.", + "pattern": "*.{fa,fasta}{.gz,}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1919" + }, + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + { + "compress": { + "type": "boolean", + "description": "Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded." + } + } + ], + "output": { + "alignment": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" + } + }, + { + "*.aln{.gz,}": { + "type": "file", + "description": "Alignment file. May be gzipped or uncompressed, depending on if `compress` is set to `true` or `false`.", + "pattern": "*.{aln}{.gz,}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2554" + }, + { + "edam": "http://edamontology.org/format_1921" + }, + { + "edam": "http://edamontology.org/format_1984" + } + ] + } + } + ] + ], + "versions_kalign": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "kalign": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "kalign -v | sed \"s/^.*kalign[[:space:]]*//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_pigz": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "pigz": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pigz --version 2>&1 | sed \"s/^.*pigz[[:space:]]*//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "kalign": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "kalign -v | sed \"s/^.*kalign[[:space:]]*//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "pigz": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pigz --version 2>&1 | sed \"s/^.*pigz[[:space:]]*//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@luisas", "@JoseEspinosa"], + "maintainers": ["@luisas", "@JoseEspinosa"] }, - { - "fai": { - "type": "file", - "description": "Reference fasta index file", - "pattern": "*.fai", - "ontologies": [] - } - } - ], - { - "split": { - "type": "boolean", - "description": "Split the regions" - } - } - ], - "output": { - "bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bed": { - "type": "file", - "description": "Bed file containing split regions", - "pattern": "*.bed", - "ontologies": [] - } - } - ] - ], - "versions_goleft": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "goleft": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "goleft --version 2>&1 | sed '1!d;s/^.*goleft Version: //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "goleft": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "goleft --version 2>&1 | sed '1!d;s/^.*goleft Version: //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "multiplesequencealign", + "version": "1.1.1" + } ] - ] - }, - "authors": [ - "@matthdsm" - ], - "maintainers": [ - "@matthdsm" - ] - } - }, - { - "name": "gprofiler2_gost", - "path": "modules/nf-core/gprofiler2/gost/meta.yml", - "type": "module", - "meta": { - "name": "gprofiler2_gost", - "description": "runs a functional enrichment analysis with gprofiler2", - "keywords": [ - "gene set analysis", - "enrichment", - "gprofiler2", - "gost", - "gene set" - ], - "tools": [ - { - "gprofiler2": { - "description": "An R interface corresponding to the 2019 update of g:Profiler web tool.", - "homepage": "https://biit.cs.ut.ee/gprofiler/page/r", - "documentation": "https://rdrr.io/cran/gprofiler2/", - "tool_dev_url": "https://gl.cs.ut.ee/biit/r-gprofiler2", - "doi": "10.1093/nar/gkad347", - "licence": [ - "GPL v2" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ]\n" - } - }, - { - "de_file": { - "type": "file", - "pattern": "*.{csv,tsv}", - "description": "CSV or TSV-format tabular file with differential analysis outputs\n", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - }, - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy map" - } - }, - { - "gmt_file": { - "type": "file", - "pattern": "*.gmt", - "description": "Path to a GMT file downloaded from g:profiler that should be queried instead of the online databases\n", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy map" - } + }, + { + "name": "kallisto_index", + "path": "modules/nf-core/kallisto/index/meta.yml", + "type": "module", + "meta": { + "name": "kallisto_index", + "description": "Create kallisto index", + "keywords": ["kallisto", "kallisto/index", "index"], + "tools": [ + { + "kallisto": { + "description": "Quantifying abundances of transcripts from bulk and single-cell RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.", + "homepage": "https://pachterlab.github.io/kallisto/", + "documentation": "https://pachterlab.github.io/kallisto/manual", + "tool_dev_url": "https://github.com/pachterlab/kallisto", + "licence": ["BSD-2-Clause"], + "identifier": "biotools:kallisto" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "genome fasta file", + "pattern": "*.{fasta}", + "ontologies": [] + } + } + ] + ], + "output": { + "index": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "kallisto": { + "type": "directory", + "description": "Kallisto genome index", + "pattern": "*.idx" + } + } + ] + ], + "versions_kallisto": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "kallisto": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "kallisto 2>&1 | head -1 | sed \"s/^kallisto //; s/Usage.*//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "kallisto": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "kallisto 2>&1 | head -1 | sed \"s/^kallisto //; s/Usage.*//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@ggabernet"], + "maintainers": ["@ggabernet"] }, - { - "background_file": { - "type": "file", - "pattern": "*.{csv,tsv,txt}", - "description": "Path to a CSV/TSV/TXT file listing gene IDs that should be used as the background (will override count_file). This can be an expression matrix (see also background_column parameter); if so, will only consider those genes with an expression value > 0 in at least one sample. Alternatively, this can be a TXT file containing only a list of gene IDs.\n", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - }, - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "output": { - "all_enrich": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ]\n" - } - }, - { - "*.gprofiler2.all_enriched_pathways.tsv": { - "type": "file", - "description": "TSV file; table listing all enriched pathways that were found. This table will always be created (empty if no enrichment was found), the other output files are only created if enriched pathways were found\n", - "pattern": "*gprofiler2.*all_enriched_pathways.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "rds": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ]\n" - } - }, - { - "*.gprofiler2.gost_results.rds": { - "type": "file", - "description": "RDS file; R object containing the results of the gost query\n", - "pattern": "*gprofiler2.*gost_results.rds", - "ontologies": [] - } - } - ] - ], - "plot_png": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ]\n" - } - }, - { - "*.gprofiler2.gostplot.png": { - "type": "file", - "description": "PNG file; Manhattan plot of all enriched pathways\n", - "pattern": "*gprofiler2.*gostplot.png", - "ontologies": [] - } - } - ] - ], - "plot_html": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ]\n" - } - }, - { - "*.gprofiler2.gostplot.html": { - "type": "file", - "description": "HTML file; interactive Manhattan plot of all enriched pathways\n", - "pattern": "*gprofiler2.*gostplot.html", - "ontologies": [] - } - } - ] - ], - "sub_enrich": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ]\n" - } - }, - { - "*.gprofiler2.*.sub_enriched_pathways.tsv": { - "type": "file", - "description": "TSV file; table listing enriched pathways that were found from one particular source\n", - "pattern": "*gprofiler2.*sub_enriched_pathways.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "sub_plot": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ]\n" - } - }, - { - "*.gprofiler2.*.sub_enriched_pathways.png": { - "type": "file", - "description": "PNG file; bar plot showing the fraction of genes that were found enriched in each pathway\n", - "pattern": "*gprofiler2.*sub_enriched_pathways.png", - "ontologies": [] - } - } - ] - ], - "filtered_gmt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ]\n" - } - }, - { - "*ENSG_filtered.gmt": { - "type": "file", - "description": "GMT file that was provided as input or that was downloaded from g:profiler if no input GMT file was given; filtered for the selected datasources\n", - "pattern": "*ENSG_filtered.gmt", - "ontologies": [] - } - } - ] - ], - "session_info": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ]\n" - } - }, - { - "*R_sessionInfo.log": { - "type": "file", - "description": "Log file containing information about the R session that was run for this module\n", - "pattern": "*R_sessionInfo.log", - "ontologies": [] - } - } + "pipelines": [ + { + "name": "lncpipe", + "version": "dev" + }, + { + "name": "references", + "version": "0.1" + }, + { + "name": "riboseq", + "version": "1.2.0" + }, + { + "name": "rnaseq", + "version": "3.26.0" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "YAML file containing versions of tools used in the module", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "topics": { - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "YAML file containing versions of tools used in the module", - "ontologies": [] - } - } - ] }, - "authors": [ - "@WackerO" - ] - }, - "pipelines": [ { - "name": "differentialabundance", - "version": "1.5.0" + "name": "kallisto_quant", + "path": "modules/nf-core/kallisto/quant/meta.yml", + "type": "module", + "meta": { + "name": "kallisto_quant", + "description": "Computes equivalence classes for reads and quantifies abundances", + "keywords": ["quant", "kallisto", "pseudoalignment"], + "tools": [ + { + "kallisto": { + "description": "Quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.", + "homepage": "https://pachterlab.github.io/kallisto/", + "documentation": "https://pachterlab.github.io/kallisto/manual", + "tool_dev_url": "https://github.com/pachterlab/kallisto", + "doi": "10.1038/nbt.3519", + "licence": ["BSD_2_clause"], + "identifier": "biotools:kallisto" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", + "pattern": "*.{fastq,fastq.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "index": { + "type": "file", + "description": "Kallisto genome index.", + "pattern": "*.idx", + "ontologies": [] + } + } + ], + { + "gtf": { + "type": "file", + "description": "Optional gtf file for translation of transcripts into genomic coordinates.", + "pattern": "*.gtf", + "ontologies": [] + } + }, + { + "chromosomes": { + "type": "file", + "description": "Optional tab separated file with chromosome names and lengths.", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, + { + "fragment_length": { + "type": "integer", + "description": "For single-end mode only, the estimated average fragment length." + } + }, + { + "fragment_length_sd": { + "type": "integer", + "description": "For single-end mode only, the estimated standard deviation of the fragment length." + } + } + ], + "output": { + "results": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}": { + "type": "file", + "description": "Kallisto output file", + "ontologies": [] + } + } + ] + ], + "json_info": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.run_info.json": { + "type": "file", + "description": "JSON file containing information about the run", + "pattern": "*.run_info.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "File containing log information from running kallisto quant", + "pattern": "*.log.txt", + "ontologies": [] + } + } + ] + ], + "versions_kallisto": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "kallisto": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "kallisto version | sed 's/.*version //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "kallisto": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "kallisto version | sed 's/.*version //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@anoronh4"], + "maintainers": ["@anoronh4"] + }, + "pipelines": [ + { + "name": "riboseq", + "version": "1.2.0" + }, + { + "name": "rnaseq", + "version": "3.26.0" + } + ] }, { - 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{ - "input": { - "type": "file", - "pattern": "*.gz", - "description": "file to check compression", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "output": { - "compress_bgzip": [ - { - "meta": { - "type": "string", - "description": "environmental variable with value \"yes\" or \"no\"" - } - } - ], - "versions_grabix": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "grabix": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "grabix |& sed -n 's/^version: //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "grabix": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "grabix |& sed -n 's/^version: //p'": { - "type": "eval", - 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] - }, - "authors": [ - "@yuukiiwa", - "@drpatelh" - ], - "maintainers": [ - "@yuukiiwa", - "@drpatelh" - ] - } - }, - { - "name": "graphtyper_genotype", - "path": "modules/nf-core/graphtyper/genotype/meta.yml", - "type": "module", - "meta": { - "name": "graphtyper_genotype", - "description": "Tools for population-scale genotyping using pangenome graphs.", - "keywords": [ - "variant", - "vcf", - "bam", - "cram", - "pangenome" - ], - "tools": [ - { - "graphtyper": { - "description": "A graph-based variant caller capable of genotyping population-scale short read data sets while incorporating previously discovered variants.", - "homepage": "https://github.com/DecodeGenetics/graphtyper", - "documentation": "https://github.com/DecodeGenetics/graphtyper/wiki/User-guide", - "tool_dev_url": "https://github.com/DecodeGenetics/graphtyper", - "doi": "10.1038/ng.3964", - "licence": [ - "MIT" - ], - "identifier": "biotools:Graphtyper" + }, + { + "name": "kleborate", + "path": "modules/nf-core/kleborate/meta.yml", + "type": "module", + "meta": { + "name": "kleborate", + "description": "Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC).", + "keywords": ["screen", "assembly", "Klebsiella", "pneumoniae"], + "tools": [ + { + "kleborate": { + "description": "Screening Klebsiella genome assemblies for MLST, sub-species, and other Klebsiella related genes of interest", + "homepage": "https://github.com/katholt/Kleborate", + "documentation": "https://github.com/katholt/Kleborate/wiki", + "tool_dev_url": "https://github.com/katholt/Kleborate", + "doi": "10.1038/s41467-021-24448-3", + "licence": ["GPL v3 or later (GPL v3+)"], + "identifier": "biotools:kleborate" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fastas": { + "type": "list", + "description": "Klebsiella genome assemblies to be screened", + "pattern": "*.fasta" + } + } + ] + ], + "output": { + "txt": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "Result file generated after screening", + "pattern": "*.txt", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@abhi18av", "@rpetit3"], + "maintainers": ["@abhi18av", "@rpetit3"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM file", - "pattern": "*.{bam,cram}", - "ontologies": [] - } - }, - { - "bai": { - "type": "file", - "description": "BAM index file. This is automatically found base on BAM input file name", - "pattern": "*.{bai}", - "ontologies": [] - } + }, + { + "name": "kma_index", + "path": "modules/nf-core/kma/index/meta.yml", + "type": "module", + "meta": { + "name": "kma_index", + "description": "This module wraps the index module of the KMA alignment tool.", + "keywords": ["alignment", "kma", "index", "database", "reads"], + "tools": [ + { + "kma": { + "description": "Rapid and precise alignment of raw reads against redundant databases with KMA", + "homepage": "https://bitbucket.org/genomicepidemiology/kma/src/master/", + "documentation": "https://bitbucket.org/genomicepidemiology/kma/src/master/", + "tool_dev_url": "https://bitbucket.org/genomicepidemiology/kma/src/master/", + "doi": "10.1186/s12859-018-2336-6", + "licence": ["http://www.apache.org/licenses/LICENSE-2.0"], + "identifier": "biotools:kma" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. `[ id:'reference' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "(Multi-)FASTA file of your database sequences.", + "pattern": "*.{fa,fasta}", + "ontologies": [] + } + } + ] + ], + "output": { + "index": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'reference' ]`\n" + } + }, + { + "kmaindex": { + "type": "directory", + "description": "Directory of KMA index files", + "pattern": "*.{comp.b,length.b,name,seq.b}" + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@krannich479"], + "maintainers": ["@krannich479"] } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "ref": { - "type": "file", - "description": "Reference fasta file", - "pattern": "*.{fa, fasta, fas}", - "ontologies": [] - } + }, + { + "name": "kma_kma", + "path": "modules/nf-core/kma/kma/meta.yml", + "type": "module", + "meta": { + "name": "kma_kma", + "description": "Mapping raw reads directly against redundant databases via KMA alignment", + "keywords": ["fastq", "reads", "alignment", "kma"], + "tools": [ + { + "kma": { + "description": "Rapid and precise alignment of raw reads against redundant databases with KMA", + "homepage": "https://bitbucket.org/genomicepidemiology/kma/src/master/", + "documentation": "https://bitbucket.org/genomicepidemiology/kma/src/master/", + "tool_dev_url": "https://bitbucket.org/genomicepidemiology/kma/src/master/", + "doi": "10.1186/s12859-018-2336-6", + "licence": ["Apache-2.0"], + "identifier": "biotools:kma" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference index information\ne.g. [ id:'reference' ]\n" + } + }, + { + "index": { + "type": "file", + "description": "kma database file generated via kma_index", + "pattern": "*.{comp.b,length.b,name,seq.b}" + } + } + ], + { + "interleaved": { + "type": "boolean", + "description": "use one interleaved fastq file (true) or two paired fastq files (false)", + "pattern": "true or false" + } + } + ], + "output": { + "res": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.res": { + "type": "file", + "description": "A result overview giving the most common statistics for each mapped template.", + "pattern": "*.{res}" + } + } + ] + ], + "fsa": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.fsa": { + "type": "file", + "description": "The consensus sequences drawn from the alignments.", + "pattern": "*.{fsa}" + } + } + ] + ], + "aln": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.aln": { + "type": "file", + "description": "The consensus alignment of the reads against their template.", + "pattern": "*.{aln}" + } + } + ] + ], + "frag": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.frag.gz": { + "type": "file", + "description": "Mapping information on each mapped read, where the columns are\nread, number of equally well mapping templates, mapping score, start position,\nend position (w.r.t. template), the chosen template.\n", + "pattern": "*.{frag.gz}" + } + } + ] + ], + "matrix": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.mat.gz": { + "type": "file", + "description": "Base counts on each position in each template, (only if -matrix is enabled).", + "pattern": "*.{mat.gz}" + } + } + ] + ], + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "Compressed VCF file containing positions different from the template identified during KMA mapping against the reference database", + "pattern": "*.{vcf.gz}" + } + } + ] + ], + "sam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.sam": { + "type": "file", + "description": "SAM alignment file containing detailed mapping information from KMA mapping", + "pattern": "*.{sam}" + } + } + ] + ], + "spa": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.spa": { + "type": "file", + "description": "Text file containing the top scoring references. Note that kma\n(v1.4.15) can only use spare alignment if the kma index was also build with\nthe sparse option.\n", + "pattern": "*.{spa}" + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] + }, + "authors": ["@Krannich479", "@haidyi"], + "maintainers": ["@Krannich479", "@haidyi"] } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } + }, + { + "name": "kmcp_compute", + "path": "modules/nf-core/kmcp/compute/meta.yml", + "type": "module", + "meta": { + "name": "kmcp_compute", + "description": "Generate k-mers (sketches) from FASTA/Q sequences", + "keywords": ["metagenomics", "classify", "taxonomic profiling", "fastq", "sequences", "kmers"], + "tools": [ + { + "kmcp": { + "description": "Accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping", + "homepage": "https://github.com/shenwei356/kmcp", + "documentation": "https://github.com/shenwei356/kmcp#documents", + "tool_dev_url": "https://github.com/shenwei356/kmcp", + "doi": "10.1093/bioinformatics/btac845", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "sequences": { + "type": "file", + "description": "List of fasta files, or a directory containing FASTA files", + "pattern": "**/*.{fa,fa.gz,fasta,fasta.gz,fna,fna.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ] + ], + "output": { + "outdir": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}": { + "type": "directory", + "description": "Output directory containing all .unik files and a summary file in .txt format. Every .unik file contains the sequence/reference ID,chunk index, number of chunks, and genome size of reference.", + "pattern": "*/" + } + } + ] + ], + "info": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/_info.txt": { + "type": "file", + "description": "Summary file that is generated for later use", + "pattern": "*_info.txt", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + } + ] + ], + "versions_kmcp": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "kmcp": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "kmcp version 2>&1 | sed 's/^.*kmcp v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "kmcp": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "kmcp version 2>&1 | sed 's/^.*kmcp v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@sofstam"], + "maintainers": ["@sofstam"] }, - { - "ref_fai": { - "type": "file", - "description": "Reference index file. This is automatically found based on reference input file name.", - "pattern": "*.{.fai}", - "ontologies": [] - } - } - ], - { - "region_file": { - "type": "file", - "description": "File with a list of chromosome/locations in reference genome to genotype. One region per line in the format :-. This or `--region` (in ext.args) must be specified.", - "pattern": "*", - "ontologies": [] - } - } - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "results/*/*.vcf.gz": { - "type": "file", - "description": "VCF file with genotyped variants", - "pattern": "*.{vcf.gz}", - "ontologies": [] - } - } - ] - ], - "tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "results/*/*.vcf.gz.tbi": { - "type": "file", - "description": "VCF index file", - "pattern": "*.{vcf.gz.tbi}", - "ontologies": [] - } - } - ] - ], - "versions_graphtyper": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "graphtyper": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "graphtyper --help | tail -1 | sed 's/.* //'": { - "type": "eval", - 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{ - "bwa_index": { - "type": "directory", - "description": "OPTIONAL - The BWA index created from the reference fasta, will be generated by Gridss in the setupreference step" - } - } - ] - ], - "output": { - "bedpe": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.bedpe": { - "type": "file", - "description": "GRIDSS generated breakpoint pon bedpe file", - "pattern": "*.bedpe", - "ontologies": [] - } - } - ] - ], - "bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.bed": { - "type": "file", - "description": "GRIDSS generated breakpoint pon bed file", - "pattern": "*.bed", - "ontologies": [] - } - } - ] - ], - "versions_gridss": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process" - } - }, - { - "gridss": { - "type": "string", - "description": "The tool name" - } - }, - { - 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"bam", - "cram", - "vcf" - ], - "tools": [ - { - "gridss": { - "description": "GRIDSS: the Genomic Rearrangement IDentification Software Suite", - "documentation": "https://github.com/PapenfussLab/gridss/wiki/GRIDSS-Documentation", - "tool_dev_url": "https://github.com/PapenfussLab/gridss", - "doi": "10.1186/s13059-021-02423-x", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:gridss" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "inputs": { - "type": "file", - "description": "One or more input BAM/CRAM file(s)", - "pattern": "*.{bam,cram}", - "ontologies": [] - } + }, + { + "name": "kmergenie", + "path": "modules/nf-core/kmergenie/meta.yml", + "type": "module", + "meta": { + "name": "kmergenie", + "description": "KmerGenie estimates the best k-mer length for genome de novo assembly", + "keywords": ["k-mer", "count", "genome assembly"], + "tools": [ + { + "kmergenie": { + "description": "KmerGenie estimates the best k-mer length for genome de novo assembly. Given a set of reads, KmerGenie first computes the k-mer abundance histogram for many values of k. Then, for each value of k, it predicts the number of distinct genomic k-mers in the dataset, and returns the k-mer length which maximizes this number.", + "homepage": "http://kmergenie.bx.psu.edu/", + "documentation": "http://kmergenie.bx.psu.edu/", + "tool_dev_url": "https://github.com/movingpictures83/KMerGenie", + "doi": "10.1093/bioinformatics/btt310", + "licence": ["MIT License"], + "identifier": "biotools:kmergenie" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "Input reads in FastQ format", + "pattern": "*.{fastq.gz, fastq, fq.gz, fq}", + "ontologies": [] + } + } + ] + ], + "output": { + "html": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_report.html": { + "type": "file", + "description": "html file containing all the plotted histograms obtained from different kmer size", + "pattern": "*_report.html", + "ontologies": [] + } + } + ] + ], + "histo": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.histo": { + "type": "file", + "description": "histogram files (text) obtained from individual kmer sizes", + "pattern": "*.histo", + "ontologies": [] + } + } + ] + ], + "dat": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.dat": { + "type": "file", + "description": "text file containing number of kmer for kmer sizes and recommended coverage cut-off", + "pattern": "*.dat", + "ontologies": [] + } + } + ] + ], + "pdf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.pdf": { + "type": "file", + "description": "histogram plots obtained from individual kmer sizes", + "pattern": "*.pdf", + "ontologies": [] + } + } + ] + ], + "versions_kmergenie": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "kmergenie": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "kmergenie --version |& sed \"1!d ; s/KmerGenie //\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.kmergenie.log": { + "type": "file", + "description": "log file containing the standard output and error of the kmergenie command", + "pattern": "*.kmergenie.log" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "kmergenie": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "kmergenie --version |& sed \"1!d ; s/KmerGenie //\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@LiaOb21"], + "maintainers": ["@LiaOb21"] } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\n" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference fasta", - "pattern": "*.{fa,fna,fasta}", - "ontologies": [] - } + }, + { + "name": "knotannotsv", + "path": "modules/nf-core/knotannotsv/meta.yml", + "type": "module", + "meta": { + "name": "knotannotsv", + "description": "Simple tool to create a customizable html file (to be displayed on a web browser) from an AnnotSV output", + "keywords": ["annotation", "structural variants", "annotsv", "tsv", "html"], + "tools": [ + { + "knotannotsv": { + "description": "Simple tool to create a customizable html file (to be displayed on a web browser) from an AnnotSV output", + "homepage": "https://github.com/mobidic/knotAnnotSV", + "documentation": "https://github.com/mobidic/knotAnnotSV/blob/master/README.knotAnnotSV_latest.pdf", + "tool_dev_url": "https://github.com/mobidic/knotAnnotSV", + "licence": ["GPL-3.0"] + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "annotsv_tsv": { + "type": "file", + "description": "Annotated TSV produced by AnnotSV", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, + { + "knot_out_xl": { + "type": "boolean", + "description": "Specify 'true' to output as XLSM (rather than HTML by default)" + } + } + ] + ], + "output": { + "output_file": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.{html,xlsm}": { + "type": "file", + "description": "HTML (or XLSM if 'knot_out_xl=true') annotated file", + "pattern": "*.{html,xlsm}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2331" + }, + { + "edam": "http://edamontology.org/format_3620" + } + ] + } + } + ] + ], + "versions_knotannotsv": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "knotannotsv": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "1.1.5": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "knotannotsv": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "1.1.5": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@thomasguignard"], + "maintainers": ["@thomasguignard"] } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\n" - } - }, - { - "fasta_fai": { - "type": "file", - "description": "The index of the reference fasta", - "pattern": "*.fai", - "ontologies": [] - } + }, + { + "name": "kofamscan", + "path": "modules/nf-core/kofamscan/meta.yml", + "type": "module", + "meta": { + "name": "kofamscan", + "description": "Produces annotation using kofamscan against a Profile database and a KO list", + "keywords": ["fasta", "kegg", "kofamscan"], + "tools": [ + { + "kofamscan": { + "description": "KofamKOALA assigns K numbers to the user's sequence data by HMMER/HMMSEARCH against KOfam", + "homepage": "https://www.genome.jp/tools/kofamkoala/", + "documentation": "https://github.com/takaram/kofam_scan", + "tool_dev_url": "https://github.com/takaram/kofam_scan", + "doi": "10.1093/bioinformatics/btz859", + "licence": ["MIT License"], + "identifier": "biotools:kofamscan" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input fasta file containing query sequences", + "pattern": "*.{fa,fasta}", + "ontologies": [] + } + } + ], + { + "profiles": { + "type": "directory", + "description": "Directory containing the Profiles database", + "pattern": "*" + } + }, + { + "ko_list": { + "type": "file", + "description": "File containing list of KO entries with their data", + "pattern": "*.{fa,fasta}", + "ontologies": [] + } + } + ], + "output": { + "txt": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "Application-specific text file with hits information", + "pattern": "*.{txt}", + "ontologies": [] + } + } + ] + ], + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "Tab separated file containing with detailed hits", + "pattern": "*.{tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_kofamscan": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "kofamscan": { + "type": "string", + "description": "kofamscan version string" + } + }, + { + "exec_annotation --version 2>&1 | sed 's/exec_annotation //;'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "kofamscan": { + "type": "string", + "description": "kofamscan version string" + } + }, + { + "exec_annotation --version 2>&1 | sed 's/exec_annotation //;'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@toniher"], + "maintainers": ["@toniher"] } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing reference information\n" - } + }, + { + "name": "kraken2_add", + "path": "modules/nf-core/kraken2/add/meta.yml", + "type": "module", + "meta": { + "name": "kraken2_add", + "description": "Adds fasta files to a Kraken2 taxonomic database", + "keywords": ["metagenomics", "db", "classification", "build", "kraken2", "add"], + "tools": [ + { + "kraken2": { + "description": "Kraken2 is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies.", + "homepage": "https://ccb.jhu.edu/software/kraken2/", + "documentation": "https://github.com/DerrickWood/kraken2/wiki/Manual", + "tool_dev_url": "https://github.com/DerrickWood/kraken2", + "doi": "10.1186/s13059-019-1891-0", + "licence": ["MIT"], + "identifier": "biotools:kraken2" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "fasta file that will be added to the database", + "pattern": "*.{fa,fasta,fna,ffn}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + { + "taxonomy_names": { + "type": "file", + "description": "used for associating sequences with taxonomy IDs", + "pattern": "*.dmp", + "ontologies": [ + { + "edam": "http://edamontology.org/data_3028" + } + ] + } + }, + { + "taxonomy_nodes": { + "type": "file", + "description": "tree nodes using NCBI taxonomy nomenclature", + "pattern": "*.dmp", + "ontologies": [ + { + "edam": "http://edamontology.org/data_3028" + } + ] + } + }, + { + "accession2taxid": { + "type": "file", + "description": "associates sequence accession IDs to taxonomy IDs", + "pattern": "*.accession2taxid", + "ontologies": [ + { + "edam": "http://edamontology.org/data_3028" + } + ] + } + }, + { + "seqid2taxid": { + "type": "file", + "description": "optional premade 2 column seq2taxid map file. Must be named seq2taxid.map. If not supplied will be generated by kraken2 itself during upstream build step.", + "pattern": "seqid2taxid.map", + "ontologies": [ + { + "edam": "http://edamontology.org/data_3028" + } + ] + } + } + ], + "output": { + "library_added_files": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n", + "pattern": "*/" + } + }, + { + "${prefix}/library/added/*": { + "type": "file", + "description": "Files present in the /library/added/ directory, including FASTA files, masked FASTAs, and prelim_map files.", + "pattern": "*", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ] + ], + "seqid2taxid_map": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n", + "pattern": "*/" + } + }, + { + "${prefix}/seqid2taxid.map": { + "type": "file", + "description": "File mapping sequence IDs to taxonomy IDs, either generated or premade.", + "pattern": "seqid2taxid.map", + "ontologies": [ + { + "edam": "http://edamontology.org/data_3028" + } + ] + } + } + ] + ], + "taxonomy_files": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n", + "pattern": "*/" + } + }, + { + "${prefix}/taxonomy/*": { + "type": "file", + "description": "Files present in the /taxonomy/ directory, including nodes.dmp, names.dmp, and .accession2taxid files.", + "pattern": "*", + "ontologies": [ + { + "edam": "http://edamontology.org/data_3028" + } + ] + } + } + ] + ], + "versions_kraken2": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "kraken2": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "kraken2 --version 2>&1 | head -1 | sed \"s/^.*Kraken version //; s/ .*//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "kraken2": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "kraken2 --version 2>&1 | head -1 | sed \"s/^.*Kraken version //; s/ .*//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@alxndrdiaz"], + "maintainers": ["@alxndrdiaz", "@jfy133"] }, - { - "bwa_index": { - "type": "directory", - "description": "OPTIONAL - The BWA index created from the reference fasta, will be generated by Gridss in the setupreference step" - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.vcf.gz": { - "type": "file", - "description": "The called VCF file created by Gridss' call step", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "versions_gridss": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process" - } - }, - { - "gridss": { - "type": "string", - "description": "The tool name" - } - }, - { - "GeneratePonBedpe --version 2>&1 | sed 's/-gridss//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process" - } - }, - { - "gridss": { - "type": "string", - "description": "The tool name" - } - }, - { - "GeneratePonBedpe --version 2>&1 | sed 's/-gridss//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@nvnieuwk" - ], - "maintainers": [ - "@nvnieuwk" - ] - } - }, - { - "name": "gridss_somaticfilter", - "path": "modules/nf-core/gridss/somaticfilter/meta.yml", - "type": "module", - "meta": { - "name": "gridss_somaticfilter", - "description": "GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements.", - "keywords": [ - "gridss", - "structural variants", - "somatic variants", - "vcf" - ], - "tools": [ - { - "gridss": { - "description": "GRIDSS: the Genomic Rearrangement IDentification Software Suite", - "documentation": "https://github.com/PapenfussLab/gridss/wiki/GRIDSS-Documentation", - "tool_dev_url": "https://github.com/PapenfussLab/gridss", - "doi": "10.1186/s13059-021-02423-x", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:gridss" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "vcf": { - "type": "file", - "description": "Input VCF file, must be generated with GRIDSS", - "pattern": "*.{vcf,vcf.gz}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing information for PONDIR\ne.g. [ id:'test']\n" - } - }, - { - "pondir": { - "type": "directory", - "description": "Directory containing Panel Of Normal bed/bedpe used to filter FP somatic events. Use gridss.GeneratePonBedpe to generate the PON." - } - } - ] - ], - "output": { - "high_conf_sv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "*.high_confidence_somatic.vcf.bgz": { - "type": "file", - "description": "VCF file including high confidence somatic SVs", - "pattern": "*.vcf.bgz", - "ontologies": [] - } - } - ] - ], - "all_sv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "*.all_somatic.vcf.bgz": { - "type": "file", - "description": "VCF file including all somatic SVs", - "pattern": "*.vcf.bgz", - "ontologies": [] - } - } - ] - ], - "versions_gridss": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process" - } - }, - { - "gridss": { - "type": "string", - "description": "The tool name" - } - }, - { - "GeneratePonBedpe --version 2>&1 | sed 's/-gridss//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process" - } - }, - { - "gridss": { - "type": "string", - "description": "The tool name" - } - }, - { - "GeneratePonBedpe --version 2>&1 | sed 's/-gridss//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@kubranarci" - ], - "maintainers": [ - "@famosab" - ] - } - }, - { - "name": "gsea_gsea", - "path": "modules/nf-core/gsea/gsea/meta.yml", - "type": "module", - "meta": { - "name": "gsea_gsea", - "description": "run the Broad Gene Set Enrichment tool in GSEA mode", - "keywords": [ - "gene set analysis", - "enrichment", - "gsea", - "gene set" - ], - "tools": [ - { - "gsea": { - "description": "Gene Set Enrichment Analysis (GSEA)", - "homepage": "http://www.gsea-msigdb.org/gsea/index.jsp", - "documentation": "https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page", - "doi": "10.1073/pnas.0506580102", - "licence": [ - "BSD-3-clause" - ], - "identifier": "biotools:gsea" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ].\n" - } - }, - { - "gct": { - "type": "file", - "description": "GCT file with expression values", - "pattern": "*.{gct}", - "ontologies": [] - } - }, - { - "cls": { - "type": "file", - "description": "CL file with the classes of the samples in the GCT file", - "pattern": "*.{gct}", - "ontologies": [] - } - }, - { - "gene_sets": { - "type": "file", - "description": "GMX or GMT file with gene sets", - "pattern": "*.{gmx,gmt}", - "ontologies": [] - } - } - ], - [ - { - "reference": { - "type": "string", - "description": "String indicating which of the classes in the cls file should be used\nas the reference level of the comparison.\n" - } - }, - { - "target": { - "type": "string", - "description": "String indicating which of the classes in the cls file should be used\nas the target level of the comparison.\n" - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy map" - } - }, - { - "chip": { - "type": "file", - "description": "optional Broad-style chip file mapping identifiers in gct to\nthose in gene_sets\n", - "pattern": "*.{chip}", - "ontologies": [] - } - } - ] - ], - "output": { - "rpt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ]\n" - } - }, - { - "*.rpt": { - "type": "file", - "description": "File containing parameter settings used", - "pattern": "*.rpt", - "ontologies": [] - } - } - ] - ], - "index_html": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ]\n" - } - }, - { - "*index.html": { - "type": "file", - "description": "Top level report HTML file", - "pattern": "index.html", - "ontologies": [] - } - } - ] - ], - "heat_map_corr_plot": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ]\n" - } - }, - { - "*heat_map_corr_plot.html": { - "type": "file", - "description": "HTML file combining heatmap and rank correlation plot", - "pattern": "heat_map_corr_plot.html", - "ontologies": [] - } - } - ] - ], - "report_tsvs_ref": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ]\n" - } - }, - { - "*gsea_report_for_${reference}.tsv": { - "type": "file", - "description": "Main TSV results report file for the reference group.", - "pattern": "gsea_report_for_reference*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "report_htmls_ref": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ]\n" - } - }, - { - "*gsea_report_for_${reference}.html": { - "type": "file", - "description": "Main HTML results report file for the reference group. sample groups", - "pattern": "gsea_report_for_reference*.html", - "ontologies": [] - } - } - ] - ], - "report_tsvs_target": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ]\n" - } - }, - { - "*gsea_report_for_${target}.tsv": { - "type": "file", - "description": "Main TSV results report file for the target group.", - "pattern": "gsea_report_for_target*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "report_htmls_target": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ]\n" - } - }, - { - "*gsea_report_for_${target}.html": { - "type": "file", - "description": "Main HTML results report file for the target group.", - "pattern": "gsea_report_for_target*.html", - "ontologies": [] - } - } - ] - ], - "ranked_gene_list": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ]\n" - } - }, - { - "*ranked_gene_list*.tsv": { - "type": "file", - "description": "TSV file with ranked gene list and scores", - "pattern": "ranked_gene_list*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "gene_set_sizes": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ]\n" - } - }, - { - "*gene_set_sizes.tsv": { - "type": "file", - "description": "TSV file with gene set sizes", - "pattern": "gene_set_sizes.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "histogram": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ]\n" - } - }, - { - "*global_es_histogram.png": { - "type": "file", - "description": "Plot showing number of gene sets by enrichment score", - "pattern": "global_es_histogram.png", - "ontologies": [] - } - } - ] - ], - "heatmap": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ]\n" - } - }, - { - "*heat_map_1.png": { - "type": "file", - "description": "Heat Map of the top 50 features for each phenotype in test", - "pattern": "heat_map_1.png", - "ontologies": [] - } - } - ] - ], - "pvalues_vs_nes_plot": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ]\n" - } - }, - { - "*pvalues_vs_nes_plot.png": { - "type": "file", - "description": "Plot showing FDR q-value by normalised enrichment score", - "pattern": "pvalues_vs_nes_plot", - "ontologies": [] - } - } - ] - ], - "ranked_list_corr": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ]\n" - } - }, - { - "*ranked_list_corr_2.png": { - "type": "file", - "description": "Ranked Gene List Correlation Profile", - "pattern": "ranked_list_corr_2.png", - "ontologies": [] - } - } - ] - ], - "butterfly_plot": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ]\n" - } - }, - { - "*butterfly_plot.png": { - "type": "file", - "description": "Butterfly plot with gene rank plotted against score", - "pattern": "butterfly_plot.png", - "ontologies": [] - } - } - ] - ], - "gene_set_tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ]\n" - } - }, - { - "gene_sets_*.tsv": { - "type": "list", - "description": "Where -make_sets is not set to false, TSV files, one file for each gene set, with detail on enrichment for each gene", - "pattern": "gene_sets_*.tsv" - } - } - ] - ], - "gene_set_html": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ]\n" - } - }, - { - "gene_sets_*.html": { - "type": "list", - "description": "Where -make_sets is not set to false, HTML files, one file for each gene set, with detail on enrichment for each gene", - "pattern": "gene_sets_*.html" - } - } - ] - ], - "gene_set_heatmap": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ]\n" - } - }, - { - "gene_sets_*.png": { - "type": "list", - "description": "Where -make_sets is not set to false, PNG-format heatmaps, one file for each gene set, showing expression for each gene", - "pattern": "gene_sets_*.png" - } - } - ] - ], - "snapshot": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ]\n" - } - }, - { - "*_snapshot*.html": { - "type": "list", - "description": "HTML files, one each for positive and negative enrichment, collecting elements of gene_set_enplot", - "pattern": "*_snapshot*.html" - } - } - ] - ], - "gene_set_enplot": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ]\n" - } - }, - { - "*enplot*.png": { - "type": "list", - "description": "Where -make_sets is not set to false, PNG-format enrichment (barcode) plots, one file for each gene set, showing how genes contribute to enrichment.", - "pattern": "enplot*.png" - } - } - ] - ], - "gene_set_dist": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ]\n" - } - }, - { - "*gset_rnd_es_dist*.png": { - "type": "list", - "description": "Where -make_sets is not set to false, PNG-format enrichment score distributions plots, one file for each gene set.", - "pattern": "gset_rnd_es_dist*.png" - } - } - ] - ], - "archive": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ]\n" - } - }, - { - "*.zip": { - "type": "file", - "description": "Where -zip_report is set, a zip archive containing all outputs", - "pattern": "*.zip", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3987" - } - ] - } - } - ] - ], - "versions_gsea": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gsea": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "4.3.2": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gsea": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "4.3.2": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@pinin4fjords" - ], - "maintainers": [ - "@pinin4fjords", - "@nschcolnicov" - ] - }, - "pipelines": [ - { - "name": "differentialabundance", - "version": "1.5.0" - } - ] - }, - { - "name": "gstama_collapse", - "path": "modules/nf-core/gstama/collapse/meta.yml", - "type": "module", - "meta": { - "name": "gstama_collapse", - "description": "Collapse redundant transcript models in Iso-Seq data.", - "keywords": [ - "tama_collapse.py", - "isoseq", - "nanopore", - "long-read", - "transcriptome", - "gene model", - "TAMA" - ], - "tools": [ - { - "tama_collapse.py": { - "description": "Collapse similar gene model", - "homepage": "https://github.com/sguizard/gs-tama", - "documentation": "https://github.com/GenomeRIK/tama/wiki", - "tool_dev_url": "https://github.com/sguizard/gs-tama", - "doi": "10.1186/s12864-020-07123-7", - "licence": [ - "GNU GPL3" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "A sorted BAM or sam file of aligned reads", - "pattern": "*.{bam,sam}", - "ontologies": [] - } - } - ], - { - "fasta": { - "type": "file", - "description": "A fasta file of the genome used for the mapping", - "pattern": "*.{fasta,fa}", - "ontologies": [] - } - } - ], - "output": { - "bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*_collapsed.bed": { - "type": "file", - "description": "a bed12 format file containing the final collapsed version of your transcriptome", - "pattern": "*.bed", - "ontologies": [] - } - } - ] - ], - "bed_trans_reads": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*_trans_read.bed": { - "type": "file", - "description": "This file uses bed12 format to show the transcript model for each read based on the mapping prior to collapsing. This only contains the reads which were accepted according to the defined thresholds. You can use this file to see if there were any strange occurrences during collapsing. It also contains the relationships between reads and collapsed transcript models. The 1st subfield in the 4th column shows the final transcript ID and the 2nd subfield in the 4th column shows the read ID. If you used no_cap mode for collapsing there may be multiple lines for a single read. This happens when a 5' degraded read can match to multiple 5' longer transcript models.", - "pattern": "*_trans_read.bed", - "ontologies": [] - } - } - ] - ], - "local_density_error": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*_local_density_error.txt": { - "type": "file", - "description": "This file contains the log of filtering for local density error around the splice junctions (\"-lde\")", - "pattern": "*_local_density_error.txt", - "ontologies": [] - } - } - ] - ], - "polya": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*_polya.txt": { - "type": "file", - "description": "This file contains the reads with potential poly A truncation.", - "pattern": "*_polya.txt", - "ontologies": [] - } - } - ] - ], - "read": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*_read.txt": { - "type": "file", - "description": "This file contains information for all mapped reads from the input SAM/BAM file. It shows both accepted and discarded reads and should match the number of mapped reads in your SAM/BAM file", - "pattern": "*_read.txt", - "ontologies": [] - } - } - ] - ], - "strand_check": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*_strand_check.txt": { - "type": "file", - "description": "This file shows instances where the sam flag strand information contrasted the GMAP strand information.", - "pattern": "*_strand_check.txt", - "ontologies": [] - } - } - ] - ], - "trans_report": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*_trans_report.txt": { - "type": "file", - "description": "This file contains collapsing information for each transcript.", - "pattern": "*_trans_report.txt", - "ontologies": [] - } - } - ] - ], - "varcov": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*_varcov.txt": { - "type": "file", - "description": "This file contains the coverage information for each variant detected.", - "pattern": "*_varcov.txt", - "ontologies": [] - } - } - ] - ], - "variants": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*_variants.txt": { - "type": "file", - "description": "This file contains the variants called. Variants are only called if 5 or more reads show the variant at a specific locus. If you would like to change the threshold, please make an issue about this in the Github repo.", - "pattern": "*_variants.txt", - "ontologies": [] - } - } - ] - ], - "versions_gstama": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gstama": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "tama_collapse.py -version | sed -n 's/tc_version_date_//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gstama": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "tama_collapse.py -version | sed -n 's/tc_version_date_//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@sguizard" - ], - "maintainers": [ - "@sguizard" - ] - }, - "pipelines": [ - { - "name": "isoseq", - "version": "2.0.0" - } - ] - }, - { - "name": "gstama_merge", - "path": "modules/nf-core/gstama/merge/meta.yml", - "type": "module", - "meta": { - "name": "gstama_merge", - "description": "Merge multiple transcriptomes while maintaining source information.", - "keywords": [ - "gstama", - "gstama/merge", - "long-read", - "isoseq", - "nanopore", - "tama", - "trancriptome", - "annotation" - ], - "tools": [ - { - "gstama": { - "description": "Gene-Switch Transcriptome Annotation by Modular Algorithms", - "homepage": "https://github.com/sguizard/gs-tama", - "documentation": "https://github.com/GenomeRIK/tama/wiki", - "tool_dev_url": "https://github.com/sguizard/gs-tama", - "doi": "10.1186/s12864-020-07123-7", - "licence": [ - "GPL v3 License" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bed": { - "type": "file", - "description": "bed12 file generated by TAMA collapse", - "pattern": "*.bed", - "ontologies": [] - } - } - ], - { - "filelist": { - "type": "file", - "description": "list of files", - "ontologies": [] - } - } - ], - "output": { - "bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.bed": { - "type": "file", - "description": "This is the main merged annotation file. Transcripts are coloured according to the source support for each model. Sources are numbered based on the order supplied in the input filelist file. For example the first file named in the filelist file would have its transcripts coloured in red. If a transcript has multiple sources the colour is shown as magenta.", - "pattern": "*.bed", - "ontologies": [] - } - } - ] - ], - "gene_report": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*_gene_report.txt": { - "type": "file", - "description": "This contains a report of the genes from the merged file. \"num_clusters\" refers to the number of source transcripts that were used to make this gene model. \"num_final_trans\" refers to the number of transcripts in the final gene model.", - "pattern": "*_gene_report.txt", - "ontologies": [] - } - } - ] - ], - "merge": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*_merge.txt": { - "type": "file", - "description": "This contains a bed12 format file which shows the coordinates of each input transcript matched to the merged transcript ID. I used the \"txt\" extension even though it is a bed file just to avoid confusion with the main bed file. You can use this file to map the final merged transcript models to their pre-merged supporting transcripts. The 1st subfield in the 4th column shows the final merged transcript ID while the 2nd subfield shows the pre-merged transcript ID with source prefix.", - "pattern": "*_merge.txt", - "ontologies": [] - } - } - ] - ], - "trans_report": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*_trans_report.txt": { - "type": "file", - "description": "This contains the source information for each merged transcript.", - "pattern": "*_trans_report.txt", - "ontologies": [] - } - } - ] - ], - "versions_gstama": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gstama": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "tama_merge.py -version | sed '1!d'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gstama": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "tama_merge.py -version | sed '1!d'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@sguizard" - ], - "maintainers": [ - "@sguizard" - ] - }, - "pipelines": [ - { - "name": "isoseq", - "version": "2.0.0" - } - ] - }, - { - "name": "gstama_polyacleanup", - "path": "modules/nf-core/gstama/polyacleanup/meta.yml", - "type": "module", - "meta": { - "name": "gstama_polyacleanup", - "description": "Helper script, remove remaining polyA sequences from Full Length Non Chimeric reads (Pacbio isoseq3)", - "keywords": [ - "gstama", - "gstama/polyacleanup", - "long-read", - "isoseq", - "tama", - "trancriptome", - "annotation" - ], - "tools": [ - { - "gstama": { - "description": "Gene-Switch Transcriptome Annotation by Modular Algorithms", - "homepage": "https://github.com/sguizard/gs-tama", - "documentation": "https://github.com/GenomeRIK/tama/wiki", - "tool_dev_url": "https://github.com/sguizard/gs-tama", - "doi": "10.1186/s12864-020-07123-7", - "licence": [ - "GPL v3 License" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Full Length Non Chimeric reads in fasta format", - "pattern": "*.{fa,fasta}", - "ontologies": [] - } - } - ] - ], - "output": { - "fasta": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.fa.gz": { - "type": "file", - "description": "The Full Length Non Chimeric reads cleaned from remaining polyA tails. The sequences are in FASTA format compressed with gzip.", - "pattern": "*.fa.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "report": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_polya_flnc_report.txt.gz": { - "type": "file", - "description": "A text file describing the number of polyA tails removed and their length. Compressed with gzip.", - "pattern": "*_polya_flnc_report.txt.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "tails": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_tails.fa.gz": { - "type": "file", - "description": "A gzip compressed FASTA file of trimmed polyA tails.", - "pattern": "*_tails.fa.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "versions_gstama": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gstama": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "tama_collapse.py -version | sed -n 's/tc_version_date_//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gstama": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "tama_collapse.py -version | sed -n 's/tc_version_date_//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@sguizard" - ], - "maintainers": [ - "@sguizard" - ] - }, - "pipelines": [ - { - "name": "isoseq", - "version": "2.0.0" - } - ] - }, - { - "name": "gt_gff3", - "path": "modules/nf-core/gt/gff3/meta.yml", - "type": "module", - "meta": { - "name": "gt_gff3", - "description": "GenomeTools gt-gff3 utility to parse, possibly transform, and output GFF3 files", - "keywords": [ - "genome", - "gff3", - "annotation" - ], - "tools": [ - { - "gt": { - "description": "The GenomeTools genome analysis system", - "homepage": "https://genometools.org/index.html", - "documentation": "https://genometools.org/documentation.html", - "tool_dev_url": "https://github.com/genometools/genometools", - "doi": "10.1109/TCBB.2013.68", - "licence": [ - "ISC" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "gff3": { - "type": "file", - "description": "Input gff3 file", - "pattern": "*.{gff,gff3}", - "ontologies": [] - } - } - ] - ], - "output": { - "gt_gff3": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "*.gt.gff3": { - "type": "file", - "description": "Parsed gff3 file produced only if there is no parsing error", - "pattern": "*.gt.gff3", - "ontologies": [] - } - } - ] - ], - "error_log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "*.error.log": { - "type": "file", - "description": "Error log if gt-gff3 failed to parse the input gff3 file", - "pattern": "*.error.log", - "ontologies": [] - } - } - ] - ], - "versions_gt": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "genometools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gt --version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "genometools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gt --version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@gallvp" - ], - "maintainers": [ - "@gallvp" - ] - } - }, - { - "name": "gt_gff3validator", - "path": "modules/nf-core/gt/gff3validator/meta.yml", - "type": "module", - "meta": { - "name": "gt_gff3validator", - "description": "GenomeTools gt-gff3validator utility to strictly validate a GFF3 file", - "keywords": [ - "genome", - "gff3", - "annotation", - "validation" - ], - "tools": [ - { - "gt": { - "description": "The GenomeTools genome analysis system", - "homepage": "https://genometools.org/index.html", - "documentation": "https://genometools.org/documentation.html", - "tool_dev_url": "https://github.com/genometools/genometools", - "doi": "10.1109/TCBB.2013.68", - "licence": [ - "ISC" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "gff3": { - "type": "file", - "description": "Input gff3 file", - "pattern": "*.{gff,gff3}", - "ontologies": [] - } - } - ] - ], - "output": { - "success_log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "*.success.log": { - "type": "file", - "description": "Log file for successful validation", - "pattern": "*.success.log", - "ontologies": [] - } - } - ] - ], - "error_log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "*.error.log": { - "type": "file", - "description": "Log file for failed validation", - "pattern": "*.error.log", - "ontologies": [] - } - } - ] - ], - "versions_gt": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "genometools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gt --version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "genometools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gt --version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@GallVp" - ], - "maintainers": [ - "@GallVp" - ] - } - }, - { - "name": "gt_ltrharvest", - "path": "modules/nf-core/gt/ltrharvest/meta.yml", - "type": "module", - "meta": { - "name": "gt_ltrharvest", - "description": "Predicts LTR retrotransposons using GenomeTools gt-ltrharvest utility", - "keywords": [ - "genomics", - "genome", - "annotation", - "repeat", - "transposons", - "retrotransposons" - ], - "tools": [ - { - "gt": { - "description": "The GenomeTools genome analysis system", - "homepage": "https://genometools.org/index.html", - "documentation": "https://genometools.org/documentation.html", - "tool_dev_url": "https://github.com/genometools/genometools", - "doi": "10.1109/TCBB.2013.68", - "licence": [ - "ISC" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "index": { - "type": "directory", - "description": "Folder containing the suffixerator index files", - "pattern": "suffixerator" - } - } - ] - ], - "output": { - "tabout": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.tabout": { - "type": "file", - "description": "Old tabular output by default or when `-tabout yes` argument is present", - "pattern": "*.tabout", - "ontologies": [] - } - } - ] - ], - "gff3": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.gff3": { - "type": "file", - "description": "GFF3 output when `-tabout no` argument is present", - "pattern": "*.gff3", - "ontologies": [] - } - } - ] - ], - "fasta": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "$out_name": { - "type": "file", - "description": "FASTA output when `-out` argument is present", - "pattern": "*.{fa,fsa,fasta}", - "ontologies": [] - } - } - ] - ], - "inner_fasta": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "$outinner_name": { - "type": "file", - "description": "FASTA output for inner regions when `-outinner` argument is present", - "pattern": "*.{fa,fsa,fasta}", - "ontologies": [] - } - } - ] - ], - "versions_gt": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "genometools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gt --version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "genometools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gt --version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@GallVp" - ], - "maintainers": [ - "@GallVp" - ] - } - }, - { - "name": "gt_stat", - "path": "modules/nf-core/gt/stat/meta.yml", - "type": "module", - "meta": { - "name": "gt_stat", - "description": "GenomeTools gt-stat utility to show statistics about features contained in GFF3 files", - "keywords": [ - "genome", - "gff3", - "annotation", - "statistics", - "stats" - ], - "tools": [ - { - "gt": { - "description": "The GenomeTools genome analysis system", - "homepage": "https://genometools.org/index.html", - "documentation": "https://genometools.org/documentation.html", - "tool_dev_url": "https://github.com/genometools/genometools", - "doi": "10.1109/TCBB.2013.68", - "licence": [ - "ISC" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "gff3": { - "type": "file", - "description": "Input gff3 file", - "pattern": "*.{gff,gff3}", - "ontologies": [] - } - } - ] - ], - "output": { - "stats": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "${prefix}.yml": { - "type": "file", - "description": "Stats file in yaml format", - "pattern": "*.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - ], - "versions_gt": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "genometools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gt --version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "genometools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gt --version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@GallVp" - ], - "maintainers": [ - "@GallVp" - ] - } - }, - { - "name": "gt_suffixerator", - "path": "modules/nf-core/gt/suffixerator/meta.yml", - "type": "module", - "meta": { - "name": "gt_suffixerator", - "description": "Computes enhanced suffix array using GenomeTools gt-suffixerator utility", - "keywords": [ - "genomics", - "genome", - "fasta", - "index" - ], - "tools": [ - { - "gt": { - "description": "The GenomeTools genome analysis system", - "homepage": "https://genometools.org/index.html", - "documentation": "https://genometools.org/documentation.html", - "tool_dev_url": "https://github.com/genometools/genometools", - "doi": "10.1109/TCBB.2013.68", - "licence": [ - "ISC" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input fasta file to index", - "pattern": "*.{fsa,fa,fasta}", - "ontologies": [] - } - } - ], - { - "mode": { - "type": "string", - "description": "Mode must be one of 'dna', or 'protein'" - } - } - ], - "output": { - "index": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "$prefix": { - "type": "directory", - "description": "Folder containing the suffixerator index files", - "pattern": "suffixerator" - } - } - ] - ], - "versions_gt": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "genometools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gt --version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "genometools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gt --version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@GallVp" - ], - "maintainers": [ - "@GallVp" - ] - } - }, - { - "name": "gtdbtk_classifywf", - "path": "modules/nf-core/gtdbtk/classifywf/meta.yml", - "type": "module", - "meta": { - "name": "gtdbtk_classifywf", - "description": "GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB.", - "keywords": [ - "GTDB taxonomy", - "taxonomic classification", - "metagenomics", - "classification", - "genome taxonomy database", - "bacteria", - "archaea" - ], - "tools": [ - { - "gtdbtk": { - "description": "GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB.", - "homepage": "https://ecogenomics.github.io/GTDBTk/", - "documentation": "https://ecogenomics.github.io/GTDBTk/", - "tool_dev_url": "https://github.com/Ecogenomics/GTDBTk", - "doi": "10.1093/bioinformatics/btz848", - "licence": [ - "GNU General Public v3 (GPL v3)" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false, assembler:'spades' ]\n" - } - }, - { - "bins/*": { - "type": "file", - "description": "A list of one or more bins in FASTA format for classification", - "pattern": "*.{fasta,fna,fas,fa}{,.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - [ - { - "db_name": { - "type": "string", - "description": "The name of the GTDB database to use." - } - }, - { - "db": { - "type": "file", - "description": "Path to a directory containing a GDTB database, as uncompressed from from the 'full package' gtdbdtk_data.tar.gz file.\nYou can give the 'release' directory here.\nMust contain the 'metadata' subdirectory\n", - "pattern": "release[0-9]+/", - "ontologies": [] - } - } - ], - { - "use_pplacer_scratch_dir": { - "type": "boolean", - "description": "Set to true to reduce pplacer memory usage by writing to disk (slower)" - } - } - ], - "output": { - "gtdb_outdir": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false, assembler:'spades' ]\n", - "pattern": "*" - } - }, - { - "${prefix}": { - "type": "directory", - "description": "All files output by GTDB-Tk", - "pattern": "*" - } - } - ] - ], - "summary": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false, assembler:'spades' ]\n", - "pattern": "*" - } - }, - { - "${prefix}/classify/*.summary.tsv": { - "type": "file", - "description": "A TSV summary file for the classification", - "pattern": "*.{summary.tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "tree": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false, assembler:'spades' ]\n", - "pattern": "*" - } - }, - { - "${prefix}/classify/*.classify.tree": { - "type": "file", - "description": "Groovy Map NJ or UPGMA trees in Newick format produced from a multiple sequence\nalignment\n", - "pattern": "*.{classify.tree}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1910" - } - ] - } - } - ] - ], - "markers": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false, assembler:'spades' ]\n", - "pattern": "*" - } - }, - { - "${prefix}/identify/*.markers_summary.tsv": { - "type": "file", - "description": "A TSV summary file lineage markers used for the classification.", - "pattern": "*.{markers_summary.tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "msa": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false, assembler:'spades' ]\n", - "pattern": "*" - } - }, - { - "${prefix}/align/*.msa.fasta.gz": { - "type": "file", - "description": "Multiple sequence alignments file.", - "pattern": "*.{msa.fasta.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ], - "user_msa": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false, assembler:'spades' ]\n", - "pattern": "*" - } - }, - { - "${prefix}/align/*.user_msa.fasta.gz": { - "type": "file", - "description": "Multiple sequence alignments file for the user-provided files.", - "pattern": "*.{user_msa.fasta.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ], - "filtered": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false, assembler:'spades' ]\n", - "pattern": "*" - } - }, - { - "${prefix}/align/*.filtered.tsv": { - "type": "file", - "description": "A list of genomes with an insufficient number of amino acids in MSA", - "pattern": "*.{filtered.tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "failed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false, assembler:'spades' ]\n", - "pattern": "*" - } - }, - { - "${prefix}/identify/*.failed_genomes.tsv": { - "type": "file", - "description": "A TSV summary of the genomes which GTDB-tk failed to classify.", - "pattern": "*.{failed_genomes.tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false, assembler:'spades' ]\n", - "pattern": "*" - } - }, - { - "${prefix}/${prefix}.log": { - "type": "file", - "description": "GTDB-tk log file", - "pattern": "*.{log}", - "ontologies": [ - { - "edam": "http://edamontology.org/data_3671" - } - ] - } - } - ] - ], - "warnings": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false, assembler:'spades' ]\n", - "pattern": "*" - } - }, - { - "${prefix}/${prefix}.warnings.log": { - "type": "file", - "description": "GTDB-tk warnings log file", - "pattern": "*.{warnings.log}", - "ontologies": [ - { - "edam": "http://edamontology.org/data_3671" - } - ] - } - } - ] - ], - "versions_gtdbtk": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gtdbtk": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gtdbtk --version 2>&1 | grep -Eo '[0-9]+(\\.[0-9]+)+' | head -1": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_gtdbtk_db": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gtdb_db": { - "type": "string", - "description": "The name of the database" - } - }, - { - "grep VERSION_DATA \\$GTDBTK_DATA_PATH/metadata/metadata.txt | sed \"s/VERSION_DATA=//\"": { - "type": "eval", - "description": "The expression to obtain the version of the database" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gtdbtk": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gtdbtk --version 2>&1 | grep -Eo '[0-9]+(\\.[0-9]+)+' | head -1": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gtdb_db": { - "type": "string", - "description": "The name of the database" - } - }, - { - "grep VERSION_DATA \\$GTDBTK_DATA_PATH/metadata/metadata.txt | sed \"s/VERSION_DATA=//\"": { - "type": "eval", - "description": "The expression to obtain the version of the database" - } - } - ] - ] - }, - "authors": [ - "@skrakau", - "@prototaxites", - "@abhi18av" - ], - "maintainers": [ - "@skrakau", - "@abhi18av" - ] - }, - "pipelines": [ - { - "name": "mag", - "version": "5.4.2" - } - ] - }, - { - "name": "gtdbtk_gtdbtoncbimajorityvote", - "path": "modules/nf-core/gtdbtk/gtdbtoncbimajorityvote/meta.yml", - "type": "module", - "meta": { - "name": "gtdbtk_gtdbtoncbimajorityvote", - "description": "Converts the output classifications of GTDB-TK from GTDB taxonomy to NCBI taxonomy", - "keywords": [ - 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"eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "gunzip": { - "type": "string", - "description": "The tool name" - } - }, - { - "gunzip --version 2>&1 | head -1 | sed \"s/^.*(gzip) //; s/ Copyright.*//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "createtaxdb", + "version": "3.0.0" + } ] - ] - }, - "authors": [ - "@joseespinosa", - "@drpatelh", - "@jfy133" - ], - "maintainers": [ - "@joseespinosa", - "@drpatelh", - "@jfy133", - "@gallvp" - ] - }, - "pipelines": [ - { - "name": "atacseq", - "version": "2.1.2" - }, - { - "name": "bacass", - "version": "2.6.0" }, { - "name": "chipseq", - "version": "2.1.0" + "name": "kraken2_build", + "path": "modules/nf-core/kraken2/build/meta.yml", + "type": "module", + "meta": { + "name": "kraken2_build", + "description": "Builds Kraken2 database", + "keywords": ["metagenomics", "db", "classification", "build", "kraken2"], + "tools": [ + { + "kraken2": { + "description": "Kraken2 is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies.", + "homepage": "https://ccb.jhu.edu/software/kraken2/", + "documentation": "https://github.com/DerrickWood/kraken2/wiki/Manual", + "tool_dev_url": "https://github.com/DerrickWood/kraken2", + "doi": "10.1186/s13059-019-1891-0", + "licence": ["MIT"], + "args_id": "$args", + "identifier": "biotools:kraken2" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "library_added_files": { + "type": "file", + "description": "Files present in the /library/added/ directory, including FASTA files, masked FASTAs, and prelim_map files.", + "pattern": "*", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "seqid2taxid_map": { + "type": "file", + "description": "File mapping sequence IDs to taxonomy IDs, either generated or premade.", + "pattern": "seqid2taxid.map", + "ontologies": [ + { + "edam": "http://edamontology.org/data_3028" + } + ] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "taxonomy_files": { + "type": "file", + "description": "Files present in the /taxonomy/ directory, including nodes.dmp, names.dmp, and .accession2taxid files.", + "pattern": "*", + "ontologies": [ + { + "edam": "http://edamontology.org/data_3028" + } + ] + } + } + ], + { + "cleaning": { + "type": "boolean", + "description": "activate or deactivate (true or false) cleaning of intermediate files" + } + } + ], + "output": { + "db": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "kraken2-database": { + "type": "directory", + "description": "Directory contains the database that can be used to perform taxonomic classification\n\nIMPORTANT: this output directory will be hardcoded as 'kraken2-database/' inside the module\nto prevent issues of containers following symlinks in symlinks.\n\nTo give a user the option to provide custom name for the database directory within a pipeline, you should\ncustomise this name using during pipeline output publication via the pipeline's publishDir or workflow output customisation options.\n", + "pattern": "kraken2-database/", + "ontologies": [ + { + "edam": "http://edamontology.org/data_1049" + } + ] + } + } + ] + ], + "db_separated": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "kraken2-database/*k2d": { + "type": "file", + "description": "Kraken2 k2d binary database files", + "pattern": "*.k2d", + "ontologies": [] + } + }, + { + "kraken2-database/*map": { + "type": "file", + "description": "Kraken2 k2d binary database taxonomy to sequencing mapping file", + "pattern": "*.map", + "ontologies": [] + } + }, + { + "kraken2-database/library/added/*": { + "type": "file", + "description": "Kraken2 masked FASTA files used to build the database", + "pattern": "*.fasta", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + }, + { + "kraken2-database/taxonomy/*": { + "type": "file", + "description": "Kraken2 nodes.dmp, names.dmp, and .accession2taxid taxonomy files", + "pattern": "*.{dmp,accession2taxid}", + "ontologies": [ + { + "edam": "http://edamontology.org/data_3028" + } + ] + } + } + ] + ], + "versions_kraken2": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "kraken2": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "kraken2 --version 2>&1 | head -1 | sed \"s/^.*Kraken version //; s/ .*//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "unmapped": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "kraken2-database/unmapped*.txt": { + "type": "file", + "description": "List of unmapped sequence files, i.e. accessions that did not map to any taxonomy ID\nand were excluded\n", + "pattern": "unmapped*.txt", + "ontologies": [ + { + "edam": "http://edamontology.org/data_2526" + } + ] + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "kraken2": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "kraken2 --version 2>&1 | head -1 | sed \"s/^.*Kraken version //; s/ .*//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@alxndrdiaz"], + "maintainers": ["@alxndrdiaz", "@jfy133"] + }, + "pipelines": [ + { + "name": "createtaxdb", + "version": "3.0.0" + } + ] }, { - "name": "cutandrun", - "version": "3.2.2" + "name": "kraken2_buildstandard", + "path": "modules/nf-core/kraken2/buildstandard/meta.yml", + "type": "module", + "meta": { + "name": "kraken2_buildstandard", + "description": "Downloads and builds Kraken2 standard database", + "keywords": ["metagenomics", "db", "classification", "build", "kraken2", "standard", "download"], + "tools": [ + { + "kraken2": { + "description": "Kraken2 is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies.", + "homepage": "https://ccb.jhu.edu/software/kraken2/", + "documentation": "https://github.com/DerrickWood/kraken2/wiki/Manual", + "tool_dev_url": "https://github.com/DerrickWood/kraken2", + "doi": "10.1186/s13059-019-1891-0", + "licence": ["MIT"], + "args_id": "$args", + "identifier": "biotools:kraken2" + } + } + ], + "input": [ + { + "cleaning": { + "type": "boolean", + "description": "activate or deactivate (true or false) cleaning of intermediate files" + } + } + ], + "output": { + "db": [ + { + "${prefix}": { + "type": "directory", + "description": "Directory containing the Kraken2 'standard' database that can be used to perform taxonomic classification", + "pattern": "*/", + "ontologies": [ + { + "edam": "http://edamontology.org/data_1049" + } + ] + } + } + ], + "versions_kraken2": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "kraken2": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "kraken2 --version 2>&1 | head -1 | sed \"s/^.*Kraken version //; s/ .*//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "kraken2": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "kraken2 --version 2>&1 | head -1 | sed \"s/^.*Kraken version //; s/ .*//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@egreenberg7"], + "maintainers": ["@egreenberg7"] + } }, { - "name": "differentialabundance", - "version": "1.5.0" + "name": "kraken2_kraken2", + "path": "modules/nf-core/kraken2/kraken2/meta.yml", + "type": "module", + "meta": { + "name": "kraken2_kraken2", + "description": "Classifies metagenomic sequence data", + "keywords": ["classify", "metagenomics", "fastq", "db"], + "tools": [ + { + "kraken2": { + "description": "Kraken2 is a taxonomic sequence classifier that assigns taxonomic labels to sequence reads\n", + "homepage": "https://ccb.jhu.edu/software/kraken2/", + "documentation": "https://github.com/DerrickWood/kraken2/wiki/Manual", + "doi": "10.1186/s13059-019-1891-0", + "licence": ["MIT"], + "identifier": "biotools:kraken2" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", + "ontologies": [] + } + } + ], + { + "db": { + "type": "directory", + "description": "Kraken2 database" + } + }, + { + "save_output_fastqs": { + "type": "string", + "description": "If true, optional commands are added to save classified and unclassified reads\nas fastq files\n" + } + }, + { + "save_reads_assignment": { + "type": "string", + "description": "If true, an optional command is added to save a file reporting the taxonomic\nclassification of each input read\n" + } + } + ], + "output": { + "classified_reads_fastq": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.classified{.,_}*": { + "type": "file", + "description": "Reads classified as belonging to any of the taxa\non the Kraken2 database.\n", + "pattern": "*{fastq.gz}", + "ontologies": [] + } + } + ] + ], + "unclassified_reads_fastq": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.unclassified{.,_}*": { + "type": "file", + "description": "Reads not classified to any of the taxa\non the Kraken2 database.\n", + "pattern": "*{fastq.gz}", + "ontologies": [] + } + } + ] + ], + "classified_reads_assignment": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*classifiedreads.txt": { + "type": "file", + "description": "Kraken2 output file indicating the taxonomic assignment of\neach input read\n", + "ontologies": [] + } + } + ] + ], + "report": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*report.txt": { + "type": "file", + "description": "Kraken2 report containing stats about classified\nand not classified reads.\n", + "pattern": "*.{report.txt}", + "ontologies": [] + } + } + ] + ], + "versions_kraken2": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "kraken2": { + "type": "string", + "description": "The tool name" + } + }, + { + "kraken2 --version 2>&1 | head -1 | sed \"s/^.*Kraken version //; s/ .*//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_pigz": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "pigz": { + "type": "string", + "description": "The tool name" + } + }, + { + "pigz --version 2>&1 | sed \"s/pigz //g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "kraken2": { + "type": "string", + "description": "The tool name" + } + }, + { + "kraken2 --version 2>&1 | head -1 | sed \"s/^.*Kraken version //; s/ .*//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "pigz": { + "type": "string", + "description": "The tool name" + } + }, + { + "pigz --version 2>&1 | sed \"s/pigz //g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@joseespinosa", "@drpatelh"], + "maintainers": ["@joseespinosa", "@drpatelh"] + }, + "pipelines": [ + { + "name": "ampliseq", + "version": "2.17.0" + }, + { + "name": "bacass", + "version": "2.6.0" + }, + { + "name": "coproid", + "version": "2.0.1" + }, + { + "name": "demultiplex", + "version": "1.7.1" + }, + { + "name": "detaxizer", + "version": "1.3.0" + }, + { + "name": "hgtseq", + "version": "1.1.0" + }, + { + "name": "rnaseq", + "version": "3.26.0" + }, + { + "name": "taxprofiler", + "version": "2.0.0" + }, + { + "name": "viralmetagenome", + "version": "1.1.1" + }, + { + "name": "viralrecon", + "version": "3.0.0" + } + ] }, { - "name": "epitopeprediction", - "version": "3.1.0" + "name": "krakentools_combinekreports", + "path": "modules/nf-core/krakentools/combinekreports/meta.yml", + "type": "module", + "meta": { + "name": "krakentools_combinekreports", + "description": "Takes multiple kraken-style reports and combines them into a single report file", + "keywords": ["kraken", "krakentools", "metagenomics", "table", "combining", "merging"], + "tools": [ + { + "krakentools": { + "description": "KrakenTools is a suite of scripts to be used for post-analysis of Kraken/KrakenUniq/Kraken2/Bracken results. Please cite the relevant paper if using KrakenTools with any of the listed programs.", + "homepage": "https://github.com/jenniferlu717/KrakenTools", + "licence": ["GPL v3"], + "identifier": "biotools:krakentools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "kreports": { + "type": "file", + "description": "List of kraken-style report files", + "pattern": "*.{txt,kreport}", + "ontologies": [] + } + } + ] + ], + "output": { + "txt": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "Combined kreport file of all input files", + "pattern": "*.txt", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@jfy133"], + "maintainers": ["@jfy133"] + }, + "pipelines": [ + { + "name": "taxprofiler", + "version": "2.0.0" + } + ] }, { - "name": "evexplorer", - "version": "dev" + "name": "krakentools_extractkrakenreads", + "path": "modules/nf-core/krakentools/extractkrakenreads/meta.yml", + "type": "module", + "meta": { + "name": "krakentools_extractkrakenreads", + "description": "Extract reads classified at any user-specified taxonomy IDs.", + "keywords": ["kraken2", "krakentools", "metagenomics"], + "tools": [ + { + "krakentools": { + "description": "KrakenTools is a suite of scripts to be used for post-analysis of Kraken/KrakenUniq/Kraken2/Bracken results. Please cite the relevant paper if using KrakenTools with any of the listed programs.", + "homepage": "https://github.com/jenniferlu717/KrakenTools", + "documentation": "https://github.com/jenniferlu717/KrakenTools?tab=readme-ov-file#extract_kraken_readspy", + "tool_dev_url": "https://github.com/jenniferlu717/KrakenTools", + "doi": "10.1038/s41596-022-00738-y", + "licence": ["GPL v3"], + "identifier": "biotools:krakentools" + } + } + ], + "input": [ + { + "taxid": { + "type": "string", + "description": "A list of taxid separated by spaces" + } + }, + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "classified_reads_assignment": { + "type": "file", + "description": "A file contains the taxonomic classification of each input read.", + "pattern": "*.{classifiedreads.txt}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "classified_reads_fastq": { + "type": "file", + "description": "Classified reads as belonging to any of the taxa on the kraken2 database.", + "pattern": "*.{fastq.gz}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "report": { + "type": "file", + "description": "Optional Kraken2 report containing stats about classified and not classified reads.", + "pattern": "*.{report.txt}", + "ontologies": [] + } + } + ] + ], + "output": { + "extracted_kraken2_reads": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.{fastq.gz,fasta.gz}": { + "type": "file", + "description": "Reads assigned to a taxid list.", + "pattern": "*.{fastq.gz,fasta.gz}", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@LilyAnderssonLee"], + "maintainers": ["@LilyAnderssonLee"] + } }, { - "name": "funcprofiler", - "version": "dev" + "name": "krakentools_kreport2krona", + "path": "modules/nf-core/krakentools/kreport2krona/meta.yml", + "type": "module", + "meta": { + "name": "krakentools_kreport2krona", + "description": "Takes a Kraken report file and prints out a krona-compatible TEXT file", + "keywords": ["kraken", "krona", "metagenomics", "visualization"], + "tools": [ + { + "krakentools": { + "description": "KrakenTools is a suite of scripts to be used for post-analysis of Kraken/KrakenUniq/Kraken2/Bracken results. Please cite the relevant paper if using KrakenTools with any of the listed programs.", + "homepage": "https://github.com/jenniferlu717/KrakenTools", + "licence": ["GPL v3"], + "identifier": "biotools:krakentools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "kreport": { + "type": "file", + "description": "Kraken report", + "pattern": "*.{txt,kreport}", + "ontologies": [] + } + } + ] + ], + "output": { + "txt": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "Krona text-based input file converted from Kraken report", + "pattern": "*.{txt,krona}", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@MillironX"], + "maintainers": ["@MillironX"] + }, + "pipelines": [ + { + "name": "taxprofiler", + "version": "2.0.0" + }, + { + "name": "viralmetagenome", + "version": "1.1.1" + } + ] }, { - "name": "funcscan", - "version": "3.0.0" + "name": "krakenuniq_build", + "path": "modules/nf-core/krakenuniq/build/meta.yml", + "type": "module", + "meta": { + "name": "krakenuniq_build", + "description": "Download and build (custom) KrakenUniq databases", + "keywords": ["metagenomics", "krakenuniq", "database", "build", "ncbi"], + "tools": [ + { + "krakenuniq": { + "description": "Metagenomics classifier with unique k-mer counting for more specific results", + "homepage": "https://github.com/fbreitwieser/krakenuniq", + "documentation": "https://github.com/fbreitwieser/krakenuniq", + "tool_dev_url": "https://github.com/fbreitwieser/krakenuniq", + "doi": "10.1186/s13059-018-1568-0", + "licence": ["MIT"], + "identifier": "biotools:KrakenUniq" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "custom_library_dir": { + "type": "file", + "description": "List of custom fasta files for adding to database build", + "pattern": "*" + } + }, + { + "custom_taxonomy_dir": { + "type": "file", + "description": "List of NCBI style taxdmp files (at a minimum: nodes.dmp, names.dmp)\n", + "pattern": "*" + } + }, + { + "custom_seqid2taxid": { + "type": "file", + "description": "Custom seqid2taxid file of mapping sequence accessions to taxid", + "ontologies": [] + } + } + ], + { + "keep_intermediate": { + "type": "boolean", + "description": "Keep intermediate files that are not used by the database itself", + "pattern": "true|false" + } + } + ], + "output": { + "db": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/": { + "type": "directory", + "description": "Directory containing KrakenUniq database", + "pattern": "*/" + } + } + ] + ], + "versions_krakenuniq": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "krakenuniq": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "krakenuniq --version | sed '1!d;s/KrakenUniq version //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "krakenuniq": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "krakenuniq --version | sed '1!d;s/KrakenUniq version //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@jfy133"], + "maintainers": ["@jfy133"] + }, + "pipelines": [ + { + "name": "createtaxdb", + "version": "3.0.0" + } + ] }, { - "name": "genomeannotator", - "version": "dev" + "name": "krakenuniq_download", + "path": "modules/nf-core/krakenuniq/download/meta.yml", + "type": "module", + "meta": { + "name": "krakenuniq_download", + "description": "Download KrakenUniq databases and related fles", + "keywords": ["metagenomics", "krakenuniq", "database", "download", "ncbi"], + "tools": [ + { + "krakenuniq": { + "description": "Metagenomics classifier with unique k-mer counting for more specific results", + "homepage": "https://github.com/fbreitwieser/krakenuniq", + "documentation": "https://github.com/fbreitwieser/krakenuniq", + "tool_dev_url": "https://github.com/fbreitwieser/krakenuniq", + "doi": "10.1186/s13059-018-1568-0", + "licence": ["MIT"], + "identifier": "biotools:KrakenUniq" + } + } + ], + "input": [ + { + "pattern": { + "type": "string", + "description": "Pattern indicating what type of NCBI data to download. See KrakenUniq documnation for possibilities." + } + } + ], + "output": { + "output": [ + { + "${pattern}/": { + "type": "directory", + "description": "Directory containing downloaded data with directory naming being the user provided pattern." + } + } + ], + "versions_krakenuniq": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "krakenuniq": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "krakenuniq --version | sed '1!d;s/KrakenUniq version //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "krakenuniq": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "krakenuniq --version | sed '1!d;s/KrakenUniq version //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@jfy133"], + "maintainers": ["@jfy133"] + } }, { - "name": "genomicrelatedness", - "version": "dev" + "name": "krakenuniq_preloadedkrakenuniq", + "path": "modules/nf-core/krakenuniq/preloadedkrakenuniq/meta.yml", + "type": "module", + "meta": { + "name": "krakenuniq_preloadedkrakenuniq", + "description": "Classifies metagenomic sequence data using unique k-mer counts", + "keywords": ["classify", "metagenomics", "kmers", "fastq", "db"], + "tools": [ + { + "krakenuniq": { + "description": "Metagenomics classifier with unique k-mer counting for more specific results", + "homepage": "https://github.com/fbreitwieser/krakenuniq", + "documentation": "https://github.com/fbreitwieser/krakenuniq", + "doi": "10.1186/s13059-018-1568-0", + "licence": ["MIT"], + "identifier": "biotools:KrakenUniq" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "sequences": { + "type": "file", + "description": "List of input files containing sequences. All of them must be either in FASTA or FASTQ format.", + "ontologies": [] + } + }, + { + "prefixes": { + "type": "string", + "description": "List of sample identifiers or filename prefixes. Must correspond in order and length to the 'sequences', or to the number of sequencing pairs.\n" + } + } + ], + { + "sequence_type": { + "type": "string", + "description": "Format of all given sequencing files as literal string, either 'fasta' or 'fastq'.", + "pattern": "{fasta,fastq}" + } + }, + { + "db": { + "type": "directory", + "description": "KrakenUniq database" + } + }, + { + "save_output_reads": { + "type": "boolean", + "description": "Optionally, commands are added to save classified and unclassified reads\nas FASTQ or FASTA files depending on the input format. When the input\nis paired-end, the single output FASTQ contains merged reads.\n" + } + }, + { + "report_file": { + "type": "boolean", + "description": "Whether to generate a report of relative abundances." + } + }, + { + "save_output": { + "type": "boolean", + "description": "Whether to save a file reporting the taxonomic classification of each input read." + } + } + ], + "output": { + "classified_reads": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.classified.${sequence_type}.gz": { + "type": "file", + "description": "Reads classified as belonging to any of the taxa\nin the KrakenUniq reference database.\n", + "pattern": "*.classified.{fastq,fasta}.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ] + ], + "unclassified_reads": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.unclassified.${sequence_type}.gz": { + "type": "file", + "description": "Reads not classified to any of the taxa\nin the KrakenUniq reference database.\n", + "pattern": "*.unclassified.{fastq,fasta}.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ] + ], + "classified_assignment": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.krakenuniq.classified.txt": { + "type": "file", + "description": "KrakenUniq output file indicating the taxonomic assignment of\neach input read ## DOUBLE CHECK!!\n", + "pattern": "*.krakenuniq.classified.txt", + "ontologies": [] + } + } + ] + ], + "report": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.krakenuniq.report.txt": { + "type": "file", + "description": "KrakenUniq report containing statistics about classified\nand unclassified reads.\n", + "pattern": "*.krakenuniq.report.txt", + "ontologies": [] + } + } + ] + ], + "versions_krakenuniq": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "krakenuniq": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "krakenuniq --version | sed '1!d;s/KrakenUniq version //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "krakenuniq": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "krakenuniq --version | sed '1!d;s/KrakenUniq version //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@mjamy", "@Midnighter"], + "maintainers": ["@mjamy", "@Midnighter"] + }, + "pipelines": [ + { + "name": "taxprofiler", + "version": "2.0.0" + } + ] }, { - "name": "hicar", - "version": "1.0.0" + "name": "krona_kronadb", + "path": "modules/nf-core/krona/kronadb/meta.yml", + "type": "module", + "meta": { + "name": "krona_kronadb", + "description": "KronaTools Update Taxonomy downloads a taxonomy database", + "deprecated": true, + "keywords": ["database", "taxonomy", "krona"], + "tools": [ + { + "krona": { + "description": "Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files.", + "homepage": "https://github.com/marbl/Krona/wiki/KronaTools", + "documentation": "https://github.com/marbl/Krona/wiki/Installing", + "doi": "10.1186/1471-2105-12-385", + "identifier": "biotools:krona" + } + } + ], + "output": { + "db": [ + { + "taxonomy/taxonomy.tab": { + "type": "file", + "description": "A TAB separated file that contains a taxonomy database.", + "pattern": "*.{tab}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@mjakobs"], + "maintainers": ["@mjakobs"] + } }, { - "name": "hlatyping", - "version": "2.2.0" + "name": "krona_ktimportkrona", + "path": "modules/nf-core/krona/ktimportkrona/meta.yml", + "type": "module", + "meta": { + "name": "krona_ktimportkrona", + "description": "Collect multiple krona reports into a single html file", + "keywords": ["plot", "taxonomy", "interactive", "html", "visualisation", "krona chart"], + "tools": [ + { + "krona": { + "description": "Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files.", + "homepage": "https://github.com/marbl/Krona/wiki/KronaTools", + "documentation": "http://manpages.ubuntu.com/manpages/impish/man1/ktImportTaxonomy.1.html", + "doi": "10.1186/1471-2105-12-385", + "identifier": "biotools:krona" + } + } + ], + "input": [ + { + "html": { + "type": "file", + "description": "One or multiple html files each containing a krona single plot", + "pattern": "*.html", + "ontologies": [] + } + } + ], + "output": { + "html": [ + { + "${prefix}.html": { + "type": "file", + "description": "HTML file containing all input HTML Krona plots with a selection bar to choose which one to look at", + "pattern": "*.krona.html" + } + } + ], + "versions_krona": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "krona": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "ktImportKrona | grep -Po '(?<=KronaTools )[0-9.]+'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "krona": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "ktImportKrona | grep -Po '(?<=KronaTools )[0-9.]+'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@paulwolk"], + "maintainers": ["@paulwolk"] + } }, { - "name": "isoseq", - "version": "2.0.0" + "name": "krona_ktimporttaxonomy", + "path": "modules/nf-core/krona/ktimporttaxonomy/meta.yml", + "type": "module", + "meta": { + "name": "krona_ktimporttaxonomy", + "description": "KronaTools Import Taxonomy imports taxonomy classifications and produces an interactive Krona plot.", + "keywords": ["plot", "taxonomy", "interactive", "html", "visualisation", "krona chart"], + "tools": [ + { + "krona": { + "description": "Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files.", + "homepage": "https://github.com/marbl/Krona/wiki/KronaTools", + "documentation": "http://manpages.ubuntu.com/manpages/impish/man1/ktImportTaxonomy.1.html", + "doi": "10.1186/1471-2105-12-385", + "identifier": "biotools:krona" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "report": { + "type": "file", + "description": "A tab-delimited file with taxonomy IDs and (optionally) query IDs, magnitudes, and scores. Query IDs are taken from column 1, taxonomy IDs from column 2, and scores from column 3. Lines beginning with # will be ignored.", + "pattern": "*.{tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + { + "taxonomy": { + "type": "file", + "description": "Path to a Krona taxonomy .tab file normally downloaded and generated by\nkrona/ktUpdateTaxonomy. Custom taxonomy files can have any name, but\nmust end in `.tab`.\n", + "pattern": "*tab", + "ontologies": [] + } + } + ], + "output": { + "html": [ + [ + { + "meta": { + "type": "file", + "description": "A html file containing an interactive krona plot.", + "pattern": "*.{html}", + "ontologies": [] + } + }, + { + "*.html": { + "type": "file", + "description": "A html file containing an interactive krona plot.", + "pattern": "*.{html}", + "ontologies": [] + } + } + ] + ], + "versions_krona": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "krona": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "ktImportTaxonomy | grep -Po '(?<=KronaTools )[0-9.]+'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "krona": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "ktImportTaxonomy | grep -Po '(?<=KronaTools )[0-9.]+'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@mjakobs"], + "maintainers": ["@mjakobs"] + }, + "pipelines": [ + { + "name": "hgtseq", + "version": "1.1.0" + }, + { + "name": "taxprofiler", + "version": "2.0.0" + } + ] }, { - "name": "lncpipe", - "version": "dev" + "name": "krona_ktimporttext", + "path": "modules/nf-core/krona/ktimporttext/meta.yml", + "type": "module", + "meta": { + "name": "krona_ktimporttext", + "description": "Creates a Krona chart from text files listing quantities and lineages.", + "keywords": ["plot", "taxonomy", "interactive", "html", "visualisation", "krona chart", "metagenomics"], + "tools": [ + { + "krona": { + "description": "Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files.", + "homepage": "https://github.com/marbl/Krona/wiki/KronaTools", + "documentation": "http://manpages.ubuntu.com/manpages/impish/man1/ktImportTaxonomy.1.html", + "tool_dev_url": "https://github.com/marbl/Krona", + "doi": "10.1186/1471-2105-12-385", + "licence": ["https://raw.githubusercontent.com/marbl/Krona/master/KronaTools/LICENSE.txt"], + "identifier": "biotools:krona" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "report": { + "type": "file", + "description": "Tab-delimited text file. Each line should be a number followed by a list of wedges to contribute to (starting from the highest level). If no wedges are listed (and just a quantity is given), it will contribute to the top level. If the same lineage is listed more than once, the values will be added. Quantities can be omitted if -q is specified. Lines beginning with '#' will be ignored.", + "pattern": "*.{txt}", + "ontologies": [] + } + } + ] + ], + "output": { + "html": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.html": { + "type": "file", + "description": "A html file containing an interactive krona plot.", + "pattern": "*.{html}", + "ontologies": [] + } + } + ] + ], + "versions_krona": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "krona": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "ktImportText | grep -Po '(?<=KronaTools )[0-9.]+'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "krona": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "ktImportText | grep -Po '(?<=KronaTools )[0-9.]+'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@jianhong"], + "maintainers": ["@jianhong"] + }, + "pipelines": [ + { + "name": "taxprofiler", + "version": "2.0.0" + }, + { + "name": "viralmetagenome", + "version": "1.1.1" + } + ] }, { - 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May be compressed with gzip.\n", + "pattern": "*.{fasta,fasta.gz,fastq,fastq.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ] + ], + "output": { + "index": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "lastdb": { + "type": "directory", + "description": "directory containing the files of the LAST index", + "pattern": "lastdb/" + } + } + ] + ], + "versions_last": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "last": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "lastal --version | sed 's/lastal //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "last": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "lastal --version | sed 's/lastal //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@charles-plessy"], + "maintainers": ["@charles-plessy"] + }, + "pipelines": [ + { + "name": "pairgenomealign", + "version": "2.2.3" + }, + { + "name": "raredisease", + "version": "3.0.0" + } + ] }, { - "name": "nascent", - "version": "2.3.0" + "name": "last_mafconvert", + "path": "modules/nf-core/last/mafconvert/meta.yml", + "type": "module", + "meta": { + "name": "last_mafconvert", + "description": "Converts MAF alignments in another format.", + "keywords": ["LAST", "convert", "alignment", "MAF"], + "tools": [ + { + "last": { + "description": "LAST finds & aligns related regions of sequences.", + "homepage": "https://gitlab.com/mcfrith/last", + "documentation": "https://gitlab.com/mcfrith/last/-/blob/main/doc/", + "tool_dev_url": "https://gitlab.com/mcfrith/last", + "licence": ["GPL v3-or-later"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "maf": { + "type": "file", + "description": "Multiple Alignment Format (MAF) file, optionally compressed with gzip", + "pattern": "*.{maf.gz,maf}", + "ontologies": [] + } + }, + { + "format": { + "type": "string", + "description": "Output format (one of axt, bam, blast, blasttab, cram, chain, gff, html, psl, sam, or tab)" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Genome file in FASTA format for CRAM conversion. If compressed it must be done in BGZF format (like with the bgzip tool).", + "pattern": "*.{fasta,fasta.gz,fasta.bgz,fasta.bgzf}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "fai": { + "type": "file", + "description": "Genome index file needed for CRAM conversion.", + "pattern": "*.fai", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "gzi": { + "type": "file", + "description": "Genome index file needed for CRAM conversion when the genome file was compressed with the BGZF algorithm.", + "pattern": "*.gzi", + "ontologies": [] + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "dict": { + "type": "file", + "description": "Samtools dictionary of the genome file.", + "pattern": "*.dict", + "ontologies": [] + } + } + ] + ], + "output": { + "alignment": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.{axt.gz,bam,bed.gz,blast.gz,blasttab.gz,chain.gz,cram,gff.gz,html.gz,psl.gz,sam.gz,tab.gz}": { + "type": "file", + "description": "Pairwise alignment exported to Axt, BAM, BED, BLAST, Chain, CRAM, GFF, HTML PSL, SAM or Tab format.", + "pattern": "*.{axt.gz,bam,bed.gz,blast.gz,blasttab.gz,chain.gz,cram,gff.gz,html.gz,psl.gz,sam.gz,tab.gz}", + "ontologies": [] + } + } + ] + ], + "versions_last": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "last": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "lastal --version | sed 's/lastal //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "last": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "lastal --version | sed 's/lastal //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@aleksandrabliznina", "@charles-plessy"], + "maintainers": ["@charles-plessy"] + }, + "pipelines": [ + { + "name": "pairgenomealign", + "version": "2.2.3" + } + ] }, { - "name": "pacsomatic", - "version": "dev" + "name": "last_mafswap", + "path": "modules/nf-core/last/mafswap/meta.yml", + "type": "module", + "meta": { + "name": "last_mafswap", + "description": "Reorder alignments in a MAF file", + "keywords": ["LAST", "reorder", "alignment", "MAF"], + "tools": [ + { + "last": { + "description": "LAST finds & aligns related regions of 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masking", + "keywords": ["LAST", "mask", "alignment", "MAF"], + "tools": [ + { + "last": { + "description": "LAST finds & aligns related regions of sequences.", + "homepage": "https://gitlab.com/mcfrith/last", + "documentation": "https://gitlab.com/mcfrith/last/-/blob/main/doc/last-postmask.rst", + "tool_dev_url": "https://gitlab.com/mcfrith/last", + "doi": "10.1371/journal.pone.0028819", + "licence": ["GPL v3-or-later"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "maf": { + "type": "file", + "description": "Multiple Alignment Format (MAF) file, optionally compressed with gzip", + "pattern": "*.{maf.gz,maf}", + "ontologies": [] + } + } + ] + ], + "output": { + "maf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + 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{ + "primers": { + "type": "file", + "description": "Fasta file, sequences of primers", + "pattern": "*.fasta", + "ontologies": [] + } + } + ], + "output": { + "counts": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.counts": { + "type": "file", + "description": "A tabulated file of describing pairs of primers", + "pattern": "*.counts", + "ontologies": [] + } + } + ] + ], + "report": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.report": { + "type": "file", + "description": "A tab-separated file about each ZMW, unfiltered", + "pattern": "*.report", + "ontologies": [] + } + } + ] + ], + "summary": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.summary": { + "type": "file", + "description": "This file shows how many ZMWs have been filtered, how ZMWs many are same/different, and how many reads have been filtered.", + "pattern": "*.summary", + "ontologies": [] + } + } + ] + ], + "versions_lima": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "lima": { + "type": "string", + "description": "The tool name" + } + }, + { + "lima --version | head -n1 | sed 's/lima //g' | sed 's/ (.\\+//g'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ], + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "A bam file of ccs purged of primers", + "pattern": "*.bam", + "ontologies": [] + } + } + ] + ], + "pbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.bam.pbi": { + "type": "file", + "description": "Pacbio index file of ccs purged of primers", + "pattern": "*.bam", + "ontologies": [] + } + } + ] + ], + "fasta": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.{fa,fasta}": { + "type": "file", + "description": "A fasta file of ccs purged of primers.", + "pattern": "*.fa", + "ontologies": [] + } + } + ] + ], + "fastagz": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.{fa.gz,fasta.gz}": { + "type": "file", + "description": "A fasta.gz file of ccs purged of primers.", + "pattern": "*.fasta.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "fastq": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.fastq": { + "type": "file", + "description": "A fastq file of ccs purged of primers.", + "pattern": "*.fastq", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ] + ], + "fastqgz": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.fastq.gz": { + "type": "file", + "description": "A fastq.gz file of ccs purged of primers.", + "pattern": "*.fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "xml": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.xml": { + "type": "file", + "description": "An XML file representing a set of a particular sequence data type such as subreads, references or aligned subreads.", + "pattern": "*.xml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2332" + } + ] + } + } + ] + ], + "json": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.json": { + "type": "file", + "description": "A metadata json file", + "pattern": "*.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "clips": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.clips": { + "type": "file", + "description": "A fasta file of clipped primers", + "pattern": "*.clips", + "ontologies": [] + } + } + ] + ], + "guess": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.guess": { + "type": "file", + "description": "A second tabulated file of describing pairs of primers (no doc available)", + "pattern": "*.guess", + "ontologies": [] + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "lima": { + "type": "string", + "description": "The tool name" + } + }, + { + "lima --version | head -n1 | sed 's/lima //g' | sed 's/ (.\\+//g'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@sguizard"], + "maintainers": ["@sguizard"] + }, + "pipelines": [ + { + "name": "genomeassembler", + "version": "1.1.0" + }, + { + "name": "isoseq", + "version": "2.0.0" + }, + { + "name": "pacvar", + "version": "1.0.1" + } + ] }, { - "name": "rnasplice", - "version": "1.0.4" + "name": "limma_differential", + "path": "modules/nf-core/limma/differential/meta.yml", + "type": "module", + "meta": { + "name": "limma_differential", + "description": "runs a differential expression analysis with Limma", + "keywords": ["differential", "expression", "microarray", "limma"], + "tools": [ + { + "limma": { + "description": "Linear Models for Microarray Data", + "homepage": "https://bioconductor.org/packages/release/bioc/html/limma.html", + "documentation": "https://bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf", + "tool_dev_url": "https://github.com/cran/limma\"\"", + "doi": "10.18129/B9.bioc.limma", + "licence": ["LGPL >=3"], + "identifier": "biotools:limma" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing contrast information. This can be used at the\nworkflow level to pass optional parameters to the module, e.g.\n[ id:'contrast1', blocking:'patient' ] passed in as ext.args like:\n'--blocking_variable $meta.blocking'.\n" + } + }, + { + "contrast_variable": { + "type": "string", + "description": "(Optional, required if reference and target are used) The column in the sample sheet that should be used to define groups for\ncomparison\n" + } + }, + { + "reference": { + "type": "string", + "description": "(Optional, required if contrast_variable and target are used) The value within the contrast_variable column of the sample sheet that\nshould be used to derive the reference samples\n" + } + }, + { + "target": { + "type": "string", + "description": "(Optional, required if contrast_variable and reference are used) The value within the contrast_variable column of the sample sheet that\nshould be used to derive the target samples\n" + } + }, + { + "formula": { + "type": "string", + "description": "(Optional, requires comparison if used) R formula string used for modeling, e.g. '~ treatment'." + } + }, + { + "comparison": { + "type": "string", + "description": "(Optional, mandatory if formula is used) Literal string passed to `limma::makeContrasts`, e.g. 'treatmentmCherry'." + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy map containing study-wide metadata related to the sample sheet\nand matrix\n" + } + }, + { + "samplesheet": { + "type": "file", + "description": "Sample sheet file", + "ontologies": [] + } + }, + { + "intensities": { + "type": "file", + "description": "Raw TSV or CSV format expression matrix with probes by row and samples\nby column\n", + "ontologies": [] + } + } + ] + ], + "output": { + "results": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing contrast information. This can be used at the\nworkflow level to pass optional parameters to the module, e.g.\n[ id:'contrast1', blocking:'patient' ] passed in as ext.args like:\n'--blocking_variable $meta.blocking'.\n" + } + }, + { + "*.limma.results.tsv": { + "type": "file", + "description": "TSV-format table of differential expression information as output by Limma", + "pattern": "*.limma.results.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "md_plot": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing contrast information. This can be used at the\nworkflow level to pass optional parameters to the module, e.g.\n[ id:'contrast1', blocking:'patient' ] passed in as ext.args like:\n'--blocking_variable $meta.blocking'.\n" + } + }, + { + "*.limma.mean_difference.png": { + "type": "file", + "description": "Limma mean difference plot", + "pattern": "*.mean_difference.png", + "ontologies": [] + } + } + ] + ], + "rdata": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing contrast information. This can be used at the\nworkflow level to pass optional parameters to the module, e.g.\n[ id:'contrast1', blocking:'patient' ] passed in as ext.args like:\n'--blocking_variable $meta.blocking'.\n" + } + }, + { + "*.MArrayLM.limma.rds": { + "type": "file", + "description": "Serialised MArrayLM object", + "pattern": "*.MArrayLM.limma.rds", + "ontologies": [] + } + } + ] + ], + "model": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing contrast information. This can be used at the\nworkflow level to pass optional parameters to the module, e.g.\n[ id:'contrast1', blocking:'patient' ] passed in as ext.args like:\n'--blocking_variable $meta.blocking'.\n" + } + }, + { + "*.limma.model.txt": { + "type": "file", + "description": "TXT-format limma model", + "pattern": "*.limma.model.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "session_info": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing contrast information. This can be used at the\nworkflow level to pass optional parameters to the module, e.g.\n[ id:'contrast1', blocking:'patient' ] passed in as ext.args like:\n'--blocking_variable $meta.blocking'.\n" + } + }, + { + "*.R_sessionInfo.log": { + "type": "file", + "description": "dump of R SessionInfo", + "pattern": "*.log", + "ontologies": [] + } + } + ] + ], + "normalised_counts": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing contrast information. This can be used at the\nworkflow level to pass optional parameters to the module, e.g.\n[ id:'contrast1', blocking:'patient' ] passed in as ext.args like:\n'--blocking_variable $meta.blocking'.\n" + } + }, + { + "*.normalised_counts.tsv": { + "type": "file", + "description": "normalised TSV format expression matrix with probes by row and samples by column", + "pattern": "*.normalised_counts.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "topics": { + "versions": [ + { + "versions.yml": { + "type": "string", + "description": "The name of the process" + } + } + ] + }, + "authors": ["@pinin4fjords"], + "maintainers": ["@pinin4fjords"] + }, + "pipelines": [ + { + "name": "differentialabundance", + "version": "1.5.0" + } + ] }, { - "name": "rnavar", - "version": "1.2.3" + "name": "links", + "path": "modules/nf-core/links/meta.yml", + "type": "module", + "meta": { + "name": "links", + "description": "LINKS is a genomics application for scaffolding genome assemblies with long reads,\nsuch as those produced by Oxford Nanopore Technologies Ltd.\nIt can be used to scaffold high-quality draft genome assemblies with any long sequences\n(eg. ONT reads, PacBio reads, other draft genomes, etc).\nIt is also used to scaffold contig pairs linked by ARCS/ARKS.\nThis module is for LINKS >=2.0.0 and does not support MPET input.\n", + "keywords": ["scaffold", "long-reads", "genomics"], + "tools": [ + { + "links": { + "description": "Long Interval Nucleotide K-mer Scaffolder", + "homepage": "https://www.bcgsc.ca/resources/software/links", + "documentation": "https://github.com/bcgsc/LINKS", + "tool_dev_url": "https://github.com/bcgsc/LINKS", + "doi": "10.1186/s13742-015-0076-3", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "assembly": { + "type": "file", + "description": "(Multi-)fasta file containing the draft assembly", + "pattern": "*.{fa,fasta,fa.gz,fasta.gz}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "reads": { + "type": "file", + "description": "fastq file(s) containing the long reads to be used for scaffolding", + "pattern": "*.{fq,fastq,fq.gz,fastq.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ] + ], + "output": { + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "*.log": { + "type": "file", + "description": "text file; Logs execution time / errors / pairing stats.", + "pattern": "*.log", + "ontologies": [] + } + } + ] + ], + "pairing_distribution": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "*.pairing_distribution.csv": { + "type": "file", + "description": "comma-separated file; 1st column is the calculated distance\nfor each pair (template) with reads that assembled logically\nwithin the same contig. 2nd column is the number of pairs at\nthat distance.\n", + "pattern": "*.pairing_distribution.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "pairing_issues": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "*.pairing_issues": { + "type": "file", + "description": "text file; Lists all pairing issues encountered between contig\npairs and illogical/out-of-bounds pairing.\n", + "pattern": "*.pairing_issues", + "ontologies": [] + } + } + ] + ], + "scaffolds_csv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "*.scaffolds": { + "type": "file", + "description": "comma-separated file; containing the new scaffold(s)", + "pattern": "*.scaffolds", + "ontologies": [] + } + } + ] + ], + "scaffolds_fasta": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "*.scaffolds.fa": { + "type": "file", + "description": "fasta file of the new scaffold sequence", + "pattern": "*.scaffolds.fa", + "ontologies": [] + } + } + ] + ], + "bloom": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "*.bloom": { + "type": "file", + "description": "Bloom filter created by shredding the -f input\ninto k-mers of size -k\n", + "pattern": "*.bloom", + "ontologies": [] + } + } + ] + ], + "scaffolds_graph": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "*.gv": { + "type": "file", + "description": "scaffold graph (for visualizing merges), can be rendered\nin neato, graphviz, etc\n", + "pattern": "*.gv", + "ontologies": [] + } + } + ] + ], + "assembly_correspondence": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "*.assembly_correspondence.tsv": { + "type": "file", + "description": "correspondence file lists the scaffold ID,\ncontig ID, original_name, #linking kmer pairs,\nlinks ratio, gap or overlap\n", + "pattern": "*.assembly_correspondence.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "simplepair_checkpoint": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "*.simplepair_checkpoint.tsv": { + "type": "file", + "description": "checkpoint file, contains info to rebuild datastructure for .gv graph", + "pattern": "*.simplepair_checkpoint.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "tigpair_checkpoint": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "*.tigpair_checkpoint.tsv": { + "type": "file", + "description": "if -b BASNAME.tigpair_checkpoint.tsv is present,\nLINKS will skip the kmer pair extraction and contig pairing stages.\nDelete this file to force LINKS to start at the beginning.\nThis file can be used to:\n1) quickly test parameters (-l min. links / -a min. links ratio),\n2) quickly recover from crash,\n3) explore very large kmer spaces,\n4) scaffold with output of ARCS\n", + "pattern": "*.tigpair_checkpoint.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_links": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "liftoff": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "echo \\$(LINKS | grep -o 'LINKS v.*' | sed 's/LINKS v//')": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "liftoff": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "echo \\$(LINKS | grep -o 'LINKS v.*' | sed 's/LINKS v//')": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@nschan"], + "maintainers": ["@nschan"] + }, + "pipelines": [ + { + "name": "genomeassembler", + "version": "1.1.0" + } + ] }, { - "name": "sammyseq", - "version": "dev" + "name": "lissero", + "path": "modules/nf-core/lissero/meta.yml", + "type": "module", + "meta": { + "name": "lissero", + "description": "Serogrouping Listeria monocytogenes assemblies", + "keywords": ["fasta", "Listeria monocytogenes", "serogroup"], + "tools": [ + { + "lissero": { + "description": "In silico serotyping of Listeria monocytogenes", + "homepage": "https://github.com/MDU-PHL/LisSero/blob/master/README.md", + "documentation": "https://github.com/MDU-PHL/LisSero/blob/master/README.md", + "tool_dev_url": "https://github.com/MDU-PHL/lissero", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA assembly file", + "pattern": "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}", + "ontologies": [] + } + } + ] + ], + "output": { + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "Tab-delimited result file", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@rpetit3"], + "maintainers": ["@rpetit3"] + } }, { - "name": "sarek", - "version": "3.8.1" + "name": "llamacpppython_run", + "path": "modules/nf-core/llamacpppython/run/meta.yml", + "type": "module", + "meta": { + "name": "llamacpppython_run", + "description": "Python wrapper for running locally-hosted LLM with llama.cpp", + "keywords": ["inference", "llama", "llm", "local-inference", "offline-llm"], + "tools": [ + { + "llama-cpp-python": { + "description": "Python wrapper for llama.cpp LLM inference tool", + "homepage": "https://llama-cpp-python.readthedocs.io/en/latest/", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + 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], - { - "format": { - "type": "string", - "description": "Type of report file to be produced", - "pattern": "tsv|json" + }, + { + "name": "longphase_haplotag", + "path": "modules/nf-core/longphase/haplotag/meta.yml", + "type": "module", + "meta": { + "name": "longphase_haplotag", + "description": "LongPhase is an ultra-fast program for simultaneously co-phasing SNPs, small indels, large SVs, and (5mC) modifications for Nanopore and PacBio platforms.", + "keywords": ["haplotag", "long-read", "genomics"], + "tools": [ + { + "longphase": { + "description": "LongPhase is an ultra-fast program for simultaneously co-phasing SNPs, small indels, large SVs, and (5mC) modifications for Nanopore and PacBio platforms.", + "homepage": "https://github.com/twolinin/longphase", + "documentation": "https://github.com/twolinin/longphase", + "tool_dev_url": "https://github.com/twolinin/longphase", + "doi": "10.1093/bioinformatics/btac058", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "bam": { + "type": "file", + "description": "Sorted BAM/CRAM file", + "pattern": "*.{bam,cram}", + "ontologies": [] + } + }, + { + "bai": { + "type": "file", + "description": "Index of sorted BAM/CRAM file", + "pattern": "*.{bai,crai,csi}", + "ontologies": [] + } + }, + { + "snps": { + "type": "file", + "description": "VCF file with SNPs (and INDELs)", + "pattern": "*.{vcf,vcf.gz}", + "ontologies": [] + } + }, + { + "svs": { + "type": "file", + "description": "VCF file with SVs", + "pattern": "*.{vcf,vcf.gz}", + "ontologies": [] + } + }, + { + "mods": { + "type": "file", + "description": "modcall-generated VCF with modifications", + "pattern": "*.{vcf,vcf.gz}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. `[ id:'hg38' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference fasta file", + "pattern": "*.fasta", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. `[ id:'hg38' ]`\n" + } + }, + { + "fai": { + "type": "file", + "description": "Reference fai index", + "pattern": "*.fai", + "ontologies": [] + } + } + ] + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.{bam,cram}": { + "type": "file", + "description": "BAM file with haplotagged reads", + "pattern": "*.bam", + "ontologies": [] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.log": { + "type": "file", + "description": "Log file", + "pattern": "*.log", + "ontologies": [] + } + } + ] + ], + "versions_longphase": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "longphase": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "longphase --version | head -n 1 | sed 's/Version: //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "longphase": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "longphase --version | head -n 1 | sed 's/Version: //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@fellen31"], + "maintainers": ["@fellen31"] } - 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}, - { - "reference_db_version": { - "type": "string", - "description": "Database version of ncbi_AMRfinder used", - "pattern": "[0-9]-[0-9]-[0-9].[0-9]" - } - } - ], - "output": { - "json": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.json": { - "type": "file", - "description": "hAMRonised report in JSON format", - "pattern": "*.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "hAMRonised report in TSV format", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_hamronization": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "hamronization": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "hamronize --version 2>&1 | sed 's/hamronize //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "hamronization": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "hamronize --version 2>&1 | sed 's/hamronize //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@louperelo" - ], - "maintainers": [ - "@louperelo" - ] - }, - "pipelines": [ - { - "name": "funcscan", - "version": "3.0.0" - } - ] - }, - { - "name": "hamronization_deeparg", - "path": "modules/nf-core/hamronization/deeparg/meta.yml", - "type": "module", - "meta": { - "name": "hamronization_deeparg", - "description": "Tool to convert and summarize DeepARG outputs using the hAMRonization specification", - "keywords": [ - "amr", - "antimicrobial resistance", - "reporting", - "deeparg" - ], - "tools": [ - { - "hamronization": { - "description": "Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification", - "homepage": "https://github.com/pha4ge/hAMRonization/", - "documentation": "https://github.com/pha4ge/hAMRonization/", - "tool_dev_url": "https://github.com/pha4ge/hAMRonization", - "licence": [ - "GNU Lesser General Public v3 (LGPL v3)" - ], - "identifier": "biotools:hamronization" + }, + { + "name": "longstitch", + "path": "modules/nf-core/longstitch/meta.yml", + "type": "module", + "meta": { + "name": "longstitch", + "description": "\"A genome assembly correction and scaffolding pipeline using long reads, consisting of up to three steps:\n - Tigmint cuts the draft assembly at potentially misassembled regions\n - ntLink is then used to scaffold the corrected assembly\n - followed by ARKS for further scaffolding (optional)\"\n", + "keywords": ["scaffolding", "long read", "assembly correction"], + "tools": [ + { + "longstitch": { + "description": "A genome assembly correction and scaffolding pipeline using long reads", + "homepage": "https://github.com/bcgsc/longstitch", + "documentation": "https://github.com/bcgsc/longstitch", + "tool_dev_url": "https://github.com/bcgsc/longstitch", + "doi": "10.1186/s12859-021-04451-7", + "licence": ["GPL v3-or-later", "GPL v3"], + "identifier": "biotools:longstitch" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "assembly": { + "type": "file", + "description": "Draft assembly", + "pattern": "*.{fa,fasta,fa.gz,fasta.gz}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "reads": { + "type": "file", + "description": "long reads", + "pattern": "*.{fq,fastq,fq.gz,fastq.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ], + { + "command": { + "type": "string", + "description": "Longstitch command to run. Valid options are:\n[\"run\", \"tigmint-ntLink-arks\", \"tigmint-ntLink\", \"ntLink-arks\"]\n" + } + }, + { + "span": { + "type": "string", + "description": "min number of spanning molecules to be considered correctly assembled.\nEither span or genomesize need to be provided.\n" + } + }, + { + "genomesize": { + "type": "string", + "description": "Expected genome size. Either span or genomesize need to be provided.\n" + } + }, + { + "longmap": { + "type": "string", + "description": "Type of long-read (passed to minimap2). Valid options are:\n[ \"ont\", \"pb\", \"hifi\" ]\n" + } + } + ], + "output": { + "tigmint_ntLink_fasta": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.tigmint-ntLink.fa": { + "type": "file", + "description": "Fasta file after tigmint and ntLink", + "pattern": "*.tigmint-ntLink.fa", + "ontologies": [] + } + } + ] + ], + "tigmint_ntLink_arcs_fasta": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.tigmint-ntLink-arks.fa": { + "type": "file", + "description": "Fasta file after tigmint, ntLink and arcs+links", + "pattern": "*.tigmint-ntLink-arks.fa", + "ontologies": [] + } + } + ] + ], + "ntLink_arcs_fasta": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.ntLink-arks.fa": { + "type": "file", + "description": "Fasta file after ntLink and arcs+links", + "pattern": "*.ntLink-arks.fa", + "ontologies": [] + } + } + ] + ], + "scaffold_dot": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*k*.w*.z*.n*.scaffold.dot": { + "type": "file", + "description": "Scaffold dot file", + "pattern": "*k*.w*.z*.n*.scaffold.dot", + "ontologies": [] + } + } + ] + ], + "links_scaffolds_dist_gv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*k*.w*.z*.ntLink.scaffolds_*.dist.gv": { + "type": "file", + "description": "ntLink scaffold distance gv file", + "pattern": "*k*.w*.z*.ntLink.scaffolds_*.dist.gv", + "ontologies": [] + } + } + ] + ], + "links_assembly_correspondence_tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*k*.w*.z*.ntLink.scaffolds_*_l*.assembly_correspondence.tsv": { + "type": "file", + "description": "ntLink assembly correspondance table", + "pattern": "*k*.w*.z*.ntLink.scaffolds_*_l*.assembly_correspondence.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "links_gv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*k*.w*.z*.ntLink.scaffolds_*_l*.gv": { + "type": "file", + "description": "Links graph", + "pattern": "*k*.w*.z*.ntLink.scaffolds_*_l*.gv", + "ontologies": [] + } + } + ] + ], + "links_log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*k*.w*.z*.ntLink.scaffolds_*_l*.log": { + "type": "file", + "description": "Links logfile", + "pattern": "*k*.w*.z*.ntLink.scaffolds_*_l*.log", + "ontologies": [] + } + } + ] + ], + "links_scaffolds": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*k*.w*.z*.ntLink.scaffolds_*_l*.scaffolds": { + "type": "file", + "description": "links scaffolds", + "pattern": "*k*.w*.z*.ntLink.scaffolds_*_l*.scaffolds", + "ontologies": [] + } + } + ] + ], + "links_scaffolds_fa": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*k*.w*.z*.ntLink.scaffolds_*_l*.scaffolds.fa": { + "type": "file", + "description": "links scaffolds fasta", + "pattern": "*k*.w*.z*.ntLink.scaffolds_*_l*.scaffolds.fa", + "ontologies": [] + } + } + ] + ], + "links_checkpoint_tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*k*.w*.z*.ntLink.scaffolds_*_l*.*.tigpair_checkpoint.tsv": { + "type": "file", + "description": "tigpair checkpoint for links", + "pattern": "*k*.w*.z*.ntLink.scaffolds_*_l*.tigpair_checkpoint.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "arcs_tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*k*.w*.z*.ntLink.scaffolds_*_main.tsv": { + "type": "file", + "description": "arcs tsv file", + "pattern": "*k*.w*.z*.ntLink.scaffolds_*_main.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "arcs_gv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*k*.w*.z*.ntLink.scaffolds_*_original.gv": { + "type": "file", + "description": "arcs graph", + "pattern": "*k*.w*.z*.ntLink.scaffolds_*_original.gv", + "ontologies": [] + } + } + ] + ], + "arcs_checkpoint_tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*k*.w*.z*.ntLink.scaffolds_*.tigpair_checkpoint.tsv": { + "type": "file", + "description": "tigpair checkpoint for arcs", + "pattern": "*k*.w*.z*.ntLink.scaffolds_*.tigpair_checkpoint.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "arcs_scaffolds_fa": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*k*.w*.z*.ntLink.scaffolds.fa": { + "type": "file", + "description": "arcs scaffolds fasta", + "pattern": "*k*.w*.z*.ntLink.scaffolds.fa", + "ontologies": [] + } + } + ] + ], + "arcs_scaffolds_renamed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*k*.w*.z*.ntLink.scaffolds.renamed.fa": { + "type": "file", + "description": "renamed arcs scaffolds fasta file", + "pattern": "*k*.w*.z*.ntLink.scaffolds.renamed.fa", + "ontologies": [] + } + } + ] + ], + "abyss_scaffolds_fa": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*k*.w*.z*.stitch.abyss-scaffold.fa": { + "type": "file", + "description": "abyss scaffolds fasta file", + "pattern": "*k*.w*.z*.stitch.abyss-scaffold.fa", + "ontologies": [] + } + } + ] + ], + "stitch_path": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*k*.w*.z*.stitch.path": { + "type": "file", + "description": "stitch paths", + "pattern": "*k*.w*.z*.stitch.path", + "ontologies": [] + } + } + ] + ], + "trimmed_scaffolds_agp": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*k*.w*.z*.trimmed_scafs.agp": { + "type": "file", + "description": "trimmed scaffolds in agp format", + "pattern": "*k*.w*.z*.trimmed_scafs.agp", + "ontologies": [] + } + } + ] + ], + "trimmed_scaffolds_fasta": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*k*.w*.z*.trimmed_scafs.fa": { + "type": "file", + "description": "trimmed scaffolds in fasta format", + "pattern": "*k*.w*.z*.trimmed_scafs.fa", + "ontologies": [] + } + } + ] + ], + "trimmed_scaffolds_path": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*k*.w*.z*.trimmed_scafs.path": { + "type": "file", + "description": "trimmed scaffolds path", + "pattern": "*k*.w*.z*.trimmed_scafs.path", + "ontologies": [] + } + } + ] + ], + "trimmed_scaffolds_tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*k*.w*.z*.trimmed_scafs.tsv": { + "type": "file", + "description": "trimmed scaffolds tsv", + "pattern": "*k*.w*.z*.trimmed_scafs.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "verbose_mapping_tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*k*.w*.z*.verbose_mapping.tsv": { + "type": "file", + "description": "trimmed scaffolds mapping", + "pattern": "*k*.w*.z*.verbose_mapping.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.k*.w???.tsv": { + "type": "file", + "description": "scaffolding tsv file", + "pattern": "*.k*.w???.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@nschan"], + "maintainers": ["@nschan"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "report": { - "type": "file", - "description": "Output .mapping.ARG file from DeepARG", - "pattern": "*.mapping.ARG", - "ontologies": [] - } + }, + { + "name": "lsa_cosine", + "path": "modules/nf-core/lsa/cosine/meta.yml", + "type": "module", + "meta": { + "name": "lsa_cosine", + "description": "Calculates the cosine similarity matrix between samples based on a gene expression matrix.", + "keywords": ["similarity", "cosine", "clustering", "rnaseq", "heatmap"], + "tools": [ + { + "lsa": { + "description": "Latent Semantic Analysis (LSA) package for R.", + "homepage": "https://cran.r-project.org/web/packages/lsa/index.html", + "documentation": "https://cran.r-project.org/web/packages/lsa/lsa.pdf", + "licence": ["GPL-2"], + "identifier": "" + } + }, + { + "pheatmap": { + "description": "Pretty Heatmaps package for R.", + "homepage": "https://cran.r-project.org/web/packages/pheatmap/index.html", + "documentation": "https://cran.r-project.org/web/packages/pheatmap/pheatmap.pdf", + "licence": ["GPL-2"], + "identifier": "biotools:pheatmap" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information, e.g. [ id:'test' ].\n" + } + }, + { + "expression_matrix": { + "type": "file", + "description": "CSV file containing the expression matrix.\nRows should be features (genes) and columns should be samples.\n", + "pattern": "*.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "output": { + "matrix": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information, e.g. [ id:'test' ].\n" + } + }, + { + "*_matrix.csv": { + "type": "file", + "description": "A square matrix (CSV) containing pairwise similarity scores.", + "pattern": "*_matrix.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "heatmap": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information, e.g. [ id:'test' ].\n" + } + }, + { + "*_heatmap.png": { + "type": "file", + "description": "A PNG image visualizing the similarity matrix as a heatmap.", + "pattern": "*_heatmap.png", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions.", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@miguelrosell"], + "maintainers": ["@miguelrosell"] } - ], - { - "format": { - "type": "string", - "description": "Type of report file to be produced", - "pattern": "tsv|json" + }, + { + "name": "ltrfinder", + "path": "modules/nf-core/ltrfinder/meta.yml", + "type": "module", + "meta": { + "name": "ltrfinder", + "description": "Finds full-length LTR retrotranspsons in genome sequences using the\nparallel version of LTR_Finder\n", + "keywords": [ + "genomics", + "annotation", + "parallel", + "repeat", + "long terminal retrotransposon", + "retrotransposon" + ], + "tools": [ + { + "LTR_FINDER_parallel": { + "description": "A Perl wrapper for LTR_FINDER", + "homepage": "https://github.com/oushujun/LTR_FINDER_parallel", + "documentation": "https://github.com/oushujun/LTR_FINDER_parallel", + "tool_dev_url": "https://github.com/oushujun/LTR_FINDER_parallel", + "doi": "10.1186/s13100-019-0193-0", + "licence": ["MIT"], + "identifier": "" + } + }, + { + "LTR_Finder": { + "description": "An efficient program for finding full-length LTR retrotranspsons in genome sequences", + "homepage": "https://github.com/xzhub/LTR_Finder", + "documentation": "https://github.com/xzhub/LTR_Finder", + "tool_dev_url": "https://github.com/xzhub/LTR_Finder", + "doi": "10.1093/nar/gkm286", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Genome sequences in fasta format", + "pattern": "*.{fsa,fa,fasta}", + "ontologies": [] + } + } + ] + ], + "output": { + "scn": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.scn": { + "type": "file", + "description": "Annotation in LTRharvest or LTR_FINDER format", + "pattern": "*.scn", + "ontologies": [] + } + } + ] + ], + "gff": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.gff3": { + "type": "file", + "description": "Annotation in gff3 format", + "pattern": "*.gff3", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@GallVp"], + "maintainers": ["@GallVp"] } - }, - { - "software_version": { - "type": "string", - "description": "Version of DeepARG used", - "pattern": "[0-9].[0-9].[0-9]" + }, + { + "name": "ltrharvest", + "path": "modules/nf-core/ltrharvest/meta.yml", + "type": "module", + "meta": { + "name": "ltrharvest", + "description": "Predicts LTR retrotransposons using the parallel version of GenomeTools gt-ltrharvest\nutility included in the EDTA toolchain\n", + "keywords": ["genomics", "genome", "annotation", "repeat", "transposons", "retrotransposons"], + "tools": [ + { + "LTR_HARVEST_parallel": { + "description": "A Perl wrapper for LTR_harvest", + "homepage": "https://github.com/oushujun/EDTA/tree/v2.2.0/bin/LTR_HARVEST_parallel", + "documentation": "https://github.com/oushujun/EDTA/tree/v2.2.0/bin/LTR_HARVEST_parallel", + "tool_dev_url": "https://github.com/oushujun/EDTA/tree/v2.2.0/bin/LTR_HARVEST_parallel", + "licence": ["MIT"], + "identifier": "" + } + }, + { + "gt": { + "description": "The GenomeTools genome analysis system", + "homepage": "https://genometools.org/index.html", + "documentation": "https://genometools.org/documentation.html", + "tool_dev_url": "https://github.com/genometools/genometools", + "doi": "10.1109/TCBB.2013.68", + "licence": ["ISC"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input genome fasta", + "pattern": "*.{fsa,fa,fasta}", + "ontologies": [] + } + } + ] + ], + "output": { + "gff3": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.gff3": { + "type": "file", + "description": "Predicted LTR candidates in gff3 format", + "pattern": "*.gff3", + "ontologies": [] + } + } + ] + ], + "scn": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.scn": { + "type": "file", + "description": "Predicted LTR candidates in scn format", + "pattern": "*.scn", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@GallVp"], + "maintainers": ["@GallVp"] } - }, - { - "reference_db_version": { - "type": "integer", - "description": "Database version of DeepARG used", - "pattern": "[0-9]" + }, + { + "name": "ltrretriever_lai", + "path": "modules/nf-core/ltrretriever/lai/meta.yml", + "type": "module", + "meta": { + "name": "ltrretriever_lai", + "description": "Estimates the mean LTR sequence identity in the genome. The input genome fasta should\nhave short alphanumeric IDs without comments\n", + "keywords": [ + "genomics", + "annotation", + "repeat", + "long terminal retrotransposon", + "retrotransposon", + "stats", + "qc" + ], + "tools": [ + { + "lai": { + "description": "Assessing genome assembly quality using the LTR Assembly Index (LAI)", + "homepage": "https://github.com/oushujun/LTR_retriever", + "documentation": "https://github.com/oushujun/LTR_retriever", + "tool_dev_url": "https://github.com/oushujun/LTR_retriever", + "doi": "10.1093/nar/gky730", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The genome file that is used to generate everything", + "pattern": "*.{fsa,fa,fasta}", + "ontologies": [] + } + } + ], + { + "pass_list": { + "type": "file", + "description": "A list of intact LTR-RTs generated by LTR_retriever", + "pattern": "*.pass.list", + "ontologies": [] + } + }, + { + "annotation_out": { + "type": "file", + "description": "RepeatMasker annotation of all LTR sequences in the genome", + "pattern": "*.out", + "ontologies": [] + } + }, + { + "monoploid_seqs": { + "type": "file", + "description": "This parameter is mainly for ployploid genomes. User provides a list of\nsequence names that represent a monoploid (1x). LAI will be calculated only\non these sequences if provided.\n", + "pattern": "*.txt", + "ontologies": [] + } + } + ], + "output": { + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.LAI.log": { + "type": "file", + "description": "Log from LAI", + "pattern": "*.LAI.log", + "ontologies": [] + } + } + ] + ], + "lai_out": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.LAI.out": { + "type": "file", + "description": "Output file from LAI if LAI is able to estimate the index from the inputs\n", + "pattern": "*.LAI.out", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@GallVp"], + "maintainers": ["@GallVp"] } - } - ], - "output": { - "json": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.json": { - "type": "file", - "description": "hAMRonised report in JSON format", - "pattern": "*.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "hAMRonised report in TSV format", - "pattern": "*.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "versions_hamronization": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "hamronization": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "hamronize --version 2>&1 | sed 's/hamronize //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "hamronization": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "hamronize --version 2>&1 | sed 's/hamronize //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@jfy133" - ], - "maintainers": [ - "@jfy133" - ] - }, - "pipelines": [ - { - "name": "funcscan", - "version": "3.0.0" - } - ] - }, - { - "name": "hamronization_fargene", - "path": "modules/nf-core/hamronization/fargene/meta.yml", - "type": "module", - "meta": { - "name": "hamronization_fargene", - "description": "Tool to convert and summarize fARGene outputs using the hAMRonization specification", - "keywords": [ - "amr", - "antimicrobial resistance", - "arg", - "antimicrobial resistance genes", - "reporting", - "fARGene" - ], - "tools": [ - { - "hamronization": { - "description": "Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification", - "homepage": "https://github.com/pha4ge/hAMRonization/", - "documentation": "https://github.com/pha4ge/hAMRonization/", - "tool_dev_url": "https://github.com/pha4ge/hAMRonization", - "licence": [ - "GNU Lesser General Public v3 (LGPL v3)" - ], - "identifier": "biotools:hamronization" + }, + { + "name": "ltrretriever_ltrretriever", + "path": "modules/nf-core/ltrretriever/ltrretriever/meta.yml", + "type": "module", + "meta": { + "name": "ltrretriever_ltrretriever", + "description": "Identifies LTR retrotransposons using LTR_retriever", + "keywords": ["genomics", "annotation", "repeat", "long terminal repeat", "retrotransposon"], + "tools": [ + { + "LTR_retriever": { + "description": "Sensitive and accurate identification of LTR retrotransposons", + "homepage": "https://github.com/oushujun/LTR_retriever", + "documentation": "https://github.com/oushujun/LTR_retriever", + "tool_dev_url": "https://github.com/oushujun/LTR_retriever", + "doi": "10.1104/pp.17.01310", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "genome": { + "type": "file", + "description": "Genomic sequences in fasta format", + "pattern": "*.{fsa,fa,fasta}", + "ontologies": [] + } + } + ], + { + "harvest": { + "type": "file", + "description": "LTR-RT candidates from GenomeTools ltrharvest in the old tabular format", + "pattern": "*.tabout", + "ontologies": [] + } + }, + { + "finder": { + "type": "file", + "description": "LTR-RT candidates from LTR_FINDER", + "pattern": "*.scn", + "ontologies": [] + } + }, + { + "mgescan": { + "type": "file", + "description": "LTR-RT candidates from MGEScan_LTR", + "pattern": "*.out", + "ontologies": [] + } + }, + { + "non_tgca": { + "type": "file", + "description": "Non-canonical LTR-RT candidates from GenomeTools ltrharvest in the old tabular format", + "pattern": "*.tabout", + "ontologies": [] + } + } + ], + "output": { + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.log": { + "type": "file", + "description": "Output log from LTR_retriever", + "pattern": "*.log", + "ontologies": [] + } + } + ] + ], + "pass_list": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}.pass.list": { + "type": "file", + "description": "Intact LTR-RTs with coordinate and structural information in summary table format", + "pattern": "*.pass.list", + "ontologies": [] + } + } + ] + ], + "pass_list_gff": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.pass.list.gff3": { + "type": "file", + "description": "Intact LTR-RTs with coordinate and structural information in gff3 format", + "pattern": "*.pass.list.gff3", + "ontologies": [] + } + } + ] + ], + "ltrlib": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.LTRlib.fa": { + "type": "file", + "description": "All non-redundant LTR-RTs", + "pattern": "*.LTRlib.fa", + "ontologies": [] + } + } + ] + ], + "annotation_out": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}.out": { + "type": "file", + "description": "Whole-genome LTR-RT annotation by the non-redundant library", + "pattern": "*.out", + "ontologies": [] + } + } + ] + ], + "annotation_gff": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.out.gff3": { + "type": "file", + "description": "Whole-genome LTR-RT annotation by the non-redundant library in gff3 format", + "pattern": "*.out.gff3", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@GallVp"], + "maintainers": ["@GallVp"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } + }, + { + "name": "macrel_contigs", + "path": "modules/nf-core/macrel/contigs/meta.yml", + "type": "module", + "meta": { + "name": "macrel_contigs", + "description": "A tool that mines antimicrobial peptides (AMPs) from (meta)genomes by predicting peptides from genomes (provided as contigs) and outputs all the predicted anti-microbial peptides found.", + "keywords": ["AMP", "antimicrobial peptides", "genome mining", "metagenomes", "peptide prediction"], + "tools": [ + { + "macrel": { + "description": "A pipeline for AMP (antimicrobial peptide) prediction", + "homepage": "https://macrel.readthedocs.io/en/latest/", + "documentation": "https://macrel.readthedocs.io/en/latest/", + "tool_dev_url": "https://github.com/BigDataBiology/macrel", + "doi": "10.7717/peerj.10555", + "licence": ["MIT"], + "identifier": "biotools:macrel" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "A fasta file with nucleotide sequences.", + "pattern": "*.{fasta,fa,fna,fasta.gz,fa.gz,fna.gz}", + "ontologies": [] + } + } + ] + ], + "output": { + "smorfs": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*/*.smorfs.faa.gz": { + "type": "file", + "description": "A zipped fasta file containing aminoacid sequences showing the general gene prediction information in the contigs.", + "pattern": "*.smorfs.faa.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "all_orfs": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*/*.all_orfs.faa.gz": { + "type": "file", + "description": "A zipped fasta file containing amino acid sequences showing the general gene prediction information in the contigs.", + "pattern": "*.all_orfs.faa.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "amp_prediction": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*/*.prediction.gz": { + "type": "file", + "description": "A zipped file, with all predicted amps in a table format.", + "pattern": "*.prediction.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "readme_file": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*/*.md": { + "type": "file", + "description": "A readme file containing tool specific information (e.g. citations, details about the output, etc.).", + "pattern": "*.md", + "ontologies": [] + } + } + ] + ], + "log_file": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*/*_log.txt": { + "type": "file", + "description": "A log file containing the information pertaining to the run.", + "pattern": "*_log.txt", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@darcy220606"], + "maintainers": ["@darcy220606"] }, - { - "report": { - "type": "file", - "description": "Output .txt file from fARGene", - "pattern": "*.txt", - "ontologies": [] - } - } - ], - { - "format": { - "type": "string", - "description": "Type of report file to be produced", - "pattern": "tsv|json" - } - }, - { - "software_version": { - "type": "string", - "description": "Version of fARGene used", - "pattern": "[0-9].[0-9].[0-9]" - } - }, - { - "reference_db_version": { - "type": "string", - "description": "Database version of fARGene used", - "pattern": "[0-9].[0-9].[0-9]" - } - } - ], - "output": { - "json": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.json": { - "type": "file", - "description": "hAMRonised report in JSON format", - "pattern": "*.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "hAMRonised report in TSV format", - "pattern": "*.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "versions_hamronization": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "hamronization": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "hamronize --version 2>&1 | sed 's/hamronize //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "hamronization": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "hamronize --version 2>&1 | sed 's/hamronize //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "funcscan", + "version": "3.0.0" + } ] - ] - }, - "authors": [ - "@jfy133" - ], - "maintainers": [ - "@jfy133" - ] - }, - "pipelines": [ - { - "name": "funcscan", - "version": "3.0.0" - } - ] - }, - { - "name": "hamronization_rgi", - "path": "modules/nf-core/hamronization/rgi/meta.yml", - "type": "module", - "meta": { - "name": "hamronization_rgi", - "description": "Tool to convert and summarize RGI outputs using the hAMRonization specification.", - "keywords": [ - "amr", - "antimicrobial resistance", - "arg", - "antimicrobial resistance genes", - "reporting", - "rgi" - ], - "tools": [ - { - "hamronization": { - "description": "Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification", - "homepage": "https://github.com/pha4ge/hAMRonization/", - "documentation": "https://github.com/pha4ge/hAMRonization/", - "tool_dev_url": "https://github.com/pha4ge/hAMRonization", - "licence": [ - "GNU Lesser General Public v3 (LGPL v3)" - ], - "identifier": "biotools:hamronization" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } + }, + { + "name": "macs2_callpeak", + "path": "modules/nf-core/macs2/callpeak/meta.yml", + "type": "module", + "meta": { + "name": "macs2_callpeak", + "description": "Peak calling of enriched genomic regions of ChIP-seq and ATAC-seq experiments", + "keywords": ["alignment", "atac-seq", "chip-seq", "peak-calling"], + "tools": [ + { + "macs2": { + "description": "Model Based Analysis for ChIP-Seq data", + "documentation": "https://docs.csc.fi/apps/macs2/", + "tool_dev_url": "https://github.com/macs3-project/MACS", + "doi": "10.1101/496521", + "licence": ["BSD"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "ipbam": { + "type": "file", + "description": "The ChIP-seq treatment file", + "ontologies": [] + } + }, + { + "controlbam": { + "type": "file", + "description": "The control file", + "ontologies": [] + } + } + ], + { + "macs2_gsize": { + "type": "string", + "description": "Effective genome size. It can be 1.0e+9 or 1000000000, or shortcuts:'hs' for human (2.7e9), 'mm' for mouse (1.87e9), 'ce' for C. elegans (9e7) and 'dm' for fruitfly (1.2e8)" + } + } + ], + "output": { + "peak": [ + [ + { + "meta": { + "type": "file", + "description": "BED file containing annotated peaks", + "pattern": "*.gappedPeak,*.narrowPeak}", + "ontologies": [] + } + }, + { + "*.{narrowPeak,broadPeak}": { + "type": "file", + "description": "BED file containing annotated peaks", + "pattern": "*.gappedPeak,*.narrowPeak}", + "ontologies": [] + } + } + ] + ], + "xls": [ + [ + { + "meta": { + "type": "file", + "description": "BED file containing annotated peaks", + "pattern": "*.gappedPeak,*.narrowPeak}", + "ontologies": [] + } + }, + { + "*.xls": { + "type": "file", + "description": "xls file containing annotated peaks", + "pattern": "*.xls", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software version", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ], + "gapped": [ + [ + { + "meta": { + "type": "file", + "description": "BED file containing annotated peaks", + "pattern": "*.gappedPeak,*.narrowPeak}", + "ontologies": [] + } + }, + { + "*.gappedPeak": { + "type": "file", + "description": "Optional BED file containing gapped peak", + "pattern": "*.gappedPeak", + "ontologies": [] + } + } + ] + ], + "bed": [ + [ + { + "meta": { + "type": "file", + "description": "BED file containing annotated peaks", + "pattern": "*.gappedPeak,*.narrowPeak}", + "ontologies": [] + } + }, + { + "*.bed": { + "type": "file", + "description": "Optional BED file containing peak summits locations for every peak", + "pattern": "*.bed", + "ontologies": [] + } + } + ] + ], + "bdg": [ + [ + { + "meta": { + "type": "file", + "description": "BED file containing annotated peaks", + "pattern": "*.gappedPeak,*.narrowPeak}", + "ontologies": [] + } + }, + { + "*.bdg": { + "type": "file", + "description": "Optional bedGraph files for input and treatment input samples", + "pattern": "*.bdg", + "ontologies": [] + } + } + ] + ] + }, + "authors": ["@ntoda03", "@JoseEspinosa", "@jianhong"], + "maintainers": ["@ntoda03", "@JoseEspinosa", "@jianhong"] }, - { - "report": { - "type": "file", - "description": "Output .txt file from RGI", - "pattern": "*.txt", - "ontologies": [] - } - } - ], - { - "format": { - "type": "string", - "description": "Type of report file to be produced", - "pattern": "tsv|json" - } - }, - { - "software_version": { - "type": "string", - "description": "Version of DeepARG used", - "pattern": "[0-9].[0-9].[0-9]" - } - }, - { - "reference_db_version": { - "type": "string", - "description": "Database version of DeepARG used", - "pattern": "[0-9].[0-9].[0-9]" - } - } - ], - "output": { - "json": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.json": { - "type": "file", - "description": "hAMRonised report in JSON format", - "pattern": "*.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "hAMRonised report in TSV format", - "pattern": "*.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "versions_hamronization": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "hamronization": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "hamronize --version 2>&1 | sed 's/hamronize //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "hamronization": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "hamronize --version 2>&1 | sed 's/hamronize //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@louperelo" - ], - "maintainers": [ - "@louperelo" - ] - }, - "pipelines": [ - { - "name": "funcscan", - "version": "3.0.0" - } - ] - }, - { - "name": "hamronization_summarize", - "path": "modules/nf-core/hamronization/summarize/meta.yml", - "type": "module", - "meta": { - "name": "hamronization_summarize", - "description": "Tool to summarize and combine all hAMRonization reports into a single file", - "keywords": [ - "amr", - "antimicrobial resistance", - "reporting" - ], - "tools": [ - { - "hamronization": { - "description": "Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification", - "homepage": "https://github.com/pha4ge/hAMRonization/", - "documentation": "https://github.com/pha4ge/hAMRonization/", - "tool_dev_url": "https://github.com/pha4ge/hAMRonization", - "licence": [ - "GNU Lesser General Public v3 (LGPL v3)" - ], - "identifier": "biotools:hamronization" - } - } - ], - "input": [ - { - "reports": { - "type": "file", - "description": "List of multiple hAMRonization reports in either JSON or TSV format", - "pattern": "*.{json,tsv}", - "ontologies": [ + "pipelines": [ { - "edam": "http://edamontology.org/format_3464" + "name": "atacseq", + "version": "2.1.2" }, { - "edam": "http://edamontology.org/format_3475" + "name": "cutandrun", + "version": "3.2.2" + }, + { + "name": "hicar", + "version": "1.0.0" } - ] - } - }, - { - "format": { - "type": "string", - "description": "Type of final combined report file to be produced", - "pattern": "tsv|json|interactive" - } - } - ], - "output": { - "json": [ - { - "hamronization_combined_report.json": { - "type": "file", - "description": "hAMRonised summary in JSON format", - "pattern": "*.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ], - "tsv": [ - { - "hamronization_combined_report.tsv": { - "type": "file", - "description": "hAMRonised summary in TSV format", - "pattern": "*.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ], - "html": [ - { - "hamronization_combined_report.html": { - "type": "file", - "description": "hAMRonised summary in HTML format", - "pattern": "*.html", - "ontologies": [] - } - } - ], - "versions_hamronization": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "hamronization": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "hamronize --version 2>&1 | sed 's/hamronize //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "hamronization": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "hamronize --version 2>&1 | sed 's/hamronize //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@jfy133" - ], - "maintainers": [ - "@jfy133" - ] - }, - "pipelines": [ - { - "name": "funcscan", - "version": "3.0.0" - } - ] - }, - { - "name": "hapibd", - "path": "modules/nf-core/hapibd/meta.yml", - "type": "module", - "meta": { - "name": "hapibd", - "description": "The hap-ibd program detects identity-by-descent (IBD) segments and homozygosity-by-descent (HBD) segments in phased genotype data. The hap-ibd program can analyze data sets with hundreds of thousands of samples.", - "keywords": [ - "ibd", - "hbd", - "beagle" - ], - "tools": [ - { - "hapibd": { - "description": "Hap-ibd Detects identity-by-descent (IBD) segments and homozygosity-by-descent (HBD) segments in phased genotype data.", - "homepage": "https://github.com/browning-lab/hap-ibd/blob/master/README.md", - "documentation": "https://github.com/browning-lab/hap-ibd/blob/master/README.md", - "doi": "10.1016/j.ajhg.2020.02.010", - "licence": [ - "Apache-2.0" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing cohort information\ne.g. [ id:'test' ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "phased VCF file with a GT FORMAT subfield with no missing alleles", - "pattern": "*.{vcf,vcf.gz}", - "ontologies": [] - } - } - ], - { - "map": { - "type": "file", - "description": "genetic map with cM units in PLINK format", - "pattern": "*.{map,map.gz,map.zip}", - "ontologies": [] - } - }, - { - "exclude": { - "type": "file", - "description": "text file containing samples one sample per line to be excluded from the analysis", - "pattern": "*.*", - "ontologies": [] - } - } - ], - "output": { - "hbd": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing cohort information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.hbd.gz": { - "type": "file", - "description": "contains HBD segments within individuals", - "pattern": "*.hbd.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "ibd": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing cohort information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.ibd.gz": { - "type": "file", - "description": "contains IBD segments shared between individuals", - "pattern": "*.ibd.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing cohort information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.log": { - "type": "file", - "description": "contains a summary of the analysis which includes the analysis parameters the number of markers the number of samples the number of output HBD and IBD segments and the mean number of HBD and IBD segments per sample", - "pattern": "*.log", - "ontologies": [] - } - } - ] - ], - "versions_hapibd": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "hapibd": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "hap-ibd 2>&1 | sed '1!d;s/^.* version //;s/,.*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "hapibd": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "hap-ibd 2>&1 | sed '1!d;s/^.* version //;s/,.*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@ashotmarg" - ], - "maintainers": [ - "@ashotmarg" - ] - } - }, - { - "name": "haplocheck", - "path": "modules/nf-core/haplocheck/meta.yml", - "type": "module", - "meta": { - "name": "haplocheck", - "description": "Haplocheck detects contamination patterns in mtDNA AND WGS sequencing studies by analyzing\nthe mitochondrial DNA. Haplocheck also works as a proxy tool for nDNA studies and provides\nusers a graphical report to investigate the contamination further. Internally, it uses the\nHaplogrep tool, that supports rCRS and RSRS mitochondrial versions.\n", - "keywords": [ - "mitochondrial", - "mtDNA", - "contamination" - ], - "tools": [ - { - "haplocheck": { - "description": "Detects in-sample contamination in mtDNA or WGS sequencing studies by analyzing the mitochondrial content.", - "homepage": "https://github.com/genepi/haplocheck", - "documentation": "https://github.com/genepi/haplocheck", - "tool_dev_url": "https://github.com/genepi/haplocheck", - "doi": "10.1101/gr.256545.119", - "licence": [ - "MIT" - ], - "identifier": "biotools:haplocheck" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + }, + { + "name": "macs3_callpeak", + "path": "modules/nf-core/macs3/callpeak/meta.yml", + "type": "module", + "meta": { + "name": "macs3_callpeak", + "description": "Peak calling of enriched genomic regions of ChIP-seq and ATAC-seq experiments", + "keywords": ["alignment", "atac-seq", "chip-seq", "peak-calling"], + "tools": [ + { + "macs3": { + "description": "Model Based Analysis for ChIP-Seq data", + "homepage": "https://macs3-project.github.io/MACS/", + "documentation": "https://macs3-project.github.io/MACS/", + "tool_dev_url": "https://github.com/macs3-project/MACS/", + "doi": "10.1101/496521", + "licence": ["BSD-3-clause"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample_1', single_end:false ]`\n" + } + }, + { + "ipbam": { + "type": "file", + "description": "The ChIP-seq treatment file", + "ontologies": [] + } + }, + { + "controlbam": { + "type": "file", + "description": "The control file", + "ontologies": [] + } + } + ], + { + "macs3_gsize": { + "type": "string", + "description": "Effective genome size. It can be 1.0e+9 or 1000000000,\nor shortcuts:'hs' for human (2,913,022,398), 'mm' for mouse\n(2,652,783,500), 'ce' for C. elegans (100,286,401)\nand 'dm' for fruitfly (142,573,017), Default:hs.\n" + } + } + ], + "output": { + "peak": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.{narrowPeak,broadPeak}": { + "type": "file", + "description": "BED file containing annotated peaks", + "pattern": "*.gappedPeak,*.narrowPeak}", + "ontologies": [] + } + } + ] + ], + "xls": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.xls": { + "type": "file", + "description": "xls file containing annotated peaks", + "pattern": "*.xls", + "ontologies": [] + } + } + ] + ], + "gapped": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.gappedPeak": { + "type": "file", + "description": "Optional BED file containing gapped peak", + "pattern": "*.gappedPeak", + "ontologies": [] + } + } + ] + ], + "bed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "Optional BED file containing peak summits locations for every peak", + "pattern": "*.bed", + "ontologies": [] + } + } + ] + ], + "bdg": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.bdg": { + "type": "file", + "description": "Optional bedGraph files for input and treatment input samples", + "pattern": "*.bdg", + "ontologies": [] + } + } + ] + ], + "versions_macs3": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "macs3": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "macs3 --version | sed -e 's/macs3 //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "macs3": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "macs3 --version | sed -e 's/macs3 //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@JoseEspinosa"], + "maintainers": ["@JoseEspinosa", "@Kevin-Brockers"] }, - { - "vcf": { - "type": "file", - "description": "VCF file", - "pattern": "*.{vcf.gz}", - "ontologies": [] - } - } - ] - ], - "output": { - "txt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.txt": { - "type": "file", - "description": "Raw report in txt format", - "pattern": "*.{txt}", - "ontologies": [] - } - } - ] - ], - "html": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.html": { - "type": "file", - "description": "Haplocheck HTML report", - "pattern": "*.{html}", - "ontologies": [] - } - } - ] - ], - "versions_haplocheck": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "haplocheck": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "haplocheck --version 2>&1 | sed -n 's/^haplocheck //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "haplocheck": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "haplocheck --version 2>&1 | sed -n 's/^haplocheck //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "chipseq", + "version": "2.1.0" + } ] - ] - }, - "authors": [ - "@lmtani" - ], - "maintainers": [ - "@lmtani" - ] - }, - "pipelines": [ - { - "name": "variantcatalogue", - "version": "dev" - } - ] - }, - { - "name": "haplogrep2_classify", - "path": "modules/nf-core/haplogrep2/classify/meta.yml", - "type": "module", - "meta": { - "name": "haplogrep2_classify", - "description": "classification into haplogroups", - "keywords": [ - "haplogroups", - "classify", - "mtDNA" - ], - "tools": [ - { - "haplogrep2": { - "description": "A tool for mtDNA haplogroup classification.", - "homepage": "https://github.com/seppinho/haplogrep-cmd", - "documentation": "https://github.com/seppinho/haplogrep-cmd", - "tool_dev_url": "https://github.com/seppinho/haplogrep-cmd", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "inputfile": { - "type": "file", - "description": "valid options are hsd, vcf, or fasta files", - "pattern": "*.{vcf,vcf.gz,fasta,hsd}", - "ontologies": [] - } + }, + { + "name": "macse_refinealignment", + "path": "modules/nf-core/macse/refinealignment/meta.yml", + "type": "module", + "meta": { + "name": "macse_refinealignment", + "description": "improves the input nucleotide alignment in a codon-aware manner", + "keywords": ["multiple sequence alignment", "codon-aware", "fasta"], + "tools": [ + { + "macse": { + "description": "MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons.", + "homepage": "https://www.agap-ge2pop.org/macse/", + "documentation": "https://www.agap-ge2pop.org/macse/macse-documentation/", + "tool_dev_url": "https://github.com/nf-core/masce", + "doi": "10.1371/journal.pone.0022594", + "licence": ["CeCILL 2.1"], + "identifier": "biotools:macse" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Aligned sequences in FASTA format. May be gzipped or uncompressed.", + "pattern": "*.{fa,fas,fasta,aln}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2554" + }, + { + "edam": "http://edamontology.org/format_1921" + }, + { + "edam": "http://edamontology.org/format_1984" + } + ] + } + } + ] + ], + "output": { + "nt": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_NT.{fa,fas,fasta,aln}": { + "type": "file", + "description": "Aligned sequences in FASTA format. May be gzipped or uncompressed.", + "pattern": "*_NT.{fa,fas,fasta,aln}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2554" + }, + { + "edam": "http://edamontology.org/format_1921" + }, + { + "edam": "http://edamontology.org/format_1984" + } + ] + } + } + ] + ], + "aa": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_AA.{fa,fas,fasta,aln}": { + "type": "file", + "description": "Aligned sequences in FASTA format. May be gzipped or uncompressed.", + "pattern": "*_AA.{fa,fas,fasta,aln}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2554" + }, + { + "edam": "http://edamontology.org/format_1921" + }, + { + "edam": "http://edamontology.org/format_1984" + } + ] + } + } + ] + ], + "versions_macse": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "macse": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "macse --version | sed -n 's/.*V\\([0-9]*\\.[0-9]*\\).*/\\1/p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "macse": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "macse --version | sed -n 's/.*V\\([0-9]*\\.[0-9]*\\).*/\\1/p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@charles-plessy", "@pmuskusv", "@takiifujita-ui", "@leapicard"], + "maintainers": ["@leapicard"] } - ], - { - "format": { - "type": "string", - "description": "either \"vcf\", \"fasta\" or \"hsd\"" + }, + { + "name": "macsyfinder_download", + "path": "modules/nf-core/macsyfinder/download/meta.yml", + "type": "module", + "meta": { + "name": "macsyfinder_download", + "description": "Download MacSyFinder models using msf_data", + "keywords": ["genomics", "protein", "macromolecular systems", "models", "database"], + "tools": [ + { + "macsyfinder": { + "description": "Detection of macromolecular systems in protein datasets using systems\nmodelling and similarity search\n", + "homepage": "https://github.com/gem-pasteur/macsyfinder", + "documentation": "https://macsyfinder.readthedocs.io", + "tool_dev_url": "https://github.com/gem-pasteur/macsyfinder", + "doi": "10.24072/pcjournal.250", + "licence": ["GPL v3"], + "identifier": "biotools:macsyfinder" + } + } + ], + "input": [ + { + "model_name": { + "type": "string", + "description": "Name of the MacSyFinder model to download (e.g., 'TXSScan', 'CasFinder')" + } + } + ], + "output": { + "models": [ + { + "models": { + "type": "directory", + "description": "Directory containing downloaded MacSyFinder model definitions", + "pattern": "models" + } + } + ], + "versions_macsyfinder": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "macsyfinder": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "macsyfinder --version 2>&1 | sed \"1!d;s/^.*MacSyFinder //;s/ .*$//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_macsydata": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "msf_data": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "msf_data --version 2>&1 | sed \"4!d;s/^- MacSyLib //;s/ *$//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "macsyfinder": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "macsyfinder --version 2>&1 | sed \"1!d;s/^.*MacSyFinder //;s/ .*$//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "msf_data": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "msf_data --version 2>&1 | sed \"4!d;s/^- MacSyLib //;s/ *$//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@brovolia"], + "maintainers": ["@brovolia"] } - } - ], - "output": { - "txt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.txt": { - "type": "file", - "description": "text file with classification information", - "pattern": "*.{txt}", - "ontologies": [] - } - } - ] - ], - "versions_haplogrep2": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "haplogrep2": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "haplogrep --version 2>&1 | sed '2!d;s/.*v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "haplogrep2": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "haplogrep --version 2>&1 | sed '2!d;s/.*v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@lucpen" - ], - "maintainers": [ - "@lucpen" - ] - } - }, - { - "name": "haplogrep3_classify", - "path": "modules/nf-core/haplogrep3/classify/meta.yml", - "type": "module", - "meta": { - "name": "haplogrep3_classify", - "description": "classification into haplogroups", - "keywords": [ - "haplogroups", - "classify", - "mtDNA" - ], - "tools": [ - { - "haplogrep3": { - "description": "A tool for mtDNA haplogroup classification.", - "homepage": "https://github.com/genepi/haplogrep3", - "documentation": "https://github.com/genepi/haplogrep3", - "tool_dev_url": "https://github.com/genepi/haplogrep3", - "licence": [ - "MIT" - ], - "identifier": "" + }, + { + "name": "macsyfinder_search", + "path": "modules/nf-core/macsyfinder/search/meta.yml", + "type": "module", + "meta": { + "name": "macsyfinder_search", + "description": "Search for macromolecular systems in protein datasets using MacSyFinder", + "notes": "The current input structure searches all specified models in a single MacSyFinder process\n(using internal parallelization via --worker). For Nextflow-level parallelization across\nindividual models, the inputs could be combined into a single tuple:\ntuple val(meta), path(proteins), path(models), val(model_names)\n", + "keywords": ["genomics", "protein", "macromolecular systems", "hmmer", "search"], + "tools": [ + { + "macsyfinder": { + "description": "Detection of macromolecular systems in protein datasets using systems\nmodelling and similarity search\n", + "homepage": "https://github.com/gem-pasteur/macsyfinder", + "documentation": "https://macsyfinder.readthedocs.io", + "tool_dev_url": "https://github.com/gem-pasteur/macsyfinder", + "doi": "10.24072/pcjournal.250", + "licence": ["GPL v3"], + "identifier": "biotools:macsyfinder" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "proteins": { + "type": "file", + "description": "Protein sequence file in FASTA format", + "pattern": "*.{fasta,faa,fa}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + { + "models": { + "type": "directory", + "description": "Directory containing MacSyFinder model(s)", + "pattern": "*" + } + }, + { + "model_names": { + "type": "string", + "description": "Space-separated list of model names to search for. If not provided, all models in the directory will be used." + } + } + ], + "output": { + "results": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', db_type:'gembase' ]`\n" + } + }, + { + "${prefix}/*": { + "type": "directory", + "description": "Directory containing all MacSyFinder results", + "pattern": "${prefix}/*" + } + } + ] + ], + "hmmer": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', db_type:'gembase' ]`\n" + } + }, + { + "${prefix}/hmmer_results": { + "type": "directory", + "description": "Directory containing HMMER search results (may contain variable content like timestamps)", + "pattern": "${prefix}/hmmer_results" + } + } + ] + ], + "stdout": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', db_type:'gembase' ]`\n" + } + }, + { + "${prefix}/macsyfinder.out": { + "type": "file", + "description": "MacSyFinder standard output", + "pattern": "${prefix}/macsyfinder.out", + "ontologies": [] + } + } + ] + ], + "stderr": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', db_type:'gembase' ]`\n" + } + }, + { + "${prefix}/macsyfinder.err": { + "type": "file", + "description": "MacSyFinder standard error", + "pattern": "${prefix}/macsyfinder.err", + "ontologies": [] + } + } + ] + ], + "summary": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', db_type:'gembase' ]`\n" + } + }, + { + "${prefix}/all_systems.tsv": { + "type": "file", + "description": "Summary table of all detected systems", + "pattern": "${prefix}/all_systems.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "best_solutions": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', db_type:'gembase' ]`\n" + } + }, + { + "${prefix}/all_best_solutions*": { + "type": "file", + "description": "Best solution files for detected systems", + "pattern": "${prefix}/all_best_solutions*", + "ontologies": [] + } + } + ] + ], + "versions_macsyfinder": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "macsyfinder": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "macsyfinder --version 2>&1 | sed \"1!d;s/^.*MacSyFinder //;s/ .*$//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_hmmer": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "hmmer": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "hmmsearch -h 2>&1 | sed \"2!d;s/^# HMMER //;s/ .*$//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "macsyfinder": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "macsyfinder --version 2>&1 | sed \"1!d;s/^.*MacSyFinder //;s/ .*$//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "hmmer": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "hmmsearch -h 2>&1 | sed \"2!d;s/^# HMMER //;s/ .*$//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@brovolia"], + "maintainers": ["@brovolia"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + }, + { + "name": "mafft_align", + "path": "modules/nf-core/mafft/align/meta.yml", + "type": "module", + "meta": { + "name": "mafft_align", + "description": "Multiple sequence alignment using MAFFT", + "keywords": ["fasta", "msa", "multiple sequence alignment"], + "tools": [ + { + "mafft": { + "description": "Multiple alignment program for amino acid or nucleotide sequences based on fast Fourier transform", + "homepage": "https://mafft.cbrc.jp/alignment/software/", + "documentation": "https://mafft.cbrc.jp/alignment/software/manual/manual.html", + "tool_dev_url": "https://mafft.cbrc.jp/alignment/software/source.html", + "doi": "10.1093/nar/gkf436", + "licence": ["BSD"], + "identifier": "biotools:MAFFT" + } + }, + { + "pigz": { + "description": "Parallel implementation of the gzip algorithm.", + "homepage": "https://zlib.net/pigz/", + "documentation": "https://zlib.net/pigz/pigz.pdf", + "identifier": "biotools:MAFFT" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA file containing the sequences to align. May be gzipped or uncompressed.", + "pattern": "*.{fa,fasta}{.gz,}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1919" + }, + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "add": { + "type": "file", + "description": "FASTA file containing sequences to align to the sequences in `fasta` using `--add`. May be gzipped or uncompressed.", + "pattern": "*.{fa,fasta}{.gz,}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1919" + }, + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "addfragments": { + "type": "file", + "description": "FASTA file containing sequences to align to the sequences in `fasta` using `--addfragments`. May be gzipped or uncompressed.", + "pattern": "*.{fa,fasta}{.gz,}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1919" + }, + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "addfull": { + "type": "file", + "description": "FASTA file containing sequences to align to the sequences in `fasta` using `--addfull`. May be gzipped or uncompressed.", + "pattern": "*.{fa,fasta}{.gz,}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1919" + }, + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "addprofile": { + "type": "file", + "description": "FASTA file containing sequences to align to the sequences in `fasta` using `--addprofile`. May be gzipped or uncompressed.", + "pattern": "*.{fa,fasta}{.gz,}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1919" + }, + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + [ + { + "meta6": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "addlong": { + "type": "file", + "description": "FASTA file containing sequences to align to the sequences in `fasta` using `--addlong`. May be gzipped or uncompressed.", + "pattern": "*.{fa,fasta}{.gz,}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1919" + }, + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + { + "compress": { + "type": "boolean", + "description": "Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded." + } + } + ], + "output": { + "fas": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fas{.gz,}": { + "type": "file", + "description": "Aligned sequences in FASTA format. May be gzipped or uncompressed.", + "pattern": "*.fas{.gz,}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2554" + }, + { + "edam": "http://edamontology.org/format_1921" + }, + { + "edam": "http://edamontology.org/format_1984" + } + ] + } + } + ] + ], + "versions_mafft": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process name" + } + }, + { + "mafft": { + "type": "string", + "description": "The tool name" + } + }, + { + "mafft --version 2>&1 | sed 's/ (.*) //g'": { + "type": "eval", + "description": "The tool version" + } + } + ] + ], + "versions_pigz": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process name" + } + }, + { + "pigz": { + "type": "string", + "description": "The tool name" + } + }, + { + "pigz --version 2>&1 | sed 's/pigz //g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process name" + } + }, + { + "mafft": { + "type": "string", + "description": "The tool name" + } + }, + { + "mafft --version 2>&1 | sed 's/ (.*) //g'": { + "type": "eval", + "description": "The tool version" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The process name" + } + }, + { + "pigz": { + "type": "string", + "description": "The tool name" + } + }, + { + "pigz --version 2>&1 | sed 's/pigz //g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@MillironX"], + "maintainers": ["@MillironX", "@Joon-Klaps"] }, - { - "inputfile": { - "type": "file", - "description": "valid options are hsd, vcf, or fasta files", - "pattern": "*.{vcf,vcf.gz,fasta,hsd}", - "ontologies": [] - } - } - ] - ], - "output": { - "txt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.txt": { - "type": "file", - "description": "text file with classification information", - "pattern": "*.{txt}", - "ontologies": [] - } - } - ] - ], - "versions_haplogrep3": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "haplogrep3": { - "type": "string", - "description": "The tool name" - } - }, - { - "haplogrep3 | sed -n 's/.*Haplogrep 3 \\([0-9.]\\+\\).*/\\1/p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "haplogrep3": { - "type": "string", - "description": "The tool name" - } - }, - { - "haplogrep3 | sed -n 's/.*Haplogrep 3 \\([0-9.]\\+\\).*/\\1/p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "ampliseq", + "version": "2.17.0" + }, + { + "name": "multiplesequencealign", + "version": "1.1.1" + }, + { + "name": "pathogensurveillance", + "version": "1.1.0" + }, + { + "name": "phyloplace", + "version": "2.0.0" + }, + { + "name": "proteinfamilies", + "version": "2.3.0" + }, + { + "name": "viralmetagenome", + "version": "1.1.1" + } ] - ] - }, - "authors": [ - "@lucpen" - ], - "maintainers": [ - "@lucpen", - "@ramprasadn" - ] - } - }, - { - "name": "happy_ftxpy", - "path": "modules/nf-core/happy/ftxpy/meta.yml", - "type": "module", - "meta": { - "name": "happy_ftxpy", - "description": "Somatic VCF Feature Extraction tool from hap.y.", - "keywords": [ - "happy", - "featuretable", - "somatic", - "extraction" - ], - "tools": [ - { - "happy": { - "description": "Haplotype VCF comparison tools", - "homepage": "https://www.illumina.com/products/by-type/informatics-products/basespace-sequence-hub/apps/hap-py-benchmarking.html", - "documentation": "https://github.com/Illumina/hap.py", - "tool_dev_url": "https://github.com/Illumina/hap.py", - "licence": [ - "BSD-2-clause" - ], - "identifier": "biotools:happy" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF file to process", - "pattern": "*.{vcf,vcf.gz}", - "ontologies": [] - } - }, - { - "regions_bed": { - "type": "file", - "description": "BED file. Restrict analysis to given (sparse) regions.", - "pattern": "*.bed", - "ontologies": [] - } - }, - { - "targets_bed": { - "type": "file", - "description": "Restrict analysis to given (dense) regions.", - "pattern": "*.bed", - "ontologies": [] - } - }, - { - "bam": { - "type": "file", - "description": "Pass one or more BAM files for feature table extraction", - "pattern": "*.bam", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information for reference fasta\ne.g. [ id:'test2']\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA file of the reference genome", - "pattern": "*.{fa,fasta}", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information for reference fai\ne.g. [ id:'test3' ]\n" - } + }, + { + "name": "mafft_guidetree", + "path": "modules/nf-core/mafft/guidetree/meta.yml", + "type": "module", + "meta": { + "name": "mafft_guidetree", + "description": "Guide tree rendering using MAFFT", + "keywords": ["fasta", "msa", "guide tree"], + "tools": [ + { + "mafft": { + "description": "Multiple alignment program for amino acid or nucleotide sequences based on fast Fourier transform", + "homepage": "https://mafft.cbrc.jp/alignment/software/", + "documentation": "https://mafft.cbrc.jp/alignment/software/manual/manual.html", + "tool_dev_url": "https://mafft.cbrc.jp/alignment/software/source.html", + "doi": "10.1093/nar/gkf436", + "licence": ["BSD"], + "identifier": "biotools:MAFFT" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA file containing the sequences to be used to render the guidetree.", + "pattern": "*.{fa,fasta}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1919" + }, + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ] + ], + "output": { + "tree": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "*.dnd": { + "type": "file", + "description": "Guide tree in Newick format.", + "pattern": "*.dnd", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2006" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@luisas"], + "maintainers": ["@luisas"] }, - { - "fasta_fai": { - "type": "file", - "description": "The index of the reference FASTA", - "pattern": "*.fai", - "ontologies": [] - } - } - ] - ], - "output": { - "features": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.csv": { - "type": "file", - "description": "Fuature table", - "pattern": "*.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "versions_happy": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "happy": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "0.3.15": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "happy": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "0.3.15": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "multiplesequencealign", + "version": "1.1.1" + } ] - ] - }, - "authors": [ - "@kubranarci" - ], - "maintainers": [ - "@kubranarci" - ] - } - }, - { - "name": "happy_happy", - "path": "modules/nf-core/happy/happy/meta.yml", - "type": "module", - "meta": { - "name": "happy_happy", - "description": "Hap.py is a tool to compare diploid genotypes at haplotype level. Rather than comparing VCF records row by row, hap.py will generate and match alternate sequences in a superlocus. A superlocus is a small region of the genome (sized between 1 and around 1000 bp) that contains one or more variants.", - "keywords": [ - "happy", - "benchmark", - "haplotype", - "validation" - ], - "tools": [ - { - "happy": { - "description": "Haplotype VCF comparison tools", - "homepage": "https://www.illumina.com/products/by-type/informatics-products/basespace-sequence-hub/apps/hap-py-benchmarking.html", - "documentation": "https://github.com/Illumina/hap.py", - "tool_dev_url": "https://github.com/Illumina/hap.py", - "licence": [ - "BSD-2-clause" - ], - "identifier": "biotools:happy" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "query_vcf": { - "type": "file", - "description": "VCF/GVCF file to query", - "pattern": "*.{gvcf,vcf}.gz", - "ontologies": [] - } - }, - { - "truth_vcf": { - "type": "file", - "description": "gold standard VCF file", - "pattern": "*.{gvcf,vcf}.gz", - "ontologies": [] - } - }, - { - "regions_bed": { - "type": "file", - "description": "Sparse regions to restrict the analysis to", - "pattern": "*.bed", - "ontologies": [] - } - }, - { - "targets_bed": { - "type": "file", - "description": "Dense regions to restrict the analysis to", - "pattern": "*.bed", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing fasta file information\ne.g. [ id:'test2']\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA file of the reference genome", - "pattern": "*.{fa,fasta}", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing fai file information\ne.g. [ id:'test3']\n" - } - }, - { - "fasta_fai": { - "type": "file", - "description": "The index of the reference FASTA", - "pattern": "*.fai", - "ontologies": [] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing false_positives_bed file information\ne.g. [ id:'test4']\n" - } - }, - { - "false_positives_bed": { - "type": "file", - "description": "False positive / confident call regions. 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} - ] - } - } - ] - ], - "roc_indel_locations_csv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.roc.Locations.INDEL.csv.gz": { - "type": "file", - "description": "A CSV file containing ROC values for all indels", - "pattern": "*.roc.Locations.INDEL.csv.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "roc_indel_locations_pass_csv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.roc.Locations.INDEL.PASS.csv.gz": { - "type": "file", - "description": "A CSV file containing ROC values for all indels that passed all filters", - "pattern": "*.roc.Locations.INDEL.PASS.csv.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "roc_snp_locations_csv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.roc.Locations.SNP.csv.gz": { - "type": "file", - "description": "A CSV file containing ROC values for all SNPs", - "pattern": "*.roc.Locations.SNP.csv.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "roc_snp_locations_pass_csv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.roc.Locations.SNP.PASS.csv.gz": { - "type": "file", - "description": "A CSV file containing ROC values for all SNPs that passed all filters", - "pattern": "*.roc.Locations.SNP.PASS.csv.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "extended_csv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.extended.csv": { - "type": "file", - "description": "A CSV file containing extended info of the benchmarking", - "pattern": "*.extended.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "runinfo": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.runinfo.json": { - "type": "file", - "description": "A JSON file containing the benchmarking metrics", - "pattern": "*.metrics.json.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "metrics_json": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.metrics.json.gz": { - "type": "file", - "description": "A JSON file containing the run info", - "pattern": "*.runinfo.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.vcf.gz": { - "type": "file", - "description": "An annotated VCF", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tbi": { - "type": "file", - "description": "The index of the annotated VCF", - "pattern": "*.tbi", - "ontologies": [] - } - } - ] - ], - "versions_happy": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "happy": { - "type": "string", - "description": "The tool name" - } - }, - { - "0.3.15": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "happy": { - "type": "string", - "description": "The tool name" - } - }, - { - "0.3.15": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "crisprseq", + "version": "2.3.0" + } ] - ] - }, - "authors": [ - "@nvnieuwk" - ], - "maintainers": [ - "@nvnieuwk" - ] - }, - "pipelines": [ - { - "name": "variantbenchmarking", - "version": "1.5.0" - } - ] - }, - { - "name": "happy_prepy", - "path": "modules/nf-core/happy/prepy/meta.yml", - "type": "module", - "meta": { - "name": "happy_prepy", - "description": "Pre.py is a preprocessing tool made to preprocess VCF files for Hap.py", - "keywords": [ - "happy", - "benchmark", - "haplotype" - ], - "tools": [ - { - "happy": { - "description": "Haplotype VCF comparison tools", - "homepage": "https://www.illumina.com/products/by-type/informatics-products/basespace-sequence-hub/apps/hap-py-benchmarking.html", - "documentation": "https://github.com/Illumina/hap.py", - "tool_dev_url": "https://github.com/Illumina/hap.py", - "licence": [ - "BSD-2-clause" - ], - "identifier": "biotools:happy" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF file to preprocess", - "pattern": "*.{vcf,vcf.gz}", - "ontologies": [] - } - }, - { - "bed": { - "type": "file", - "description": "BED file", - "pattern": "*.bed", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information for reference fasta\ne.g. [ id:'test2']\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA file of the reference genome", - "pattern": "*.{fa,fasta}", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information for reference fai\ne.g. [ id:'test3' ]\n" - } + }, + { + "name": "mageck_mle", + "path": "modules/nf-core/mageck/mle/meta.yml", + "type": "module", + "meta": { + "name": "mageck_mle", + "description": "maximum-likelihood analysis of gene essentialities computation", + "keywords": ["sort", "maximum-likelihood", "CRISPR"], + "tools": [ + { + "mageck": { + "description": "MAGeCK (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout), an algorithm to process, QC, analyze and visualize CRISPR screening data.", + "homepage": "https://sourceforge.net/p/mageck/wiki/Home/#mle", + "documentation": "https://sourceforge.net/p/mageck/wiki/Home/", + "tool_dev_url": "https://bitbucket.org/liulab/mageck/src", + "doi": "10.1186/s13059-015-0843-6", + "licence": ["BSD"], + "identifier": "biotools:mageck" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "count_table": { + "type": "file", + "description": "Count table file.\nEach line in the table should include\nsgRNA name (1st column), target gene (2nd column)\nand read counts in each sample.\n", + "pattern": "*.{txt,tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + { + "design_matrix": { + "type": "file", + "description": "Design matrix describing the samples and conditions", + "pattern": "*.{txt,tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + "output": { + "gene_summary": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.gene_summary.txt": { + "type": "file", + "description": "Gene summary file describing the fitness score\nand associated p-values.\n", + "pattern": "*.{gene_summary}", + "ontologies": [] + } + } + ] + ], + "sgrna_summary": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.sgrna_summary.txt": { + "type": "file", + "description": "sgRNA summary file describing the sgRNA and\nassociated gene\n", + "pattern": "*.{gene_summary}", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@LaurenceKuhl"], + "maintainers": ["@LaurenceKuhl"] }, - { - "fasta_fai": { - "type": "file", - "description": "The index of the reference FASTA", - "pattern": "*.fai", - "ontologies": [] - } - } - ] - ], - "output": { - "preprocessed_vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.vcf.gz": { - "type": "file", - "description": "Preprocessed VCF file", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "versions_happy": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "happy": { - "type": "string", - "description": "The tool name" - } - }, - { - "0.3.15": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "happy": { - "type": "string", - "description": "The tool name" - } - }, - { - "0.3.15": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "crisprseq", + "version": "2.3.0" + } ] - ] - }, - "authors": [ - "@nvnieuwk" - ], - "maintainers": [ - "@nvnieuwk" - ] - }, - "pipelines": [ - { - "name": "variantbenchmarking", - "version": "1.5.0" - } - ] - }, - { - "name": "happy_sompy", - "path": "modules/nf-core/happy/sompy/meta.yml", - "type": "module", - "meta": { - "name": "happy_sompy", - "description": "Hap.py is a tool to compare diploid genotypes at haplotype level. som.py is a part of hap.py compares somatic variations.", - "keywords": [ - "happy", - "sompy", - "benchmark", - "haplotype", - "validation", - "somatic variants" - ], - "tools": [ - { - "sompy": { - "description": "Haplotype VCF comparison tools somatic variant comparison", - "homepage": "https://www.illumina.com/products/by-type/informatics-products/basespace-sequence-hub/apps/hap-py-benchmarking.html", - "documentation": "https://github.com/Illumina/hap.py/blob/master/doc/sompy.md", - "tool_dev_url": "https://github.com/Illumina/hap.py", - "licence": [ - "BSD-2-clause" - ], - "identifier": "biotools:happy" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "query_vcf": { - "type": "file", - "description": "VCF/GVCF file to query", - "pattern": "*.{gvcf,vcf}.gz", - "ontologies": [] - } - }, - { - "truth_vcf": { - "type": "file", - "description": "gold standard VCF file", - "pattern": "*.{gvcf,vcf}.gz", - "ontologies": [] - } - }, - { - "regions_bed": { - "type": "file", - "description": "Sparse regions to restrict the analysis to", - "pattern": "*.bed", - "ontologies": [] - } - }, - { - "targets_bed": { - "type": "file", - "description": "Dense regions to restrict the analysis to", - "pattern": "*.bed", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing fasta file information\ne.g. [ id:'test2']\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA file of the reference genome", - "pattern": "*.{fa,fasta}", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing fai file information\ne.g. [ id:'test3']\n" - } - }, - { - "fasta_fai": { - "type": "file", - "description": "The index of the reference FASTA", - "pattern": "*.fai", - "ontologies": [] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing false_positives_bed file information\ne.g. [ id:'test4']\n" - } - }, - { - "false_positives_bed": { - "type": "file", - "description": "False positive / confident call regions. Calls outside these regions will be labelled as UNK.", - "pattern": "*.{bed,bed.gz}", - "ontologies": [] - } - } - ], - [ - { - "meta5": { - "type": "map", - "description": "Groovy Map containing ambiguous_beds file information\ne.g. [ id:'test5']\n" - } - }, - { - "ambiguous_beds": { - "type": "file", - "description": "Ambiguous regions", - "pattern": "*.{bed,bed.gz}", - "ontologies": [] - } - } - ], - [ - { - "meta6": { - "type": "map", - "description": "Groovy Map containing bam file information\ne.g. [ id:'test6']\n" - } + }, + { + "name": "mageck_test", + "path": "modules/nf-core/mageck/test/meta.yml", + "type": "module", + "meta": { + "name": "mageck_test", + "description": "Mageck test performs a robust ranking aggregation (RRA) to identify positively or negatively selected genes in functional genomics screens.", + "keywords": ["sort", "rra", "CRISPR"], + "tools": [ + { + "mageck": { + "description": "MAGeCK (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout), an algorithm to process, QC, analyze and visualize CRISPR screening data.", + "homepage": "https://sourceforge.net/p/mageck/wiki/Home/#mle", + "documentation": "https://sourceforge.net/p/mageck/wiki/Home/", + "tool_dev_url": "https://bitbucket.org/liulab/mageck/src", + "doi": "10.1186/s13059-015-0843-6", + "licence": ["BSD License"], + "identifier": "biotools:mageck" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "count_table": { + "type": "file", + "description": "Count table file.\nEach line in the table should include\nsgRNA name (1st column), target gene (2nd column)\nand read counts in each sample.\n", + "pattern": "*.{txt,tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "output": { + "gene_summary": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.gene_summary.txt": { + "type": "file", + "description": "Gene summary file describing the fitness score\nand associated p-values.\n", + "pattern": "*.{gene_summary.txt}", + "ontologies": [] + } + } + ] + ], + "sgrna_summary": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.sgrna_summary.txt": { + "type": "file", + "description": "sgRNA summary file describing the sgRNA and\nassociated gene\n", + "pattern": "*.{sgrna_summary.txt}", + "ontologies": [] + } + } + ] + ], + "r_script": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.R": { + "type": "file", + "description": "R script allowing to output plots\nfrom main hit genes\n", + "pattern": "*.R", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3999" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@LaurenceKuhl"], + "maintainers": ["@LaurenceKuhl"] }, - { - "bams": { - "type": "file", - "description": "one or more BAM files for feature table extraction", - "pattern": "*.bam", - "ontologies": [] - } - } - ] - ], - "output": { - "features": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.features.csv": { - "type": "file", - "description": "One or more than one (if AF count is on ) CSV file containing feature information", - "pattern": "*.features.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "metrics": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.metrics.json": { - "type": "file", - "description": "One or more than one (if AF count is on ) JSON file with metrics", - "pattern": "*.metrics.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "stats": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.stats.csv": { - "type": "file", - "description": "One or more than one (if AF count is on ) CSV file with benchmark stats", - "pattern": "*.stats.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "versions_happy": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "happy": { - "type": "string", - "description": "The tool name" - } - }, - { - "0.3.15": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "happy": { - "type": "string", - "description": "The tool name" - } - }, - { - "0.3.15": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "crisprseq", + "version": "2.3.0" + } ] - ] }, - "authors": [ - "@kubranarci" - ] - }, - "pipelines": [ { - "name": "variantbenchmarking", - "version": "1.5.0" - } - ] - }, - { - "name": "hasheddrops", - "path": "modules/nf-core/hasheddrops/meta.yml", - "type": "module", - "meta": { - "name": "hasheddrops", - "description": "Generating cell hashing calls from a matrix of count data.", - "keywords": [ - "demultiplexing", - "hashing-based deconvolution", - "single-cell" - ], - "tools": [ - { - "hasheddrops": { - "description": "Demultiplex cell barcodes into their samples of origin based on the most abundant hash tag oligo (HTO). Also identify potential doublets based on the presence of multiple significant HTOs.", - "homepage": "https://rdrr.io/github/MarioniLab/DropletUtils/man/hashedDrops.html", - "documentation": "https://rdrr.io/github/MarioniLab/DropletUtils/man/hashedDrops.html", - "tool_dev_url": "https://github.com/MarioniLab/DropletUtils", - "doi": "10.18129/B9.bioc.DropletUtils", - "licence": [ - "GPL-3" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "hto_matrix": { - "type": "file", - "description": "Directory that contains the HTO matrix in a 10X format.\n", - "ontologies": [ - { - "edam": "http://edamontology.org/data_3917" - } - ] - } - }, - { - "runEmptyDrops": { - "type": "boolean", - "description": "Run EmptyDrops() before hashedDrops() (\"TRUE\") or not (\"FALSE\").\n" - } + "name": "magus_align", + "path": "modules/nf-core/magus/align/meta.yml", + "type": "module", + "meta": { + "name": "magus_align", + "description": "Multiple Sequence Alignment using Graph Clustering", + "keywords": ["MSA", "alignment", "genomics", "graph"], + "tools": [ + { + "magus": { + "description": "Multiple Sequence Alignment using Graph Clustering", + "homepage": "https://github.com/vlasmirnov/MAGUS", + "documentation": "https://github.com/vlasmirnov/MAGUS", + "tool_dev_url": "https://github.com/vlasmirnov/MAGUS", + "doi": "10.1093/bioinformatics/btaa992", + "licence": ["MIT"], + "identifier": "biotools:magus" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing the fasta meta information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input sequences in FASTA format.", + "pattern": "*.{fa,fna,fasta}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1919" + }, + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information for the specified guide tree (if supplied)\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "tree": { + "type": "file", + "description": "Optional path to a file containing a guide tree in newick format to use as input. If empty, or overwritten by passing `-t [fasttree|fasttree-noml|clustal|parttree]`, MAGUS will construct its own guide tree. If empty, `fasttree` is used as a default.", + "pattern": "*.{dnd,tree}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2006" + } + ] + } + } + ], + { + "compress": { + "type": "boolean", + "description": "Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded." + } + } + ], + "output": { + "alignment": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample meta information.\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.aln{.gz,}": { + "type": "file", + "description": "File containing the output alignment, in FASTA format containing gaps. The sequences may be in a different order than in the input FASTA. The output file may or may not be gzipped, depending on the value supplied to `compress`.", + "pattern": "*.aln{.gz,}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2554" + }, + { + "edam": "http://edamontology.org/format_1921" + }, + { + "edam": "http://edamontology.org/format_1984" + } + ] + } + } + ] + ], + "versions_magus": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "magus": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "magus --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_pigz": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "pigz": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pigz --version 2>&1 | sed \"s/^.*pigz[[:space:]]*//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "magus": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "magus --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "pigz": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pigz --version 2>&1 | sed \"s/^.*pigz[[:space:]]*//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@lrauschning"] }, - { - "rna_matrix": { - "type": "file", - "description": "Path to RNA count matrix, which is only uses if runEmptyDrops == \"TRUE\".\n", - "ontologies": [ - { - "edam": "http://edamontology.org/data_3917" - } - ] - } - } - ] - ], - "output": { - "empty_drops_plot": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*_emptyDrops.png": { - "type": "file", - "description": "EmptyDrops results plot\n", - "pattern": "_emptyDrops.png", - "ontologies": [] - } - } - ] - ], - "empty_drops_csv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*_emptyDrops.csv": { - "type": "file", - "description": "EmptyDrops results in CSV format\n", - "pattern": "_emptyDrops.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "empty_drops_rds": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*_emptyDrops.rds": { - "type": "file", - "description": "EmptyDrops results in RDS format\n", - "pattern": "_emptyDrops.rds", - "ontologies": [] - } - } - ] - ], - "results": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*_results_hasheddrops.csv": { - "type": "file", - "description": "HashedDrops results\n", - "pattern": "_results_hasheddrops.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "id_to_hash": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*_id_to_hash.csv": { - "type": "file", - "description": "A table mapping integer indices used by hashedDrops results (e.g. the column `Best` or `Second`) to HTO names (or combinations of HTO names joined with `+` if `combinations` is speficied in `ext.args`).\n", - "pattern": "_id_to_hash.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "rds": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*_hasheddrops.rds": { - "type": "file", - "description": "HashedDrops results in RDS format\n", - "pattern": "_hasheddrops.rds", - "ontologies": [] - } - } - ] - ], - "plot": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*_plot_hasheddrops.png": { - "type": "file", - "description": "HashedDrops plot\n", - "pattern": "_plot_hasheddrops.png", - "ontologies": [] - } - } - ] - ], - "params": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*_params_hasheddrops.csv": { - "type": "file", - "description": "The used parameters to call hashedDrops() in the R-Script.\n", - "pattern": "_params_hasheddrops.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } + "pipelines": [ + { + "name": "multiplesequencealign", + "version": "1.1.1" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "topics": { - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@LuisHeinzlmeier" - ], - "maintainers": [ - "@LuisHeinzlmeier" - ] - } - }, - { - "name": "helitronscanner_draw", - "path": "modules/nf-core/helitronscanner/draw/meta.yml", - "type": "module", - "meta": { - "name": "helitronscanner_draw", - "description": "HelitronScanner draw tool for Helitron transposons in genomes", - "keywords": [ - "genomics", - "helitron", - "scanner" - ], - "tools": [ - { - "helitronscanner": { - "description": "HelitronScanner uncovers a large overlooked cache of Helitron transposons in many genomes", - "homepage": "https://sourceforge.net/projects/helitronscanner", - "documentation": "https://sourceforge.net/projects/helitronscanner", - "tool_dev_url": "https://sourceforge.net/projects/helitronscanner", - "doi": "10.1073/pnas.1410068111", - "licence": [ - "GPL v3-or-later" - ], - "identifier": "" + }, + { + "name": "magus_guidetree", + "path": "modules/nf-core/magus/guidetree/meta.yml", + "type": "module", + "meta": { + "name": "magus_guidetree", + "description": "Multiple Sequence Alignment using Graph Clustering", + "keywords": ["MSA", "guidetree", "genomics", "graph"], + "tools": [ + { + "magus": { + "description": "Multiple Sequence Alignment using Graph Clustering", + "homepage": "https://github.com/vlasmirnov/MAGUS", + "documentation": "https://github.com/vlasmirnov/MAGUS", + "tool_dev_url": "https://github.com/vlasmirnov/MAGUS", + "doi": "10.1093/bioinformatics/btaa992", + "licence": ["MIT"], + "identifier": "biotools:magus" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing fasta meta information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input sequences in FASTA format.", + "pattern": "*.{fa,fna,fasta}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1919" + }, + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ] + ], + "output": { + "tree": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.tree": { + "type": "file", + "description": "File containing the output guidetree, in newick format.", + "pattern": "*.tree", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2006" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@lrauschning"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Genome data to scan for Helitrons", - "pattern": "*.{fa,fsa,fasta}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "head": { - "type": "file", - "description": "Output of the HelitronScanner head command", - "pattern": "*.{head}", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "tail": { - "type": "file", - "description": "Output of the HelitronScanner tail command", - "pattern": "*.{tail}", - "ontologies": [] - } - } - ] - ], - "output": { - "draw": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n", - "pattern": "*.{draw}" - } - }, - { - "*.draw": { - "type": "map", - "description": "The draw output from HelitronScanner\n", - "pattern": "*.{draw}" - } - } - ] - ], - "versions_helitronscanner": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "helitronscanner": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "HelitronScanner |& sed -n 's/HelitronScanner V//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "helitronscanner": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "HelitronScanner |& sed -n 's/HelitronScanner V//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@GallVp", - "@jguhlin" - ], - "maintainers": [ - "@GallVp" - ] - } - }, - { - "name": "helitronscanner_scan", - "path": "modules/nf-core/helitronscanner/scan/meta.yml", - "type": "module", - "meta": { - "name": "helitronscanner_scan", - "description": "HelitronScanner scanHead and scanTail tools for Helitron transposons in genomes", - "keywords": [ - "genomics", - "helitron", - "scanner" - ], - "tools": [ - { - "helitronscanner": { - "description": "HelitronScanner uncovers a large overlooked cache of Helitron transposons in many genomes", - "homepage": "https://sourceforge.net/projects/helitronscanner", - "documentation": "https://sourceforge.net/projects/helitronscanner", - "tool_dev_url": "https://sourceforge.net/projects/helitronscanner", - "doi": "10.1073/pnas.1410068111", - "licence": [ - "GPL v3-or-later" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Genome data to scan for Helitrons", - "pattern": "*.{fa,fsa,fasta}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - { - "command": { - "type": "string", - "description": "Command to execute. One of [ 'head', 'tail' ]" - } - }, - { - "lcv_filepath": { - "type": "file", - "description": "LCV file path. If not provided by setting it to [], the LCV file packaged with the module will be used", - "pattern": "*.lcvs", - "ontologies": [] - } - }, - { - "buffer_size": { - "type": "integer", - "description": "Genome slice size (use negative or zero for non-buffer, i.e. treat every whole chromosome)" - } - } - ], - "output": { - "scan": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.$command": { - "type": "file", - "description": "Head or tail file depending on the command", - "pattern": "*.$command", - "ontologies": [] - } - } - ] - ], - "versions_helitronscanner": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "helitronscanner": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "HelitronScanner |& sed -n 's/HelitronScanner V//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "helitronscanner": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "HelitronScanner |& sed -n 's/HelitronScanner V//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@GallVp" - ], - "maintainers": [ - "@GallVp" - ] - } - }, - { - "name": "hhsuite_hhblits", - "path": "modules/nf-core/hhsuite/hhblits/meta.yml", - "type": "module", - "meta": { - "name": "hhsuite_hhblits", - "description": "Fast and sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs)", - "keywords": [ - "sensitive search", - "HMM", - "alignment" - ], - "tools": [ - { - "hhsuite": { - "description": "HH-suite3 for fast remote homology detection and deep protein annotation", - "homepage": "https://github.com/soedinglab/hh-suite", - "documentation": "https://github.com/soedinglab/hh-suite/wiki", - "tool_dev_url": "https://github.com/soedinglab/hh-suite", - "doi": "10.1371/journal.pone.0082138", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:hh-suite" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "aln": { - "type": "file", - "description": "Input multiple sequence alignment file in a2m or a3m format", - "pattern": "*.{a2m,a2m.gz,a3m,a3m.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3281" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "hh_db": { - "type": "directory", - "description": "Input hhsuite formatted database", - "pattern": "*/" - } - } - ] - ], - "output": { - "hhr": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.hhr": { - "type": "file", - "description": "Human-readable result file in a custom text format designed by the HH-suite", - "pattern": "*.hhr", - "ontologies": [] - } - } - ] - ], - "versions_hhsuite": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "hhsuite": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "hhblits -h 2>&1 | sed '1!d;s/^HHblits //;s/://'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "hhsuite": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "hhblits -h 2>&1 | sed '1!d;s/^HHblits //;s/://'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@vagkaratzas" - ], - "maintainers": [ - "@vagkaratzas" - ] - } - }, - { - "name": "hhsuite_hhsearch", - "path": "modules/nf-core/hhsuite/hhsearch/meta.yml", - "type": "module", - "meta": { - "name": "hhsuite_hhsearch", - "description": "Sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs)", - "keywords": [ - "sensitive search", - "HMM", - "alignment" - ], - "tools": [ - { - "hhsuite": { - "description": "HH-suite3 for fast remote homology detection and deep protein annotation", - "homepage": "https://github.com/soedinglab/hh-suite", - "documentation": "https://github.com/soedinglab/hh-suite/wiki", - "tool_dev_url": "https://github.com/soedinglab/hh-suite", - "doi": "10.1371/journal.pone.0082138", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:hh-suite" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "aln": { - "type": "file", - "description": "Input multiple sequence alignment file in a2m or a3m format", - "pattern": "*.{a2m,a2m.gz,a3m,a3m.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3281" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "hh_db": { - "type": "directory", - "description": "Input hhsuite formatted database", - "pattern": "*/" - } - } - ] - ], - "output": { - "hhr": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.hhr": { - "type": "file", - "description": "Human-readable result file in a custom text format designed by the HH-suite", - "pattern": "*.hhr", - "ontologies": [] - } - } - ] - ], - "versions_hhsuite": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "hhsuite": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "hhblits -h 2>&1 | sed '1!d;s/^HHblits //;s/://'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "hhsuite": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "hhblits -h 2>&1 | sed '1!d;s/^HHblits //;s/://'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@vagkaratzas" - ], - "maintainers": [ - "@vagkaratzas" - ] - } - }, - { - "name": "hhsuite_reformat", - "path": "modules/nf-core/hhsuite/reformat/meta.yml", - "type": "module", - "meta": { - "name": "hhsuite_reformat", - "description": "Reformat a Multiple Sequence Alignment (MSA) file", - "keywords": [ - "reformat", - "MSA", - "hhsuite", - "alignment" - ], - "tools": [ - { - "hhsuite": { - "description": "HH-suite3 for fast remote homology detection and deep protein annotation", - "homepage": "https://github.com/soedinglab/hh-suite", - "documentation": "https://github.com/soedinglab/hh-suite/wiki", - "tool_dev_url": "https://github.com/soedinglab/hh-suite", - "doi": "10.1371/journal.pone.0082138", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:hh-suite" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "aln": { - "type": "file", - "description": "Input MSA file", - "pattern": "*.{fa,fasta,fas,a2m,a3m,sto,psi,clu,fa.gz,fasta.gz,fas.gz,a2m.gz,a3m.gz,sto.gz,psi.gz,clu.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - }, - { - "edam": "http://edamontology.org/format_1984" - }, - { - "edam": "http://edamontology.org/format_3281" - }, - { - "edam": "http://edamontology.org/format_1961" - }, - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ], - { - "informat": { - "type": "string", - "description": "Format of the input MSA file", - "enum": [ - "fas", - "a2m", - "a3m", - "sto", - "psi", - "clu" - ] - } - }, - { - "outformat": { - "type": "string", - "description": "Format of the output MSA file", - "enum": [ - "fas", - "a2m", - "a3m", - "sto", - "psi", - "clu" - ] - } - } - ], - "output": { - "msa": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}.${outformat}.gz": { - "type": "file", - "description": "Gzipped reformatted output MSA file", - "pattern": "*.{fas.gz,a2m.gz,a3m.gz,sto.gz,psi.gz,clu.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "versions_hhsuite": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "hhsuite": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "hhblits -h 2>&1 | sed '1!d;s/^HHblits //;s/://'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "hhsuite": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "hhblits -h 2>&1 | sed '1!d;s/^HHblits //;s/://'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@vagkaratzas" - ], - "maintainers": [ - "@vagkaratzas" - ] - }, - "pipelines": [ - { - "name": "proteinfamilies", - "version": "2.3.0" - } - ] - }, - { - "name": "hicap", - "path": "modules/nf-core/hicap/meta.yml", - "type": "module", - "meta": { - "name": "hicap", - "description": "Identify cap locus serotype and structure in your Haemophilus influenzae assemblies", - "keywords": [ - "fasta", - "serotype", - "Haemophilus influenzae" - ], - "tools": [ - { - "hicap": { - "description": "In silico typing of the H. influenzae capsule locus", - "homepage": "https://github.com/scwatts/hicap", - "documentation": "https://github.com/scwatts/hicap", - "tool_dev_url": "https://github.com/scwatts/hicap", - "doi": "10.1128/JCM.00190-19", - "licence": [ - "GPL v3" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA formatted assembly file", - "pattern": "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}", - "ontologies": [] - } - } - ], - { - "database_dir": { - "type": "directory", - "description": "Optional - Directory containing locus database", - "pattern": "*/*" - } - }, - { - "model_fp": { - "type": "file", - "description": "Optional - Prodigal model to use for gene prediction", - "pattern": "*.{bin}", - "ontologies": [] - } - } - ], - "output": { - "gbk": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.gbk": { - "type": "file", - "description": "GenBank file and cap locus annotations", - "pattern": "*.gbk", - "ontologies": [] - } - } - ] - ], - "svg": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.svg": { - "type": "file", - "description": "Visualization of annotated cap locus", - "pattern": "*.svg", - "ontologies": [] - } - } - ] - ], - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "Detailed summary of cap locus annotations", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_hicap": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "hicap": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "hicap --version 2>&1 | sed 's/^.*hicap //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "hicap": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "hicap --version 2>&1 | sed 's/^.*hicap //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@rpetit3" - ], - "maintainers": [ - "@rpetit3" - ] - } - }, - { - "name": "hicexplorer_hicpca", - "path": "modules/nf-core/hicexplorer/hicpca/meta.yml", - "type": "module", - "meta": { - "name": "hicexplorer_hicpca", - "description": "Computes PCA eigenvectors for a Hi-C matrix.", - "keywords": [ - "eigenvectors", - "PCA", - "hicPCA" - ], - "tools": [ - { - "hicexplorer": { - "description": "Set of programs to process, analyze and visualize Hi-C and capture Hi-C data", - "homepage": "https://hicexplorer.readthedocs.io", - "documentation": "https://hicexplorer.readthedocs.io", - "tool_dev_url": "https://github.com/deeptools/HiCExplorer", - "doi": "10.1038/s41467-017-02525-w", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:hicexplorer" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', bin:50000 ]\n" - } - }, - { - "matrix": { - "type": "file", - "description": "HiCExplorer matrix in h5 format", - "ontologies": [] - } - } - ] - ], - "output": { - "results": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', bin:50000 ]\n" - } - }, - { - "${prefix}_*": { - "type": "file", - "description": "Outputs of hicPCA", - "ontologies": [] - } - } - ] - ], - "pca1": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', bin:50000 ]\n" - } - }, - { - "${prefix}_pca1.$format": { - "type": "file", - "description": "PCA1 file", - "ontologies": [] - } - } - ] - ], - "pca2": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', bin:50000 ]\n" - } - }, - { - "${prefix}_pca2.$format": { - "type": "file", - "description": "PCA2 file", - "ontologies": [] - } - } - ] - ], - "versions_hicexplorer": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "hicexplorer": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "hicPCA --version 2>&1 | sed 's/hicPCA //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "hicexplorer": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "hicPCA --version 2>&1 | sed 's/hicPCA //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@jianhong" - ], - "maintainers": [ - "@jianhong" - ] - } - }, - { - "name": "hifiadapterfilt_downloaddb", - "path": "modules/nf-core/hifiadapterfilt/downloaddb/meta.yml", - "type": "module", - "meta": { - "name": "hifiadapterfilt_downloaddb", - "description": "Downloads the pre-built PacBio adapter BLAST database from the HiFiAdapterFilt\nGitHub repository. The database contains two adapter sequences: NGB00972.1\n(Pacific Biosciences Blunt Adapter, 45 bp) and NGB00973.1 (C2 Primer, 35 bp).\nThis module is consumed by hifiadapterfilt/hifiadapterfilt as a prerequisite to\nprovide the BLAST database for adapter detection.\n", - "keywords": [ - "pacbio", - "hifi", - "adapter", - "blast", - "database", - "download" - ], - "tools": [ - { - "hifiadapterfilt": { - "description": "HiFiAdapterFilt uses BLAST to identify and remove adapter sequences\nfrom PacBio HiFi reads, producing adapter-filtered FASTQ output along\nwith detailed statistics.\n", - "homepage": "https://github.com/sheinasim/HiFiAdapterFilt", - "documentation": "https://github.com/sheinasim/HiFiAdapterFilt", - "tool_dev_url": "https://github.com/sheinasim/HiFiAdapterFilt", - "licence": [ - "MIT" - ], - "identifier": "biotools:HiFiAdapterFilt" - } - } - ], - "input": [], - "output": { - "db": [ - { - "DB": { - "type": "directory", - "description": "Directory containing the pre-built BLAST nucleotide database for PacBio\nadapter sequences. Contains pacbio_vectors_db.* files (NGB00972.1 Blunt\nAdapter and NGB00973.1 C2 Primer).\n", - "pattern": "DB" - } - } - ], - "versions_hifiadapterfilt": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "hifiadapterfilt": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "hifiadapterfilt.sh --version 2>&1 | head -1": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "hifiadapterfilt": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "hifiadapterfilt.sh --version 2>&1 | head -1": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@vagkaratzas" - ], - "maintainers": [ - "@vagkaratzas" - ] - } - }, - { - "name": "hifiadapterfilt_hifiadapterfilt", - "path": "modules/nf-core/hifiadapterfilt/hifiadapterfilt/meta.yml", - "type": "module", - "meta": { - "name": "hifiadapterfilt_hifiadapterfilt", - "description": "Remove adapter sequences from PacBio HiFi (CCS) reads using BLAST-based\ndetection. Produces filtered FASTQ output, filtering statistics, BLAST hits,\nand a list of blocked read IDs.\n", - "keywords": [ - "pacbio", - "hifi", - "adapter", - "filtering", - "long reads", - "ccs" - ], - "tools": [ - { - "hifiadapterfilt": { - "description": "HiFiAdapterFilt uses BLAST to identify and remove adapter sequences\nfrom PacBio HiFi reads, producing adapter-filtered FASTQ output along\nwith detailed statistics.\n", - "homepage": "https://github.com/sheinasim/HiFiAdapterFilt", - "documentation": "https://github.com/sheinasim/HiFiAdapterFilt", - "tool_dev_url": "https://github.com/sheinasim/HiFiAdapterFilt", - "licence": [ - "MIT" - ], - "identifier": "biotools:HiFiAdapterFilt" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "reads": { - "type": "file", - "description": "PacBio HiFi reads in BAM or FASTQ (compressed or uncompressed) format", - "pattern": "*.{bam,fastq|fq(.gz)}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - }, - { - "edam": "http://edamontology.org/format_1930" - }, - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - }, - { - "db": { - "type": "directory", - "description": "Directory containing the pre-built BLAST nucleotide database for PacBio\nadapter sequences, as produced by the hifiadapterfilt/downloaddb module.\nMust contain pacbio_vectors_db.* files.\n", - "pattern": "DB" - } - } - ] - ], - "output": { - "fastq": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}.filt.fastq.gz": { - "type": "file", - "description": "Adapter-filtered reads in gzipped FASTQ format", - "pattern": "*.filt.fastq.gz", - "ontologies": [ + }, + { + "name": "malt_build", + "path": "modules/nf-core/malt/build/meta.yml", + "type": "module", + "meta": { + "name": "malt_build", + "description": "MALT, an acronym for MEGAN alignment tool, is a sequence alignment and analysis tool designed for processing high-throughput sequencing data, especially in the context of metagenomics.", + "keywords": [ + "malt", + "alignment", + "metagenomics", + "ancient DNA", + "aDNA", + "palaeogenomics", + "archaeogenomics", + "microbiome", + "database" + ], + "tools": [ + { + "malt": { + "description": "A tool for mapping metagenomic data", + "homepage": "https://www.wsi.uni-tuebingen.de/lehrstuehle/algorithms-in-bioinformatics/software/malt/", + "documentation": "https://software-ab.cs.uni-tuebingen.de/download/malt/manual.pdf", + "doi": "10.1038/s41559-017-0446-6", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ { - "edam": "http://edamontology.org/format_1930" + "fastas": { + "type": "file", + "description": "Directory of, or list of FASTA reference files for indexing", + "pattern": "*/|*.fasta", + "ontologies": [] + } }, { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "stats": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}.stats": { - "type": "file", - "description": "Filtering statistics file", - "pattern": "*.stats", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3671" - } - ] - } - } - ] - ], - "blastout": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}.contaminant.blastout": { - "type": "file", - "description": "BLAST tabular output for reads containing adapter sequences", - "pattern": "*.contaminant.blastout", - "ontologies": [] - } - } - ] - ], - "blocklist": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}.blocklist": { - "type": "file", - "description": "List of read IDs blocked due to adapter contamination", - "pattern": "*.blocklist", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3671" - } - ] - } - } - ] - ], - "versions_hifiadapterfilt": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "hifiadapterfilt": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "hifiadapterfilt.sh --version 2>&1 | head -1": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "hifiadapterfilt": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "hifiadapterfilt.sh --version 2>&1 | head -1": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@vagkaratzas" - ], - "maintainers": [ - "@vagkaratzas" - ] - } - }, - { - "name": "hifiasm", - "path": "modules/nf-core/hifiasm/meta.yml", - "type": "module", - "meta": { - "name": "hifiasm", - "description": "Whole-genome assembly using PacBio HiFi reads", - "keywords": [ - "genome assembly", - "haplotype resolution", - "phasing", - "PacBio", - "HiFi", - "long reads" - ], - "tools": [ - { - "hifiasm": { - "description": "Haplotype-resolved assembler for accurate HiFi reads", - "homepage": "https://github.com/chhylp123/hifiasm", - "documentation": "https://github.com/chhylp123/hifiasm", - "tool_dev_url": "https://github.com/chhylp123/hifiasm", - "doi": "10.1038/s41592-020-01056-5", - "licence": [ - "MIT" - ], - "identifier": "biotools:hifiasm" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "long_reads": { - "type": "file", - "description": "Long reads PacBio HiFi reads or ONT reads (requires ext.arg '--ont').", - "ontologies": [] - } - }, - { - "ul_reads": { - "type": "file", - "description": "ONT long reads to use with --ul.", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing information about parental kmers.\n" - } - }, - { - "paternal_kmer_dump": { - "type": "file", - "description": "Yak kmer dump file for paternal reads (can be used for haplotype resolution). It can have an arbitrary extension.", - "ontologies": [] - } - }, - { - "maternal_kmer_dump": { - "type": "file", - "description": "Yak kmer dump file for maternal reads (can be used for haplotype resolution). It can have an arbitrary extension.", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing information about Hi-C reads\n" - } - }, - { - "hic_read1": { - "type": "file", - "description": "Hi-C data Forward reads.", - "ontologies": [] - } - }, - { - "hic_read2": { - "type": "file", - "description": "Hi-C data Reverse reads.", - "ontologies": [] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing information about the input bin files\n" - } - }, - { - "bin_files": { - "type": "file", - "description": "bin files produced during a previous Hifiasm run", - "ontologies": [] - } - } - ] - ], - "output": { - "raw_unitigs": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.r_utg.gfa": { - "type": "file", - "description": "Raw unitigs", - "pattern": "*.r_utg.gfa", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3975" - } - ] - } - } - ] - ], - "bin_files": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bin": { - "type": "file", - "description": "Binary files containing processed data for hifiasm, including\nerror-corrected reads, read overlaps, and Hi-C alignments. Can\nbe re-used as an input for subsequent re-runs of hifiasm with new\ninputs or modified parameters in order to save recomputation of\ninitial results, which are the most computationally-expensive\nsteps.\n", - "pattern": "*.bin", - "ontologies": [] - } - } - ] - ], - "processed_unitigs": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.p_utg.gfa": { - "type": "file", - "description": "Processed unitigs", - "pattern": "*.p_utg.gfa", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3975" - } - ] - } - } - ] - ], - "primary_contigs": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.{p_ctg,bp.p_ctg,hic.p_ctg}.gfa": { - "type": "file", - "description": "Contigs representing the primary assembly", - "pattern": "${prefix}.{p_ctg,bp.p_ctg,hic.p_ctg}.gfa", - "ontologies": [] - } - } - ] - ], - "alternate_contigs": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.{a_ctg,hic.a_ctg}.gfa": { - "type": "file", - "description": "Contigs representing the alternative assembly", - "pattern": "${prefix}.{a_ctg,hic.a_ctg}.gfa", - "ontologies": [] - } - } - ] - ], - "hap1_contigs": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.*.hap1.p_ctg.gfa": { - "type": "file", - "description": "Contigs for the first haplotype. How the haplotypes are represented\ndepends on the input mode; in standard HiFi-only mode, these\nare partially-phased parental contigs. In Hi-C mode, they\nare fully phased parental contigs, but the phasing is not maintained\nbetween contigs. In trio mode, they are fully phased paternal contigs\nall originating from a single parental haplotype.\n", - "pattern": "${prefix}.*.hap1.p_ctg.gfa", - "ontologies": [] - } - } - ] - ], - "hap2_contigs": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.*.hap2.p_ctg.gfa": { - "type": "file", - "description": "Contigs for the second haplotype. How the haplotypes are represented\ndepends on the input mode; in standard HiFi-only mode, these\nare partially-phased parental contigs. In Hi-C mode, they\nare fully phased parental contigs, but the phasing is not maintained\nbetween contigs. In trio mode, they are fully phased paternal contigs\nall originating from a single parental haplotype.\n", - "pattern": "${prefix}.*.hap2.p_ctg.gfa", - "ontologies": [] - } - } - ] - ], - "corrected_reads": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.ec.fa.gz": { - "type": "file", - "description": "If option --write-ec specified, a gzipped fasta file containing the error corrected\nreads produced by the hifiasm error correction module\n", - "pattern": "*.ec.fa.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "read_overlaps": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.ovlp.paf.gz": { - "type": "file", - "description": "If option --write-paf specified, a gzipped paf file describing the overlaps\namong all error-corrected reads\n", - "pattern": "*.ovlp.paf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.stderr.log": { - "type": "file", - "description": "Stderr log", - "pattern": "*.stderr.log", - "ontologies": [] - } - } - ] - ], - "versions_hifiasm": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "hifiasm": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "hifiasm --version 2>&1": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "hifiasm": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "hifiasm --version 2>&1": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@sidorov-si", - "@scorreard", - "@mbeavitt", - "@schmytzi", - "@prototaxites" - ], - "maintainers": [ - "@sidorov-si", - "@scorreard" - ] - }, - "pipelines": [ - { - "name": "genomeassembler", - "version": "1.1.0" - } - ] - }, - { - "name": "hificnv", - "path": "modules/nf-core/hificnv/meta.yml", - "type": "module", - "meta": { - "name": "hificnv", - "description": "Copy number variant calling from PacBio HiFi reads", - "keywords": [ - "copy number variation", - "cnv", - "PacBio", - "HiFi", - "long reads", - "structural variation" - ], - "tools": [ - { - "hificnv": { - "description": "Copy number variant caller designed for PacBio HiFi reads", - "homepage": "https://github.com/PacificBiosciences/HiFiCNV", - "documentation": "https://github.com/PacificBiosciences/HiFiCNV", - "tool_dev_url": "https://github.com/PacificBiosciences/HiFiCNV", - "doi": "10.1093/bioinformatics/btac808", - "licence": [ - "Pacific Biosciences Software License Agreement" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM or CRAM file from PacBio HiFi reads", - "pattern": "*.{bam,cram}", - "ontologies": [] - } - }, - { - "bai": { - "type": "file", - "description": "BAM index file (CSI, CRAI, or BAI format)", - "pattern": "*.{bai,csi,crai}", - "ontologies": [] - } - }, - { - "maf": { - "type": "file", - "description": "Minor allele frequency file (VCF format)", - "pattern": "*.{vcf,vcf.gz}", - "optional": true, - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference genome information\ne.g. `[ id:'GATK.GRCh38' ]`\n" - } - }, - { - "ref": { - "type": "file", - "description": "Reference genome FASTA file", - "pattern": "*.{fa,fasta,fa.gz,fasta.gz}", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing exclude regions information\ne.g. `[ id:'excluded_regions' ]`\n" - } - }, - { - "exclude": { - "type": "file", - "description": "BED file containing regions to exclude from CNV calling", - "pattern": "*.{bed,bed.gz}", - "optional": true, - "ontologies": [] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing expected copy number information\ne.g. `[ id:'male_expected_cn' ]`\n" - } - }, - { - "expected_cn": { - "type": "file", - "description": "BED file containing expected copy number regions", - "pattern": "*.{bed,bed.gz}", - "optional": true, - "ontologies": [] - } - } - ] - ], - "output": { - "copynum": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*.copynum.bedgraph": { - "type": "file", - "description": "Copy number bedGraph file", - "pattern": "*.copynum.bedgraph", - "ontologies": [] - } - } - ] - ], - "depth": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*.depth.bw": { - "type": "file", - "description": "Depth coverage bigWig file", - "pattern": "*.depth.bw", - "ontologies": [] - } - } - ] - ], - "maf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*.maf.bw": { - "type": "file", - "description": "Minor allele frequency bigWig file", - "pattern": "*.maf.bw", - "optional": true, - "ontologies": [] - } - } - ] - ], - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*.vcf.gz": { - "type": "file", - "description": "Copy number variants in VCF format", - "pattern": "*.{vcf.gz}", - "ontologies": [] - } - } - ] - ], - "versions_hificnv": [ - [ - { - "${task.process}": { - "type": "string", - "description": "Name of the process" - } - }, - { - "hificnv": { - "type": "string", - "description": "Name of the tool" - } - }, - { - "hificnv --version | sed 's/.* //g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "Name of the process" - } - }, - { - "hificnv": { - "type": "string", - "description": "Name of the tool" - } - }, - { - "hificnv --version | sed 's/.* //g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@chaochaowong" - ], - "maintainers": [ - "@chaochaowong" - ] - } - }, - { - "name": "hifitrimmer_filterbam", - "path": "modules/nf-core/hifitrimmer/filterbam/meta.yml", - "type": "module", - "meta": { - "name": "hifitrimmer_filterbam", - "description": "Run hifi_trimmer filter_bam to filter and trim adapter hits from PacBio HiFi reads (BAM/FASTA/FASTQ) using BLAST against\nadapter sequences. Primary output is filtered FASTA/FASTQ.\n", - "keywords": [ - "pacbio", - "bam", - "fasta", - "hifi_trimmer", - "filtering", - "trimming", - "quality control", - "adapter removal" - ], - "tools": [ - { - "hifi_trimmer": { - "description": "hifi_trimmer: tools for processing HiFi read BLAST results and filtering/trimming\nread files to output processed FASTA/FASTQ and accompanying summary and hit (optional) files.\n", - "homepage": "https://github.com/sanger-tol/hifi-trimmer", - "documentation": "https://github.com/sanger-tol/hifi-trimmer", - "licence": [ - "MIT" - ] - } - }, - { - "samtools": { - "description": "SAMtools is a set of utilities for interacting with and post-processing\nshort DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.\nThese files are generated as output by short read aligners like BWA.\n", - "homepage": "http://www.htslib.org/", - "documentation": "http://www.htslib.org/doc/samtools.html", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "identifier": "biotools:samtools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "input": { - "type": "file", - "description": "Input BAM/FASTA/FASTQ file to filter", - "pattern": "*.{bam,fa,fasta,fa.gz,fasta.gz,fastq,fq,fastq.gz,fq.gz}" - } - }, - { - "bed": { - "type": "file", - "description": "Input gzipped bed file contains regions to filter/trim", - "pattern": "*.bed.gz" - } - } - ] - ], - "output": { - "filtered": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.fast{q,a}.gz": { - "type": "file", - "description": "Gzipped FASTA/FASTQ produced by hifi_trimmer", - "pattern": "*.fast{q,a}.gz", - "ontologies": [ + "gff": { + "type": "file", + "description": "Directory of, or GFF3 files of input FASTA files", + "pattern": "*/|*.gff|*.gff3", + "ontologies": [] + } + }, { - "edam": "http://edamontology.org/format_1930" + "mapping_db": { + "type": "file", + "description": "An uncompressed MEGAN mapping file from https://software-ab.cs.uni-tuebingen.de/download/megan6/welcome.html (either mapping db, or acc2* .abin file)", + "pattern": "*.{db,abin}", + "ontologies": [] + } }, { - "edam": "http://edamontology.org/format_1929" + "map_type": { + "type": "string", + "description": "The type of map file provided to the pipeline. Must be a valid string corresponding to a single-dash parameter, for example '-a2tax' or '-a2interpro2go'", + "pattern": "mdb|a2t|s2t|a2ec|s2ec|t4ec|a2eggnog|s2eggnog|t4eggnog|a2gtdb|s2gtdb|t4gtdb|a2interpro2go|s2interpro2go|t4interprotogo|a2kegg|s2kegg|t4kegg|a2pgpt|s2pgpt|t4pgpt|a2seed|s2seed|t4seed" + } } - ] + ], + "output": { + "index": [ + { + "malt_index/": { + "type": "directory", + "description": "Directory containing MALT database index directory", + "pattern": "malt_index/" + } + } + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ], + "log": [ + { + "malt-build.log": { + "type": "file", + "description": "Log file from STD out of malt-build", + "pattern": "malt-build.log", + "ontologies": [] + } + } + ] + }, + "authors": ["@jfy133", "@LilyAnderssonLee"], + "maintainers": ["@jfy133", "@LilyAnderssonLee"] + }, + "pipelines": [ + { + "name": "createtaxdb", + "version": "3.0.0" } - } - ] - ], - "versions_hifitrimmer": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "hifi_trimmer": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "hifi_trimmer --version | cut -d' ' -f3": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_samtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "Name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "Name of the tool" - } - }, - { - "samtools --version | head -1 | sed -e \"s/samtools //\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "hifi_trimmer": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "hifi_trimmer --version | cut -d' ' -f3": { - "type": "eval", - "description": "The expression to obtain the version" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "Name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "Name of the tool" - } - }, - { - "samtools --version | head -1 | sed -e \"s/samtools //\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } ] - ] - }, - "authors": [ - "@sainsachiko" - ], - "maintainers": [ - "@sainsachiko" - ] - } - }, - { - "name": "hifitrimmer_processblast", - "path": "modules/nf-core/hifitrimmer/processblast/meta.yml", - "type": "module", - "meta": { - "name": "hifitrimmer_processblast", - "description": "Run hifi_trimmer process_blast to process a BLAST search of adapter sequences against PacBio HiFi reads.\nPrimary output is a BED describing regions to exclude, a json of summary information, and an optional hits file.\n", - "keywords": [ - "pacbio", - "bam", - "hifi_trimmer", - "processblast", - "quality control", - "adapter removal" - ], - "tools": [ - { - "hifi_trimmer": { - "description": "hifi_trimmer: tools for processing HiFi read BLAST results and filtering/trimming\nBAM files to output processed FASTA/FASTQ and accompanying summary and hit (optional) files.\n", - "homepage": "https://github.com/sanger-tol/hifi-trimmer", - "documentation": "https://github.com/sanger-tol/hifi-trimmer", - "licence": [ - "MIT" - ] - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "blast": { - "type": "file", - "description": "BLAST TSV output file used by hifi_trimmer (e.g. .blast, .out). Must be generated using \"blastn -query -db -outfmt '6 std qlen'\".", - "pattern": "*.blast" - } - } - ], - [ - { - "meta1": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } + }, + { + "name": "malt_run", + "path": "modules/nf-core/malt/run/meta.yml", + "type": "module", + "meta": { + "name": "malt_run", + "description": "MALT, an acronym for MEGAN alignment tool, is a sequence alignment and analysis tool designed for processing high-throughput sequencing data, especially in the context of metagenomics.", + "keywords": [ + "malt", + "alignment", + "metagenomics", + "ancient DNA", + "aDNA", + "palaeogenomics", + "archaeogenomics", + "microbiome" + ], + "tools": [ + { + "malt": { + "description": "A tool for mapping metagenomic data", + "homepage": "https://www.wsi.uni-tuebingen.de/lehrstuehle/algorithms-in-bioinformatics/software/malt/", + "documentation": "https://software-ab.cs.uni-tuebingen.de/download/malt/manual.pdf", + "doi": "10.1038/s41559-017-0446-6", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fastqs": { + "type": "file", + "description": "Input FASTQ files", + "pattern": "*.{fastq.gz,fq.gz}", + "ontologies": [] + } + } + ], + { + "index": { + "type": "directory", + "description": "Index/database directory from malt-build", + "pattern": "*/" + } + } + ], + "output": { + "rma6": [ + [ + { + "meta": { + "type": "file", + "description": "MEGAN6 RMA6 file", + "pattern": "*.rma6", + "ontologies": [] + } + }, + { + "*.rma6": { + "type": "file", + "description": "MEGAN6 RMA6 file", + "pattern": "*.rma6", + "ontologies": [] + } + } + ] + ], + "alignments": [ + [ + { + "meta": { + "type": "file", + "description": "MEGAN6 RMA6 file", + "pattern": "*.rma6", + "ontologies": [] + } + }, + { + "*.{tab,text,sam,tab.gz,text.gz,sam.gz}": { + "type": "file", + "description": "Alignment files in Tab, Text or MEGAN-compatible SAM format", + "pattern": "*.{tab,txt,sam}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "file", + "description": "MEGAN6 RMA6 file", + "pattern": "*.rma6", + "ontologies": [] + } + }, + { + "*.log": { + "type": "file", + "description": "Log of verbose MALT stdout", + "pattern": "*-malt-run.log", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@jfy133"], + "maintainers": ["@jfy133"] }, - { - "yaml": { - "type": "file", - "description": "YAML file contain trimming/filtering configuration for `hifi_trimmer`", - "pattern": "*.{yaml,yml}" - } - } - ] - ], - "output": { - "bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + "pipelines": [ + { + "name": "taxprofiler", + "version": "2.0.0" } - }, - { - "*.bed.gz": { - "type": "file", - "description": "Gzipped BED file of selected reads", - "pattern": "*.bed.gz", - "ontologies": [ + ] + }, + { + "name": "maltextract", + "path": "modules/nf-core/maltextract/meta.yml", + "type": "module", + "meta": { + "name": "maltextract", + "description": "Tool for evaluation of MALT results for true positives of ancient metagenomic taxonomic screening", + "keywords": [ + "malt", + "MaltExtract", + "HOPS", + "alignment", + "metagenomics", + "ancient DNA", + "aDNA", + "palaeogenomics", + "archaeogenomics", + "microbiome", + "authentication", + "damage", + "edit distance" + ], + "tools": [ + { + "maltextract": { + "description": "Java tool to work with ancient metagenomics", + "homepage": "https://github.com/rhuebler/hops", + "documentation": "https://github.com/rhuebler/hops", + "tool_dev_url": "https://github.com/rhuebler/hops", + "doi": "10.1186/s13059-019-1903-0", + "licence": ["GPL 3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "rma6": { + "type": "file", + "description": "RMA6 files from MALT", + "pattern": "*.rma6", + "ontologies": [] + } + } + ], { - "edam": "http://edamontology.org/format_3003" + "taxon_list": { + "type": "file", + "description": "List of target taxa to evaluate", + "pattern": "*.txt", + "ontologies": [] + } }, { - "edam": "http://edamontology.org/format_3989" + "ncbi_dir": { + "type": "directory", + "description": "Directory containing NCBI taxonomy map and tre files", + "pattern": "${ncbi_dir}/" + } } - ] - } - } - ] - ], - "summary": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.summary.json": { - "type": "file", - "description": "JSON summary including trimming and filtering information", - "pattern": "*.summary.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "hits": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.hits": { - "type": "file", - "description": "Optional hits file produced by hifi_trimmer (may be absent when no hits found or '-hf' is not specified)", - "pattern": "*.hits", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_hifitrimmer": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "hifi_trimmer": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "hifi_trimmer --version | cut -d' ' -f3": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "hifi_trimmer": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "hifi_trimmer --version | cut -d' ' -f3": { - "type": "eval", - "description": "The expression to obtain the version" - } - } - ] - ] - }, - "authors": [ - "@sainsachiko" - ], - "maintainers": [ - "@sainsachiko" - ] - } - }, - { - "name": "hiphase", - "path": "modules/nf-core/hiphase/meta.yml", - "type": "module", - "meta": { - "name": "hiphase", - "description": "Small and structural variant phasing tool for PacBio HiFi reads, supporting co-phasing of SNVs and SVs across multiple BAM files and samples", - "keywords": [ - "pacbio", - "structural variant", - "phasing", - "pacbio hifi", - "snv", - "haplotagging" - ], - "tools": [ - { - "hiphase": { - "description": "Small and structural variant phasing tool for PacBio HiFi reads", - "homepage": "https://github.com/PacificBiosciences/HiPhase", - "documentation": "https://github.com/PacificBiosciences/HiPhase", - "tool_dev_url": "https://github.com/PacificBiosciences/HiPhase", - "licence": [ - "Pacific Biosciences Software License Agreement" - ], - "identifier": "biotools:hiphase" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "bams": { - "type": "file", - "description": "One or more sorted BAM/CRAM files", - "pattern": "*.{bam,cram}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - }, - { - "bais": { - "type": "file", - "description": "Index files associated with the BAM/CRAM files", - "pattern": "*.{bai,crai,csi}", - "ontologies": [] - } - }, - { - "snv": { - "type": "file", - "description": "Compressed VCF file containing SNV/small variants to phase (optional)", - "pattern": "*.{vcf.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - } - ] - } - }, - { - "snv_index": { - "type": "file", - "description": "Index file for the SNV VCF (optional)", - "pattern": "*.{tbi,csi}", - "ontologies": [] - } - }, - { - "sv": { - "type": "file", - "description": "Compressed VCF file containing structural variants to co-phase (optional)", - "pattern": "*.{vcf.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - } - ] - } - }, - { - "sv_index": { - "type": "file", - "description": "Index file for the SV VCF (optional)", - "pattern": "*.{tbi,csi}", - "ontologies": [] - } - }, - { - "samples": { - "type": "list", - "description": "List of sample names to phase within the VCF, if empty only the first sample is phased." - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference genome information\ne.g. `[ id:'GRCh38' ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome FASTA file used for the BAM alignment", - "pattern": "*.{fasta,fa}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - }, - { - "fai": { - "type": "file", - "description": "FASTA index file (.fai) for the reference genome", - "pattern": "*.fai", - "ontologies": [] - } - } - ], - { - "output_bam": { - "type": "boolean", - "description": "Whether to output haplotagged BAM files. Set to true to emit phased BAM files with haplotag information." - } - }, - { - "summary_file": { - "type": "boolean", - "description": "Whether to output a phasing summary file." - } - }, - { - "blocks_file": { - "type": "boolean", - "description": "Whether to output a phasing blocks file." - } - }, - { - "stats_file": { - "type": "boolean", - "description": "Whether to output a per-read phasing statistics file." - } - }, - { - "haplotag_file": { - "type": "boolean", - "description": "Whether to output a haplotag assignments file." + ], + "output": { + "results": [ + [ + { + "meta": { + "type": "directory", + "description": "Directory containing MaltExtract text results files", + "pattern": "results/" + } + }, + { + "results": { + "type": "directory", + "description": "Directory containing MaltExtract text results files", + "pattern": "results/" + } + } + ] + ], + "versions_maltextract": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "maltextract": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "MaltExtract --help | head -n 2 | tail -n 1 | sed 's/MaltExtract version//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "maltextract": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "MaltExtract --help | head -n 2 | tail -n 1 | sed 's/MaltExtract version//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@jfy133"], + "maintainers": ["@jfy133"] } - }, - { - "file_format": { - "type": "string", - "description": "Output file format for summary/blocks/stats/haplotag files, either 'tsv' or 'csv'." + }, + { + "name": "manta_convertinversion", + "path": "modules/nf-core/manta/convertinversion/meta.yml", + "type": "module", + "meta": { + "name": "manta_convertinversion", + "description": "Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. This script reformats inversions into single inverted sequence junctions which was the format used in Manta versions <= 1.4.0.", + "keywords": ["structural variants", "conversion", "indels"], + "tools": [ + { + "manta": { + "description": "Structural variant and indel caller for mapped sequencing data", + "homepage": "https://github.com/Illumina/manta", + "documentation": "https://github.com/Illumina/manta/blob/v1.6.0/docs/userGuide/README.md", + "tool_dev_url": "https://github.com/Illumina/manta", + "doi": "10.1093/bioinformatics/btv710", + "licence": ["GPL v3"], + "identifier": "biotools:manta_sv" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF file produces by Manta", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing fasta information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The reference fasta file", + "pattern": "*.{fasta,fa,fna}", + "ontologies": [] + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "VCF file with reformatted inversions", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz.tbi": { + "type": "file", + "description": "TBI file produces by Manta", + "pattern": "*.vcf.gz.tbi", + "ontologies": [] + } + } + ] + ], + "versions_manta": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "manta": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "configManta.py --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_samtools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "samtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "samtools --version | head -1 | sed -e s'/samtools //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "manta": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "configManta.py --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "samtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "samtools --version | head -1 | sed -e s'/samtools //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@FriederikeHanssen"], + "maintainers": ["@FriederikeHanssen"] } - } - ], - "output": { - "vcfs": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*_snv_phased.vcf.gz": { - "type": "file", - "description": "Phased and compressed SNV VCF file (optional, only emitted when SNV VCF input is provided)", - "pattern": "*_snv_phased.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - }, + }, + { + "name": "manta_germline", + "path": "modules/nf-core/manta/germline/meta.yml", + "type": "module", + "meta": { + "name": "manta_germline", + "description": "Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs.", + "keywords": ["somatic", "wgs", "wxs", "panel", "vcf", "structural variants", "small indels"], + "tools": [ + { + "manta": { + "description": "Structural variant and indel caller for mapped sequencing data", + "homepage": "https://github.com/Illumina/manta", + "documentation": "https://github.com/Illumina/manta/blob/v1.6.0/docs/userGuide/README.md", + "tool_dev_url": "https://github.com/Illumina/manta", + "doi": "10.1093/bioinformatics/btv710", + "licence": ["GPL v3"], + "identifier": "biotools:manta_sv" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM/SAM file. For joint calling use a list of files.", + "pattern": "*.{bam,cram,sam}", + "ontologies": [] + } + }, + { + "index": { + "type": "file", + "description": "BAM/CRAM/SAM index file. For joint calling use a list of files.", + "pattern": "*.{bai,crai,sai}", + "ontologies": [] + } + }, + { + "target_bed": { + "type": "file", + "description": "BED file containing target regions for variant calling", + "pattern": "*.{bed}", + "ontologies": [] + } + }, + { + "target_bed_tbi": { + "type": "file", + "description": "Index for BED file containing target regions for variant calling", + "pattern": "*.{bed.tbi}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Genome reference FASTA file", + "pattern": "*.{fa,fasta}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Genome reference FASTA index file", + "pattern": "*.{fa.fai,fasta.fai}", + "ontologies": [] + } + } + ], { - "edam": "http://edamontology.org/format_3989" + "config": { + "type": "file", + "description": "Manta configuration file", + "pattern": "*.{ini,conf,config}", + "ontologies": [] + } } - ] + ], + "output": { + "candidate_small_indels_vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*candidate_small_indels.vcf.gz": { + "type": "file", + "description": "Gzipped VCF file containing variants", + "pattern": "*.{vcf.gz}", + "ontologies": [] + } + } + ] + ], + "candidate_small_indels_vcf_tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*candidate_small_indels.vcf.gz.tbi": { + "type": "file", + "description": "Index for gzipped VCF file containing variants", + "pattern": "*.{vcf.gz.tbi}", + "ontologies": [] + } + } + ] + ], + "candidate_sv_vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*candidate_sv.vcf.gz": { + "type": "file", + "description": "Gzipped VCF file containing variants", + "pattern": "*.{vcf.gz}", + "ontologies": [] + } + } + ] + ], + "candidate_sv_vcf_tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*candidate_sv.vcf.gz.tbi": { + "type": "file", + "description": "Index for gzipped VCF file containing variants", + "pattern": "*.{vcf.gz.tbi}", + "ontologies": [] + } + } + ] + ], + "diploid_sv_vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*diploid_sv.vcf.gz": { + "type": "file", + "description": "Gzipped VCF file containing variants", + "pattern": "*.{vcf.gz}", + "ontologies": [] + } + } + ] + ], + "diploid_sv_vcf_tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*diploid_sv.vcf.gz.tbi": { + "type": "file", + "description": "Index for gzipped VCF file containing variants", + "pattern": "*.{vcf.gz.tbi}", + "ontologies": [] + } + } + ] + ], + "versions_manta": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "manta": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "configManta.py --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "manta": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "configManta.py --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@maxulysse", "@ramprasadn", "@nvnieuwk"], + "maintainers": ["@maxulysse", "@ramprasadn", "@nvnieuwk"] + }, + "pipelines": [ + { + "name": "raredisease", + "version": "3.0.0" + }, + { + "name": "sarek", + "version": "3.8.1" } - } ] - ], - "sv_vcfs": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*_sv_phased.vcf.gz": { - "type": "file", - "description": "Phased and compressed SV VCF file (optional, only emitted when SV VCF input is provided)", - "pattern": "*_sv_phased.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - }, + }, + { + "name": "manta_somatic", + "path": "modules/nf-core/manta/somatic/meta.yml", + "type": "module", + "meta": { + "name": "manta_somatic", + "description": "Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs.", + "keywords": ["somatic", "wgs", "wxs", "panel", "vcf", "structural variants", "small indels"], + "tools": [ + { + "manta": { + "description": "Structural variant and indel caller for mapped sequencing data", + "homepage": "https://github.com/Illumina/manta", + "documentation": "https://github.com/Illumina/manta/blob/v1.6.0/docs/userGuide/README.md", + "tool_dev_url": "https://github.com/Illumina/manta", + "doi": "10.1093/bioinformatics/btv710", + "licence": ["GPL v3"], + "identifier": "biotools:manta_sv" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input_normal": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}", + "ontologies": [] + } + }, + { + "input_index_normal": { + "type": "file", + "description": "BAM/CRAM/SAM index file", + "pattern": "*.{bai,crai,sai}", + "ontologies": [] + } + }, + { + "input_tumor": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}", + "ontologies": [] + } + }, + { + "input_index_tumor": { + "type": "file", + "description": "BAM/CRAM/SAM index file", + "pattern": "*.{bai,crai,sai}", + "ontologies": [] + } + }, + { + "target_bed": { + "type": "file", + "description": "BED file containing target regions for variant calling", + "pattern": "*.{bed}", + "ontologies": [] + } + }, + { + "target_bed_tbi": { + "type": "file", + "description": "Index for BED file containing target regions for variant calling", + "pattern": "*.{bed.tbi}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Genome reference FASTA file", + "pattern": "*.{fa,fasta}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Genome reference FASTA index file", + "pattern": "*.{fa.fai,fasta.fai}", + "ontologies": [] + } + } + ], { - "edam": "http://edamontology.org/format_3989" + "config": { + "type": "file", + "description": "Manta configuration file", + "pattern": "*.{ini,conf,config}", + "ontologies": [] + } } - ] + ], + "output": { + "candidate_small_indels_vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.candidate_small_indels.vcf.gz": { + "type": "file", + "description": "Gzipped VCF file containing variants", + "pattern": "*.{vcf.gz}", + "ontologies": [] + } + } + ] + ], + "candidate_small_indels_vcf_tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.candidate_small_indels.vcf.gz.tbi": { + "type": "file", + "description": "Index for gzipped VCF file containing variants", + "pattern": "*.{vcf.gz.tbi}", + "ontologies": [] + } + } + ] + ], + "candidate_sv_vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.candidate_sv.vcf.gz": { + "type": "file", + "description": "Gzipped VCF file containing variants", + "pattern": "*.{vcf.gz}", + "ontologies": [] + } + } + ] + ], + "candidate_sv_vcf_tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.candidate_sv.vcf.gz.tbi": { + "type": "file", + "description": "Index for gzipped VCF file containing variants", + "pattern": "*.{vcf.gz.tbi}", + "ontologies": [] + } + } + ] + ], + "diploid_sv_vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.diploid_sv.vcf.gz": { + "type": "file", + "description": "Gzipped VCF file containing variants", + "pattern": "*.{vcf.gz}", + "ontologies": [] + } + } + ] + ], + "diploid_sv_vcf_tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.diploid_sv.vcf.gz.tbi": { + "type": "file", + "description": "Index for gzipped VCF file containing variants", + "pattern": "*.{vcf.gz.tbi}", + "ontologies": [] + } + } + ] + ], + "somatic_sv_vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.somatic_sv.vcf.gz": { + "type": "file", + "description": "Gzipped VCF file containing variants", + "pattern": "*.{vcf.gz}", + "ontologies": [] + } + } + ] + ], + "somatic_sv_vcf_tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.somatic_sv.vcf.gz.tbi": { + "type": "file", + "description": "Index for gzipped VCF file containing variants", + "pattern": "*.{vcf.gz.tbi}", + "ontologies": [] + } + } + ] + ], + "versions_manta": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "manta": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "configManta.py --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "manta": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "configManta.py --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@FriederikeHanssen", "@nvnieuwk"], + "maintainers": ["@FriederikeHanssen", "@nvnieuwk"] + }, + "pipelines": [ + { + "name": "rnadnavar", + "version": "dev" + }, + { + "name": "sarek", + "version": "3.8.1" } - } - ] - ], - "vcfs_indexes": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*_snv_phased.vcf.gz.{tbi,csi}": { - "type": "file", - "description": "Index file for the phased SNV VCF (optional)", - "pattern": "*_snv_phased.vcf.gz.{tbi,csi}", - "ontologies": [] - } - } - ] - ], - "sv_vcfs_indexes": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*_sv_phased.vcf.gz.{tbi,csi}": { - "type": "file", - "description": "Index file for the phased SV VCF (optional)", - "pattern": "*_sv_phased.vcf.gz.{tbi,csi}", - "ontologies": [] - } - } - ] - ], - "summary_tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.summary.tsv": { - "type": "file", - "description": "TSV file containing phasing summary statistics (optional)", - "pattern": "*.summary.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "summary_csv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.summary.csv": { - "type": "file", - "description": "CSV file containing phasing summary statistics (optional)", - "pattern": "*.summary.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "blocks_tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.blocks.tsv": { - "type": "file", - "description": "TSV file containing phasing block information (optional)", - "pattern": "*.blocks.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "blocks_csv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.blocks.csv": { - "type": "file", - "description": "CSV file containing phasing block information (optional)", - "pattern": "*.blocks.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "stats_tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.stats.tsv": { - "type": "file", - "description": "TSV file containing per-read phasing statistics (optional)", - "pattern": "*.stats.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "stats_csv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.stats.csv": { - "type": "file", - "description": "CSV file containing per-read phasing statistics (optional)", - "pattern": "*.stats.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - 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Supports only single-end or merged paired-end data (mandatory)\n", + "pattern": "*.{bam,cram,fastq,fastq.gz,fq,fq.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "index": { + "type": "file", + "description": "mapAD genome index files (mandatory)", + "pattern": "*.{tbw,tle,toc,tos,tpi,trt,tsa}", + "ontologies": [] + } + } + ], + { + "mismatch_parameter": { + "type": "float", + "description": "Minimum probability of the number of mismatches under `-D` base error rate\n" + } + }, + { + "double_stranded_library": { + "type": "boolean", + "description": "Library preparation method - specify if double stranded else it's assumed single stranded" + } + }, + { + "five_prime_overhang": { + "type": "float", + "description": "5'-overhang length parameter" + } + }, + { + "three_prime_overhang": { + "type": "float", + "description": "3'-overhang length parameter" + } + }, + { + "deam_rate_double_stranded": { + "type": "float", + "description": "Deamination rate in double-stranded stem of a read" + } + }, + { + "deam_rate_single_stranded": { + "type": "float", + "description": "Deamination rate in single-stranded ends of a read" + } + }, + { + "indel_rate": { + "type": "float", + "description": "Expected rate of indels between reads and reference" + } + } + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Output BAM/SAM file containing read alignments", + "pattern": "*.bam", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": 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"description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false]" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file", + "pattern": "*.{bam}", + "ontologies": [] + } + } + ], + { + "fasta": { + "type": "file", + "description": "Fasta file, the reference the input BAM was mapped against", + "pattern": "*.{fasta}", + "ontologies": [] + } + } + ], + "output": { + "runtime_log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false]" + } + }, + { + "results_*/Runtime_log.txt": { + "type": "file", + "description": "Log file with a summary of command lines used and timestamps.", + "pattern": "Runtime_log.txt", + "ontologies": [] + } + } + ] + ], + "fragmisincorporation_plot": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false]" + } + }, + { + "results_*/Fragmisincorporation_plot.pdf": { + 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"ontologies": [] - } - } - ] - ], - "output": { - "sam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample1', single_end:false ]\n" - } - }, - { - "*.sam": { - "type": "file", - "description": "Output SAM file containing read alignments", - "pattern": "*.sam", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2573" - } - ] - } - } - ] - ], - "summary": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample1', single_end:false ]\n" - } - }, - { - "*.log": { - "type": "file", - "description": "Alignment summary log", - "pattern": "*.log", - "ontologies": [] - } - } - ] - ], - "versions_hisat3n": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "hisat-3n": { - "type": "string", - "description": "The tool name" - } - }, - { - "hisat-3n --version 2>&1 | head -1 | sed 's/.* //'": { - "type": "eval", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "hisat-3n": { - "type": "string", - "description": "The tool name" - } - }, - { - "hisat-3n --version 2>&1 | head -1 | sed 's/.* //'": { - "type": "eval", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@emmcauley" - ], - "maintainers": [ - "@emmcauley" - ] - } - }, - { - "name": "hisat3n_build", - "path": "modules/nf-core/hisat3n/build/meta.yml", - "type": "module", - "meta": { - "name": "hisat3n_build", - "description": "Build HISAT-3N index for nucleotide conversion sequencing alignment", - "keywords": [ - "build", - "index", - "fasta", - "genome", - "reference", - "bisulfite", - "methylation" - ], - "tools": [ - { - "hisat-3n": { - "description": "HISAT-3N is designed for nucleotide conversion sequencing technologies and implemented based on HISAT2.", - "homepage": "http://daehwankimlab.github.io/hisat2/hisat-3n/", - "documentation": "http://daehwankimlab.github.io/hisat2/hisat-3n/", - "tool_dev_url": "https://github.com/DaehwanKimLab/hisat2/tree/hisat-3n", - "doi": "10.1101/gr.275193.120", - "licence": [ - "GPL v3" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. `[ id:'genome' ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference FASTA file", - "pattern": "*.{fa,fasta,fna}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ], - "output": { - "index": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. `[ id:'genome' ]`\n" - } - }, - { - "hisat3n": { - "type": "directory", - "description": "Directory containing HISAT-3N index files", - "pattern": "hisat3n", - "ontologies": [] - } - } - ] - ], - "versions_hisat3n": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "hisat-3n": { - "type": "string", - "description": "The tool name" - } - }, - { - "hisat-3n --version 2>&1 | head -1 | sed 's/.* //'": { - "type": "eval", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "hisat-3n": { - "type": "string", - "description": "The tool name" - } - }, - { - "hisat-3n --version 2>&1 | head -1 | sed 's/.* //'": { - "type": "eval", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@emmcauley" - ], - "maintainers": [ - "@emmcauley" - ] - } - }, - { - "name": "hlala_preparegraph", - "path": "modules/nf-core/hlala/preparegraph/meta.yml", - "type": "module", - "meta": { - "name": "hlala_preparegraph", - "description": "Pre-compute the graph index structure.", - "keywords": [ - "hla", - "hlala", - "hla_typing", - "hlala_typing" - ], - "tools": [ - { - "hlala": { - "description": "HLA typing from short and long reads", - "homepage": "https://github.com/DiltheyLab/HLA-LA", - "documentation": "https://github.com/DiltheyLab/HLA-LA#running-hlala", - "tool_dev_url": "https://github.com/DiltheyLab/HLA-LA", - "doi": "10.1093/bioinformatics/btz235", - "licence": [ - "GPL" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "graph": { - "type": "directory", - "description": "PRG graph directory" - } - } - ] - ], - "output": { - "graph": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${graph}": { - "type": "directory", - "description": "PRG graph directory" - } - } - ] - ], - "versions_hlala": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "hla-la": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "echo 1.0.4": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "hla-la": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "echo 1.0.4": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@mapo9" - ], - "maintainers": [ - "@mapo9" - ] - } - }, - { - "name": "hlala_typing", - "path": "modules/nf-core/hlala/typing/meta.yml", - "type": "module", - "meta": { - "name": "hlala_typing", - "description": "Performs HLA typing based on a population reference graph and employs a new linear projection method to align reads to the graph.", - "keywords": [ - "hla", - "hlala", - "hla_typing", - "hlala_typing" - ], - "tools": [ - { - "hlala": { - "description": "HLA typing from short and long reads", - "homepage": "https://github.com/DiltheyLab/HLA-LA", - "documentation": "https://github.com/DiltheyLab/HLA-LA#running-hlala", - "tool_dev_url": "https://github.com/DiltheyLab/HLA-LA", - "doi": "10.1093/bioinformatics/btz235", - "licence": [ - "GPL" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } - }, - { - "bai": { - "type": "file", - "description": "BAM index file", - "pattern": "*.{bai}", - "ontologies": [] - } - }, - { - "graph": { - "type": "directory", - "description": "Path to prepared graph with hla-la --action prepareGraph" - } - } - ] - ], - "output": { - "results": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "${prefix}": { - "type": "directory", - "description": "Per-sample HLA-LA output directory" - } - } - ] - ], - "extraction": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "${prefix}/extraction.bam": { - "type": "file", - "description": "Extraction BAM file", - "pattern": "*.bam", - "ontologies": [] - } - } - ] - ], - "extraction_index": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "${prefix}/extraction.bam.bai": { - "type": "file", - "description": "Extraction BAM index file", - "pattern": "*.bam.bai", - "ontologies": [] - } - } - ] - ], - "extraction_mapped": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "${prefix}/extraction_mapped.bam": { - "type": "file", - "description": "Extraction mapped BAM file", - "pattern": "*.bam", - "ontologies": [] - } - } - ] - ], - "extraction_unmpapped": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "${prefix}/extraction_unmapped.bam": { - "type": "file", - "description": "Extraction unmapped BAM file", - "pattern": "*.bam", - "ontologies": [] - } - } - ] - ], - "hla": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "${prefix}/hla/*": { - "type": "file", - "description": "HLA results", - "ontologies": [] - } - } - ] - ], - "fastq": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "${prefix}/*.fastq": { - "type": "file", - "description": "Fastq file", - "pattern": "*.fastq", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "reads_per_level": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "${prefix}/reads_per_level.txt": { - "type": "file", - "description": "Reads per level", - "pattern": "*.txt", - "ontologies": [] - } - } - ] - ], - "remapped": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "${prefix}/remapped_with_a.bam": { - "type": "file", - "description": "Remapped BAM file", - "pattern": "*.bam", - "ontologies": [] - } - } - ] - ], - "remapped_index": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "${prefix}/remapped_with_a.bam.bai": { - "type": "file", - "description": "Remapped BAM index file", - "pattern": "*.bam.bai", - "ontologies": [] - } - } - ] - ], - "versions_hlala": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "hla-la": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "echo 1.0.4": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "hla-la": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "echo 1.0.4": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@mapo9" - ], - "maintainers": [ - "@mapo9" - ] - } - }, - { - "name": "hmmcopy_gccounter", - "path": "modules/nf-core/hmmcopy/gccounter/meta.yml", - "type": "module", - "meta": { - "name": "hmmcopy_gccounter", - "description": "gcCounter function from HMMcopy utilities, used to generate GC content in non-overlapping windows from a fasta reference", - "keywords": [ - "hmmcopy", - "gccounter", - "cnv" - ], - "tools": [ - { - "hmmcopy": { - "description": "C++ based programs for analyzing BAM files and preparing read counts -- used with bioconductor-hmmcopy", - "homepage": "https://github.com/shahcompbio/hmmcopy_utils", - "documentation": "https://github.com/shahcompbio/hmmcopy_utils", - "tool_dev_url": "https://github.com/shahcompbio/hmmcopy_utils", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:hmmcopy" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input genome fasta file", - "ontologies": [] - } - } - ] - ], - "output": { - "wig": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.wig": { - "type": "file", - "description": "wig file containing gc content of each window of the genome", - "pattern": "*.wig", - "ontologies": [] - } - } - ] - ], - "versions_hmmcopy": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "hmmcopy": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "0.1.1": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "hmmcopy": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "0.1.1": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@sppearce", - "@adamrtalbot" - ], - "maintainers": [ - "@sppearce", - "@adamrtalbot" - ] - } - }, - { - "name": "hmmcopy_generatemap", - "path": "modules/nf-core/hmmcopy/generatemap/meta.yml", - "type": "module", - "meta": { - "name": "hmmcopy_generatemap", - "description": "Perl script (generateMap.pl) generates the mappability of a genome given a certain size of reads, for input to hmmcopy mapcounter. Takes a very long time on large genomes, is not parallelised at all.", - "keywords": [ - "hmmcopy", - "mapcounter", - "mappability" - ], - "tools": [ - { - "hmmcopy": { - "description": "C++ based programs for analyzing BAM files and preparing read counts -- used with bioconductor-hmmcopy", - "homepage": "https://github.com/shahcompbio/hmmcopy_utils", - "documentation": "https://github.com/shahcompbio/hmmcopy_utils", - "tool_dev_url": "https://github.com/shahcompbio/hmmcopy_utils", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:hmmcopy" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input genome fasta file", - "ontologies": [] - } - } - ] - ], - "output": { - "bigwig": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bw": { - "type": "file", - "description": "bigwig file containing the mappability of the genome", - "pattern": "*.bw", - "ontologies": [] - } - } - ] - ], - "versions_hmmcopy": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "hmmcopy": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "0.1.1": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "hmmcopy": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "0.1.1": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@sppearce", - "@adamrtalbot" - ], - "maintainers": [ - "@sppearce", - "@adamrtalbot" - ] - } - }, - { - "name": "hmmcopy_mapcounter", - "path": "modules/nf-core/hmmcopy/mapcounter/meta.yml", - "type": "module", - "meta": { - "name": "hmmcopy_mapcounter", - "description": "mapCounter function from HMMcopy utilities, used to generate mappability in non-overlapping windows from a bigwig file", - "keywords": [ - "hmmcopy", - "mapcounter", - "cnv" - ], - "tools": [ - { - "hmmcopy": { - "description": "C++ based programs for analyzing BAM files and preparing read counts -- used with bioconductor-hmmcopy", - "homepage": "https://github.com/shahcompbio/hmmcopy_utils", - "documentation": "https://github.com/shahcompbio/hmmcopy_utils", - "tool_dev_url": "https://github.com/shahcompbio/hmmcopy_utils", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:hmmcopy" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bigwig": { - "type": "file", - "description": "BigWig file with the mappability score of the genome, for instance made with generateMap function.", - "pattern": "*.wig", - "ontologies": [] - } - } - ] - ], - "output": { - "wig": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.wig": { - "type": "file", - "description": "wig file containing mappability of each window of the genome", - "pattern": "*.wig", - "ontologies": [] - } - } - ] - ], - "versions_hmmcopy": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "hmmcopy": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "0.1.1": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "hmmcopy": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "0.1.1": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@sppearce" - ], - "maintainers": [ - "@sppearce" - ] - } - }, - { - "name": "hmmcopy_readcounter", - "path": "modules/nf-core/hmmcopy/readcounter/meta.yml", - "type": "module", - "meta": { - "name": "hmmcopy_readcounter", - "description": "readCounter function from HMMcopy utilities, used to generate read in windows", - "keywords": [ - "hmmcopy", - "readcounter", - "cnv" - ], - "tools": [ - { - "hmmcopy": { - "description": "C++ based programs for analyzing BAM files and preparing read counts -- used with bioconductor-hmmcopy", - "homepage": "https://github.com/shahcompbio/hmmcopy_utils", - "documentation": "https://github.com/shahcompbio/hmmcopy_utils", - "tool_dev_url": "https://github.com/shahcompbio/hmmcopy_utils", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:hmmcopy" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM file", - "pattern": "*.{bam,cram}", - "ontologies": [] - } - }, - { - "bai": { - "type": "file", - "description": "BAM/CRAM index file", - "pattern": "*.{bai}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Genome fasta file. Required when using a CRAM file.", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ], - "output": { - "wig": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.wig": { - "type": "file", - "description": "A wig file with the number of reads lying within each window in each chromosome", - "pattern": "*.wig", - "ontologies": [] - } - } - ] - ], - "versions_hmmcopy": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "hmmcopy": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "0.1.1": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_samtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "hmmcopy": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "0.1.1": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@sppearce" - ], - "maintainers": [ - "@sppearce" - ] - } - }, - { - "name": "hmmer_eslalimask", - 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"type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "mag", + "version": "5.4.2" + } ] - ] }, - "authors": [ - "@erikrikarddaniel" - ], - "maintainers": [ - "@erikrikarddaniel" - ] - }, - "pipelines": [ { - "name": "ampliseq", - "version": "2.17.0" + "name": "maxquant_lfq", + "path": "modules/nf-core/maxquant/lfq/meta.yml", + "type": "module", + "meta": { + "name": "maxquant_lfq", + "description": "Run standard proteomics data analysis with MaxQuant, mostly dedicated to label-free. Paths to fasta and raw files needs to be marked by \"PLACEHOLDER\"", + "keywords": ["sort", "proteomics", "mass-spectroscopy"], + "tools": [ + { + "maxquant": { + "description": "MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. License restricted.", + "homepage": "https://www.maxquant.org/", + "documentation": "http://coxdocs.org/doku.php?id=maxquant:start", + "licence": ["http://www.coxdocs.org/lib/exe/fetch.php?media=license_agreement.pdf"], + "identifier": "biotools:maxquant" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "fasta file with protein sequences", + "pattern": "*.{fasta}", + "ontologies": [] + } + }, + { + "paramfile": { + "type": "file", + "description": "MaxQuant parameter file", + "ontologies": [] + } + } + ], + { + "raw": { + "type": "file", + "description": "raw files with mass spectra", + "pattern": "*.{raw,RAW,Raw}", + "ontologies": [] + } + } + ], + "output": { + "maxquant_txt": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/*.txt": { + "type": "file", + "description": "tables with peptides and protein information", + "pattern": "*.{txt}", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software version", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@veitveit"], + "maintainers": ["@veitveit"] + } }, { - "name": "phyloplace", - "version": "2.0.0" - } - ] - }, - { - "name": "hmmer_hmmalign", - "path": "modules/nf-core/hmmer/hmmalign/meta.yml", - "type": "module", - "meta": { - "name": "hmmer_hmmalign", - "description": "hmmalign from the HMMER suite aligns a number of sequences to an HMM profile", - "keywords": [ - "alignment", - "HMMER", - "profile", - "amino acid", - "nucleotide" - ], - "tools": [ - { - "hmmer": { - "description": "Biosequence analysis using profile hidden Markov models", - "homepage": "http://hmmer.org/", - "documentation": "http://hmmer.org/documentation.html", - "doi": "10.1371/journal.pcbi.1002195", - "licence": [ - "BSD-3-Clause" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } + "name": "mcquant", + "path": "modules/nf-core/mcquant/meta.yml", + "type": "module", + "meta": { + "name": "mcquant", + "description": "Mcquant extracts single-cell data given a multi-channel image and a segmentation mask.", + "keywords": ["quantification", "image_analysis", "mcmicro", "highly_multiplexed_imaging"], + "tools": [ + { + "mcquant": { + "description": "Module for single-cell data extraction given a segmentation mask and multi-channel image. The CSV structure is aligned with histoCAT output.", + "homepage": "https://github.com/labsyspharm/quantification", + "documentation": "https://github.com/labsyspharm/quantification/blob/master/README.md", + "tool_dev_url": "https://github.com/labsyspharm/quantification", + "doi": "10.1038/s41592-021-01308-y", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "image": { + "type": "file", + "description": "Multi-channel image file", + "pattern": "*.{tiff,tif,h5,hdf5}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3590" + }, + { + "edam": "http://edamontology.org/format_3591" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "mask": { + "type": "file", + "description": "Labeled segmentation mask for image", + "pattern": "*.{tiff,tif,h5,hdf5}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3590" + }, + { + "edam": "http://edamontology.org/format_3591" + } + ] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "markerfile": { + "type": "file", + "description": "Marker file with channel names for image to quantify", + "pattern": "*.{csv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "output": { + "csv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.csv": { + "type": "file", + "description": "Quantified regionprops_table", + "pattern": "*.{csv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "versions_mcquant": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "mcquant": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "1.5.4": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "mcquant": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "1.5.4": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@FloWuenne"], + "maintainers": ["@FloWuenne"] }, - { - "fasta": { - "type": "file", - "description": "Amino acid or nucleotide gzipped compressed fasta file", - "pattern": "*.{fna.gz,faa.gz,fasta.gz,fa.gz}", - "ontologies": [] - } - } - ], - { - "hmm": { - "type": "file", - "description": "A gzipped HMM file", - "pattern": "*.hmm.gz", - "ontologies": [ + "pipelines": [ { - "edam": "http://edamontology.org/format_3989" + "name": "mcmicro", + "version": "dev" } - ] - } - } - ], - "output": { - "sto": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.sto.gz": { - "type": "file", - "description": "Multiple alignment in gzipped Stockholm format", - "pattern": "*.sto.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "versions_hmmer": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "hmmer": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "hmmsearch -h | sed '2!d;s/^# HMMER *//;s/ .*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "hmmer": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "hmmsearch -h | sed '2!d;s/^# HMMER *//;s/ .*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } ] - ] }, - "authors": [ - "@erikrikarddaniel", - "@jfy133" - ], - "maintainers": [ - "@erikrikarddaniel", - "@jfy133", - "@vagkaratzas" - ] - }, - "pipelines": [ { - "name": "ampliseq", - "version": "2.17.0" - }, - { - "name": "phyloplace", - "version": "2.0.0" + "name": "mcroni", + "path": "modules/nf-core/mcroni/meta.yml", + "type": "module", + "meta": { + "name": "mcroni", + "description": "Analysis of mcr-1 gene (mobilized colistin resistance) for sequence variation", + "keywords": ["resistance", "fasta", "mcr-1"], + "tools": [ + { + "mcroni": { + "description": "Scripts for finding and processing promoter variants upstream of mcr-1", + "homepage": "https://github.com/liampshaw/mcroni", + "documentation": "https://github.com/liampshaw/mcroni", + "tool_dev_url": "https://github.com/liampshaw/mcroni", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "A fasta file.", + "pattern": "*.{fasta.gz,fasta,fa.gz,fa,fna.gz,fna}", + "ontologies": [] + } + } + ] + ], + "output": { + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "mcroni results in TSV format", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "fa": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fa": { + "type": "file", + "description": "mcr-1 matching sequences", + "pattern": "*.fa", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@rpetit3"], + "maintainers": ["@rpetit3"] + } }, { - "name": "proteinfamilies", - "version": "2.3.0" - } - ] - }, - { - "name": "hmmer_hmmbuild", - "path": "modules/nf-core/hmmer/hmmbuild/meta.yml", - "type": "module", - "meta": { - "name": "hmmer_hmmbuild", - "description": "create an hmm profile from a multiple sequence alignment", - "keywords": [ - "search", - "hidden Markov model", - "HMM", - "hmmer", - "hmmsearch" - ], - "tools": [ - { - "hmmer": { - "description": "Biosequence analysis using profile hidden Markov models", - "homepage": "http://hmmer.org", - "documentation": "http://hmmer.org/documentation.html", - "tool_dev_url": "https://github.com/EddyRivasLab/hmmer", - "doi": "10.1371/journal.pcbi.1002195", - "licence": [ - "BSD" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "alignment": { - "type": "file", - "description": "multiple sequence alignment in fasta, clustal, stockholm or phylip format", - "pattern": "*", - "ontologies": [ - { - "edam": "http://edamontology.org/data_0863" - }, - { - "edam": "http://edamontology.org/format_1929" - }, - { - "edam": "http://edamontology.org/format_1997" - }, - { - "edam": "http://edamontology.org/format_1961" - } - ] - } - } - ], - { - "mxfile": { - "type": "file", - "description": "read substitution score matrix, for use when building profiles from single sequences (--singlemx option)", - "pattern": "*", - "ontologies": [] - } - } - ], - "output": { - "hmm": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.hmm.gz": { - "type": "file", - "description": "Gzipped HMM file", - "pattern": "*.{hmm.gz}", - "ontologies": [] - } - } - ] - ], - "hmmbuildout": [ - { - "*.hmmbuild.txt": { - "type": "file", - "description": "HMM build output", - "ontologies": [] - } + "name": "mcstaging_imc2mc", + "path": "modules/nf-core/mcstaging/imc2mc/meta.yml", + "type": "module", + "meta": { + "name": "mcstaging_imc2mc", + "description": "Staging module for MCMICRO transforming Imaging Mass Cytometry .txt files to .tif files with OME-XML metadata. Includes optional hot pixel removal.", + "deprecated": true, + "keywords": ["imaging", "ome-tif", "staging", "MCMICRO"], + "tools": [ + { + "mcstaging": { + "description": "Staging modules for MCMICRO", + "homepage": "https://github.com/SchapiroLabor/imc2mc", + "documentation": "https://github.com/SchapiroLabor/imc2mc/README.md", + "tool_dev_url": "https://github.com/SchapiroLabor/imc2mc", + "licence": ["GPL-3.0 license"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "txtfile": { + "type": "file", + "description": "Acquisition .txt file", + "pattern": "*.{txt}", + "ontologies": [] + } + } + ] + ], + "output": { + "tif": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.tif": { + "type": "file", + "description": "One output .tif file containing acquisition and metadata", + "pattern": "*.{tif}", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@MargotCh"], + "maintainers": ["@MargotCh"] } - ], - "versions_hmmer": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "hmmer": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "hmmsearch -h | sed '2!d;s/^# HMMER *//;s/ .*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "hmmer": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "hmmsearch -h | sed '2!d;s/^# HMMER *//;s/ .*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] }, - "authors": [ - "@erikrikarddaniel" - ], - "maintainers": [ - "@erikrikarddaniel" - ] - }, - "pipelines": [ { - "name": "ampliseq", - "version": "2.17.0" + "name": "mcstaging_macsima2mc", + "path": "modules/nf-core/mcstaging/macsima2mc/meta.yml", + "type": "module", + "meta": { + "name": "mcstaging_macsima2mc", + "description": "Staging module for MCMICRO transforming MACSima data sets for being registered with ASHLAR in MCMICRO.", + "keywords": ["imaging", "ome-tif", "mcmicro", "staging", "spatial-omics", "macsima"], + "tools": [ + { + "macsima2mc": { + "description": "Staging module for MCMICRO", + "homepage": "https://github.com/SchapiroLabor/macsima2mc", + "documentation": "https://github.com/SchapiroLabor/macsima2mc/README.md", + "tool_dev_url": "https://github.com/SchapiroLabor/macsima2mc", + "licence": ["BSD-3-Clause"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "input_dir": { + "type": "directory", + "description": "Absolute path to the the parent folder of the raw tiles, whose name follows the pattern X_Cycle_N,where N represents the cycle number", + "pattern": "*Cycle*" + } + }, + { + "output_dir": { + "type": "string", + "description": "Absolute path to the directory in which the outputs will be saved. If the output directory doesn't exist it will be created." + } + } + ] + ], + "output": { + "out_dir": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${output_dir}/*": { + "type": "directory", + "description": "Output directory containing subdirectories per well-rack-roi-exp combination.\nEach subdirectory contains a markers.csv table and a raw/ folder with ome.tif files.\n", + "pattern": "*/" + } + } + ] + ], + "versions_macsima2mc": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "macsima2mc": { + "type": "string", + "description": "The tool name" + } + }, + { + "python -m pip show macsima2mc | grep \"Version\" | sed -e \"s/Version: //g\"": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "macsima2mc": { + "type": "string", + "description": "The tool name" + } + }, + { + "python -m pip show macsima2mc | grep \"Version\" | sed -e \"s/Version: //g\"": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@EfraMP"], + "maintainers": ["@EfraMP", "@VictorDidier"] + } }, { - "name": "phyloplace", - "version": "2.0.0" + "name": "mcstaging_phenoimager2mc", + "path": "modules/nf-core/mcstaging/phenoimager2mc/meta.yml", + "type": "module", + "meta": { + "name": "mcstaging_phenoimager2mc", + "description": "Staging module for MCMICRO transforming PhenoImager .tif files into stacked and normalized ome-tif files per cycle, compatible as ASHLAR input.", + "deprecated": true, + "keywords": ["imaging", "registration", "ome-tif", "Staging", "MCMICRO"], + "tools": [ + { + "mcstaging": { + "description": "Staging modules for MCMICRO", + "homepage": "https://github.com/SchapiroLabor/phenoimager2mc", + "documentation": "https://github.com/SchapiroLabor/phenoimager2mc/README.md", + "tool_dev_url": "https://github.com/SchapiroLabor/phenoimager2mc", + "licence": ["GPL-2.0 license"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "tiles": { + "type": "list", + "description": "Folder or list with .tif files of one cycle from PhenoImager" + } + } + ] + ], + "output": { + "tif": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.tif": { + "type": "file", + "description": "One output .tif file containing concatenated tiles of the cycle.", + "pattern": "*.{tif,tiff}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3591" + } + ] + } + } + ] + ], + "versions_phenoimager2mc": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "phenoimager2mc": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python /phenoimager2mc/scripts/phenoimager2mc.py --version | sed \"s/v//g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "phenoimager2mc": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python /phenoimager2mc/scripts/phenoimager2mc.py --version | sed \"s/v//g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@chiarasch"], + "maintainers": ["@chiarasch"] + } }, { - "name": "proteinfamilies", - "version": "2.3.0" - } - ] - }, - { - "name": "hmmer_hmmfetch", - "path": "modules/nf-core/hmmer/hmmfetch/meta.yml", - "type": "module", - "meta": { - "name": "hmmer_hmmfetch", - "description": "extract hmm from hmm database file or create index for hmm database", - "keywords": [ - "hidden Markov model", - "HMM", - "hmmer", - "hmmfetch" - ], - "tools": [ - { - "hmmer": { - "description": "Biosequence analysis using profile hidden Markov models", - "homepage": "http://hmmer.org/", - "documentation": "http://hmmer.org/documentation.html", - "tool_dev_url": "https://github.com/EddyRivasLab/hmmer", - "doi": "10.1371/journal.pcbi.1002195", - "licence": [ - "BSD" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + "name": "md5sum", + "path": "modules/nf-core/md5sum/meta.yml", + "type": "module", + "meta": { + "name": "md5sum", + "description": "Create MD5 (128-bit) checksums", + "keywords": ["checksum", "MD5", "128 bit"], + "tools": [ + { + "md5sum": { + "description": "Create MD5 (128-bit) checksums for each file", + "homepage": "https://www.gnu.org", + "documentation": "https://man7.org/linux/man-pages/man1/md5sum.1.html", + "licence": ["GPL-3.0-or-later"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "files": { + "type": "file", + "description": "Any number of files. One md5sum file will be generated for each.", + "pattern": "*.*", + "ontologies": [] + } + } + ], + { + "as_separate_files": { + "type": "boolean", + "description": "If true, each file will have its own md5sum file. If false, all files will be\nchecksummed into a single md5sum file.\n" + } + } + ], + "output": { + "checksum": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.md5": { + "type": "file", + "description": "File containing checksum", + "pattern": "*.md5", + "ontologies": [] + } + } + ] + ], + "versions_md5sum": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "md5sum": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "md5sum --version | sed '1!d; s/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "md5sum": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "md5sum --version | sed '1!d; s/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@matthdsm"], + "maintainers": ["@matthdsm"] }, - { - "hmm": { - "type": "file", - "description": "HMM file with multiple HMM models", - "pattern": "*.hmm", - "ontologies": [] - } - } - ], - { - "key": { - "type": "string", - "description": "Name of HMM to extract. Specify either this or keyfile. If none is specified, an index will be built." - } - }, - { - "keyfile": { - "type": "file", - "description": "File containing list of HMM models to extract. Specify either this or key. If none is specified, an index will be built.", - "pattern": "*.txt", - "ontologies": [ + "pipelines": [ { - "edam": "http://edamontology.org/format_2330" + "name": "demultiplex", + "version": "1.7.1" } - ] - } - }, - { - "index": { - "type": "file", - "description": "Index file from another run.", - "ontologies": [] - } - } - ], - "output": { - "hmm": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.hmm": { - "type": "file", - "description": "File with one or more HMM models", - "pattern": "selection.hmm", - "ontologies": [] - } - } ] - ], - "index": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.ssi": { - "type": "file", - "description": "Index for HMM database. Created if neither key nor keyfile is specified.", - "pattern": "*.ssi", - "ontologies": [] - } - } - ] - ], - "versions_hmmer": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "hmmer": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "hmmsearch -h | sed '2!d;s/^# HMMER *//;s/ .*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "hmmer": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "hmmsearch -h | sed '2!d;s/^# HMMER *//;s/ .*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@erikrikarddaniel" - ], - "maintainers": [ - "@erikrikarddaniel" - ] - } - }, - { - "name": "hmmer_hmmpress", - 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Software Tools for masking low-complexity DNA sequences", + "homepage": "https://github.com/lh3/mdust", + "documentation": "https://github.com/lh3/mdust", + "tool_dev_url": "https://github.com/lh3/mdust", + "licence": ["The Artistic License"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input fasta file", + "pattern": "*.{fa,fsa,faa,fas,fasta}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ] + ], + "output": { + "fasta": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.fasta": { + "type": "file", + "description": "Output fasta file", + "pattern": "*.{fasta}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@GallVp"], + "maintainers": ["@GallVp"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + }, + { + "name": "medaka", + "path": "modules/nf-core/medaka/meta.yml", + "type": "module", + "meta": { + "name": "medaka", + "description": "A tool to create consensus sequences and variant calls from nanopore sequencing data", + "keywords": ["assembly", "polishing", "nanopore"], + "tools": [ + { + "medaka": { + "description": "Neural network sequence error correction.", + "homepage": "https://nanoporetech.github.io/medaka/index.html", + "documentation": "https://nanoporetech.github.io/medaka/index.html", + "tool_dev_url": "https://github.com/nanoporetech/medaka", + "licence": ["Mozilla Public License 2.0"], + "identifier": "biotools:medaka" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input nanopore fasta/FastQ files", + "pattern": "*.{fasta,fa,fastq,fastq.gz,fq,fq.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + }, + { + "assembly": { + "type": "file", + "description": "Genome assembly", + "pattern": "*.{fasta,fa}", + "ontologies": [] + } + } + ] + ], + "output": { + "assembly": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fa.gz": { + "type": "file", + "description": "Polished genome assembly", + "pattern": "*.fa.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "versions_medaka": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "medaka": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "medaka --version 2>&1 | sed \"s/medaka //g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "medaka": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "medaka --version 2>&1 | sed \"s/medaka //g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@avantonder"], + "maintainers": ["@avantonder"] }, - { - "hmmfile": { - "type": "file", - "description": "HMMER flatfile database of HMM profiles", - "pattern": "*", - "ontologies": [] - } - } - ] - ], - "output": { - "compressed_db": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.h3?": { - "type": "list", - "description": "Binary files with compressed profiles and their index", - "pattern": "*.h3?" - } - } - ] - ], - "versions_hmmer": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "hmmer": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "hmmsearch -h | sed '2!d;s/^# HMMER *//;s/ .*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "hmmer": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "hmmsearch -h | sed '2!d;s/^# HMMER *//;s/ .*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "crisprseq", + "version": "2.3.0" + } ] - ] - }, - "authors": [ - "@ochkalova" - ], - "maintainers": [ - "@ochkalova" - ] - } - }, - { - "name": "hmmer_hmmrank", - "path": "modules/nf-core/hmmer/hmmrank/meta.yml", - "type": "module", - "meta": { - "name": "hmmer_hmmrank", - "description": "R script that scores output from multiple runs of hmmer/hmmsearch", - "keywords": [ - "hmmer", - "hmmsearch", - "rank" - ], - "tools": [ - { - "hmmer": { - "description": "Biosequence analysis using profile hidden Markov models", - "homepage": "http://hmmer.org/", - "documentation": "http://hmmer.org/documentation.html", - "tool_dev_url": "https://github.com/EddyRivasLab/hmmer", - "doi": "10.1371/journal.pcbi.1002195", - "licence": [ - "BSD" - ], - "identifier": "" - } - }, - { - "R": { - "description": "A Language and Environment for Statistical Computing", - "homepage": "https://www.r-project.org/", - "documentation": "https://www.r-project.org/", - "licence": [ - "GPL v2" - ], - "identifier": "" - } - }, - { - "Tidyverse": { - "description": "Tidyverse: R packages for data science", - "homepage": "https://www.tidyverse.org/", - "documentation": "https://www.tidyverse.org/", - "tool_dev_url": "https://github.com/tidyverse", - "doi": "10.21105/joss.01686", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } + }, + { + "name": "megahit", + "path": "modules/nf-core/megahit/meta.yml", + "type": "module", + "meta": { + "name": "megahit", + "description": "An ultra-fast metagenomic assembler for large and complex metagenomics", + "keywords": ["megahit", "denovo", "assembly", "debruijn", "metagenomics"], + "tools": [ + { + "megahit": { + "description": "An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph", + "homepage": "https://github.com/voutcn/megahit", + "documentation": "https://github.com/voutcn/megahit", + "tool_dev_url": "https://github.com/voutcn/megahit", + "doi": "10.1093/bioinformatics/btv033", + "licence": ["GPL v3"], + "args_id": "$args", + "identifier": "biotools:megahit" + } + }, + { + "pigz": { + "description": "Parallel implementation of the gzip algorithm.", + "homepage": "https://zlib.net/pigz/", + "documentation": "https://zlib.net/pigz/pigz.pdf", + "args_id": "$args2", + "identifier": "biotools:megahit" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information and input single, or paired-end FASTA/FASTQ files (optionally decompressed)\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads1": { + "type": "file", + "description": "A single or list of input FastQ files for single-end or R1 of paired-end library(s),\nrespectively in gzipped or uncompressed FASTQ or FASTA format.\n", + "ontologies": [] + } + }, + { + "reads2": { + "type": "file", + "description": "A single or list of input FastQ files for R2 of paired-end library(s),\nrespectively in gzipped or uncompressed FASTQ or FASTA format.\n", + "ontologies": [] + } + } + ] + ], + "output": { + "contigs": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.contigs.fa.gz": { + "type": "file", + "description": "Final final contigs result of the assembly in FASTA format.", + "pattern": "*.contigs.fa.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "k_contigs": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "intermediate_contigs/k*.contigs.fa.gz": { + "type": "file", + "description": "Contigs assembled from the de Bruijn graph of order-K", + "pattern": "k*.contigs.fa.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "addi_contigs": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "intermediate_contigs/k*.addi.fa.gz": { + "type": "file", + "description": "Contigs assembled after iteratively removing local low coverage unitigs in the de Bruijn graph of order-K", + "pattern": "k*.addi.fa.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "local_contigs": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "intermediate_contigs/k*.local.fa.gz": { + "type": "file", + "description": "Contigs of the locally assembled contigs for k=K", + "pattern": "k*.local.fa.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "kfinal_contigs": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "intermediate_contigs/k*.final.contigs.fa.gz": { + "type": "file", + "description": "Stand-alone contigs for k=K; if local assembly is turned on, the file will be empty", + "pattern": "k*.final.contigs.fa.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "Log file containing statistics of the assembly output", + "pattern": "*.log", + "ontologies": [] + } + } + ] + ], + "versions_megahit": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "megahit": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "megahit -v | sed 's/MEGAHIT v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "megahit": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "megahit -v | sed 's/MEGAHIT v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@jfy133"], + "maintainers": ["@jfy133"] }, - { - "tblouts": { - "type": "file", - "description": "table outputs from hmmsearch", - "pattern": "*.tsv.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "output": { - "hmmrank": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.hmmrank.tsv.gz": { - "type": "file", - "description": "TSV file with ranked hmmer results", - "pattern": "*.hmmrank.tsv.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } + "pipelines": [ + { + "name": "bacass", + "version": "2.6.0" + }, + { + "name": "mag", + "version": "5.4.2" + }, + { + "name": "viralmetagenome", + "version": "1.1.1" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "topics": { - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] }, - "authors": [ - 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"input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "daa": { + "type": "file", + "description": "DAA file from DIAMOND", + "pattern": "*.daa", + "ontologies": [] + } + } + ], + { + "megan_summary": { + "type": "boolean", + "description": "Specify whether to generate a MEGAN summary file" + } + } + ], + "output": { + "txt_gz": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt.gz": { + "type": "file", + "description": "Compressed text file", + "pattern": "*.txt.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "megan": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.megan": { + "type": "file", + "description": "Optionally generated MEGAN summary file", + "pattern": "*.megan", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@jfy133"], + "maintainers": ["@jfy133"] + } }, { - "name": "phyloplace", - "version": "2.0.0" - } - ] - }, - { - "name": "hmmer_hmmsearch", - "path": "modules/nf-core/hmmer/hmmsearch/meta.yml", - "type": "module", - "meta": { - "name": "hmmer_hmmsearch", - "description": "search profile(s) against a sequence database", - "keywords": [ - "Hidden Markov Model", - "HMM", - "hmmer", - "hmmsearch" - ], - "tools": [ - { - "hmmer": { - "description": "Biosequence analysis using profile hidden Markov models", - "homepage": "http://hmmer.org/", - "documentation": "http://hmmer.org/documentation.html", - "tool_dev_url": 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Specify with 'true' to save." - } - }, - { - "write_target": { - "type": "boolean", - "description": "Flag to save optional per target summary. Specify with 'true' to save." - } + "name": "megan_rma2info", + "path": "modules/nf-core/megan/rma2info/meta.yml", + "type": "module", + "meta": { + "name": "megan_rma2info", + "description": "Analyses an RMA file and exports information in text format", + "keywords": ["megan", "rma6", "classification", "conversion"], + "tools": [ + { + "megan": { + "description": "A tool for studying the taxonomic content of a set of DNA reads", + "homepage": "https://uni-tuebingen.de/fakultaeten/mathematisch-naturwissenschaftliche-fakultaet/fachbereiche/informatik/lehrstuehle/algorithms-in-bioinformatics/software/megan6/", + "documentation": "https://software-ab.cs.uni-tuebingen.de/download/megan6/welcome.html", + "tool_dev_url": "https://github.com/husonlab/megan-ce", + "doi": "10.1371/journal.pcbi.1004957", + "licence": ["GPL >=3"], + "identifier": "biotools:megan" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "rma6": { + "type": "file", + "description": "RMA6 file from MEGAN or MALT", + "pattern": "*.rma6", + "ontologies": [] + } + } + ], + { + "megan_summary": { + "type": "boolean", + "description": "Specify whether to generate an MEGAN summary file" + } + } + ], + "output": { + "txt": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt.gz": { + "type": "file", + "description": "Compressed text file", + "pattern": "*.txt.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "megan_summary": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.megan": { + "type": "file", + "description": "Optionally generated MEGAN summary file", + "pattern": "*.megan", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@jfy133"], + "maintainers": ["@jfy133"] }, - { - "write_domain": { - "type": "boolean", - "description": "Flag to save optional per domain summary. 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The subtool -hist estimates the QV (quality value of [Merqury](https://github.com/marbl/merqury)) for each scaffold/contig and genome-wide averages. In addition, Merfin produces a QV* estimate, which accounts also for kmers that are seen in excess with respect to their expected multiplicity predicted from the reads.", + "homepage": "https://github.com/arangrhie/merfin", + "documentation": "https://github.com/arangrhie/merfin/wiki/Best-practices-for-Merfin", + "doi": "10.1038/s41592-022-01445-y", + "licence": ["Apache-2.0"], + "identifier": "biotools:merfin" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "fasta_assembly": { + "type": "file", + "description": "Genome assembly in FASTA; uncompressed, gz compressed [REQUIRED]", + "pattern": "*.{fasta, fasta.gz}", + "ontologies": [] + } + } + ], + [ + { + "meta1": { + "type": "map", + "description": "Groovy Map containing sample read information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "meryl_db_reads": { + "type": "file", + "description": "K-mer database produced from raw reads using Meryl [REQUIRED]", + "pattern": "*.{meryl_db}", + "ontologies": [] + } + } + ], + { + "lookup_table": { + "type": "file", + "description": "Input vector of k-mer probabilities (obtained by genomescope2 with parameter --fitted_hist) [OPTIONAL]", + "pattern": "lookup_table.txt", + "ontologies": [] + } + }, + { + "seqmers": { + "type": "file", + "description": "Input for pre-built sequence meryl db. By default, the sequence meryl db will be generated from the input genome assembly [OPTIONAL]", + "pattern": "*.{meryl_db}", + "ontologies": [] + } + }, + { + "peak": { + "type": "float", + "description": "Input to hard set copy 1 and infer multiplicity to copy number. Can be calculated using genomescope2 [REQUIRED]" + } + } + ], + "output": { + "hist": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.hist": { + "type": "file", + "description": "The generated 0-centered k* histogram for sequences in .\nPositive k* values are expected collapsed copies. Negative k* values are expected\nexpanded copies. Closer to 0 means the expected and found k-mers are well\nbalanced, 1:1.\n", + "pattern": "*.{hist}", + "ontologies": [] + } + } + ] + ], + "log_stderr": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.hist.stderr.log": { + "type": "file", + "description": "Log (stderr) of hist tool execution. The QV and QV* metrics are reported at the end.", + "pattern": "*.{hist.stderr.log}", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@rodtheo"], + "maintainers": ["@rodtheo"] + } }, { - "name": "proteinannotator", - "version": "1.1.0" + "name": "merqury_hapmers", + "path": "modules/nf-core/merqury/hapmers/meta.yml", + "type": "module", + "meta": { + "name": "merqury_hapmers", + "description": "A script to generate hap-mer dbs for trios", + "keywords": ["genomics", "quality check", "qc", "kmer"], + "tools": [ + { + "merqury": { + "description": "Evaluate genome assemblies with k-mers and more.", + "tool_dev_url": "https://github.com/marbl/merqury", + "doi": "10.1186/s13059-020-02134-9", + "licence": ["United States Government Work"], + "identifier": "biotools:merqury" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "child_meryl": { + "type": "directory", + "description": "Childs' k-mers (all, from WGS reads)", + "pattern": "*.meryl" + } + } + ], + { + "maternal_meryl": { + "type": "directory", + "description": "Haplotype1 k-mers (all, ex. maternal)", + "pattern": "*.meryl" + } + }, + { + "paternal_meryl": { + "type": "directory", + "description": "Haplotype2 k-mers (all, ex. paternal)", + "pattern": "*.meryl" + } + } + ], + "output": { + "mat_hapmer_meryl": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_mat.hapmer.meryl": { + "type": "directory", + "description": "Inherited maternal hap-mer dbs", + "pattern": "*_mat.hapmer.meryl" + } + } + ] + ], + "pat_hapmer_meryl": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_pat.hapmer.meryl": { + "type": "directory", + "description": "Inherited paternal hap-mer dbs", + "pattern": "*_pat.hapmer.meryl" + } + } + ] + ], + "inherited_hapmers_fl_png": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_inherited_hapmers.fl.png": { + "type": "file", + "description": "k-mer distribution of the inherited dbs and cutoffs used to generate hap-mer dbs", + "pattern": "*_inherited_hapmers.fl.png", + "ontologies": [] + } + } + ] + ], + "inherited_hapmers_ln_png": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_inherited_hapmers.ln.png": { + "type": "file", + "description": "k-mer distribution of the inherited dbs and cutoffs used to generate hap-mer dbs", + "pattern": "*_inherited_hapmers.ln.png", + "ontologies": [] + } + } + ] + ], + "inherited_hapmers_st_png": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_inherited_hapmers.st.png": { + "type": "file", + "description": "k-mer distribution of the inherited dbs and cutoffs used to generate hap-mer dbs", + "pattern": "*_inherited_hapmers.st.png", + "ontologies": [] + } + } + ] + ], + "versions_merqury": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "merqury": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "\"1.3\"": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "merqury": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "\"1.3\"": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@GallVp"], + "maintainers": ["@GallVp"] + } }, { - 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"versions_hmtnote": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "hmtnote": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "hmtnote --version 2>&1 | sed 's/.*version //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "hmtnote": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "hmtnote --version 2>&1 | sed 's/.*version //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@sysbiocoder" - ], - "maintainers": [ - "@sysbiocoder" - ] - } - }, - { - "name": "homer_annotatepeaks", - "path": "modules/nf-core/homer/annotatepeaks/meta.yml", - "type": "module", - "meta": { - "name": 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{ + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_only.wig": { + "type": "file", + "description": "The positions of the k-mers found only in an assembly for further investigation in .wig", + "pattern": "*_only.wig", + "ontologies": [] + } + } + ] + ], + "stats": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.completeness.stats": { + "type": "file", + "description": "Assembly statistics file", + "pattern": "*.completeness.stats", + "ontologies": [] + } + } + ] + ], + "dist_hist": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.dist_only.hist": { + "type": "file", + "description": "Histogram", + "pattern": "*.dist_only.hist", + "ontologies": [] + } + } + ] + ], + "spectra_cn_fl_png": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.spectra-cn.fl.png": { + "type": "file", + "description": "Unstacked copy number spectra filled plot in PNG format", + "pattern": "*.spectra-cn.fl.png", + "optional": true, + "ontologies": [] + } + } + ] + ], + "spectra_cn_hist": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.spectra-cn.hist": { + "type": "file", + "description": "Copy number spectra histogram", + "pattern": "*.spectra-cn.hist", + "ontologies": [] + } + } + ] + ], + "spectra_cn_ln_png": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.spectra-cn.ln.png": { + "type": "file", + "description": "Unstacked copy number spectra line plot in PNG format", + "pattern": "*.spectra-cn.ln.png", + "ontologies": [] + } + } + ] + ], + "spectra_cn_st_png": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.spectra-cn.st.png": { + "type": "file", + "description": "Stacked copy number spectra line plot in PNG format", + "pattern": "*.spectra-cn.st.png", + "optional": true, + "ontologies": [] + } + } + ] + ], + "spectra_asm_fl_png": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.spectra-asm.fl.png": { + "type": "file", + "description": "Unstacked assembly spectra filled plot in PNG format", + "pattern": "*.spectra-asm.fl.png", + "optional": true, + "ontologies": [] + } + } + ] + ], + "spectra_asm_hist": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.spectra-asm.hist": { + "type": "file", + "description": "Assembly spectra histogram", + "pattern": "*.spectra-asm.hist", + "ontologies": [] + } + } + ] + ], + "spectra_asm_ln_png": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.spectra-asm.ln.png": { + "type": "file", + "description": "Unstacked assembly spectra line plot in PNG format", + "pattern": "*.spectra-asm.ln.png", + "ontologies": [] + } + } + ] + ], + "spectra_asm_st_png": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.spectra-asm.st.png": { + "type": "file", + "description": "Stacked assembly spectra line plot in PNG format", + "pattern": "*.spectra-asm.st.png", + "optional": true, + "ontologies": [] + } + } + ] + ], + "assembly_qv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.qv": { + "type": "file", + "description": "Assembly consensus quality estimation", + "pattern": "*.qv", + "ontologies": [] + } + } + ] + ], + "scaffold_qv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.*.qv": { + "type": "file", + "description": "Scaffold consensus quality estimation", + "pattern": "*.qv", + "ontologies": [] + } + } + ] + ], + "read_ploidy": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.hist.ploidy": { + "type": "file", + "description": "Ploidy estimate from read k-mer database", + "pattern": "*.hist.ploidy", + "ontologies": [] + } + } + ] + ], + "hapmers_blob_png": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.hapmers.blob.png": { + "type": "file", + "description": "Hap-mer blob plot", + "pattern": "*.hapmers.blob.png", + "optional": true, + "ontologies": [] + } + } + ] + ], + "versions_merqury": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "merqury": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "\"1.3\"": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "merqury": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "\"1.3\"": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@mahesh-panchal"], + "maintainers": ["@mahesh-panchal", "@gallvp"] }, - { - "peak": { - "type": "file", - "description": "Peak file to annotate", - "ontologies": [] - } - } - ], - { - "fasta": { - "type": "file", - "description": "Fasta file of reference genome", - "pattern": "*.fasta", - "ontologies": [] - } - }, - { - "gtf": { - "type": "file", - "description": "GTF file of reference genome", - "pattern": "*.gtf", - "ontologies": [] - } - } - ], - "output": { - "txt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*annotatePeaks.txt": { - "type": "file", - "description": "Annotated peaks in txt file", - "pattern": "*annotatePeaks.txt", - "ontologies": [] - } - } - ] - ], - "stats": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*annStats.txt": { - "type": "file", - "description": "Annotation statistics in txt file", - "pattern": "*annStats.txt", - "ontologies": [] - } - } - ] - ], - "versions_homer": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "homer": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "4.11": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "homer": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "4.11": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "genomeassembler", + "version": "1.1.0" + }, + { + "name": "genomeqc", + "version": "dev" + } ] - ] }, - "authors": [ - "@drpatelh", - "@kevinmenden" - ], - "maintainers": [ - "@drpatelh", - "@kevinmenden" - ] - }, - "pipelines": [ { - "name": "atacseq", - "version": "2.1.2" + "name": "merquryfk_hapmaker", + "path": "modules/nf-core/merquryfk/hapmaker/meta.yml", + "type": "module", + "meta": { + "name": "merquryfk_hapmaker", + "description": "Produces maternal and paternal FastK kmer tables from maternal, paternal and child\nFastK tables\n", + "keywords": ["k-mer frequency", "trio binning", "reference-free", "assembly evaluation"], + "tools": [ + { + "merquryfk": { + "description": "FastK based version of Merqury", + "homepage": "https://github.com/thegenemyers/MERQURY.FK", + "tool_dev_url": "https://github.com/thegenemyers/MERQURY.FK", + "license": ["https://github.com/thegenemyers/MERQURY.FK/blob/main/LICENSE"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing maternal sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "matktab": { + "type": "file", + "description": "maternal ktab files from the program FastK", + "pattern": "*.ktab*", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing paternal sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "patktab": { + "type": "file", + "description": "paternal ktab files from the program FastK", + "pattern": "*.ktab*", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing child sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "childktab": { + "type": "file", + "description": "child ktab files from the program FastK", + "pattern": "*.ktab*", + "ontologies": [] + } + } + ] + ], + "output": { + "mat_hap_ktab": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing maternal sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*${input_mat}.hap.ktab*": { + "type": "file", + "description": "Maternal haplotype-specific k-mer table files generated by HAPmaker from FastK tables.\n", + "pattern": "*.hap.ktab*", + "ontologies": [] + } + } + ] + ], + "pat_hap_ktab": [ + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing paternal sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*${input_pat}.hap.ktab*": { + "type": "file", + "description": "Paternal haplotype-specific k-mer table files generated by HAPmaker from FastK tables.\n", + "pattern": "*.hap.ktab*", + "ontologies": [] + } + } + ] + ], + "versions_merquryfk": [ + [ + { + "${task.process}": { + "type": "string", + "description": "Name of the process" + } + }, + { + "merquryfk": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "1.2": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_fastk": [ + [ + { + "${task.process}": { + "type": "string", + "description": "Name of the process" + } + }, + { + "fastk": { + "type": "string", + "description": "Name of the tool" + } + }, + { + "1.2": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "Name of the process" + } + }, + { + "merquryfk": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "1.2": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "Name of the process" + } + }, + { + "fastk": { + "type": "string", + "description": "Name of the tool" + } + }, + { + "1.2": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@prototaxites", "@yumisims"], + "maintainers": ["@prototaxites", "@yumisims"] + } }, { - "name": "chipseq", - "version": "2.1.0" - } - ] - }, - { - "name": "homer_findpeaks", - "path": "modules/nf-core/homer/findpeaks/meta.yml", - "type": "module", - "meta": { - "name": "homer_findpeaks", - "description": "Find peaks with HOMER suite", - "keywords": [ - "annotation", - "peaks", - "enrichment" - ], - "tools": [ - { - "homer": { - "description": "HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.\n", - "homepage": "http://homer.ucsd.edu/homer/index.html", - "documentation": "http://homer.ucsd.edu/homer/", - "tool_dev_url": "http://homer.ucsd.edu/homer/ngs/peaks.html", - "doi": "10.1016/j.molcel.2010.05.004.", - "licence": [ - "GPL-3.0-or-later" - ], - "identifier": "biotools:homer" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "tagDir": { - "type": "directory", - "description": "The 'Tag Directory'", - "pattern": "tagDir" - } - } - ], - { - "uniqmap": { - "type": "directory", - "description": "(directory of binary files specifying uniquely mappable locations) Download from http://biowhat.ucsd.edu/homer/groseq/", - "pattern": "uniqmap/" - } - } - ], - "output": { - "txt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.peaks.txt": { - "type": "file", - "description": "Peaks in txt file", - "pattern": "*.peaks.txt", - "ontologies": [] - } - } - ] - ], - "versions_homer": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "homer": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "4.11": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - 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"biotools:homer" - } - }, - { - "samtools": { - "description": "SAMtools is a set of utilities for interacting with and post-processing\nshort DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.\nThese files are generated as output by short read aligners like BWA.\n", - "homepage": "http://www.htslib.org/", - "documentation": "http://www.htslib.org/doc/samtools.html", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "identifier": "biotools:homer" - } - }, - { - "DESeq2": { - "description": "Differential gene expression analysis based on the negative binomial distribution\n", - "homepage": "https://bioconductor.org/packages/DESeq2", - "documentation": "https://bioconductor.org/packages/DESeq2", - "tool_dev_url": "https://github.com/mikelove/DESeq2", - "doi": "10.18129/B9.bioc.DESeq2", - "licence": [ - "LGPL-3.0-or-later" - ], - "identifier": "biotools:homer" - } - }, - { - "edgeR": { - "description": "Empirical Analysis of Digital 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"versions_merquryfk": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "merquryfk": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "1.2": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_fastk": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "fastk": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "1.2": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_r": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "R": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "R --version | sed \"1!d; s/.*version //; s/ .*//\"": { + "type": "eval", + "description": "The expression to obtain the 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+ "type": "map", + "description": "Groovy Map containing paternal sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "pathaptab": { + "type": "file", + "description": "trio paternal histogram ktab files from the program FastK (option -t)", + "pattern": "*.ktab*", + "ontologies": [] + } + } + ] + ], + "output": { + "stats": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.completeness.stats": { + "type": "file", + "description": "Assembly statistics file", + "pattern": "*.completeness.stats", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "bed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.*_only.bed": { + "type": "file", + "description": "Assembly only kmer positions not supported 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"type": "module", - "meta": { - "name": "htodemux", - "description": "Demultiplex samples based on data from cell hashing.", - "keywords": [ - "demultiplexing", - "hashing-based deconvolution", - "single-cell" - ], - "tools": [ - { - "htodemux": { - "description": "HTODemux is the demultiplexing module of Seurat, which demultiplex samples based on data from cell hashing.", - "homepage": "https://satijalab.org/seurat/articles/hashing_vignette", - "documentation": "https://satijalab.org/seurat/reference/htodemux", - "tool_dev_url": "https://github.com/satijalab/seurat", - "doi": "10.1186/s13059-018-1603-1", - "licence": [ - "MIT" - ], - "identifier": "" + }, + { + "name": "metabuli_build", + "path": "modules/nf-core/metabuli/build/meta.yml", + "type": "module", + "meta": { + "name": "metabuli_build", + "description": "Builds a database for classification with metabuli from FASTA files and a taxonomy", + "keywords": ["database", "taxonomic classification", "classification", "metagenomics"], + "tools": [ + { + "metabuli": { + "description": "Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid", + "homepage": "https://github.com/steineggerlab/Metabuli", + "documentation": "https://github.com/steineggerlab/Metabuli", + "tool_dev_url": "https://github.com/steineggerlab/Metabuli", + "doi": "10.1101/2023.05.31.543018", + "licence": ["GPL v3"], + "identifier": "biotools:metabuli" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\n" + } + }, + { + "fasta": { + "type": "file", + "description": "List of fasta files with input assemblies", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + { + "taxonomy_names": { + "type": "file", + "description": "File describing individual members of a taxonomic tree in NCBI nodes.dmp format", + "ontologies": [ + { + "edam": "http://edamontology.org/data_3028" + } + ] + } + }, + { + "taxonomy_nodes": { + "type": "file", + "description": "File describing parent-child relationships of a taxonomic tree in NCBI nodes.dmp format", + "ontologies": [ + { + "edam": "http://edamontology.org/data_3028" + } + ] + } + }, + { + "taxonomy_merged": { + "type": "file", + "description": "Optional input to map old/deprecated TaxID to new ones", + "ontologies": [ + { + "edam": "http://edamontology.org/data_3028" + } + ] + } + }, + { + "accession2taxid": { + "type": "directory", + "description": "TSV file (with no header) of first column with mapping accession (from first part of each fasta entry) and second column the corresponding TaxID", + "ontologies": [ + { + "edam": "http://edamontology.org/data_3028" + } + ] + } + }, + { + "cds_info": { + "type": "file", + "description": "List of files to cds files", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1936" + } + ] + } + } + ], + "output": { + "db": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "$prefix": { + "type": "directory", + "description": "metabuli database directory for classification" + } + } + ] + ], + "versions_metabuli": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "metabuli": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "metabuli 2>&1 | awk '/metabuli Version:/ {print $3}'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "metabuli": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "metabuli 2>&1 | awk '/metabuli Version:/ {print $3}'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@pawelciurkaardigen", "@MichalStachowiakArdigen", "@sofstam"], + "maintainers": ["@pawelciurkaardigen", "@MichalStachowiakArdigen", "@softam"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "seurat_object": { - "type": "file", - "description": "A `.rds` file containing the seurat object. Assumes that the hash tag oligo (HTO) data has been added and normalized.\n", - "ontologies": [] - } + }, + { + "name": "metacache_build", + "path": "modules/nf-core/metacache/build/meta.yml", + "type": "module", + "meta": { + "name": "metacache_build", + "description": "Taxonomic profiling database building with MetaCache", + "keywords": [ + "genomics", + "metagenomics", + "taxonomy", + "short reads", + "long reads", + "kmer", + "k-mer", + "metacache", + "build", + "reference" + ], + "tools": [ + { + "metacache": { + "description": "MetaCache is a classification system for mapping genomic sequences (short reads, long reads, contigs, ...) from metagenomic samples to their most likely taxon of origin. It aims to reduce the memory requirement usually associated with k-mer based methods while retaining their speed. MetaCache uses locality sensitive hashing to quickly identify candidate regions within one or multiple reference genomes. A read is then classified based on the similarity to those regions.\n\nFor an independent comparison to other tools in terms of classification accuracy see the LEMMI benchmarking site.\n\nThe latest version of MetaCache classifies around 60 Million reads (of length 100) per minute against all complete bacterial, viral and archaea genomes from NCBI RefSeq Release 97 running with 88 threads on a workstation with 2 Intel(R) Xeon(R) Gold 6238 CPUs.\n", + "homepage": "https://muellan.github.io/metacache", + "documentation": "https://github.com/muellan/metacache/tree/master/docs", + "tool_dev_url": "https://github.com/muellan/metacache", + "licence": ["GPL v3-or-later"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "genome_files": { + "type": "file", + "description": "(possibly gzipped) fasta or fastq files of full genomes, for example from an NCBI assembly", + "pattern": "*.{fna,fa,fasta,fnq,fq,fastq}{,.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + }, + { + "edam": "http://edamontology.org/format_1930" + }, + { + "edam": "http://edamontology.org/format_1954" + }, + { + "edam": "http://edamontology.org/data_2044" + } + ] + } + } + ], + { + "taxonomy": { + "type": "file", + "description": "NCBI taxonomy formatted files nodes.dmp and names.dmp", + "pattern": "{names,nodes,merged}.dmp", + "ontologies": [ + { + "edam": "http://edamontology.org/data_3028" + } + ] + } + }, + { + "seq2taxid": { + "type": "file", + "description": "NCBI-style 'accession2taxid' tab-separated file with 3 or 4 columns: accession, accession_version, taxid, and gid (optional)\n", + "pattern": "*", + "ontologies": [] + } + } + ], + "output": { + "db": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.meta": { + "type": "file", + "description": "sequence signature database binary file", + "pattern": "*.meta", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2333" + } + ] + } + }, + { + "*.cache*": { + "type": "file", + "description": "sequence signature database binary files", + "pattern": "*.cache+([0-9])", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2333" + } + ] + } + } + ] + ], + "versions_metacache": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "metacache": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "metacache info |& sed -n 's/^MetaCache version \\+\\([0-9.]\\+\\).*\\$/\\1/p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "metacache": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "metacache info |& sed -n 's/^MetaCache version \\+\\([0-9.]\\+\\).*\\$/\\1/p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@Gullumluvl"], + "maintainers": ["@Gullumluvl"] }, - { - "assay": { - "type": "string", - "description": "Name of the Hashtag assay, usually called \"HTO\" by default. Use the custom name if the assay has been named differently.\n" - } - } - ] - ], - "output": { - "params": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*_params_htodemux.csv": { - "type": "file", - "description": "The used parameters to call HTODemux in the R-Script.", - "pattern": "params_htodemux.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "assignment": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*_assignment_htodemux.csv": { - "type": "file", - "description": "Assignment results.", - "pattern": "assignment_htodemux.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "classification": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*_classification_htodemux.csv": { - "type": "file", - "description": "Classification results.", - "pattern": "classification_htodemux.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "rds": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*_htodemux.rds": { - "type": "file", - "description": "SeuratObject saved as RDS.", - "pattern": "htodemux.rds", - "ontologies": [] - } - } + "pipelines": [ + { + "name": "createtaxdb", + "version": "3.0.0" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@LuisHeinzlmeier" - ], - "maintainers": [ - "@LuisHeinzlmeier" - ] - } - }, - { - "name": "htseq_count", - "path": "modules/nf-core/htseq/count/meta.yml", - "type": "module", - "meta": { - "name": "htseq_count", - "description": "count how many reads map to each feature", - "keywords": [ - "htseq", - "count", - "gtf", - "annotation" - ], - "tools": [ - { - "htseq/count": { - "description": "HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.", - "homepage": "https://htseq.readthedocs.io/en/latest/", - "documentation": "https://htseq.readthedocs.io/en/latest/index.html", - "doi": "10.1093/bioinformatics/btu638", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:htseq" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "input": { - "type": "file", - "description": "Sorted BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } - }, - { - "index": { - "type": "file", - "description": "Contains indexed bam file", - "pattern": "*.bai", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": ".gtf file information\ne.g. `[ id:'test' ]`\n" - } + }, + { + "name": "metacache_query", + "path": "modules/nf-core/metacache/query/meta.yml", + "type": "module", + "meta": { + "name": "metacache_query", + "description": "Metacache query command for taxonomic classification", + "keywords": ["metagenomics", "classification", "metacache"], + "tools": [ + { + "metacache": { + "description": "MetaCache is a classification system for mapping genomic sequences (short reads, long reads, contigs, ...) from metagenomic samples to their most likely taxon of origin.", + "homepage": "https://github.com/muellan/metacache", + "documentation": "https://muellan.github.io/metacache/", + "tool_dev_url": "https://github.com/muellan/metacache", + "doi": "10.1093/bioinformatics/btx520", + "licence": ["GPL-3.0 license"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "reads": { + "type": "file", + "description": "FASTA or FASTQ files", + "pattern": "*.{fasta,fa,fastq,fq}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ], + { + "db": { + "type": "directory", + "description": "A MetaCache database contains taxonomic information and min-hash signatures of reference sequences (complete genomes, scaffolds, contigs, ...)." + } + }, + { + "do_abundances": { + "type": "boolean", + "description": "Flag indicating whether to produce the abundance table." + } + } + ], + "output": { + "mapping_results": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*mapping.txt": { + "type": "file", + "description": "Output file containing mapping results", + "pattern": "*mapping.txt", + "ontologies": [] + } + } + ] + ], + "abundances": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*abundances.txt": { + "type": "file", + "description": "Output file showing absolute and relative abundance of each taxon", + "pattern": "*abundances.txt", + "ontologies": [] + } + } + ] + ], + "versions_metacache": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "metacache": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "metacache info |& sed -n 's/^MetaCache version \\+\\([0-9.]\\+\\).*\\$/\\1/p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "metacache": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "metacache info |& sed -n 's/^MetaCache version \\+\\([0-9.]\\+\\).*\\$/\\1/p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@sofstam", "@Gullumluvl"], + "maintainers": ["@sofstam", "@Gullumluvl"] }, - { - "gtf": { - "type": "file", - "description": "Contains the features in the GTF format", - "pattern": "*.gtf", - "ontologies": [] - } - } - ] - ], - "output": { - "txt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*.txt": { - "type": "file", - "description": "File containing feature counts output", - "pattern": ".txt", - "ontologies": [] - } - } + "pipelines": [ + { + "name": "taxprofiler", + "version": "2.0.0" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@zehrahazalsezer" - ], - "maintainers": [ - "@zehrahazalsezer" - ] - }, - "pipelines": [ - { - "name": "lncpipe", - "version": "dev" - } - ] - }, - { - "name": "htslib_bgziptabix", - "path": "modules/nf-core/htslib/bgziptabix/meta.yml", - "type": "module", - "meta": { - "name": "htslib_bgziptabix", - "description": "Multi-purpose module to compress, decompress and index files using bgzip and tabix.", - "keywords": [ - "compress", - "decompress", - "index", - "bgzip", - "tabix", - "gzip", - "bzip", - "xz" - ], - "tools": [ - { - "htslib": { - "description": "C library for high-throughput sequencing data formats.", - "homepage": "http://www.htslib.org/", - "documentation": "http://www.htslib.org/doc/", - "tool_dev_url": "https://github.com/samtools/htslib", - "doi": "10.1093/gigascience/giab007", - "licence": [ - "MIT" - ], - "identifier": "biotools:htslib" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample1' ]\n" - } - }, - { - "infile": { - "type": "file", - "description": "Input file to compress or decompress", - "pattern": "*", - "ontologies": [] - } - }, - { - "infile_tbi": { - "type": "file", - "description": "Optional tabix index for the input file.", - "pattern": "*.{tbi,csi}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3616" - } - ] - } + }, + { + "name": "metaeuk_easypredict", + "path": "modules/nf-core/metaeuk/easypredict/meta.yml", + "type": "module", + "meta": { + "name": "metaeuk_easypredict", + "description": "Annotation of eukaryotic metagenomes using MetaEuk", + "keywords": ["genomics", "annotation", "fasta"], + "tools": [ + { + "metaeuk": { + "description": "MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics", + "homepage": "https://github.com/soedinglab/metaeuk", + "documentation": "https://github.com/soedinglab/metaeuk", + "tool_dev_url": "https://github.com/soedinglab/metaeuk", + "doi": "10.1186/s40168-020-00808-x", + "licence": ["GPL v3"], + "identifier": "biotools:MetaEuk" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Nucleotide FASTA file for annotation", + "pattern": "*.{fasta,fa,fasta.gz,fa.gz}", + "ontologies": [] + } + } + ], + { + "database": { + "type": "file", + "description": "Either a fasta file containing protein sequences, or a directory containing an mmseqs2-formatted protein database", + "ontologies": [] + } + } + ], + "output": { + "faa": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.fas": { + "type": "file", + "description": "Protein FASTA file containing the exons from the input FASTA file", + "pattern": "*.{fas}", + "ontologies": [] + } + } + ] + ], + "codon": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.codon.fas": { + "type": "file", + "description": "Nucleotide FASTA file of protein-coding sequences", + "pattern": "*.{codon.fas}", + "ontologies": [] + } + } + ] + ], + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "TSV file containing locations of each protein coding sequence in the input fasta", + "pattern": "*.headersMap.{tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "gff": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.gff": { + "type": "file", + "description": "Annotation file in GFF format", + "pattern": "*.{gff}", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@prototaxites"], + "maintainers": ["@prototaxites"] }, - { - "regions": { - "type": "file", - "description": "Optional file of regions to extract (BED or chr:start-end format). Only used when creating an index for the output file.", - "pattern": "*.{bed,txt,tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - }, - { - "edam": "http://edamontology.org/format_3003" - } - ] - } - } - ], - { - "action": { - "type": "string", - "description": "Action to perform, either `compress` or `decompress`" - } - }, - { - "make_index": { - "type": "boolean", - "description": "Whether to create a tabix index for the output file; only used if `action` is `compress`" - } - }, - { - "out_ext": { - "type": "string", - "description": "Output file extension without `.gz` suffix (for example `vcf`)" - } - } - ], - "output": { - "output": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample1' ]\n" - } - }, - { - "${outfile}": { - "type": "file", - "description": "Compressed or decompressed output file", - "pattern": "*", - "ontologies": [] - } - } - ] - ], - "index": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample1' ]\n" - } - }, - { - "${outfile}.{tbi,csi}": { - "type": "file", - "description": "Tabix index file for the compressed output file", - "pattern": "*.{tbi,csi}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3616" - } - ] - } - } - ] - ], - "versions_htslib": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "htslib": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bgzip --version | sed '1! d; s/bgzip (htslib) //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_xz": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "xz": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "xz --version | sed '1! d; s/xz (XZ Utils) //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "htslib": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bgzip --version | sed '1! d; s/bgzip (htslib) //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "xz": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "xz --version | sed '1! d; s/xz (XZ Utils) //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "mag", + "version": "5.4.2" + } ] - ] - }, - "authors": [ - "@itrujnara" - ], - "maintainers": [ - "@itrujnara" - ] - } - }, - { - "name": "htsnimtools_vcfcheck", - "path": "modules/nf-core/htsnimtools/vcfcheck/meta.yml", - "type": "module", - "meta": { - "name": "htsnimtools_vcfcheck", - "description": "This tools takes a background VCF, such as gnomad, that has full genome (though in some cases, users will instead want whole exome) coverage and uses that as an expectation of variants.", - "keywords": [ - "validation", - "check", - "variation" - ], - "tools": [ - { - "htsnimtools": { - "description": "useful command-line tools written to show-case hts-nim", - "homepage": "https://github.com/brentp/hts-nim-tools", - "documentation": "https://github.com/brentp/hts-nim-tools", - "tool_dev_url": "https://github.com/brentp/hts-nim-tools", - "licence": [ - "MIT" - ], - "identifier": "" + }, + { + "name": "metamaps_classify", + "path": "modules/nf-core/metamaps/classify/meta.yml", + "type": "module", + "meta": { + "name": "metamaps_classify", + "description": "Strain-level metagenomic assignment", + "keywords": ["metamaps", "long reads", "metagenomics", "taxonomy"], + "tools": [ + { + "metamaps": { + "description": "MetaMaps is a tool for long-read metagenomic analysis", + "homepage": "https://github.com/DiltheyLab/MetaMaps", + "documentation": "https://github.com/DiltheyLab/MetaMaps/blob/master/README.md", + "tool_dev_url": "https://github.com/DiltheyLab/MetaMaps", + "doi": "10.1038/s41467-019-10934-2", + "licence": ["Public Domain"], + "identifier": "biotools:metamaps" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "classification_res": { + "type": "file", + "description": "Coordinates where reads map", + "pattern": "*.{classification_res}", + "ontologies": [] + } + }, + { + "meta_file": { + "type": "file", + "description": "Statistics for mapping result", + "pattern": "*.{classification_res.meta}", + "ontologies": [] + } + }, + { + "meta_unmappedreadsLengths": { + "type": "file", + "description": "Statistics for length of unmapped reads", + "pattern": "*.{classification_res.meta.unmappedReadsLengths}", + "ontologies": [] + } + }, + { + "para_file": { + "type": "file", + "description": "Log with parameters", + "pattern": "*.{classification_res.parameters}", + "ontologies": [] + } + } + ], + { + "database_folder": { + "type": "directory", + "description": "Path to MetaMaps database", + "pattern": "*" + } + } + ], + "output": { + "wimp": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*classification_res.EM.WIMP": { + "type": "file", + "description": "Sample composition at different taxonomic levels", + "pattern": "*.{classification_res.EM.WIMP}", + "ontologies": [] + } + } + ] + ], + "evidence_unknown_species": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*classification_res.EM.evidenceUnknownSpecies": { + "type": "file", + "description": "Statistics on read identities and zero-coverage regions", + "pattern": "*.{classification_res.EM.evidenceUnknownSpecies}", + "ontologies": [] + } + } + ] + ], + "reads2taxon": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*classification_res.EM.reads2Taxon": { + "type": "file", + "description": "Taxon ID assignment of reads", + "pattern": "*.{classification_res.EM.reads2Taxon}", + "ontologies": [] + } + } + ] + ], + "em": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*classification_res.EM": { + "type": "file", + "description": "The final and complete set of approximate read mappings", + "pattern": "*.{classification_res.EM}", + "ontologies": [] + } + } + ] + ], + "contig_coverage": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*classification_res.EM.contigCoverage": { + "type": "file", + "description": "Read coverage for contigs", + "pattern": "*.{classification_res.EM.contigCoverage}", + "ontologies": [] + } + } + ] + ], + "length_and_id": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*classification_res.EM.lengthAndIdentitiesPerMappingUnit": { + "type": "file", + "description": "Read length and estimated identity for all reads", + "pattern": "*.{classification_res.EM.lengthAndIdentitiesPerMappingUnit}", + "ontologies": [] + } + } + ] + ], + "krona": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*classification_res.EM.reads2Taxon.krona": { + "type": "file", + "description": "Taxon ID assignment of reads in Krona format", + "pattern": "*.{classification_res.EM.reads2Taxon.krona}", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@henningonsbring", "@sofstam"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "vcf": { - "type": "file", - "description": "The query VCF file", - "pattern": "*.{vcf,vcf.gz,bcf}", - "ontologies": [] - } - }, - { - "tbi": { - "type": "file", - "description": "The index of the query VCF file", - "pattern": "*.{tbi}", - "ontologies": [] - } + }, + { + "name": "metamaps_mapdirectly", + "path": "modules/nf-core/metamaps/mapdirectly/meta.yml", + "type": "module", + "meta": { + "name": "metamaps_mapdirectly", + "description": "Maps long reads to a metamaps database", + "keywords": ["metamaps", "long reads", "metagenomics", "taxonomy"], + "tools": [ + { + "metamaps": { + "description": "MetaMaps is a tool for long-read metagenomic analysis", + "homepage": "https://github.com/DiltheyLab/MetaMaps", + "documentation": "https://github.com/DiltheyLab/MetaMaps/blob/master/README.md", + "tool_dev_url": "https://github.com/DiltheyLab/MetaMaps", + "doi": "10.1038/s41467-019-10934-2", + "licence": ["Public Domain"], + "identifier": "biotools:metamaps" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "Input fastq file containing query sequences", + "pattern": "*.{fq,fastq,fastq.gz,fq.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ], + { + "database": { + "type": "file", + "description": "Database file in fasta format", + "pattern": "*.{fa,fasta}", + "ontologies": [] + } + } + ], + "output": { + "classification_res": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*classification_res": { + "type": "file", + "description": "Coordinates where reads map", + "pattern": "*.{classification_res}", + "ontologies": [] + } + } + ] + ], + "meta_file": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*classification_res.meta": { + "type": "file", + "description": "Statistics for mapping result", + "pattern": "*.{classification_res.meta}", + "ontologies": [] + } + } + ] + ], + "meta_unmappedreadsLengths": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*classification_res.meta.unmappedReadsLengths": { + "type": "file", + "description": "Statistics for length of unmapped reads", + "pattern": "*.{classification_res.meta.unmappedReadsLengths}", + "ontologies": [] + } + } + ] + ], + "para_file": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*classification_res.parameters": { + "type": "file", + "description": "Log with parameters", + "pattern": "*.{classification_res.parameters}", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@henningonsbring", "@sofstam"], + "maintainers": ["@sofstam"] } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing background VCF information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "background_vcf": { - "type": "file", - "description": "The background VCF file", - "pattern": "*.{vcf,vcf.gz,bcf}", - "ontologies": [] - } + }, + { + "name": "metamdbg_asm", + "path": "modules/nf-core/metamdbg/asm/meta.yml", + "type": "module", + "meta": { + "name": "metamdbg_asm", + "description": "Metagenome assembler for long-read sequences (HiFi and ONT).", + "keywords": ["assembly", "long reads", "metagenome", "metagenome assembler"], + "tools": [ + { + "metamdbg": { + "description": "MetaMDBG: a lightweight assembler for long and accurate metagenomics reads.", + "homepage": "https://github.com/GaetanBenoitDev/metaMDBG", + "documentation": "https://github.com/GaetanBenoitDev/metaMDBG", + "tool_dev_url": "https://github.com/GaetanBenoitDev/metaMDBG", + "doi": "10.1038/s41587-023-01983-6", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "reads": { + "type": "file", + "description": "Long read sequence data from ONT or HiFi in fasta format (can be gzipped)", + "pattern": "*.{fa,fasta,fa.gz,fasta.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + { + "input_type": { + "type": "string", + "description": "Sequencing technology for reads - either \"hifi\" for PacBio HiFi reads or \"ont\" for Oxford Nanopore reads." + } + } + ], + "output": { + "contigs": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.contigs.fasta.gz": { + "type": "file", + "description": "Gzipped fasta file containing the assembled contigs from the input\nreads.\n", + "pattern": "*.contigs.fasta.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.metaMDBG.log": { + "type": "file", + "description": "Log file describing the metaMDBG run.", + "pattern": "*.metaMDBG.log", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3671" + } + ] + } + } + ] + ], + "versions_metamdbg": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "metamdbg": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "metaMDBG | sed -n \"s/.*Version: //p\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "metamdbg": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "metaMDBG | sed -n \"s/.*Version: //p\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@prototaxites", "@eit-maxlcummins"], + "maintainers": ["@prototaxites"] }, - { - "background_tbi": { - "type": "file", - "description": "The index of the background VCF file", - "pattern": "*.{tbi}", - "ontologies": [] - } - } - ] - ], - "output": { - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "A tab-delimited file comparing the variant count of each region in the query VCF and background VCF", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } + "pipelines": [ + { + "name": "mag", + "version": "5.4.2" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@nvnieuwk" - ], - "maintainers": [ - "@nvnieuwk" - ] - } - }, - { - "name": "huggingface_download", - "path": "modules/nf-core/huggingface/download/meta.yml", - "type": "module", - "meta": { - "name": "huggingface_download", - "description": "Download a file from a Hugging Face Hub repository using the `hf` CLI", - "keywords": [ - "download", - "gguf", - "huggingface", - "hub", - "inference", - "llm", - "model" - ], - "tools": [ - { - "huggingface_hub": { - "description": "Client library for interacting with the Hugging Face Hub, providing the `hf` CLI for downloading and uploading repositories, models and datasets.", - "homepage": "https://huggingface.co/docs/huggingface_hub", - "documentation": "https://huggingface.co/docs/huggingface_hub/guides/cli", - "tool_dev_url": "https://github.com/huggingface/huggingface_hub", - "licence": [ - "Apache-2.0" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "hf_repo": { - "type": "string", - "description": "Hugging Face repository identifier in `/` form,\ne.g. `ggml-org/gemma-3-1b-it-GGUF`.\n" - } - }, - { - "hf_file": { - "type": "string", - "description": "Path of the file to download within the repository,\ne.g. `gemma-3-1b-it-Q4_K_M.gguf`. The downloaded file is emitted\nwith this name in the task work directory.\n" - } + }, + { + "name": "metaphlan3_mergemetaphlantables", + "path": "modules/nf-core/metaphlan3/mergemetaphlantables/meta.yml", + "type": "module", + "meta": { + "name": "metaphlan3_mergemetaphlantables", + "description": "Merges output abundance tables from MetaPhlAn3", + "keywords": ["metagenomics", "classification", "merge", "table", "profiles"], + "tools": [ + { + "metaphlan3": { + "description": "Identify clades (phyla to species) present in the metagenome obtained from a microbiome sample and their relative abundance", + "homepage": "https://huttenhower.sph.harvard.edu/metaphlan/", + "documentation": "https://github.com/biobakery/MetaPhlAn", + "doi": "10.7554/eLife.65088", + "licence": ["MIT License"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "profiles": { + "type": "file", + "description": "List of per-sample MetaPhlAn3 taxonomic abundance tables", + "pattern": "*", + "ontologies": [] + } + } + ] + ], + "output": { + "txt": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.txt": { + "type": "file", + "description": "Combined MetaPhlAn3 table", + "pattern": "*.txt", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@jfy133"], + "maintainers": ["@jfy133"] } - ] - ], - "output": { - "output": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "hf_file": { - "type": "file", - "description": "Downloaded file from the Hugging Face repository", - "ontologies": [] - } - } - ] - ], - "versions_huggingface_hub": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "huggingface_hub": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "hf --version 2>&1 | tail -n1 | awk '{print \\$NF}'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "huggingface_hub": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "hf --version 2>&1 | tail -n1 | awk '{print \\$NF}'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@toniher", - "@lucacozzuto" - ], - "maintainers": [ - "@toniher", - "@lucacozzuto" - ] - } - }, - { - "name": "humann3_humann", - "path": "modules/nf-core/humann3/humann/meta.yml", - "type": "module", - "meta": { - "name": "humann3_humann", - "description": "Functional analysis of metagenome or metatranscriptome data", - "keywords": [ - "function", - "metagenomics", - "metatranscriptomics", - "profiling", - "community" - ], - "tools": [ - { - "humann": { - "description": "HUMAnN: The HMP Unified Metabolic Analysis Network", - "homepage": "http://huttenhower.sph.harvard.edu/humann", - "documentation": "https://github.com/biobakery/biobakery/wiki/humann3", - "tool_dev_url": "https://github.com/biobakery/humann", - "doi": "10.7554/eLife.65088", - "licence": [ - "MIT" - ], - "identifier": "" + }, + { + "name": "metaphlan3_metaphlan3", + "path": "modules/nf-core/metaphlan3/metaphlan3/meta.yml", + "type": "module", + "meta": { + "name": "metaphlan3_metaphlan3", + "description": "MetaPhlAn is a tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.", + "keywords": ["metagenomics", "classification", "fastq", "bam", "fasta"], + "tools": [ + { + "metaphlan3": { + "description": "Identify clades (phyla to species) present in the metagenome obtained from a microbiome sample and their relative abundance", + "homepage": "https://huttenhower.sph.harvard.edu/metaphlan/", + "documentation": "https://github.com/biobakery/MetaPhlAn", + "doi": "10.7554/eLife.65088", + "licence": ["MIT License"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "Metaphlan 3.0 can classify the metagenome from a variety of input data types, including FASTQ files (single-end and paired-end), FASTA, bowtie2-produced SAM files (produced from alignments to the MetaPHlAn marker database) and intermediate bowtie2 alignment files (bowtie2out)", + "pattern": "*.{fastq.gz, fasta, fasta.gz, sam, bowtie2out.txt}", + "ontologies": [] + } + } + ], + { + "metaphlan_db": { + "type": "file", + "description": "Directory containing pre-downloaded and uncompressed MetaPhlAn3 database downloaded from: http://cmprod1.cibio.unitn.it/biobakery3/metaphlan_databases/.\nNote that you will also need to specify `--index` and the database version name (e.g. 'mpa_v31_CHOCOPhlAn_201901') in your module.conf ext.args for METAPHLAN3_METAPHLAN3!\n", + "pattern": "*/", + "ontologies": [] + } + } + ], + "output": { + "profile": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_profile.txt": { + "type": "file", + "description": "Tab-separated output file of the predicted taxon relative abundances", + "pattern": "*.{txt}", + "ontologies": [] + } + } + ] + ], + "biom": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.biom": { + "type": "file", + "description": "General-use format for representing biological sample by observation contingency tables", + "pattern": "*.{biom}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3746" + } + ] + } + } + ] + ], + "bt2out": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bowtie2out.txt": { + "type": "file", + "description": "Bowtie2 output file", + "pattern": "*.{bowtie2out.txt}", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@MGordon09"], + "maintainers": ["@MGordon09"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "input": { - "type": "file", - "description": "A metagenome (DNA reads) or metatranscriptome (RNA reads) [fastq,fastq.gz,fasta,fasta.gz]\nOR pre-computed mappings [sam,bam,blastm8]\nOR pre-computed abundance tables [tsv,biom]\n", - "pattern": "*.{fastq,fastq.gz,fasta,fasta.gz,sam,bam,blastm8,tsv,biom}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - }, - { - "edam": "http://edamontology.org/format_3475" - }, - { - "edam": "http://edamontology.org/format_3746" - } - ] - } + }, + { + "name": "metaphlan_makedb", + "path": "modules/nf-core/metaphlan/makedb/meta.yml", + "type": "module", + "meta": { + "name": "metaphlan_makedb", + "description": "Build MetaPhlAn database for taxonomic profiling.", + "keywords": ["metaphlan", "index", "database", "metagenomics"], + "tools": [ + { + "metaphlan": { + "description": "Identify clades (phyla to species) present in the metagenome obtained from a microbiome sample and their relative abundance", + "homepage": "https://huttenhower.sph.harvard.edu/metaphlan/", + "documentation": "https://github.com/biobakery/MetaPhlAn", + "doi": "10.7554/eLife.65088", + "licence": ["MIT License"], + "identifier": "biotools:metaphlan" + } + } + ], + "output": { + "db": [ + { + "metaphlan_db_latest": { + "type": "directory", + "description": "Output directory containing the indexed METAPHLAN database", + "pattern": "*/" + } + } + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@LilyAnderssonLee"], + "maintainers": ["@LilyAnderssonLee"] } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } + }, + { + "name": "metaphlan_mergemetaphlantables", + "path": "modules/nf-core/metaphlan/mergemetaphlantables/meta.yml", + "type": "module", + "meta": { + "name": "metaphlan_mergemetaphlantables", + "description": "Merges output abundance tables from MetaPhlAn4", + "keywords": ["metagenomics", "classification", "merge", "table", "profiles"], + "tools": [ + { + "metaphlan4": { + "description": "Identify clades (phyla to species) present in the metagenome obtained from a microbiome sample and their relative abundance", + "homepage": "https://huttenhower.sph.harvard.edu/metaphlan/", + "documentation": "https://github.com/biobakery/MetaPhlAn", + "doi": "10.1038/s41587-023-01688-w", + "licence": ["MIT License"], + "identifier": "biotools:metaphlan" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "profiles": { + "type": "file", + "description": "List of per-sample MetaPhlAn4 taxonomic abundance tables", + "pattern": "*", + "ontologies": [] + } + } + ] + ], + "output": { + "txt": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.txt": { + "type": "file", + "description": "Combined MetaPhlAn4 table", + "pattern": "*.txt", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@jfy133", "@LilyAnderssonLee"], + "maintainers": ["@jfy133", "@LilyAnderssonLee"] }, - { - "profile": { - "type": "file", - "description": "Pre-computed MetaPhlAn taxonomic profile", - "pattern": "*.{txt}", - "ontologies": [] - } - } - ], - { - "nucleotide_db": { - "type": "directory", - "description": "ChocoPhlAn nucleotide database directory (v3: *.ffn.gz, v4: *.fna.gz)\n" - } - }, - { - "protein_db": { - "type": "directory", - "description": "UniRef protein database directory containing *.dmnd files\n" - } - }, - { - "utility_db": { - "type": "directory", - "description": "HUMAnN utility mapping database directory\n" - } - } - ], - "output": { - "genefamilies": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*_genefamilies.tsv.gz": { - "type": "file", - "description": "Compressed gene families abundance table", - "pattern": "*.{tsv.gz}", - "ontologies": [] - } - } - ] - ], - "pathabundance": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*_pathabundance.tsv.gz": { - "type": "file", - "description": "Compressed pathway abundance table", - "pattern": "*.{tsv.gz}", - "ontologies": [] - } - } - ] - ], - "pathcoverage": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*_pathcoverage.tsv.gz": { - "type": "file", - "description": "Compressed pathway coverage table", - "pattern": "*.{tsv.gz}", - "ontologies": [] - } - } - ] - ], - "reactions": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*_reactions.tsv.gz": { - "type": "file", - "description": "Compressed reactions abundance table", - "pattern": "*.{tsv.gz}", - "ontologies": [] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.log": { - "type": "file", - "description": "HUMAnN run log file", - "pattern": "*.{log}", - "ontologies": [] - } - } - ] - ], - "versions_humann": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "HUMAnN": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "humann --version 2>&1 | sed 's/humann v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_metaphlan": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "MetaPhlAn": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "metaphlan --version 2>&1 | sed 's/MetaPhlAn version //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_python": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "Python": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python --version 2>&1 | sed 's/Python //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "HUMAnN": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "humann --version 2>&1 | sed 's/humann v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "MetaPhlAn": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "metaphlan --version 2>&1 | sed 's/MetaPhlAn version //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "Python": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python --version 2>&1 | sed 's/Python //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "taxprofiler", + "version": "2.0.0" + } ] - ] - }, - "authors": [ - "@nickp60", - "@d4straub", - "@vinisalazar" - ], - "maintainers": [ - "@nickp60", - "@vinisalazar" - ] - }, - "pipelines": [ - { - "name": "funcprofiler", - "version": "dev" - } - ] - }, - { - "name": "humann3_regroup", - "path": "modules/nf-core/humann3/regroup/meta.yml", - "type": "module", - "meta": { - "name": "humann3_regroup", - "description": "Regrouping genes to other functional categories", - "keywords": [ - "function", - "metagenomics", - "metatranscriptomics", - "profiling", - "community" - ], - "tools": [ - { - "humann": { - "description": "HUMAnN: The HMP Unified Metabolic Analysis Network, version 3", - "homepage": "http://huttenhower.sph.harvard.edu/humann", - "documentation": "https://github.com/biobakery/biobakery/wiki/humann3", - "tool_dev_url": "https://github.com/biobakery/humann", - "doi": "10.7554/eLife.65088", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } + }, + { + "name": "metaphlan_metaphlan", + "path": "modules/nf-core/metaphlan/metaphlan/meta.yml", + "type": "module", + "meta": { + "name": "metaphlan_metaphlan", + "description": "MetaPhlAn is a tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.", + "keywords": ["metagenomics", "classification", "fastq", "fasta", "sam"], + "tools": [ + { + "metaphlan": { + "description": "Identify clades (phyla to species) present in the metagenome obtained from a microbiome sample and their relative abundance", + "homepage": "https://huttenhower.sph.harvard.edu/metaphlan/", + "documentation": "https://github.com/biobakery/MetaPhlAn", + "doi": "10.1038/s41587-023-01688-w", + "licence": ["MIT License"], + "identifier": "biotools:metaphlan" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "Metaphlan can classify the metagenome from a variety of input data types, including FASTQ files (single-end and paired-end), FASTA, bowtie2-produced SAM files (produced from alignments to the MetaPHlAn marker database) and intermediate bowtie2 alignment files (bowtie2out)", + "pattern": "*.{fastq.gz, fasta, fasta.gz, sam, bowtie2out.txt}", + "ontologies": [] + } + } + ], + { + "metaphlan_db_latest": { + "type": "file", + "description": "Directory containing pre-downloaded and uncompressed MetaPhlAn database downloaded from: http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/.\nNote that you will also need to specify `--index` and the database version name (e.g. 'mpa_vJan21_TOY_CHOCOPhlAnSGB_202103') in your module.conf ext.args for METAPHLAN_METAPHLAN!\n", + "pattern": "*/", + "ontologies": [] + } + }, + { + "save_samfile": { + "type": "boolean", + "description": "Whether to save the SAM file produced by MetaPhlAn of read alignments to MetaPhlAn database gene sequences\n" + } + } + ], + "output": { + "profile": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_profile.txt": { + "type": "file", + "description": "Tab-separated output file of the predicted taxon relative abundances", + "pattern": "*.{txt}", + "ontologies": [] + } + } + ] + ], + "biom": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.biom": { + "type": "file", + "description": "General-use format for representing biological sample by observation contingency tables", + "pattern": "*.{biom}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3746" + } + ] + } + } + ] + ], + "bt2out": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bowtie2out.txt": { + "type": "file", + "description": "Intermediate Bowtie2 output produced from mapping the metagenome against the MetaPHlAn marker database ( not compatible with `bowtie2out` files generated with MetaPhlAn versions below 3 )", + "pattern": "*.{bowtie2out.txt}", + "ontologies": [] + } + } + ] + ], + "sam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.sam": { + "type": "file", + "description": "SAM file produced by MetaPPhlAn of read alignments to MetaPhlAn database gene sequences", + "pattern": "*.{sam}", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@MGordon09", "@LilyAnderssonLee"], + "maintainers": ["@MGordon09", "@LilyAnderssonLee"] }, - { - "input": { - "type": "file", - "description": "Tab separated abundance file of HUMAnN3", - "pattern": "*.{tsv.gz,tsv}" - } - } - ], - { - "groups": { - "type": "string", - "description": "Regroup abundance values to a functional category (e.g. uniref90_rxn, uniref50_rxn)", - "pattern": "{uniref90_rxn,uniref50_rxn}" - } - }, - { - "utility_db": { - "type": "directory", - "description": "HUMAnN utility mapping database directory" - } - } - ], - "output": { - "regroup": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*_regroup.tsv.gz": { - "type": "file", - "description": "Re-grouped compressed tab separated text file", - "pattern": "*.{tsv.gz}" - } - } - ] - ], - "versions_humann": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "HUMAnN": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "humann --version 2>&1 | sed 's/humann v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_metaphlan": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "MetaPhlAn": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "metaphlan --version 2>&1 | sed 's/MetaPhlAn version //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_python": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "Python": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python --version 2>&1 | sed 's/Python //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "HUMAnN": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "humann --version 2>&1 | sed 's/humann v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "MetaPhlAn": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "metaphlan --version 2>&1 | sed 's/MetaPhlAn version //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "Python": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python --version 2>&1 | sed 's/Python //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "funcprofiler", + "version": "dev" + }, + { + "name": "taxprofiler", + "version": "2.0.0" + } ] - ] - }, - "authors": [ - "@d4straub", - "@nickp60", - "@vinisalazar" - ], - "maintainers": [ - "@nickp60", - "@vinisalazar" - ] - }, - "pipelines": [ - { - "name": "funcprofiler", - "version": "dev" - } - ] - }, - { - "name": "humann3_renorm", - "path": "modules/nf-core/humann3/renorm/meta.yml", - "type": "module", - "meta": { - "name": "humann3_renorm", - "description": "Normalizing RPKs to relative abundance", - "keywords": [ - "function", - "metagenomics", - "metatranscriptomics", - "profiling", - "community" - ], - "tools": [ - { - "humann": { - "description": "HUMAnN: The HMP Unified Metabolic Analysis Network, version 3", - "homepage": "http://huttenhower.sph.harvard.edu/humann", - "documentation": "https://github.com/biobakery/biobakery/wiki/humann3", - "tool_dev_url": "https://github.com/biobakery/humann", - "doi": "10.7554/eLife.65088", - "licence": [ - "MIT" - ], - "identifier": "" + }, + { + "name": "metaspace_converter", + "path": "modules/nf-core/metaspace/converter/meta.yml", + "type": "module", + "meta": { + "name": "metaspace_converter", + "description": "Export METASPACE datasets to AnnData and SpatialData objects", + "keywords": ["anndata", "spatialdata", "metabolomics", "mass spectrometry", "imaging"], + "tools": [ + { + "metaspace_converter": { + "description": "Python package to download and convert datasets from the METASPACE knowledge base to common formats for single-cell and spatial omics analysis", + "homepage": "https://metaspace2020.github.io/metaspace-converter/", + "documentation": "https://metaspace2020.github.io/metaspace-converter/", + "tool_dev_url": "https://github.com/metaspace2020/metaspace-converter", + "licence": ["Apache 2.0 license"], + "identifier": "biotools:metaspace" + } + } + ], + "input": [ + { + "ds_id": { + "type": "string", + "description": "METASPACE dataset identifier to retrieve and convert to AnnData and SpatialData formats." + } + }, + { + "database_name_": { + "type": "string", + "description": "Name of the metabolite annotation database to use (e.g., HMDB)" + } + }, + { + "database_version_": { + "type": "string", + "description": "Version of the annotation database to use (e.g., v4)" + } + }, + { + "fdr_": { + "type": "string", + "description": "False Discovery Rate threshold for filtering metabolite annotations.", + "pattern": "^(0(\\.[0-9]+)?|1(\\.0+)?)$" + } + }, + { + "use_tic_": { + "type": "string", + "description": "Controls whether intensity values are scaled by the total ion count per pixel.\n", + "pattern": "^(true|false)$" + } + }, + { + "metadata_as_obs_": { + "type": "string", + "description": "Whether to store metadata in the obs dataframe instead of uns.\n", + "pattern": "^(true|false)$" + } + } + ], + "output": { + "adata_object": [ + { + "AnnData_${ds_id}.h5ad": { + "type": "file", + "description": "AnnData object in .h5ad format. Obs are single pixels and vars are metabolites", + "ontologies": [] + } + } + ], + "sdata_object": [ + { + "SpatialData_${ds_id}.zarr": { + "type": "directory", + "description": "SpatialData format in .zarr format" + } + } + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@bisho2122"], + "maintainers": ["@bisho2122"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "input": { - "type": "file", - "description": "Tab separated abundance file of HUMAnN3", - "pattern": "*.{tsv.gz,tsv}" - } + }, + { + "name": "metaspace_download", + "path": "modules/nf-core/metaspace/download/meta.yml", + "type": "module", + "meta": { + "name": "metaspace_download", + "description": "A module to download dataset results from the METASPACE platform and save them as CSV files, using a containerized Python script. Inputs are provided via a CSV file or a list of datasets, with results saved to a specified output directory.", + "keywords": ["metaspace", "metabolite annotation", "data-download", "csv"], + "tools": [ + { + "metaspace2020": { + "description": "Python package providing programmatic access to the METASPACE platform", + "homepage": "https://metaspace2020.readthedocs.io", + "documentation": "https://metaspace2020.readthedocs.io", + "tool_dev_url": "https://github.com/metaspace2020/metaspace/tree/master/metaspace/python-client", + "licence": ["Apache-2.0 license"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "dataset_id": { + "type": "string", + "description": "The ID of the dataset to process.\nThe ID is the last part of the dataset URL.\nFor example, in the URL `https://metaspace2020.org/dataset/2022-08-05_17h28m56s`,\nthe `dataset_id` is `2022-08-05_17h28m56s`.\n", + "optional": false + } + }, + { + "database": { + "type": "string", + "description": "The database to download the dataset from (default: 'HMDB').\nIf not provided, all dataset will be included.\n", + "optional": true + } + }, + { + "version": { + "type": "string", + "description": "The version of the database to download the dataset from (default: 'v4').\nIf not provided, all versions will be included.\n", + "optional": true + } + } + ] + ], + "output": { + "results": [ + { + "${dataset_id}_*.csv": { + "type": "file", + "description": "CSV file containing the downloaded dataset results, saved to the directory specified by the output parameter.\nFilename format is '{dataset_id}_*.csv'.\n", + "pattern": "*.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752:latest" + }, + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ], + "log": [ + { + "emit:": { + "type": "string", + "description": "The standard output (stdout) of the script, containing log messages.\nYou can print the last log to see the download progress of all the datasets.\nExample:\n METASPACE_DOWNLOAD.out.log.view { \"${it.split('\\n').last().trim()}\" }\nIt will print the last log message of the script.\nFor Example:\n \"❌ {dataset_id} Dataset not found or inaccessible. Skipping this dataset.\"\n \"❌ {dataset_id} could not find database: {database}\"\n \"❌ {dataset_id} has no annotation data in database: {database}.\"\n \"⚠️ {dataset_id} has multiple {database} version. All the version saved to {filename}\"\n \"✅ {dataset_id} with {database} database are saved to {filename}\"\n \"✅ {dataset_id} with all database are saved to {filename}\"\n" + } + } + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "YAML file containing the versions of the tools used in the pipeline.\nThis file is automatically generated by the pipeline and should not be modified.\n", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + }, + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@Dewey-Wang"], + "maintainers": ["@Dewey-Wang"] } - ] - ], - "output": { - "renorm": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*_renorm.tsv.gz": { - "type": "file", - "description": "Normalized compressed tab separated text file", - "pattern": "*.{tsv.gz}" - } - } - ] - ], - "versions_humann": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "HUMAnN": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "humann --version 2>&1 | sed 's/humann v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_metaphlan": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "MetaPhlAn": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "metaphlan --version 2>&1 | sed 's/MetaPhlAn version //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_python": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "Python": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python --version 2>&1 | sed 's/Python //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "HUMAnN": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "humann --version 2>&1 | sed 's/humann v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "MetaPhlAn": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "metaphlan --version 2>&1 | sed 's/MetaPhlAn version //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "Python": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python --version 2>&1 | sed 's/Python //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@d4straub", - "@nickp60", - "@vinisalazar" - ], - "maintainers": [ - "@nickp60", - "@vinisalazar" - ] - }, - "pipelines": [ - { - "name": "funcprofiler", - "version": "dev" - } - ] - }, - { - "name": "humid", - "path": "modules/nf-core/humid/meta.yml", - "type": "module", - "meta": { - "name": "humid", - "description": "HUMID is a tool to quickly and easily remove duplicate reads from FastQ files, with or without UMIs.", - "keywords": [ - "umi", - "fastq", - "deduplication", - "hamming-distance", - "clustering" - ], - "tools": [ - { - "humid": { - "description": "HUMID -- High-performance UMI Deduplicator", - "homepage": "https://github.com/jfjlaros/HUMID", - "documentation": "https://humid.readthedocs.io/en/latest/", - "tool_dev_url": "https://github.com/jfjlaros/HUMID", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "reads": { - "type": "file", - "description": "Fastq file(s) to deduplicate", - "pattern": "*.{fastq,fq,fastq.gz,fq.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "umi_file": { - "type": "file", - "description": "UMI file", - "ontologies": [] - } - } - ] - ], - "output": { - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "${prefix}.log": { - "type": "file", - "description": "Log file of humid, containing progress and errors", - "pattern": "*.log", - "ontologies": [] - } - } - ] - ], - "dedup": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*_dedup*.fastq.gz": { - "type": "file", - "description": "Deduplicated Fastq file(s)", - "pattern": "*.{fastq,fq,fastq.gz,fq.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "annotated": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*_annotated*.fastq.gz": { - "type": "file", - "description": "Annotated Fastq file(s)", - "pattern": "*.{fastq,fq,fastq.gz,fq.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "stats": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "${prefix}": { - "type": "directory", - "description": "Directory containing statistics file, use for multiqc.", - "pattern": "${prefix}/" - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@Joon-Klaps" - ], - "maintainers": [ - "@Joon-Klaps" - ] - }, - "pipelines": [ - { - "name": "viralmetagenome", - "version": "1.1.1" - } - ] - }, - { - "name": "hypo", - "path": "modules/nf-core/hypo/meta.yml", - "type": "module", - "meta": { - "name": "hypo", - "description": "Assembly polisher using short (and long) reads", - "keywords": [ - "assembly", - "polishing", - "nanopore", - "illumina" - ], - "tools": [ - { - "hypo": { - "description": "Super Fast and Accurate Polisher for Long Read Genome Assemblies.", - "homepage": "https://github.com/kensung-lab/hypo", - "documentation": "https://github.com/kensung-lab/hypo/blob/master/README.md", - "tool_dev_url": "https://github.com/kensung-lab/hypo", - "doi": "10.1101/2019.12.19.882506", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:hypo" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "sr_bam": { - "type": "file", - "description": "Aligned short-read BAM/SAM file. Must have CIGAR information.", - "pattern": "*.{bam,sam}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "Short reads file(s). In fastq or fasta, compressed or uncompressed", - "ontologies": [] - } - } - ], - { - "draft": { - "type": "file", - "description": "Input (fasta) file containing draft contig assembly", - "ontologies": [] - } - }, - { - "genome_size": { - "type": "string", - "description": "Estimated size of the genome. 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"description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@drpatelh", - "@joseespinosa" - ], - "maintainers": [ - "@drpatelh", - "@joseespinosa" - ] - } - }, - { - "name": "igv_js", - "path": "modules/nf-core/igv/js/meta.yml", - "type": "module", - "meta": { - "name": "igv_js", - "description": "igv.js is an embeddable interactive genome visualization component", - "keywords": [ - "igv", - "igv.js", - "js", - "genome browser" - ], - "tools": [ - { - "igv": { - "description": "Create an embeddable interactive genome browser component.\nOutput files are expected to be present in the same directory as the genome browser html file.\nTo visualise it, files have to be served. Check the documentation at:\n https://github.com/igvteam/igv-webapp for an example and\n https://github.com/igvteam/igv.js/wiki/Data-Server-Requirements for server requirements\n", - "homepage": "https://github.com/igvteam/igv.js", - "documentation": "https://github.com/igvteam/igv.js/wiki", - "tool_dev_url": "https://github.com/igvteam/igv.js", - "doi": "10.1093/bioinformatics/btac830", - "licence": [ - "MIT" - ], - "identifier": "biotools:igv" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "alignment": { - "type": "file", - "description": "Sorted BAM/CRAM file", - "pattern": "*.{bam,cram}", - "ontologies": [] - } + }, + { + "name": "miniasm", + "path": "modules/nf-core/miniasm/meta.yml", + "type": "module", + "meta": { + "name": "miniasm", + "description": "A very fast OLC-based de novo assembler for noisy long reads", + "keywords": ["assembly", "pacbio", "nanopore"], + "tools": [ + { + "miniasm": { + "description": "Ultrafast de novo assembly for long noisy reads (though having no consensus step)", + "homepage": "https://github.com/lh3/miniasm", + "documentation": "https://github.com/lh3/miniasm", + "tool_dev_url": "https://github.com/lh3/miniasm", + "doi": "10.1093/bioinformatics/btw152", + "licence": ["MIT"], + "identifier": "biotools:miniasm" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input PacBio/ONT FastQ files.", + "pattern": "*.{fastq,fastq.gz,fq,fq.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + }, + { + "paf": { + "type": "file", + "description": "Alignment in PAF format", + "pattern": "*{.paf,.paf.gz}", + "ontologies": [] + } + } + ] + ], + "output": { + "gfa": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.gfa.gz": { + "type": "file", + "description": "Assembly graph", + "pattern": "*.gfa.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "assembly": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fasta.gz": { + "type": "file", + "description": "Genome assembly", + "pattern": "*.fasta.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "versions_miniasm": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "miniasm": { + "type": "string", + "description": "The tool name" + } + }, + { + "miniasm -V 2>&1": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "miniasm": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "miniasm -V 2>&1": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@avantonder"], + "maintainers": ["@avantonder"] }, - { - "index": { - "type": "file", - "description": "Index of sorted BAM/CRAM file", - "pattern": "*.{bai,crai}", - "ontologies": [] - } - } - ] - ], - "output": { - "browser": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_genome-browser.html": { - "type": "file", - "description": "Genome browser HTML file", - "pattern": "*.{html}", - "ontologies": [] - } - } - ] - ], - "align_files": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "alignment": { - "type": "file", - "description": "Copy of the input sorted BAM/CRAM file", - "pattern": "*.{bam,cram}", - "ontologies": [] - } - } - ] - ], - "index_files": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "index": { - "type": "file", - "description": "Copy of the input index of sorted BAM/CRAM file", - "pattern": "*.{bai,crai}", - "ontologies": [] - } - } + "pipelines": [ + { + "name": "bacass", + "version": "2.6.0" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@mirpedrol" - ], - "maintainers": [ - "@mirpedrol" - ] - } - }, - { - "name": "igvreports", - "path": "modules/nf-core/igvreports/meta.yml", - "type": "module", - "meta": { - "name": "igvreports", - "description": "A Python application to generate self-contained HTML reports for variant review and other genomic applications", - "keywords": [ - "vcf", - "variant", - "genomics" - ], - "tools": [ - { - "igvreports": { - "description": "Creates self-contained html pages for visual variant review with IGV (igv.js).", - "homepage": "https://github.com/igvteam/igv-reports", - "documentation": "https://github.com/igvteam/igv-reports", - "tool_dev_url": "https://github.com/igvteam/igv-reports", - "doi": "10.1093/bioinformatics/btac830", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "sites": { - "type": "file", - "description": "VCF, BED, MAF, BEDPE, or generic tab delimited file of genomic variant sites\n", - "ontologies": [] - } - }, - { - "tracks": { - "type": "file", - "description": "List of any set of files of the types that IGV can display,\neg BAM/CRAM, GTF/GFF, VCF, BED, etc\n", - "ontologies": [] - } - }, - { - "tracks_indices": { - "type": "file", - "description": "List of indices for the tracks\n", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing genome information\ne.g. [ id:'genome_name' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference fasta file", - "pattern": "*.{fasta,fa}", - "ontologies": [] - } + }, + { + "name": "minimac4_compressref", + "path": "modules/nf-core/minimac4/compressref/meta.yml", + "type": "module", + "meta": { + "name": "minimac4_compressref", + "description": "Compression of a reference panel for genotype imputation to `.msav` format", + "keywords": ["haplotypes", "reference compression", "genomics"], + "tools": [ + { + "minimac4": { + "description": "Computationally efficient genotype imputation", + "homepage": "https://github.com/statgen/Minimac4", + "documentation": "https://github.com/statgen/Minimac4", + "tool_dev_url": "https://github.com/statgen/Minimac4", + "doi": "10.1038/ng.3656", + "licence": ["GPL v3-or-later"], + "identifier": "biotools:minimac4" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "ref": { + "type": "file", + "description": "Variant reference panel file", + "pattern": "*.{vcf,vcf.gz,bcf}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + }, + { + "edam": "http://edamontology.org/format_3020" + } + ] + } + }, + { + "ref_index": { + "type": "file", + "description": "Index file for the reference panel", + "pattern": "*.{tbi,csi}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3700" + } + ] + } + } + ] + ], + "output": { + "msav": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.msav": { + "type": "file", + "description": "Multy-sample variant compressed file", + "pattern": "*.{msav}", + "ontologies": [] + } + } + ] + ], + "versions_minimac4": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "minimac4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "minimac4 --version |& sed '1!d ; s/minimac v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "minimac4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "minimac4 --version |& sed '1!d ; s/minimac v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@LouisLeNezet"], + "maintainers": ["@LouisLeNezet"] }, - { - "fai": { - "type": "file", - "description": "Reference fasta file index", - "pattern": "*.{fai}", - "ontologies": [] - } - } - ] - ], - "output": { - "report": [ - [ - { - "meta": { - "type": "file", - "description": "html report with a table of genomic sites and an embedded\nIGV genome browser for viewing data for each site\n", - "pattern": "*.{html}", - "ontologies": [] - } - }, - { - "*.html": { - "type": "file", - "description": "html report with a table of genomic sites and an embedded\nIGV genome browser for viewing data for each site\n", - "pattern": "*.{html}", - "ontologies": [] - } - } + "pipelines": [ + { + "name": "phaseimpute", + "version": "1.1.0" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@souljamie" - ], - "maintainers": [ - "@souljamie" - ] - } - }, - { - "name": "ilastik_multicut", - "path": "modules/nf-core/ilastik/multicut/meta.yml", - "type": "module", - "meta": { - "name": "ilastik_multicut", - "description": "Ilastik is a tool that utilizes machine learning algorithms to classify pixels, segment, track and count cells in images. Ilastik contains a graphical user interface to interactively label pixels. However, this nextflow module will implement the --headless mode, to apply pixel classification using a pre-trained .ilp file on an input image.", - "keywords": [ - "multicut", - "segmentation", - "pixel classification" - ], - "tools": [ - { - "ilastik": { - "description": "Ilastik is a user friendly tool that enables pixel classification, segmentation and analysis.", - "homepage": "https://www.ilastik.org/", - "documentation": "https://www.ilastik.org/documentation/", - "tool_dev_url": "https://github.com/ilastik/ilastik", - "license": [ - "GPL3" - ], - "identifier": "biotools:ilastik" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "h5": { - "type": "file", - "description": "h5 file containing image stack to classify file", - "pattern": "*.{h5,hdf5}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3590" - } - ] - } + }, + { + "name": "minimac4_impute", + "path": "modules/nf-core/minimac4/impute/meta.yml", + "type": "module", + "meta": { + "name": "minimac4_impute", + "description": "Imputation of genotypes using a reference panel", + "keywords": ["impute", "haploype", "genomics"], + "tools": [ + { + "minimac4": { + "description": "Computationally efficient genotype imputation", + "homepage": "https://github.com/statgen/Minimac4", + "documentation": "https://github.com/statgen/Minimac4", + "tool_dev_url": "https://github.com/statgen/Minimac4", + "doi": "10.1038/ng.3656", + "licence": ["GPL v3-or-later"], + "identifier": "biotools:minimac4" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "target_vcf": { + "type": "file", + "description": "Target VCF/BCF file", + "pattern": "*.{vcf,bcf,vcf.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + }, + { + "edam": "http://edamontology.org/format_3020" + } + ] + } + }, + { + "target_index": { + "type": "file", + "description": "Target VCF/BCF file index", + "pattern": "*.{csi,tbi}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3700" + } + ] + } + }, + { + "ref_msav": { + "type": "file", + "description": "Reference compressed MSAV file obtain through `minimac4 --compress-reference`", + "pattern": "*.{msav}", + "ontologies": [] + } + }, + { + "sites_vcf": { + "type": "file", + "description": "Sites VCF/BCF file containing the sites to impute", + "pattern": "*.{vcf,bcf,vcf.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + }, + { + "edam": "http://edamontology.org/format_3020" + } + ] + } + }, + { + "sites_index": { + "type": "file", + "description": "Sites VCF/BCF file index", + "pattern": "*.{csi,tbi}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3700" + } + ] + } + }, + { + "map": { + "type": "file", + "description": "Genetic map file", + "pattern": "*.map", + "ontologies": [ + { + "edam": "http://edamontology.org/data_1278" + } + ] + } + }, + { + "region": { + "type": "string", + "description": "Region to perform imputation", + "pattern": "(chr)?\\d*:\\d*-\\d*" + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.{bcf,sav,vcf.gz,vcf,ubcf,usav}": { + "type": "file", + "description": "Imputed variants file", + "pattern": "*.{bcf,sav,vcf.gz,vcf,ubcf,usav}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + }, + { + "edam": "http://edamontology.org/format_3020" + } + ] + } + } + ] + ], + "versions_minimac4": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "minimac4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "minimac4 --version |& sed '1!d ; s/minimac v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "minimac4": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "minimac4 --version |& sed '1!d ; s/minimac v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@LouisLeNezet"], + "maintainers": ["@LouisLeNezet"] }, - { - "probs": { - "type": "file", - "description": "Probability map for boundary based segmentation as exported by the pixel classification workflow.", - "pattern": "*.{h5,hdf5}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3590" - } - ] - } - } - ], - { - "ilp": { - "type": "file", - "description": "Trained 'Boundary-based Segmentation with Multicut' .ilp project file", - "pattern": "*.{ilp}", - "ontologies": [] - } - } - ], - "output": { - "mask": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tiff": { - "type": "file", - "description": "Multicut segmentation mask output.", - "pattern": "*.{tiff}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3591" - } - ] - } - } - ] - ], - "versions_ilastik": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "ilastik": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "/opt/ilastik-1.4.0-Linux/run_ilastik.sh --headless --version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "ilastik": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "/opt/ilastik-1.4.0-Linux/run_ilastik.sh --headless --version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "phaseimpute", + "version": "1.1.0" + } ] - ] }, - "authors": [ - "@FloWuenne" - ], - "maintainers": [ - "@FloWuenne" - ] - }, - "pipelines": [ { - "name": "mcmicro", - "version": "dev" + "name": "minimap2_align", + "path": "modules/nf-core/minimap2/align/meta.yml", + "type": "module", + "meta": { + "name": "minimap2_align", + "description": "A versatile pairwise aligner for genomic and spliced nucleotide sequences", + "keywords": ["align", "fasta", "fastq", "genome", "paf", "reference"], + "tools": [ + { + "minimap2": { + "description": "A versatile pairwise aligner for genomic and spliced nucleotide sequences.\n", + "homepage": "https://github.com/lh3/minimap2", + "documentation": "https://github.com/lh3/minimap2#uguide", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FASTA or FASTQ files of size 1 and 2 for single-end\nand paired-end data, respectively.\n", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test_ref']\n" + } + }, + { + "reference": { + "type": "file", + "description": "Reference database in FASTA format.\n", + "ontologies": [] + } + } + ], + { + "bam_format": { + "type": "boolean", + "description": "Specify that output should be in BAM format" + } + }, + { + "bam_index_extension": { + "type": "string", + "description": "BAM alignment index extension (e.g. \"bai\")" + } + }, + { + "cigar_paf_format": { + "type": "boolean", + "description": "Specify that output CIGAR should be in PAF format" + } + }, + { + "cigar_bam": { + "type": "boolean", + "description": "Write CIGAR with >65535 ops at the CG tag. This is recommended when\ndoing XYZ (https://github.com/lh3/minimap2#working-with-65535-cigar-operations)\n" + } + } + ], + "output": { + "paf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.paf": { + "type": "file", + "description": "Alignment in PAF format", + "pattern": "*.paf", + "ontologies": [] + } + } + ] + ], + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Alignment in BAM format", + "pattern": "*.bam", + "ontologies": [] + } + } + ] + ], + "index": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam.${bam_index_extension}": { + "type": "file", + "description": "BAM alignment index", + "pattern": "*.bam.*", + "ontologies": [] + } + } + ] + ], + "versions_minimap2": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process name" + } + }, + { + "minimap2": { + "type": "string", + "description": "The tool name" + } + }, + { + "minimap2 --version": { + "type": "eval", + "description": "The tool version" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process name" + } + }, + { + "minimap2": { + "type": "string", + "description": "The tool name" + } + }, + { + "minimap2 --version": { + "type": "eval", + "description": "The tool version" + } + } + ] + ] + }, + "authors": ["@heuermh", "@sofstam", "@sateeshperi", "@jfy133", "@fellen31"], + "maintainers": ["@heuermh", "@sofstam", "@sateeshperi", "@jfy133", "@fellen31"] + }, + "pipelines": [ + { + "name": "abotyper", + "version": "dev" + }, + { + "name": "bacass", + "version": "2.6.0" + }, + { + "name": "circdna", + "version": "1.1.0" + }, + { + "name": "crisprseq", + "version": "2.3.0" + }, + { + "name": "evexplorer", + "version": "dev" + }, + { + "name": "genomeassembler", + "version": "1.1.0" + }, + { + "name": "isoseq", + "version": "2.0.0" + }, + { + "name": "mag", + "version": "5.4.2" + }, + { + "name": "methylong", + "version": "2.0.0" + }, + { + "name": "radseq", + "version": "dev" + }, + { + "name": "scnanoseq", + "version": "1.2.2" + }, + { + "name": "taxprofiler", + "version": "2.0.0" + }, + { + "name": "viralmetagenome", + "version": "1.1.1" + } + ] }, { - "name": "molkart", - "version": "1.2.0" - } - ] - }, - { - "name": "ilastik_pixelclassification", - "path": "modules/nf-core/ilastik/pixelclassification/meta.yml", - "type": "module", - "meta": { - "name": "ilastik_pixelclassification", - "description": "Ilastik is a tool that utilizes machine learning algorithms to classify pixels, segment, track and count cells in images. Ilastik contains a graphical user interface to interactively label pixels. However, this nextflow module will implement the --headless mode, to apply pixel classification using a pre-trained .ilp file on an input image.", - "keywords": [ - "pixel_classification", - "segmentation", - "probability_maps" - ], - "tools": [ - { - "ilastik": { - "description": "Ilastik is a user friendly tool that enables pixel classification, segmentation and analysis.", - "homepage": "https://www.ilastik.org/", - "documentation": "https://www.ilastik.org/documentation/", - "tool_dev_url": "https://github.com/ilastik/ilastik", - "licence": [ - "GPL3" - ], - "identifier": "biotools:ilastik" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information for h5 file\ne.g. [ id:'test' ]\n" - } - }, - { - "input_img": { - "type": "file", - "description": "Input img file containing image stack to classify. Input format is specified within the .ilp project file.", - "ontologies": [] - } - }, - { - "output_format": { - "type": "string", - "description": "String specifying the output format passed as the file extension to the output file specified with the `output_filename_format` parameter." - } + "name": "minimap2_index", + "path": "modules/nf-core/minimap2/index/meta.yml", + "type": "module", + "meta": { + "name": "minimap2_index", + "description": "Provides fasta index required by minimap2 alignment.", + "keywords": ["index", "fasta", "reference"], + "tools": [ + { + "minimap2": { + "description": "A versatile pairwise aligner for genomic and spliced nucleotide sequences.\n", + "homepage": "https://github.com/lh3/minimap2", + "documentation": "https://github.com/lh3/minimap2#uguide", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference database in FASTA format.\n", + "ontologies": [] + } + } + ] + ], + "output": { + "index": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.mmi": { + "type": "file", + "description": "Minimap2 fasta index.", + "pattern": "*.mmi", + "ontologies": [] + } + } + ] + ], + "versions_minimap2": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "minimap2": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "minimap2 --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "minimap2": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "minimap2 --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@yuukiiwa", "@drpatelh"], + "maintainers": ["@yuukiiwa", "@drpatelh"] }, - { - "export_source": { - "type": "string", - "description": "String passed to the `export_source` parameter - valid options are 'probabilities', '\"simple segmentation\"', 'uncertainty', 'features', 'labels']" - } - } - ], - { - "ilp": { - "type": "file", - "description": "Trained ilastik pixel classification .ilp project file", - "pattern": "*.{ilp}", - "ontologies": [] - } - } - ], - "output": { - "output": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.${output_format}": { - "type": "file", - "description": "Output file from ilastik pixel classification, as specified by the `output_format` parameter.", - "ontologies": [] - } - } - ] - ], - "versions_ilastik": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "ilastik": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "/opt/ilastik-1.4.0-Linux/run_ilastik.sh --headless --version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "ilastik": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "/opt/ilastik-1.4.0-Linux/run_ilastik.sh --headless --version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "crisprseq", + "version": "2.3.0" + }, + { + "name": "evexplorer", + "version": "dev" + }, + { + "name": "mag", + "version": "5.4.2" + }, + { + "name": "radseq", + "version": "dev" + }, + { + "name": "scnanoseq", + "version": "1.2.2" + }, + { + "name": "taxprofiler", + "version": "2.0.0" + }, + { + "name": "viralmetagenome", + "version": "1.1.1" + } ] - ] }, - "authors": [ - "@FloWuenne" - ], - "maintainers": [ - "@FloWuenne" - ] - }, - "pipelines": [ { - "name": "mcmicro", - "version": "dev" + "name": "miniprot_align", + "path": "modules/nf-core/miniprot/align/meta.yml", + "type": "module", + "meta": { + "name": "miniprot_align", + "description": "A versatile pairwise aligner for genomic and spliced nucleotide sequences", + "keywords": ["align", "fasta", "protein", "genome", "paf", "gff"], + "tools": [ + { + "miniprot": { + "description": "A versatile pairwise aligner for genomic and protein sequences.\n", + "homepage": "https://github.com/lh3/miniprot", + "documentation": "https://github.com/lh3/miniprot", + "licence": ["MIT"], + "identifier": "biotools:miniprot" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "pep": { + "type": "file", + "description": "a fasta file contains one or multiple protein sequences", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\n" + } + }, + { + "ref": { + "type": "file", + "description": "Reference database in FASTA format or miniprot index format.", + "ontologies": [] + } + } + ] + ], + "output": { + "paf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.paf": { + "type": "file", + "description": "Alignment in PAF format", + "pattern": "*.paf", + "ontologies": [] + } + } + ] + ], + "gff": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.gff": { + "type": "file", + "description": "Alignment in gff format", + "pattern": "*.gff", + "ontologies": [] + } + } + ] + ], + "versions_miniprot": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "miniprot": { + "type": "string", + "description": "The tool name" + } + }, + { + "miniprot --version": { + "type": "eval", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "miniprot": { + "type": "string", + "description": "The tool name" + } + }, + { + "miniprot --version": { + "type": "eval", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@yumisims", "@muffato"], + "maintainers": ["@yumisims", "@muffato"] + } }, { - "name": "molkart", - "version": "1.2.0" - } - ] - }, - { - "name": "imc2mc", - "path": "modules/nf-core/imc2mc/meta.yml", - "type": "module", - "meta": { - "name": "imc2mc", - "description": "Staging module transforming Imaging Mass Cytometry .txt files to .tif files with OME-XML metadata. Includes optional hot pixel removal.", - "keywords": [ - "imaging", - "ome-tif", - "staging", - "MCMICRO" - ], - "tools": [ - { - "imc2mc": { - "description": "Formatting Imaging Mass Cytrometry (IMC) output files to be compatible with the MCMICRO pipeline.", - "homepage": "https://github.com/SchapiroLabor/imc2mc", - "documentation": "https://github.com/SchapiroLabor/imc2mc/README.md", - "tool_dev_url": "https://github.com/SchapiroLabor/imc2mc", - "licence": [ - "GPL-3.0 license" - ], - "identifier": "" + "name": "miniprot_index", + "path": "modules/nf-core/miniprot/index/meta.yml", + "type": "module", + "meta": { + "name": "miniprot_index", + "description": "Provides fasta index required by miniprot alignment.", + "keywords": ["index", "fasta", "genome", "reference"], + "tools": [ + { + "miniprot": { + "description": "A versatile pairwise aligner for genomic and protein sequences.\n", + "homepage": "https://github.com/lh3/miniprot", + "documentation": "https://github.com/lh3/miniprot", + "licence": ["MIT"], + "identifier": "biotools:miniprot" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference database in FASTA format.\n", + "ontologies": [] + } + } + ] + ], + "output": { + "index": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.mpi": { + "type": "file", + "description": "miniprot fasta index.", + "pattern": "*.mpi", + "ontologies": [] + } + } + ] + ], + "versions_miniprot": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "miniprot": { + "type": "string", + "description": "The tool name" + } + }, + { + "miniprot --version": { + "type": "eval", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "miniprot": { + "type": "string", + "description": "The tool name" + } + }, + { + "miniprot --version": { + "type": "eval", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@yumisims", "@muffato"], + "maintainers": ["@yumisims", "@muffato"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } + }, + { + "name": "miranda", + "path": "modules/nf-core/miranda/meta.yml", + "type": "module", + "meta": { + "name": "miranda", + "description": "miRanda is an algorithm for finding genomic targets for microRNAs", + "keywords": ["microrna", "mirna", "target prediction"], + "tools": [ + { + "miranda": { + "description": "An algorithm for finding genomic targets for microRNAs", + "homepage": "https://cbio.mskcc.org/miRNA2003/miranda.html", + "documentation": "https://cbio.mskcc.org/miRNA2003/miranda.html", + "doi": "10.1186/gb-2003-5-1-r1", + "licence": ["GNU Public License"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "query": { + "type": "file", + "description": "FASTA file containing the microRNA query sequences", + "pattern": "*.{fa,fasta}", + "ontologies": [] + } + } + ], + { + "mirbase": { + "type": "file", + "description": "FASTA file containing the sequence(s) to be scanned", + "pattern": "*.{fa,fasta}", + "ontologies": [] + } + } + ], + "output": { + "txt": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "Reformatted TXT file containing microRNA targets", + "pattern": "*.{txt}", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@BarryDigby"], + "maintainers": ["@BarryDigby"] }, - 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It integrates the mapping of sequencing reads to the genome and predicts miRNA precursors and mature miRNAs.\n", + "keywords": ["mirdeep2", "miRNA", "RNA sequencing"], + "tools": [ + { + "mirdeep2": { + "description": "miRDeep2 is a tool that discovers microRNA genes by analyzing sequenced RNAs.\nIt includes three main scripts: `miRDeep2.pl`, `mapper.pl`, and `quantifier.pl` for comprehensive miRNA detection and quantification.\n", + "homepage": "https://www.mdc-berlin.de/content/mirdeep2-documentation", + "documentation": "https://www.mdc-berlin.de/content/mirdeep2-documentation", + "tool_dev_url": "https://github.com/rajewsky-lab/mirdeep2", + "doi": "10.1093/nar/gkn491", + "licence": ["GPL V3"], + "identifier": "biotools:mirdeep2" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information, e.g. `[ id:'sample1', single_end:false ]`" + } + }, + { + "processed_reads": { + "type": "file", + "description": "FASTA file containing the processed sequencing reads.", + "pattern": "*.fa", + "ontologies": [] + } + }, + { + "genome_mappings": { + "type": "file", + "description": "ARF format file with mapped reads to the genome.", + "pattern": "*.arf", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map for genome FASTA file metadata, e.g. `[ id:'genome']`" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA file of the corresponding genome.", + "pattern": "*.fa", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map for miRNA metadata, e.g. `[ id:'mirbase', single_end:false ]`" + } + }, + { + "mature": { + "type": "file", + "description": "FASTA file containing known mature miRNAs of the species being analyzed.", + "pattern": "*.fa", + "ontologies": [] + } + }, + { + "hairpin": { + "type": "file", + "description": "FASTA file containing hairpin sequences (miRNA precursors).", + "pattern": "*.fa", + "ontologies": [] + } + }, + { + "mature_other_species": { + "type": "file", + "description": "FASTA file containing known mature miRNAs of other species.", + "pattern": "*.fa", + "ontologies": [] + } + } + ] + ], + "output": { + "outputs": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`" + } + }, + { + "result*.{bed,csv,html}": { + "type": "file", + "description": "Output files, including BED, CSV, and HTML results files with an overview of detected miRNAs.", + "pattern": "result*.{bed,csv,html}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@atrigila"], + "maintainers": ["@atrigila"] }, - { - "seqdb": { - "type": "file", - "description": "A FASTA file of sequences to search the covariance models\nagainst. 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} - }, - { - "*.IS/output/*.IS_scaffold_info.tsv": { - "type": "file", - "description": "Scaffold information", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } + "pipelines": [ + { + "name": "smrnaseq", + "version": "2.4.1" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@mrolm" - ], - "maintainers": [ - "@mrolm" - ] - }, - "pipelines": [ - { - "name": "phageannotator", - "version": "dev" - } - ] - }, - { - "name": "integronfinder", - "path": "modules/nf-core/integronfinder/meta.yml", - "type": "module", - "meta": { - "name": "integronfinder", - "description": "Detect integrons in DNA sequences", - "keywords": [ - "bacteria", - "fasta", - "mobile genetic elements", - "integron" - ], - "tools": [ - { - "integronfinder": { - 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"description": "Read coverage plot for mitochondrial contigs", + "pattern": "coverage_plot.png", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3603" + } + ] + } + } + ] + ], + "final_mitogenome_annotation": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "final_mitogenome.annotation.png": { + "type": "file", + "description": "Graphical representation of annotated genes for the final\nmitogenome contig\n", + "pattern": "final_mitogenome.annotation.png", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3603" + } + ] + } + } + ] + ], + "final_mitogenome_choice": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "final_mitogenome_choice/": { + "type": "directory", + "description": "Files with potential contigs clusterings and alignments", + "pattern": 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information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads_mapping_and_assembly/": { + "type": "directory", + "description": "Read mapping files for run from the raw reads", + "pattern": "reads_mapping_and_assembly/" + } + } + ] + ], + "shared_genes": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "shared_genes.tsv": { + "type": "directory", + "description": "Report on genes shared with the reference genome", + "pattern": "shared_genes.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "directory", + "description": "Log file describing Mitohifi run", + "pattern": "*.log", + "ontologies": [ + { + "edam": 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obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@ksenia-krasheninnikova", "@prototaxites"], + "maintainers": ["@ksenia-krasheninnikova"] } - ] }, - "authors": [ - "@avantonder", - "@aunderwo" - ], - "maintainers": [ - "@avantonder", - "@aunderwo" - ] - }, - "pipelines": [ { - "name": "pathogensurveillance", - "version": "1.1.0" + "name": "mitorsaw_haplotype", + "path": "modules/nf-core/mitorsaw/haplotype/meta.yml", + "type": "module", + "meta": { + "name": "mitorsaw_haplotype", + "description": "Mitorsaw analyses mitochondrial variants and identifies heteroplasmy and homoplasmy", + "keywords": ["heteroplasmy", "homoplasmy", "mitochondrial", "mitorsaw", "haplotype"], + "tools": [ + { + "mitorsaw": { + "description": "A tool for mitochondrial analysis for HiFi sequencing data", + "homepage": "https://github.com/PacificBiosciences/mitorsaw", + "documentation": "https://github.com/PacificBiosciences/mitorsaw/tree/main/docs", + "tool_dev_url": 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id:'sample1' ]\n" + } + }, + { + "*${prefix}.vcf.gz.tbi": { + "type": "file", + "description": "Index file for the compressed VCF file", + "pattern": "*.vcf.gz.tbi", + "ontologies": [] + } + } + ] + ], + "stats": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample1' ]\n" + } + }, + { + "${prefix}.json": { + "type": "file", + "description": "Mitorsaw statistics in JSON format", + "pattern": "*.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "coverage_stats": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample1' ]\n" + } + }, + { + "${prefix}_debug/coverage_stats.json": { + "type": "file", + "description": "Coverage statistics in JSON format", + "pattern": "coverage_stats.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "sequences_chrM": [ + [ + { + 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"documentation": "https://github.com/PacificBiosciences/IsoSeq/blob/master/isoseq-clustering.md", - "tool_dev_url": "https://github.com/PacificBiosciences/IsoSeq/blob/master/isoseq-clustering.md", - "licence": [ - "BSD-3-Clause-Clear" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test ]\n" - } + }, + { + "name": "mmseqs_createdb", + "path": "modules/nf-core/mmseqs/createdb/meta.yml", + "type": "module", + "meta": { + "name": "mmseqs_createdb", + "description": "Create an MMseqs database from an existing FASTA/Q file", + "keywords": ["protein sequence", "databases", "clustering", "searching", "indexing", "mmseqs2"], + "tools": [ + { + "mmseqs": { + "description": "MMseqs2: ultra fast and sensitive sequence search and clustering suite", + "homepage": "https://github.com/soedinglab/MMseqs2", + "documentation": "https://mmseqs.com/latest/userguide.pdf", + "tool_dev_url": "https://github.com/soedinglab/MMseqs2", + "doi": "10.1093/bioinformatics/btw006", + "licence": ["GPL v3"], + "identifier": "biotools:mmseqs" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "sequence": { + "type": "file", + "description": "Input sequences in FASTA/Q (zipped or unzipped) format to parse into an mmseqs database", + "pattern": "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,fastq,fastq.gz,fq,fq.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ] + ], + "output": { + "db": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "${prefix}/": { + "type": "directory", + "description": "The created MMseqs2 database" + } + } + ] + ], + "versions_mmseqs": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "mmseqs": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "mmseqs version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "mmseqs": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "mmseqs version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@Joon-Klaps"], + "maintainers": ["@Joon-Klaps", "@vagkaratzas"] }, - { - "bam": { - "type": "file", - "description": "BAM file, cleaned ccs generated by lima", - "pattern": "*.bam", - "ontologies": [] - } - } - ], - { - "primers": { - "type": "file", - "description": "fasta file of primers", - "pattern": "*.fasta", - "ontologies": [] - } - } - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "Set of complete reads (with polyA tail), where the polyA has been trimmed", - "pattern": "*.bam", - "ontologies": [] - } - } - ] - ], - "pbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.bam.pbi": { - "type": "file", - "description": "Pacbio index file from polyA trimmed reads", - "pattern": "*.pbi", - "ontologies": [] - } - } - ] - ], - "consensusreadset": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.consensusreadset.xml": { - "type": "file", - "description": "Metadata about read library", - "pattern": "*.xml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2332" - } - ] - } - } - ] - ], - "summary": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.filter_summary.report.json": { - "type": "file", - "description": "json file describing number of full length reads, full length non chimeric reads and full length non chimeric polyA reads", - "pattern": "*.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "report": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.report.csv": { - "type": "file", - "description": "Metadata about primer and polyA detection (primers/polyA/insert length, strand, primer name)", - "pattern": "*.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } + "pipelines": [ + { + "name": "funcscan", + "version": "3.0.0" + }, + { + "name": "proteinfamilies", + "version": "2.3.0" + }, + { + "name": "viralmetagenome", + "version": "1.1.1" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@sguizard" - ], - "maintainers": [ - "@sguizard" - ] - }, - "pipelines": [ - { - "name": "isoseq", - "version": "2.0.0" - } - ] - }, - { - "name": "ivar_consensus", - "path": "modules/nf-core/ivar/consensus/meta.yml", - "type": "module", - "meta": { - "name": "ivar_consensus", - "description": "Generate a consensus sequence from a BAM file using iVar", - "keywords": [ - "amplicon sequencing", - "consensus", - "fasta" - ], - "tools": [ - { - "ivar": { - "description": "iVar - a computational package that contains functions broadly useful for viral amplicon-based sequencing.\n", - "homepage": "https://github.com/andersen-lab/ivar", - "documentation": "https://andersen-lab.github.io/ivar/html/manualpage.html", - "licence": [ - "GPL-3.0-or-later" - ], - "identifier": "biotools:andersen-lab_ivar" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + }, + { + "name": "mmseqs_createindex", + "path": "modules/nf-core/mmseqs/createindex/meta.yml", + "type": "module", + "meta": { + "name": "mmseqs_createindex", + "description": "Creates sequence index for mmseqs database", + "keywords": ["protein sequence", "databases", "clustering", "searching", "indexing"], + "tools": [ + { + "mmseqs": { + "description": "MMseqs2: ultra fast and sensitive sequence search and clustering suite", + "homepage": "https://github.com/soedinglab/MMseqs2", + "documentation": "https://mmseqs.com/latest/userguide.pdf", + "tool_dev_url": "https://github.com/soedinglab/MMseqs2", + "doi": "10.1093/bioinformatics/btw006", + "licence": ["GPL v3"], + "identifier": "biotools:mmseqs" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "db": { + "type": "directory", + "description": "Directory containing the DB to be indexed\n", + "pattern": "*" + } + } + ] + ], + "output": { + "db_indexed": [ + [ + { + "meta": { + "type": "directory", + "description": "Directory containing the DB and the generated indexes\n", + "pattern": "*" + } + }, + { + "db": { + "type": "directory", + "description": "Directory containing the DB and the generated indexes\n", + "pattern": "*" + } + } + ] + ], + "versions_mmseqs": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "mmseqs": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "mmseqs version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "mmseqs": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "mmseqs version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@JoseEspinosa"], + "maintainers": ["@JoseEspinosa"] }, - { - "bam": { - "type": "file", - "description": "A sorted (with samtools sort) and trimmed (with iVar trim) bam file", - "pattern": "*.bam", - "ontologies": [] - } - } - ], - { - "fasta": { - "type": "file", - "description": "The reference sequence used for mapping and generating the BAM file", - "pattern": "*.fa", - "ontologies": [] - } - }, - { - "save_mpileup": { - "type": "boolean", - "description": "Save mpileup file generated by ivar consensus", - "pattern": "*.mpileup" - } - } - ], - "output": { - "fasta": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.fa": { - "type": "file", - "description": "iVar generated consensus sequence", - "pattern": "*.fa", - "ontologies": [] - } - } - ] - ], - "qual": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.qual.txt": { - "type": "file", - "description": "iVar generated quality file", - "pattern": "*.qual.txt", - "ontologies": [] - } - } - ] - ], - "mpileup": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.mpileup": { - "type": "file", - "description": "mpileup output from samtools mpileup [OPTIONAL]", - "pattern": "*.mpileup", - "ontologies": [] - } - } + "pipelines": [ + { + "name": "proteinfold", + "version": "2.0.0" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] }, - "authors": [ - "@andersgs", - "@drpatelh" - ], - "maintainers": [ - "@andersgs", - "@drpatelh" - ] - }, - "pipelines": [ { - "name": "viralmetagenome", - "version": "1.1.1" + "name": "mmseqs_createtaxdb", + "path": "modules/nf-core/mmseqs/createtaxdb/meta.yml", + "type": "module", + "meta": { + "name": "mmseqs_createtaxdb", + "description": "Adds taxonomy information to an existing MMseqs2 database", + "keywords": ["protein sequence", "databases", "clustering", "searching", "taxonomy"], + "tools": [ + { + "mmseqs": { + "description": "MMseqs2: ultra fast and sensitive sequence search and clustering suite", + "homepage": "https://github.com/soedinglab/MMseqs2", + "documentation": "https://mmseqs.com/latest/userguide.pdf", + "tool_dev_url": "https://github.com/soedinglab/MMseqs2", + "doi": "10.1093/bioinformatics/btw006", + "licence": ["GPL v3"], + "identifier": "biotools:mmseqs" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "db": { + "type": "directory", + "description": "Directory containing the MMseqs2 database\n", + "pattern": "*" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "taxdump_dir": { + "type": "directory", + "description": "Directory containing NCBI taxonomy dump files (names.dmp, nodes.dmp, merged.dmp).\nIf not provided, the module will attempt to download them from NCBI\n", + "pattern": "*" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "tax_mapping_file": { + "type": "file", + "description": "File mapping sequence IDs to taxonomy IDs.\nIf not provided, the module will attempt to download the Uniprot id mapping file\n", + "pattern": "*", + "ontologies": [] + } + } + ] + ], + "output": { + "db_with_taxonomy": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "db": { + "type": "directory", + "description": "Directory containing the database with added taxonomy information\n", + "pattern": "*" + } + } + ] + ], + "versions_mmseqs": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "mmseqs": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "mmseqs | grep 'Version' | sed 's/MMseqs2 Version: //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "mmseqs": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "mmseqs | grep 'Version' | sed 's/MMseqs2 Version: //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@dialvarezs"], + "maintainers": ["@dialvarezs"] + } }, { - "name": "viralrecon", - "version": "3.0.0" - } - ] - }, - { - "name": "ivar_trim", - "path": "modules/nf-core/ivar/trim/meta.yml", - "type": "module", - "meta": { - "name": "ivar_trim", - "description": "Trim primer sequences rom a BAM file with iVar", - "keywords": [ - "amplicon sequencing", - "trimming", - "fasta" - ], - "tools": [ - { - "ivar": { - "description": "iVar - a computational package that contains functions broadly useful for viral amplicon-based sequencing.\n", - "homepage": "https://github.com/andersen-lab/ivar", - "documentation": "https://andersen-lab.github.io/ivar/html/manualpage.html", - "licence": [ - "GPL-3.0-or-later" - ], - "identifier": "biotools:andersen-lab_ivar" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "Co-ordinate sorted BAM file", - "pattern": "*.bam", - "ontologies": [] - } + "name": "mmseqs_createtsv", + "path": "modules/nf-core/mmseqs/createtsv/meta.yml", + "type": "module", + "meta": { + "name": "mmseqs_createtsv", + "description": "Create a tsv file from a query and a target database as well as the result database", + "keywords": ["protein sequence", "databases", "clustering", "searching", "indexing", "mmseqs2", "tsv"], + "tools": [ + { + "mmseqs": { + "description": "MMseqs2: ultra fast and sensitive sequence search and clustering suite", + "homepage": "https://github.com/soedinglab/MMseqs2", + "documentation": "https://mmseqs.com/latest/userguide.pdf", + "tool_dev_url": "https://github.com/soedinglab/MMseqs2", + "doi": "10.1093/bioinformatics/btw006", + "licence": ["GPL v3"], + "identifier": "biotools:mmseqs" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "db_result": { + "type": "directory", + "description": "an MMseqs2 database with result data" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "db_query": { + "type": "directory", + "description": "an MMseqs2 database with query data" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "db_target": { + "type": "directory", + "description": "an MMseqs2 database with target data" + } + } + ] + ], + "output": { + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "The resulting tsv file created using the query, target and result MMseqs databases", + "pattern": "*.{tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_mmseqs": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "mmseqs": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "mmseqs version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "mmseqs": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "mmseqs version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@Joon-Klaps"], + "maintainers": ["@Joon-Klaps"] }, - { - "bai": { - "type": "file", - "description": "Index file for co-ordinate sorted BAM file", - "pattern": "*.bai", - "ontologies": [] - } - } - ], - { - "bed": { - "type": "file", - "description": "BED file with primer labels and positions", - "pattern": "*.bed", - "ontologies": [] - } - } - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "iVar generated trimmed bam file (unsorted)", - "pattern": "*.bam", - "ontologies": [] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.log": { - "type": "file", - "description": "Log file generated by iVar for use with MultiQC", - "pattern": "*.log", - "ontologies": [] - } - } + "pipelines": [ + { + "name": "funcscan", + "version": "3.0.0" + }, + { + "name": "proteinfamilies", + "version": "2.3.0" + }, + { + "name": "viralmetagenome", + "version": "1.1.1" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@andersgs", - "@drpatelh" - ], - "maintainers": [ - "@andersgs", - "@drpatelh" - ] - }, - "pipelines": [ - { - "name": "viralrecon", - "version": "3.0.0" - } - ] - }, - { - "name": "ivar_variants", - "path": "modules/nf-core/ivar/variants/meta.yml", - "type": "module", - "meta": { - "name": "ivar_variants", - "description": "Call variants from a BAM file using iVar", - "keywords": [ - "amplicon sequencing", - "variants", - "fasta" - ], - "tools": [ - { - "ivar": { - "description": "iVar - a computational package that contains functions broadly useful for viral amplicon-based sequencing.\n", - "homepage": "https://github.com/andersen-lab/ivar", - "documentation": "https://andersen-lab.github.io/ivar/html/manualpage.html", - "licence": [ - "GPL-3.0-or-later" - ], - "identifier": "biotools:andersen-lab_ivar" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + }, + { + "name": "mmseqs_databases", + "path": "modules/nf-core/mmseqs/databases/meta.yml", + "type": "module", + "meta": { + "name": "mmseqs_databases", + "description": "Download an mmseqs-formatted database", + "keywords": ["database", "indexing", "clustering", "searching"], + "tools": [ + { + "mmseqs": { + "description": "MMseqs2: ultra fast and sensitive sequence search and clustering suite", + "homepage": "https://github.com/soedinglab/MMseqs2", + "documentation": "https://mmseqs.com/latest/userguide.pdf", + "tool_dev_url": "https://github.com/soedinglab/MMseqs2", + "doi": "10.1093/bioinformatics/btw006", + "licence": ["GPL v3"], + "identifier": "biotools:mmseqs" + } + } + ], + "input": [ + { + "database": { + "type": "string", + "description": "Database available through the mmseqs2 databases interface - see https://github.com/soedinglab/MMseqs2/wiki#downloading-databases for details" + } + } + ], + "output": { + "database": [ + { + "${prefix}/": { + "type": "directory", + "description": "Directory containing processed mmseqs database" + } + } + ], + "versions_mmseqs": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "mmseqs": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "mmseqs version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "mmseqs": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "mmseqs version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@prototaxites"], + "maintainers": ["@prototaxites"] }, - { - "bam": { - "type": "file", - "description": "A sorted (with samtools sort) and trimmed (with iVar trim) bam file", - "pattern": "*.bam", - "ontologies": [] - } - } - ], - { - "fasta": { - "type": "file", - "description": "The reference sequence used for mapping and generating the BAM file", - "pattern": "*.fa", - "ontologies": [] - } - }, - { - "fai": { - "type": "file", - "description": "The index for the reference sequence used for mapping and generating the BAM file", - "pattern": "*.fai", - "ontologies": [] - } - }, - { - "gff": { - "type": "file", - "description": "A GFF file in the GFF3 format can be supplied to specify coordinates of open reading frames (ORFs). In absence of GFF file, amino acid translation will not be done.", - "pattern": "*.gff", - "ontologies": [] - } - }, - { - "save_mpileup": { - "type": "boolean", - "description": "Save mpileup file generated by ivar variants", - "pattern": "*.mpileup" - } - } - ], - "output": { - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "iVar generated TSV file with the variants", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "mpileup": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.mpileup": { - "type": "file", - "description": "mpileup output from samtools mpileup [OPTIONAL]", - "pattern": "*.mpileup", - "ontologies": [] - } - } + "pipelines": [ + { + "name": "funcscan", + "version": "3.0.0" + }, + { + "name": "mag", + "version": "5.4.2" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] }, - "authors": [ - "@andersgs", - "@drpatelh" - ], - "maintainers": [ - "@andersgs", - "@drpatelh" - ] - }, - "pipelines": [ { - "name": "viralmetagenome", - "version": "1.1.1" + "name": "mmseqs_easycluster", + "path": "modules/nf-core/mmseqs/easycluster/meta.yml", + "type": "module", + "meta": { + "name": "mmseqs_easycluster", + "description": "Cluster sequences using MMSeqs2 easy cluster.", + "keywords": ["protein sequence", "databases", "clustering", "searching", "mmseqs2"], + "tools": [ + { + "mmseqs": { + "description": "MMseqs2: ultra fast and sensitive sequence search and clustering suite", + "homepage": "https://github.com/soedinglab/MMseqs2", + "documentation": "https://mmseqs.com/latest/userguide.pdf", + "tool_dev_url": "https://github.com/soedinglab/MMseqs2", + "doi": "10.1093/bioinformatics/btw006", + "licence": ["GPL v3"], + "identifier": "biotools:mmseqs" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "sequence": { + "type": "file", + "description": "Input sequence file in FASTA/FASTQ format for clustering", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1920" + } + ] + } + } + ] + ], + "output": { + "representatives": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*rep_seq.fasta": { + "type": "file", + "description": "a fasta file containing the cluster representatives", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ] + ], + "fasta": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*all_seqs.fasta": { + "type": "file", + "description": "a fasta-like file per cluster", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ] + ], + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "an adjacency list file containing the clusters", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_mmseqs": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "mmseqs": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "mmseqs version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "mmseqs": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "mmseqs version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@Joon-Klaps"], + "maintainers": ["@Joon-Klaps"] + } }, { - "name": "viralrecon", - "version": "3.0.0" - } - ] - }, - { - "name": "jasminesv", - "path": "modules/nf-core/jasminesv/meta.yml", - "type": "module", - "meta": { - "name": "jasminesv", - "description": "Jointly Accurate Sv Merging with Intersample Network Edges", - "keywords": [ - "jasminesv", - "jasmine", - "structural variants", - "vcf", - "bam" - ], - "tools": [ - { - "jasminesv": { - "description": "Software for merging structural variants between individuals", - "homepage": "https://github.com/mkirsche/Jasmine/wiki/Jasmine-User-Manual", - "documentation": "https://github.com/mkirsche/Jasmine/wiki/Jasmine-User-Manual", - "tool_dev_url": "https://github.com/mkirsche/Jasmine", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcfs": { - "type": "list", - "description": "The VCF files that need to be merged\n", - "pattern": "*.{vcf,vcf.gz}" - } - }, - { - "bams": { - "type": "list", - "description": "Optional - The BAM files from which the VCFs were created", - "pattern": "*.bam" - } - }, - { - "bais": { - "type": "list", - "description": "Optional - The BAM index files from which the VCFs were created", - "pattern": "*.bai" - } - }, - { - "sample_dists": { - "type": "file", - "description": "Optional - A txt file containing the distance thresholds for each sample", - "pattern": "*.txt", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing fasta information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Optional - The reference FASTA file used to create the VCFs", - "pattern": "*.{fasta,fa}", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing fasta index information\ne.g. [ id:'test', single_end:false ]\n" - } + "name": "mmseqs_easysearch", + "path": "modules/nf-core/mmseqs/easysearch/meta.yml", + "type": "module", + "meta": { + "name": "mmseqs_easysearch", + "description": "Searches for the sequences of a fasta file in a database using MMseqs2", + "keywords": ["protein sequence", "databases", "searching", "mmseqs2"], + "tools": [ + { + "mmseqs": { + "description": "MMseqs2: ultra fast and sensitive sequence search and clustering suite", + "homepage": "https://github.com/soedinglab/MMseqs2", + "documentation": "https://mmseqs.com/latest/userguide.pdf", + "tool_dev_url": "https://github.com/soedinglab/MMseqs2", + "doi": "10.1093/bioinformatics/btw006", + "licence": ["GPL v3"], + "identifier": "biotools:mmseqs" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing input fasta file information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Fasta file", + "pattern": "*.{fa,fasta}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing database information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "db_target": { + "type": "directory", + "description": "an MMseqs2 database with target data, e.g. uniref90" + } + } + ] + ], + "output": { + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing input fasta file information\ne.g. `[ id:'test']`\n" + } + }, + { + "${prefix}.tsv": { + "type": "file", + "description": "tsv file with the results of the search", + "pattern": "*.{tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_mmseqs": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "mmseqs": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "mmseqs version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "mmseqs": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "mmseqs version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@luisas"], + "maintainers": ["@luisas"] }, - { - "fasta_fai": { - "type": "file", - "description": "Optional - The index of the reference FASTA file used to create the VCFs", - "pattern": "*.fai", - "ontologies": [] - } - } - ], - { - "chr_norm": { - "type": "file", - "description": "Optional - A txt file containing the chromosomes and their aliases for normalization", - "pattern": "*.txt", - "ontologies": [] - } - } - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.vcf.gz": { - "type": "file", - "description": "The merged VCF file", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "versions_jasminesv": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "jasminesv": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "jasmine 2>&1 | grep \"version\" | sed \"s/Jasmine version //\"": { - "type": "eval", - "description": "The version of the tool" - } - } - ] - ], - "versions_bgzip": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bgzip": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bgzip --version | head -1 | sed -e \"s/bgzip (htslib) //\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "jasminesv": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "jasmine 2>&1 | grep \"version\" | sed \"s/Jasmine version //\"": { - "type": "eval", - "description": "The version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bgzip": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bgzip --version | head -1 | sed -e \"s/bgzip (htslib) //\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "viralmetagenome", + "version": "1.1.1" + } ] - ] - }, - "authors": [ - "@nvnieuwk" - ], - "maintainers": [ - "@nvnieuwk" - ] - } - }, - { - "name": "jellyfish_count", - "path": "modules/nf-core/jellyfish/count/meta.yml", - "type": "module", - "meta": { - "name": "jellyfish_count", - "description": "Efficiently counts k-mers from DNA sequencing reads using a fast, memory-efficient, parallelized algorithm", - "keywords": [ - "k-mer", - "DNA", - "substrings" - ], - "tools": [ - { - "jellyfish": { - "description": "Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence", - "homepage": "https://github.com/gmarcais/Jellyfish", - "documentation": "https://github.com/gmarcais/Jellyfish/blob/master/doc/Readme.md", - "tool_dev_url": "https://github.com/gmarcais/Jellyfish", - "doi": "10.1093/bioinformatics/btr011", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:jellyfish" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } + }, + { + "name": "mmseqs_linclust", + "path": "modules/nf-core/mmseqs/linclust/meta.yml", + "type": "module", + "meta": { + "name": "mmseqs_linclust", + "description": "Cluster sequences in linear time using MMSeqs2 linclust.", + "keywords": ["protein sequence", "databases", "clustering", "searching", "indexing", "mmseqs2"], + "tools": [ + { + "mmseqs": { + "description": "MMseqs2: ultra fast and sensitive sequence search and clustering suite", + "homepage": "https://github.com/soedinglab/MMseqs2", + "documentation": "https://mmseqs.com/latest/userguide.pdf", + "tool_dev_url": "https://github.com/soedinglab/MMseqs2", + "doi": "10.1093/bioinformatics/btw006", + "licence": ["GPL v3"], + "identifier": "biotools:mmseqs" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "db_input": { + "type": "file", + "description": "Input database", + "ontologies": [] + } + } + ] + ], + "output": { + "db_cluster": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "${prefix}/": { + "type": "directory", + "description": "a clustered MMseqs2 database" + } + } + ] + ], + "versions_mmseqs": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "mmseqs": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "mmseqs version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "mmseqs": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "mmseqs version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@vagkaratzas"], + "maintainers": ["@vagkaratzas"] }, - { - "fasta": { - "type": "file", - "description": "Nucleotide sequences in FASTA format", - "pattern": "*.{fasta,fa,fna,faa}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - { - "kmer_length": { - "type": "integer", - "description": "k-mer size to use" - } - }, - { - "size": { - "type": "string", - "description": "Specifies the memory hash size (in bytes) to allocate for the k-mer counting hash table (e.g., '100M').\nA mean estimation could be carried with this formula: 'genome size + (genome size * coverage * kmer-length * error rate)'\n" - } - } - ], - "output": { - "jf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}.jf": { - "type": "file", - "description": "Jellyfish binary k-mer database", - "pattern": "*.jf", - "ontologies": [] - } - } + "pipelines": [ + { + "name": "proteinfamilies", + "version": "2.3.0" + }, + { + "name": "viralmetagenome", + "version": "1.1.1" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@vagkaratzas" - ], - "maintainers": [ - "@vagkaratzas" - ] - } - }, - { - "name": "jellyfish_dump", - "path": "modules/nf-core/jellyfish/dump/meta.yml", - "type": "module", - "meta": { - "name": "jellyfish_dump", - "description": "Dumps the results from a jellyfish binary file into a human readable format", - "keywords": [ - "k-mer", - "DNA", - "substrings" - ], - "tools": [ - { - "jellyfish": { - "description": "Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence", - "homepage": "https://github.com/gmarcais/Jellyfish", - "documentation": "https://github.com/gmarcais/Jellyfish/blob/master/doc/Readme.md", - "tool_dev_url": "https://github.com/gmarcais/Jellyfish", - "doi": "10.1093/bioinformatics/btr011", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:jellyfish" + }, + { + "name": "mmseqs_makepaddedseqdb", + "path": "modules/nf-core/mmseqs/makepaddedseqdb/meta.yml", + "type": "module", + "meta": { + "name": "mmseqs_makepaddedseqdb", + "description": "Create an MMseqs padded database from an existing MMseqs database", + "keywords": ["protein sequence", "databases", "clustering", "searching", "indexing", "mmseqs2"], + "tools": [ + { + "mmseqs": { + "description": "MMseqs2: ultra fast and sensitive sequence search and clustering suite", + "homepage": "https://github.com/soedinglab/MMseqs2", + "documentation": "https://mmseqs.com/latest/userguide.pdf", + "tool_dev_url": "https://github.com/soedinglab/MMseqs2", + "doi": "10.1093/bioinformatics/btw006", + "licence": ["GPL v3"], + "identifier": "biotools:mmseqs" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "db_in": { + "type": "directory", + "description": "Input of existing MMseqs database" + } + } + ] + ], + "output": { + "db_padded": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "${prefix}/": { + "type": "directory", + "description": "The padded MMseqs2 database" + } + } + ] + ], + "versions_mmseqs": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "mmseqs": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "mmseqs version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "mmseqs": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "mmseqs version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@nbtm-sh"], + "maintainers": ["@nbtm-sh"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "jf": { - "type": "file", - "description": "Jellyfish binary k-mer database", - "pattern": "*.jf", - "ontologies": [] - } + }, + { + "name": "mmseqs_search", + "path": "modules/nf-core/mmseqs/search/meta.yml", + "type": "module", + "meta": { + "name": "mmseqs_search", + "description": "Search and calculate a score for similar sequences in a query and a target database.", + "keywords": ["protein sequence", "databases", "clustering", "searching", "indexing", "mmseqs2"], + "tools": [ + { + "mmseqs": { + "description": "MMseqs2: ultra fast and sensitive sequence search and clustering suite", + "homepage": "https://github.com/soedinglab/MMseqs2", + "documentation": "https://mmseqs.com/latest/userguide.pdf", + "tool_dev_url": "https://github.com/soedinglab/MMseqs2", + "doi": "10.1093/bioinformatics/btw006", + "licence": ["GPL v3"], + "identifier": "biotools:mmseqs" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "db_query": { + "type": "file", + "description": "Query database", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "db_target": { + "type": "file", + "description": "Target database", + "ontologies": [] + } + } + ] + ], + "output": { + "db_search": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "${prefix}/": { + "type": "directory", + "description": "an MMseqs2 database with search results" + } + } + ] + ], + "versions_mmseqs": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "mmseqs": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "mmseqs version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "mmseqs": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "mmseqs version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@Joon-Klaps"], + "maintainers": ["@Joon-Klaps"] } - ] - ], - "output": { - "output": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}.${extension}": { - "type": "file", - "description": "Human readable k-mer database in fasta format, or in 2-column space delimited format if the -c argument is provided", - "pattern": "*.{fa,txt}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - }, + }, + { + "name": "mmseqs_taxonomy", + "path": "modules/nf-core/mmseqs/taxonomy/meta.yml", + "type": "module", + "meta": { + "name": "mmseqs_taxonomy", + "description": "Computes the lowest common ancestor by identifying the query sequence homologs against the target database.", + "keywords": ["protein sequence", "nucleotide sequence", "databases", "taxonomy", "homologs", "mmseqs2"], + "tools": [ + { + "mmseqs": { + "description": "MMseqs2: ultra fast and sensitive sequence search and clustering suite", + "homepage": "https://github.com/soedinglab/MMseqs2", + "documentation": "https://mmseqs.com/latest/userguide.pdf", + "tool_dev_url": "https://github.com/soedinglab/MMseqs2", + "doi": "10.1093/bioinformatics/btw006", + "licence": ["GPL v3"], + "identifier": "biotools:mmseqs" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "db_query": { + "type": "directory", + "description": "An MMseqs2 database with query data" + } + } + ], { - "edam": "http://edamontology.org/format_2330" + "db_target": { + "type": "directory", + "description": "an MMseqs2 database with target data including the taxonomy classification" + } } - ] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@vagkaratzas" - ], - "maintainers": [ - "@vagkaratzas" - ] - } - }, - { - "name": "juicertools_pre", - "path": "modules/nf-core/juicertools/pre/meta.yml", - "type": "module", - "meta": { - "name": "juicertools_pre", - "description": "Create a multi-resolution .hic contact matrix for analysis with Juicer", - "keywords": [ - "hic", - "contact map", - "genomics" - ], - "tools": [ - { - "juicertools": { - "description": "Visualization and analysis software for Hi-C data", - "homepage": "https://github.com/aidenlab/juicer", - "documentation": "https://github.com/aidenlab/juicer", - 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See https://github.com/aidenlab/juicer/wiki/Pre#file-format\nfor details.\n", - "pattern": "*.{pairs,tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "genome_id": { - "type": "string", - "description": "String of a supported genome ID, see https://github.com/aidenlab/juicer/wiki/Pre#usage\nfor details. Incompatible with chromsizes option.\n" - } - }, - { - "chromsizes": { - "type": "file", - "description": "Headerless TSV file describing chromosome sizes with format:\nchrom_name\\tlength\n\nIncompatible with genome_id option.\n", - "pattern": "*.{tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "output": { - "hic": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.hic": { - "type": "file", - "description": ".hic file for analysis and visualisation in Juicer", - "pattern": "*.{hic}", - "ontologies": [] - } - } - ] - ], - "versions_juicertools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "juicer_tools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "juicer_tools -V | grep \"Version\" | sed \"s/Juicer Tools Version //\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "juicer_tools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "juicer_tools -V | grep \"Version\" | sed \"s/Juicer Tools Version //\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@prototaxites" - ], - "maintainers": [ - "@prototaxites" - ] - } - }, - { - "name": "jupyternotebook", - "path": "modules/nf-core/jupyternotebook/meta.yml", - "type": "module", - "meta": { - "name": "jupyternotebook", - "description": "Render jupyter (or jupytext) notebooks to HTML reports. Supports parametrization\nthrough papermill.\n", - "keywords": [ - "Python", - "Jupyter", - "jupytext", - "papermill", - "notebook", - "reports" - ], - "tools": [ - { - "jupytext": { - "description": "Jupyter notebooks as plain text scripts or markdown documents", - "homepage": "https://github.com/mwouts/jupytext/", - "documentation": "https://jupyter.org/documentation", - "tool_dev_url": "https://github.com/mwouts/jupytext/", - "license": [ - "MIT" - ], - "identifier": "" - } - }, - { - "papermill": { - "description": "Parameterize, execute, and analyze notebooks", - "homepage": "https://github.com/nteract/papermill", - "documentation": "http://papermill.readthedocs.io/en/latest/", - "tool_dev_url": "https://github.com/nteract/papermill", - "license": [ - "BSD 3-clause" - ], - "identifier": "" - } - }, - { - "nbconvert": { - "description": "Parameterize, execute, and analyze notebooks", - "homepage": "https://nbconvert.readthedocs.io/en/latest/", - "documentation": "https://nbconvert.readthedocs.io/en/latest/", - "tool_dev_url": "https://github.com/jupyter/nbconvert", - "license": [ - "BSD 3-clause" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "notebook": { - "type": "file", - "description": "Jupyter notebook or jupytext representation thereof", - "pattern": "*.{ipynb,py,md,Rmd,myst}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3996" - }, - { - "edam": "http://edamontology.org/format_4000" - } - ] - } - } - ], - { - "parameters": { - "type": "map", - "description": "Groovy map with notebook parameters which will be passed\nto papermill in order to create parametrized reports.\n" - } - }, - { - "input_files": { - "type": "file", - "description": "One or multiple files serving as input data for the notebook.", - "pattern": "*", - "ontologies": [] - } - }, - { - "kernel_": { - "type": "string", - "description": "Name of the kernel to use." - } - } - ], - "output": { - "report": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.html": { - "type": "file", - "description": "HTML report generated from Jupyter notebook", - "pattern": "*.html", - "ontologies": [] - } - } - ] - ], - "artifacts": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "artifacts/": { - "type": "directory", - "description": "Directory containing all artifacts generated by the notebook", - "pattern": "artifacts/" - } - } - ] - ], - "versions_jupytext": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "jupytext": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "jupytext --version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_ipykernel": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "ipykernel": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python -c \"import ipykernel; print(ipykernel.__version__)\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_nbconvert": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "nbconvert": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "jupyter nbconvert --version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_papermill": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "papermill": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "papermill --version | cut -f1 -d\" \"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "jupytext": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "jupytext --version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "ipykernel": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python -c \"import ipykernel; print(ipykernel.__version__)\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "nbconvert": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "jupyter nbconvert --version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "papermill": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "papermill --version | cut -f1 -d\" \"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@grst" - ], - "maintainers": [ - "@grst" - ] - } - }, - { - "name": "jvarkit_dict2bed", - "path": "modules/nf-core/jvarkit/dict2bed/meta.yml", - "type": "module", - "meta": { - "name": "jvarkit_dict2xml", - "description": "Extract BED file from hts files containing a dictionary (VCF,BAM, CRAM, DICT, etc...)", - "keywords": [ - "vcf", - "bcf", - "bed", - "dict", - "dictionary", - "fasta", - "fai" - ], - "tools": [ - { - "jvarkit": { - "description": "Java utilities for Bioinformatics.", - "homepage": "https://github.com/lindenb/jvarkit", - "documentation": "https://jvarkit.readthedocs.io/", - "tool_dev_url": "https://github.com/lindenb/jvarkit", - "doi": "10.6084/m9.figshare.1425030", - "licence": [ - "MIT License" - ], - "args_id": "$args", - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing dict file information\ne.g. [ id:'test_reference' ]\n" - } - }, - { - "dict_files": { - "type": "file", - "description": "File(s) containing a dictionary VCF/BCF/BAM/DICT etc...", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz,dict,fai,bam,cram,interval_list}", - "ontologies": [] - } - } - ] - ], - "output": { - "bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing VCF information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bed": { - "type": "file", - "description": "BED output file", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@lindenb" - ], - "maintainers": [ - "@lindenb" - ] - } - }, - { - "name": "jvarkit_sam2tsv", - "path": "modules/nf-core/jvarkit/sam2tsv/meta.yml", - "type": "module", - "meta": { - "name": "jvarkit_sam2tsv", - "description": "Convert sam files to tsv files", - "keywords": [ - "sam", - "tsv", - "jvarkit" - ], - "tools": [ - { - "jvarkit": { - "description": "Java utilities for Bioinformatics.", - "homepage": "https://github.com/lindenb/jvarkit", - "documentation": "https://jvarkit.readthedocs.io/", - "tool_dev_url": "https://github.com/lindenb/jvarkit", - "doi": "10.6084/m9.figshare.1425030", - "licence": [ - "MIT License" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM file from alignment", - "pattern": "*.{bam,cram}", - "ontologies": [] - } - }, - { - "bai": { - "type": "file", - "description": "BAI/CRAI file from alignment", - "pattern": "*.{bai,crai}", - "ontologies": [] - } - }, - { - "regions_file": { - "type": "file", - "description": "Optional. Restrict to regions listed in a file", - "pattern": "*.{vcf,bed,gtf,gff,vcf.gz,bed.gz,gtf.gz,gff.gz}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [id: 'reference']\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome", - "pattern": "*.{fasta,fa}", - "ontologies": [] - } - }, - { - "fasta_index": { - "type": "file", - "description": "Reference genome information for fasta index", - "pattern": "*.{fasta.fai,fa.fai}", - "ontologies": [] - } - }, - { - "fasta_dict": { - "type": "file", - "description": "Reference genome information for fasta dict", - "pattern": "*.{.dict}", - "ontologies": [] - } - } - ] - ], - "output": { - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing TSV information e.g. [ id:'test' ]" - } - }, - { - "*.tsv": { - "type": "file", - "description": "Output file", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@lmfaber" - ], - "maintainers": [ - "@lmfaber" - ] - } - }, - { - "name": "jvarkit_vcf2table", - "path": "modules/nf-core/jvarkit/vcf2table/meta.yml", - "type": "module", - "meta": { - "name": "jvarkit_vcf2table", - "description": "Convert VCF to a user friendly table", - "keywords": [ - "vcf", - "bcf", - "text", - "html", - "visualization" - ], - "tools": [ - { - "jvarkit": { - "description": "Java utilities for Bioinformatics.", - "homepage": "https://github.com/lindenb/jvarkit", - "documentation": "https://jvarkit.readthedocs.io/", - "tool_dev_url": "https://github.com/lindenb/jvarkit", - "doi": "10.6084/m9.figshare.1425030", - "licence": [ - "MIT" - ], - "args_id": "$args2", - "identifier": "" - } - }, - { - "bcftools": { - "description": "View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF\n", - "homepage": "http://samtools.github.io/bcftools/bcftools.html", - "documentation": "http://www.htslib.org/doc/bcftools.html", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "args_id": "$args1", - "identifier": "biotools:samtools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing VCF information\ne.g. [ id:'genome' ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "Input vcf/bcf file", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", - "ontologies": [] - } - }, - { - "tbi": { - "type": "file", - "description": "Optional index file for the VCF", - "pattern": "*.{tbi,csi}", - "ontologies": [] - } - }, - { - "regions_file": { - "type": "file", - "description": "Optional. Restrict to regions listed in a file", - "pattern": "*.{bed,bed.gz,txt,tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing pedigree information\n" - } + ], + "output": { + "db_taxonomy": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "${prefix}_taxonomy": { + "type": "directory", + "description": "An MMseqs2 database with target data including the taxonomy classification" + } + } + ] + ], + "versions_mmseqs": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "mmseqs": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "mmseqs version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "mmseqs": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "mmseqs version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@darcy220606"], + "maintainers": ["@darcy220606"] }, - { - "pedigree": { - "type": "file", - "description": "Optional pedigree for jvarkit", - "pattern": "*.{ped,pedigree}", - "ontologies": [] - } - } - ] - ], - "output": { - "output": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing VCF information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.${extension}": { - "type": "file", - "description": "Output file", - "pattern": "*.{txt,html}", - "ontologies": [] - } - } + "pipelines": [ + { + "name": "funcscan", + "version": "3.0.0" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@lindenb" - ], - "maintainers": [ - "@lindenb" - ] - } - }, - { - "name": "jvarkit_vcffilterjdk", - "path": "modules/nf-core/jvarkit/vcffilterjdk/meta.yml", - "type": "module", - "meta": { - "name": "jvarkit_vcffilterjdk", - "description": "Filtering VCF with dynamically-compiled java expressions", - "keywords": [ - "vcf", - "bcf", - "filter", - "variant", - "java", - "script" - ], - "tools": [ - { - "jvarkit": { - "description": "Java utilities for Bioinformatics.", - "homepage": "https://github.com/lindenb/jvarkit", - "documentation": "https://jvarkit.readthedocs.io/", - "tool_dev_url": "https://github.com/lindenb/jvarkit", - "doi": "10.1093/bioinformatics/btx734 ", - "licence": [ - "MIT License" - ], - "args_id": "$args2", - "identifier": "" - } - }, - { - "bcftools": { - "description": "View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF\n", - "homepage": "http://samtools.github.io/bcftools/bcftools.html", - "documentation": "http://www.htslib.org/doc/bcftools.html", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "args_id": [ - "$args1", - "$args3" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing VCF information\ne.g. [ id:'test_reference' ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "Input VCF/BCF file", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", - "ontologies": [] - } - }, - { - "tbi": { - "type": "file", - "description": "Optional VCF/BCF index file", - "pattern": "*.{tbi,csi}", - "ontologies": [] - } - }, - { - "regions_file": { - "type": "file", - "description": "Optional. Restrict to regions listed in a file", - "pattern": "*.{bed,bed.gz,txt,tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing fasta information\ne.g. [ id:'test_reference' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Fasta reference file", - "pattern": "*.fasta", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing fasta.fai information\ne.g. [ id:'test_reference' ]\n" - } - }, - { - "fai": { - "type": "file", - "description": "Fasta file index", - "pattern": "*.fasta.fai", - "ontologies": [] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing fasta.dict information\ne.g. [ id:'test_reference' ]\n" - } - }, - { - "dict": { - "type": "file", - "description": "GATK sequence dictionary", - "pattern": "*.dict", - "ontologies": [] - } - } - ], - [ - { - "meta5": { - "type": "map", - "description": "Groovy Map containing code information\ne.g. [ id:'test_reference' ]\n" - } - }, - { - "code": { - "type": "file", - "description": "File containing custom user code . May be empty if script if provided via `task.ext.args2`.", - "pattern": "*.{code,script,txt,tsv,java,js}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - [ - { - "meta6": { - "type": "map", - "description": "Groovy Map containing pedigree information\ne.g. [ id:'test_reference' ]\n" - } + }, + { + "name": "mmseqs_tsv2exprofiledb", + "path": "modules/nf-core/mmseqs/tsv2exprofiledb/meta.yml", + "type": "module", + "meta": { + "name": "mmseqs_tsv2exprofiledb", + "description": "Conversion of expandable profile to databases to the MMseqs2 databases format", + "keywords": ["protein sequence", "databases", "clustering", "searching", "indexing"], + "tools": [ + { + "mmseqs": { + "description": "MMseqs2: ultra fast and sensitive sequence search and clustering suite", + "homepage": "https://github.com/soedinglab/MMseqs2", + "documentation": "https://mmseqs.com/latest/userguide.pdf", + "tool_dev_url": "https://github.com/soedinglab/MMseqs2", + "doi": "10.1093/bioinformatics/btw006", + "licence": ["GPL v3"], + "identifier": "biotools:mmseqs" + } + } + ], + "input": [ + { + "database": { + "type": "directory", + "description": "Directory containing the database to be indexed\n", + "pattern": "*" + } + } + ], + "output": { + "db_exprofile": [ + { + "database": { + "type": "directory", + "description": "Directory containing the expandable profile database\n", + "pattern": "*" + } + } + ], + "versions_mmseqs": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "mmseqs": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "mmseqs version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "mmseqs": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "mmseqs version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@JoseEspinosa"], + "maintainers": ["@JoseEspinosa", "@sateeshperi"] }, - { - "pedigree": { - "type": "file", - "description": "Optional jvarkit pedigree.", - "pattern": "*.{tsv,ped,pedigree}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing VCF information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.${extension}": { - "type": "file", - "description": "VCF filtered output file", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", - "ontologies": [] - } - } - ] - ], - "tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing VCF information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tbi": { - "type": "file", - "description": "Alternative VCF file index", - "pattern": "*.tbi", - "ontologies": [] - } - } - ] - ], - "csi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing VCF information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.csi": { - "type": "file", - "description": "Default VCF file index", - "pattern": "*.csi", - "ontologies": [] - } - } + "pipelines": [ + { + "name": "proteinfold", + "version": "2.0.0" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@lindenb" - ], - "maintainers": [ - "@lindenb" - ] - } - }, - { - "name": "jvarkit_vcfpolyx", - "path": "modules/nf-core/jvarkit/vcfpolyx/meta.yml", - "type": "module", - "meta": { - "name": "jvarkit_vcfpolyx", - "description": "annotate VCF files for poly repeats", - "keywords": [ - "vcf", - "bcf", - "annotation", - "repeats" - ], - "tools": [ - { - "jvarkit": { - "description": "Java utilities for Bioinformatics.", - "homepage": "https://github.com/lindenb/jvarkit", - "documentation": "https://jvarkit.readthedocs.io/", - "tool_dev_url": "https://github.com/lindenb/jvarkit", - "doi": "10.6084/m9.figshare.1425030", - "licence": [ - "MIT License" - ], - "identifier": "" - } - }, - { - "bcftools": { - "description": "View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF\n", - "homepage": "http://samtools.github.io/bcftools/bcftools.html", - "documentation": "http://www.htslib.org/doc/bcftools.html", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing VCF information\n" - } - }, - { - "vcf": { - "type": "file", - "description": "Groovy Map containing reference genome information for vcf", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", - "ontologies": [] - } - }, - { - "tbi": { - "type": "file", - "description": "Alternative VCF file index", - "pattern": "*.tbi", - "ontologies": [] - } - }, - { - "regions_file": { - "type": "file", - "description": "Regions file", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing fasta information\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Groovy Map containing reference genome information for fai reference fasta file", - "pattern": "*.fasta", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing fasta.fai information\n" - } - }, - { - "fai": { - "type": "file", - "description": "Groovy Map containing reference genome information for fai", - "pattern": "*.fasta.fai", - "ontologies": [] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing fasta.dict information\n" - } + }, + { + "name": "mobster", + "path": "modules/nf-core/mobster/meta.yml", + "type": "module", + "meta": { + "name": "mobster", + "description": "Subclonal deconvolution of cancer genome sequencing data.", + "keywords": ["subclonal deconvolution", "genomics", "cancer evolution"], + "tools": [ + { + "mobster": { + "description": "mobster is a package that implements a model-based approach for subclonal deconvolution of\ncancer genome sequencing data.\n\nThe package integrates evolutionary theory (i.e., population) and Machine-Learning to analyze\n(e.g., whole-genome) bulk data from cancer samples. This analysis relates to clustering; we\napproach it via a maximum-likelihood formulation of Dirichlet mixture models, and use bootstrap\nroutines to assess the confidence of the parameters.\n", + "homepage": "https://caravagnalab.github.io/mobster/", + "documentation": "https://caravagnalab.github.io/mobster/", + "tool_dev_url": "https://github.com/caravagnalab/mobster", + "doi": "10.1038/s41588-020-0675-5", + "licence": ["GPL-3.0"], + "identifier": "biotools:mobster-R" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "rds_join": { + "type": "file", + "description": "Either a .rds object of class mCNAqc or a .csv mutations table", + "pattern": "*.{rds,csv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "output": { + "mobster_rds": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_mobster_fit.rds": { + "type": "file", + "description": "Full mobster fit as an .rds object", + "pattern": "*_mobster_fit.rds", + "ontologies": [] + } + } + ] + ], + "mobster_best_rds": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_mobster_best_fit.rds": { + "type": "file", + "description": "Best mobster fit as an .rds object", + "pattern": "*_mobster_best_fit.rds", + "ontologies": [] + } + } + ] + ], + "mobster_best_plots_rds": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_mobster_best_plots.rds": { + "type": "file", + "description": "Final plots as an .rds object", + "pattern": "*_mobster_best_plots.rds", + "ontologies": [] + } + } + ] + ], + "mobster_report_rds": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_mobster_report.rds": { + "type": "file", + "description": "Final report plots as an .rds object", + "pattern": "*_mobster_report.rds", + "ontologies": [] + } + } + ] + ], + "mobster_report_pdf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_mobster_report.pdf": { + "type": "file", + "description": "Final report plots as a .pdf file", + "pattern": "*_mobster_report.pdf", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3508" + } + ] + } + } + ] + ], + "mobster_report_png": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_mobster_report.png": { + "type": "file", + "description": "Final report plots as a .png file", + "pattern": "*_mobster_report.png", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3603" + } + ] + } + } + ] + ], + "versions_mobster": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "topics": { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@elena-buscaroli"], + "maintainers": ["@elena-buscaroli"] }, - { - "dict": { - "type": "file", - "description": "Groovy Map containing reference genome information for GATK sequence dictionary", - "pattern": "*.dict", - "ontologies": [] - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing VCF information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.${extension}": { - "type": "file", - "description": "VCF filtered output file", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", - "ontologies": [] - } - } - ] - ], - "tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing VCF information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tbi": { - "type": "file", - "description": "Alternative VCF file index", - "pattern": "*.tbi", - "ontologies": [] - } - } - ] - ], - "csi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing VCF information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.csi": { - "type": "file", - "description": "Default VCF file index", - "pattern": "*.csi", - "ontologies": [] - } - } + "pipelines": [ + { + "name": "tumourevo", + "version": "dev" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@lindenb" - ], - "maintainers": [ - "@lindenb" - ] - } - }, - { - "name": "jvarkit_wgscoverageplotter", - "path": "modules/nf-core/jvarkit/wgscoverageplotter/meta.yml", - "type": "module", - "meta": { - "name": "jvarkit_wgscoverageplotter", - "description": "Plot whole genome coverage from BAM/CRAM file as SVG", - "keywords": [ - "bam", - "cram", - "depth", - "coverage", - "xml", - "svg", - "visualization" - ], - "tools": [ - { - "jvarkit": { - "description": "Java utilities for Bioinformatics.", - "homepage": "https://github.com/lindenb/jvarkit", - "documentation": "https://jvarkit.readthedocs.io/", - "tool_dev_url": "https://github.com/lindenb/jvarkit", - "doi": "10.6084/m9.figshare.1425030", - "licence": [ - "MIT License" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM file from alignment", - "pattern": "*.{bam,cram}", - "ontologies": [] - } - }, - { - "bai": { - "type": "file", - "description": "BAI/CRAI file from alignment", - "pattern": "*.{bai,crai}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test_reference' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference fasta file", - "pattern": "*.fasta", - "ontologies": [] - } + }, + { + "name": "mobsuite_recon", + "path": "modules/nf-core/mobsuite/recon/meta.yml", + "type": "module", + "meta": { + "name": "mobsuite_recon", + "description": "A tool to reconstruct plasmids in bacterial assemblies", + "keywords": ["bacteria", "plasmid", "cluster"], + "tools": [ + { + "mobsuite": { + "description": "Software tools for clustering, reconstruction and typing of plasmids from draft assemblies.", + "homepage": "https://github.com/phac-nml/mob-suite", + "documentation": "https://github.com/phac-nml/mob-suite", + "tool_dev_url": "https://github.com/phac-nml/mob-suite", + "doi": "10.1099/mgen.0.000435", + "licence": ["Apache License, Version 2.0"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "A bacterial genome assembly in FASTA format", + "pattern": "*.{fasta,fa,fna}", + "ontologies": [] + } + } + ] + ], + "output": { + "chromosome": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "results/chromosome.fasta": { + "type": "file", + "description": "FASTA file of all contigs found to belong to the chromosome", + "pattern": "chromosome.fasta", + "ontologies": [] + } + } + ] + ], + "contig_report": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "results/contig_report.txt": { + "type": "file", + "description": "Assignment of the contig to chromosome or a particular plasmid grouping", + "pattern": "contig_report.txt", + "ontologies": [] + } + } + ] + ], + "plasmids": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "results/plasmid_*.fasta": { + "type": "file", + "description": "Each plasmid group is written to an individual FASTA", + "pattern": "plasmid_*.fasta", + "ontologies": [] + } + } + ] + ], + "mobtyper_results": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "results/mobtyper_results.txt": { + "type": "file", + "description": "Aggregate MOB-typer report files for all identified plasmid", + "pattern": "mobtyper_results.txt", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@rpetit3"], + "maintainers": ["@rpetit3"] } - 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+ } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "clahe": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python /local/scripts/molkart_clahe.py --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "scikit-image": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python -c 'import skimage; print(skimage.__version__)'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@kbestak"], + "maintainers": ["@kbestak"] + } }, { - "name": "viralmetagenome", - "version": "1.1.1" - } - ] - }, - { - "name": "kaiju_kaiju2table", - "path": "modules/nf-core/kaiju/kaiju2table/meta.yml", - "type": "module", - "meta": { - "name": "kaiju_kaiju2table", - "description": "write your description here", - "keywords": [ - "classify", - "metagenomics", - "taxonomic profiling" - ], - "tools": [ - { - "kaiju": { - "description": "Fast and sensitive taxonomic classification for metagenomics", - "homepage": "https://kaiju.binf.ku.dk/", - "documentation": "https://github.com/bioinformatics-centre/kaiju/blob/master/README.md", - "tool_dev_url": "https://github.com/bioinformatics-centre/kaiju", - "doi": "10.1038/ncomms11257", - "licence": [ - "GNU GPL v3" - ], - "identifier": "biotools:kaiju" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "Kaiju input file", - "ontologies": [] - } - } - ], - { - "db": { - "type": "file", - "description": "Kaiju database", - "ontologies": [] - } - }, - { - "taxon_rank": { - "type": "string", - "description": "Taxonomic rank to display in report\npattern: \"phylum|class|order|family|genus|species\"\n" - } - } - ], - "output": { - "summary": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.txt": { - "type": "file", - "description": "Kaiju output file", - "pattern": "*.txt", - "ontologies": [] - } - } - ] - ], - "versions_kaiju": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "kaiju": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "kaiju -h 2>&1 | sed -n 1p | sed 's/^.*Kaiju //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "kaiju": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "kaiju -h 2>&1 | sed -n 1p | sed 's/^.*Kaiju //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@sofstam", - "@talnor", - "@jfy133" - ], - "maintainers": [ - "@sofstam", - "@talnor", - "@jfy133" - ] - }, - "pipelines": [ - { - "name": "taxprofiler", - "version": "2.0.0" - }, - { - "name": "viralmetagenome", - "version": "1.1.1" - } - ] - }, - { - "name": "kaiju_mergeoutputs", - "path": "modules/nf-core/kaiju/mergeoutputs/meta.yml", - "type": "module", - "meta": { - "name": "kaiju_mergeoutputs", - "description": "Merge two tab-separated output files of Kaiju and Kraken in the column format", - "keywords": [ - "classify", - "metagenomics", - "fastq", - "taxonomic profiling" - ], - "tools": [ - { - "kaiju": { - "description": "Fast and sensitive taxonomic classification for metagenomics", - "homepage": "https://kaiju.binf.ku.dk/", - "documentation": "https://github.com/bioinformatics-centre/kaiju/blob/master/README.md", - "tool_dev_url": "https://github.com/bioinformatics-centre/kaiju", - "doi": "10.1038/ncomms11257", - "licence": [ - "GNU GPL v3" - ], - "identifier": "biotools:kaiju" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "kaiju": { - "type": "file", - "description": "Results with taxonomic classification of each read from Kaiju\n", - "ontologies": [] - } - }, - { - "kraken": { - "type": "file", - "description": "Results with taxonomic classification of each read from Kraken\n", - "pattern": "*.{tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - { - "db": { - "type": "directory", - "description": "List containing the database and nodes files for Kaiju\ne.g. [ 'database.fmi', 'nodes.dmp' ]\n" - } - } - ], - "output": { - "merged": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "Results with merged taxonomic classification of each read based on the given strategy '1', '2', 'lca' [default] or 'lowest'", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_kaiju": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "kaiju": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "kaiju -h 2>&1 | sed -n 1p | sed 's/^.*Kaiju //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "kaiju": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "kaiju -h 2>&1 | sed -n 1p | sed 's/^.*Kaiju //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@Joon-Klaps" - ], - "maintainers": [ - "@Joon-Klaps" - ] - } - }, - { - "name": "kaiju_mkfmi", - "path": "modules/nf-core/kaiju/mkfmi/meta.yml", - "type": "module", - "meta": { - "name": "kaiju_mkfmi", - "description": "Make Kaiju FMI-index file from a protein FASTA file", - "keywords": [ - "classify", - "metagenomics", - "fastq", - "taxonomic profiling", - "database", - "index" - ], - "tools": [ - { - "kaiju": { - "description": "Fast and sensitive taxonomic classification for metagenomics", - "homepage": "https://bioinformatics-centre.github.io/kaiju/", - "documentation": "https://github.com/bioinformatics-centre/kaiju/blob/master/README.md", - "tool_dev_url": "https://github.com/bioinformatics-centre/kaiju", - "doi": "10.1038/ncomms11257", - "licence": [ - "GNU GPL v3" - ], - "identifier": "biotools:kaiju" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } + "name": "mosdepth", + "path": "modules/nf-core/mosdepth/meta.yml", + "type": "module", + "meta": { + "name": "mosdepth", + "description": "Calculates genome-wide sequencing coverage.", + "keywords": ["mosdepth", "bam", "cram", "coverage"], + "tools": [ + { + "mosdepth": { + "description": "Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing.\n", + "documentation": "https://github.com/brentp/mosdepth", + "doi": "10.1093/bioinformatics/btx699", + "licence": ["MIT"], + "identifier": "biotools:mosdepth" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "Input BAM/CRAM file", + "pattern": "*.{bam,cram}", + "ontologies": [] + } + }, + { + "bai": { + "type": "file", + "description": "Index for BAM/CRAM file", + "pattern": "*.{bai,crai}", + "ontologies": [] + } + }, + { + "bed": { + "type": "file", + "description": "BED file with intersected intervals", + "pattern": "*.{bed}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing bed information\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference genome FASTA file", + "pattern": "*.{fa,fasta}", + "ontologies": [] + } + } + ], + { + "quantize_labels": { + "type": "list", + "description": "List of labels for quantized coverage bins, e.g. [ \"NO_COVERAGE\", \"LOW_COVERAGE\", \"MEDIUM_COVERAGE\", \"HIGH_COVERAGE\" ]\nThe first value will be assigned to the `MOSDEPTH_Q0` environment variable, the second to `MOSDEPTH_Q1`, and so on.\nThese can then be used in the `--quantize` option of mosdepth to assign labels to quantized coverage bins.\n" + } + } + ], + "output": { + "global_txt": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.global.dist.txt": { + "type": "file", + "description": "Text file with global cumulative coverage distribution", + "pattern": "*.{global.dist.txt}", + "ontologies": [] + } + } + ] + ], + "summary_txt": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.summary.txt": { + "type": "file", + "description": "Text file with summary mean depths per chromosome and regions", + "pattern": "*.{summary.txt}", + "ontologies": [] + } + } + ] + ], + "regions_txt": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.region.dist.txt": { + "type": "file", + "description": "Text file with region cumulative coverage distribution", + "pattern": "*.{region.dist.txt}", + "ontologies": [] + } + } + ] + ], + "per_base_d4": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.per-base.d4": { + "type": "file", + "description": "D4 file with per-base coverage", + "pattern": "*.{per-base.d4}", + "ontologies": [] + } + } + ] + ], + "per_base_bed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.per-base.bed.gz": { + "type": "file", + "description": "BED file with per-base coverage", + "pattern": "*.{per-base.bed.gz}", + "ontologies": [] + } + } + ] + ], + "per_base_csi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.per-base.bed.gz.csi": { + "type": "file", + "description": "Index file for BED file with per-base coverage", + "pattern": "*.{per-base.bed.gz.csi}", + "ontologies": [] + } + } + ] + ], + "regions_bed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.regions.bed.gz": { + "type": "file", + "description": "BED file with per-region coverage", + "pattern": "*.{regions.bed.gz}", + "ontologies": [] + } + } + ] + ], + "regions_csi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.regions.bed.gz.csi": { + "type": "file", + "description": "Index file for BED file with per-region coverage", + "pattern": "*.{regions.bed.gz.csi}", + "ontologies": [] + } + } + ] + ], + "quantized_bed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.quantized.bed.gz": { + "type": "file", + "description": "BED file with binned coverage", + "pattern": "*.{quantized.bed.gz}", + "ontologies": [] + } + } + ] + ], + "quantized_csi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.quantized.bed.gz.csi": { + "type": "file", + "description": "Index file for BED file with binned coverage", + "pattern": "*.{quantized.bed.gz.csi}", + "ontologies": [] + } + } + ] + ], + "thresholds_bed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.thresholds.bed.gz": { + "type": "file", + "description": "BED file with the number of bases in each region that are covered at or above each threshold", + "pattern": "*.{thresholds.bed.gz}", + "ontologies": [] + } + } + ] + ], + "thresholds_csi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.thresholds.bed.gz.csi": { + "type": "file", + "description": "Index file for BED file with threshold coverage", + "pattern": "*.{thresholds.bed.gz.csi}", + "ontologies": [] + } + } + ] + ], + "versions_mosdepth": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "mosdepth": { + "type": "string", + "description": "The tool name" + } + }, + { + "mosdepth --version | sed 's/mosdepth //g'": { + "type": "eval", + "description": "The command used to generate the version of the tool" + } + } + ] + ], + "versions_gzip": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "gzip": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gzip -V 2>&1 | sed 's/gzip \\([0-9.]*\\).*/\\1/;q'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "mosdepth": { + "type": "string", + "description": "The tool name" + } + }, + { + "mosdepth --version | sed 's/mosdepth //g'": { + "type": "eval", + "description": "The command used to generate the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "gzip": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gzip -V 2>&1 | sed 's/gzip \\([0-9.]*\\).*/\\1/;q'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@joseespinosa", "@drpatelh", "@ramprasadn", "@matthdsm"], + "maintainers": ["@joseespinosa", "@ramprasadn", "@matthdsm"] }, - { - "fasta": { - "type": "file", - "description": "Uncompressed Protein FASTA file (mandatory)", - "pattern": "*.{fa,faa,fasta}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - { - "nodes_dmp": { - "type": "file", - "description": "NCBI nodes.dmp file (mandatory)", - "pattern": "nodes.dmp", - "ontologies": [ + "pipelines": [ { - "edam": "http://edamontology.org/format_3751" - } - ] - } - }, - { - "names_dmp": { - "type": "file", - "description": "NCBI names.dmp file (mandatory)", - "pattern": "names.dmp", - "ontologies": [ + "name": "createpanelrefs", + "version": "dev" + }, + { + "name": "genomicrelatedness", + "version": "dev" + }, + { + "name": "pacsomatic", + "version": "dev" + }, + { + "name": "raredisease", + "version": "3.0.0" + }, + { + "name": "rnadnavar", + "version": "dev" + }, + { + "name": "rnavar", + "version": "1.2.3" + }, + { + "name": "sarek", + "version": "3.8.1" + }, + { + "name": "variantcatalogue", + "version": "dev" + }, + { + "name": "viralmetagenome", + "version": "1.1.1" + }, { - "edam": "http://edamontology.org/format_3751" + "name": "viralrecon", + "version": "3.0.0" } - ] - } - }, - { - "keep_intermediate": { - "type": "boolean", - "description": "Keep intermediate files", - "pattern": "true|false" - } - } - ], - "output": { - "fmi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*.{fmi,dmp}": { - "type": "file", - "description": "Kaiju FM-index file, and input {names,nodes}.dmp NCBI taxonomy files required for downstream Kaiju commands", - "pattern": "*.{fmi,dmp}", - "ontologies": [] - } - } - ] - ], - "bwt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*.bwt": { - "type": "file", - "description": "Kaiju intermedite bwt-index file (not needed for classification)", - "pattern": "*.{bwt}", - "ontologies": [] - } - } ] - ], - "sa": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*.sa": { - "type": "file", - "description": "Kaiju intermedite bwt-index file (not needed for classification)", - "pattern": "*.{sa}", - "ontologies": [] - } - } - ] - ], - "versions_kaiju": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "kaiju": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "kaiju -h 2>&1 | sed -n 1p | sed 's/^.*Kaiju //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "kaiju": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "kaiju -h 2>&1 | sed -n 1p | sed 's/^.*Kaiju //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] }, - "authors": [ - "@alxndrdiaz", - "@jfy133" - ] - }, - "pipelines": [ { - "name": "createtaxdb", - "version": "3.0.0" - } - ] - }, - { - "name": "kalign_align", - "path": "modules/nf-core/kalign/align/meta.yml", - "type": "module", - "meta": { - "name": "kalign_align", - "description": "Aligns sequences using kalign", - "keywords": [ - "alignment", - "MSA", - "genomics" - ], - "tools": [ - { - "kalign": { - "description": "Kalign is a fast and accurate multiple sequence alignment algorithm.", - "homepage": "https://msa.sbc.su.se/cgi-bin/msa.cgi", - "documentation": "https://github.com/TimoLassmann/kalign", - "tool_dev_url": "https://github.com/TimoLassmann/kalign", - "doi": "10.1093/bioinformatics/btz795", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:kalign" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input sequences in FASTA format. May be gzipped or uncompressed.", - "pattern": "*.{fa,fasta}{.gz,}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1919" - }, - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - { - "compress": { - "type": "boolean", - "description": "Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded." - } - } - ], - "output": { - "alignment": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" - } - }, - { - "*.aln{.gz,}": { - "type": "file", - "description": "Alignment file. May be gzipped or uncompressed, depending on if `compress` is set to `true` or `false`.", - "pattern": "*.{aln}{.gz,}", - "ontologies": [ + "name": "motus_downloaddb", + "path": "modules/nf-core/motus/downloaddb/meta.yml", + "type": "module", + "meta": { + "name": "motus_downloaddb", + "description": "Download the mOTUs database", + "keywords": ["classify", "metagenomics", "fastq", "taxonomic profiling", "database", "download"], + "tools": [ + { + "motus": { + "description": "The mOTU profiler is a computational tool that estimates relative taxonomic abundance of known and currently unknown microbial community members using metagenomic shotgun sequencing data.", + "documentation": "https://github.com/motu-tool/mOTUs/wiki", + "tool_dev_url": "https://github.com/motu-tool/mOTUs", + "doi": "10.1186/s40168-022-01410-z", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ { - "edam": "http://edamontology.org/format_2554" - }, + "motus_downloaddb_script": { + "type": "file", + "description": "The script to download the mOTUs database", + "ontologies": [] + } + } + ], + "output": { + "db": [ + { + "db_mOTU/": { + "type": "directory", + "description": "The mOTUs database directory", + "pattern": "db_mOTU" + } + } + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@jianhong"], + "maintainers": ["@jianhong"] + } + }, + { + "name": "motus_merge", + "path": "modules/nf-core/motus/merge/meta.yml", + "type": "module", + "meta": { + "name": "motus_merge", + "description": "Taxonomic meta-omics profiling using universal marker genes", + "keywords": [ + "classify", + "metagenomics", + "fastq", + "taxonomic profiling", + "merging", + "merge", + "otu table" + ], + "tools": [ + { + "motus": { + "description": "Marker gene-based OTU (mOTU) profiling", + "homepage": "https://motu-tool.org/", + "documentation": "https://github.com/motu-tool/mOTUs/wiki", + "tool_dev_url": "https://github.com/motu-tool/mOTUs", + "doi": "10.1186/s40168-022-01410-z", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "input": { + "type": "file", + "description": "List of output files (more than one) from motus profile,\nor a single directory containing motus output files.\n", + "ontologies": [] + } + } + ], { - "edam": "http://edamontology.org/format_1921" + "db": { + "type": "directory", + "description": "mOTUs database downloaded by `motus downloadDB`\npattern: \"db_mOTU/\"\n" + } }, { - "edam": "http://edamontology.org/format_1984" + "profile_version_yml": { + "type": "file", + "description": "A single versions.yml file output from motus/profile. motus/merge cannot reconstruct\nthis itself without having the motus database present and configured with the tool\nso here we take it from what is already reported by the upstream module.\n", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } } - ] - } - } - ] - ], - "versions_kalign": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "kalign": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "kalign -v | sed \"s/^.*kalign[[:space:]]*//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_pigz": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pigz": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pigz --version 2>&1 | sed \"s/^.*pigz[[:space:]]*//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "kalign": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "kalign -v | sed \"s/^.*kalign[[:space:]]*//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pigz": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pigz --version 2>&1 | sed \"s/^.*pigz[[:space:]]*//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@luisas", - "@JoseEspinosa" - ], - "maintainers": [ - "@luisas", - "@JoseEspinosa" - ] - }, - "pipelines": [ - { - "name": "multiplesequencealign", - "version": "1.1.1" - } - ] - }, - { - "name": "kallisto_index", - "path": "modules/nf-core/kallisto/index/meta.yml", - "type": "module", - "meta": { - "name": "kallisto_index", - "description": "Create kallisto index", - "keywords": [ - "kallisto", - "kallisto/index", - "index" - ], - "tools": [ - { - "kallisto": { - "description": "Quantifying abundances of transcripts from bulk and single-cell RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.", - "homepage": "https://pachterlab.github.io/kallisto/", - "documentation": "https://pachterlab.github.io/kallisto/manual", - "tool_dev_url": "https://github.com/pachterlab/kallisto", - "licence": [ - "BSD-2-Clause" - ], - "identifier": "biotools:kallisto" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } + ], + "output": { + "txt": [ + [ + { + "meta": { + "type": "file", + "description": "OTU table in txt format, if BIOM format not requested", + "pattern": "*.txt", + "ontologies": [] + } + }, + { + "*.txt": { + "type": "file", + "description": "OTU table in txt format, if BIOM format not requested", + "pattern": "*.txt", + "ontologies": [] + } + } + ] + ], + "biom": [ + [ + { + "meta": { + "type": "file", + "description": "OTU table in txt format, if BIOM format not requested", + "pattern": "*.txt", + "ontologies": [] + } + }, + { + "*.biom": { + "type": "file", + "description": "OTU table in biom format, if BIOM format requested", + "pattern": "*.biom", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3746" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@jfy133"], + "maintainers": ["@jfy133"] }, - { - "fasta": { - "type": "file", - "description": "genome fasta file", - "pattern": "*.{fasta}", - "ontologies": [] - } - } - ] - ], - "output": { - "index": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "kallisto": { - "type": "directory", - "description": "Kallisto genome index", - "pattern": "*.idx" - } - } - ] - ], - "versions_kallisto": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "kallisto": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "kallisto 2>&1 | head -1 | sed \"s/^kallisto //; s/Usage.*//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "kallisto": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "kallisto 2>&1 | head -1 | sed \"s/^kallisto //; s/Usage.*//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "taxprofiler", + "version": "2.0.0" + } ] - ] - }, - "authors": [ - "@ggabernet" - ], - "maintainers": [ - "@ggabernet" - ] - }, - "pipelines": [ - { - "name": "lncpipe", - "version": "dev" - }, - { - "name": "references", - "version": "0.1" }, { - "name": "riboseq", - "version": "1.2.0" - }, - { - "name": "rnaseq", - "version": "3.26.0" - } - ] - }, - { - "name": "kallisto_quant", - "path": "modules/nf-core/kallisto/quant/meta.yml", - "type": "module", - "meta": { - "name": "kallisto_quant", - "description": "Computes equivalence classes for reads and quantifies abundances", - "keywords": [ - "quant", - "kallisto", - "pseudoalignment" - ], - "tools": [ - { - "kallisto": { - "description": "Quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.", - "homepage": "https://pachterlab.github.io/kallisto/", - "documentation": "https://pachterlab.github.io/kallisto/manual", - "tool_dev_url": "https://github.com/pachterlab/kallisto", - "doi": "10.1038/nbt.3519", - "licence": [ - "BSD_2_clause" - ], - "identifier": "biotools:kallisto" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", - "pattern": "*.{fastq,fastq.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + "name": "motus_preplong", + "path": "modules/nf-core/motus/preplong/meta.yml", + "type": "module", + "meta": { + "name": "motus_preplong", + "description": "Taxonomic meta-omics profiling using universal marker genes", + "keywords": ["classify", "metagenomics", "fastq", "taxonomic profiling"], + "tools": [ + { + "motus": { + "description": "Marker gene-based operational taxonomic unit (mOTU) profiling", + "homepage": "https://motu-tool.org/", + "documentation": "https://github.com/motu-tool/mOTUs/wiki", + "tool_dev_url": "https://github.com/motu-tool/mOTUs", + "doi": "10.1186/s40168-022-01410-z", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "reads": { + "type": "file", + "description": "Long read file to convert, can be fasta(.gz) or fastq(.gz)", + "pattern": "*.{gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ], + { + "db": { + "type": "directory", + "description": "mOTUs database downloaded by `motus downloadDB`\npattern: \"db_mOTU/\"\n" + } + } + ], + "output": { + "out": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.gz": { + "type": "file", + "description": "converted file (gzipped), ready to be used by motus profile", + "pattern": "*.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@sofstam"], + "maintainers": ["@sofstam"] }, - { - "index": { - "type": "file", - "description": "Kallisto genome index.", - "pattern": "*.idx", - "ontologies": [] - } - } - ], - { - "gtf": { - "type": "file", - "description": "Optional gtf file for translation of transcripts into genomic coordinates.", - "pattern": "*.gtf", - "ontologies": [] - } - }, - { - "chromosomes": { - "type": "file", - "description": "Optional tab separated file with chromosome names and lengths.", - "pattern": "*.tsv", - "ontologies": [ + "pipelines": [ { - "edam": "http://edamontology.org/format_3475" + "name": "taxprofiler", + "version": "2.0.0" } - ] - } - }, - { - "fragment_length": { - "type": "integer", - "description": "For single-end mode only, the estimated average fragment length." - } - }, - { - "fragment_length_sd": { - "type": "integer", - "description": "For single-end mode only, the estimated standard deviation of the fragment length." - } - } - ], - "output": { - "results": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}": { - "type": "file", - "description": "Kallisto output file", - "ontologies": [] - } - } - ] - ], - "json_info": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.run_info.json": { - "type": "file", - "description": "JSON file containing information about the run", - "pattern": "*.run_info.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.log": { - "type": "file", - "description": "File containing log information from running kallisto quant", - "pattern": "*.log.txt", - "ontologies": [] - } - } ] - ], - "versions_kallisto": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "kallisto": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "kallisto version | sed 's/.*version //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "kallisto": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "kallisto version | sed 's/.*version //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@anoronh4" - ], - "maintainers": [ - "@anoronh4" - ] - }, - "pipelines": [ - { - "name": "riboseq", - "version": "1.2.0" }, { - "name": "rnaseq", - "version": "3.26.0" - } - ] - }, - { - "name": "kallistobustools_count", - "path": "modules/nf-core/kallistobustools/count/meta.yml", - "type": "module", - "meta": { - "name": "kallistobustools_count", - "description": "quantifies scRNA-seq data from fastq files using kb-python.", - "keywords": [ - "scRNA-seq", - "count", - "single-cell", - "kallisto", - "bustools" - ], - "tools": [ - { - "kb": { - "description": "kallisto and bustools are wrapped in an easy-to-use program called kb", - "homepage": "https://www.kallistobus.tools/", - "documentation": "https://kb-python.readthedocs.io/en/latest/index.html", - "tool_dev_url": "https://github.com/pachterlab/kb_python", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", - "ontologies": [] - } - } - ], - { - "index": { - "type": "file", - "description": "kb-ref index file (.idx)", - "pattern": "*.{idx}", - "ontologies": [] - } - }, - { - "t2g": { - "type": "file", - "description": "t2g file from kallisto", - "pattern": "*t2g.txt", - "ontologies": [] - } - }, - { - "t1c": { - "type": "file", - "description": "kb ref's c1 cdna_t2c file", - "pattern": "*.{cdna_t2c.txt}", - "ontologies": [] - } - }, - { - "t2c": { - "type": "file", - "description": "kb ref's c2 intron_t2c file", - "pattern": "*.{intron_t2c.txt}", - "ontologies": [] - } - }, - { - "technology": { - "type": "string", - "description": "String value defining the sequencing technology used.", - "pattern": "{10XV1,10XV2,10XV3,CELSEQ,CELSEQ2,DROPSEQ,INDROPSV1,INDROPSV2,INDROPSV3,SCRUBSEQ,SURECELL,SMARTSEQ}" - } - }, - { - "workflow_mode": { - "type": "string", - "description": "String value defining workflow to use, can be one of \"standard\", \"nac\", \"lamanno\" (obsolete)", - "pattern": "{standard,lamanno,nac}" - } - } - ], - "output": { - "count": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "*.count": { - "type": "file", - "description": "kb count output folder", - "pattern": "*.{count}", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ], - "matrix": [ - { - "*.count/*/*.mtx": { - "type": "file", - "description": "file containing the count matrix", - "pattern": "*.mtx", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3916" - } - ] - } - } - ] - }, - "authors": [ - "@flowuenne" - ], - "maintainers": [ - "@flowuenne" - ] - }, - "pipelines": [ - { - "name": "scrnaseq", - "version": "4.1.0" - } - ] - }, - { - "name": "kallistobustools_ref", - "path": "modules/nf-core/kallistobustools/ref/meta.yml", - "type": "module", - "meta": { - "name": "kallistobustools_ref", - "description": "index creation for kb count quantification of single-cell data.", - "keywords": [ - "scRNA-seq", - "count", - "single-cell", - "kallisto", - "bustools", - "index" - ], - "tools": [ - { - "kb": { - "description": "kallisto|bustools (kb) is a tool developed for fast and efficient processing of single-cell OMICS data.", - "homepage": "https://www.kallistobus.tools/", - "documentation": "https://kb-python.readthedocs.io/en/latest/index.html", - "tool_dev_url": "https://github.com/pachterlab/kb_python", - "doi": "10.22002/D1.1876", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - { - "fasta": { - "type": "file", - "description": "Genomic DNA fasta file", - "pattern": "*.{fasta,fasta.gz}", - "ontologies": [] - } - }, - { - "gtf": { - "type": "file", - "description": "Genomic gtf file", - "pattern": "*.{gtf,gtf.gz}", - "ontologies": [] - } - }, - { - "workflow_mode": { - "type": "string", - "description": "String value defining workflow to use, can be one of \"standard\", \"nac\", \"lamanno\" (obsolete)", - "pattern": "{standard,lamanno,nac}" - } - } - ], - "output": { - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ], - "index": [ - { - "kb_ref_out.idx": { - "type": "file", - "description": "kb ref index file", - "pattern": "*kb_ref_out.idx", - "ontologies": [] - } - } - ], - "t2g": [ - { - "t2g.txt": { - "type": "file", - "description": "Transcript to gene table", - "pattern": "*t2g.{txt}", - "ontologies": [] - } - } - ], - "cdna": [ - { - "cdna.fa": { - "type": "file", - "description": "cDNA fasta file", - "pattern": "*cdna.{fa}", - "ontologies": [] - } - } - ], - "intron": [ - { - "intron.fa": { - "type": "file", - "description": "Intron fasta file", - "pattern": "*intron.{fa}", - "ontologies": [] - } - } - ], - "cdna_t2c": [ - { - "cdna_t2c.txt": { - "type": "file", - "description": "cDNA transcript to capture file", - "pattern": "*cdna_t2c.{txt}", - "ontologies": [] - } - } - ], - "intron_t2c": [ - { - "intron_t2c.txt": { - "type": "file", - "description": "Intron transcript to capture file", - "pattern": "*intron_t2c.{txt}", - "ontologies": [] - } - } - ] - }, - "authors": [ - "@flowuenne" - ], - "maintainers": [ - "@flowuenne" - ] - }, - "pipelines": [ - { - "name": "scrnaseq", - "version": "4.1.0" - } - ] - }, - { - "name": "kat_hist", - "path": "modules/nf-core/kat/hist/meta.yml", - "type": "module", - "meta": { - "name": "kat_hist", - "description": "Creates a histogram of the number of distinct k-mers having a given frequency.", - "deprecated": true, - "keywords": [ - "k-mer", - "histogram", - "count" - ], - "tools": [ - { - "kat": { - "description": "KAT is a suite of tools that analyse jellyfish hashes or sequence files (fasta or fastq) using kmer counts", - "homepage": "https://www.earlham.ac.uk/kat-tools", - "documentation": "https://kat.readthedocs.io/en/latest/index.html", - "tool_dev_url": "https://github.com/TGAC/KAT", - "doi": "10.1093/bioinformatics/btw663", - "licence": [ - "GPL v3" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", - "ontologies": [] - } - } - ] - ], - "output": { - "hist": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.hist": { - "type": "file", - "description": "KAT histogram of k-mer counts", - "pattern": "*.hist", - "ontologies": [] - } - } - ] - ], - "json": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.hist.dist_analysis.json": { - "type": "file", - "description": "KAT histogram summary of distance analysis", - "pattern": "*.hist.dist_analysis.json", - "ontologies": [ - 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] - ], - "jellyfish_hash": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*-hash.jf*": { - "type": "file", - "description": "Jellyfish hash file", - "pattern": "*-hist.jf*", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@mahesh-panchal" - ], - "maintainers": [ - "@mahesh-panchal" - ] - } - }, - { - "name": "khmer_normalizebymedian", - "path": "modules/nf-core/khmer/normalizebymedian/meta.yml", - "type": "module", - "meta": { - "name": "khmer_normalizebymedian", - "description": "Module that calls normalize-by-median.py from khmer. 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"keywords": [ - "quality control", - "genomics", - "filtering", - "reads", - "khmer", - "k-mer" - ], - "tools": [ - { - "khmer": { - "description": "khmer k-mer counting library", - "homepage": "https://github.com/dib-lab/khmer", - "documentation": "https://khmer.readthedocs.io/en/latest/", - "tool_dev_url": "https://github.com/dib-lab/khmer", - "doi": "10.12688/f1000research.6924.1", - "licence": [ - "BSD License" - ], - "identifier": "biotools:khmer" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "seq_file": { - "type": "file", - "description": "fasta/fastq file", - "pattern": "*.{fa,fasta,fas,fq,fastq}", - "ontologies": [ - { - "edam": "http://edamontology.org/data_2044" - }, - { - "edam": "http://edamontology.org/format_1929" - }, - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "output": { - "trimmed": [ - [ - { - "meta": { - "type": "map", - 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"edam": "http://edamontology.org/format_1930" + "db": { + "type": "directory", + "description": "mOTUs database downloaded by `motus downloadDB`\n" + } } - ] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@zachary-foster" - ], - "maintainers": [ - "@zachary-foster" - ] - } - }, - { - "name": "khmer_uniquekmers", - "path": "modules/nf-core/khmer/uniquekmers/meta.yml", - "type": "module", - "meta": { - "name": "khmer_uniquekmers", - "description": "In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more", - "keywords": [ - "khmer", - "k-mer", - "effective genome size" - ], - "tools": [ - { - "khmer": { - "description": "khmer k-mer counting library", - "homepage": "https://github.com/dib-lab/khmer", - "documentation": "https://khmer.readthedocs.io/en/latest/", - "tool_dev_url": "https://github.com/dib-lab/khmer", - "doi": "10.12688/f1000research.6924.1", - "licence": [ - "BSD License" - ], - "identifier": "biotools:khmer" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } + ], + "output": { + "out": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.out": { + "type": "file", + "description": "Results with taxonomic classification of each read", + "pattern": "*.out", + "ontologies": [] + } + } + ] + ], + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Optional intermediate sorted BAM file from BWA", + "pattern": "*.{bam}", + "ontologies": [] + } + } + ] + ], + "mgc": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.mgc": { + "type": "file", + "description": "Optional intermediate mgc read count table file saved with `-M`.", + "pattern": "*.{mgc}", + "ontologies": [] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "Standard error logging file containing summary statistics", + "pattern": "*.log", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@jianhong"], + "maintainers": ["@jianhong"] }, - { - "fasta": { - "type": "file", - "description": "fasta file", - "pattern": "*.{fa,fasta}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - { - "kmer_size": { - "type": "integer", - "description": "k-mer size to use" - } - } - ], - "output": { - "report": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.report.txt": { - "type": "file", - "description": "Text file containing unique-kmers.py execution report", - "pattern": "*.report.txt", - "ontologies": [] - } - } - ] - ], - "kmers": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.kmers.txt": { - "type": "file", - "description": "Text file containing number of kmers", - "pattern": "*.kmers.txt", - "ontologies": [] - } - } + "pipelines": [ + { + "name": "taxprofiler", + "version": "2.0.0" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@JoseEspinosa" - ], - "maintainers": [ - "@JoseEspinosa" - ] - }, - "pipelines": [ - { - "name": "atacseq", - "version": "2.1.2" }, { - "name": "chipseq", - "version": "2.1.0" - } - ] - }, - { - "name": "kleborate", - "path": "modules/nf-core/kleborate/meta.yml", - "type": "module", - "meta": { - "name": "kleborate", - "description": "Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC).", - "keywords": [ - "screen", - "assembly", - "Klebsiella", - "pneumoniae" - ], - "tools": [ - { - "kleborate": { - "description": "Screening Klebsiella genome assemblies for MLST, sub-species, and other Klebsiella related genes of interest", - "homepage": "https://github.com/katholt/Kleborate", - "documentation": "https://github.com/katholt/Kleborate/wiki", - 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} - ] - } - } - ] - }, - "authors": [ - "@abhi18av", - "@rpetit3" - ], - "maintainers": [ - "@abhi18av", - "@rpetit3" - ] - } - }, - { - "name": "kma_index", - "path": "modules/nf-core/kma/index/meta.yml", - "type": "module", - "meta": { - "name": "kma_index", - "description": "This module wraps the index module of the KMA alignment tool.", - "keywords": [ - "alignment", - "kma", - "index", - "database", - "reads" - ], - "tools": [ - { - "kma": { - "description": "Rapid and precise alignment of raw reads against redundant databases with KMA", - "homepage": "https://bitbucket.org/genomicepidemiology/kma/src/master/", - "documentation": "https://bitbucket.org/genomicepidemiology/kma/src/master/", - "tool_dev_url": "https://bitbucket.org/genomicepidemiology/kma/src/master/", - "doi": "10.1186/s12859-018-2336-6", - "licence": [ - "http://www.apache.org/licenses/LICENSE-2.0" - ], - "identifier": "biotools:kma" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. `[ id:'reference' ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "(Multi-)FASTA file of your database sequences.", - "pattern": "*.{fa,fasta}", - "ontologies": [] - } - } - ] - ], - "output": { - "index": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'reference' ]`\n" - } - }, - { - "kmaindex": { - "type": "directory", - "description": "Directory of KMA index files", - "pattern": "*.{comp.b,length.b,name,seq.b}" - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@krannich479" - ], - "maintainers": [ - "@krannich479" - ] - } - }, - { - "name": "kma_kma", - "path": "modules/nf-core/kma/kma/meta.yml", - "type": "module", - "meta": { - "name": "kma_kma", - "description": "Mapping raw reads directly against redundant databases via KMA alignment", - "keywords": [ - "fastq", - "reads", - "alignment", - "kma" - ], - "tools": [ - { - "kma": { - "description": "Rapid and precise alignment of raw reads against redundant databases with KMA", - "homepage": "https://bitbucket.org/genomicepidemiology/kma/src/master/", - "documentation": "https://bitbucket.org/genomicepidemiology/kma/src/master/", - "tool_dev_url": "https://bitbucket.org/genomicepidemiology/kma/src/master/", - "doi": "10.1186/s12859-018-2336-6", - "licence": [ - "Apache-2.0" - ], - "identifier": "biotools:kma" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference index information\ne.g. [ id:'reference' ]\n" - } - }, - { - "index": { - "type": "file", - "description": "kma database file generated via kma_index", - "pattern": "*.{comp.b,length.b,name,seq.b}" - } - } - ], - { - "interleaved": { - "type": "boolean", - "description": "use one interleaved fastq file (true) or two paired fastq files (false)", - "pattern": "true or false" - } - } - ], - "output": { - "res": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.res": { - "type": "file", - "description": "A result overview giving the most common statistics for each mapped template.", - "pattern": "*.{res}" - } - } - ] - ], - "fsa": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.fsa": { - "type": "file", - "description": "The consensus sequences drawn from the alignments.", - "pattern": "*.{fsa}" - } - } - ] - ], - "aln": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.aln": { - "type": "file", - "description": "The consensus alignment of the reads against their template.", - "pattern": "*.{aln}" - } - } - ] - ], - "frag": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.frag.gz": { - "type": "file", - "description": "Mapping information on each mapped read, where the columns are\nread, number of equally well mapping templates, mapping score, start position,\nend position (w.r.t. template), the chosen template.\n", - "pattern": "*.{frag.gz}" - } - } - ] - ], - "matrix": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.mat.gz": { - "type": "file", - "description": "Base counts on each position in each template, (only if -matrix is enabled).", - "pattern": "*.{mat.gz}" - } - } - ] - ], - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.vcf.gz": { - "type": "file", - "description": "Compressed VCF file containing positions different from the template identified during KMA mapping against the reference database", - "pattern": "*.{vcf.gz}" - } - } - ] - ], - "sam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.sam": { - "type": "file", - "description": "SAM alignment file containing detailed mapping information from KMA mapping", - "pattern": "*.{sam}" - } - } - ] - ], - "spa": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.spa": { - "type": "file", - "description": "Text file containing the top scoring references. Note that kma\n(v1.4.15) can only use spare alignment if the kma index was also build with\nthe sparse option.\n", - "pattern": "*.{spa}" - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - } - ] - }, - "authors": [ - "@Krannich479", - "@haidyi" - ], - "maintainers": [ - "@Krannich479", - "@haidyi" - ] - } - }, - { - "name": "kmcp_compute", - "path": "modules/nf-core/kmcp/compute/meta.yml", - "type": "module", - "meta": { - "name": "kmcp_compute", - "description": "Generate k-mers (sketches) from FASTA/Q sequences", - "keywords": [ - "metagenomics", - "classify", - "taxonomic profiling", - "fastq", - "sequences", - "kmers" - ], - "tools": [ - { - "kmcp": { - "description": "Accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping", - "homepage": "https://github.com/shenwei356/kmcp", - "documentation": "https://github.com/shenwei356/kmcp#documents", - "tool_dev_url": "https://github.com/shenwei356/kmcp", - "doi": "10.1093/bioinformatics/btac845", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "sequences": { - "type": "file", - "description": "List of fasta files, or a directory containing FASTA files", - "pattern": "**/*.{fa,fa.gz,fasta,fasta.gz,fna,fna.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ], - "output": { - "outdir": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}": { - "type": "directory", - "description": "Output directory containing all .unik files and a summary file in .txt format. Every .unik file contains the sequence/reference ID,chunk index, number of chunks, and genome size of reference.", - "pattern": "*/" - } - } - ] - ], - "info": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/_info.txt": { - "type": "file", - "description": "Summary file that is generated for later use", - "pattern": "*_info.txt", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2330" - } - ] - } - } - ] - ], - "versions_kmcp": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "kmcp": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "kmcp version 2>&1 | sed 's/^.*kmcp v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "kmcp": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "kmcp version 2>&1 | sed 's/^.*kmcp v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@sofstam" - ], - "maintainers": [ - "@sofstam" - ] - }, - "pipelines": [ - { - "name": "createtaxdb", - "version": "3.0.0" - } - ] - }, - { - "name": "kmcp_index", - "path": "modules/nf-core/kmcp/index/meta.yml", - "type": "module", - "meta": { - "name": "kmcp_index", - "description": "Construct KMCP database from k-mer files", - "keywords": [ - "metagenomics", - "classify", - "taxonomic profiling", - "fastq", - "sequences", - "kmers", - "index" - ], - "tools": [ - { - "kmcp": { - "description": "Accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping", - "homepage": "https://github.com/shenwei356/kmcp", - "documentation": "https://github.com/shenwei356/kmcp#documents", - "tool_dev_url": "https://github.com/shenwei356/kmcp", - "doi": "10.1093/bioinformatics/btac845", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "compute_dir": { - "type": "directory", - "description": "Output directory generated by \"kmcp compute\"", - "pattern": "*/" - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "taxdmp": { - "type": "directory", - "description": "List or directory containing NCBI-like taxdmp files\n(nodes.dmp, names.dmp, and optionally, merged.dmp, delnodes.dmp)\n", - "pattern": "*/" - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "seq2taxidmap": { - "type": "file", - "description": "Kraken2 style sequence to taxid mapping file, with two columns:\nsequence ID and taxid\n(e.g. \"accession1\\t12345\")\n", - "pattern": "*.map" - } - } - ] - ], - "output": { - "kmcp": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}": { - "type": "directory", - "description": "Output directory containing the database from k-mer files.", - "pattern": "*/" - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.log": { - "type": "file", - "description": "A log of kmcp/index output", - "pattern": "*.log", - "ontologies": [] - } - } - ] - ], - "versions_kmcp": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "kmcp": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "kmcp version 2>&1 | sed 's/^.*kmcp v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "kmcp": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "kmcp version 2>&1 | sed 's/^.*kmcp v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@sofstam" - ], - "maintainers": [ - "@sofstam" - ] - }, - "pipelines": [ - { - "name": "createtaxdb", - "version": "3.0.0" - } - ] - }, - { - "name": "kmcp_merge", - "path": "modules/nf-core/kmcp/merge/meta.yml", - "type": "module", - "meta": { - "name": "kmcp_merge", - "description": "Merge search results from multiple databases.", - "keywords": [ - "metagenomics", - "classify", - "taxonomic profiling", - "fastq", - "sequences", - "kmers" - ], - "tools": [ - { - "kmcp": { - "description": "Accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping", - "homepage": "https://github.com/shenwei356/kmcp", - "documentation": "https://github.com/shenwei356/kmcp#documents", - "tool_dev_url": "https://github.com/shenwei356/kmcp", - "doi": "10.1093/bioinformatics/btac845", - "license": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "search_out": { - "type": "file", - "description": "The output file created by kmcp search", - "pattern": "*.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "output": { - "result": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.gz": { - "type": "file", - "description": "Output file in gzipped format", - "pattern": "*.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "versions_kmcp": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "kmcp": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "kmcp version 2>&1 | sed 's/^.*kmcp v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "kmcp": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "kmcp version 2>&1 | sed 's/^.*kmcp v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@sofstam" - ], - "maintainers": [ - "@sofstam" - ] - } - }, - { - "name": "kmcp_profile", - "path": "modules/nf-core/kmcp/profile/meta.yml", - "type": "module", - "meta": { - "name": "kmcp_profile", - "description": "Generate taxonomic profile from search results", - "keywords": [ - "metagenomics", - "classify", - "taxonomic profiling", - "fastq", - "sequences", - "kmers", - "index" - ], - "tools": [ - { - "kmcp": { - "description": "Accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping", - "homepage": "https://github.com/shenwei356/kmcp", - "documentation": "https://bioinf.shenwei.me/kmcp/usage/#profile", - "tool_dev_url": "https://github.com/shenwei356/kmcp", - "doi": "10.1093/bioinformatics/btac845", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "search_results": { - "type": "file", - "description": "Gzipped file output from kmcp search module", - "pattern": "*.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ], - { - "db": { - "type": "directory", - "description": "Database directory containing taxdump files and taxid file" - } - }, - { - "level": { - "type": "string", - "description": "Taxonomic rank to generate profile at (e.g. \"species\", \"strain\", \"assembly\")" - } - } - ], - "output": { - "profile": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.profile": { - "type": "file", - "description": "Tab-delimited format file with 17 columns.", - "pattern": "*.profile", - "ontologies": [] - } - } - ] - ], - "versions_kmcp": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "kmcp": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "kmcp version 2>&1 | sed 's/^.*kmcp v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "kmcp": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "kmcp version 2>&1 | sed 's/^.*kmcp v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@sofstam" - ], - "maintainers": [ - "@sofstam" - ] - }, - "pipelines": [ - { - "name": "taxprofiler", - "version": "2.0.0" - } - ] - }, - { - "name": "kmcp_search", - "path": "modules/nf-core/kmcp/search/meta.yml", - "type": "module", - "meta": { - "name": "kmcp_search", - "description": "Search sequences against database", - "keywords": [ - "metagenomics", - "classify", - "taxonomic profiling", - "fastq", - "sequences", - "kmers" - ], - "tools": [ - { - "kmcp": { - "description": "Accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping", - "homepage": "https://github.com/shenwei356/kmcp", - "documentation": "https://github.com/shenwei356/kmcp#documents", - "tool_dev_url": "https://github.com/shenwei356/kmcp", - "doi": "10.1093/bioinformatics/btac845", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "gzipped fasta or fastq files", - "pattern": "*.{fq.gz,fastq.gz,fa.gz}", - "ontologies": [] - } - } - ], - { - "db": { - "type": "directory", - "description": "Database directory created by \"kmcp index\"", - "pattern": "*" - } - } - ], - "output": { - "result": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.gz": { - "type": "file", - "description": "Output file in tab-delimited format with 15 columns", - "pattern": "*.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "versions_kmcp": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "kmcp": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "kmcp version 2>&1 | sed 's/^.*kmcp v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "kmcp": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "kmcp version 2>&1 | sed 's/^.*kmcp v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@sofstam" - ], - "maintainers": [ - "@sofstam" - ] - }, - "pipelines": [ - { - "name": "taxprofiler", - "version": "2.0.0" - } - ] - }, - { - "name": "kmergenie", - "path": "modules/nf-core/kmergenie/meta.yml", - "type": "module", - "meta": { - "name": "kmergenie", - "description": "KmerGenie estimates the best k-mer length for genome de novo assembly", - "keywords": [ - "k-mer", - "count", - "genome assembly" - ], - "tools": [ - { - "kmergenie": { - "description": "KmerGenie estimates the best k-mer length for genome de novo assembly. Given a set of reads, KmerGenie first computes the k-mer abundance histogram for many values of k. Then, for each value of k, it predicts the number of distinct genomic k-mers in the dataset, and returns the k-mer length which maximizes this number.", - "homepage": "http://kmergenie.bx.psu.edu/", - "documentation": "http://kmergenie.bx.psu.edu/", - "tool_dev_url": "https://github.com/movingpictures83/KMerGenie", - "doi": "10.1093/bioinformatics/btt310", - "licence": [ - "MIT License" - ], - "identifier": "biotools:kmergenie" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "Input reads in FastQ format", - "pattern": "*.{fastq.gz, fastq, fq.gz, fq}", - "ontologies": [] - } - } - ] - ], - "output": { - "html": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_report.html": { - "type": "file", - "description": "html file containing all the plotted histograms obtained from different kmer size", - "pattern": "*_report.html", - "ontologies": [] - } - } - ] - ], - "histo": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.histo": { - "type": "file", - "description": "histogram files (text) obtained from individual kmer sizes", - "pattern": "*.histo", - "ontologies": [] - } - } - ] - ], - "dat": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.dat": { - "type": "file", - "description": "text file containing number of kmer for kmer sizes and recommended coverage cut-off", - "pattern": "*.dat", - "ontologies": [] - } - } - ] - ], - "pdf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.pdf": { - "type": "file", - "description": "histogram plots obtained from individual kmer sizes", - "pattern": "*.pdf", - "ontologies": [] - } - } - ] - ], - "versions_kmergenie": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "kmergenie": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "kmergenie --version |& sed \"1!d ; s/KmerGenie //\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.kmergenie.log": { - "type": "file", - "description": "log file containing the standard output and error of the kmergenie command", - "pattern": "*.kmergenie.log" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "kmergenie": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "kmergenie --version |& sed \"1!d ; s/KmerGenie //\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@LiaOb21" - ], - "maintainers": [ - "@LiaOb21" - ] - } - }, - { - "name": "knotannotsv", - "path": "modules/nf-core/knotannotsv/meta.yml", - "type": "module", - "meta": { - "name": "knotannotsv", - "description": "Simple tool to create a customizable html file (to be displayed on a web browser) from an AnnotSV output", - "keywords": [ - "annotation", - "structural variants", - "annotsv", - "tsv", - "html" - ], - "tools": [ - { - "knotannotsv": { - "description": "Simple tool to create a customizable html file (to be displayed on a web browser) from an AnnotSV output", - "homepage": "https://github.com/mobidic/knotAnnotSV", - "documentation": "https://github.com/mobidic/knotAnnotSV/blob/master/README.knotAnnotSV_latest.pdf", - "tool_dev_url": "https://github.com/mobidic/knotAnnotSV", - "licence": [ - "GPL-3.0" - ] - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "annotsv_tsv": { - "type": "file", - "description": "Annotated TSV produced by AnnotSV", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - }, - { - "knot_out_xl": { - "type": "boolean", - "description": "Specify 'true' to output as XLSM (rather than HTML by default)" - } - } - ] - ], - "output": { - "output_file": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.{html,xlsm}": { - "type": "file", - "description": "HTML (or XLSM if 'knot_out_xl=true') annotated file", - "pattern": "*.{html,xlsm}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2331" - }, - { - "edam": "http://edamontology.org/format_3620" + "name": "msisensor2_msi", + "path": "modules/nf-core/msisensor2/msi/meta.yml", + "type": "module", + "meta": { + "name": "msisensor2_msi", + "description": "msisensor2 detection of MSI regions.", + "keywords": ["msi", "microsatellite", "microsatellite instability", "tumor", "cfDNA"], + "tools": [ + { + "msisensor2": { + "description": "MSIsensor2 is a novel algorithm based machine learning, featuring a large upgrade in the microsatellite instability (MSI) detection for tumor only sequencing data, including Cell-Free DNA (cfDNA), Formalin-Fixed Paraffin-Embedded(FFPE) and other sample types. The original MSIsensor is specially designed for tumor/normal paired sequencing data.", + "homepage": "https://github.com/niu-lab/msisensor2", + "documentation": "https://github.com/niu-lab/msisensor2/blob/master/README.md", + "tool_dev_url": "https://github.com/niu-lab/msisensor2", + "license": ["GPL-3.0"], + "identifier": "" + } } - ] - } - } - ] - ], - "versions_knotannotsv": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "knotannotsv": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "1.1.5": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "knotannotsv": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "1.1.5": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@thomasguignard" - ], - "maintainers": [ - "@thomasguignard" - ] - } - }, - { - "name": "kofamscan", - "path": "modules/nf-core/kofamscan/meta.yml", - "type": "module", - "meta": { - "name": "kofamscan", - "description": "Produces annotation using kofamscan against a Profile database and a KO list", - "keywords": [ - "fasta", - "kegg", - "kofamscan" - ], - "tools": [ - { - "kofamscan": { - "description": "KofamKOALA assigns K numbers to the user's sequence data by HMMER/HMMSEARCH against KOfam", - "homepage": "https://www.genome.jp/tools/kofamkoala/", - "documentation": "https://github.com/takaram/kofam_scan", - "tool_dev_url": "https://github.com/takaram/kofam_scan", - "doi": "10.1093/bioinformatics/btz859", - "licence": [ - "MIT License" - ], - "identifier": "biotools:kofamscan" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input fasta file containing query sequences", - "pattern": "*.{fa,fasta}", - "ontologies": [] - } - } - ], - { - "profiles": { - "type": "directory", - "description": "Directory containing the Profiles database", - "pattern": "*" - } - }, - { - "ko_list": { - "type": "file", - "description": "File containing list of KO entries with their data", - "pattern": "*.{fa,fasta}", - "ontologies": [] - } - } - ], - "output": { - "txt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.txt": { - "type": "file", - "description": "Application-specific text file with hits information", - "pattern": "*.{txt}", - "ontologies": [] - } - } - ] - ], - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "Tab separated file containing with detailed hits", - "pattern": "*.{tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_kofamscan": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "kofamscan": { - "type": "string", - "description": "kofamscan version string" - } - }, - { - "exec_annotation --version 2>&1 | sed 's/exec_annotation //;'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "kofamscan": { - "type": "string", - "description": "kofamscan version string" - } - }, - { - "exec_annotation --version 2>&1 | sed 's/exec_annotation //;'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@toniher" - ], - "maintainers": [ - "@toniher" - ] - } - }, - { - "name": "kraken2_add", - "path": "modules/nf-core/kraken2/add/meta.yml", - "type": "module", - "meta": { - "name": "kraken2_add", - "description": "Adds fasta files to a Kraken2 taxonomic database", - "keywords": [ - "metagenomics", - "db", - "classification", - "build", - "kraken2", - "add" - ], - "tools": [ - { - "kraken2": { - "description": "Kraken2 is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies.", - "homepage": "https://ccb.jhu.edu/software/kraken2/", - "documentation": "https://github.com/DerrickWood/kraken2/wiki/Manual", - "tool_dev_url": "https://github.com/DerrickWood/kraken2", - "doi": "10.1186/s13059-019-1891-0", - "licence": [ - "MIT" - ], - "identifier": "biotools:kraken2" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "tumor_bam": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}", + "ontologies": [] + } + }, + { + "tumor_bam_index": { + "type": "file", + "description": "BAM/CRAM/SAM index file", + "pattern": "*.{bai,crai}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "models": { + "type": "file", + "description": "Folder of MSISensor2 models (available from Github or as a product of msisensor2/scan)", + "pattern": "*/*", + "ontologies": [] + } + } + ] + ], + "output": { + "msi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}": { + "type": "file", + "description": "MSI classifications as a text file", + "ontologies": [] + } + } + ] + ], + "distribution": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}_dis": { + "type": "file", + "description": "Read count distributions of MSI regions", + "ontologies": [] + } + } + ] + ], + "somatic": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}_somatic": { + "type": "file", + "description": "Somatic MSI regions detected.", + "ontologies": [] + } + } + ] + ], + "versions_msisensor2": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "msisensor2": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "msisensor2 2> >(grep Version) | sed 's/Version: v//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "msisensor2": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "msisensor2 2> >(grep Version) | sed 's/Version: v//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@adamrtalbot"], + "maintainers": ["@adamrtalbot"] }, - { - "fasta": { - "type": "file", - "description": "fasta file that will be added to the database", - "pattern": "*.{fa,fasta,fna,ffn}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - { - "taxonomy_names": { - "type": "file", - "description": "used for associating sequences with taxonomy IDs", - "pattern": "*.dmp", - "ontologies": [ - { - "edam": "http://edamontology.org/data_3028" - } - ] - } - }, - { - "taxonomy_nodes": { - "type": "file", - "description": "tree nodes using NCBI taxonomy nomenclature", - "pattern": "*.dmp", - "ontologies": [ - { - "edam": "http://edamontology.org/data_3028" - } - ] - } - }, - { - "accession2taxid": { - "type": "file", - "description": "associates sequence accession IDs to taxonomy IDs", - "pattern": "*.accession2taxid", - "ontologies": [ - { - "edam": "http://edamontology.org/data_3028" - } - ] - } - }, - { - "seqid2taxid": { - "type": "file", - "description": "optional premade 2 column seq2taxid map file. Must be named seq2taxid.map. If not supplied will be generated by kraken2 itself during upstream build step.", - "pattern": "seqid2taxid.map", - "ontologies": [ + "pipelines": [ { - "edam": "http://edamontology.org/data_3028" + "name": "sarek", + "version": "3.8.1" } - ] - } - } - ], - "output": { - "library_added_files": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n", - "pattern": "*/" - } - }, - { - "${prefix}/library/added/*": { - "type": "file", - "description": "Files present in the /library/added/ directory, including FASTA files, masked FASTAs, and prelim_map files.", - "pattern": "*", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ], - "seqid2taxid_map": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n", - "pattern": "*/" - } - }, - { - "${prefix}/seqid2taxid.map": { - "type": "file", - "description": "File mapping sequence IDs to taxonomy IDs, either generated or premade.", - "pattern": "seqid2taxid.map", - "ontologies": [ - { - "edam": "http://edamontology.org/data_3028" - } - ] - } - } - ] - ], - "taxonomy_files": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n", - "pattern": "*/" - } - }, - { - "${prefix}/taxonomy/*": { - "type": "file", - "description": "Files present in the /taxonomy/ directory, including nodes.dmp, names.dmp, and .accession2taxid files.", - "pattern": "*", - "ontologies": [ - { - "edam": "http://edamontology.org/data_3028" - } - ] - } - } - ] - ], - "versions_kraken2": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "kraken2": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "kraken2 --version 2>&1 | head -1 | sed \"s/^.*Kraken version //; s/ .*//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "kraken2": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "kraken2 --version 2>&1 | head -1 | sed \"s/^.*Kraken version //; s/ .*//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@alxndrdiaz" - ], - "maintainers": [ - "@alxndrdiaz", - "@jfy133" - ] - }, - "pipelines": [ - { - "name": "createtaxdb", - "version": "3.0.0" - } - ] - }, - { - "name": "kraken2_build", - "path": "modules/nf-core/kraken2/build/meta.yml", - "type": "module", - "meta": { - "name": "kraken2_build", - "description": "Builds Kraken2 database", - "keywords": [ - "metagenomics", - "db", - "classification", - "build", - "kraken2" - ], - "tools": [ - { - "kraken2": { - "description": "Kraken2 is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies.", - "homepage": "https://ccb.jhu.edu/software/kraken2/", - "documentation": "https://github.com/DerrickWood/kraken2/wiki/Manual", - "tool_dev_url": "https://github.com/DerrickWood/kraken2", - "doi": "10.1186/s13059-019-1891-0", - "licence": [ - "MIT" - ], - "args_id": "$args", - "identifier": "biotools:kraken2" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "library_added_files": { - "type": "file", - "description": "Files present in the /library/added/ directory, including FASTA files, masked FASTAs, and prelim_map files.", - "pattern": "*", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "seqid2taxid_map": { - "type": "file", - "description": "File mapping sequence IDs to taxonomy IDs, either generated or premade.", - "pattern": "seqid2taxid.map", - "ontologies": [ - { - "edam": "http://edamontology.org/data_3028" - } - ] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "taxonomy_files": { - "type": "file", - "description": "Files present in the /taxonomy/ directory, including nodes.dmp, names.dmp, and .accession2taxid files.", - "pattern": "*", - "ontologies": [ - { - "edam": "http://edamontology.org/data_3028" - } - ] - } - } - ], - { - "cleaning": { - "type": "boolean", - "description": "activate or deactivate (true or false) cleaning of intermediate files" - } - } - ], - "output": { - "db": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "kraken2-database": { - "type": "directory", - "description": "Directory contains the database that can be used to perform taxonomic classification\n\nIMPORTANT: this output directory will be hardcoded as 'kraken2-database/' inside the module\nto prevent issues of containers following symlinks in symlinks.\n\nTo give a user the option to provide custom name for the database directory within a pipeline, you should\ncustomise this name using during pipeline output publication via the pipeline's publishDir or workflow output customisation options.\n", - "pattern": "kraken2-database/", - "ontologies": [ - { - "edam": "http://edamontology.org/data_1049" - } - ] - } - } - ] - ], - "db_separated": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "kraken2-database/*k2d": { - "type": "file", - "description": "Kraken2 k2d binary database files", - "pattern": "*.k2d", - "ontologies": [] - } - }, - { - "kraken2-database/*map": { - "type": "file", - "description": "Kraken2 k2d binary database taxonomy to sequencing mapping file", - "pattern": "*.map", - "ontologies": [] - } - }, - { - "kraken2-database/library/added/*": { - "type": "file", - "description": "Kraken2 masked FASTA files used to build the database", - "pattern": "*.fasta", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - }, - { - "kraken2-database/taxonomy/*": { - "type": "file", - "description": "Kraken2 nodes.dmp, names.dmp, and .accession2taxid taxonomy files", - "pattern": "*.{dmp,accession2taxid}", - "ontologies": [ - { - "edam": "http://edamontology.org/data_3028" - } - ] - } - } - ] - ], - "versions_kraken2": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "kraken2": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "kraken2 --version 2>&1 | head -1 | sed \"s/^.*Kraken version //; s/ .*//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "unmapped": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "kraken2-database/unmapped*.txt": { - "type": "file", - "description": "List of unmapped sequence files, i.e. accessions that did not map to any taxonomy ID\nand were excluded\n", - "pattern": "unmapped*.txt", - "ontologies": [ - { - "edam": "http://edamontology.org/data_2526" - } - ] - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "kraken2": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "kraken2 --version 2>&1 | head -1 | sed \"s/^.*Kraken version //; s/ .*//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@alxndrdiaz" - ], - "maintainers": [ - "@alxndrdiaz", - "@jfy133" - ] - }, - "pipelines": [ - { - "name": "createtaxdb", - "version": "3.0.0" - } - ] - }, - { - "name": "kraken2_buildstandard", - "path": "modules/nf-core/kraken2/buildstandard/meta.yml", - "type": "module", - "meta": { - "name": "kraken2_buildstandard", - "description": "Downloads and builds Kraken2 standard database", - "keywords": [ - "metagenomics", - "db", - "classification", - "build", - "kraken2", - "standard", - "download" - ], - "tools": [ - { - "kraken2": { - "description": "Kraken2 is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies.", - "homepage": "https://ccb.jhu.edu/software/kraken2/", - "documentation": "https://github.com/DerrickWood/kraken2/wiki/Manual", - "tool_dev_url": "https://github.com/DerrickWood/kraken2", - "doi": "10.1186/s13059-019-1891-0", - "licence": [ - "MIT" - ], - "args_id": "$args", - "identifier": "biotools:kraken2" - } - } - ], - "input": [ - { - "cleaning": { - "type": "boolean", - "description": "activate or deactivate (true or false) cleaning of intermediate files" - } - } - ], - "output": { - "db": [ - { - "${prefix}": { - "type": "directory", - "description": "Directory containing the Kraken2 'standard' database that can be used to perform taxonomic classification", - "pattern": "*/", - "ontologies": [ - { - "edam": "http://edamontology.org/data_1049" - } - ] - } - } - ], - "versions_kraken2": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "kraken2": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "kraken2 --version 2>&1 | head -1 | sed \"s/^.*Kraken version //; s/ .*//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "kraken2": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "kraken2 --version 2>&1 | head -1 | sed \"s/^.*Kraken version //; s/ .*//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@egreenberg7" - ], - "maintainers": [ - "@egreenberg7" - ] - } - }, - { - "name": "kraken2_kraken2", - "path": "modules/nf-core/kraken2/kraken2/meta.yml", - "type": "module", - "meta": { - "name": "kraken2_kraken2", - "description": "Classifies metagenomic sequence data", - "keywords": [ - "classify", - "metagenomics", - "fastq", - "db" - ], - "tools": [ - { - "kraken2": { - "description": "Kraken2 is a taxonomic sequence classifier that assigns taxonomic labels to sequence reads\n", - "homepage": "https://ccb.jhu.edu/software/kraken2/", - "documentation": "https://github.com/DerrickWood/kraken2/wiki/Manual", - "doi": "10.1186/s13059-019-1891-0", - "licence": [ - "MIT" - ], - "identifier": "biotools:kraken2" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", - "ontologies": [] - } - } - ], - { - "db": { - "type": "directory", - "description": "Kraken2 database" - } - }, - { - "save_output_fastqs": { - "type": "string", - "description": "If true, optional commands are added to save classified and unclassified reads\nas fastq files\n" - } - }, - { - "save_reads_assignment": { - "type": "string", - "description": "If true, an optional command is added to save a file reporting the taxonomic\nclassification of each input read\n" - } - } - ], - "output": { - "classified_reads_fastq": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.classified{.,_}*": { - "type": "file", - "description": "Reads classified as belonging to any of the taxa\non the Kraken2 database.\n", - "pattern": "*{fastq.gz}", - "ontologies": [] - } - } - ] - ], - "unclassified_reads_fastq": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.unclassified{.,_}*": { - "type": "file", - "description": "Reads not classified to any of the taxa\non the Kraken2 database.\n", - "pattern": "*{fastq.gz}", - "ontologies": [] - } - } - ] - ], - "classified_reads_assignment": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*classifiedreads.txt": { - "type": "file", - "description": "Kraken2 output file indicating the taxonomic assignment of\neach input read\n", - "ontologies": [] - } - } - ] - ], - "report": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*report.txt": { - "type": "file", - "description": "Kraken2 report containing stats about classified\nand not classified reads.\n", - "pattern": "*.{report.txt}", - "ontologies": [] - } - } - ] - ], - "versions_kraken2": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "kraken2": { - "type": "string", - "description": "The tool name" - } - }, - { - "kraken2 --version 2>&1 | head -1 | sed \"s/^.*Kraken version //; s/ .*//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } ] - ], - "versions_pigz": [ - [ - { - "${task.process}": { - "type": "string", - 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- ] - }, - "pipelines": [ { - "name": "taxprofiler", - "version": "2.0.0" + "name": "msisensorpro_pro", + "path": "modules/nf-core/msisensorpro/pro/meta.yml", + "type": "module", + "meta": { + "name": "msisensorpro_pro", + "description": "MSIsensor-pro/pro is a tool used to evaluate MSI using single (tumor) sample sequencing data", + "keywords": ["msisensor-pro", "pro", "micro-satellite"], + "tools": [ + { + "msisensorpro": { + "description": "Microsatellite Instability (MSI) detection using high-throughput sequencing data.", + "homepage": "https://github.com/xjtu-omics/msisensor-pro", + "documentation": "https://github.com/xjtu-omics/msisensor-pro/wiki", + "tool_dev_url": "https://github.com/xjtu-omics/msisensor-pro", + "doi": "10.1016/j.gpb.2020.02.001", + "licence": ["Custom Licence"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "input": { + "type": "file", + "description": "sorted BAM/CRAM file", + "pattern": "*.{bam,cram}", + "ontologies": [] + } + }, + { + "index": { + "type": "file", + "description": "index file for input", + "pattern": "*.{bai,crai}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "list": { + "type": "file", + "description": "micro-satellite list", + "pattern": "*.{list}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "reference genome used to create micro-satellite list", + "pattern": "*.{fasta}", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "fai": { + "type": "file", + "description": "index file for reference fasta", + "pattern": "*.{fai}", + "ontologies": [] + } + } + ] + ], + "output": { + "summary_msi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}": { + "type": "file", + "description": "txt file containing summary of results", + "ontologies": [] + } + } + ] + ], + "all_msi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}_all": { + "type": "file", + "description": "txt file containing all results", + "ontologies": [] + } + } + ] + ], + "dis_msi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}_dis": { + "type": "file", + "description": "txt file containing the allele length distribution", + "ontologies": [] + } + } + ] + ], + "unstable_msi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}_unstable": { + "type": "file", + "description": "txt file containing unstable micro-satellite sites", + "ontologies": [] + } + } + ] + ], + "versions_msisensorpro": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "msisensor-pro": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "msisensor-pro --version 2>&1 | sed -nE 's/Version:\\s*//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "msisensor-pro": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "msisensor-pro --version 2>&1 | sed -nE 's/Version:\\s*//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@Tuur-ds"], + "maintainers": ["@Tuur-ds"] + } }, { - "name": "viralmetagenome", - "version": "1.1.1" - } - ] - }, - { - "name": "krakenuniq_build", - "path": "modules/nf-core/krakenuniq/build/meta.yml", - "type": "module", - "meta": { - "name": "krakenuniq_build", - "description": "Download and build (custom) KrakenUniq databases", - "keywords": [ - "metagenomics", - "krakenuniq", - "database", - "build", - "ncbi" - ], - "tools": [ - { - "krakenuniq": { - "description": "Metagenomics classifier with unique k-mer counting for more specific results", - "homepage": "https://github.com/fbreitwieser/krakenuniq", - "documentation": "https://github.com/fbreitwieser/krakenuniq", - "tool_dev_url": "https://github.com/fbreitwieser/krakenuniq", - "doi": "10.1186/s13059-018-1568-0", - "licence": [ - "MIT" - ], - "identifier": "biotools:KrakenUniq" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "custom_library_dir": { - "type": "file", - "description": "List of custom fasta files for adding to database build", - "pattern": "*" - } - }, - { - "custom_taxonomy_dir": { - "type": "file", - "description": "List of NCBI style taxdmp files (at a minimum: nodes.dmp, names.dmp)\n", - "pattern": "*" - } - }, - { - "custom_seqid2taxid": { - "type": "file", - "description": "Custom seqid2taxid file of mapping sequence accessions to taxid", - "ontologies": [] - } - } - ], - { - "keep_intermediate": { - "type": "boolean", - "description": "Keep intermediate files that are not used by the database itself", - "pattern": "true|false" - } - } - ], - "output": { - "db": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/": { - "type": "directory", - "description": "Directory containing KrakenUniq database", - "pattern": "*/" - } - } - ] - ], - "versions_krakenuniq": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "krakenuniq": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "krakenuniq --version | sed '1!d;s/KrakenUniq version //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "krakenuniq": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "krakenuniq --version | sed '1!d;s/KrakenUniq version //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@jfy133" - ], - "maintainers": [ - "@jfy133" - ] - }, - "pipelines": [ - { - "name": "createtaxdb", - "version": "3.0.0" - } - ] - }, - { - "name": "krakenuniq_download", - "path": "modules/nf-core/krakenuniq/download/meta.yml", - "type": "module", - "meta": { - "name": "krakenuniq_download", - "description": "Download KrakenUniq databases and related fles", - "keywords": [ - "metagenomics", - "krakenuniq", - "database", - "download", - "ncbi" - ], - "tools": [ - { - "krakenuniq": { - "description": "Metagenomics classifier with unique k-mer counting for more specific results", - "homepage": "https://github.com/fbreitwieser/krakenuniq", - "documentation": "https://github.com/fbreitwieser/krakenuniq", - "tool_dev_url": "https://github.com/fbreitwieser/krakenuniq", - "doi": "10.1186/s13059-018-1568-0", - "licence": [ - "MIT" - ], - "identifier": "biotools:KrakenUniq" - } - } - ], - "input": [ - { - "pattern": { - "type": "string", - "description": "Pattern indicating what type of NCBI data to download. See KrakenUniq documnation for possibilities." - } - } - ], - "output": { - "output": [ - { - "${pattern}/": { - "type": "directory", - "description": "Directory containing downloaded data with directory naming being the user provided pattern." - } - } - ], - "versions_krakenuniq": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "krakenuniq": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "krakenuniq --version | sed '1!d;s/KrakenUniq version //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "krakenuniq": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "krakenuniq --version | sed '1!d;s/KrakenUniq version //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@jfy133" - ], - "maintainers": [ - "@jfy133" - ] - } - }, - { - "name": "krakenuniq_preloadedkrakenuniq", - "path": "modules/nf-core/krakenuniq/preloadedkrakenuniq/meta.yml", - "type": "module", - "meta": { - "name": "krakenuniq_preloadedkrakenuniq", - "description": "Classifies metagenomic sequence data using unique k-mer counts", - "keywords": [ - "classify", - "metagenomics", - "kmers", - "fastq", - "db" - ], - "tools": [ - { - "krakenuniq": { - "description": "Metagenomics classifier with unique k-mer counting for more specific results", - "homepage": "https://github.com/fbreitwieser/krakenuniq", - "documentation": "https://github.com/fbreitwieser/krakenuniq", - "doi": "10.1186/s13059-018-1568-0", - "licence": [ - "MIT" - ], - "identifier": "biotools:KrakenUniq" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "sequences": { - "type": "file", - "description": "List of input files containing sequences. All of them must be either in FASTA or FASTQ format.", - "ontologies": [] - } + "name": "msisensorpro_scan", + "path": "modules/nf-core/msisensorpro/scan/meta.yml", + "type": "module", + "meta": { + "name": "msisensorpro_scan", + "description": "MSIsensor-pro evaluates Microsatellite Instability (MSI) for cancer patients with next generation sequencing data. It accepts the whole genome sequencing, whole exome sequencing and target region (panel) sequencing data as input", + "keywords": ["micro-satellite-scan", "msisensor-pro", "scan"], + "tools": [ + { + "msisensorpro": { + "description": "Microsatellite Instability (MSI) detection using high-throughput sequencing data.", + "homepage": "https://github.com/xjtu-omics/msisensor-pro", + "documentation": "https://github.com/xjtu-omics/msisensor-pro/wiki", + "tool_dev_url": "https://github.com/xjtu-omics/msisensor-pro", + "doi": "10.1016/j.gpb.2020.02.001", + "licence": ["Custom Licence"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference genome", + "pattern": "*.{fasta}", + "ontologies": [] + } + } + ] + ], + "output": { + "list": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.list": { + "type": "file", + "description": "File containing microsatellite list", + "pattern": "*.{list}", + "ontologies": [] + } + } + ] + ], + "versions_msisensorpro": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "msisensor-pro": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "msisensor-pro --version 2>&1 | sed -nE 's/Version:\\s*//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "msisensor-pro": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "msisensor-pro --version 2>&1 | sed -nE 's/Version:\\s*//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@FriederikeHanssen"], + "maintainers": ["@FriederikeHanssen"] }, - { - "prefixes": { - "type": "string", - "description": "List of sample identifiers or filename prefixes. Must correspond in order and length to the 'sequences', or to the number of sequencing pairs.\n" - } - } - ], - { - "sequence_type": { - "type": "string", - "description": "Format of all given sequencing files as literal string, either 'fasta' or 'fastq'.", - "pattern": "{fasta,fastq}" - } - }, - { - "db": { - "type": "directory", - "description": "KrakenUniq database" - } - }, - { - "save_output_reads": { - "type": "boolean", - "description": "Optionally, commands are added to save classified and unclassified reads\nas FASTQ or FASTA files depending on the input format. When the input\nis paired-end, the single output FASTQ contains merged reads.\n" - } - }, - { - "report_file": { - "type": "boolean", - "description": "Whether to generate a report of relative abundances." - } - }, - { - "save_output": { - "type": "boolean", - "description": "Whether to save a file reporting the taxonomic classification of each input read." - } - } - ], - "output": { - "classified_reads": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.classified.${sequence_type}.gz": { - "type": "file", - "description": "Reads classified as belonging to any of the taxa\nin the KrakenUniq reference database.\n", - "pattern": "*.classified.{fastq,fasta}.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "unclassified_reads": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.unclassified.${sequence_type}.gz": { - "type": "file", - "description": "Reads not classified to any of the taxa\nin the KrakenUniq reference database.\n", - "pattern": "*.unclassified.{fastq,fasta}.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "classified_assignment": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.krakenuniq.classified.txt": { - "type": "file", - "description": "KrakenUniq output file indicating the taxonomic assignment of\neach input read ## DOUBLE CHECK!!\n", - "pattern": "*.krakenuniq.classified.txt", - "ontologies": [] - } - } - ] - ], - "report": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.krakenuniq.report.txt": { - "type": "file", - "description": "KrakenUniq report containing statistics about classified\nand unclassified reads.\n", - "pattern": "*.krakenuniq.report.txt", - "ontologies": [] - } - } - ] - ], - "versions_krakenuniq": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "krakenuniq": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "krakenuniq --version | sed '1!d;s/KrakenUniq version //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "krakenuniq": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "krakenuniq --version | sed '1!d;s/KrakenUniq version //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@mjamy", - "@Midnighter" - ], - "maintainers": [ - "@mjamy", - "@Midnighter" - ] - }, - "pipelines": [ - { - "name": "taxprofiler", - "version": "2.0.0" - } - ] - }, - { - "name": "krona_kronadb", - "path": "modules/nf-core/krona/kronadb/meta.yml", - "type": "module", - "meta": { - "name": "krona_kronadb", - "description": "KronaTools Update Taxonomy downloads a taxonomy database", - "deprecated": true, - "keywords": [ - "database", - "taxonomy", - "krona" - ], - "tools": [ - { - "krona": { - "description": "Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files.", - "homepage": "https://github.com/marbl/Krona/wiki/KronaTools", - "documentation": "https://github.com/marbl/Krona/wiki/Installing", - "doi": "10.1186/1471-2105-12-385", - "identifier": "biotools:krona" - } - } - ], - "output": { - "db": [ - { - "taxonomy/taxonomy.tab": { - "type": "file", - "description": "A TAB separated file that contains a taxonomy database.", - "pattern": "*.{tab}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@mjakobs" - ], - "maintainers": [ - "@mjakobs" - ] - } - }, - { - "name": "krona_ktimportkrona", - "path": "modules/nf-core/krona/ktimportkrona/meta.yml", - "type": "module", - "meta": { - "name": "krona_ktimportkrona", - "description": "Collect multiple krona reports into a single html file", - "keywords": [ - "plot", - "taxonomy", - "interactive", - "html", - "visualisation", - "krona chart" - ], - "tools": [ - { - "krona": { - "description": "Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files.", - "homepage": "https://github.com/marbl/Krona/wiki/KronaTools", - "documentation": "http://manpages.ubuntu.com/manpages/impish/man1/ktImportTaxonomy.1.html", - "doi": "10.1186/1471-2105-12-385", - "identifier": "biotools:krona" - } - } - ], - "input": [ - { - "html": { - "type": "file", - "description": "One or multiple html files each containing a krona single plot", - "pattern": "*.html", - "ontologies": [] - } - } - ], - "output": { - "html": [ - { - "${prefix}.html": { - "type": "file", - "description": "HTML file containing all input HTML Krona plots with a selection bar to choose which one to look at", - "pattern": "*.krona.html" - } - } - ], - "versions_krona": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "krona": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "ktImportKrona | grep -Po '(?<=KronaTools )[0-9.]+'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "krona": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "ktImportKrona | grep -Po '(?<=KronaTools )[0-9.]+'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "references", + "version": "0.1" + }, + { + "name": "sarek", + "version": "3.8.1" + } ] - ] - }, - "authors": [ - "@paulwolk" - ], - "maintainers": [ - "@paulwolk" - ] - } - }, - { - "name": "krona_ktimporttaxonomy", - "path": "modules/nf-core/krona/ktimporttaxonomy/meta.yml", - "type": "module", - "meta": { - "name": "krona_ktimporttaxonomy", - "description": "KronaTools Import Taxonomy imports taxonomy classifications and produces an interactive Krona plot.", - "keywords": [ - "plot", - "taxonomy", - "interactive", - "html", - "visualisation", - "krona chart" - ], - "tools": [ - { - "krona": { - "description": "Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files.", - "homepage": "https://github.com/marbl/Krona/wiki/KronaTools", - "documentation": "http://manpages.ubuntu.com/manpages/impish/man1/ktImportTaxonomy.1.html", - "doi": "10.1186/1471-2105-12-385", - "identifier": "biotools:krona" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } + }, + { + "name": "mtmalign_align", + "path": "modules/nf-core/mtmalign/align/meta.yml", + "type": "module", + "meta": { + "name": "mtmalign_align", + "description": "Aligns protein structures using mTM-align", + "keywords": ["alignment", "MSA", "genomics", "structure"], + "tools": [ + { + "mTM-align": { + "description": "Algorithm for structural multiple sequence alignments", + "homepage": "http://yanglab.nankai.edu.cn/mTM-align/", + "documentation": "http://yanglab.nankai.edu.cn/mTM-align/help/", + "tool_dev_url": "http://yanglab.nankai.edu.cn/mTM-align/", + "doi": "10.1093/bioinformatics/btx828", + "licence": ["None"], + "identifier": "" + } + }, + { + "pigz": { + "description": "Parallel implementation of the gzip algorithm.", + "homepage": "https://zlib.net/pigz/", + "documentation": "https://zlib.net/pigz/pigz.pdf", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" + } + }, + { + "pdbs": { + "type": "file", + "description": "Input protein structures in PDB format. Files may be gzipped or uncompressed. They should contain exactly one chain!", + "pattern": "*.{pdb}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1476" + }, + { + "edam": "http://edamontology.org/format_1477" + } + ] + } + } + ], + { + "compress": { + "type": "boolean", + "description": "Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded." + } + } + ], + "output": { + "alignment": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" + } + }, + { + "${prefix}.aln${compress ? '.gz' : ''}": { + "type": "file", + "description": "Alignment in FASTA format. May be gzipped or uncompressed.", + "pattern": "*.aln{.gz,}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2554" + }, + { + "edam": "http://edamontology.org/format_1921" + }, + { + "edam": "http://edamontology.org/format_1984" + } + ] + } + } + ] + ], + "structure": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" + } + }, + { + "${prefix}.pdb${compress ? '.gz' : ''}": { + "type": "file", + "description": "Overlaid structures in PDB format. May be gzipped or uncompressed.", + "pattern": "${prefix}.pdb{.gz,}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1476" + } + ] + } + } + ] + ], + "versions_mtmalign": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "mtm-align": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "mtm-align -h | sed -n \"s/.*Version \\([0-9]*\\).*/\\1/p\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_pigz": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "pigz": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pigz --version 2>&1 | sed \"s/^.*pigz[[:space:]]*//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "mtm-align": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "mtm-align -h | sed -n \"s/.*Version \\([0-9]*\\).*/\\1/p\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "pigz": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pigz --version 2>&1 | sed \"s/^.*pigz[[:space:]]*//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@lrauschning"], + "maintainers": ["@lrauschning"] }, - { - "report": { - "type": "file", - "description": "A tab-delimited file with taxonomy IDs and (optionally) query IDs, magnitudes, and scores. Query IDs are taken from column 1, taxonomy IDs from column 2, and scores from column 3. Lines beginning with # will be ignored.", - "pattern": "*.{tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - { - "taxonomy": { - "type": "file", - "description": "Path to a Krona taxonomy .tab file normally downloaded and generated by\nkrona/ktUpdateTaxonomy. Custom taxonomy files can have any name, but\nmust end in `.tab`.\n", - "pattern": "*tab", - "ontologies": [] - } - } - ], - "output": { - "html": [ - [ - { - "meta": { - "type": "file", - "description": "A html file containing an interactive krona plot.", - "pattern": "*.{html}", - "ontologies": [] - } - }, - { - "*.html": { - "type": "file", - "description": "A html file containing an interactive krona plot.", - "pattern": "*.{html}", - "ontologies": [] - } - } - ] - ], - "versions_krona": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "krona": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "ktImportTaxonomy | grep -Po '(?<=KronaTools )[0-9.]+'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "krona": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "ktImportTaxonomy | grep -Po '(?<=KronaTools )[0-9.]+'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "multiplesequencealign", + "version": "1.1.1" + } ] - ] }, - "authors": [ - "@mjakobs" - ], - "maintainers": [ - "@mjakobs" - ] - }, - "pipelines": [ { - "name": "hgtseq", - "version": "1.1.0" + "name": "mtnucratio", + "path": "modules/nf-core/mtnucratio/meta.yml", + "type": "module", + "meta": { + "name": "mtnucratio", + "description": "A small Java tool to calculate ratios between MT and nuclear sequencing reads in a given BAM file.", + "keywords": [ + "mtnucratio", + "ratio", + "reads", + "bam", + "mitochondrial to nuclear ratio", + "mitochondria", + "statistics" + ], + "tools": [ + { + "mtnucratio": { + "description": "A small tool to determine MT to Nuclear ratios for NGS data.", + "homepage": "https://github.com/apeltzer/MTNucRatioCalculator", + "documentation": "https://github.com/apeltzer/MTNucRatioCalculator", + "tool_dev_url": "https://github.com/apeltzer/MTNucRatioCalculator", + "doi": "10.1186/s13059-016-0918-z", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "(coordinate) sorted BAM/SAM file", + "pattern": "*.{bam,sam}", + "ontologies": [] + } + } + ], + { + "mt_id": { + "type": "string", + "description": "Identifier of the contig/chromosome of interest (e.g. chromosome, contig) as in the aligned against reference FASTA file, e.g. mt or chrMT for mitochondria" + } + } + ], + "output": { + "mtnucratio": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.mtnucratio": { + "type": "file", + "description": "Text file containing metrics (mtreads, mt_cov_avg, nucreads, nuc_cov_avg, mt_nuc_ratio)", + "pattern": "*.mtnucratio", + "ontologies": [] + } + } + ] + ], + "json": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.json": { + "type": "file", + "description": "JSON file, containing metadata map with sample name, tool name and version, and metrics as in txt file", + "pattern": "*.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@louperelo"], + "maintainers": ["@louperelo"] + } }, { - "name": "taxprofiler", - "version": "2.0.0" - } - ] - }, - { - "name": "krona_ktimporttext", - "path": "modules/nf-core/krona/ktimporttext/meta.yml", - "type": "module", - "meta": { - "name": "krona_ktimporttext", - "description": "Creates a Krona chart from text files listing quantities and lineages.", - "keywords": [ - "plot", - "taxonomy", - "interactive", - "html", - "visualisation", - "krona chart", - "metagenomics" - ], - "tools": [ - { - "krona": { - "description": "Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files.", - "homepage": "https://github.com/marbl/Krona/wiki/KronaTools", - "documentation": "http://manpages.ubuntu.com/manpages/impish/man1/ktImportTaxonomy.1.html", - "tool_dev_url": "https://github.com/marbl/Krona", - "doi": "10.1186/1471-2105-12-385", - "licence": [ - "https://raw.githubusercontent.com/marbl/Krona/master/KronaTools/LICENSE.txt" - ], - "identifier": "biotools:krona" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "report": { - "type": "file", - "description": "Tab-delimited text file. Each line should be a number followed by a list of wedges to contribute to (starting from the highest level). If no wedges are listed (and just a quantity is given), it will contribute to the top level. If the same lineage is listed more than once, the values will be added. Quantities can be omitted if -q is specified. Lines beginning with '#' will be ignored.", - "pattern": "*.{txt}", - "ontologies": [] - } + "name": "mudskipper_bulk", + "path": "modules/nf-core/mudskipper/bulk/meta.yml", + "type": "module", + "meta": { + "name": "mudskipper_bulk", + "description": "Convert genomic BAM/SAM files to transcriptomic BAM/RAD files.", + "keywords": ["bam", "transcriptome", "transcriptomic", "mudskipper", "sam", "rad"], + "tools": [ + { + "mudskipper": { + "description": "mudskipper is a tool for converting genomic BAM/SAM files to transcriptomic BAM/RAD files.", + "homepage": "https://github.com/OceanGenomics/mudskipper", + "documentation": "https://github.com/OceanGenomics/mudskipper", + "tool_dev_url": "https://github.com/OceanGenomics/mudskipper", + "licence": ["BSD 3-clause"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "bam": { + "type": "file", + "description": "Name-Sorted BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}", + "ontologies": [] + } + } + ], + { + "index": { + "type": "directory", + "description": "Annotation index created by mudskipper/index" + } + }, + { + "gtf": { + "type": "file", + "description": "Annotation file", + "pattern": "*.{gtf,gff,gff3}", + "ontologies": [] + } + }, + { + "rad": { + "type": "string", + "description": "File type" + } + } + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "${prefix}.bam": { + "type": "file", + "description": "Sorted BAM file", + "pattern": "*.bam", + "ontologies": [] + } + } + ] + ], + "rad": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "${prefix}.rad": { + "type": "file", + "description": "RAD file", + "pattern": "*.rad", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@anoronh4"] } - ] - ], - "output": { - "html": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.html": { - "type": "file", - "description": "A html file containing an interactive krona plot.", - "pattern": "*.{html}", - "ontologies": [] - } - } - ] - ], - "versions_krona": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "krona": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "ktImportText | grep -Po '(?<=KronaTools )[0-9.]+'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "krona": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "ktImportText | grep -Po '(?<=KronaTools )[0-9.]+'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] }, - "authors": [ - "@jianhong" - ], - "maintainers": [ - "@jianhong" - ] - }, - "pipelines": [ { - "name": "taxprofiler", - "version": "2.0.0" + "name": "mudskipper_index", + "path": "modules/nf-core/mudskipper/index/meta.yml", + "type": "module", + "meta": { + "name": "mudskipper_index", + "description": "Build and store a gtf index, which is useful for converting genomic BAM/SAM files to transcriptomic BAM/SAM files.", + "keywords": ["bam", "transcriptome", "transcriptomic", "index", "mudskipper", "sam"], + "tools": [ + { + "mudskipper": { + "description": "mudskipper is a tool for converting genomic BAM/SAM files to transcriptomic BAM/RAD files.", + "homepage": "https://github.com/OceanGenomics/mudskipper", + "documentation": "https://github.com/OceanGenomics/mudskipper", + "tool_dev_url": "https://github.com/OceanGenomics/mudskipper", + "licence": ["BSD 3-clause"], + "identifier": "" + } + } + ], + "input": [ + { + "gtf": { + "type": "file", + "description": "Transcript annotation file.", + "pattern": "*.{gtf,gff,gff3}", + "ontologies": [] + } + } + ], + "output": { + "index": [ + { + "index/": { + "type": "directory", + "description": "Mudskipper index for running mudskipper conversion tools", + "pattern": "*/" + } + } + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@anoronh4"] + } }, { - "name": "viralmetagenome", - "version": "1.1.1" - } - ] - }, - { - "name": "krona_ktupdatetaxonomy", - "path": "modules/nf-core/krona/ktupdatetaxonomy/meta.yml", - "type": "module", - "meta": { - "name": "krona_ktupdatetaxonomy", - "description": "KronaTools Update Taxonomy downloads a taxonomy database", - "keywords": [ - "database", - "taxonomy", - "krona", - "visualisation" - ], - "tools": [ - { - "krona": { - "description": "Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files.", - "homepage": "https://github.com/marbl/Krona/wiki/KronaTools", - "documentation": "https://github.com/marbl/Krona/wiki/Installing", - "doi": "10.1186/1471-2105-12-385", - "identifier": "biotools:krona" - } - } - ], - "output": { - "db": [ - { - "taxonomy/taxonomy.tab": { - "type": "file", - "description": "A TAB separated file that contains a taxonomy database.", - "pattern": "*.{tab}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - "versions_krona": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "krona": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "ktImportTaxonomy | grep -Po '(?<=KronaTools )[0-9.]+'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "krona": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "ktImportTaxonomy | grep -Po '(?<=KronaTools )[0-9.]+'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@mjakobs" - ], - "maintainers": [ - "@mjakobs" - ] - }, - "pipelines": [ - { - "name": "hgtseq", - "version": "1.1.0" - } - ] - }, - { - "name": "last_dotplot", - "path": "modules/nf-core/last/dotplot/meta.yml", - "type": "module", - "meta": { - "name": "last_dotplot", - "description": "Makes a dotplot (Oxford Grid) of pair-wise sequence alignments", - "keywords": [ - "LAST", - "plot", - "pair", - "alignment", - "MAF" - ], - "tools": [ - { - "last": { - "description": "LAST finds & aligns related regions of sequences.", - "homepage": "https://gitlab.com/mcfrith/last", - "documentation": "https://gitlab.com/mcfrith/last/-/blob/main/doc/last-dotplot.rst", - "tool_dev_url": "https://gitlab.com/mcfrith/last", - "licence": [ - "GPL v3-or-later" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "maf": { - "type": "file", - "description": "Multiple Alignment Format (MAF) file, compressed with gzip", - "pattern": "*.{maf.gz}", - "ontologies": [] - } - }, - { - "annot_b": { - "type": "file", - "description": "Annotation file in BED, Repeamasker, genePred or AGP format for the second (vertical) sequence", - "pattern": "*.{bed,bed.gz,out,out.gz,rmsk.txt,rmsk.txt.gz,genePred,genePred.gz,gff,gff.gz,gtf,gtf.gz,gap.txt,gap.txt.gz}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample2', single_end:false ]`\n" - } - }, - { - "annot_a": { - "type": "file", - "description": "Annotation file in BED, Repeamasker, genePred or AGP format for the first (horizontal) sequence", - "pattern": "*.{bed,bed.gz,out,out.gz,rmsk.txt,rmsk.txt.gz,genePred,genePred.gz,gff,gff.gz,gtf,gtf.gz,gap.txt,gap.txt.gz}", - "ontologies": [] - } - } - ], - { - "format": { - "type": "string", - "description": "Output format (PNG or GIF)." - } - }, - { - "filter": { - "type": "boolean", - "description": "Remove isolated alignments using the `maf-linked` software." - } - } - ], - "output": { - "plot": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.{gif,png}": { - "type": "file", - "description": "Pairwise alignment dot plot image, in GIF or PNG format.", - "pattern": "*.{gif,png}", - "ontologies": [] - } - } - ] - ], - "versions_last": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "last": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "lastal --version | sed 's/lastal //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "last": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "lastal --version | sed 's/lastal //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@charles-plessy" - ], - "maintainers": [ - "@charles-plessy" - ] - }, - "pipelines": [ - { - "name": "pairgenomealign", - "version": "2.2.3" - } - ] - }, - { - "name": "last_lastal", - "path": "modules/nf-core/last/lastal/meta.yml", - "type": "module", - "meta": { - "name": "last_lastal", - "description": "Aligns query sequences to target sequences indexed with lastdb", - "keywords": [ - "LAST", - "align", - "fastq", - "fasta" - ], - "tools": [ - { - "last": { - "description": "LAST finds & aligns related regions of sequences.", - "homepage": "https://gitlab.com/mcfrith/last", - "documentation": "https://gitlab.com/mcfrith/last/-/blob/main/doc/last-train.rst", - "tool_dev_url": "https://gitlab.com/mcfrith/last", - "licence": [ - "GPL v3-or-later" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "fastx": { - "type": "file", - "description": "FASTA/FASTQ file", - "pattern": "*.{fasta,fastq}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - }, - { - "param_file": { - "type": "file", - "description": "Trained parameter file", - "pattern": "*.train", - "ontologies": [] - } - } - ], - { - "index": { - "type": "directory", - "description": "Directory containing the files of the LAST index", - "pattern": "lastdb/" - } - } - ], - "output": { - "maf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.maf.gz": { - "type": "file", - "description": "Gzipped MAF (Multiple Alignment Format) file", - "pattern": "*.{maf.gz}", - "ontologies": [] - } - } - ] - ], - "multiqc": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "Summary reporting the total alignment length (including gaps) and the\npercent identity computed with and without taking gaps in\nconsideration (because there is no standard definition of percent\nidentity).\n", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_last": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "last": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "lastal --version | sed 's/lastal //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "last": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "lastal --version | sed 's/lastal //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@charles-plessy" - ], - "maintainers": [ - "@charles-plessy" - ] - }, - "pipelines": [ - { - "name": "pairgenomealign", - "version": "2.2.3" - 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}, - { - "last": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "lastal --version | sed 's/lastal //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "abotyper", + "version": "dev" + }, + { + "name": "airrflow", + "version": "5.0.0" + }, + { + "name": "alleleexpression", + "version": "dev" + }, + { + "name": "ampliseq", + "version": "2.17.0" + }, + { + "name": "bacass", + "version": "2.6.0" + }, + { + "name": "bamtofastq", + "version": "2.2.1" + }, + { + "name": "callingcards", + "version": "1.0.0" + }, + { + "name": "cellpainting", + "version": "dev" + }, + { + "name": "chipseq", + "version": "2.1.0" + }, + { + "name": "circrna", + "version": "dev" + }, + { + "name": "coproid", + "version": "2.0.1" + }, + { + "name": "createpanelrefs", + "version": "dev" + }, + { + "name": "createtaxdb", + "version": "3.0.0" + }, + { + "name": "crisprseq", + "version": "2.3.0" + }, + { + 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{ + "name": "mitodetect", + "version": "dev" + }, + { + "name": "molkart", + "version": "1.2.0" + }, + { + "name": "multiplesequencealign", + "version": "1.1.1" + }, + { + "name": "nanoseq", + "version": "3.1.0" + }, + { + "name": "nanostring", + "version": "1.3.3" + }, + { + "name": "nascent", + "version": "2.3.0" + }, + { + "name": "ncrnannotator", + "version": "dev" + }, + { + "name": "omicsgenetraitassociation", + "version": "dev" + }, + { + "name": "pacsomatic", + "version": "dev" + }, + { + "name": "pacvar", + "version": "1.0.1" + }, + { + "name": "pairgenomealign", + "version": "2.2.3" + }, + { + "name": "pangenome", + "version": "1.1.3" + }, + { + "name": "panoramaseq", + "version": "dev" + }, + { + "name": "pathogensurveillance", + "version": "1.1.0" + }, + { + "name": "phageannotator", + "version": "dev" + }, + { + "name": "phaseimpute", + "version": "1.1.0" + }, + { + "name": "phyloplace", + "version": "2.0.0" + }, + { + "name": "proteinannotator", + "version": "1.1.0" + }, 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+ { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample1', single_end:false ]\n" + } + }, + { + "runinfo_xml": { + "type": "file", + "description": "Illumina RunInfo.xml file", + "pattern": "RunInfo.xml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2332" + } + ] + } + }, + { + "interop_bin": { + "type": "file", + "description": "Illumina InterOp binary files", + "pattern": "InterOp/*.bin", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2333" + } + ] + } + }, + { + "extra_multiqc_files": { + "type": "file", + "description": "List of reports / files rec ognised by MultiQC, for example the html and zip output of FastQC\n", + "ontologies": [] + } + }, + { + "multiqc_config": { + "type": "file", + "description": "Optional config yml for MultiQC", + "pattern": "*.{yml,yaml}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + }, + { + "extra_multiqc_config": { + "type": "file", + "description": "Second optional config yml for MultiQC. Will override common sections in multiqc_config.", + "pattern": "*.{yml,yaml}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + }, + { + "multiqc_logo": { + "type": "file", + "description": "Optional logo file for MultiQC", + "pattern": "*.{png}", + "ontologies": [] + } + }, + { + "replace_names": { + "type": "file", + "description": "Optional two-column sample renaming file. First column a set of\npatterns, second column a set of corresponding replacements. Passed via\nMultiQC's `--replace-names` option.\n", + "pattern": "*.{tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, + { + "sample_names": { + "type": "file", + "description": "Optional TSV file with headers, passed to the MultiQC --sample_names\nargument.\n", + "pattern": "*.{tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "output": { + "report": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample1', single_end:false ]\n" + } + }, + { + "*.html": { + "type": "file", + "description": "MultiQC report file", + "pattern": ".html", + "ontologies": [] + } + } + ] + ], + "data": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample1', single_end:false ]\n" + } + }, + { + "*_data": { + "type": "directory", + "description": "MultiQC data dir", + "pattern": "multiqc_data" + } + } + ] + ], + "plots": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample1', single_end:false ]\n" + } + }, + { + "*_plots": { + "type": "file", + "description": "Plots created by MultiQC", + "pattern": "*_data", + "ontologies": [] + } + } + ] + ], + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "multiqc": { + "type": "string", + "description": "The tool name" + } + }, + { + "multiqc --version | sed \"s/.* //g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_multiqc_sav": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "multiqc_sav": { + "type": "string", + "description": "The tool name" + } + }, + { + "python -c \"import multiqc_sav; print(multiqc_sav.__version__)\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_interop": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "interop": { + "type": "string", + "description": "The tool name" + } + }, + { + "python -c \"import interop; print(interop.__version__)\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@matthdsm", "@delfiterradas"], + "maintainers": ["@matthdsm"] + } }, { - "name": "raredisease", - "version": "3.0.0" - } - ] - }, - { - "name": "last_mafconvert", - "path": "modules/nf-core/last/mafconvert/meta.yml", - "type": "module", - "meta": { - "name": "last_mafconvert", - "description": "Converts MAF alignments in another format.", - "keywords": [ - "LAST", - "convert", - "alignment", - "MAF" - ], - "tools": [ - { - "last": { - "description": "LAST finds & aligns related regions of sequences.", - "homepage": "https://gitlab.com/mcfrith/last", - "documentation": "https://gitlab.com/mcfrith/last/-/blob/main/doc/", - "tool_dev_url": "https://gitlab.com/mcfrith/last", - "licence": [ - "GPL v3-or-later" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "maf": { - "type": "file", - "description": "Multiple Alignment Format (MAF) file, optionally compressed with gzip", - "pattern": "*.{maf.gz,maf}", - "ontologies": [] - } - }, - { - "format": { - "type": "string", - "description": "Output format (one of axt, bam, blast, blasttab, cram, chain, gff, html, psl, sam, or tab)" - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Genome file in FASTA format for CRAM conversion. If compressed it must be done in BGZF format (like with the bgzip tool).", - "pattern": "*.{fasta,fasta.gz,fasta.bgz,fasta.bgzf}", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "fai": { - "type": "file", - "description": "Genome index file needed for CRAM conversion.", - "pattern": "*.fai", - "ontologies": [] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "gzi": { - "type": "file", - "description": "Genome index file needed for CRAM conversion when the genome file was compressed with the BGZF algorithm.", - "pattern": "*.gzi", - "ontologies": [] - } - } - ], - [ - { - "meta5": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "dict": { - "type": "file", - "description": "Samtools dictionary of the genome file.", - "pattern": "*.dict", - "ontologies": [] - } - } - ] - ], - "output": { - "alignment": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.{axt.gz,bam,bed.gz,blast.gz,blasttab.gz,chain.gz,cram,gff.gz,html.gz,psl.gz,sam.gz,tab.gz}": { - "type": "file", - "description": "Pairwise alignment exported to Axt, BAM, BED, BLAST, Chain, CRAM, GFF, HTML PSL, SAM or Tab format.", - "pattern": "*.{axt.gz,bam,bed.gz,blast.gz,blasttab.gz,chain.gz,cram,gff.gz,html.gz,psl.gz,sam.gz,tab.gz}", - "ontologies": [] - } - } - ] - ], - "versions_last": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "last": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "lastal --version | sed 's/lastal //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "last": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "lastal --version | sed 's/lastal //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@aleksandrabliznina", - "@charles-plessy" - ], - "maintainers": [ - "@charles-plessy" - ] - }, - "pipelines": [ - { - "name": "pairgenomealign", - "version": "2.2.3" - } - ] - }, - { - "name": "last_mafswap", - "path": "modules/nf-core/last/mafswap/meta.yml", - "type": "module", - "meta": { - "name": "last_mafswap", - "description": "Reorder alignments in a MAF file", - "keywords": [ - "LAST", - "reorder", - "alignment", - "MAF" - ], - "tools": [ - { - "last": { - "description": "LAST finds & aligns related regions of sequences.", - "homepage": "https://gitlab.com/mcfrith/last", - "documentation": "https://gitlab.com/mcfrith/last/-/blob/main/doc/", - "tool_dev_url": "https://gitlab.com/mcfrith/last", - "licence": [ - "GPL v3-or-later" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "maf": { - "type": "file", - "description": "Multiple Alignment Format (MAF) file, optionally compressed with gzip", - "pattern": "*.{maf.gz,maf}", - "ontologies": [] - } - } - ] - ], - "output": { - "maf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.maf.gz": { - "type": "file", - "description": "Multiple Alignment Format (MAF) file, compressed with gzip", - "pattern": "*.{maf.gz}", - "ontologies": [] - } - } - ] - ], - "versions_last": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "last": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "lastal --version | sed 's/lastal //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "last": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "lastal --version | sed 's/lastal //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@charles-plessy" - ], - "maintainers": [ - "@charles-plessy" - ] - } - }, - { - "name": "last_postmask", - "path": "modules/nf-core/last/postmask/meta.yml", - "type": "module", - "meta": { - "name": "last_postmask", - "description": "Post-alignment masking", - "keywords": [ - "LAST", - "mask", - "alignment", - "MAF" - ], - "tools": [ - { - "last": { - "description": "LAST finds & aligns related regions of sequences.", - "homepage": "https://gitlab.com/mcfrith/last", - "documentation": "https://gitlab.com/mcfrith/last/-/blob/main/doc/last-postmask.rst", - "tool_dev_url": "https://gitlab.com/mcfrith/last", - "doi": "10.1371/journal.pone.0028819", - "licence": [ - "GPL v3-or-later" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "maf": { - "type": "file", - "description": "Multiple Alignment Format (MAF) file, optionally compressed with gzip", - "pattern": "*.{maf.gz,maf}", - "ontologies": [] - } - } - ] - ], - "output": { - "maf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.maf.gz": { - "type": "file", - "description": "Multiple Alignment Format (MAF) file, compressed with gzip", - "pattern": "*.{maf.gz}", - "ontologies": [] - } - } - ] - ], - "versions_last": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "last": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "lastal --version | sed 's/lastal //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "last": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "lastal --version | sed 's/lastal //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@charles-plessy" - ], - "maintainers": [ - "@charles-plessy" - ] - } - }, - { - "name": "last_split", - "path": "modules/nf-core/last/split/meta.yml", - "type": "module", - "meta": { - "name": "last_split", - "description": "Find split or spliced alignments in a MAF file", - "keywords": [ - "LAST", - "split", - "spliced", - "alignment", - "MAF" - ], - "tools": [ - { - "last": { - "description": "LAST finds & aligns related regions of sequences.", - "homepage": "https://gitlab.com/mcfrith/last", - "documentation": "https://gitlab.com/mcfrith/last/-/blob/main/doc/", - "tool_dev_url": "https://gitlab.com/mcfrith/last", - "licence": [ - "GPL v3-or-later" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "maf": { - "type": "file", - "description": "Multiple Alignment Format (MAF) file, compressed with gzip", - "pattern": "*.{maf.gz}", - "ontologies": [] - } - } - ] - ], - "output": { - "maf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.maf.gz": { - "type": "file", - "description": "Multiple Alignment Format (MAF) file, compressed with gzip", - "pattern": "*.{maf.gz}", - "ontologies": [] - } - } - ] - ], - "multiqc": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "Summary reporting the total alignment length (including gaps) and the\npercent identity computed with and without taking gaps in\nconsideration (because there is no standard definition of percent\nidentity).\n", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_last": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "last": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "lastal --version | sed 's/lastal //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "last": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "lastal --version | sed 's/lastal //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@aleksandrabliznina", - "@charles-plessy" - ], - "maintainers": [ - "@charles-plessy" - ] - }, - "pipelines": [ - { - "name": "pairgenomealign", - "version": "2.2.3" - } - ] - }, - { - "name": "last_train", - "path": "modules/nf-core/last/train/meta.yml", - "type": "module", - "meta": { - "name": "last_train", - "description": "Find suitable score parameters for sequence alignment", - "keywords": [ - "LAST", - "train", - "fastq", - "fasta" - ], - "tools": [ - { - "last": { - "description": "LAST finds & aligns related regions of sequences.", - "homepage": "https://gitlab.com/mcfrith/last", - "documentation": "https://gitlab.com/mcfrith/last/-/blob/main/doc/last-train.rst", - "tool_dev_url": "https://gitlab.com/mcfrith/last", - "licence": [ - "GPL v3-or-later" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "fastx": { - "type": "file", - "description": "FASTA/FASTQ file", - "pattern": "*.{fasta,fastq}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ], - { - "index": { - "type": "directory", - "description": "Directory containing the files of the LAST index", - "pattern": "lastdb/" - } - } - ], - "output": { - "param_file": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.train": { - "type": "file", - "description": "Trained parameter file", - "pattern": "*.train", - "ontologies": [] - } - } - ] - ], - "multiqc": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "Alignment parameter summary for MultiQC", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_last": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "last": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "lastal --version | sed 's/lastal //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "last": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "lastal --version | sed 's/lastal //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@aleksandrabliznina", - "@charles-plessy", - "@U13bs1125" - ], - "maintainers": [ - "@charles-plessy" - ] - }, - "pipelines": [ - { - "name": "pairgenomealign", - "version": "2.2.3" - } - ] - }, - { - "name": "learnmsa_align", - "path": "modules/nf-core/learnmsa/align/meta.yml", - "type": "module", - "meta": { - "name": "learnmsa_align", - "description": "Align sequences using learnMSA", - "keywords": [ - "alignment", - "MSA", - "genomics" - ], - "tools": [ - { - "learnmsa": { - "description": "learnMSA: Learning and Aligning large Protein Families", - "homepage": "https://github.com/Gaius-Augustus/learnMSA", - "documentation": "https://github.com/Gaius-Augustus/learnMSA", - "tool_dev_url": "https://github.com/Gaius-Augustus/learnMSA", - "doi": "10.1093/gigascience/giac104", - "licence": [ - "MIT" - ], - "identifier": "biotools:learnMSA" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input sequences in FASTA format.", - "pattern": "*.{fa,fasta}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1919" - }, - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ], - "output": { - "alignment": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" - } - }, - { - "*.aln": { - "type": "file", - "description": "Alignment file, in FASTA format.", - "pattern": "*.aln", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2554" + "name": "multiqcsav", + "path": "modules/nf-core/multiqcsav/meta.yml", + "type": "module", + "meta": { + "name": "multiqcsav", + "description": "Aggregate results from bioinformatics analyses across many samples into a single report, with support for multiqc_sav plugin", + "keywords": [ + "QC", + "bioinformatics tools", + "Beautiful stand-alone HTML report", + "Illumina", + "Sequencing Analysis Viewer", + "SAV" + ], + "tools": [ + { + "multiqc": { + "description": "MultiQC searches a given directory for analysis logs and compiles a HTML report.\nIt's a general use tool, perfect for summarising the output from numerous bioinformatics tools.\n", + "homepage": "https://multiqc.info/", + "documentation": "https://multiqc.info/docs/", + "licence": ["GPL-3.0-or-later"], + "identifier": "biotools:multiqc" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample1', single_end:false ]\n" + } + }, + { + "xml": { + "type": "file", + "description": "xml files from an Illumina sequencing run", + "pattern": "*.xml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2332" + } + ] + } + }, + { + "interop_bin": { + "type": "file", + "description": "Illumina InterOp binary files", + "pattern": "InterOp/*.bin", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2333" + } + ] + } + }, + { + "extra_multiqc_files": { + "type": "file", + "description": "List of reports / files recognised by MultiQC, for example the html and zip output of FastQC\n", + "ontologies": [] + } + }, + { + "multiqc_config": { + "type": "file", + "description": "Optional config yml for MultiQC", + "pattern": "*.{yml,yaml}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + }, + { + "multiqc_logo": { + "type": "file", + "description": "Optional logo file for MultiQC", + "pattern": "*.{png}", + "ontologies": [] + } + }, + { + "replace_names": { + "type": "file", + "description": "Optional two-column sample renaming file. First column a set of\npatterns, second column a set of corresponding replacements. Passed via\nMultiQC's `--replace-names` option.\n", + "pattern": "*.{tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, + { + "sample_names": { + "type": "file", + "description": "Optional TSV file with headers, passed to the MultiQC --sample_names\nargument.\n", + "pattern": "*.{tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "output": { + "report": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample1', single_end:false ]\n" + } + }, + { + "*.html": { + "type": "file", + "description": "MultiQC report file", + "pattern": ".html", + "ontologies": [] + } + } + ] + ], + "data": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample1', single_end:false ]\n" + } + }, + { + "*_data": { + "type": "directory", + "description": "MultiQC data dir", + "pattern": "multiqc_data" + } + } + ] + ], + "plots": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample1', single_end:false ]\n" + } + }, + { + "*_plots": { + "type": "file", + "description": "Plots created by MultiQC", + "pattern": "*_data", + "ontologies": [] + } + } + ] + ], + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "multiqc": { + "type": "string", + "description": "The tool name" + } + }, + { + "multiqc --version | sed \"s/.* //g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_interop": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "interop": { + "type": "string", + "description": "The tool name" + } + }, + { + "python -c \"import interop; print(interop.__version__)\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_multiqcsav": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "multiqcsav": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python -c \"import multiqc_sav; print(multiqc_sav.__version__)\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@matthdsm", "@delfiterradas"], + "maintainers": ["@matthdsm"], + "containers": { + "conda": { + "linux/amd64": { + "lock_file": "modules/nf-core/multiqcsav/.conda-lock/linux_amd64-bd-d497f2c0ee14021c_1.txt" + }, + "linux/arm64": { + "lock_file": "modules/nf-core/multiqcsav/.conda-lock/linux_arm64-bd-63d3faa1f4fa1fa6_1.txt" + } }, - { - "edam": "http://edamontology.org/format_1921" + "docker": { + "linux/amd64": { + "name": "community.wave.seqera.io/library/multiqc_multiqc_sav_pip_interop:d497f2c0ee14021c", + "build_id": "bd-d497f2c0ee14021c_1", + "scan_id": "sc-872ef428e7dd759e_1" + }, + "linux/arm64": { + "name": "community.wave.seqera.io/library/multiqc_multiqc_sav_pip_interop:63d3faa1f4fa1fa6", + "build_id": "bd-63d3faa1f4fa1fa6_1", + "scan_id": "sc-d2c09f2fb4caa3ad_1" + } }, - { - "edam": "http://edamontology.org/format_1984" + "singularity": { + "linux/amd64": { + "name": "oras://community.wave.seqera.io/library/multiqc_multiqc_sav_pip_interop:f4f70d0f966edec3", + "build_id": "bd-f4f70d0f966edec3_1", + "https": "https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/80/80a772836e24ece3afc4eb53f6584a311000842e6323b8e725d37fd88b566768/data" + }, + "linux/arm64": { + "name": "oras://community.wave.seqera.io/library/multiqc_multiqc_sav_pip_interop:8285dbf19c66f011", + "build_id": "bd-8285dbf19c66f011_1", + "https": "https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/20/20f8e844c2df1a8893ac3897249bf3166752c17c41822271c12a51821b13c685/data" + } } - ] } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@luisas", - "@JoseEspinosa" - ], - "maintainers": [ - "@luisas", - "@JoseEspinosa" - ] - }, - "pipelines": [ - { - "name": "multiplesequencealign", - "version": "1.1.1" - } - ] - }, - { - "name": "leehom", - "path": "modules/nf-core/leehom/meta.yml", - "type": "module", - "meta": { - "name": "leehom", - "description": "Bayesian reconstruction of ancient DNA fragments", - "keywords": [ - "ancient DNA", - "adapter removal", - "clipping", - "trimming", - "merging", - "collapsing", - "preprocessing", - "bayesian" - ], - "tools": [ - { - "leehom": { - "description": "Bayesian reconstruction of ancient DNA fragments", - "homepage": "https://grenaud.github.io/leeHom/", - "documentation": "https://github.com/grenaud/leeHom", - "tool_dev_url": "https://github.com/grenaud/leeHom", - "doi": "10.1093/nar/gku699", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:leehom" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "Unaligned BAM or one or two gzipped FASTQ file(s)", - "pattern": "*.{bam,fq.gz,fastq.gz}", - "ontologies": [] - } - } - ] - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.bam": { - "type": "file", - "description": "BAM file", - "pattern": "*.bam", - "ontologies": [] - } - } - ] - ], - "fq_pass": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.fq.gz": { - "type": "file", - "description": "Trimmed and merged FASTQ", - "pattern": "*.fq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "fq_fail": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.fail.fq.gz": { - "type": "file", - "description": "Failed trimmed and merged FASTQs", - "pattern": "*.fail.fq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "unmerged_r1_fq_pass": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}_r1.fq.gz": { - "type": "file", - "description": "Passed unmerged R1 FASTQs", - "pattern": "*.r1.fq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "unmerged_r1_fq_fail": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}_r1.fail.fq.gz": { - "type": "file", - "description": "Failed unmerged R1 FASTQs", - "pattern": "*.r1.fail.fq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "unmerged_r2_fq_pass": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}_r2.fq.gz": { - "type": "file", - "description": "Passed unmerged R2 FASTQs", - "pattern": "*.r2.fq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "unmerged_r2_fq_fail": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}_r2.fail.fq.gz": { - "type": "file", - "description": "Failed unmerged R2 FASTQs", - "pattern": "*.r2.fail.fq.gz", - 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} - ] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@rpetit3" - ], - "maintainers": [ - "@rpetit3" - ] - } - }, - { - "name": "leviosam2_index", - "path": "modules/nf-core/leviosam2/index/meta.yml", - "type": "module", - "meta": { - "name": "leviosam2_index", - "description": "Index chain files for lift over", - "keywords": [ - "leviosam2", - "index", - "lift" - ], - "tools": [ - { - "leviosam2": { - "description": "Fast and accurate coordinate conversion between assemblies", - "homepage": "https://github.com/milkschen/leviosam2/blob/main/workflow/README.md", - "documentation": "https://github.com/milkschen/leviosam2/blob/main/workflow/README.md", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'reference' ]`\n" - } }, - { - "fai": { - "type": "file", - "description": "FAI (FASTA index) file of the target reference", - "pattern": "*.{fai}", - "ontologies": [] - } - } - ], - { - "chain": { - "type": "file", - "description": "Chain file to index.", - "pattern": "*.{chain}", - "ontologies": [ + "pipelines": [ { - "edam": "http://edamontology.org/format_3982" + "name": "demultiplex", + "version": "1.7.1" } - ] - } - } - ], - "output": { - "clft": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'reference' ]`\n" - } - }, - { - "*.clft": { - "type": "file", - "description": "Clft file of indexed chain", - "pattern": "*.{clft}", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@lgrochowalski" - ], - "maintainers": [ - "@lgrochowalski" - ] - } - }, - { - "name": "leviosam2_lift", - "path": "modules/nf-core/leviosam2/lift/meta.yml", - "type": "module", - "meta": { - "name": "leviosam2_lift", - "description": "Converting aligned short and long reads records from one reference to another", - "keywords": [ - "leviosam2", - "index", - "lift" - ], - "tools": [ - { - "leviosam2": { - "description": "Fast and accurate coordinate conversion between assemblies", - "homepage": "https://github.com/milkschen/leviosam2/blob/main/workflow/README.md", - "documentation": "https://github.com/milkschen/leviosam2/blob/main/workflow/README.md", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "input": { - "type": "file", - "description": "SAM/BAM/CRAM file to be lifted", - "pattern": "*.{bam}", - "ontologies": [] - } - } - ], - [ - { - "meta_ref": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. `[ id:'reference' ]`\n" - } - }, - { - "clft": { - "type": "file", - "description": "Clft file of indexed ChainMap.", - "pattern": "*.{clft}", - "ontologies": [] - } - } - ] - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'reference' ]`\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "Lifted bam file", - "pattern": "*.{bam}", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@lgrochowalski" - ], - "maintainers": [ - "@lgrochowalski" - ] - } - }, - { - "name": "liftoff", - "path": "modules/nf-core/liftoff/meta.yml", - "type": "module", - "meta": { - "name": "liftoff", - "description": "Uses Liftoff to accurately map annotations in GFF or GTF between assemblies of the same,\nor closely-related species\n", - "keywords": [ - "genome", - "annotation", - "gff3", - "gtf", - "liftover" - ], - "tools": [ - { - "liftoff": { - "description": "Liftoff is a tool that accurately maps annotations in GFF or GTF between assemblies of the same,\nor closely-related species\n", - "homepage": "https://github.com/agshumate/Liftoff", - "documentation": "https://github.com/agshumate/Liftoff", - "tool_dev_url": "https://github.com/agshumate/Liftoff", - "doi": "10.1093/bioinformatics/bty191", - "licence": [ - "GPL v3 License" - ], - "identifier": "biotools:liftoff" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "target_fa": { - "type": "file", - "description": "Target assembly in fasta format (can be gzipped)", - "pattern": "*.{fa,fa.gz,fasta,fasta.gz,fas,fas.gz,fsa,fsa.gz}", - "ontologies": [] - } - } - ], - { - "ref_fa": { - "type": "file", - "description": "Reference assembly in fasta format (can be gzipped)", - "pattern": "*.{fa,fa.gz,fasta,fasta.gz,fas,fas.gz,fsa,fsa.gz}", - "ontologies": [] - } - }, - { - "ref_annotation": { - "type": "file", - "description": "Reference assembly annotations in gtf or gff3 format", - "pattern": "*.{gtf,gff3}", - "ontologies": [] - } - }, - { - "ref_db": { - "type": "file", - "description": "Name of feature database; if not specified, the -g argument must\nbe provided and a database will be built automatically\n", - "ontologies": [] - } - } - ], - "output": { - "gff3": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "${prefix}.gff3": { - "type": "file", - "description": "Lifted annotations for the target assembly in gff3 format", - "pattern": "*.gff3", - "ontologies": [] - } - } - ] - ], - "polished_gff3": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "*.polished.gff3": { - "type": "file", - "description": "Polished lifted annotations for the target assembly in gff3 format", - "pattern": "*.polished.gff3", - "ontologies": [] - } - } - ] - ], - "unmapped_txt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "*.unmapped.txt": { - "type": "file", - "description": "List of unmapped reference annotations", - "pattern": "*.unmapped.txt", - "ontologies": [] - } - } - ] - ], - "versions_liftoff": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "liftoff": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "liftoff --version | sed \"s/v//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "liftoff": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "liftoff --version | sed \"s/v//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] }, - "authors": [ - "@GallVp" - ], - "maintainers": [ - "@GallVp" - ] - }, - "pipelines": [ { - "name": "bacass", - "version": "2.6.0" + "name": "multiseqdemux", + "path": "modules/nf-core/multiseqdemux/meta.yml", + "type": "module", + "meta": { + "name": "multiseqdemux", + "description": "Identify singlets, doublets and negative cells from multiplexing experiments. Annotate singlets by tags.", + "keywords": ["demultiplexing", "hashing-based deconvolution", "single-cell"], + "tools": [ + { + "multiseqdemux": { + "description": "MULTIseqDemux is the demultiplexing module of Seurat, which demultiplex samples based on data from cell hashing.", + "homepage": "https://satijalab.org/seurat/reference/multiseqdemux", + "documentation": "https://satijalab.org/seurat/reference/multiseqdemux", + "tool_dev_url": "https://github.com/satijalab/seurat", + "doi": "10.1038/s41592-019-0433-8", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "seurat_object": { + "type": "file", + "description": "A `.rds` file containing the seurat object. Assumes that the hash tag oligo (HTO) data has been added and normalized.\n", + "ontologies": [] + } + }, + { + "assay": { + "type": "string", + "description": "Name of the Hashtag assay, usually called \"HTO\" by default. Use the custom name if the assay has been named differently.\n" + } + } + ] + ], + "output": { + "params": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_params_multiseqdemux.csv": { + "type": "file", + "description": "The used parameters to call MULTIseqDemux in the R-Script.", + "pattern": "_params_multiseqdemux.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "results": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_res_multiseqdemux.csv": { + "type": "file", + "description": "Resuls of MULTIseqDemux.", + "pattern": "_res_multiseqdemux.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "rds": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_multiseqdemux.rds": { + "type": "file", + "description": "SeuratObject saved as RDS.", + "pattern": "_multiseqdemux.rds", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@LuisHeinzlmeier"], + "maintainers": ["@LuisHeinzlmeier"] + } }, { - "name": "genomeassembler", - "version": "1.1.0" - } - ] - }, - { - "name": "lima", - "path": "modules/nf-core/lima/meta.yml", - "type": "module", - "meta": { - "name": "lima", - "description": "lima - The PacBio Barcode Demultiplexer and Primer Remover", - "keywords": [ - "isoseq", - "ccs", - "primer", - "pacbio", - "barcode" - ], - "tools": [ - { - "lima": { - "description": "lima - The PacBio Barcode Demultiplexer and Primer Remover", - "homepage": "https://github.com/PacificBiosciences/pbbioconda", - "documentation": "https://lima.how/", - "tool_dev_url": "https://github.com/pacificbiosciences/barcoding/", - "licence": [ - "BSD-3-Clause-Clear" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "ccs": { - "type": "file", - "description": "A BAM or fasta or fasta.gz or fastq or fastq.gz file of subreads or ccs", - "pattern": "*.{bam,fasta,fasta.gz,fastq,fastq.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ], - { - "primers": { - "type": "file", - "description": "Fasta file, sequences of primers", - "pattern": "*.fasta", - "ontologies": [] + "name": "multivcfanalyzer", + "path": "modules/nf-core/multivcfanalyzer/meta.yml", + "type": "module", + "meta": { + "name": "multivcfanalyzer", + "description": "SNP table generator from GATK UnifiedGenotyper with functionality geared for aDNA", + "keywords": ["vcf", "ancient DNA", "aDNA", "SNP", "GATK UnifiedGenotyper", "SNP table"], + "tools": [ + { + "multivcfanalyzer": { + "description": "MultiVCFAnalyzer is a VCF file post-processing tool tailored for aDNA. License on Github repository.", + "homepage": "https://github.com/alexherbig/MultiVCFAnalyzer", + "documentation": "https://github.com/alexherbig/MultiVCFAnalyzer", + "tool_dev_url": "https://github.com/alexherbig/MultiVCFAnalyzer", + "doi": "10.1038/nature13591", + "licence": ["GPL >=3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "vcfs": { + "type": "file", + "description": "One or a list of gzipped or uncompressed VCF file", + "pattern": "*.vcf", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference genome VCF was generated against", + "pattern": "*.{fasta,fna,fa}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "snpeff_results": { + "type": "file", + "description": "Results from snpEff in txt format (Optional)", + "pattern": "*.txt", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "gff": { + "type": "file", + "description": "GFF file corresponding to reference genome fasta (Optional)", + "pattern": "*.gff", + "ontologies": [] + } + } + ], + { + "allele_freqs": { + "type": "boolean", + "description": "Whether to include the percentage of reads a given allele is\npresent in in the SNP table.\n" + } + }, + { + "genotype_quality": { + "type": "integer", + "description": "Minimum GATK genotyping threshold threshold of which a SNP call\nfalling under is 'discarded'\n" + } + }, + { + "coverage": { + "type": "integer", + "description": "Minimum number of a reads that a position must be covered by to be\nreported\n" + } + }, + { + "homozygous_freq": { + "type": "integer", + "description": "Fraction of reads a base must have to be called 'homozygous'" + } + }, + { + "heterozygous_freq": { + "type": "integer", + "description": "Fraction of which whereby if a call falls above this value, and lower\nthan the homozygous threshold, a base will be called 'heterozygous'.\n" + } + }, + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "gff_exclude": { + "type": "file", + "description": "file listing positions that will be 'filtered' (i.e. ignored)\n(Optional)\n", + "pattern": "*.vcf", + "ontologies": [] + } + } + ] + ], + "output": { + "full_alignment": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*fullAlignment.fasta.gz": { + "type": "file", + "description": "Fasta a fasta file of all positions contained in the VCF files i.e. including ref calls", + "pattern": ".fasta.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3615" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "info_txt": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*info.txt": { + "type": "file", + "description": "Information about the run", + "pattern": ".txt", + "ontologies": [] + } + } + ] + ], + "snp_alignment": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*snpAlignment.fasta.gz": { + "type": "file", + "description": "A fasta file of just SNP positions with samples only", + "pattern": ".fasta.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3615" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "snp_genome_alignment": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*snpAlignmentIncludingRefGenome.fasta.gz": { + "type": "file", + "description": "A fasta file of just SNP positions with reference genome", + "pattern": ".fasta.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3615" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "snpstatistics": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*snpStatistics.tsv": { + "type": "file", + "description": "Some basic statistics about the SNP calls of each sample", + "pattern": ".tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "snptable": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*snpTable.tsv": { + "type": "file", + "description": "Basic SNP table of combined positions taken from each VCF file", + "pattern": ".tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "snptable_snpeff": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*snpTableForSnpEff.tsv": { + "type": "file", + "description": "Input file for SnpEff", + "pattern": ".tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "snptable_uncertainty": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*snpTableWithUncertaintyCalls.tsv": { + "type": "file", + "description": "Same as above, but with lower case characters indicating uncertain calls", + "pattern": ".tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "structure_genotypes": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*structureGenotypes.tsv": { + "type": "file", + "description": "Input file for STRUCTURE", + "pattern": ".tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "structure_genotypes_nomissing": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*structureGenotypes_noMissingData-Columns.tsv": { + "type": "file", + "description": "Alternate input file for STRUCTURE", + "pattern": ".tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "json": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*MultiVCFAnalyzer.json": { + "type": "file", + "description": "Summary statistics in MultiQC JSON format", + "pattern": ".json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "versions_multivcfanalyzer": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "multivcfanalyzer": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "multivcfanalyzer -h | head -n 1 | cut -f 3 -d \" \"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_tabix": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "tabix": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "tabix -h 2>&1 | grep Version | cut -f 2 -d \" \"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "multivcfanalyzer": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "multivcfanalyzer -h | head -n 1 | cut -f 3 -d \" \"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "tabix": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "tabix -h 2>&1 | grep Version | cut -f 2 -d \" \"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@jfy133"], + "maintainers": ["@jfy133", "@TCLamnidis"] } - } - ], - "output": { - "counts": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.counts": { - "type": "file", - "description": "A tabulated file of describing pairs of primers", - "pattern": "*.counts", - "ontologies": [] - } - } - ] - ], - "report": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.report": { - "type": "file", - "description": "A tab-separated file about each ZMW, unfiltered", - "pattern": "*.report", - "ontologies": [] - } - } - ] - ], - "summary": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.summary": { - "type": "file", - "description": "This file shows how many ZMWs have been filtered, how ZMWs many are same/different, and how many reads have been filtered.", - "pattern": "*.summary", - "ontologies": [] - } - } - ] - ], - "versions_lima": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "lima": { - "type": "string", - "description": "The tool name" - } - }, - { - "lima --version | head -n1 | sed 's/lima //g' | sed 's/ (.\\+//g'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ], - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "A bam file of ccs purged of primers", - "pattern": "*.bam", - "ontologies": [] - } - } - ] - ], - "pbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.bam.pbi": { - "type": "file", - "description": "Pacbio index file of ccs purged of primers", - "pattern": "*.bam", - "ontologies": [] - } - } - ] - ], - "fasta": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.{fa,fasta}": { - "type": "file", - "description": "A fasta file of ccs purged of primers.", - "pattern": "*.fa", - "ontologies": [] - } - } - ] - ], - "fastagz": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.{fa.gz,fasta.gz}": { - "type": "file", - "description": "A fasta.gz file of ccs purged of primers.", - "pattern": "*.fasta.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "fastq": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.fastq": { - "type": "file", - "description": "A fastq file of ccs purged of primers.", - "pattern": "*.fastq", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "fastqgz": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.fastq.gz": { - "type": "file", - "description": "A fastq.gz file of ccs purged of primers.", - "pattern": "*.fastq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "xml": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.xml": { - "type": "file", - "description": "An XML file representing a set of a particular sequence data type such as subreads, references or aligned subreads.", - "pattern": "*.xml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2332" - } - ] - } - } - ] - ], - "json": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.json": { - "type": "file", - "description": "A metadata json file", - "pattern": "*.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "clips": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.clips": { - "type": "file", - "description": "A fasta file of clipped primers", - "pattern": "*.clips", - "ontologies": [] - } - } - ] - ], - "guess": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.guess": { - "type": "file", - "description": "A second tabulated file of describing pairs of primers (no doc available)", - "pattern": "*.guess", - "ontologies": [] - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "lima": { - "type": "string", - "description": "The tool name" - } - }, - { - "lima --version | head -n1 | sed 's/lima //g' | sed 's/ (.\\+//g'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] }, - "authors": [ - "@sguizard" - ], - "maintainers": [ - "@sguizard" - ] - }, - "pipelines": [ { - "name": "genomeassembler", - "version": "1.1.0" + "name": "mummer", + "path": "modules/nf-core/mummer/meta.yml", + "type": "module", + "meta": { + "name": "mummer", + "description": "MUMmer is a system for rapidly aligning entire genomes", + "keywords": ["align", "genome", "fasta"], + "tools": [ + { + "mummer": { + "description": "MUMmer is a system for rapidly aligning entire genomes", + "homepage": "http://mummer.sourceforge.net/", + "documentation": "http://mummer.sourceforge.net/", + "tool_dev_url": "http://mummer.sourceforge.net/", + "doi": "10.1186/gb-2004-5-2-r12", + "licence": ["The Artistic License"], + "identifier": "biotools:mummer" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "ref": { + "type": "file", + "description": "FASTA file of the reference sequence", + "pattern": "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}", + "ontologies": [] + } + }, + { + "query": { + "type": "file", + "description": "FASTA file of the query sequence", + "pattern": "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}", + "ontologies": [] + } + } + ] + ], + "output": { + "coords": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.coords": { + "type": "file", + "description": "File containing coordinates of matches between reference and query sequence", + "pattern": "*.coords", + "ontologies": [] + } + } + ] + ], + "versions_mummer": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "mummer": { + "type": "string", + "description": "The tool name" + } + }, + { + "3.23": { + "type": "string", + "description": "The version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "mummer": { + "type": "string", + "description": "The tool name" + } + }, + { + "3.23": { + "type": "string", + "description": "The version of the tool" + } + } + ] + ] + }, + "authors": ["@mjcipriano", "@sateeshperi"], + "maintainers": ["@mjcipriano", "@sateeshperi"] + } }, { - "name": "isoseq", - "version": "2.0.0" + "name": "muscle", + "path": "modules/nf-core/muscle/meta.yml", + "type": "module", + "meta": { + "name": "muscle", + "description": "MUSCLE is a program for creating multiple alignments of amino acid or nucleotide sequences. A range of options are provided that give you the choice of optimizing accuracy, speed, or some compromise between the two", + "keywords": ["msa", "multiple sequence alignment", "phylogeny"], + "tools": [ + { + "muscle": { + "description": "MUSCLE is a multiple sequence alignment tool with high accuracy and throughput", + "homepage": "https://www.drive5.com/muscle", + "documentation": "http://www.drive5.com/muscle/muscle.html#_Toc81224840", + "doi": "10.1093/nar/gkh340", + "licence": ["http://www.drive5.com/muscle/manual/license.html"], + "identifier": "biotools:muscle" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input sequences for alignment must be in FASTA format", + "pattern": "*.{fasta,fa,fna}", + "ontologies": [] + } + } + ] + ], + "output": { + "aligned_fasta": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.afa": { + "type": "file", + "description": "Multiple sequence alignment produced in FASTA format", + "pattern": "*.{afa}", + "ontologies": [] + } + } + ] + ], + "phyi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.phyi": { + "type": "file", + "description": "Multiple sequence alignment produced in PHYLIP interleaved format", + "pattern": "*.{phyi}", + "ontologies": [] + } + } + ] + ], + "phys": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.phys": { + "type": "file", + "description": "Multiple sequence alignment produced in PHYLIP sequential format", + "pattern": "*.{phys}", + "ontologies": [] + } + } + ] + ], + "clustalw": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.clw": { + "type": "file", + "description": "Multiple sequence alignment produced in ClustalW format without base/residue numbering", + "pattern": "*.{clw}", + "ontologies": [] + } + } + ] + ], + "html": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.html": { + "type": "file", + "description": "Multiple sequence alignment produced in HTML format", + "pattern": "*.{html}", + "ontologies": [] + } + } + ] + ], + "msf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.msf": { + "type": "file", + "description": "GCG Multiple Sequence File (MSF) alignment format (similar to CLUSTALW)", + "pattern": "*.{msf}", + "ontologies": [] + } + } + ] + ], + "tree": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.tree": { + "type": "file", + "description": "NJ or UPGMA tree in Newick format produced from a multiple sequence alignment", + "pattern": "*.{tree}", + "ontologies": [] + } + } + ] + ], + "log": [ + { + "*.log": { + "type": "file", + "description": "Log file of MUSCLE run", + "pattern": "*{.log}", + "ontologies": [] + } + } + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@MGordon"], + "maintainers": ["@MGordon"] + } }, { - "name": "pacvar", - "version": "1.0.1" - } - ] - }, - { - "name": "limma_differential", - "path": "modules/nf-core/limma/differential/meta.yml", - "type": "module", - "meta": { - "name": "limma_differential", - "description": "runs a differential expression analysis with Limma", - "keywords": [ - "differential", - "expression", - "microarray", - "limma" - ], - "tools": [ - { - "limma": { - "description": "Linear Models for Microarray Data", - "homepage": "https://bioconductor.org/packages/release/bioc/html/limma.html", - "documentation": "https://bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf", - "tool_dev_url": "https://github.com/cran/limma\"\"", - "doi": "10.18129/B9.bioc.limma", - "licence": [ - "LGPL >=3" - ], - "identifier": "biotools:limma" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing contrast information. This can be used at the\nworkflow level to pass optional parameters to the module, e.g.\n[ id:'contrast1', blocking:'patient' ] passed in as ext.args like:\n'--blocking_variable $meta.blocking'.\n" - } - }, - { - "contrast_variable": { - "type": "string", - "description": "(Optional, required if reference and target are used) The column in the sample sheet that should be used to define groups for\ncomparison\n" - } - }, - { - "reference": { - "type": "string", - "description": "(Optional, required if contrast_variable and target are used) The value within the contrast_variable column of the sample sheet that\nshould be used to derive the reference samples\n" - } - }, - { - "target": { - "type": "string", - "description": "(Optional, required if contrast_variable and reference are used) The value within the contrast_variable column of the sample sheet that\nshould be used to derive the target samples\n" - } - }, - { - "formula": { - "type": "string", - "description": "(Optional, requires comparison if used) R formula string used for modeling, e.g. '~ treatment'." - } - }, - { - "comparison": { - "type": "string", - "description": "(Optional, mandatory if formula is used) Literal string passed to `limma::makeContrasts`, e.g. 'treatmentmCherry'." - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy map containing study-wide metadata related to the sample sheet\nand matrix\n" - } - }, - { - "samplesheet": { - "type": "file", - "description": "Sample sheet file", - "ontologies": [] - } - }, - { - "intensities": { - "type": "file", - "description": "Raw TSV or CSV format expression matrix with probes by row and samples\nby column\n", - "ontologies": [] - } - } - ] - ], - "output": { - "results": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing contrast information. This can be used at the\nworkflow level to pass optional parameters to the module, e.g.\n[ id:'contrast1', blocking:'patient' ] passed in as ext.args like:\n'--blocking_variable $meta.blocking'.\n" - } - }, - { - "*.limma.results.tsv": { - "type": "file", - "description": "TSV-format table of differential expression information as output by Limma", - "pattern": "*.limma.results.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "md_plot": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing contrast information. This can be used at the\nworkflow level to pass optional parameters to the module, e.g.\n[ id:'contrast1', blocking:'patient' ] passed in as ext.args like:\n'--blocking_variable $meta.blocking'.\n" - } - }, - { - "*.limma.mean_difference.png": { - "type": "file", - "description": "Limma mean difference plot", - "pattern": "*.mean_difference.png", - "ontologies": [] - } - } - ] - ], - "rdata": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing contrast information. This can be used at the\nworkflow level to pass optional parameters to the module, e.g.\n[ id:'contrast1', blocking:'patient' ] passed in as ext.args like:\n'--blocking_variable $meta.blocking'.\n" - } - }, - { - "*.MArrayLM.limma.rds": { - "type": "file", - "description": "Serialised MArrayLM object", - "pattern": "*.MArrayLM.limma.rds", - "ontologies": [] - } - } - ] - ], - "model": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing contrast information. This can be used at the\nworkflow level to pass optional parameters to the module, e.g.\n[ id:'contrast1', blocking:'patient' ] passed in as ext.args like:\n'--blocking_variable $meta.blocking'.\n" - } - }, - { - "*.limma.model.txt": { - "type": "file", - "description": "TXT-format limma model", - "pattern": "*.limma.model.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "session_info": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing contrast information. This can be used at the\nworkflow level to pass optional parameters to the module, e.g.\n[ id:'contrast1', blocking:'patient' ] passed in as ext.args like:\n'--blocking_variable $meta.blocking'.\n" - } - }, - { - "*.R_sessionInfo.log": { - "type": "file", - "description": "dump of R SessionInfo", - "pattern": "*.log", - "ontologies": [] - } - } - ] - ], - "normalised_counts": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing contrast information. This can be used at the\nworkflow level to pass optional parameters to the module, e.g.\n[ id:'contrast1', blocking:'patient' ] passed in as ext.args like:\n'--blocking_variable $meta.blocking'.\n" - } - }, - { - "*.normalised_counts.tsv": { - "type": "file", - "description": "normalised TSV format expression matrix with probes by row and samples by column", - "pattern": "*.normalised_counts.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "topics": { - "versions": [ - { - "versions.yml": { - "type": "string", - "description": "The name of the process" - } - } - ] - }, - "authors": [ - "@pinin4fjords" - ], - "maintainers": [ - "@pinin4fjords" - ] - }, - "pipelines": [ - { - "name": "differentialabundance", - "version": "1.5.0" - } - ] - }, - { - "name": "links", - "path": "modules/nf-core/links/meta.yml", - "type": "module", - "meta": { - "name": "links", - "description": "LINKS is a genomics application for scaffolding genome assemblies with long reads,\nsuch as those produced by Oxford Nanopore Technologies Ltd.\nIt can be used to scaffold high-quality draft genome assemblies with any long sequences\n(eg. ONT reads, PacBio reads, other draft genomes, etc).\nIt is also used to scaffold contig pairs linked by ARCS/ARKS.\nThis module is for LINKS >=2.0.0 and does not support MPET input.\n", - "keywords": [ - "scaffold", - "long-reads", - "genomics" - ], - "tools": [ - { - "links": { - "description": "Long Interval Nucleotide K-mer Scaffolder", - "homepage": "https://www.bcgsc.ca/resources/software/links", - "documentation": "https://github.com/bcgsc/LINKS", - "tool_dev_url": "https://github.com/bcgsc/LINKS", - "doi": "10.1186/s13742-015-0076-3", - "licence": [ - "GPL v3" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "assembly": { - "type": "file", - "description": "(Multi-)fasta file containing the draft assembly", - "pattern": "*.{fa,fasta,fa.gz,fasta.gz}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } + "name": "muscle5_super5", + "path": "modules/nf-core/muscle5/super5/meta.yml", + "type": "module", + "meta": { + "name": "muscle5_super5", + "description": "Muscle is a program for creating multiple alignments of amino acid or nucleotide sequences. This particular module uses the super5 algorithm for very big alignments. It can permutate the guide tree according to a set of flags.", + "keywords": ["align", "msa", "multiple sequence alignment"], + "tools": [ + { + "muscle -super5": { + "description": "Muscle v5 is a major re-write of MUSCLE based on new algorithms.", + "homepage": "https://drive5.com/muscle5/", + "documentation": "https://drive5.com/muscle5/manual/", + "doi": "10.1101/2021.06.20.449169", + "licence": ["Public Domain"], + "identifier": "" + } + }, + { + "pigz": { + "description": "Parallel implementation of the gzip algorithm.", + "homepage": "https://zlib.net/pigz/", + "documentation": "https://zlib.net/pigz/pigz.pdf", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input sequences for alignment must be in FASTA format", + "pattern": "*.{fasta,fa,fna}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1919" + }, + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + { + "compress": { + "type": "boolean", + "description": "Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded." + } + } + ], + "output": { + "alignment": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.aln{.gz,}": { + "type": "file", + "description": "Multiple sequence alignment produced in gzipped FASTA format. If '-perm all' is passed in ext.args, this will be multiple files per input!", + "pattern": "*.{aln.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2554" + }, + { + "edam": "http://edamontology.org/format_1921" + }, + { + "edam": "http://edamontology.org/format_1984" + } + ] + } + } + ] + ], + "versions_muscle": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "muscle": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "muscle -version | head -n 1 | cut -d \" \" -f 2 | sed \"s/.linux64//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_pigz": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "pigz": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pigz --version 2>&1 | sed \"s/^.*pigz[[:space:]]*//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "muscle": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "muscle -version | head -n 1 | cut -d \" \" -f 2 | sed \"s/.linux64//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "pigz": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pigz --version 2>&1 | sed \"s/^.*pigz[[:space:]]*//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@alessiovignoli", "@JoseEspinosa"], + "maintainers": ["@alessiovignoli", "@JoseEspinosa", "@lrauschning"] }, - { - "reads": { - "type": "file", - "description": "fastq file(s) containing the long reads to be used for scaffolding", - "pattern": "*.{fq,fastq,fq.gz,fastq.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "output": { - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } - }, - { - "*.log": { - "type": "file", - "description": "text file; Logs execution time / errors / pairing stats.", - "pattern": "*.log", - "ontologies": [] - } - } - ] - ], - "pairing_distribution": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } - }, - { - "*.pairing_distribution.csv": { - "type": "file", - "description": "comma-separated file; 1st column is the calculated distance\nfor each pair (template) with reads that assembled logically\nwithin the same contig. 2nd column is the number of pairs at\nthat distance.\n", - "pattern": "*.pairing_distribution.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "pairing_issues": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } - }, - { - "*.pairing_issues": { - "type": "file", - "description": "text file; Lists all pairing issues encountered between contig\npairs and illogical/out-of-bounds pairing.\n", - "pattern": "*.pairing_issues", - "ontologies": [] - } - } - ] - ], - "scaffolds_csv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } - }, - { - "*.scaffolds": { - "type": "file", - "description": "comma-separated file; containing the new scaffold(s)", - "pattern": "*.scaffolds", - "ontologies": [] - } - } - ] - ], - "scaffolds_fasta": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } - }, - { - "*.scaffolds.fa": { - "type": "file", - "description": "fasta file of the new scaffold sequence", - "pattern": "*.scaffolds.fa", - "ontologies": [] - } - } - ] - ], - "bloom": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } - }, - { - "*.bloom": { - "type": "file", - "description": "Bloom filter created by shredding the -f input\ninto k-mers of size -k\n", - "pattern": "*.bloom", - "ontologies": [] - } - } - ] - ], - "scaffolds_graph": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } - }, - { - "*.gv": { - "type": "file", - "description": "scaffold graph (for visualizing merges), can be rendered\nin neato, graphviz, etc\n", - "pattern": "*.gv", - "ontologies": [] - } - } - ] - ], - "assembly_correspondence": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } - }, - { - "*.assembly_correspondence.tsv": { - "type": "file", - "description": "correspondence file lists the scaffold ID,\ncontig ID, original_name, #linking kmer pairs,\nlinks ratio, gap or overlap\n", - "pattern": "*.assembly_correspondence.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "simplepair_checkpoint": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } - }, - { - "*.simplepair_checkpoint.tsv": { - "type": "file", - "description": "checkpoint file, contains info to rebuild datastructure for .gv graph", - "pattern": "*.simplepair_checkpoint.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "tigpair_checkpoint": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } - }, - { - "*.tigpair_checkpoint.tsv": { - "type": "file", - "description": "if -b BASNAME.tigpair_checkpoint.tsv is present,\nLINKS will skip the kmer pair extraction and contig pairing stages.\nDelete this file to force LINKS to start at the beginning.\nThis file can be used to:\n1) quickly test parameters (-l min. links / -a min. links ratio),\n2) quickly recover from crash,\n3) explore very large kmer spaces,\n4) scaffold with output of ARCS\n", - "pattern": "*.tigpair_checkpoint.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_links": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "liftoff": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "echo \\$(LINKS | grep -o 'LINKS v.*' | sed 's/LINKS v//')": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "liftoff": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "echo \\$(LINKS | grep -o 'LINKS v.*' | sed 's/LINKS v//')": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "multiplesequencealign", + "version": "1.1.1" + } ] - ] - }, - "authors": [ - "@nschan" - ], - "maintainers": [ - "@nschan" - ] - }, - "pipelines": [ - { - "name": "genomeassembler", - "version": "1.1.0" - } - ] - }, - { - "name": "lissero", - "path": "modules/nf-core/lissero/meta.yml", - "type": "module", - "meta": { - "name": "lissero", - "description": "Serogrouping Listeria monocytogenes assemblies", - "keywords": [ - "fasta", - "Listeria monocytogenes", - "serogroup" - ], - "tools": [ - { - "lissero": { - "description": "In silico serotyping of Listeria monocytogenes", - "homepage": "https://github.com/MDU-PHL/LisSero/blob/master/README.md", - "documentation": "https://github.com/MDU-PHL/LisSero/blob/master/README.md", - "tool_dev_url": "https://github.com/MDU-PHL/lissero", - "licence": [ - "GPL v3" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + }, + { + "name": "muse_call", + "path": "modules/nf-core/muse/call/meta.yml", + "type": "module", + "meta": { + "name": "muse_call", + "description": "pre-filtering and calculating position-specific summary statistics using the Markov substitution model", + "keywords": ["variant calling", "somatic", "wgs", "wxs", "vcf"], + "tools": [ + { + "MuSE": { + "description": "Somatic point mutation caller based on Markov substitution model for molecular evolution", + "homepage": "https://bioinformatics.mdanderson.org/public-software/muse/", + "documentation": "https://github.com/wwylab/MuSE", + "tool_dev_url": "https://github.com/wwylab/MuSE", + "doi": "10.1101/gr.278456.123", + "licence": ["https://github.com/danielfan/MuSE/blob/master/LICENSE"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "tumor_bam": { + "type": "file", + "description": "Sorted tumor BAM file", + "pattern": "*.bam", + "ontologies": [] + } + }, + { + "tumor_bai": { + "type": "file", + "description": "Index file for the tumor BAM file", + "pattern": "*.bai", + "ontologies": [] + } + }, + { + "normal_bam": { + "type": "file", + "description": "Sorted matched normal BAM file", + "pattern": "*.bam", + "ontologies": [] + } + }, + { + "normal_bai": { + "type": "file", + "description": "Index file for the normal BAM file", + "pattern": "*.bai", + "ontologies": [] + } + }, + { + "reference": { + "type": "file", + "description": "reference genome file", + "pattern": ".fasta", + "ontologies": [] + } + } + ] + ], + "output": { + "txt": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.MuSE.txt": { + "type": "file", + "description": "position-specific summary statistics", + "pattern": "*.MuSE.txt", + "ontologies": [] + } + } + ] + ], + "versions_muse": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "muse": { + "type": "string", + "description": "The tool name" + } + }, + { + "MuSE --version | sed -e 's/MuSE, version //g' | sed -e 's/MuSE v//g'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "muse": { + "type": "string", + "description": "The tool name" + } + }, + { + "MuSE --version | sed -e 's/MuSE, version //g' | sed -e 's/MuSE v//g'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@famosab"], + "maintainers": ["@famosab"] }, - { - "fasta": { - "type": "file", - "description": "FASTA assembly file", - "pattern": "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}", - "ontologies": [] - } - } - ] - ], - "output": { - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "Tab-delimited result file", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } + "pipelines": [ + { + "name": "sarek", + "version": "3.8.1" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@rpetit3" - ], - "maintainers": [ - "@rpetit3" - ] - } - }, - { - "name": "llamacpppython_run", - "path": "modules/nf-core/llamacpppython/run/meta.yml", - "type": "module", - "meta": { - "name": "llamacpppython_run", - "description": "Python wrapper for running locally-hosted LLM with llama.cpp", - "keywords": [ - "inference", - "llama", - "llm", - "local-inference", - "offline-llm" - ], - "tools": [ - { - "llama-cpp-python": { - "description": "Python wrapper for llama.cpp LLM inference tool", - "homepage": "https://llama-cpp-python.readthedocs.io/en/latest/", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "prompt_file": { - "type": "file", - "description": "Prompt file\nStructure: [ val(meta), path(prompt_file) ]\n", - "ontologies": [] - } + }, + { + "name": "muse_sump", + "path": "modules/nf-core/muse/sump/meta.yml", + "type": "module", + "meta": { + "name": "muse_sump", + "description": "Computes tier-based cutoffs from a sample-specific error model which is generated by muse/call and reports the finalized variants", + "keywords": ["variant calling", "somatic", "wgs", "wxs", "vcf"], + "tools": [ + { + "MuSE": { + "description": "Somatic point mutation caller based on Markov substitution model for molecular evolution", + "homepage": "https://bioinformatics.mdanderson.org/public-software/muse/", + "documentation": "https://github.com/wwylab/MuSE", + "tool_dev_url": "https://github.com/wwylab/MuSE", + "doi": "10.1101/gr.278456.123", + "licence": ["https://github.com/danielfan/MuSE/blob/master/LICENSE"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "muse_call_txt": { + "type": "file", + "description": "single input file generated by 'MuSE call'", + "pattern": "*.MuSE.txt", + "ontologies": [] + } + }, + { + "ref_vcf": { + "type": "file", + "description": "dbSNP vcf file that should be bgzip compressed, tabix indexed and\nbased on the same reference genome used in 'MuSE call'\n", + "pattern": ".vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + }, + { + "ref_vcf_tbi": { + "type": "file", + "description": "Tabix index for the dbSNP vcf file", + "pattern": ".vcf.gz.tbi", + "ontologies": [] + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.vcf.gz": { + "type": "map", + "description": "bgzipped vcf file with called variants", + "pattern": "*.vcf.gz" + } + } + ] + ], + "tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.vcf.gz.tbi": { + "type": "map", + "description": "tabix index of bgzipped vcf file with called variants", + "pattern": "*.vcf.gz.tbi" + } + } + ] + ], + "versions_muse": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "muse": { + "type": "string", + "description": "The tool name" + } + }, + { + "MuSE --version | sed -e 's/MuSE, version //g' | sed -e 's/MuSE v//g'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ], + "versions_bgzip": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bgzip": { + "type": "string", + "description": "The tool name" + } + }, + { + "bgzip --version | sed -n 's/bgzip (htslib) \\([0-9.]*\\)/\\1/p'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "muse": { + "type": "string", + "description": "The tool name" + } + }, + { + "MuSE --version | sed -e 's/MuSE, version //g' | sed -e 's/MuSE v//g'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bgzip": { + "type": "string", + "description": "The tool name" + } + }, + { + "bgzip --version | sed -n 's/bgzip (htslib) \\([0-9.]*\\)/\\1/p'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@famosab"], + "maintainers": ["@famosab"] }, - { - "gguf_model": { - "type": "file", - "description": "GGUF model\nStructure: [ val(meta), path(gguf_model) ]\n", - "ontologies": [] - } - } - ] - ], - "output": { - "output": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}.txt": { - "type": "file", - "description": "File with the output of LLM inference request", - "ontologies": [] - } - } + "pipelines": [ + { + "name": "sarek", + "version": "3.8.1" + } ] - ], - "versions_llama_cpp_python": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } + }, + { + "name": "mygene", + "path": "modules/nf-core/mygene/meta.yml", + "type": "module", + "meta": { + "name": "mygene", + "description": "Fetch the GO concepts for a list of genes", + "keywords": ["mygene", "go", "annotation"], + "tools": [ + { + "mygene": { + "description": "A python wrapper to query/retrieve gene annotation data from Mygene.info.", + "homepage": "https://mygene.info/", + "documentation": "https://docs.mygene.info/projects/mygene-py/en/latest/", + "tool_dev_url": "https://github.com/biothings/mygene.py", + "doi": "10.1093/nar/gks1114", + "licence": ["Apache-2.0"], + "identifier": "biotools:mygene" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "gene_list": { + "type": "file", + "description": "A tsv/csv file that contains a list of gene ids in one of the columns. By default, the column name should be \"gene_id\", but this can be changed by using \"--columname gene_id\" in ext.args.", + "pattern": "*.{csv,tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + }, + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "output": { + "gmt": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.gmt": { + "type": "file", + "description": "Each row contains the GO id, a description, and a list of gene ids.\n", + "pattern": "*.gmt", + "ontologies": [] + } + } + ] + ], + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "(optional) A tsv file with the following columns:\nquery, mygene_id, go_id, go_term, go_evidence, go_category, symbol, name, taxid\n", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_mygene": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "mygene": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "3.2.2": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "mygene": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "3.2.2": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@suzannejin"], + "maintainers": ["@suzannejin"] } - ] - }, - "topics": { - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } + }, + { + "name": "mykrobe_predict", + "path": "modules/nf-core/mykrobe/predict/meta.yml", + "type": "module", + "meta": { + "name": "mykrobe_predict", + "description": "AMR predictions for supported species", + "keywords": ["fastq", "bam", "antimicrobial resistance"], + "tools": [ + { + "mykrobe": { + "description": "Antibiotic resistance prediction in minutes", + "homepage": "http://www.mykrobe.com/", + "documentation": "https://github.com/Mykrobe-tools/mykrobe/wiki", + "tool_dev_url": "https://github.com/Mykrobe-tools/mykrobe", + "doi": "10.1038/ncomms10063", + "licence": ["MIT"], + "identifier": "biotools:Mykrobe" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "seqs": { + "type": "file", + "description": "BAM or FASTQ file", + "pattern": "*.{bam,fastq.gz,fq.gz}", + "ontologies": [] + } + } + ], + { + "species": { + "type": "string", + "description": "Species to make AMR prediction against", + "pattern": "*" + } + } + ], + "output": { + "csv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.csv": { + "type": "file", + "description": "AMR predictions in CSV format", + "pattern": "*.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "json": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.json": { + "type": "file", + "description": "AMR predictions in JSON format", + "pattern": "*.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@rpetit3"], + "maintainers": ["@rpetit3"] } - ] - }, - "authors": [ - "@toniher", - "@lucacozzuto" - ], - "maintainers": [ - "@toniher", - "@lucacozzuto" - ] - } - }, - { - "name": "localcdsearch_annotate", - "path": "modules/nf-core/localcdsearch/annotate/meta.yml", - "type": "module", - "meta": { - "name": "localcdsearch_annotate", - "description": "A command-line tool for local protein domain annotation using NCBI's Conserved Domain Database (CDD)", - "keywords": [ - "cdd", - "rpsblast", - "rpsbproc", - "protein", - "domain", - "annotation" - ], - "tools": [ - { - "localcdsearch": { - "description": "Protein annotation using local PSSM databases from CDD.", - "homepage": "https://github.com/apcamargo/local-cd-search", - "documentation": "https://github.com/apcamargo/local-cd-search", - "tool_dev_url": "https://github.com/apcamargo/local-cd-search", - "licence": [ - "MIT" - ], - "identifier": "" + }, + { + "name": "myloasm", + "path": "modules/nf-core/myloasm/meta.yml", + "type": "module", + "meta": { + "name": "myloasm", + "description": "Myloasm is a de novo metagenome assembler for long-read sequencing data.\nIt takes sequencing reads and outputs polished contigs in a single command.\n", + "keywords": ["assembly", "metagenome", "long-read", "pacbio", "nanopore"], + "tools": [ + { + "myloasm": { + "description": "Myloasm is a long-read assembler for metagenomes", + "homepage": "https://myloasm-docs.github.io", + "documentation": "https://myloasm-docs.github.io", + "tool_dev_url": "https://github.com/bluenote-1577/myloasm/tree/main", + "doi": "10.1101/2025.09.05.674543", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "reads": { + "type": "file", + "description": "Input long reads in FASTQ or FASTA format (FASTQ preferred for base quality information)", + "pattern": "*.{fastq,fq,fastq.gz,fq.gz,fasta,fa,fasta.gz,fa.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + }, + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ] + ], + "output": { + "results": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "${prefix}": { + "type": "directory", + "description": "Directory containing all myloasm output files and folders", + "pattern": "*" + } + } + ] + ], + "contigs": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "${prefix}/assembly_primary.fa": { + "type": "file", + "description": "Primary assembly contigs in FASTA format", + "pattern": "assembly_primary.fa", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ] + ], + "gfa": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "${prefix}/final_contig_graph.gfa": { + "type": "file", + "description": "Final contig graph in GFA format", + "pattern": "final_contig_graph.gfa", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3975" + } + ] + } + } + ] + ], + "contigs_alt": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "${prefix}/alternate_assemblies/assembly_alternate.fa": { + "type": "file", + "description": "Alternative assembly contigs in FASTA format", + "pattern": "assembly_alternate.fa", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ] + ], + "contigs_dup": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "${prefix}/alternate_assemblies/duplicated_contigs.fa": { + "type": "file", + "description": "Duplicated contigs in FASTA format", + "pattern": "duplicated_contigs.fa", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ] + ], + "mapping": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "${prefix}/3-mapping/map_to_unitigs.paf.gz": { + "type": "file", + "description": "Mapping of reads to unitigs in PAF format (compressed)", + "pattern": "map_to_unitigs.paf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "${prefix}/*.log": { + "type": "file", + "description": "MyloAsm log files containing assembly process information", + "pattern": "*.log", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + } + ] + ], + "versions_myloasm": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "myloasm": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "myloasm --version | sed 's/.* //'": { + "type": "eval", + "description": "The expression used to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "myloasm": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "myloasm --version | sed 's/.* //'": { + "type": "eval", + "description": "The expression used to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@vagkaratzas"], + "maintainers": ["@vagkaratzas"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } + }, + { + "name": "nacho_normalize", + "path": "modules/nf-core/nacho/normalize/meta.yml", + "type": "module", + "meta": { + "name": "nacho_normalize", + "description": "NACHO (NAnostring quality Control dasHbOard) is developed for NanoString nCounter data.\nNanoString nCounter data is a messenger-RNA/micro-RNA (mRNA/miRNA) expression assay and works with fluorescent barcodes.\nEach barcode is assigned a mRNA/miRNA, which can be counted after bonding with its target.\nAs a result each count of a specific barcode represents the presence of its target mRNA/miRNA.\n", + "keywords": ["nacho", "nanostring", "mRNA", "miRNA", "qc"], + "tools": [ + { + "NACHO": { + "description": "R package that uses two main functions to summarize and visualize NanoString RCC files,\nnamely: `load_rcc()` and `visualise()`. It also includes a function `normalise()`, which (re)calculates\nsample specific size factors and normalises the data.\nFor more information `vignette(\"NACHO\")` and `vignette(\"NACHO-analysis\")`\n", + "homepage": "https://github.com/mcanouil/NACHO", + "documentation": "https://cran.r-project.org/web/packages/NACHO/vignettes/NACHO.html", + "doi": "10.1093/bioinformatics/btz647", + "licence": ["GPL-3.0"], + "identifier": "", + "args_id": "$args" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "rcc_files": { + "type": "file", + "description": "List of RCC files for all samples, which are direct outputs from NanoString runs\n", + "pattern": "*.RCC", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing file information\ne.g. [ id:'test_samplesheet' ]\n" + } + }, + { + "sample_sheet": { + "type": "file", + "pattern": "*.csv", + "description": "Comma-separated file with 3 columns: RCC_FILE, RCC_FILE_NAME, and SAMPLE_ID\n", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "output": { + "normalized_counts": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "normalized_counts.tsv": { + "type": "file", + "description": "Tab-separated file with gene normalized counts for the samples\n", + "pattern": "normalized_counts.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "normalized_counts_wo_HK": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "normalized_counts_wo_HKnorm.tsv": { + "type": "file", + "description": "Tab-separated file with gene normalized counts for the samples, without housekeeping genes.\n", + "pattern": "normalized_counts_wo_HKnorm.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions\n", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@alanmmobbs93"], + "maintainers": ["@alanmmobbs93"] }, - 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It also includes a function `normalise()`, which (re)calculates\nsample specific size factors and normalises the data.\nFor more information `vignette(\"NACHO\")` and `vignette(\"NACHO-analysis\")`\n", + "homepage": "https://github.com/mcanouil/NACHO", + "documentation": "https://cran.r-project.org/web/packages/NACHO/vignettes/NACHO.html", + "doi": "10.1093/bioinformatics/btz647", + "licence": ["GPL-3.0"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "rcc_files": { + "type": "file", + "description": "List of RCC files for all samples, which are direct outputs from NanoString runs\n", + "pattern": "*.RCC", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing file information\ne.g. [ id:'test_samplesheet' ]\n" + } + }, + { + "sample_sheet": { + "type": "file", + "pattern": "*.csv", + "description": "Comma-separated file with 3 columns: RCC_FILE, RCC_FILE_NAME, and SAMPLE_ID\n", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "output": { + "nacho_qc_reports": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.html": { + "type": "file", + "description": "HTML report\n", + "pattern": "*.html", + "ontologies": [] + } + } + ] + ], + "nacho_qc_png": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*_mqc.png": { + "type": "file", + "description": "Output PNG files\n", + "pattern": "*_mqc.png", + "ontologies": [] + } + } + ] + ], + "nacho_qc_txt": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*_mqc.txt": { + "type": "file", + "description": "Plain text reports\n", + "pattern": "*_mqc.txt", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions\n", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@alanmmobbs93"], + "maintainers": ["@alanmmobbs93"] }, - 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Specify with 'true' to save." + } + } + ], + "output": { + "output": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.txt": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*.{txt}" + } + } + ] + ], + "target_summary": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.tbl": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "results.tbl" + } + } + ] + ], + "alignments": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.ali": { + "type": "map", + "description": "Groovy Map containing 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It's indelqual programme inserts indel qualities in a BAM file", - "homepage": "https://csb5.github.io/lofreq/", - "doi": "10.1093/nar/gks918", - "licence": [ - "MIT" - ], - "identifier": "biotools:lofreq" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file", - "pattern": "*.{bam}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information about the reference fasta\ne.g. [ id:'reference' ]\n" - } + }, + { + "name": "nanoq", + "path": "modules/nf-core/nanoq/meta.yml", + "type": "module", + "meta": { + "name": "nanoq", + "description": "Nanoq implements ultra-fast read filters and summary reports for high-throughput nanopore reads.", + "keywords": ["nanoq", "Read filters", "Read trimming", "Read report"], + "tools": [ + { + "nanoq": { + "description": "Ultra-fast quality control and summary reports for nanopore reads", + "homepage": "https://github.com/esteinig/nanoq", + "documentation": "https://github.com/esteinig/nanoq", + "tool_dev_url": "https://github.com/esteinig/nanoq", + "doi": "10.21105/joss.02991", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "ontreads": { + "type": "file", + "description": "Compressed or uncompressed nanopore reads in fasta or fastq formats.", + "pattern": "*.{fa,fna,faa,fasta,fq,fastq}{,.gz,.bz2,.xz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ], + { + "output_format": { + "type": "string", + "description": "Specifies the output format. One of these formats: fasta, fastq; fasta.gz, fastq.gz; fasta.bz2, fastq.bz2; fasta.lzma, fastq.lzma." + } + } + ], + "output": { + "stats": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.{stats,json}": { + "type": "file", + "description": "Summary report of reads statistics.", + "pattern": "*.{stats,json}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "reads": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}.${output_format}": { + "type": "file", + "description": "Filtered reads.", + "pattern": "*.{fasta,fastq}{,.gz,.bz2,.lzma}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ] + ], + "versions_nanoq": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "nanoq": { + "type": "string", + "description": "The tool name" + } + }, + { + "nanoq --version | sed -e 's/nanoq //g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "nanoq": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "nanoq --version | sed -e 's/nanoq //g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@LilyAnderssonLee"], + "maintainers": ["@LilyAnderssonLee"] }, - { - "fasta": { - "type": "file", - "description": "Reference genome FASTA file", - "pattern": "*.{fasta,fa}", - "ontologies": [] - } - } - ] - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map 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alignments when tumor-normal paired samples are available", - "keywords": [ - "variant calling", - "low frequency variant calling", - "somatic", - "variants", - "vcf" - ], - "tools": [ - { - "lofreq": { - "description": "A fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data", - "homepage": "https://csb5.github.io/lofreq/", - "documentation": "https://csb5.github.io/lofreq/commands/", - "doi": "10.1093/nar/gks918", - "licence": [ - "MIT" - ], - "identifier": "biotools:lofreq" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]" - } - }, - { - "tumor": { - "type": "file", - "description": "tumor sample input BAM file", - "pattern": "*.{bam}", - "ontologies": [] - } - }, - { - "tumor_index": { - "type": "file", - "description": "tumor sample BAM index file", - "pattern": "*.{bam.bai}", - "ontologies": [] - } - }, - { - "normal": { - "type": "file", - "description": "normal sample input BAM file", - "pattern": "*.{bam}", - "ontologies": [] - } - }, - { - "normal_index": { - "type": "file", - "description": "normal sample BAM index file", - "pattern": "*.{bam.bai}", - "ontologies": [] - } - }, - { - "target_bed": { - "type": "file", - "description": "BED file containing target regions for variant calling", - "pattern": "*.{bed}", - "ontologies": [] - } + }, + { + "name": "narfmap_align", + "path": "modules/nf-core/narfmap/align/meta.yml", + "type": "module", + "meta": { + "name": "narfmap_align", + "description": "Performs fastq alignment to a reference using NARFMAP", + "keywords": ["alignment", "map", "fastq", "bam", "sam"], + "tools": [ + { + "narfmap": { + "description": "narfmap is a fork of the Dragen mapper/aligner Open Source Software.", + "homepage": "https://github.com/bioinformaticsorphanage/NARFMAP", + "documentation": "https://github.com/bioinformaticsorphanage/NARFMAP/blob/main/doc/usage.md#basic-command-line-usage", + "tool_dev_url": "https://github.com/bioinformaticsorphanage/NARFMAP", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "hashmap": { + "type": "file", + "description": "NARFMAP hash table", + "pattern": "Directory containing NARFMAP hash table *.{cmp,.bin,.txt}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference genome in FASTA format", + "pattern": "*.{fasta,fa,fna}", + "ontologies": [] + } + } + ], + { + "sort_bam": { + "type": "boolean", + "description": "Sort the BAM file after alignment" + } + } + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "file", + "description": "Output BAM file containing read alignments", + "pattern": "*.{bam}", + "ontologies": [] + } + }, + { + "*.bam": { + "type": "file", + "description": "Output BAM file containing read alignments", + "pattern": "*.{bam}", + "ontologies": [] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "file", + "description": "Output BAM file containing read alignments", + "pattern": "*.{bam}", + "ontologies": [] + } + }, + { + "*.log": { + "type": "file", + "description": "Log file of NARFMAP run", + "pattern": "*{.log}", + "ontologies": [] + } + } + ] + ], + "versions_narfmap": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "narfmap": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "dragen-os --version 2>&1": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_samtools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "samtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "samtools version | sed '1!d;s/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_pigz": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "pigz": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pigz --version 2>&1 | sed 's/pigz //g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "narfmap": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "dragen-os --version 2>&1": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "samtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "samtools version | sed '1!d;s/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "pigz": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pigz --version 2>&1 | sed 's/pigz //g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@edmundmiller"], + "maintainers": ["@edmundmiller"] } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome FASTA file", - "pattern": "*.{fasta}", - "ontologies": [] - } + }, + { + "name": "narfmap_hashtable", + "path": "modules/nf-core/narfmap/hashtable/meta.yml", + "type": "module", + "meta": { + "name": "narfmap_hashtable", + "description": "Create DRAGEN hashtable for reference genome", + "keywords": ["index", "fasta", "genome", "reference"], + "tools": [ + { + "narfmap": { + "description": "narfmap is a fork of the Dragen mapper/aligner Open Source Software.", + "homepage": "https://github.com/edmundmiller/narfmap", + "documentation": "https://github.com/edmundmiller/NARFMAP/blob/main/doc/usage.md#basic-command-line-usage", + "tool_dev_url": "https://github.com/edmundmiller/narfmap", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input genome fasta file", + "ontologies": [] + } + } + ] + ], + "output": { + "hashmap": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "narfmap": { + "type": "file", + "description": "NARFMAP hash table", + "pattern": "*.{cmp,.bin,.txt}", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@edmundmiller"], + "maintainers": ["@edmundmiller"] } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information" - } + }, + { + "name": "ncbigenomedownload", + "path": "modules/nf-core/ncbigenomedownload/meta.yml", + "type": "module", + "meta": { + "name": "ncbigenomedownload", + "description": "A tool to quickly download assemblies from NCBI's Assembly database", + "keywords": ["fasta", "download", "assembly"], + "tools": [ + { + "ncbigenomedownload": { + "description": "Download genome files from the NCBI FTP server.", + "homepage": "https://github.com/kblin/ncbi-genome-download", + "documentation": "https://github.com/kblin/ncbi-genome-download", + "tool_dev_url": "https://github.com/kblin/ncbi-genome-download", + "licence": ["Apache Software License"], + "identifier": "" + } + } + ], + "input": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "accessions": { + "type": "file", + "description": "List of accessions (one per line) to download", + "pattern": "*.txt", + "ontologies": [] + } + }, + { + "taxids": { + "type": "file", + "description": "List of taxids (one per line) to download", + "pattern": "*.txt", + "ontologies": [] + } + }, + { + "groups": { + "type": "string", + "description": "NCBI taxonomic groups to download. Can be a comma-separated list. Options are ['all', 'archaea', 'bacteria', 'fungi', 'invertebrate', 'metagenomes', 'plant', 'protozoa', 'vertebrate_mammalian', 'vertebrate_other', 'viral']" + } + } + ], + "output": { + "gbk": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_genomic.gbff.gz": { + "type": "file", + "description": "GenBank format of the genomic sequence(s) in the assembly", + "pattern": "*_genomic.gbff.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "fna": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_genomic.fna.gz": { + "type": "file", + "description": "FASTA format of the genomic sequence(s) in the assembly.", + "pattern": "*_genomic.fna.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "rm": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_rm.out.gz": { + "type": "file", + "description": "RepeatMasker output for eukaryotes.", + "pattern": "*_rm.out.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "features": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_feature_table.txt.gz": { + "type": "file", + "description": "Tab-delimited text file reporting locations and attributes for a subset of annotated features", + "pattern": "*_feature_table.txt.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "gff": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_genomic.gff.gz": { + "type": "file", + "description": "Annotation of the genomic sequence(s) in GFF3 format", + "pattern": "*_genomic.gff.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "faa": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_protein.faa.gz": { + "type": "file", + "description": "FASTA format of the accessioned protein products annotated on the genome assembly.", + "pattern": "*_protein.faa.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "gpff": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_protein.gpff.gz": { + "type": "file", + "description": "GenPept format of the accessioned protein products annotated on the genome assembly.", + 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higher mismatch rates than comparable algorithms while\nstill outperforming them in terms of runtime\n", + "homepage": "https://github.com/Cibiv/NextGenMap", + "documentation": "https://github.com/Cibiv/NextGenMap/wiki", + "doi": "10.1093/bioinformatics/btt468", + "licence": ["MIT"], + "identifier": "biotools:nextgenmap" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1, if meta.single_end is true, and 2\nif meta.single_end is false.\n", + "ontologies": [] + } + } + ], + { + "fasta": { + "type": "file", + "description": "Genomic reference fasta file\n", + "pattern": "*.{fa,fa.gz,fas,fas.gz,fna,fna.gz,fasta,fasta.gz}", + "ontologies": [] + } + } + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information. First item of tuple with\nbam, below.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Output BAM file containing read alignments. Second item of tuple with\nmeta, above\n", + "pattern": "*.{bam}", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@cmatkhan"], + "maintainers": ["@cmatkhan"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM/CRAM file(s)", - "pattern": "*.{bam,cram}", - "ontologies": [] - } - }, - { - "bai": { - "type": "file", - "description": "Index of sorted BAM/CRAM file(s)", - "pattern": "*.{bai,crai,csi}", - "ontologies": [] - } - }, - { - "snvs": { - "type": "file", - "description": "VCF file with SNPs (and INDELs)", - "pattern": "*.{vcf,vcf.gz}", - "ontologies": [] - } - }, - { - "svs": { - "type": "file", - "description": "VCF file with SVs", - "pattern": "*.{vcf,vcf.gz}", - "ontologies": [] - } - }, - { - "mods": { - "type": "file", - "description": "modcall-generated VCF with modifications", - "pattern": "*.{vcf,vcf.gz}", - "ontologies": [] - } + }, + { + "name": "ngmaster", + "path": "modules/nf-core/ngmaster/meta.yml", + "type": "module", + "meta": { + "name": "ngmaster", + "description": "Serotyping Neisseria gonorrhoeae assemblies", + "keywords": ["fasta", "Neisseria gonorrhoeae", "serotype"], + "tools": [ + { + "ngmaster": { + "description": "In silico multi-antigen sequence typing for Neisseria gonorrhoeae (NG-MAST)", + "homepage": "https://github.com/MDU-PHL/ngmaster/blob/master/README.md", + "documentation": "https://github.com/MDU-PHL/ngmaster/blob/master/README.md", + "tool_dev_url": "https://github.com/MDU-PHL/ngmaster", + "doi": "10.1099/mgen.0.000076", + "licence": ["GPL v3 only"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA assembly file", + "pattern": "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}", + "ontologies": [] + } + } + ] + ], + "output": { + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "Tab-delimited result file", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@rpetit3"], + "maintainers": ["@rpetit3"] } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. `[ id:'hg38' ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference fasta file", - "pattern": "*.fasta", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. `[ id:'hg38' ]`\n" - } - }, - { - "fai": { - "type": "file", - "description": "Reference fai index", - "pattern": "*.fai", - "ontologies": [] - } - } - ] - ], - "output": { - "snv_vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "${prefix}.vcf.gz": { - "type": "file", - "description": "Compressed VCF file with phased SNVs and indels", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "sv_vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "${prefix}_SV.vcf.gz": { - "type": "file", - "description": "Compressed VCF file with phased SVs", - "pattern": "*_SV.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "mod_vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "${prefix}_mod.vcf.gz": { - "type": "file", - "description": "Compressed VCF file with phased modifications", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "versions_longphase": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "longphase": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "longphase --version | head -n 1 | sed 's/Version: //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "longphase": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "longphase --version | head -n 1 | sed 's/Version: //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@fellen31" - ], - "maintainers": [ - "@fellen31" - ] - } - }, - { - "name": "longstitch", - "path": "modules/nf-core/longstitch/meta.yml", - "type": "module", - "meta": { - "name": "longstitch", - "description": "\"A genome assembly correction and scaffolding pipeline using long reads, consisting of up to three steps:\n - Tigmint cuts the draft assembly at potentially misassembled regions\n - ntLink is then used to scaffold the corrected assembly\n - followed by ARKS for further scaffolding (optional)\"\n", - "keywords": [ - "scaffolding", - "long read", - "assembly correction" - ], - "tools": [ - { - "longstitch": { - "description": "A genome assembly correction and scaffolding pipeline using long reads", - "homepage": "https://github.com/bcgsc/longstitch", - "documentation": "https://github.com/bcgsc/longstitch", - "tool_dev_url": "https://github.com/bcgsc/longstitch", - "doi": "10.1186/s12859-021-04451-7", - "licence": [ - "GPL v3-or-later", - "GPL v3" - ], - "identifier": "biotools:longstitch" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "assembly": { - "type": "file", - "description": "Draft assembly", - "pattern": "*.{fa,fasta,fa.gz,fasta.gz}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "reads": { - "type": "file", - "description": "long reads", - "pattern": "*.{fq,fastq,fq.gz,fastq.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ], - { - "command": { - "type": "string", - "description": "Longstitch command to run. Valid options are:\n[\"run\", \"tigmint-ntLink-arks\", \"tigmint-ntLink\", \"ntLink-arks\"]\n" - } - }, - { - "span": { - "type": "string", - "description": "min number of spanning molecules to be considered correctly assembled.\nEither span or genomesize need to be provided.\n" - } - }, - { - "genomesize": { - "type": "string", - "description": "Expected genome size. Either span or genomesize need to be provided.\n" - } - }, - { - "longmap": { - "type": "string", - "description": "Type of long-read (passed to minimap2). Valid options are:\n[ \"ont\", \"pb\", \"hifi\" ]\n" - } - } - ], - "output": { - "tigmint_ntLink_fasta": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.tigmint-ntLink.fa": { - "type": "file", - "description": "Fasta file after tigmint and ntLink", - "pattern": "*.tigmint-ntLink.fa", - "ontologies": [] - } - } - ] - ], - "tigmint_ntLink_arcs_fasta": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.tigmint-ntLink-arks.fa": { - "type": "file", - "description": "Fasta file after tigmint, ntLink and arcs+links", - "pattern": "*.tigmint-ntLink-arks.fa", - "ontologies": [] - } - } - ] - ], - "ntLink_arcs_fasta": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.ntLink-arks.fa": { - "type": "file", - "description": "Fasta file after ntLink and arcs+links", - "pattern": "*.ntLink-arks.fa", - "ontologies": [] - } - } - ] - ], - "scaffold_dot": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*k*.w*.z*.n*.scaffold.dot": { - "type": "file", - "description": "Scaffold dot file", - "pattern": "*k*.w*.z*.n*.scaffold.dot", - "ontologies": [] - } - } - ] - ], - "links_scaffolds_dist_gv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*k*.w*.z*.ntLink.scaffolds_*.dist.gv": { - "type": "file", - "description": "ntLink scaffold distance gv file", - "pattern": "*k*.w*.z*.ntLink.scaffolds_*.dist.gv", - "ontologies": [] - } - } - ] - ], - "links_assembly_correspondence_tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*k*.w*.z*.ntLink.scaffolds_*_l*.assembly_correspondence.tsv": { - "type": "file", - "description": "ntLink assembly correspondance table", - "pattern": "*k*.w*.z*.ntLink.scaffolds_*_l*.assembly_correspondence.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "links_gv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*k*.w*.z*.ntLink.scaffolds_*_l*.gv": { - "type": "file", - "description": "Links graph", - "pattern": "*k*.w*.z*.ntLink.scaffolds_*_l*.gv", - "ontologies": [] - } - } - ] - ], - "links_log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*k*.w*.z*.ntLink.scaffolds_*_l*.log": { - "type": "file", - "description": "Links logfile", - "pattern": "*k*.w*.z*.ntLink.scaffolds_*_l*.log", - "ontologies": [] - } - } - ] - ], - "links_scaffolds": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*k*.w*.z*.ntLink.scaffolds_*_l*.scaffolds": { - "type": "file", - "description": "links scaffolds", - "pattern": "*k*.w*.z*.ntLink.scaffolds_*_l*.scaffolds", - "ontologies": [] - } - } - ] - ], - "links_scaffolds_fa": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*k*.w*.z*.ntLink.scaffolds_*_l*.scaffolds.fa": { - "type": "file", - "description": "links scaffolds fasta", - "pattern": "*k*.w*.z*.ntLink.scaffolds_*_l*.scaffolds.fa", - "ontologies": [] - } - } - ] - ], - "links_checkpoint_tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*k*.w*.z*.ntLink.scaffolds_*_l*.*.tigpair_checkpoint.tsv": { - "type": "file", - "description": "tigpair checkpoint for links", - "pattern": "*k*.w*.z*.ntLink.scaffolds_*_l*.tigpair_checkpoint.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "arcs_tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*k*.w*.z*.ntLink.scaffolds_*_main.tsv": { - "type": "file", - "description": "arcs tsv file", - "pattern": "*k*.w*.z*.ntLink.scaffolds_*_main.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "arcs_gv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*k*.w*.z*.ntLink.scaffolds_*_original.gv": { - "type": "file", - "description": "arcs graph", - "pattern": "*k*.w*.z*.ntLink.scaffolds_*_original.gv", - "ontologies": [] - } - } - ] - ], - "arcs_checkpoint_tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*k*.w*.z*.ntLink.scaffolds_*.tigpair_checkpoint.tsv": { - "type": "file", - "description": "tigpair checkpoint for arcs", - "pattern": "*k*.w*.z*.ntLink.scaffolds_*.tigpair_checkpoint.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "arcs_scaffolds_fa": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*k*.w*.z*.ntLink.scaffolds.fa": { - "type": "file", - "description": "arcs scaffolds fasta", - "pattern": "*k*.w*.z*.ntLink.scaffolds.fa", - "ontologies": [] - } - } - ] - ], - "arcs_scaffolds_renamed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*k*.w*.z*.ntLink.scaffolds.renamed.fa": { - "type": "file", - "description": "renamed arcs scaffolds fasta file", - "pattern": "*k*.w*.z*.ntLink.scaffolds.renamed.fa", - "ontologies": [] - } - } - ] - ], - "abyss_scaffolds_fa": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*k*.w*.z*.stitch.abyss-scaffold.fa": { - "type": "file", - "description": "abyss scaffolds fasta file", - "pattern": "*k*.w*.z*.stitch.abyss-scaffold.fa", - "ontologies": [] - } - } - ] - ], - "stitch_path": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*k*.w*.z*.stitch.path": { - "type": "file", - "description": "stitch paths", - "pattern": "*k*.w*.z*.stitch.path", - "ontologies": [] - } - } - ] - ], - "trimmed_scaffolds_agp": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*k*.w*.z*.trimmed_scafs.agp": { - "type": "file", - "description": "trimmed scaffolds in agp format", - "pattern": "*k*.w*.z*.trimmed_scafs.agp", - "ontologies": [] - } - } - ] - ], - "trimmed_scaffolds_fasta": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*k*.w*.z*.trimmed_scafs.fa": { - "type": "file", - "description": "trimmed scaffolds in fasta format", - "pattern": "*k*.w*.z*.trimmed_scafs.fa", - "ontologies": [] - } - } - ] - ], - "trimmed_scaffolds_path": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*k*.w*.z*.trimmed_scafs.path": { - "type": "file", - "description": "trimmed scaffolds path", - "pattern": "*k*.w*.z*.trimmed_scafs.path", - "ontologies": [] - } - } - ] - ], - "trimmed_scaffolds_tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*k*.w*.z*.trimmed_scafs.tsv": { - "type": "file", - "description": "trimmed scaffolds tsv", - "pattern": "*k*.w*.z*.trimmed_scafs.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "verbose_mapping_tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*k*.w*.z*.verbose_mapping.tsv": { - "type": "file", - "description": "trimmed scaffolds mapping", - "pattern": "*k*.w*.z*.verbose_mapping.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.k*.w???.tsv": { - "type": "file", - "description": "scaffolding tsv file", - "pattern": "*.k*.w???.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@nschan" - ], - "maintainers": [ - "@nschan" - ] - } - }, - { - "name": "lsa_cosine", - "path": "modules/nf-core/lsa/cosine/meta.yml", - "type": "module", - "meta": { - "name": "lsa_cosine", - "description": "Calculates the cosine similarity matrix between samples based on a gene expression matrix.", - "keywords": [ - "similarity", - "cosine", - "clustering", - "rnaseq", - "heatmap" - ], - "tools": [ - { - "lsa": { - "description": "Latent Semantic Analysis (LSA) package for R.", - "homepage": "https://cran.r-project.org/web/packages/lsa/index.html", - "documentation": "https://cran.r-project.org/web/packages/lsa/lsa.pdf", - "licence": [ - "GPL-2" - ], - "identifier": "" - } - }, - { - "pheatmap": { - "description": "Pretty Heatmaps package for R.", - "homepage": "https://cran.r-project.org/web/packages/pheatmap/index.html", - "documentation": "https://cran.r-project.org/web/packages/pheatmap/pheatmap.pdf", - "licence": [ - "GPL-2" - ], - "identifier": "biotools:pheatmap" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information, e.g. [ id:'test' ].\n" - } - }, - { - "expression_matrix": { - "type": "file", - "description": "CSV file containing the expression matrix.\nRows should be features (genes) and columns should be samples.\n", - "pattern": "*.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "output": { - "matrix": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information, e.g. [ id:'test' ].\n" - } - }, - { - "*_matrix.csv": { - "type": "file", - "description": "A square matrix (CSV) containing pairwise similarity scores.", - "pattern": "*_matrix.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "heatmap": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information, e.g. [ id:'test' ].\n" - } - }, - { - "*_heatmap.png": { - "type": "file", - "description": "A PNG image visualizing the similarity matrix as a heatmap.", - "pattern": "*_heatmap.png", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions.", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@miguelrosell" - ], - "maintainers": [ - "@miguelrosell" - ] - } - }, - { - "name": "ltrfinder", - "path": "modules/nf-core/ltrfinder/meta.yml", - "type": "module", - "meta": { - "name": "ltrfinder", - "description": "Finds full-length LTR retrotranspsons in genome sequences using the\nparallel version of LTR_Finder\n", - "keywords": [ - "genomics", - "annotation", - "parallel", - "repeat", - "long terminal retrotransposon", - "retrotransposon" - ], - "tools": [ - { - "LTR_FINDER_parallel": { - "description": "A Perl wrapper for LTR_FINDER", - "homepage": "https://github.com/oushujun/LTR_FINDER_parallel", - "documentation": "https://github.com/oushujun/LTR_FINDER_parallel", - "tool_dev_url": "https://github.com/oushujun/LTR_FINDER_parallel", - "doi": "10.1186/s13100-019-0193-0", - "licence": [ - "MIT" - ], - "identifier": "" - } - }, - { - "LTR_Finder": { - "description": "An efficient program for finding full-length LTR retrotranspsons in genome sequences", - "homepage": "https://github.com/xzhub/LTR_Finder", - "documentation": "https://github.com/xzhub/LTR_Finder", - "tool_dev_url": "https://github.com/xzhub/LTR_Finder", - "doi": "10.1093/nar/gkm286", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Genome sequences in fasta format", - "pattern": "*.{fsa,fa,fasta}", - "ontologies": [] - } - } - ] - ], - "output": { - "scn": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.scn": { - "type": "file", - "description": "Annotation in LTRharvest or LTR_FINDER format", - "pattern": "*.scn", - "ontologies": [] - } - } - ] - ], - "gff": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.gff3": { - "type": "file", - "description": "Annotation in gff3 format", - "pattern": "*.gff3", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@GallVp" - ], - "maintainers": [ - "@GallVp" - ] - } - }, - { - "name": "ltrharvest", - "path": "modules/nf-core/ltrharvest/meta.yml", - "type": "module", - "meta": { - "name": "ltrharvest", - "description": "Predicts LTR retrotransposons using the parallel version of GenomeTools gt-ltrharvest\nutility included in the EDTA toolchain\n", - "keywords": [ - "genomics", - "genome", - "annotation", - "repeat", - "transposons", - "retrotransposons" - ], - "tools": [ - { - "LTR_HARVEST_parallel": { - "description": "A Perl wrapper for LTR_harvest", - "homepage": "https://github.com/oushujun/EDTA/tree/v2.2.0/bin/LTR_HARVEST_parallel", - "documentation": "https://github.com/oushujun/EDTA/tree/v2.2.0/bin/LTR_HARVEST_parallel", - "tool_dev_url": "https://github.com/oushujun/EDTA/tree/v2.2.0/bin/LTR_HARVEST_parallel", - "licence": [ - "MIT" - ], - "identifier": "" - } - }, - { - "gt": { - "description": "The GenomeTools genome analysis system", - "homepage": "https://genometools.org/index.html", - "documentation": "https://genometools.org/documentation.html", - "tool_dev_url": "https://github.com/genometools/genometools", - "doi": "10.1109/TCBB.2013.68", - "licence": [ - "ISC" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input genome fasta", - "pattern": "*.{fsa,fa,fasta}", - "ontologies": [] - } - } - ] - ], - "output": { - "gff3": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.gff3": { - "type": "file", - "description": "Predicted LTR candidates in gff3 format", - "pattern": "*.gff3", - "ontologies": [] - } - } - ] - ], - "scn": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.scn": { - "type": "file", - "description": "Predicted LTR candidates in scn format", - "pattern": "*.scn", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@GallVp" - ], - "maintainers": [ - "@GallVp" - ] - } - }, - { - "name": "ltrretriever_lai", - "path": "modules/nf-core/ltrretriever/lai/meta.yml", - "type": "module", - "meta": { - "name": "ltrretriever_lai", - "description": "Estimates the mean LTR sequence identity in the genome. The input genome fasta should\nhave short alphanumeric IDs without comments\n", - "keywords": [ - "genomics", - "annotation", - "repeat", - "long terminal retrotransposon", - "retrotransposon", - "stats", - "qc" - ], - "tools": [ - { - "lai": { - "description": "Assessing genome assembly quality using the LTR Assembly Index (LAI)", - "homepage": "https://github.com/oushujun/LTR_retriever", - "documentation": "https://github.com/oushujun/LTR_retriever", - "tool_dev_url": "https://github.com/oushujun/LTR_retriever", - "doi": "10.1093/nar/gky730", - "licence": [ - "GPL v3" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "The genome file that is used to generate everything", - "pattern": "*.{fsa,fa,fasta}", - "ontologies": [] - } - } - ], - { - "pass_list": { - "type": "file", - "description": "A list of intact LTR-RTs generated by LTR_retriever", - "pattern": "*.pass.list", - "ontologies": [] - } - }, - { - "annotation_out": { - "type": "file", - "description": "RepeatMasker annotation of all LTR sequences in the genome", - "pattern": "*.out", - "ontologies": [] - } - }, - { - "monoploid_seqs": { - "type": "file", - "description": "This parameter is mainly for ployploid genomes. User provides a list of\nsequence names that represent a monoploid (1x). LAI will be calculated only\non these sequences if provided.\n", - "pattern": "*.txt", - "ontologies": [] - } - } - ], - "output": { - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.LAI.log": { - "type": "file", - "description": "Log from LAI", - "pattern": "*.LAI.log", - "ontologies": [] - } - } - ] - ], - "lai_out": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.LAI.out": { - "type": "file", - "description": "Output file from LAI if LAI is able to estimate the index from the inputs\n", - "pattern": "*.LAI.out", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@GallVp" - ], - "maintainers": [ - "@GallVp" - ] - } - }, - { - "name": "ltrretriever_ltrretriever", - "path": "modules/nf-core/ltrretriever/ltrretriever/meta.yml", - "type": "module", - "meta": { - "name": "ltrretriever_ltrretriever", - "description": "Identifies LTR retrotransposons using LTR_retriever", - "keywords": [ - "genomics", - "annotation", - "repeat", - "long terminal repeat", - "retrotransposon" - ], - "tools": [ - { - "LTR_retriever": { - "description": "Sensitive and accurate identification of LTR retrotransposons", - "homepage": "https://github.com/oushujun/LTR_retriever", - "documentation": "https://github.com/oushujun/LTR_retriever", - "tool_dev_url": "https://github.com/oushujun/LTR_retriever", - "doi": "10.1104/pp.17.01310", - "licence": [ - "GPL v3" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "genome": { - "type": "file", - "description": "Genomic sequences in fasta format", - "pattern": "*.{fsa,fa,fasta}", - "ontologies": [] - } - } - ], - { - "harvest": { - "type": "file", - "description": "LTR-RT candidates from GenomeTools ltrharvest in the old tabular format", - "pattern": "*.tabout", - "ontologies": [] - } - }, - { - "finder": { - "type": "file", - "description": "LTR-RT candidates from LTR_FINDER", - "pattern": "*.scn", - "ontologies": [] - } - }, - { - "mgescan": { - "type": "file", - "description": "LTR-RT candidates from MGEScan_LTR", - "pattern": "*.out", - "ontologies": [] - } - }, - { - "non_tgca": { - "type": "file", - "description": "Non-canonical LTR-RT candidates from GenomeTools ltrharvest in the old tabular format", - "pattern": "*.tabout", - "ontologies": [] + }, + { + "name": "ngmerge", + "path": "modules/nf-core/ngmerge/meta.yml", + "type": "module", + "meta": { + "name": "ngmerge", + "description": "Merging paired-end reads and removing sequencing adapters.", + "keywords": ["sort", "reads merging", "merge mate pairs"], + "tools": [ + { + "ngmerge": { + "description": "Merging paired-end reads and removing sequencing adapters.", + "homepage": "https://github.com/jsh58/NGmerge", + "documentation": "https://github.com/jsh58/NGmerge", + "tool_dev_url": "https://github.com/jsh58/NGmerge", + "doi": "10.1186/s12859-018-2579-2", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 2; i.e., paired-end data.\n", + "pattern": "*.{fa,fasta,fastq,fq,fa.gz,fasta.gz,fastq.gz,fq.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ] + ], + "output": { + "merged_reads": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.merged.fq.gz": { + "type": "file", + "description": "fastq file merged reads", + "pattern": "*.{fa,fasta,fastq,fq,fa.gz,fasta.gz,fastq.gz,fq.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ] + ], + "unstitched_read1": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*_1.fastq.gz": { + "type": "file", + "description": "fastq file unstitched read 1", + "pattern": "*.{fa,fasta,fastq,fq,fa.gz,fasta.gz,fastq.gz,fq.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ] + ], + "unstitched_read2": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*_2.fastq.gz": { + "type": "file", + "description": "fastq file unstitched read 2", + "pattern": "*.{fa,fasta,fastq,fq,fa.gz,fasta.gz,fastq.gz,fq.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@charlotteanne", "@jsh58"], + "maintainers": ["@charlotteanne", "@jsh58"] } - } - ], - "output": { - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.log": { - "type": "file", - "description": "Output log from LTR_retriever", - "pattern": "*.log", - "ontologies": [] - } - } - ] - ], - "pass_list": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}.pass.list": { - "type": "file", - "description": "Intact LTR-RTs with coordinate and structural information in summary table format", - "pattern": "*.pass.list", - "ontologies": [] - } - } - ] - ], - "pass_list_gff": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.pass.list.gff3": { - "type": "file", - "description": "Intact LTR-RTs with coordinate and structural information in gff3 format", - "pattern": "*.pass.list.gff3", - "ontologies": [] - } - } - ] - ], - "ltrlib": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.LTRlib.fa": { - "type": "file", - "description": "All non-redundant LTR-RTs", - "pattern": "*.LTRlib.fa", - "ontologies": [] - } - } - ] - ], - "annotation_out": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}.out": { - "type": "file", - "description": "Whole-genome LTR-RT annotation by the non-redundant library", - "pattern": "*.out", - "ontologies": [] - } - } - ] - ], - "annotation_gff": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.out.gff3": { - "type": "file", - "description": "Whole-genome LTR-RT annotation by the non-redundant library in gff3 format", - "pattern": "*.out.gff3", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } + }, + { + "name": "ngsbits_bedannotategc", + "path": "modules/nf-core/ngsbits/bedannotategc/meta.yml", + "type": "module", + "meta": { + "name": "ngsbits_bedannotategc", + "description": "Annotates GC content fraction to regions in a BED file.", + "keywords": ["gc", "bed", "regions"], + "tools": [ + { + "ngsbits": { + "description": "Short-read sequencing tools", + "homepage": "https://github.com/imgag/ngs-bits", + "documentation": "https://github.com/imgag/ngs-bits", + "tool_dev_url": "https://github.com/imgag/ngs-bits", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "bed": { + "type": "file", + "description": "Input BED file containing regions to annotate", + "pattern": "*.bed", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference fasta information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The reference FASTA to use", + "pattern": "*.{fasta,fa,fna}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference fasta information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "fai": { + "type": "file", + "description": "The index file from the reference FASTA", + "pattern": "*.fai", + "ontologies": [] + } + } + ] + ], + "output": { + "output": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "Annotated BED file with GC content fraction", + "pattern": "*.bed", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@nvnieuwk"], + "maintainers": ["@nvnieuwk"] } - ] - }, - "authors": [ - "@GallVp" - ], - "maintainers": [ - "@GallVp" - ] - } - }, - { - "name": "macrel_contigs", - "path": "modules/nf-core/macrel/contigs/meta.yml", - "type": "module", - "meta": { - "name": "macrel_contigs", - "description": "A tool that mines antimicrobial peptides (AMPs) from (meta)genomes by predicting peptides from genomes (provided as contigs) and outputs all the predicted anti-microbial peptides found.", - "keywords": [ - "AMP", - "antimicrobial peptides", - "genome mining", - "metagenomes", - "peptide prediction" - ], - "tools": [ - { - "macrel": { - "description": "A pipeline for AMP (antimicrobial peptide) prediction", - "homepage": "https://macrel.readthedocs.io/en/latest/", - "documentation": "https://macrel.readthedocs.io/en/latest/", - "tool_dev_url": "https://github.com/BigDataBiology/macrel", - "doi": "10.7717/peerj.10555", - "licence": [ - "MIT" - ], - "identifier": "biotools:macrel" + }, + { + "name": "ngsbits_bedcoverage", + "path": "modules/nf-core/ngsbits/bedcoverage/meta.yml", + "type": "module", + "meta": { + "name": "ngsbits_bedcoverage", + "description": "Annotates a BED file with the average coverage of the regions from one or several BAM/CRAM file(s).", + "keywords": ["bed", "coverage", "regions"], + "tools": [ + { + "ngsbits": { + "description": "Short-read sequencing tools", + "homepage": "https://github.com/imgag/ngs-bits", + "documentation": "https://github.com/imgag/ngs-bits", + "tool_dev_url": "https://github.com/imgag/ngs-bits", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "reads": { + "type": "file", + "description": "Input BAM/CRAM/SAM file(s), can be one file or a list of files", + "pattern": "*.{bam,cram,sam}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_25722" + }, + { + "edam": "http://edamontology.org/format_2573" + }, + { + "edam": "http://edamontology.org/format_3462" + } + ] + } + }, + { + "reads_index": { + "type": "file", + "description": "The index file(s) from the input BAM/CRAM/SAM file(s)", + "pattern": "*.{bai,crai}", + "ontologies": [] + } + }, + { + "bed": { + "type": "file", + "description": "Input BED file containing regions to annotate", + "pattern": "*.bed", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference fasta information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The reference FASTA to use (mandatory when CRAM files are used, otherwise optional)", + "pattern": "*.{fasta,fa,fna}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference fasta information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "fai": { + "type": "file", + "description": "The index file from the reference FASTA", + "pattern": "*.fai", + "ontologies": [] + } + } + ] + ], + "output": { + "bed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "Output BED file with average coverage of the regions", + "pattern": "*.bed", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@nvnieuwk"], + "maintainers": ["@nvnieuwk"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + }, + { + "name": "ngsbits_samplegender", + "path": "modules/nf-core/ngsbits/samplegender/meta.yml", + "type": "module", + "meta": { + "name": "ngsbits_samplegender", + "description": "Determines the gender of a sample from the BAM/CRAM file.", + "keywords": ["gender", "cram", "bam", "short reads"], + "tools": [ + { + "ngsbits": { + "description": "Short-read sequencing tools", + "homepage": "https://github.com/imgag/ngs-bits", + "documentation": "https://github.com/imgag/ngs-bits", + "tool_dev_url": "https://github.com/imgag/ngs-bits", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "One or more BAM/CRAM files to determine the gender of", + "pattern": "*.{bam,cram}", + "ontologies": [] + } + }, + { + "bai": { + "type": "file", + "description": "The index file(s) from the input BAM/CRAM file(s)", + "pattern": "*.{bai,crai}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference fasta information\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The reference FASTA to use (mandatory when CRAM files are used)", + "pattern": "*.{fasta,fa,fna}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference fasta information\ne.g. [ id:'test' ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "The index file from the reference FASTA", + "pattern": "*.fai", + "ontologies": [] + } + } + ], + { + "method": { + "type": "string", + "description": "The method to use to define the gender (possibilities are 'xy', 'hetx' and 'sry')", + "pattern": "(xy|hetx|sry)" + } + } + ], + "output": { + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "An output TSV file containing the results of the gender prediction", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_ngsbits": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "ngsbits": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "SampleGender --version 2>&1 | sed 's/SampleGender //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "ngsbits": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "SampleGender --version 2>&1 | sed 's/SampleGender //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@nvnieuwk"], + "maintainers": ["@nvnieuwk"] }, - { - "fasta": { - "type": "file", - "description": "A fasta file with nucleotide sequences.", - "pattern": "*.{fasta,fa,fna,fasta.gz,fa.gz,fna.gz}", - "ontologies": [] - } - } - ] - ], - "output": { - "smorfs": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*/*.smorfs.faa.gz": { - "type": "file", - "description": "A zipped fasta file containing aminoacid sequences showing the general gene prediction information in the contigs.", - "pattern": "*.smorfs.faa.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "all_orfs": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*/*.all_orfs.faa.gz": { - "type": "file", - "description": "A zipped fasta file containing amino acid sequences showing the general gene prediction information in the contigs.", - "pattern": "*.all_orfs.faa.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "amp_prediction": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*/*.prediction.gz": { - "type": "file", - "description": "A zipped file, with all predicted amps in a table format.", - "pattern": "*.prediction.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "readme_file": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*/*.md": { - "type": "file", - "description": "A readme file containing tool specific information (e.g. citations, details about the output, etc.).", - "pattern": "*.md", - "ontologies": [] - } - } - ] - ], - "log_file": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*/*_log.txt": { - "type": "file", - "description": "A log file containing the information pertaining to the run.", - "pattern": "*_log.txt", - "ontologies": [] - } - } + "pipelines": [ + { + "name": "raredisease", + "version": "3.0.0" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } + }, + { + "name": "ngsbits_updhunter", + "path": "modules/nf-core/ngsbits/updhunter/meta.yml", + "type": "module", + "meta": { + "name": "ngsbits_updhunter", + "description": "UPD detection from trio variant data.", + "keywords": ["upd", "vcf", "genomics"], + "tools": [ + { + "ngsbits": { + "description": "Short-read sequencing tools", + "homepage": "https://github.com/imgag/ngs-bits", + "documentation": "https://github.com/imgag/ngs-bits", + "tool_dev_url": "https://github.com/imgag/ngs-bits", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "vcf": { + "type": "file", + "description": "vcf file", + "pattern": "*.vcf{,.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + } + ] + } + }, + { + "bed": { + "type": "file", + "description": "bed file with regions to exclude", + "pattern": "*.bed", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3003" + } + ] + } + } + ] + ], + "output": { + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "TSV file containing the detected UPDs", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "igv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.igv": { + "type": "file", + "description": "IGV file containing informative variants", + "pattern": "*.igv", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@matthdsm"], + "maintainers": ["@matthdsm"] } - ] - }, - "authors": [ - "@darcy220606" - ], - "maintainers": [ - "@darcy220606" - ] - }, - "pipelines": [ - { - "name": "funcscan", - "version": "3.0.0" - } - ] - }, - { - "name": "macs2_callpeak", - "path": "modules/nf-core/macs2/callpeak/meta.yml", - "type": "module", - "meta": { - "name": "macs2_callpeak", - "description": "Peak calling of enriched genomic regions of ChIP-seq and ATAC-seq experiments", - "keywords": [ - "alignment", - "atac-seq", - "chip-seq", - "peak-calling" - ], - "tools": [ - { - "macs2": { - "description": "Model Based Analysis for ChIP-Seq data", - "documentation": "https://docs.csc.fi/apps/macs2/", - "tool_dev_url": "https://github.com/macs3-project/MACS", - "doi": "10.1101/496521", - "licence": [ - "BSD" - ], - "identifier": "" + }, + { + "name": "ngscheckmate_fastq", + "path": "modules/nf-core/ngscheckmate/fastq/meta.yml", + "type": "module", + "meta": { + "name": "ngscheckmate_fastq", + "description": "Determining whether sequencing data comes from the same individual by using SNP matching. This module generates vaf files for individual fastq file(s), ready for the vafncm module.", + "keywords": ["ngscheckmate", "matching", "snp", "qc"], + "tools": [ + { + "ngscheckmate": { + "description": "NGSCheckMate is a software package for identifying next generation sequencing (NGS) data files from the same individual, including matching between DNA and RNA.", + "homepage": "https://github.com/parklab/NGSCheckMate", + "documentation": "https://github.com/parklab/NGSCheckMate", + "tool_dev_url": "https://github.com/parklab/NGSCheckMate", + "doi": "10.1093/nar/gkx193", + "licence": ["MIT"], + "identifier": "biotools:ngscheckmate" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information about the fastq files\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "reads": { + "type": "file", + "description": "Raw fastq files for one sample, single or paired end.", + "pattern": "*.{fastq.gz}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "file", + "description": "Groovy Map containing sample information about the NGSCheckMate SNP pt file\ne.g. `[ id:'test', single_end:false ]`\n", + "ontologies": [] + } + }, + { + "snp_pt": { + "type": "file", + "description": "PT file containing SNP data, generated by ngscheckmate/patterngenerator. For human data, use the files from NGSCheckMate's github repository.", + "pattern": "*.{pt}", + "ontologies": [] + } + } + ] + ], + "output": { + "vaf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.vaf": { + "type": "file", + "description": "Text file containing reference/alt allele depth for each SNP position contained in the PT file.", + "pattern": "*.{vaf}", + "ontologies": [] + } + } + ] + ], + "versions_ngscheckmate": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "ngscheckmate": { + "type": "string", + "description": "The tool name" + } + }, + { + "ncm.py --help | sed '7!d;s/.* v//g'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "ngscheckmate": { + "type": "string", + "description": "The tool name" + } + }, + { + "ncm.py --help | sed '7!d;s/.* v//g'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@sppearce"], + "maintainers": ["@sppearce"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "ipbam": { - "type": "file", - "description": "The ChIP-seq treatment file", - "ontologies": [] - } + }, + { + "name": "ngscheckmate_ncm", + "path": "modules/nf-core/ngscheckmate/ncm/meta.yml", + "type": "module", + "meta": { + "name": "ngscheckmate_ncm", + "description": "Determining whether sequencing data comes from the same individual by using SNP matching. Designed for humans on vcf or bam files.", + "keywords": ["ngscheckmate", "matching", "snp"], + "tools": [ + { + "ngscheckmate": { + "description": "NGSCheckMate is a software package for identifying next generation sequencing (NGS) data files from the same individual, including matching between DNA and RNA.", + "homepage": "https://github.com/parklab/NGSCheckMate", + "documentation": "https://github.com/parklab/NGSCheckMate", + "tool_dev_url": "https://github.com/parklab/NGSCheckMate", + "doi": "10.1093/nar/gkx193", + "licence": ["MIT"], + "identifier": "biotools:ngscheckmate" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "files": { + "type": "file", + "description": "VCF or BAM files for each sample, in a merged channel (possibly gzipped). BAM files require an index too.", + "pattern": "*.{vcf,vcf.gz,bam,bai}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing SNP information\ne.g. [ id:'test' ]\n" + } + }, + { + "snp_bed": { + "type": "file", + "description": "BED file containing the SNPs to analyse", + "pattern": "*.{bed}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference fasta index information\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "fasta file for the genome, only used in the bam mode", + "pattern": "*.{fasta}", + "ontologies": [] + } + }, + { + "fai": { + "type": "file", + "description": "fasta index file for the genome, only used in the bam mode", + "pattern": "*.{fai}", + "ontologies": [] + } + } + ] + ], + "output": { + "corr_matrix": [ + [ + { + "meta": { + "type": "file", + "description": "A text file containing the correlation matrix between each sample", + "pattern": "*corr_matrix.txt", + "ontologies": [] + } + }, + { + "*_corr_matrix.txt": { + "type": "file", + "description": "A text file containing the correlation matrix between each sample", + "pattern": "*corr_matrix.txt", + "ontologies": [] + } + } + ] + ], + "matched": [ + [ + { + "meta": { + "type": "file", + "description": "A text file containing the correlation matrix between each sample", + "pattern": "*corr_matrix.txt", + "ontologies": [] + } + }, + { + "*_matched.txt": { + "type": "file", + "description": "A txt file containing only the samples that match with each other", + "pattern": "*matched.txt", + "ontologies": [] + } + } + ] + ], + "all": [ + [ + { + "meta": { + "type": "file", + "description": "A text file containing the correlation matrix between each sample", + "pattern": "*corr_matrix.txt", + "ontologies": [] + } + }, + { + "*_all.txt": { + "type": "file", + "description": "A txt file containing all the sample comparisons, whether they match or not", + "pattern": "*all.txt", + "ontologies": [] + } + } + ] + ], + "pdf": [ + [ + { + "meta": { + "type": "file", + "description": "A text file containing the correlation matrix between each sample", + "pattern": "*corr_matrix.txt", + "ontologies": [] + } + }, + { + "*.pdf": { + "type": "file", + "description": "A pdf containing a dendrogram showing how the samples match up", + "pattern": "*.{pdf}", + "ontologies": [] + } + } + ] + ], + "vcf": [ + [ + { + "meta": { + "type": "file", + "description": "A text file containing the correlation matrix between each sample", + "pattern": "*corr_matrix.txt", + "ontologies": [] + } + }, + { + "*.vcf": { + "type": "file", + "description": "If ran in bam mode, vcf files for each sample giving the SNP calls used", + "pattern": "*.vcf", + "ontologies": [] + } + } + ] + ], + "versions_ngscheckmate": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "ngscheckmate": { + "type": "string", + "description": "The tool name" + } + }, + { + "ncm.py --help | sed '7!d;s/.* v//g'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "ngscheckmate": { + "type": "string", + "description": "The tool name" + } + }, + { + "ncm.py --help | sed '7!d;s/.* v//g'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@sppearce"], + "maintainers": ["@sppearce"] }, - { - "controlbam": { - "type": "file", - "description": "The control file", - "ontologies": [] - } - } - ], - { - "macs2_gsize": { - "type": "string", - "description": "Effective genome size. It can be 1.0e+9 or 1000000000, or shortcuts:'hs' for human (2.7e9), 'mm' for mouse (1.87e9), 'ce' for C. elegans (9e7) and 'dm' for fruitfly (1.2e8)" - } - } - ], - "output": { - "peak": [ - [ - { - "meta": { - "type": "file", - "description": "BED file containing annotated peaks", - "pattern": "*.gappedPeak,*.narrowPeak}", - "ontologies": [] - } - }, - { - "*.{narrowPeak,broadPeak}": { - "type": "file", - "description": "BED file containing annotated peaks", - "pattern": "*.gappedPeak,*.narrowPeak}", - "ontologies": [] - } - } - ] - ], - "xls": [ - [ - { - "meta": { - "type": "file", - "description": "BED file containing annotated peaks", - "pattern": "*.gappedPeak,*.narrowPeak}", - "ontologies": [] - } - }, - { - "*.xls": { - "type": "file", - "description": "xls file containing annotated peaks", - "pattern": "*.xls", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software version", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ], - "gapped": [ - [ - { - "meta": { - "type": "file", - "description": "BED file containing annotated peaks", - "pattern": "*.gappedPeak,*.narrowPeak}", - "ontologies": [] - } - }, - { - "*.gappedPeak": { - "type": "file", - "description": "Optional BED file containing gapped peak", - "pattern": "*.gappedPeak", - "ontologies": [] - } - } - ] - ], - "bed": [ - [ - { - "meta": { - "type": "file", - "description": "BED file containing annotated peaks", - "pattern": "*.gappedPeak,*.narrowPeak}", - "ontologies": [] - } - }, - { - "*.bed": { - "type": "file", - "description": "Optional BED file containing peak summits locations for every peak", - "pattern": "*.bed", - "ontologies": [] - } - } - ] - ], - "bdg": [ - [ - { - "meta": { - "type": "file", - "description": "BED file containing annotated peaks", - "pattern": "*.gappedPeak,*.narrowPeak}", - "ontologies": [] - } - }, - { - "*.bdg": { - "type": "file", - "description": "Optional bedGraph files for input and treatment input samples", - "pattern": "*.bdg", - "ontologies": [] - } - } + "pipelines": [ + { + "name": "sarek", + "version": "3.8.1" + } ] - ] }, - "authors": [ - "@ntoda03", - "@JoseEspinosa", - "@jianhong" - ], - "maintainers": [ - "@ntoda03", - "@JoseEspinosa", - "@jianhong" - ] - }, - "pipelines": [ { - "name": "atacseq", - "version": "2.1.2" + "name": "ngscheckmate_patterngenerator", + "path": "modules/nf-core/ngscheckmate/patterngenerator/meta.yml", + "type": "module", + "meta": { + "name": "ngscheckmate_patterngenerator", + "description": "Determining whether sequencing data comes from the same individual by using SNP matching. This module generates PT files from a bed file containing individual positions.", + "keywords": ["ngscheckmate", "matching", "snp", "qc"], + "tools": [ + { + "ngscheckmate": { + "description": "NGSCheckMate is a software package for identifying next generation sequencing (NGS) data files from the same individual, including matching between DNA and RNA.", + "homepage": "https://github.com/parklab/NGSCheckMate", + "documentation": "https://github.com/parklab/NGSCheckMate", + "tool_dev_url": "https://github.com/parklab/NGSCheckMate", + "doi": "10.1093/nar/gkx193", + "licence": ["MIT"], + "identifier": "biotools:ngscheckmate" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information about the bed file\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "bed": { + "type": "file", + "description": "BED file containing population-level SNPs to use", + "pattern": "*.bed", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information about the fasta genome\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Genome fasta file", + "pattern": "*.fasta", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "bowtie_index": { + "type": "directory", + "description": "Folder of Bowtie genome index files" + } + } + ] + ], + "output": { + "pt": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.pt": { + "type": "file", + "description": "Generated binary pattern file, containing FASTQ strings to match from within raw data", + "pattern": "*.pt", + "ontologies": [] + } + } + ] + ], + "versions_ngscheckmate": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "ngscheckmate": { + "type": "string", + "description": "The tool name" + } + }, + { + "ncm.py --help | sed '7!d;s/.* v//g'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "ngscheckmate": { + "type": "string", + "description": "The tool name" + } + }, + { + "ncm.py --help | sed '7!d;s/.* v//g'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@sppearce"], + "maintainers": ["@sppearce"] + } }, { - "name": "cutandrun", - "version": "3.2.2" + "name": "ngscheckmate_vafncm", + "path": "modules/nf-core/ngscheckmate/vafncm/meta.yml", + "type": "module", + "meta": { + "name": "ngscheckmate_vafncm", + "description": "Determining whether sequencing data comes from the same individual by using SNP matching. This module generates PT files from a bed file containing individual positions.", + "keywords": ["ngscheckmate", "matching", "snp", "qc"], + "tools": [ + { + "ngscheckmate": { + "description": "NGSCheckMate is a software package for identifying next generation sequencing (NGS) data files from the same individual, including matching between DNA and RNA.", + "homepage": "https://github.com/parklab/NGSCheckMate", + "documentation": "https://github.com/parklab/NGSCheckMate", + "tool_dev_url": "https://github.com/parklab/NGSCheckMate", + "doi": "10.1093/nar/gkx193", + "licence": ["MIT"], + "identifier": "biotools:ngscheckmate" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information about the combined set of files\ne.g. `[ id:'combined' ]`\n" + } + }, + { + "vafs": { + "type": "file", + "description": "Text files containing information about reference/alternate allele depths for the SNP positions, generated by ngscheckmate/fastq", + "pattern": "*.{vaf}", + "ontologies": [] + } + } + ] + ], + "output": { + "pdf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information about the combined set of files\ne.g. `[ id:'combined' ]`\n" + } + }, + { + "*.pdf": { + "type": "file", + "description": "A pdf containing a dendrogram showing how the samples match up.| Note due to a bug in the R script used by the tool this is not produced when only two samples are given.", + "pattern": "*.{pdf}", + "ontologies": [] + } + } + ] + ], + "corr_matrix": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information about the combined set of files\ne.g. `[ id:'combined' ]`\n" + } + }, + { + "*_corr_matrix.txt": { + "type": "file", + "description": "A text file containing the correlation matrix between each sample", + "pattern": "*corr_matrix.txt", + "ontologies": [] + } + } + ] + ], + "all": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information about the combined set of files\ne.g. `[ id:'combined' ]`\n" + } + }, + { + "*_all.txt": { + "type": "file", + "description": "A txt file containing all the sample comparisons, whether they match or not", + "pattern": "*all.txt", + "ontologies": [] + } + } + ] + ], + "matched": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information about the combined set of files\ne.g. `[ id:'combined' ]`\n" + } + }, + { + "*_matched.txt": { + "type": "file", + "description": "A txt file containing only the samples that match with each other", + "pattern": "*matched.txt", + "ontologies": [] + } + } + ] + ], + "versions_ngscheckmate": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "ngscheckmate": { + "type": "string", + "description": "The tool name" + } + }, + { + "ncm.py --help | sed '7!d;s/.* v//g'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "ngscheckmate": { + "type": "string", + "description": "The tool name" + } + }, + { + "ncm.py --help | sed '7!d;s/.* v//g'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@sppearce"], + "maintainers": ["@sppearce"] + } }, { - "name": "hicar", - "version": "1.0.0" - } - ] - }, - { - "name": "macs3_callpeak", - "path": "modules/nf-core/macs3/callpeak/meta.yml", - "type": "module", - "meta": { - "name": "macs3_callpeak", - "description": "Peak calling of enriched genomic regions of ChIP-seq and ATAC-seq experiments", - "keywords": [ - "alignment", - "atac-seq", - "chip-seq", - "peak-calling" - ], - "tools": [ - { - "macs3": { - "description": "Model Based Analysis for ChIP-Seq data", - "homepage": "https://macs3-project.github.io/MACS/", - "documentation": "https://macs3-project.github.io/MACS/", - "tool_dev_url": "https://github.com/macs3-project/MACS/", - "doi": "10.1101/496521", - "licence": [ - "BSD-3-clause" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample_1', single_end:false ]`\n" - } - }, - { - "ipbam": { - "type": "file", - "description": "The ChIP-seq treatment file", - "ontologies": [] - } - }, - { - "controlbam": { - "type": "file", - "description": "The control file", - "ontologies": [] - } - } - ], - { - "macs3_gsize": { - "type": "string", - "description": "Effective genome size. It can be 1.0e+9 or 1000000000,\nor shortcuts:'hs' for human (2,913,022,398), 'mm' for mouse\n(2,652,783,500), 'ce' for C. elegans (100,286,401)\nand 'dm' for fruitfly (142,573,017), Default:hs.\n" - } - } - ], - "output": { - "peak": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.{narrowPeak,broadPeak}": { - "type": "file", - "description": "BED file containing annotated peaks", - "pattern": "*.gappedPeak,*.narrowPeak}", - "ontologies": [] - } - } - ] - ], - "xls": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.xls": { - "type": "file", - "description": "xls file containing annotated peaks", - "pattern": "*.xls", - "ontologies": [] - } - } - ] - ], - "gapped": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.gappedPeak": { - "type": "file", - "description": "Optional BED file containing gapped peak", - "pattern": "*.gappedPeak", - "ontologies": [] - } - } - ] - ], - "bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.bed": { - "type": "file", - "description": "Optional BED file containing peak summits locations for every peak", - "pattern": "*.bed", - "ontologies": [] - } - } - ] - ], - "bdg": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.bdg": { - "type": "file", - "description": "Optional bedGraph files for input and treatment input samples", - "pattern": "*.bdg", - "ontologies": [] - } - } - ] - ], - "versions_macs3": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "macs3": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "macs3 --version | sed -e 's/macs3 //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "macs3": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "macs3 --version | sed -e 's/macs3 //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@JoseEspinosa" - ], - "maintainers": [ - "@JoseEspinosa", - "@Kevin-Brockers" - ] - }, - "pipelines": [ - { - "name": "chipseq", - "version": "2.1.0" - } - ] - }, - { - "name": "macse_refinealignment", - "path": "modules/nf-core/macse/refinealignment/meta.yml", - "type": "module", - "meta": { - "name": "macse_refinealignment", - "description": "improves the input nucleotide alignment in a codon-aware manner", - "keywords": [ - "multiple sequence alignment", - "codon-aware", - "fasta" - ], - "tools": [ - { - "macse": { - "description": "MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons.", - "homepage": "https://www.agap-ge2pop.org/macse/", - "documentation": "https://www.agap-ge2pop.org/macse/macse-documentation/", - "tool_dev_url": "https://github.com/nf-core/masce", - "doi": "10.1371/journal.pone.0022594", - "licence": [ - "CeCILL 2.1" - ], - "identifier": "biotools:macse" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + "name": "nonpareil_curve", + "path": "modules/nf-core/nonpareil/curve/meta.yml", + "type": "module", + "meta": { + "name": "nonpareil_curve", + "description": "Visualise metagenome redundancy curve in PNG format from a single Nonpareil npo file", + "keywords": [ + "metagenomics", + "statistics", + "coverage", + "complexity", + "redundancy", + "diversity", + "visualisation" + ], + "tools": [ + { + "nonpareil": { + "description": "Estimate average coverage and create curves for metagenomic datasets", + "homepage": "https://github.com/lmrodriguezr/nonpareil", + "documentation": "https://nonpareil.readthedocs.io/en/latest/", + "tool_dev_url": "https://github.com/lmrodriguezr/nonpareil", + "doi": "10.1128/msystems.00039-", + "licence": ["Artistic License 2.0"], + "identifier": "biotools:nonpareil" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "npo": { + "type": "file", + "description": "Single npo redundancy summary file from nonpareil itself", + "pattern": "*.npo", + "ontologies": [] + } + } + ] + ], + "output": { + "png": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.png": { + "type": "file", + "description": "PNG file of the Nonpareil curve", + "pattern": "*.png", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@jfy133"], + "maintainers": ["@jfy133"] }, - { - "fasta": { - "type": "file", - "description": "Aligned sequences in FASTA format. May be gzipped or uncompressed.", - "pattern": "*.{fa,fas,fasta,aln}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2554" - }, - { - "edam": "http://edamontology.org/format_1921" - }, - { - "edam": "http://edamontology.org/format_1984" - } - ] - } - } - ] - ], - "output": { - "nt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + "pipelines": [ + { + "name": "taxprofiler", + "version": "2.0.0" } - }, - { - "*_NT.{fa,fas,fasta,aln}": { - "type": "file", - "description": "Aligned sequences in FASTA format. May be gzipped or uncompressed.", - "pattern": "*_NT.{fa,fas,fasta,aln}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2554" - }, + ] + }, + { + "name": "nonpareil_nonpareil", + "path": "modules/nf-core/nonpareil/nonpareil/meta.yml", + "type": "module", + "meta": { + "name": "nonpareil_nonpareil", + "description": "Calculate metagenome redundancy curve from FASTQ files", + "keywords": ["metagenomics", "statistics", "coverage", "redundancy", "diversity", "complexity"], + "tools": [ + { + "nonpareil": { + "description": "Estimate average coverage and create curves for metagenomic datasets", + "homepage": "https://github.com/lmrodriguezr/nonpareil", + "documentation": "https://nonpareil.readthedocs.io/en/latest/", + "tool_dev_url": "https://github.com/lmrodriguezr/nonpareil", + "doi": "10.1128/msystems.00039-", + "licence": ["Artistic License 2.0"], + "identifier": "biotools:nonpareil" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "reads": { + "type": "file", + "description": "FASTQ or FASTA file (ideally uncompressed, but not required)", + "pattern": "*.{fasta,fna,fas,fa,fastq,fq,fasta.gz,fna.gz,fas.gz,fa.gz,fastq.gz,fq.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ], { - "edam": "http://edamontology.org/format_1921" + "format": { + "type": "string", + "description": "File format of input file", + "pattern": "fasta|fastq" + } }, { - "edam": "http://edamontology.org/format_1984" + "mode": { + "type": "string", + "description": "Mode of redundancy estimation", + "pattern": "kmer|alignment" + } } - ] + ], + "output": { + "npa": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.npa": { + "type": "file", + "description": "Raw redundancy values", + "pattern": "*.npa", + "ontologies": [] + } + } + ] + ], + "npc": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.npc": { + "type": "file", + "description": "Mates distribution file", + "pattern": "*.npc", + "ontologies": [] + } + } + ] + ], + "npl": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.npl": { + "type": "file", + "description": "Log file", + "pattern": "*.npl", + "ontologies": [] + } + } + ] + ], + "npo": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.npo": { + "type": "file", + "description": "Redundancy summary file", + "pattern": "*.npo", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@jfy133"], + "maintainers": ["@jfy133"] + }, + "pipelines": [ + { + "name": "taxprofiler", + "version": "2.0.0" } - } ] - ], - "aa": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_AA.{fa,fas,fasta,aln}": { - "type": "file", - "description": "Aligned sequences in FASTA format. 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"type": "module", - "meta": { - "name": "macsyfinder_download", - "description": "Download MacSyFinder models using msf_data", - "keywords": [ - "genomics", - "protein", - "macromolecular systems", - "models", - "database" - ], - "tools": [ - { - "macsyfinder": { - "description": "Detection of macromolecular systems in protein datasets using systems\nmodelling and similarity search\n", - "homepage": "https://github.com/gem-pasteur/macsyfinder", - "documentation": "https://macsyfinder.readthedocs.io", - "tool_dev_url": "https://github.com/gem-pasteur/macsyfinder", - "doi": "10.24072/pcjournal.250", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:macsyfinder" - } - } - ], - "input": [ - { - "model_name": { - "type": "string", - "description": "Name of the MacSyFinder model to download (e.g., 'TXSScan', 'CasFinder')" - } - } - ], - "output": { - "models": [ - { - "models": { - "type": "directory", - "description": "Directory containing downloaded MacSyFinder model definitions", - "pattern": "models" - } - } - ], - "versions_macsyfinder": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "macsyfinder": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "macsyfinder --version 2>&1 | sed \"1!d;s/^.*MacSyFinder //;s/ .*$//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_macsydata": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "msf_data": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "msf_data --version 2>&1 | sed \"4!d;s/^- MacSyLib //;s/ *$//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "macsyfinder": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "macsyfinder --version 2>&1 | sed \"1!d;s/^.*MacSyFinder //;s/ .*$//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "msf_data": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "msf_data --version 2>&1 | sed \"4!d;s/^- MacSyLib //;s/ *$//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@brovolia" - ], - "maintainers": [ - "@brovolia" - ] - } - }, - { - "name": "macsyfinder_search", - "path": "modules/nf-core/macsyfinder/search/meta.yml", - "type": "module", - "meta": { - "name": "macsyfinder_search", - "description": "Search for macromolecular systems in protein datasets using MacSyFinder", - "notes": "The current input structure searches all specified models in a single MacSyFinder process\n(using internal parallelization via --worker). For Nextflow-level parallelization across\nindividual models, the inputs could be combined into a single tuple:\ntuple val(meta), path(proteins), path(models), val(model_names)\n", - "keywords": [ - "genomics", - "protein", - "macromolecular systems", - "hmmer", - "search" - ], - "tools": [ - { - "macsyfinder": { - "description": "Detection of macromolecular systems in protein datasets using systems\nmodelling and similarity search\n", - "homepage": "https://github.com/gem-pasteur/macsyfinder", - "documentation": "https://macsyfinder.readthedocs.io", - "tool_dev_url": "https://github.com/gem-pasteur/macsyfinder", - "doi": "10.24072/pcjournal.250", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:macsyfinder" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } + }, + { + "name": "nonpareil_set", + "path": "modules/nf-core/nonpareil/set/meta.yml", + "type": "module", + "meta": { + "name": "nonpareil_set", + "description": "Visualise metagenome redundancy curves in PNG format from multiple Nonpareil npo files in a single image", + "keywords": [ + "metagenomics", + "statistics", + "coverage", + "complexity", + "redundancy", + "diversity", + "visualisation" + ], + "tools": [ + { + "nonpareil": { + "description": "Estimate average coverage and create curves for metagenomic datasets", + "homepage": "https://github.com/lmrodriguezr/nonpareil", + "documentation": "https://nonpareil.readthedocs.io/en/latest/", + "tool_dev_url": "https://github.com/lmrodriguezr/nonpareil", + "doi": "10.1128/msystems.00039-", + "licence": ["Artistic License 2.0"], + "identifier": "biotools:nonpareil" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "npos": { + "type": "file", + "description": "A list of npo redundancy summary files from nonpareil itself", + "pattern": "*.npo", + "ontologies": [] + } + } + ] + ], + "output": { + "png": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.png": { + "type": "file", + "description": "PNG file of all the Nonpareil curves of the input npo files", + "pattern": "*.png", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@jfy133"], + "maintainers": ["@jfy133"] }, - { - "proteins": { - "type": "file", - "description": "Protein sequence file in FASTA format", - "pattern": "*.{fasta,faa,fa}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - { - "models": { - "type": "directory", - "description": "Directory containing MacSyFinder model(s)", - "pattern": "*" - } - }, - { - "model_names": { - "type": "string", - "description": "Space-separated list of model names to search for. If not provided, all models in the directory will be used." - } - } - ], - "output": { - "results": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', db_type:'gembase' ]`\n" - } - }, - { - "${prefix}/*": { - "type": "directory", - "description": "Directory containing all MacSyFinder results", - "pattern": "${prefix}/*" - } - } - ] - ], - "hmmer": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', db_type:'gembase' ]`\n" - } - }, - { - "${prefix}/hmmer_results": { - "type": "directory", - "description": "Directory containing HMMER search results (may contain variable content like timestamps)", - "pattern": "${prefix}/hmmer_results" - } - } - ] - ], - "stdout": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', db_type:'gembase' ]`\n" - } - }, - { - "${prefix}/macsyfinder.out": { - "type": "file", - 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} - }, - { - "fasta": { - "type": "file", - "description": "FASTA file containing the sequences to align. May be gzipped or uncompressed.", - "pattern": "*.{fa,fasta}{.gz,}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1919" - }, - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "add": { - "type": "file", - "description": "FASTA file containing sequences to align to the sequences in `fasta` using `--add`. May be gzipped or uncompressed.", - "pattern": "*.{fa,fasta}{.gz,}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1919" - }, - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "addfragments": { - "type": "file", - "description": "FASTA file containing sequences to align to the sequences in `fasta` using `--addfragments`. 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May be gzipped or uncompressed.", - "pattern": "*.{fa,fasta}{.gz,}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1919" - }, - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - { - "compress": { - "type": "boolean", - "description": "Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded." - } - } - ], - "output": { - "fas": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + "pipelines": [ + { + "name": "lsmquant", + "version": "1.0.0" } - }, - { - "*.fas{.gz,}": { - "type": "file", - "description": "Aligned sequences in FASTA format. 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{ + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*mito.ctg.fasta": { + "type": "file", + "description": "the structure-solved MT contigs", + "pattern": "*mito.ctg.fasta", + "ontologies": [] + } + } + ] + ], + "pltd_fasta": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*pltd.ctg.fasta": { + "type": "file", + "description": "the structure-solved PT contigs", + "pattern": "*pltd.ctg.fasta", + "ontologies": [] + } + } + ] + ], + "mito_bed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*mito.ctg.bed": { + "type": "file", + "description": "the gene annotation for the MT sequences", + "pattern": "*mito.ctg.bed", + "ontologies": [] + } + } + ] + ], + "pltd_bed": [ + [ + { + "meta": { + "type": 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"description": "the GFA file for the final genome assembly", + "pattern": "*utg.final.gfa", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3975" + } + ] + } + } + ] + ], + "initial_gfa": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*utg.gfa": { + "type": "file", + "description": "the GFA file for the initial genome assembly", + "pattern": "*utg.gfa", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3975" + } + ] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "log file describing oatk run", + "pattern": "*.log", + "ontologies": [ + { + "edam": "http://edamontology.org/data_2526" + } + ] + } + } + ] + ], + "versions_oatk": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "oatk": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "oatk --version 2>&1": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "oatk": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "oatk --version 2>&1": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@ksenia-krasheninnikova"] + } }, { - "name": "multiplesequencealign", - "version": "1.1.1" + "name": "octopusv_clean", + "path": "modules/nf-core/octopusv/clean/meta.yml", + "type": "module", + "meta": { + "name": "octopusv_clean", + "description": "Clean broken VCF/SVCF files using OctopuSV clean", + "keywords": ["vcf", "sv", 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"${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "octopusv": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python -c \"import importlib.metadata as m; print(m.version('octopusv'))\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@manascripts"], + "maintainers": ["@manascripts"] + } }, { - "name": "pathogensurveillance", - "version": "1.1.0" + "name": "octopusv_correct", + "path": "modules/nf-core/octopusv/correct/meta.yml", + "type": "module", + "meta": { + "name": "octopusv_correct", + "description": "Standardize a caller VCF into OctopuSV SVCF format.", + "keywords": ["structural", "variant", "sv", "svcf", "normalize"], + "tools": [ + { + "octopusv": { + "description": "End-to-end structural variant post-processing: standardize, merge, compare, and export SVs.", + "homepage": "https://github.com/ylab-hi/OctopuSV", + "documentation": "https://github.com/ylab-hi/OctopuSV", + "tool_dev_url": "https://github.com/ylab-hi/OctopuSV", + "doi": "10.1093/bioinformatics/btaf599", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "vcf": { + "type": "file", + "description": "Structural variant calls in VCF format", + "pattern": "*.{vcf,vcf.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + } + ] + } + } + ] + ], + "output": { + "svcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\n" + } + }, + { + "*.svcf": { + "type": "file", + "description": "Standardized SVCF file", + "pattern": "*.svcf", + "ontologies": [ + { + "edam": "https://github.com/ylab-hi/OctopuSV/blob/main/docs/SVCF_specifications.md" + } + ] + } + } + ] + ], + "versions_octopusv": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "octopusv": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python -c \"import importlib.metadata as m; print(m.version('octopusv'))\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "octopusv": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python -c \"import importlib.metadata as m; print(m.version('octopusv'))\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@manascripts"], + "maintainers": ["@manascripts"] + } }, { - "name": "phyloplace", - "version": "2.0.0" + "name": "octopusv_merge", + "path": "modules/nf-core/octopusv/merge/meta.yml", + "type": "module", + "meta": { + "name": "octopusv_merge", + "description": "Merge and harmonize structural variant calls from multiple samples.", + "keywords": ["structural variants", "merge", "genomics", "svcf"], + "tools": [ + { + "octopusv": { + "description": "End-to-end structural variant post-processing: standardize, merge, compare, and export SVs.", + "homepage": "https://github.com/ylab-hi/OctopuSV", + "documentation": "https://github.com/ylab-hi/OctopuSV", + "tool_dev_url": "https://github.com/ylab-hi/octopusV", + "doi": "10.1093/bioinformatics/btaf599", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "svcfs": { + "type": "file", + "description": "List of SVCF files to merge", + "pattern": "*.svcf", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + } + ] + } + }, + { + "strategy_flag": { + "type": "string", + "description": "Merge strategy for octopusv merge. Valid values: union, intersect, specific,\nmin-support, exact-support, max-support, expression. Defaults to union when this flag is empty.\nNOTE: Some flags require additional arguments.\n" + } + } + ] + ], + "output": { + "svcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.svcf": { + "type": "file", + "description": "Sorted VCF file", + "pattern": "*.svcf", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + } + ] + } + } + ] + ], + "upset_plot": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.png": { + "type": "file", + "description": "Upset plot comparing the variants in the input SVCF files (generated with --upsetr-output flag)", + "pattern": "*.png", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3603" + } + ] + } + } + ] + ], + "versions_octopusv": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "octopusv": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python -c \"import importlib.metadata as m; print(m.version('octopusv'))\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "octopusv": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python -c \"import importlib.metadata as m; print(m.version('octopusv'))\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@manascripts"], + "maintainers": ["@manascripts"] + } }, { - "name": "proteinfamilies", - "version": "2.3.0" + "name": "octopusv_plot", + "path": "modules/nf-core/octopusv/plot/meta.yml", + "type": "module", + "meta": { + "name": "octopusv_plot", + "description": "Plot structural variant statistics using octopusv stat output", + "keywords": ["summary", "structural variant", "statistics", "plot"], + "tools": [ + { + "octopusv": { + "description": "End-to-end structural variant post-processing: standardize, merge, compare, and export SVs.", + "homepage": "https://github.com/ylab-hi/OctopuSV", + "documentation": "https://github.com/ylab-hi/OctopuSV", + "tool_dev_url": "https://github.com/ylab-hi/octopusV", + "doi": "10.1093/bioinformatics/btaf599", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "txt": { + "type": "file", + "description": "OctopuSV stats text input", + "pattern": "*.txt", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + } + ] + ], + "output": { + "sv_sizes_png": [ + [ + { + "meta": { + "type": "map", + "description": "Sample information" + } + }, + { + "${prefix}_sv_sizes.png": { + "type": "file", + "description": "SV sizes plot (PNG)", + "pattern": "*_sv_sizes.png", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3603" + } + ] + } + } + ] + ], + "sv_sizes_svg": [ + [ + { + "meta": { + "type": "map", + "description": "Sample information" + } + }, + { + "${prefix}_sv_sizes.svg": { + "type": "file", + "description": "SV sizes plot (SVG)", + "pattern": "*_sv_sizes.svg", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3604" + } + ] + } + } + ] + ], + "sv_types_png": [ + [ + { + "meta": { + "type": "map", + "description": "Sample information" + } + }, + { + "${prefix}_sv_types.png": { + "type": "file", + "description": "SV types plot (PNG)", + "pattern": "*_sv_types.png", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3603" + } + ] + } + } + ] + ], + "sv_types_svg": [ + [ + { + "meta": { + "type": "map", + "description": "Sample information" + } + }, + { + "${prefix}_sv_types.svg": { + "type": "file", + "description": "SV types plot (SVG)", + "pattern": "*_sv_types.svg", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3604" + } + ] + } + } + ] + ], + "chromosome_distribution_png": [ + [ + { + "meta": { + "type": "map", + "description": "Sample information" + } + }, + { + "${prefix}_chromosome_distribution.png": { + "type": "file", + "description": "Chromosome distribution plot of structural variants (PNG)", + "pattern": "*_chromosome_distribution.png", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3603" + } + ] + } + } + ] + ], + "chromosome_distribution_svg": [ + [ + { + "meta": { + "type": "map", + "description": "Sample information" + } + }, + { + "${prefix}_chromosome_distribution.svg": { + "type": "file", + "description": "Chromosome distribution plot of structural variants (SVG)", + "pattern": "*_chromosome_distribution.svg", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3604" + } + ] + } + } + ] + ], + "versions_octopusv": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "octopusv": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python -c \"import importlib.metadata as m; print(m.version('octopusv'))\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "octopusv": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python -c \"import importlib.metadata as m; print(m.version('octopusv'))\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@manascripts"], + "maintainers": ["@manascripts"] + } }, { - "name": "viralmetagenome", - "version": "1.1.1" - } - ] - }, - { - "name": "mafft_guidetree", - "path": "modules/nf-core/mafft/guidetree/meta.yml", - "type": "module", - "meta": { - "name": "mafft_guidetree", - "description": "Guide tree rendering using MAFFT", - "keywords": [ - "fasta", - "msa", - "guide tree" - ], - "tools": [ - { - "mafft": { - "description": "Multiple alignment program for amino acid or nucleotide sequences based on fast Fourier transform", - "homepage": "https://mafft.cbrc.jp/alignment/software/", - "documentation": "https://mafft.cbrc.jp/alignment/software/manual/manual.html", - "tool_dev_url": "https://mafft.cbrc.jp/alignment/software/source.html", - "doi": "10.1093/nar/gkf436", - "licence": [ - "BSD" - ], - "identifier": "biotools:MAFFT" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA file containing the sequences to be used to render the guidetree.", - "pattern": "*.{fa,fasta}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1919" - }, - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ], - "output": { - "tree": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "*.dnd": { - "type": "file", - "description": "Guide tree in Newick format.", - "pattern": "*.dnd", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2006" - } - ] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@luisas" - ], - "maintainers": [ - "@luisas" - ] - }, - "pipelines": [ - { - "name": "multiplesequencealign", - "version": "1.1.1" - } - ] - }, - { - "name": "mageck_count", - "path": "modules/nf-core/mageck/count/meta.yml", - "type": "module", - "meta": { - "name": "mageck_count", - "description": "mageck count for functional genomics, reads are usually mapped to a specific sgRNA", - "keywords": [ - "sort", - "functional genomics", - "sgRNA", - "CRISPR-Cas9" - ], - "tools": [ - { - "mageck": { - "description": "MAGeCK (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout), an algorithm to process, QC, analyze and visualize CRISPR screening data.", - "homepage": "https://sourceforge.net/p/mageck/wiki/Home/", - "documentation": "https://sourceforge.net/p/mageck/wiki/demo/#step-4-run-the-mageck-count-command", - "doi": "10.1186/s13059-014-0554-4", - "licence": [ - "BSD License" - ], - "identifier": "biotools:mageck" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "inputfile": { - "type": "file", - "description": "library fastq file containing the sgRNA and gene name or count table containing the sgRNA and number of reads to per sample", - "pattern": "*.{fq,fastq,fastq.gz,fq.gz,csv,txt,tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - }, - { - "edam": "http://edamontology.org/format_3752" - }, - { - "edam": "http://edamontology.org/format_3475" - } - ] - } + "name": "octopusv_svcf2vcf", + "path": "modules/nf-core/octopusv/svcf2vcf/meta.yml", + "type": "module", + "meta": { + "name": "octopusv_svcf2vcf", + "description": "Converts octopusv SVCF files to the standard VCF format", + "keywords": ["structural variants", "svcf2vcf", "genomics", "vcf"], + "tools": [ + { + "octopusv": { + "description": "End-to-end structural variant post-processing: standardize, merge, compare, and export SVs.", + "homepage": "https://github.com/ylab-hi/OctopuSV", + "documentation": "https://github.com/ylab-hi/OctopuSV", + "tool_dev_url": "https://github.com/ylab-hi/octopusV", + "doi": "10.1093/bioinformatics/btaf599", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "svcf": { + "type": "file", + "description": "SVCF file to convert to a standard VCF file", + "pattern": "*.svcf", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + } + ] + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.vcf": { + "type": "file", + "description": "Sorted VCF file", + "pattern": "*.vcf", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + } + ] + } + } + ] + ], + "versions_octopusv": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "octopusv": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python -c \"import importlib.metadata as m; print(m.version('octopusv'))\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "octopusv": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python -c \"import importlib.metadata as m; print(m.version('octopusv'))\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@manascripts"], + "maintainers": ["@manascripts"] } - ], - { - "library": { - "type": "file", - "description": "library file containing the sgRNA and gene name", - "pattern": "*.{csv,txt,tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" + }, + { + "name": "odgi_build", + "path": "modules/nf-core/odgi/build/meta.yml", + "type": "module", + "meta": { + "name": "odgi_build", + "description": "Construct a dynamic succinct variation graph in ODGI format from a GFAv1.", + "keywords": ["variation graph", "pangenome graph", "gfa", "graph construction"], + "tools": [ + { + "odgi": { + "description": "An optimized dynamic genome/graph implementation", + "homepage": "https://github.com/pangenome/odgi", + "documentation": "https://odgi.readthedocs.io/en/latest/", + "tool_dev_url": "https://github.com/pangenome/odgi", + "doi": "10.1093/bioinformatics/btac308", + "licence": ["MIT"], + "identifier": "biotools:odgi" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "graph": { + "type": "file", + "description": "Pangenome graph in GFA v1.0 format", + "pattern": "*.{gfa}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3975" + } + ] + } + } + ] + ], + "output": { + "og": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.og": { + "type": "file", + "description": "File containing a pangenome graph in ODGI binary format. Usually ends with '.og'", + "pattern": "*.{og}", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] }, + "authors": ["@subwaystation"], + "maintainers": ["@subwaystation"] + }, + "pipelines": [ { - "edam": "http://edamontology.org/format_3475" + "name": "pangenome", + "version": "1.1.3" } - ] - } - } - ], - "output": { - "count": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*count.txt": { - "type": "file", - "description": "File containing read counts", - "pattern": "*.countsummary.txt", - "ontologies": [] - } - } - ] - ], - "norm": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.count_normalized.txt": { - "type": "file", - "description": "File containing normalized read counts", - "pattern": "*.count_normalized.txt", - "ontologies": [] - } - } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@LaurenceKuhl" - ], - "maintainers": [ - "@LaurenceKuhl" - ] - }, - "pipelines": [ - { - "name": "crisprseq", - "version": "2.3.0" - } - ] - }, - { - "name": "mageck_mle", - "path": "modules/nf-core/mageck/mle/meta.yml", - "type": "module", - "meta": { - "name": "mageck_mle", - "description": "maximum-likelihood analysis of gene essentialities computation", - "keywords": [ - "sort", - "maximum-likelihood", - "CRISPR" - ], - "tools": [ - { - "mageck": { - "description": "MAGeCK (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout), an algorithm to process, QC, analyze and visualize CRISPR screening data.", - "homepage": "https://sourceforge.net/p/mageck/wiki/Home/#mle", - "documentation": "https://sourceforge.net/p/mageck/wiki/Home/", - "tool_dev_url": "https://bitbucket.org/liulab/mageck/src", - "doi": "10.1186/s13059-015-0843-6", - "licence": [ - "BSD" - ], - "identifier": "biotools:mageck" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + }, + { + "name": "odgi_draw", + "path": "modules/nf-core/odgi/draw/meta.yml", + "type": "module", + "meta": { + "name": "odgi_draw", + "description": "Draw previously-determined 2D layouts of the graph with diverse annotations.", + "keywords": ["variation graph", "pangenome graph", "gfa", "graph drawing"], + "tools": [ + { + "odgi": { + "description": "An optimized dynamic genome/graph implementation", + "homepage": "https://github.com/pangenome/odgi", + "documentation": "https://odgi.readthedocs.io/en/latest/", + "tool_dev_url": "https://github.com/pangenome/odgi", + "doi": "10.1093/bioinformatics/btac308", + "licence": ["MIT"], + "identifier": "biotools:odgi" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "graph": { + "type": "file", + "description": "Pangenome graph in GFA v1.0 format or ODGI binary format", + "pattern": "*.{gfa,og}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3975" + } + ] + } + }, + { + "lay": { + "type": "file", + "description": "2D layout from 'odgi layout' in LAY binary format", + "pattern": "*.{lay}", + "ontologies": [] + } + } + ] + ], + "output": { + "png": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.png": { + "type": "file", + "description": "File in PNG format containing a 2D drawing of a pangenome graph", + "pattern": "*.{png}", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@subwaystation"], + "maintainers": ["@subwaystation"] }, - { - "count_table": { - "type": "file", - "description": "Count table file.\nEach line in the table should include\nsgRNA name (1st column), target gene (2nd column)\nand read counts in each sample.\n", - "pattern": "*.{txt,tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - { - "design_matrix": { - "type": "file", - "description": "Design matrix describing the samples and conditions", - "pattern": "*.{txt,tsv}", - "ontologies": [ + "pipelines": [ { - "edam": "http://edamontology.org/format_3475" + "name": "pangenome", + "version": "1.1.3" } - ] - } - } - ], - "output": { - "gene_summary": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.gene_summary.txt": { - "type": "file", - "description": "Gene summary file describing the fitness score\nand associated p-values.\n", - "pattern": "*.{gene_summary}", - "ontologies": [] - } - } - ] - ], - "sgrna_summary": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.sgrna_summary.txt": { - "type": "file", - "description": "sgRNA summary file describing the sgRNA and\nassociated gene\n", - "pattern": "*.{gene_summary}", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@LaurenceKuhl" - ], - "maintainers": [ - "@LaurenceKuhl" - ] - }, - "pipelines": [ - { - "name": "crisprseq", - "version": "2.3.0" - } - ] - }, - { - "name": "mageck_test", - "path": "modules/nf-core/mageck/test/meta.yml", - "type": "module", - "meta": { - "name": "mageck_test", - "description": "Mageck test performs a robust ranking aggregation (RRA) to identify positively or negatively selected genes in functional genomics screens.", - "keywords": [ - "sort", - "rra", - "CRISPR" - ], - "tools": [ - { - "mageck": { - "description": "MAGeCK (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout), an algorithm to process, QC, analyze and visualize CRISPR screening data.", - "homepage": "https://sourceforge.net/p/mageck/wiki/Home/#mle", - "documentation": "https://sourceforge.net/p/mageck/wiki/Home/", - "tool_dev_url": "https://bitbucket.org/liulab/mageck/src", - "doi": "10.1186/s13059-015-0843-6", - "licence": [ - "BSD License" - ], - "identifier": "biotools:mageck" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "count_table": { - "type": "file", - "description": "Count table file.\nEach line in the table should include\nsgRNA name (1st column), target gene (2nd column)\nand read counts in each sample.\n", - "pattern": "*.{txt,tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "output": { - "gene_summary": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.gene_summary.txt": { - "type": "file", - "description": "Gene summary file describing the fitness score\nand associated p-values.\n", - "pattern": "*.{gene_summary.txt}", - "ontologies": [] - } - } ] - ], - "sgrna_summary": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.sgrna_summary.txt": { - "type": "file", - "description": "sgRNA summary file describing the sgRNA and\nassociated gene\n", - "pattern": "*.{sgrna_summary.txt}", - "ontologies": [] - } - } - ] - ], - "r_script": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.R": { - "type": "file", - "description": "R script allowing to output plots\nfrom main hit genes\n", - "pattern": "*.R", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3999" - } - ] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@LaurenceKuhl" - ], - "maintainers": [ - "@LaurenceKuhl" - ] - }, - "pipelines": [ - { - "name": "crisprseq", - "version": "2.3.0" - } - ] - }, - { - "name": "magus_align", - "path": "modules/nf-core/magus/align/meta.yml", - "type": "module", - "meta": { - "name": "magus_align", - "description": "Multiple Sequence Alignment using Graph Clustering", - "keywords": [ - "MSA", - "alignment", - "genomics", - "graph" - ], - "tools": [ - { - "magus": { - "description": "Multiple Sequence Alignment using Graph Clustering", - "homepage": "https://github.com/vlasmirnov/MAGUS", - "documentation": "https://github.com/vlasmirnov/MAGUS", - "tool_dev_url": "https://github.com/vlasmirnov/MAGUS", - "doi": "10.1093/bioinformatics/btaa992", - "licence": [ - "MIT" - ], - "identifier": "biotools:magus" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing the fasta meta information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input sequences in FASTA format.", - "pattern": "*.{fa,fna,fasta}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1919" - }, - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information for the specified guide tree (if supplied)\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "tree": { - "type": "file", - "description": "Optional path to a file containing a guide tree in newick format to use as input. If empty, or overwritten by passing `-t [fasttree|fasttree-noml|clustal|parttree]`, MAGUS will construct its own guide tree. If empty, `fasttree` is used as a default.", - "pattern": "*.{dnd,tree}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2006" - } - ] - } - } - ], - { - "compress": { - "type": "boolean", - "description": "Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded." - } - } - ], - "output": { - "alignment": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample meta information.\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*.aln{.gz,}": { - "type": "file", - "description": "File containing the output alignment, in FASTA format containing gaps. The sequences may be in a different order than in the input FASTA. The output file may or may not be gzipped, depending on the value supplied to `compress`.", - "pattern": "*.aln{.gz,}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2554" - }, - { - "edam": "http://edamontology.org/format_1921" - }, - { - "edam": "http://edamontology.org/format_1984" + }, + { + "name": "odgi_layout", + "path": "modules/nf-core/odgi/layout/meta.yml", + "type": "module", + "meta": { + "name": "odgi_layout", + "description": "Establish 2D layouts of the graph using path-guided stochastic gradient descent. The graph must be sorted and id-compacted.", + "keywords": ["variation graph", "pangenome graph", "gfa", "graph layout"], + "tools": [ + { + "odgi": { + "description": "An optimized dynamic genome/graph implementation", + "homepage": "https://github.com/pangenome/odgi", + "documentation": "https://odgi.readthedocs.io/en/latest/", + "tool_dev_url": "https://github.com/pangenome/odgi", + "doi": "10.1093/bioinformatics/btac308", + "licence": ["MIT"], + "identifier": "biotools:odgi" + } } - ] + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "graph": { + "type": "file", + "description": "Pangenome graph in GFA v1.0 format or in ODGI binary format", + "pattern": "*.{gfa,og}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3975" + } + ] + } + } + ] + ], + "output": { + "lay": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.lay": { + "type": "file", + "description": "File containing a 2D layout of a pangenome graph in a binary format. Usually ends with '.lay'. Optional output specified by the `--out FILE` argument. Either this or the TSV layout output must be specified.", + "pattern": "*.{lay}", + "ontologies": [] + } + } + ] + ], + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "File containing a 2D layout of a pangenome graph in TSV format. Optional output specified by the `--tsv FILE` argument. Either this or the binary layout output must be specified.", + "pattern": "*.{tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@subwaystation"], + "maintainers": ["@subwaystation"] + }, + "pipelines": [ + { + "name": "pangenome", + "version": "1.1.3" } - } - ] - ], - "versions_magus": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "magus": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "magus --version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_pigz": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pigz": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pigz --version 2>&1 | sed \"s/^.*pigz[[:space:]]*//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "magus": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "magus --version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pigz": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pigz --version 2>&1 | sed \"s/^.*pigz[[:space:]]*//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } ] - ] }, - "authors": [ - "@lrauschning" - ] - }, - "pipelines": [ { - "name": "multiplesequencealign", - "version": "1.1.1" - } - ] - }, - { - "name": "magus_guidetree", - "path": "modules/nf-core/magus/guidetree/meta.yml", - "type": "module", - "meta": { - "name": "magus_guidetree", - "description": "Multiple Sequence Alignment using Graph Clustering", - "keywords": [ - "MSA", - "guidetree", - "genomics", - "graph" - ], - "tools": [ - { - "magus": { - "description": "Multiple Sequence Alignment using Graph Clustering", - "homepage": "https://github.com/vlasmirnov/MAGUS", - "documentation": "https://github.com/vlasmirnov/MAGUS", - "tool_dev_url": "https://github.com/vlasmirnov/MAGUS", - "doi": "10.1093/bioinformatics/btaa992", - "licence": [ - "MIT" - ], - "identifier": "biotools:magus" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing fasta meta information\ne.g. `[ id:'test', single_end:false ]`\n" - } + "name": "odgi_sort", + "path": "modules/nf-core/odgi/sort/meta.yml", + "type": "module", + "meta": { + "name": "odgi_sort", + "description": "Apply different kind of sorting algorithms to a graph. The most prominent one is the PG-SGD sorting algorithm.", + "keywords": ["variation graph", "pangenome graph", "gfa", "graph layout"], + "tools": [ + { + "odgi": { + "description": "An optimized dynamic genome/graph implementation", + "homepage": "https://github.com/pangenome/odgi", + "documentation": "https://odgi.readthedocs.io/en/latest/", + "tool_dev_url": "https://github.com/pangenome/odgi", + "doi": "10.1093/bioinformatics/btac308", + "licence": ["MIT"], + "identifier": "biotools:odgi" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "graph": { + "type": "file", + "description": "Pangenome graph in GFA v1.0 format or in ODGI binary format", + "pattern": "*.{gfa,og}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3975" + } + ] + } + } + ] + ], + "output": { + "sorted_graph": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.og": { + "type": "file", + "description": "1D sorted pangenome graph in ODGI binary format", + "pattern": "*.{og}", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@subwaystation"], + "maintainers": ["@subwaystation"] }, - { - "fasta": { - "type": "file", - "description": "Input sequences in FASTA format.", - "pattern": "*.{fa,fna,fasta}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1919" - }, - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ], - "output": { - "tree": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*.tree": { - "type": "file", - "description": "File containing the output guidetree, in newick format.", - "pattern": "*.tree", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2006" - } - ] - } - } + "pipelines": [ + { + "name": "pangenome", + "version": "1.1.3" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@lrauschning" - ] - } - }, - { - "name": "malt_build", - "path": "modules/nf-core/malt/build/meta.yml", - "type": "module", - "meta": { - "name": "malt_build", - "description": "MALT, an acronym for MEGAN alignment tool, is a sequence alignment and analysis tool designed for processing high-throughput sequencing data, especially in the context of metagenomics.", - "keywords": [ - "malt", - "alignment", - "metagenomics", - "ancient DNA", - "aDNA", - "palaeogenomics", - "archaeogenomics", - "microbiome", - "database" - ], - "tools": [ - { - "malt": { - "description": "A tool for mapping metagenomic data", - "homepage": "https://www.wsi.uni-tuebingen.de/lehrstuehle/algorithms-in-bioinformatics/software/malt/", - "documentation": "https://software-ab.cs.uni-tuebingen.de/download/malt/manual.pdf", - "doi": "10.1038/s41559-017-0446-6", - "licence": [ - "GPL v3" - ], - "identifier": "" - } - } - ], - "input": [ - { - "fastas": { - "type": "file", - "description": "Directory of, or list of FASTA reference files for indexing", - "pattern": "*/|*.fasta", - "ontologies": [] - } - }, - { - "gff": { - "type": "file", - "description": "Directory of, or GFF3 files of input FASTA files", - "pattern": "*/|*.gff|*.gff3", - "ontologies": [] - } - }, - { - "mapping_db": { - "type": "file", - "description": "An uncompressed MEGAN mapping file from https://software-ab.cs.uni-tuebingen.de/download/megan6/welcome.html (either mapping db, or acc2* .abin file)", - "pattern": "*.{db,abin}", - "ontologies": [] - } - }, - { - "map_type": { - "type": "string", - "description": "The type of map file provided to the pipeline. Must be a valid string corresponding to a single-dash parameter, for example '-a2tax' or '-a2interpro2go'", - "pattern": "mdb|a2t|s2t|a2ec|s2ec|t4ec|a2eggnog|s2eggnog|t4eggnog|a2gtdb|s2gtdb|t4gtdb|a2interpro2go|s2interpro2go|t4interprotogo|a2kegg|s2kegg|t4kegg|a2pgpt|s2pgpt|t4pgpt|a2seed|s2seed|t4seed" - } - } - ], - "output": { - "index": [ - { - "malt_index/": { - "type": "directory", - "description": "Directory containing MALT database index directory", - "pattern": "malt_index/" - } - } - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ], - "log": [ - { - "malt-build.log": { - "type": "file", - "description": "Log file from STD out of malt-build", - "pattern": "malt-build.log", - "ontologies": [] - } - } - ] - }, - "authors": [ - "@jfy133", - "@LilyAnderssonLee" - ], - "maintainers": [ - "@jfy133", - 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} - ] - } - } - ] - }, - "authors": [ - "@jch-13" - ], - "maintainers": [ - "@jch-13" - ] - } - }, - { - "name": "mapdamage2", - "path": "modules/nf-core/mapdamage2/meta.yml", - "type": "module", - "meta": { - "name": "mapdamage2", - "description": "Computational framework for tracking and quantifying DNA damage patterns among ancient DNA sequencing reads generated by Next-Generation Sequencing platforms.", - "keywords": [ - "ancient DNA", - "DNA damage", - "NGS", - "damage patterns", - "bam" - ], - "tools": [ - { - "mapdamage2": { - "description": "Tracking and quantifying damage patterns in ancient DNA sequences", - "homepage": "http://ginolhac.github.io/mapDamage/", - "documentation": "https://ginolhac.github.io/mapDamage/", - "tool_dev_url": "https://github.com/ginolhac/mapDamage", - "doi": "10.1093/bioinformatics/btt193", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false]" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file", - "pattern": "*.{bam}", - "ontologies": [] - } - } - ], - { - "fasta": { - "type": "file", - "description": "Fasta file, the reference the input BAM was mapped against", - "pattern": "*.{fasta}", - "ontologies": [] - } - } - ], - "output": { - "runtime_log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false]" - } - }, - { - "results_*/Runtime_log.txt": { - "type": "file", - "description": "Log file with a summary of command lines used and timestamps.", - "pattern": "Runtime_log.txt", - "ontologies": [] - } - } - ] - ], - "fragmisincorporation_plot": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false]" - } - }, - { - "results_*/Fragmisincorporation_plot.pdf": { - "type": "file", - "description": "A pdf file that displays both fragmentation and misincorporation patterns.", - 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[ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false]" - } - }, - { - "results_*/lgdistribution.txt": { - "type": "file", - "description": "Contains a table with read length distributions per strand.", - "pattern": "lgdistribution.txt", - "ontologies": [] - } - } - ] - ], - "dnacomp": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false]" - } - }, - { - "results_*/dnacomp.txt": { - "type": "file", - "description": "Contains a table of the reference genome base composition per position, inside reads and adjacent regions.", - "pattern": "dnacomp.txt", - "ontologies": [] - } - } - ] - ], - "stats_out_mcmc_hist": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false]" - } - }, - { - "results_*/Stats_out_MCMC_hist.pdf": { - "type": "file", - "description": "A MCMC histogram for the damage parameters and log likelihood.", - 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"type": "file", - "description": "Alignments in a FASTA file, only if flagged by -d.", - "pattern": "*.{fasta}", - "ontologies": [] - } - } - ] - ], - "folder": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false]" - } - }, - { - "*/": { - "type": "directory", - "description": "Folder created when --plot-only, --rescale and --stats-only flags are passed.", - "pattern": "*/" - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@darcy220606" - ], - "maintainers": [ - "@darcy220606" - ] - } - }, - { - "name": "mash_dist", - "path": "modules/nf-core/mash/dist/meta.yml", - "type": "module", - "meta": { - "name": "mash_dist", - "description": "Calculate Mash distances between reference and query sequences", - "keywords": [ - "distance", - "estimate", - "reference", - "query" - ], - "tools": [ - { - "mash": { - "description": "Fast sequence distance estimator that uses MinHash", - "homepage": "https://github.com/marbl/Mash", - "documentation": "https://mash.readthedocs.io/en/latest/sketches.html", - "tool_dev_url": "https://github.com/marbl/Mash", - "doi": "10.1186/s13059-016-0997-x", - "licence": [ - "https://github.com/marbl/Mash/blob/master/LICENSE.txt" - ], - "identifier": "biotools:mash" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + "name": "openms_decoydatabase", + "path": "modules/nf-core/openms/decoydatabase/meta.yml", + "type": "module", + "meta": { + "name": "openms_decoydatabase", + "description": "Create a decoy peptide database from a standard FASTA database.", + "keywords": ["decoy", "database", "openms", "proteomics", "fasta"], + "tools": [ + { + "openms": { + "description": "OpenMS is an open-source software C++ library for LC-MS data management and analyses", + "homepage": "https://openms.de", + "documentation": "https://openms.readthedocs.io/en/latest/index.html", + "tool_dev_url": "https://github.com/OpenMS/OpenMS", + "doi": "10.1038/s41592-024-02197-7", + "licence": ["BSD"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Fasta file containing protein sequences", + "pattern": "*.{fasta}", + "ontologies": [] + } + } + ] + ], + "output": { + "decoy_fasta": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.fasta": { + "type": "file", + "description": "Fasta file containing proteins and decoy proteins", + "pattern": "*.{fasta}", + "ontologies": [] + } + } + ] + ], + "versions_openms": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "openms": { + "type": "string", + "description": "The tool name" + } + }, + { + "FileInfo --help 2>&1 | sed -nE 's/^Version: ([0-9.]+).*/\\1/p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "openms": { + "type": "string", + "description": "The tool name" + } + }, + { + "FileInfo --help 2>&1 | sed -nE 's/^Version: ([0-9.]+).*/\\1/p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@jonasscheid"], + "maintainers": ["@jonasscheid", "@gallvp"] }, - 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"resistance", - "fasta", - "mcr-1" - ], - "tools": [ - { - "mcroni": { - "description": "Scripts for finding and processing promoter variants upstream of mcr-1", - "homepage": "https://github.com/liampshaw/mcroni", - "documentation": "https://github.com/liampshaw/mcroni", - "tool_dev_url": "https://github.com/liampshaw/mcroni", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + }, + { + "name": "openms_peptideindexer", + "path": "modules/nf-core/openms/peptideindexer/meta.yml", + "type": "module", + "meta": { + "name": "openms_peptideindexer", + "description": "Refreshes the protein references for all peptide hits.", + "keywords": ["refresh", "idXML", "openms", "proteomics"], + "tools": [ + { + "openms": { + "description": "OpenMS is an open-source software C++ library for LC-MS data management and analyses", + "homepage": "https://openms.de", + "documentation": "https://openms.readthedocs.io/en/latest/index.html", + "tool_dev_url": "https://github.com/OpenMS/OpenMS", + "doi": "10.1038/s41592-024-02197-7", + "licence": ["BSD"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "idxml": { + "type": "file", + "description": "idXML identification file", + "pattern": "*.idXML", + "ontologies": [] + } + }, + { + "fasta": { + "type": "file", + "description": "Input sequence database in FASTA format", + "pattern": "*.fasta", + "ontologies": [] + } + } + ] + ], + "output": { + "indexed_idxml": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.idXML": { + "type": "file", + "description": "Refreshed idXML identification file", + "pattern": "*.idXML", + "ontologies": [] + } + } + ] + ], + "versions_openms": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "openms": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "FileInfo --help 2>&1 | sed -nE 's/^Version: ([0-9.]+).*/\\1/p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "openms": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "FileInfo --help 2>&1 | sed -nE 's/^Version: ([0-9.]+).*/\\1/p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@jonasscheid"], + "maintainers": ["@jonasscheid"] }, - { - "fasta": { - "type": "file", - "description": "A fasta file.", - "pattern": "*.{fasta.gz,fasta,fa.gz,fa,fna.gz,fna}", - "ontologies": [] - } - } - ] - ], - "output": { - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "mcroni results in TSV format", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "fa": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.fa": { - "type": "file", - "description": "mcr-1 matching sequences", - "pattern": "*.fa", - "ontologies": [] - } - } + "pipelines": [ + { + "name": "mhcquant", + "version": "3.2.0" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@rpetit3" - ], - "maintainers": [ - "@rpetit3" - ] - } - }, - { - "name": "mcstaging_imc2mc", - "path": "modules/nf-core/mcstaging/imc2mc/meta.yml", - "type": "module", - "meta": { - "name": "mcstaging_imc2mc", - "description": "Staging module for MCMICRO transforming Imaging Mass Cytometry .txt files to .tif files with OME-XML metadata. Includes optional hot pixel removal.", - "deprecated": true, - "keywords": [ - "imaging", - "ome-tif", - "staging", - "MCMICRO" - ], - "tools": [ - { - "mcstaging": { - "description": "Staging modules for MCMICRO", - "homepage": "https://github.com/SchapiroLabor/imc2mc", - "documentation": "https://github.com/SchapiroLabor/imc2mc/README.md", - "tool_dev_url": "https://github.com/SchapiroLabor/imc2mc", - "licence": [ - "GPL-3.0 license" - ], - "identifier": "" + }, + { + "name": "openms_psmfeatureextractor", + "path": "modules/nf-core/openms/psmfeatureextractor/meta.yml", + "type": "module", + "meta": { + "name": "openms_psmfeatureextractor", + "description": "Computes extra features for each input PSM for use with Percolator rescoring.", + "keywords": ["features", "idXML", "openms", "percolator", "proteomics", "psm"], + "tools": [ + { + "openms": { + "description": "OpenMS is an open-source software C++ library for LC-MS data management and analyses", + "homepage": "https://openms.de", + "documentation": "https://openms.readthedocs.io/en/latest/index.html", + "tool_dev_url": "https://github.com/OpenMS/OpenMS", + "doi": "10.1038/s41592-024-02197-7", + "licence": ["BSD"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "id_file": { + "type": "file", + "description": "Peptide identification file from a search engine.", + "pattern": "*.{idXML,mzid}", + "ontologies": [] + } + } + ] + ], + "output": { + "idxml": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "${prefix}.idXML": { + "type": "file", + "description": "Peptide identification file with extra PSM features added.", + "pattern": "*.idXML", + "ontologies": [] + } + } + ] + ], + "versions_openms": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "openms": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "FileInfo --help 2>&1 | sed -nE 's/^Version: ([0-9.]+).*/\\1/p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "openms": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "FileInfo --help 2>&1 | sed -nE 's/^Version: ([0-9.]+).*/\\1/p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@jonasscheid"], + "maintainers": ["@jonasscheid"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } + }, + { + "name": "openms_textexporter", + "path": "modules/nf-core/openms/textexporter/meta.yml", + "type": "module", + "meta": { + "name": "openms_textexporter", + "description": "Exports various OpenMS XML formats (featureXML, consensusXML, idXML, mzML) to a human-readable text format.", + "keywords": ["export", "openms", "proteomics", "text", "tsv"], + "tools": [ + { + "openms": { + "description": "OpenMS is an open-source software C++ library for LC-MS data management and analyses", + "homepage": "https://openms.de", + "documentation": "https://openms.readthedocs.io/en/latest/index.html", + "tool_dev_url": "https://github.com/OpenMS/OpenMS", + "doi": "10.1038/s41592-024-02197-7", + "licence": ["BSD"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "input_file": { + "type": "file", + "description": "OpenMS data file to export to text format.", + "pattern": "*.{featureXML,consensusXML,idXML,mzML}", + "ontologies": [] + } + } + ] + ], + "output": { + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "${prefix}.tsv": { + "type": "file", + "description": "Tab-separated text export of the input data.", + "pattern": "*.tsv", + "ontologies": [] + } + } + ] + ], + "versions_openms": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "openms": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "FileInfo --help 2>&1 | sed -nE 's/^Version: ([0-9.]+).*/\\1/p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "openms": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "FileInfo --help 2>&1 | sed -nE 's/^Version: ([0-9.]+).*/\\1/p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@jonasscheid"], + "maintainers": ["@jonasscheid"] }, - { - "txtfile": { - "type": "file", - "description": "Acquisition .txt file", - "pattern": "*.{txt}", - "ontologies": [] - } - } - ] - ], - "output": { - "tif": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.tif": { - "type": "file", - "description": "One output .tif file containing acquisition and metadata", - "pattern": "*.{tif}", - "ontologies": [] - } - } + "pipelines": [ + { + "name": "mhcquant", + "version": "3.2.0" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@MargotCh" - ], - "maintainers": [ - "@MargotCh" - ] - } - }, - { - "name": "mcstaging_macsima2mc", - "path": "modules/nf-core/mcstaging/macsima2mc/meta.yml", - "type": "module", - "meta": { - "name": "mcstaging_macsima2mc", - "description": "Staging module for MCMICRO transforming MACSima data sets for being registered with ASHLAR in MCMICRO.", - "keywords": [ - "imaging", - "ome-tif", - "mcmicro", - "staging", - "spatial-omics", - "macsima" - ], - "tools": [ - { - "macsima2mc": { - "description": "Staging module for MCMICRO", - "homepage": "https://github.com/SchapiroLabor/macsima2mc", - "documentation": "https://github.com/SchapiroLabor/macsima2mc/README.md", - "tool_dev_url": "https://github.com/SchapiroLabor/macsima2mc", - "licence": [ - "BSD-3-Clause" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "input_dir": { - "type": "directory", - "description": "Absolute path to the the parent folder of the raw tiles, whose name follows the pattern X_Cycle_N,where N represents the cycle number", - "pattern": "*Cycle*" - } + }, + { + "name": "openmsthirdparty_cometadapter", + "path": "modules/nf-core/openmsthirdparty/cometadapter/meta.yml", + "type": "module", + "meta": { + "name": "openmsthirdparty_cometadapter", + "description": "Annotates MS/MS spectra using Comet.", + "keywords": ["search engine", "fasta", "mzml", "openms", "proteomics"], + "tools": [ + { + "openms": { + "description": "OpenMS is an open-source software C++ library for LC-MS data management and analyses", + "homepage": "https://openms.de", + "documentation": "https://openms.readthedocs.io/en/latest/index.html", + "tool_dev_url": "https://github.com/OpenMS/OpenMS", + "doi": "10.1038/s41592-024-02197-7", + "licence": ["BSD"], + "identifier": "" + } + }, + { + "CometAdapter": { + "description": "Annotates MS/MS spectra using Comet.", + "homepage": "https://openms.de", + "documentation": "https://openms.readthedocs.io/en/latest/index.html", + "identifier": "" + } + }, + { + "Comet": { + "description": "Comet is an open source tandem mass spectrometry (MS/MS) sequence database search tool.", + "homepage": "http://comet-ms.sourceforge.net/", + "documentation": "http://comet-ms.sourceforge.net/", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "mzml": { + "type": "file", + "description": "File containing mass spectra in mzML format", + "pattern": "*.{mzML}", + "ontologies": [] + } + }, + { + "fasta": { + "type": "file", + "description": "Protein sequence database containing targets and decoys", + "pattern": "*.{fasta}", + "ontologies": [] + } + } + ] + ], + "output": { + "idxml": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.idXML": { + "type": "file", + "description": "File containing target and decoy hits in idXML format", + "pattern": "*.{idXML}", + "ontologies": [] + } + } + ] + ], + "pin": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "TSV file tailored as Percolator input (pin) file", + "pattern": "*.{tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_cometadapter": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "CometAdapter": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "CometAdapter --help 2>&1 | sed -nE 's/^Version: ([0-9.]+).*/\\1/p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_comet": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "Comet": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "comet 2>&1 | sed -n 's/.*Comet version \" *\\(.*\\)\".*/\\1/p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "CometAdapter": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "CometAdapter --help 2>&1 | sed -nE 's/^Version: ([0-9.]+).*/\\1/p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "Comet": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "comet 2>&1 | sed -n 's/.*Comet version \" *\\(.*\\)\".*/\\1/p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@jonasscheid"], + "maintainers": ["@jonasscheid"] }, - { - "output_dir": { - "type": "string", - "description": "Absolute path to the directory in which the outputs will be saved. If the output directory doesn't exist it will be created." - } - } - ] - ], - "output": { - "out_dir": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${output_dir}/*": { - "type": "directory", - "description": "Output directory containing subdirectories per well-rack-roi-exp combination.\nEach subdirectory contains a markers.csv table and a raw/ folder with ome.tif files.\n", - "pattern": "*/" - } - } - ] - ], - "versions_macsima2mc": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "macsima2mc": { - "type": "string", - "description": "The tool name" - } - }, - { - "python -m pip show macsima2mc | grep \"Version\" | sed -e \"s/Version: //g\"": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "macsima2mc": { - "type": "string", - "description": "The tool name" - } - }, - { - "python -m pip show macsima2mc | grep \"Version\" | sed -e \"s/Version: //g\"": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } + "pipelines": [ + { + "name": "mhcquant", + "version": "3.2.0" + } ] - ] - }, - "authors": [ - "@EfraMP" - ], - "maintainers": [ - "@EfraMP", - "@VictorDidier" - ] - } - }, - { - "name": "mcstaging_phenoimager2mc", - "path": "modules/nf-core/mcstaging/phenoimager2mc/meta.yml", - "type": "module", - "meta": { - "name": "mcstaging_phenoimager2mc", - "description": "Staging module for MCMICRO transforming PhenoImager .tif files into stacked and normalized ome-tif files per cycle, compatible as ASHLAR input.", - "deprecated": true, - "keywords": [ - "imaging", - "registration", - "ome-tif", - "Staging", - "MCMICRO" - ], - "tools": [ - { - "mcstaging": { - "description": "Staging modules for MCMICRO", - "homepage": "https://github.com/SchapiroLabor/phenoimager2mc", - "documentation": "https://github.com/SchapiroLabor/phenoimager2mc/README.md", - "tool_dev_url": "https://github.com/SchapiroLabor/phenoimager2mc", - "licence": [ - "GPL-2.0 license" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } + }, + { + "name": "opt_flip", + "path": "modules/nf-core/opt/flip/meta.yml", + "type": "module", + "meta": { + "name": "opt_flip", + "description": "flip corrects probes that are aligning to the opposite strand of their intended target genes by reverse complementing them", + "keywords": ["opt", "opt flip", "transcripts", "off-target probes", "align probes"], + "tools": [ + { + "opt": { + "description": "opt is a simple program that aligns probe sequences to transcript sequences to detect potential off-target probe activity", + "homepage": "https://github.com/JEFworks-Lab/off-target-probe-tracker", + "documentation": "https://github.com/JEFworks-Lab/off-target-probe-tracker/blob/main/README.md", + "tool_dev_url": "https://github.com/JEFworks-Lab/off-target-probe-tracker", + "licence": ["GPL-3.0 license"] + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information of the probe panel sequences used for the xenium experiment\ne.g. `[ id:'breast_cancer_probe_panel_sequences' ]`\n" + } + }, + { + "probes_fasta": { + "type": "file", + "description": "Fasta file for the probe sequences used in the xenium experiment", + "pattern": "*.fasta", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing the information of the genomic features and fasta files used as references\ne.g. `[ id:'gencode_references' ]`\n" + } + }, + { + "ref_annot_gff": { + "type": "file", + "description": "Reference annotations in gff format", + "pattern": "*.gff", + "ontologies": [] + } + }, + { + "ref_annot_fa": { + "type": "file", + "description": "Reference annotations in fasta format", + "pattern": "*.fa", + "ontologies": [] + } + } + ] + ], + "output": { + "fwd_oriented_fa": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information of the forward oriented fasta generated with the probes panel sequences 'opt flip'\ne.g. `[ id:'breast_cancer_probe_panel_sequences' ]`\n" + } + }, + { + "${meta.id}/fwd_oriented.fa": { + "type": "file", + "description": "The forward oriented fasta file", + "pattern": "*.fa", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@khersameesh24"], + "maintainers": ["@khersameesh24"] }, - { - "tiles": { - "type": "list", - "description": "Folder or list with .tif files of one cycle from PhenoImager" - } - } - ] - ], - "output": { - "tif": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.tif": { - "type": "file", - "description": "One output .tif file containing concatenated tiles of the cycle.", - "pattern": "*.{tif,tiff}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3591" - } - ] - } - } - ] - ], - "versions_phenoimager2mc": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "phenoimager2mc": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python /phenoimager2mc/scripts/phenoimager2mc.py --version | sed \"s/v//g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "phenoimager2mc": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python /phenoimager2mc/scripts/phenoimager2mc.py --version | sed \"s/v//g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "spatialxe", + "version": "dev" + } ] - ] - }, - "authors": [ - "@chiarasch" - ], - "maintainers": [ - "@chiarasch" - ] - } - }, - { - "name": "md5sum", - "path": "modules/nf-core/md5sum/meta.yml", - "type": "module", - "meta": { - "name": "md5sum", - "description": "Create MD5 (128-bit) checksums", - "keywords": [ - "checksum", - "MD5", - "128 bit" - ], - "tools": [ - { - "md5sum": { - "description": "Create MD5 (128-bit) checksums for each file", - "homepage": "https://www.gnu.org", - "documentation": "https://man7.org/linux/man-pages/man1/md5sum.1.html", - "licence": [ - "GPL-3.0-or-later" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + }, + { + "name": "opt_stat", + "path": "modules/nf-core/opt/stat/meta.yml", + "type": "module", + "meta": { + "name": "opt_stat", + "description": "stat summarizes opt binding predictions", + "keywords": [ + "opt", + "opt stat", + "transcripts", + "binding predictions", + "off-target probes", + "align probes", + "summary stats" + ], + "tools": [ + { + "opt": { + "description": "opt is a simple program that aligns probe sequences to transcript sequences to detect potential off-target probe activity", + "homepage": "https://github.com/JEFworks-Lab/off-target-probe-tracker", + "documentation": "https://github.com/JEFworks-Lab/off-target-probe-tracker/blob/main/README.md", + "tool_dev_url": "https://github.com/JEFworks-Lab/off-target-probe-tracker", + "licence": ["GPL-3.0 license"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information of the probe targets generated from the panel sequences with `opt track`\ne.g. `[ id:'breast_cancer_probe_panel_sequences' ]`\n" + } + }, + { + "probe_targets": { + "type": "file", + "description": "Generated probe targets", + "pattern": "*.tsv", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing information of the forward oriented fasta generated with the probes panel sequences 'opt flip'\ne.g. `[ id:'breast_cancer_probe_panel_sequences' ]`\n" + } + }, + { + "fwd_oriented_probes": { + "type": "file", + "description": "The forward oriented fasta file", + "pattern": "*.fa", + "ontologies": [] + } + } + ], + { + "gene_synonyms": { + "type": "file", + "description": "Gene synonyms that may have been counted as off-targets but simply differ in name (optional input)", + "pattern": "*.csv", + "ontologies": [] + } + } + ], + "output": { + "summary": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing summary of the forward oriented probes generated with the panel sequences 'opt flip and track'\ne.g. `[ id:'breast_cancer_probe_panel_sequences' ]`\n" + } + }, + { + "${meta.id}/collapsed_summary.tsv": { + "type": "file", + "description": "tsv file containing the summary stats", + "pattern": "*.tsv", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@khersameesh24"], + "maintainers": ["@khersameesh24"] }, - { - "files": { - "type": "file", - "description": "Any number of files. One md5sum file will be generated for each.", - "pattern": "*.*", - "ontologies": [] - } - } - ], - { - "as_separate_files": { - "type": "boolean", - "description": "If true, each file will have its own md5sum file. If false, all files will be\nchecksummed into a single md5sum file.\n" - } - } - ], - "output": { - "checksum": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.md5": { - "type": "file", - "description": "File containing checksum", - "pattern": "*.md5", - "ontologies": [] - } - } - ] - ], - "versions_md5sum": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "md5sum": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "md5sum --version | sed '1!d; s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "md5sum": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "md5sum --version | sed '1!d; s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "spatialxe", + "version": "dev" + } ] - ] - }, - "authors": [ - "@matthdsm" - ], - "maintainers": [ - "@matthdsm" - ] - }, - "pipelines": [ - { - "name": "demultiplex", - "version": "1.7.1" - } - ] - }, - { - "name": "mdust", - "path": "modules/nf-core/mdust/meta.yml", - "type": "module", - "meta": { - "name": "mdust", - "description": "mdust from DFCI Gene Indices Software Tools for masking low-complexity DNA sequences", - "keywords": [ - "genomics", - "dna", - "low-complexity", - "masking" - ], - "tools": [ - { - "mdust": { - "description": "mdust from DFCI Gene Indices Software Tools for masking low-complexity DNA sequences", - "homepage": "https://github.com/lh3/mdust", - "documentation": "https://github.com/lh3/mdust", - "tool_dev_url": "https://github.com/lh3/mdust", - "licence": [ - "The Artistic License" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } + }, + { + "name": "opt_track", + "path": "modules/nf-core/opt/track/meta.yml", + "type": "module", + "meta": { + "name": "opt_track", + "description": "track aligns query probe sequences to any target transcriptome", + "keywords": [ + "opt", + "opt track", + "transcripts", + "off-target probes", + "align probes", + "traget transcriptome" + ], + "tools": [ + { + "opt": { + "description": "opt is a simple program that aligns probe sequences to transcript sequences to detect potential off-target probe activity", + "homepage": "https://github.com/JEFworks-Lab/off-target-probe-tracker", + "documentation": "https://github.com/JEFworks-Lab/off-target-probe-tracker/blob/main/README.md", + "tool_dev_url": "https://github.com/JEFworks-Lab/off-target-probe-tracker", + "licence": ["GPL-3.0 license"] + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information of the forward oriented fasta generated with the probes panel sequences generated with `opt flip`\ne.g. `[ id:'breast_cancer_probe_panel_sequences' ]`\n" + } + }, + { + "fwd_oriented_fa": { + "type": "file", + "description": "Forward oriented fasta file generated by the opt flip command", + "pattern": "*.fa", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing the information of the genomic features and fasta files used as references\ne.g. `[ id:'gencode_references' ]`\n" + } + }, + { + "ref_annot_gff": { + "type": "file", + "description": "Reference annotation in gff format", + "pattern": "*.gff", + "ontologies": [] + } + }, + { + "ref_annot_fa": { + "type": "file", + "description": "Reference annotation in fasta format", + "pattern": "*.fa", + "ontologies": [] + } + } + ] + ], + "output": { + "probes2target": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${meta.id}/probe2targets.tsv": { + "type": "file", + "description": "TSV file containing the gene and transcript information to which each probe aligns", + "pattern": "*.tsv", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@khersameesh24"], + "maintainers": ["@khersameesh24"] }, - { - "fasta": { - "type": "file", - "description": "Input fasta file", - "pattern": "*.{fa,fsa,faa,fas,fasta}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ], - "output": { - "fasta": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.fasta": { - "type": "file", - "description": "Output fasta file", - "pattern": "*.{fasta}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } + "pipelines": [ + { + "name": "spatialxe", + "version": "dev" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@GallVp" - ], - "maintainers": [ - "@GallVp" - ] - } - }, - { - "name": "medaka", - "path": "modules/nf-core/medaka/meta.yml", - "type": "module", - "meta": { - "name": "medaka", - "description": "A tool to create consensus sequences and variant calls from nanopore sequencing data", - "keywords": [ - "assembly", - "polishing", - "nanopore" - ], - "tools": [ - { - "medaka": { - "description": "Neural network sequence error correction.", - "homepage": "https://nanoporetech.github.io/medaka/index.html", - "documentation": "https://nanoporetech.github.io/medaka/index.html", - "tool_dev_url": "https://github.com/nanoporetech/medaka", - "licence": [ - "Mozilla Public License 2.0" - ], - "identifier": "biotools:medaka" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input nanopore fasta/FastQ files", - "pattern": "*.{fasta,fa,fastq,fastq.gz,fq,fq.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } + }, + { + "name": "optitype", + "path": "modules/nf-core/optitype/meta.yml", + "type": "module", + "meta": { + "name": "optitype", + "description": "Perform HLA-I typing of sequencing data", + "keywords": ["hla-typing", "ILP", "HLA-I"], + "tools": [ + { + "optitype": { + "description": "Precision HLA typing from next-generation sequencing data", + "homepage": "https://github.com/FRED-2/OptiType", + "documentation": "https://github.com/FRED-2/OptiType", + "doi": "10.1093/bioinformatics/btu548", + "licence": ["BSD-3-Clause"], + "identifier": "biotools:optitype" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file", + "pattern": "*.{bam}", + "ontologies": [] + } + }, + { + "bai": { + "type": "file", + "description": "BAM index file", + "pattern": "*.{bai}", + "ontologies": [] + } + } + ] + ], + "output": { + "hla_type": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', seq_type:'DNA' ]\n" + } + }, + { + "${prefix}/*.tsv": { + "type": "file", + "description": "HLA type", + "pattern": "${prefix}/*.tsv", + "ontologies": [] + } + } + ] + ], + "coverage_plot": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', seq_type:'DNA' ]\n" + } + }, + { + "${prefix}/*.pdf": { + "type": "file", + "description": "OptiType coverage plot", + "pattern": "${prefix}/*.pdf", + "ontologies": [] + } + } + ] + ], + "versions_optitype": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "optitype": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "grep \"Version:\" $(which OptiTypePipeline.py) | sed \"s/Version: //g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "optitype": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "grep \"Version:\" $(which OptiTypePipeline.py) | sed \"s/Version: //g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@apeltzer"], + "maintainers": ["@apeltzer", "@christopher-mohr"] }, - { - "assembly": { - "type": "file", - "description": "Genome assembly", - "pattern": "*.{fasta,fa}", - "ontologies": [] - } - } - ] - ], - "output": { - "assembly": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.fa.gz": { - "type": "file", - "description": "Polished genome assembly", - "pattern": "*.fa.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "versions_medaka": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "medaka": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "medaka --version 2>&1 | sed \"s/medaka //g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "medaka": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "medaka --version 2>&1 | sed \"s/medaka //g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "hlatyping", + "version": "2.2.0" + } ] - ] - }, - "authors": [ - "@avantonder" - ], - "maintainers": [ - "@avantonder" - ] - }, - "pipelines": [ - { - "name": "crisprseq", - "version": "2.3.0" - } - ] - }, - { - "name": "megahit", - "path": "modules/nf-core/megahit/meta.yml", - "type": "module", - "meta": { - "name": "megahit", - "description": "An ultra-fast metagenomic assembler for large and complex metagenomics", - "keywords": [ - "megahit", - "denovo", - "assembly", - "debruijn", - "metagenomics" - ], - "tools": [ - { - "megahit": { - "description": "An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph", - "homepage": "https://github.com/voutcn/megahit", - "documentation": "https://github.com/voutcn/megahit", - "tool_dev_url": "https://github.com/voutcn/megahit", - "doi": "10.1093/bioinformatics/btv033", - "licence": [ - "GPL v3" - ], - "args_id": "$args", - "identifier": "biotools:megahit" - } - }, - { - "pigz": { - "description": "Parallel implementation of the gzip algorithm.", - "homepage": "https://zlib.net/pigz/", - "documentation": "https://zlib.net/pigz/pigz.pdf", - "args_id": "$args2", - "identifier": "biotools:megahit" + }, + { + "name": "orfipy", + "path": "modules/nf-core/orfipy/meta.yml", + "type": "module", + "meta": { + "name": "orfipy", + "description": "orfipy is a tool written in python/cython to extract ORFs in an extremely and fast and flexible manner.", + "keywords": ["orfipy", "orfs", "open reading frames"], + "tools": [ + { + "orfipy": { + "description": "orfipy: fast and flexible search for open reading frames in fasta sequences", + "homepage": "https://github.com/urmi-21/orfipy", + "documentation": "https://github.com/urmi-21/orfipy/blob/master/README.md", + "tool_dev_url": "https://github.com/urmi-21/orfipy", + "licence": ["MIT"], + "identifier": "biotools:orfipy" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', fasta ]\n" + } + }, + { + "infile": { + "type": "file", + "description": "Input file, in plain Fasta/Fastq or gzipped format, containing Nucletide sequences", + "pattern": "*.{fasta,fa,fastq,fastq.gz,fq,fa.gz,fq.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ] + ], + "output": { + "bed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', fasta ]\n" + } + }, + { + "${prefix}/${prefix}.bed": { + "type": "file", + "description": "Output BED file containing the coordinates of predicted ORFs", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3673" + } + ] + } + } + ] + ], + "versions_orfipy": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "orfipy": { + "type": "string", + "description": "The tool name" + } + }, + { + "orfipy --version | sed 's/.*version //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "orfipy": { + "type": "string", + "description": "The tool name" + } + }, + { + "orfipy --version | sed 's/.*version //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@khersameesh24"], + "maintainers": ["@khersameesh24"] } - 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} - }, - { - "*.spectra-cn.hist": { - "type": "file", - "description": "Copy number spectra histogram", - "pattern": "*.spectra-cn.hist", - "ontologies": [] - } - } - ] - ], - "spectra_cn_ln_png": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.spectra-cn.ln.png": { - "type": "file", - "description": "Unstacked copy number spectra line plot in PNG format", - "pattern": "*.spectra-cn.ln.png", - "ontologies": [] - } - } - ] - ], - "spectra_cn_st_png": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.spectra-cn.st.png": { - "type": "file", - "description": "Stacked copy number spectra line plot in PNG format", - "pattern": "*.spectra-cn.st.png", - "optional": true, - "ontologies": [] - } - } - ] - ], - "spectra_asm_fl_png": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - 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Output from parabricks/fq2bam or gatk4/baserecalibrator.", + "pattern": "*.table", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing sample information.\ne.g. [ id:'test' ]\n" + } + }, + { + "intervals": { + "type": "file", + "description": "intervals", + "ontologies": [] + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference fasta - must be unzipped.", + "pattern": "*.fasta", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ] + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information.\ne.g. [ id:'test' ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "BAM file after applying BQSR.", + "pattern": "*.bam", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + } + ] + ], + "bai": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information.\ne.g. [ id:'test' ]\n" + } + }, + { + "*.bai": { + "type": "file", + "description": "bai index corresponding to output bam file.", + "pattern": "*.bam.bai", + "ontologies": [] + } + } + ] + ], + "versions_parabricks": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "parabricks": { + "type": "string", + "description": "The tool name" + } + }, + { + "pbrun version | grep -m1 '^pbrun:' | sed 's/^pbrun:[[:space:]]*//'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "parabricks": { + "type": "string", + "description": "The tool name" + } + }, + { + "pbrun version | grep -m1 '^pbrun:' | sed 's/^pbrun:[[:space:]]*//'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@bsiranosian"], + "maintainers": ["@bsiranosian", "@famosab"] + } }, { - "name": "genomeqc", - "version": "dev" - } - ] - }, - { - "name": "meryl_histogram", - "path": "modules/nf-core/meryl/histogram/meta.yml", - "type": "module", - "meta": { - "name": "meryl_histogram", - "description": "A genomic k-mer counter (and sequence utility) with nice features.", - "keywords": [ - "k-mer", - "histogram", - "reference-free" - ], - "tools": [ - { - "meryl": { - "description": "A genomic k-mer counter (and sequence utility) with nice features. ", - "homepage": "https://github.com/marbl/meryl", - "documentation": "https://meryl.readthedocs.io/en/latest/quick-start.html", - "tool_dev_url": "https://github.com/marbl/meryl", - "licence": [ - "GPL" - ], - "identifier": "biotools:meryl" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "meryl_db": { - "type": "directory", - "description": "Meryl k-mer database" - } - } - ], - { - "kvalue": { - "type": "integer", - "description": "An integer value of k to use as the k-mer value." - } - } - ], - "output": { - "hist": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.hist": { - "type": "file", - "description": "Histogram of k-mers", - "pattern": "*.hist", - "ontologies": [] - } - } - ] - ], - "versions_meryl": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "meryl": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "meryl --version |& sed 's/meryl //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "meryl": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "meryl --version |& sed 's/meryl //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@mahesh-panchal" - ], - "maintainers": [ - "@mahesh-panchal", - "@gallvp" - ] - } - }, - { - "name": "meryl_unionsum", - "path": "modules/nf-core/meryl/unionsum/meta.yml", - "type": "module", - "meta": { - "name": "meryl_unionsum", - "description": "A genomic k-mer counter (and sequence utility) with nice features.", - "keywords": [ - "k-mer", - "unionsum", - "reference-free" - ], - "tools": [ - { - "meryl": { - "description": "A genomic k-mer counter (and sequence utility) with nice features. ", - "homepage": "https://github.com/marbl/meryl", - "documentation": "https://meryl.readthedocs.io/en/latest/quick-start.html", - "tool_dev_url": "https://github.com/marbl/meryl", - "licence": [ - "GPL" - ], - "identifier": "biotools:meryl" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "meryl_dbs": { - "type": "directory", - "description": "Meryl k-mer databases" - } - } - ], - { - "kvalue": { - "type": "integer", - "description": "An integer value of k to use as the k-mer value." + "name": "parabricks_dbsnp", + "path": "modules/nf-core/parabricks/dbsnp/meta.yml", + "type": "module", + "meta": { + "name": "parabricks_dbsnp", + "description": "NVIDIA Clara Parabricks GPU-accelerated variant calls annotation based on dbSNP database", + "keywords": ["annotation", "dbsnp", "vcf", "germline"], + "tools": [ + { + "parabricks": { + "description": "NVIDIA Clara Parabricks GPU-accelerated genomics tools", + "homepage": "https://www.nvidia.com/en-us/clara/genomics/", + "documentation": "https://docs.nvidia.com/clara/parabricks/latest/index.html", + "licence": ["custom"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "vcf_file": { + "type": "file", + "description": "VCF file undergoing annotation.", + "pattern": "*.vcf", + "ontologies": [] + } + }, + { + "dbsnp_file": { + "type": "file", + "description": "dbSNP file required for annotation.", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + }, + { + "tabix_file": { + "type": "file", + "description": "dbSNP file index.", + "pattern": "*.vcf.gz.tbi", + "ontologies": [] + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.vcf": { + "type": "file", + "description": "VCF file.", + "pattern": "*{.vcf}", + "ontologies": [] + } + } + ] + ], + "compatible_versions": [ + { + "compatible_versions.yml": { + "type": "file", + "description": "File containing info on compatible CPU-based software versions.", + "pattern": "compatible_versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ], + "versions_parabricks": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "parabricks": { + "type": "string", + "description": "The tool name" + } + }, + { + "pbrun version | grep -m1 '^pbrun:' | sed 's/^pbrun:[[:space:]]*//'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "parabricks": { + "type": "string", + "description": "The tool name" + } + }, + { + "pbrun version | grep -m1 '^pbrun:' | sed 's/^pbrun:[[:space:]]*//'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@Furentsu"], + "maintainers": ["@famosab"] } - } - ], - "output": { - "meryl_db": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.unionsum.meryl": { - "type": "directory", - "description": "A Meryl k-mer database that is the union sum of the input databases", - "pattern": "*.unionsum.meryl" - } - } - ] - ], - "versions_meryl": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "meryl": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "meryl --version |& sed 's/meryl //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "meryl": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "meryl --version |& sed 's/meryl //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] }, - "authors": [ - "@mahesh-panchal" - ], - "maintainers": [ - "@mahesh-panchal", - "@gallvp" - ] - }, - "pipelines": [ { - "name": "genomeassembler", - "version": "1.1.0" + "name": "parabricks_deepvariant", + "path": "modules/nf-core/parabricks/deepvariant/meta.yml", + "type": "module", + "meta": { + "name": "parabricks_deepvariant", + "description": "NVIDIA Clara Parabricks GPU-accelerated germline variant calling, replicating deepvariant.", + "keywords": ["variant", "deep variant", "vcf", "haplotypecaller", "germline"], + "tools": [ + { + "parabricks": { + "description": "NVIDIA Clara Parabricks GPU-accelerated genomics tools", + "homepage": "https://www.nvidia.com/en-us/clara/genomics/", + "documentation": "https://docs.nvidia.com/clara/parabricks/latest/index.html", + "licence": ["custom"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing tumor sample information - id must match read groups for this sample.\n[ id:'test']\n" + } + }, + { + "input": { + "type": "file", + "description": "bam file for sample to be variant called.", + "pattern": "*.bam", + "ontologies": [] + } + }, + { + "input_index": { + "type": "file", + "description": "bai index corresponding to input bam file. Only necessary if intervals are provided.", + "pattern": "*.bai", + "ontologies": [] + } + }, + { + "intervals": { + "type": "file", + "description": "file or files containing genomic intervals for use in base quality score recalibration.", + "pattern": "*.{bed,interval_list,picard,list,intervals}", + "ontologies": [] + } + } + ], + [ + { + "ref_meta": { + "type": "map", + "description": "Groovy Map containing reference information.\n[ id:'test']\n" + } + }, + { + "fasta": { + "type": "file", + "description": "reference fasta - must be unzipped.", + "pattern": "*.fasta", + "ontologies": [] + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information.\ne.g. [ id:'test' ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "vcf file created with deepvariant (does not support .gz for normal vcf), optional", + "pattern": "*.vcf", + "ontologies": [] + } + } + ] + ], + "gvcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information.\ne.g. [ id:'test' ]\n" + } + }, + { + "*.g.vcf.gz": { + "type": "file", + "description": "bgzipped gvcf created with deepvariant, optional", + "pattern": "*.g.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "compatible_versions": [ + { + "compatible_versions.yml": { + "type": "file", + "description": "File containing info on compatible CPU-based software versions.", + "pattern": "compatible_versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ], + "versions_parabricks": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "parabricks": { + "type": "string", + "description": "The tool name" + } + }, + { + "pbrun version | grep -m1 '^pbrun:' | sed 's/^pbrun:[[:space:]]*//'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "parabricks": { + "type": "string", + "description": "The tool name" + } + }, + { + "pbrun version | grep -m1 '^pbrun:' | sed 's/^pbrun:[[:space:]]*//'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@bsiranosian"], + "maintainers": ["@famosab"] + } }, { - "name": "genomeqc", - "version": "dev" - } - ] - }, - { - "name": "metabat2_jgisummarizebamcontigdepths", - "path": "modules/nf-core/metabat2/jgisummarizebamcontigdepths/meta.yml", - "type": "module", - "meta": { - "name": "metabat2_jgisummarizebamcontigdepths", - "description": "Depth computation per contig step of metabat2", - "keywords": [ - "sort", - "binning", - "depth", - "bam", - "coverage", - "de novo assembly" - ], - "tools": [ - { - "metabat2": { - "description": "Metagenome binning", - "homepage": "https://bitbucket.org/berkeleylab/metabat/src/master/", - "documentation": "https://bitbucket.org/berkeleylab/metabat/src/master/", - "tool_dev_url": "https://bitbucket.org/berkeleylab/metabat/src/master/", - "doi": "10.7717/peerj.7359", - "licence": [ - "BSD-3-clause-LBNL" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM file of reads aligned on the assembled contigs", - "pattern": "*.bam", - "ontologies": [] - } - }, - { - "bai": { - "type": "file", - "description": "BAM index file", - "pattern": "*.bam.bai", - "ontologies": [] - } - } - ] - ], - "output": { - "depth": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.txt.gz": { - "type": "file", - "description": "Text file listing the coverage per contig", - "pattern": ".txt.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@maxibor" - ], - "maintainers": [ - "@maxibor" - ] - }, - "pipelines": [ - { - "name": "mag", - "version": "5.4.2" - } - ] - }, - { - "name": "metabat2_metabat2", - "path": "modules/nf-core/metabat2/metabat2/meta.yml", - "type": "module", - "meta": { - "name": "metabat2_metabat2", - "description": "Metagenome binning of contigs", - "keywords": [ - "sort", - "binning", - "depth", - "bam", - "coverage", - "de novo assembly" - ], - "tools": [ - { - "metabat2": { - "description": "Metagenome binning", - "homepage": "https://bitbucket.org/berkeleylab/metabat/src/master/", - "documentation": "https://bitbucket.org/berkeleylab/metabat/src/master/", - "tool_dev_url": "https://bitbucket.org/berkeleylab/metabat/src/master/", - "doi": "10.7717/peerj.7359", - "licence": [ - "BSD-3-clause-LBNL" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Fasta file of the assembled contigs", - "pattern": "*.{fa,fas,fasta,fna,fa.gz,fas.gz,fasta.gz,fna.gz}", - "ontologies": [] - } - }, - { - "depth": { - "type": "file", - "description": "Optional text file listing the coverage per contig pre-generated\nby metabat2_jgisummarizebamcontigdepths\n", - "pattern": "*.txt", - "ontologies": [] - } - } - ] - ], - "output": { - "tooshort": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tooShort.fa.gz": { - "type": "file", - "description": "Contigs that did not pass length filtering", - "pattern": "*.tooShort.fa.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "lowdepth": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.lowDepth.fa.gz": { - "type": "file", - "description": "Contigs that did not have sufficient depth for binning", - "pattern": "*.lowDepth.fa.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "unbinned": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.unbinned.fa.gz": { - "type": "file", - "description": "Contigs that pass length and depth filtering but could not be binned", - "pattern": "*.unbinned.fa.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "membership": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tsv.gz": { - "type": "file", - "description": "cluster memberships as a matrix format.", - "pattern": "*.tsv.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "fasta": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*[!lowDepth|tooShort|unbinned].fa.gz": { - "type": "file", - "description": "Bins created from assembled contigs in fasta file", - "pattern": "*.fa.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "versions_metabat2": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "metabat2": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "metabat2 --help 2>&1 | sed -n \"2s/.*:\\([0-9]*\\.[0-9]*\\).*/\\1/p\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "metabat2": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "metabat2 --help 2>&1 | sed -n \"2s/.*:\\([0-9]*\\.[0-9]*\\).*/\\1/p\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@maxibor", - "@jfy133" - ], - "maintainers": [ - "@maxibor", - "@jfy133" - ] - }, - "pipelines": [ - { - "name": "mag", - "version": "5.4.2" - } - ] - }, - { - "name": "metabuli_build", - "path": "modules/nf-core/metabuli/build/meta.yml", - "type": "module", - "meta": { - "name": "metabuli_build", - "description": "Builds a database for classification with metabuli from FASTA files and a taxonomy", - "keywords": [ - "database", - "taxonomic classification", - "classification", - "metagenomics" - ], - "tools": [ - { - "metabuli": { - "description": "Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid", - "homepage": "https://github.com/steineggerlab/Metabuli", - "documentation": "https://github.com/steineggerlab/Metabuli", - "tool_dev_url": "https://github.com/steineggerlab/Metabuli", - "doi": "10.1101/2023.05.31.543018", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:metabuli" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\n" - } + "name": "parabricks_fq2bam", + "path": "modules/nf-core/parabricks/fq2bam/meta.yml", + "type": "module", + "meta": { + "name": "parabricks_fq2bam", + "description": "NVIDIA Clara Parabricks GPU-accelerated alignment, sorting, BQSR calculation, and duplicate marking. Note this nf-core module requires files to be copied into the working directory and not symlinked.", + "keywords": ["align", "sort", "bqsr", "duplicates"], + "tools": [ + { + "parabricks": { + "description": "NVIDIA Clara Parabricks GPU-accelerated genomics tools", + "homepage": "https://www.nvidia.com/en-us/clara/genomics/", + "documentation": "https://docs.nvidia.com/clara/parabricks/latest/index.html", + "licence": ["custom"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "fastq.gz files", + "pattern": "*.fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing fasta information\n" + } + }, + { + "fasta": { + "type": "file", + "description": "reference fasta file - must be unzipped", + "pattern": "*.fasta", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing index information\n" + } + }, + { + "index": { + "type": "file", + "description": "reference BWA index", + "pattern": "*.{amb,ann,bwt,pac,sa}", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing index information\n" + } + }, + { + "intervals": { + "type": "file", + "description": "(optional) file(s) containing genomic intervals for use in base quality score recalibration (BQSR)", + "pattern": "*.{bed,interval_list,picard,list,intervals}", + "ontologies": [] + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing known sites information\n" + } + }, + { + "known_sites": { + "type": "file", + "description": "(optional) known sites file(s) for calculating BQSR. markdups must be true to perform BQSR.", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ], + { + "output_fmt": { + "type": "string", + "description": "Output format for the alignment. Options are 'bam' or 'cram'", + "pattern": "{bam,cram}" + } + } + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Sorted BAM file", + "pattern": "*.bam", + "ontologies": [] + } + } + ] + ], + "bai": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bai": { + "type": "file", + "description": "index corresponding to sorted BAM file", + "pattern": "*.bai", + "ontologies": [] + } + } + ] + ], + "cram": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.cram": { + "type": "file", + "description": "Sorted CRAM file", + "pattern": "*.cram", + "ontologies": [] + } + } + ] + ], + "crai": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.crai": { + "type": "file", + "description": "index corresponding to sorted CRAM file", + "pattern": "*.crai", + "ontologies": [] + } + } + ] + ], + "bqsr_table": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.table": { + "type": "file", + "description": "(optional) table from base quality score recalibration calculation, to be used with parabricks/applybqsr", + "pattern": "*.table", + "ontologies": [] + } + } + ] + ], + "qc_metrics": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_qc_metrics": { + "type": "directory", + "description": "(optional) optional directory of qc metrics", + "pattern": "*_qc_metrics" + } + } + ] + ], + "duplicate_metrics": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.duplicate-metrics.txt": { + "type": "file", + "description": "(optional) metrics calculated from marking duplicates in the bam file", + "pattern": "*.duplicate-metrics.txt", + "ontologies": [] + } + } + ] + ], + "compatible_versions": [ + { + "compatible_versions.yml": { + "type": "file", + "description": "File containing info on compatible CPU-based software versions.", + "pattern": "compatible_versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ], + "versions_parabricks": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "parabricks": { + "type": "string", + "description": "The tool name" + } + }, + { + "pbrun version | grep -m1 '^pbrun:' | sed 's/^pbrun:[[:space:]]*//'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "parabricks": { + "type": "string", + "description": "The tool name" + } + }, + { + "pbrun version | grep -m1 '^pbrun:' | sed 's/^pbrun:[[:space:]]*//'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@bsiranosian", "@adamrtalbot"], + "maintainers": ["@bsiranosian", "@adamrtalbot", "@gallvp", "@famosab"] }, - { - "fasta": { - "type": "file", - "description": "List of fasta files with input assemblies", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - { - "taxonomy_names": { - "type": "file", - "description": "File describing individual members of a taxonomic tree in NCBI nodes.dmp format", - "ontologies": [ - { - "edam": "http://edamontology.org/data_3028" - } - ] - } - }, - { - "taxonomy_nodes": { - "type": "file", - "description": "File describing parent-child relationships of a taxonomic tree in NCBI nodes.dmp format", - "ontologies": [ - { - "edam": "http://edamontology.org/data_3028" - } - ] - } - }, - { - "taxonomy_merged": { - "type": "file", - "description": "Optional input to map old/deprecated TaxID to new ones", - "ontologies": [ - { - "edam": "http://edamontology.org/data_3028" - } - ] - } - }, - { - "accession2taxid": { - "type": "directory", - "description": "TSV file (with no header) of first column with mapping accession (from first part of each fasta entry) and second column the corresponding TaxID", - "ontologies": [ + "pipelines": [ { - "edam": "http://edamontology.org/data_3028" + "name": "sarek", + "version": "3.8.1" } - ] - } - }, - { - "cds_info": { - "type": "file", - "description": "List of files to cds files", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1936" - } - ] - } - } - ], - "output": { - "db": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "$prefix": { - "type": "directory", - "description": "metabuli database directory for classification" - } - } ] - ], - "versions_metabuli": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "metabuli": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "metabuli 2>&1 | awk '/metabuli Version:/ {print $3}'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "metabuli": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "metabuli 2>&1 | awk '/metabuli Version:/ {print $3}'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@pawelciurkaardigen", - "@MichalStachowiakArdigen", - "@sofstam" - ], - "maintainers": [ - "@pawelciurkaardigen", - "@MichalStachowiakArdigen", - "@softam" - ] - } - }, - { - "name": "metacache_build", - "path": "modules/nf-core/metacache/build/meta.yml", - "type": "module", - "meta": { - "name": "metacache_build", - "description": "Taxonomic profiling database building with MetaCache", - "keywords": [ - "genomics", - "metagenomics", - "taxonomy", - "short reads", - "long reads", - "kmer", - "k-mer", - "metacache", - "build", - "reference" - ], - "tools": [ - { - "metacache": { - "description": "MetaCache is a classification system for mapping genomic sequences (short reads, long reads, contigs, ...) from metagenomic samples to their most likely taxon of origin. It aims to reduce the memory requirement usually associated with k-mer based methods while retaining their speed. MetaCache uses locality sensitive hashing to quickly identify candidate regions within one or multiple reference genomes. A read is then classified based on the similarity to those regions.\n\nFor an independent comparison to other tools in terms of classification accuracy see the LEMMI benchmarking site.\n\nThe latest version of MetaCache classifies around 60 Million reads (of length 100) per minute against all complete bacterial, viral and archaea genomes from NCBI RefSeq Release 97 running with 88 threads on a workstation with 2 Intel(R) Xeon(R) Gold 6238 CPUs.\n", - "homepage": "https://muellan.github.io/metacache", - "documentation": "https://github.com/muellan/metacache/tree/master/docs", - "tool_dev_url": "https://github.com/muellan/metacache", - "licence": [ - "GPL v3-or-later" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } + }, + { + "name": "parabricks_fq2bammeth", + "path": "modules/nf-core/parabricks/fq2bammeth/meta.yml", + "type": "module", + "meta": { + "name": "parabricks_fq2bammeth", + "description": "NVIDIA Clara Parabricks GPU-accelerated fast, accurate algorithm for mapping methylated DNA sequence reads to a reference genome, performing local alignment, and producing alignment for different parts of the query sequence", + "keywords": ["align", "sort", "bqsr", "duplicates", "bwameth"], + "tools": [ + { + "parabricks": { + "description": "NVIDIA Clara Parabricks GPU-accelerated genomics tools", + "homepage": "https://www.nvidia.com/en-us/clara/genomics/", + "documentation": "https://docs.nvidia.com/clara/parabricks/latest/index.html", + "licence": ["custom"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "fastq.gz files", + "pattern": "*.fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing fasta information\n" + } + }, + { + "fasta": { + "type": "file", + "description": "reference fasta file - must be unzipped", + "pattern": "*.fasta", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing index information\n" + } + }, + { + "index": { + "type": "file", + "description": "reference BWA index", + "pattern": "*.{amb,ann,bwt,pac,sa}", + "ontologies": [] + } + } + ], + { + "known_sites": { + "type": "file", + "description": "(optional) known sites file(s) for calculating BQSR. markdups must be true to perform BQSR.", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Sorted BAM file", + "pattern": "*.bam", + "ontologies": [] + } + } + ] + ], + "bai": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bai": { + "type": "file", + "description": "index corresponding to sorted BAM file", + "pattern": "*.bai", + "ontologies": [] + } + } + ] + ], + "qc_metrics": [ + { + "qc_metrics": { + "type": "directory", + "description": "(optional) optional directory of qc metrics", + "pattern": "qc_metrics" + } + } + ], + "bqsr_table": [ + { + "*.table": { + "type": "file", + "description": "(optional) table from base quality score recalibration calculation, to be used with parabricks/applybqsr", + "pattern": "*.table", + "ontologies": [] + } + } + ], + "duplicate_metrics": [ + { + "duplicate-metrics.txt": { + "type": "file", + "description": "(optional) metrics calculated from marking duplicates in the bam file", + "pattern": "*-duplicate-metrics.txt", + "ontologies": [] + } + } + ], + "versions_parabricks": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "parabricks": { + "type": "string", + "description": "The tool name" + } + }, + { + "pbrun version | grep -m1 '^pbrun:' | sed 's/^pbrun:[[:space:]]*//'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "parabricks": { + "type": "string", + "description": "The tool name" + } + }, + { + "pbrun version | grep -m1 '^pbrun:' | sed 's/^pbrun:[[:space:]]*//'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@sateeshperi"], + "maintainers": ["@sateeshperi", "@gallvp"] }, - { - "genome_files": { - "type": "file", - "description": "(possibly gzipped) fasta or fastq files of full genomes, for example from an NCBI assembly", - "pattern": "*.{fna,fa,fasta,fnq,fq,fastq}{,.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - }, - { - "edam": "http://edamontology.org/format_1930" - }, - { - "edam": "http://edamontology.org/format_1954" - }, - { - "edam": "http://edamontology.org/data_2044" - } - ] - } - } - ], - { - "taxonomy": { - "type": "file", - "description": "NCBI taxonomy formatted files nodes.dmp and names.dmp", - "pattern": "{names,nodes,merged}.dmp", - "ontologies": [ + "pipelines": [ { - "edam": "http://edamontology.org/data_3028" + "name": "methylseq", + "version": "4.2.0" } - ] - } - }, - { - "seq2taxid": { - "type": "file", - "description": "NCBI-style 'accession2taxid' tab-separated file with 3 or 4 columns: accession, accession_version, taxid, and gid (optional)\n", - "pattern": "*", - "ontologies": [] - } - } - ], - "output": { - "db": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.meta": { - "type": "file", - "description": "sequence signature database binary file", - "pattern": "*.meta", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2333" - } - ] - } - }, - { - "*.cache*": { - "type": "file", - "description": "sequence signature database binary files", - "pattern": "*.cache+([0-9])", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2333" - } - ] - } - } - ] - ], - "versions_metacache": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "metacache": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "metacache info |& sed -n 's/^MetaCache version \\+\\([0-9.]\\+\\).*\\$/\\1/p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "metacache": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "metacache info |& sed -n 's/^MetaCache version \\+\\([0-9.]\\+\\).*\\$/\\1/p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@Gullumluvl" - ], - "maintainers": [ - "@Gullumluvl" - ] - }, - "pipelines": [ - { - "name": "createtaxdb", - "version": "3.0.0" - } - ] - }, - { - "name": "metacache_query", - "path": "modules/nf-core/metacache/query/meta.yml", - "type": "module", - "meta": { - "name": "metacache_query", - "description": "Metacache query command for taxonomic classification", - "keywords": [ - "metagenomics", - "classification", - "metacache" - ], - "tools": [ - { - "metacache": { - "description": "MetaCache is a classification system for mapping genomic sequences (short reads, long reads, contigs, ...) from metagenomic samples to their most likely taxon of origin.", - "homepage": "https://github.com/muellan/metacache", - "documentation": "https://muellan.github.io/metacache/", - "tool_dev_url": "https://github.com/muellan/metacache", - "doi": "10.1093/bioinformatics/btx520", - "licence": [ - "GPL-3.0 license" - ], - "identifier": "" + }, + { + "name": "parabricks_genotypegvcf", + "path": "modules/nf-core/parabricks/genotypegvcf/meta.yml", + "type": "module", + "meta": { + "name": "parabricks_genotypegvcf", + "description": "NVIDIA Clara Parabricks GPU-accelerated joint genotyping, replicating GATK GenotypeGVCFs", + "keywords": ["joint-genotyping", "gvcf", "vcf", "genotypegvcf", "germline"], + "tools": [ + { + "parabricks": { + "description": "NVIDIA Clara Parabricks GPU-accelerated genomics tools", + "homepage": "https://www.nvidia.com/en-us/clara/genomics/", + "documentation": "https://docs.nvidia.com/clara/parabricks/latest/index.html", + "licence": ["custom"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "input": { + "type": "file", + "description": "gvcf file for samples to be jointly genotyped.", + "pattern": "*.{g.vcf,g.vcf.gz}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information.\n[ id:'test']\n" + } + }, + { + "fasta": { + "type": "file", + "description": "reference fasta - must be unzipped.", + "pattern": "*.fasta", + "ontologies": [] + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "*.vcf": { + "type": "file", + "description": "vcf file after gvcf conversion.", + "pattern": "*.vcf", + "ontologies": [] + } + } + ] + ], + "versions_parabricks": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "parabricks": { + "type": "string", + "description": "The tool name" + } + }, + { + "pbrun version | grep -m1 '^pbrun:' | sed 's/^pbrun:[[:space:]]*//'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "parabricks": { + "type": "string", + "description": "The tool name" + } + }, + { + "pbrun version | grep -m1 '^pbrun:' | sed 's/^pbrun:[[:space:]]*//'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@Furentsu", "@bsiranosian"], + "maintainers": ["@famosab"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "reads": { - "type": "file", - "description": "FASTA or FASTQ files", - "pattern": "*.{fasta,fa,fastq,fq}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } + }, + { + "name": "parabricks_haplotypecaller", + "path": "modules/nf-core/parabricks/haplotypecaller/meta.yml", + "type": "module", + "meta": { + "name": "parabricks_haplotypecaller", + "description": "NVIDIA Clara Parabricks GPU-accelerated germline variant calling, replicating GATK haplotypecaller.", + "keywords": ["variant", "vcf", "haplotypecaller", "germline"], + "tools": [ + { + "parabricks": { + "description": "NVIDIA Clara Parabricks GPU-accelerated genomics tools", + "homepage": "https://www.nvidia.com/en-us/clara/genomics/", + "documentation": "https://docs.nvidia.com/clara/parabricks/latest/index.html", + "licence": ["custom"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information.\n[ id:'test']\n" + } + }, + { + "input": { + "type": "file", + "description": "bam file for sample to be variant called.", + "pattern": "*.bam", + "ontologies": [] + } + }, + { + "input_index": { + "type": "file", + "description": "(Optional) bai index corresponding to input bam file. Only necessary when using intervals.", + "pattern": "*.bai", + "ontologies": [] + } + }, + { + "intervals": { + "type": "file", + "description": "file or files containing genomic intervals.", + "pattern": "*.{bed,interval_list,picard,list,intervals}", + "ontologies": [] + } + } + ], + [ + { + "ref_meta": { + "type": "map", + "description": "Groovy Map containing reference information.\n[ id:'test']\n" + } + }, + { + "fasta": { + "type": "file", + "description": "reference fasta - must be unzipped.", + "pattern": "*.fasta", + "ontologies": [] + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information.\ne.g. [ id:'test' ]\n" + } + }, + { + "*.vcf": { + "type": "file", + "description": "variant file.", + "pattern": "*.vcf", + "ontologies": [] + } + } + ] + ], + "gvcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information.\ne.g. [ id:'test' ]\n" + } + }, + { + "*.g.vcf.gz": { + "type": "file", + "description": "genomic variant file, gzipped.", + "pattern": "*.g.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "compatible_versions": [ + { + "compatible_versions.yml": { + "type": "file", + "description": "File containing info on compatible CPU-based software versions.", + "pattern": "compatible_versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ], + "versions_parabricks": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "parabricks": { + "type": "string", + "description": "The tool name" + } + }, + { + "pbrun version | grep -m1 '^pbrun:' | sed 's/^pbrun:[[:space:]]*//'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "parabricks": { + "type": "string", + "description": "The tool name" + } + }, + { + "pbrun version | grep -m1 '^pbrun:' | sed 's/^pbrun:[[:space:]]*//'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@bsiranosian"] } - ], - { - "db": { - "type": "directory", - "description": "A MetaCache database contains taxonomic information and min-hash signatures of reference sequences (complete genomes, scaffolds, contigs, ...)." + }, + { + "name": "parabricks_indexgvcf", + "path": "modules/nf-core/parabricks/indexgvcf/meta.yml", + "type": "module", + "meta": { + "name": "parabricks_indexgvcf", + "description": "NVIDIA Clara Parabricks GPU-accelerated gvcf indexing tool.", + "keywords": ["vcf", "gvcf", "tbi", "idx", "index", "GPU-accelerated"], + "tools": [ + { + "parabricks": { + "description": "NVIDIA Clara Parabricks GPU-accelerated genomics tools", + "homepage": "https://www.nvidia.com/en-us/clara/genomics/", + "documentation": "https://docs.nvidia.com/clara/parabricks/latest/index.html", + "licence": ["custom"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing gvcf information\n" + } + }, + { + "gvcf": { + "type": "file", + "description": "gvcf file to be indexed", + "pattern": "*.{vcf,vcf.gz}", + "ontologies": [] + } + } + ] + ], + "output": { + "gvcf_index": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing output information\n" + } + }, + { + "*.{idx,tbi}": { + "type": "file", + "description": "Index of the gvcf file", + "pattern": "*.{idx,tbi}", + "ontologies": [] + } + } + ] + ], + "compatible_versions": [ + { + "compatible_versions.yml": { + "type": "file", + "description": "File containing info on compatible CPU-based software versions.", + "pattern": "compatible_versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ], + "versions_parabricks": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "parabricks": { + "type": "string", + "description": "The tool name" + } + }, + { + "pbrun version | grep -m1 '^pbrun:' | sed 's/^pbrun:[[:space:]]*//'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "parabricks": { + "type": "string", + "description": "The tool name" + } + }, + { + "pbrun version | grep -m1 '^pbrun:' | sed 's/^pbrun:[[:space:]]*//'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@Furentsu", "@bsiranosian"], + "maintainers": ["@famosab"] } - }, - { - "do_abundances": { - "type": "boolean", - "description": "Flag indicating whether to produce the abundance table." + }, + { + "name": "parabricks_minimap2", + "path": "modules/nf-core/parabricks/minimap2/meta.yml", + "type": "module", + "meta": { + "name": "parabricks_minimap2", + "description": "NVIDIA Clara Parabricks GPU-accelerated minimap2 for aligning long read sequences against a large reference database using an accelerated KSW2 to convert FASTQ to BAM/CRAM.", + "keywords": ["align", "sort", "bqsr", "duplicates", "long read"], + "tools": [ + { + "parabricks": { + "description": "NVIDIA Clara Parabricks GPU-accelerated genomics tools", + "homepage": "https://www.nvidia.com/en-us/clara/genomics/", + "documentation": "https://docs.nvidia.com/clara/parabricks/latest/index.html", + "licence": ["custom"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "Input read file, supported formats - 'fastq', 'fastq.gz', 'fq', 'fq.gz', 'bam'", + "pattern": "^.*\\.(fastq|fastq\\.gz|fq|fq\\.gz|bam)$", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing fasta information\n" + } + }, + { + "fasta": { + "type": "file", + "description": "reference fasta file - must be unzipped", + "pattern": "*.fasta", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing index information\n" + } + }, + { + "intervals": { + "type": "file", + "description": "(optional) file(s) containing genomic intervals for use in base quality score recalibration (BQSR)", + "pattern": "*.{bed,interval_list,picard,list,intervals}", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing known sites information\n" + } + }, + { + "known_sites": { + "type": "file", + "description": "(optional) known sites file(s) for calculating BQSR. markdups must be true to perform BQSR.", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ], + { + "output_fmt": { + "type": "string", + "description": "Output format for the alignment. Options are 'bam' or 'cram'", + "pattern": "{bam,cram}" + } + } + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Sorted BAM file", + "pattern": "*.bam", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + } + ] + ], + "bai": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bai": { + "type": "file", + "description": "index corresponding to sorted BAM file", + "pattern": "*.bai", + "ontologies": [] + } + } + ] + ], + "cram": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.cram": { + "type": "file", + "description": "Sorted CRAM file", + "pattern": "*.cram", + "ontologies": [] + } + } + ] + ], + "crai": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.crai": { + "type": "file", + "description": "index corresponding to sorted CRAM file", + "pattern": "*.crai", + "ontologies": [] + } + } + ] + ], + "bqsr_table": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.table": { + "type": "file", + "description": "(optional) table from base quality score recalibration calculation, to be used with parabricks/applybqsr", + "pattern": "*.table", + "ontologies": [] + } + } + ] + ], + "qc_metrics": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_qc_metrics": { + "type": "directory", + "description": "(optional) optional directory of qc metrics", + "pattern": "*_qc_metrics" + } + } + ] + ], + "duplicate_metrics": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.duplicate-metrics.txt": { + "type": "file", + "description": "(optional) metrics calculated from marking duplicates in the bam file", + "pattern": "*.duplicate-metrics.txt", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + } + ] + ], + "compatible_versions": [ + { + "compatible_versions.yml": { + "type": "file", + "description": "File containing info on compatible CPU-based software versions.", + "pattern": "compatible_versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ], + "versions_parabricks": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "parabricks": { + "type": "string", + "description": "The tool name" + } + }, + { + "pbrun version | grep -m1 '^pbrun:' | sed 's/^pbrun:[[:space:]]*//'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "parabricks": { + "type": "string", + "description": "The tool name" + } + }, + { + "pbrun version | grep -m1 '^pbrun:' | sed 's/^pbrun:[[:space:]]*//'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@haidyi"], + "maintainers": ["@haidyi"] } - } - ], - "output": { - "mapping_results": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*mapping.txt": { - "type": "file", - "description": "Output file containing mapping results", - "pattern": "*mapping.txt", - "ontologies": [] - } - } - ] - ], - "abundances": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*abundances.txt": { - "type": "file", - "description": "Output file showing absolute and relative abundance of each taxon", - "pattern": "*abundances.txt", - "ontologies": [] - } - } - ] - ], - "versions_metacache": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "metacache": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "metacache info |& sed -n 's/^MetaCache version \\+\\([0-9.]\\+\\).*\\$/\\1/p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "metacache": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "metacache info |& sed -n 's/^MetaCache version \\+\\([0-9.]\\+\\).*\\$/\\1/p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@sofstam", - "@Gullumluvl" - ], - "maintainers": [ - "@sofstam", - "@Gullumluvl" - ] - }, - "pipelines": [ - { - "name": "taxprofiler", - "version": "2.0.0" - } - ] - }, - { - "name": "metaeuk_easypredict", - "path": "modules/nf-core/metaeuk/easypredict/meta.yml", - "type": "module", - "meta": { - "name": "metaeuk_easypredict", - "description": "Annotation of eukaryotic metagenomes using MetaEuk", - "keywords": [ - "genomics", - "annotation", - "fasta" - ], - "tools": [ - { - "metaeuk": { - "description": "MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics", - "homepage": "https://github.com/soedinglab/metaeuk", - "documentation": "https://github.com/soedinglab/metaeuk", - "tool_dev_url": "https://github.com/soedinglab/metaeuk", - "doi": "10.1186/s40168-020-00808-x", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:MetaEuk" + }, + { + "name": "parabricks_mutectcaller", + "path": "modules/nf-core/parabricks/mutectcaller/meta.yml", + "type": "module", + "meta": { + "name": "parabricks_mutectcaller", + "description": "NVIDIA Clara Parabricks GPU-accelerated somatic variant calling, replicating GATK Mutect2.", + "keywords": ["variant", "vcf", "mutect2", "mutect", "somatic"], + "tools": [ + { + "parabricks": { + "description": "NVIDIA Clara Parabricks GPU-accelerated genomics tools", + "homepage": "https://www.nvidia.com/en-us/clara/genomics/", + "documentation": "https://docs.nvidia.com/clara/parabricks/latest/index.html", + "licence": ["custom"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information - tumor_id and normal_id must match read groups for the respective samples.\n[ id:'test', tumor_id:'tumor', normal_id:'normal' ]\n" + } + }, + { + "tumor_bam": { + "type": "file", + "description": "bam file for tumor sample.", + "pattern": "*.bam", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + }, + { + "tumor_bam_index": { + "type": "file", + "description": "(Optional) bai index corresponding to tumor bam file. Only required if intervals are provided.", + "pattern": "*.bam.bai", + "ontologies": [] + } + }, + { + "normal_bam": { + "type": "file", + "description": "(Optional) bam file for normal sample in tumor-vs-normal calling.", + "pattern": "*.bam", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + }, + { + "normal_bam_index": { + "type": "file", + "description": "(Optional) bai index corresponding to normal bam file. Only required if intervals are provided.", + "pattern": "*.bam.bai", + "ontologies": [] + } + }, + { + "intervals": { + "type": "file", + "description": "(Optional) file or files containing genomic intervals for use in base quality score recalibration.", + "pattern": "*.{bed,interval_list,picard,list,intervals}", + "ontologies": [] + } + } + ], + [ + { + "ref_meta": { + "type": "map", + "description": "Groovy Map containing reference information\n[ id:'homo_sapiens' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "reference fasta - must be unzipped.", + "pattern": "*.fasta", + "ontologies": [] + } + } + ], + { + "panel_of_normals": { + "type": "file", + "description": "(Optional) panel of normals file.", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + }, + { + "panel_of_normals_index": { + "type": "file", + "description": "(Optional) tbi index corresponding to panel of normals file.", + "pattern": "*.tbi", + "ontologies": [] + } + } + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "Compressed variants file. Will include an annotated vcf file if panel of normals is used.", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "stats": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.vcf.gz.stats": { + "type": "file", + "description": "Variant statistics.", + "pattern": "*.vcf.gz.stats", + "ontologies": [] + } + } + ] + ], + "compatible_versions": [ + { + "compatible_versions.yml": { + "type": "file", + "description": "File containing info on compatible CPU-based software versions.", + "pattern": "compatible_versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ], + "versions_parabricks": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "parabricks": { + "type": "string", + "description": "The tool name" + } + }, + { + "pbrun version | grep -m1 '^pbrun:' | sed 's/^pbrun:[[:space:]]*//'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "parabricks": { + "type": "string", + "description": "The tool name" + } + }, + { + "pbrun version | grep -m1 '^pbrun:' | sed 's/^pbrun:[[:space:]]*//'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@bsiranosian"], + "maintainers": ["@famosab"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + }, + { + "name": "parabricks_rnafq2bam", + "path": "modules/nf-core/parabricks/rnafq2bam/meta.yml", + "type": "module", + "meta": { + "name": "parabricks_rnafq2bam", + "description": "This tool is the equivalent of fq2bam for RNA-Seq samples, receiving inputs in FASTQ format, performing alignment with the splice-aware STAR algorithm, optionally marking of duplicate reads, and outputting an aligned BAM file ready for variant and fusion calling.", + "keywords": ["align", "star", "rna"], + "tools": [ + { + "parabricks": { + "description": "NVIDIA Clara Parabricks GPU-accelerated genomics tools", + "homepage": "https://www.nvidia.com/en-us/clara/genomics/", + "documentation": "https://docs.nvidia.com/clara/parabricks/latest/index.html", + "licence": ["https://docs.nvidia.com/clara/parabricks/latest/eula.html"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "fastq.gz files", + "pattern": "*.fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + }, + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing fasta information\n" + } + }, + { + "fasta": { + "type": "file", + "description": "reference fasta file - must be unzipped", + "pattern": "*.fasta", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing genome lib dir information\n" + } + }, + { + "index": { + "type": "directory", + "description": "Path to a genome resource library directory. The indexing required to run STAR should be completed by the user beforehand.", + "pattern": "*", + "ontologies": [] + } + } + ], + { + "qc_metrics": { + "type": "boolean", + "description": "Optionally report QC metrics" + } + }, + { + "mark_duplicates": { + "type": "boolean", + "description": "Optionally mark duplicates" + } + } + ], + "output": { + "log_final": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.Log.final.out": { + "type": "file", + "description": "STAR log final out file", + "pattern": "*Log.final.out", + "ontologies": [] + } + } + ] + ], + "log_out": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.Log.out": { + "type": "file", + "description": "STAR log out file", + "pattern": "*Log.out", + "ontologies": [] + } + } + ] + ], + "log_progress": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.Log.progress.out": { + "type": "file", + "description": "STAR log progress out file", + "pattern": "*Log.progress.out", + "ontologies": [] + } + } + ] + ], + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.bam": { + "type": "file", + "description": "Output BAM file containing read alignments", + "pattern": "*.{bam}", + "ontologies": [] + } + } + ] + ], + "bai": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.bam.bai": { + "type": "file", + "description": "Output BAM index file", + "pattern": "*.{bam}.{bai}", + "ontologies": [] + } + } + ] + ], + "bam_sorted": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.sortedByCoord.out.bam": { + "type": "file", + "description": "Output BAM file of read alignments sorted by coordinate (optional)", + "pattern": "*.sortedByCoord.out.bam", + "ontologies": [] + } + } + ] + ], + "bam_sorted_aligned": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.Aligned.sortedByCoord.out.bam": { + "type": "file", + "description": "Output BAM file of read alignments sorted by coordinate (optional)", + "pattern": "*.Aligned.sortedByCoord.out.bam", + "ontologies": [] + } + } + ] + ], + "bam_transcript": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*toTranscriptome.out.bam": { + "type": "file", + "description": "Output BAM file of transcriptome alignment (optional)", + "pattern": "*toTranscriptome.out.bam", + "ontologies": [] + } + } + ] + ], + "bam_unsorted": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*Aligned.unsort.out.bam": { + "type": "file", + "description": "Unsorted BAM file of read alignments (optional)", + "pattern": "*Aligned.unsort.out.bam", + "ontologies": [] + } + } + ] + ], + "fastq": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*fastq.gz": { + "type": "file", + "description": "Unmapped FastQ files (optional)", + "pattern": "*fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "tab": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tab": { + "type": "file", + "description": "STAR output tab file(s) (optional)", + "pattern": "*.tab", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "spl_junc_tab": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.SJ.out.tab": { + "type": "file", + "description": "STAR output splice junction tab file", + "pattern": "*.SJ.out.tab", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "read_per_gene_tab": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.ReadsPerGene.out.tab": { + "type": "file", + "description": "STAR output read per gene tab file", + "pattern": "*.ReadsPerGene.out.tab", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "junction": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.out.junction": { + "type": "file", + "description": "STAR chimeric junction output file (optional)", + "pattern": "*.out.junction", + "ontologies": [] + } + } + ] + ], + "sam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.out.sam": { + "type": "file", + "description": "STAR output SAM file(s) (optional)", + "pattern": "*.out.sam", + "ontologies": [] + } + } + ] + ], + "wig": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.wig": { + "type": "file", + "description": "STAR output wiggle format file(s) (optional)", + "pattern": "*.wig", + "ontologies": [] + } + } + ] + ], + "bedgraph": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bg": { + "type": "file", + "description": "STAR output bedGraph format file(s) (optional)", + "pattern": "*.bg", + "ontologies": [] + } + } + ] + ], + "qc_metrics": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}_qc_metrics": { + "type": "directory", + "description": "Directory containing QC metrics output by STAR (optional)", + "pattern": "*_qc_metrics", + "ontologies": [] + } + } + ] + ], + "duplicate_metrics": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.duplicate-metrics.txt": { + "type": "file", + "description": "File containing duplicate metrics output by STAR (optional)", + "pattern": "*.duplicate-metrics.txt", + "ontologies": [] + } + } + ] + ], + "versions_parabricks": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "parabricks": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pbrun version 2>&1 | grep -Po '(?<=^pbrun: ).*'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "parabricks": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pbrun version 2>&1 | grep -Po '(?<=^pbrun: ).*'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@gburnett-nvidia"], + "maintainers": ["@gburnett-nvidia"] }, - { - "fasta": { - "type": "file", - "description": "Nucleotide FASTA file for annotation", - "pattern": "*.{fasta,fa,fasta.gz,fa.gz}", - "ontologies": [] - } - } - ], - { - "database": { - "type": "file", - "description": "Either a fasta file containing protein sequences, or a directory containing an mmseqs2-formatted protein database", - "ontologies": [] - } - } - ], - "output": { - "faa": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.fas": { - "type": "file", - "description": "Protein FASTA file containing the exons from the input FASTA file", - "pattern": "*.{fas}", - "ontologies": [] - } - } - ] - ], - "codon": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.codon.fas": { - "type": "file", - "description": "Nucleotide FASTA file of protein-coding sequences", - "pattern": "*.{codon.fas}", - "ontologies": [] - } - } - ] - ], - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "TSV file containing locations of each protein coding sequence in the input fasta", - "pattern": "*.headersMap.{tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "gff": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.gff": { - "type": "file", - "description": "Annotation file in GFF format", - "pattern": "*.{gff}", - "ontologies": [] - } - } + "pipelines": [ + { + "name": "rnaseq", + "version": "3.26.0" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } + }, + { + "name": "parabricks_starfusion", + "path": "modules/nf-core/parabricks/starfusion/meta.yml", + "type": "module", + "meta": { + "name": "parabricks_starfusion", + "description": "This tool uses the GPU to perform fusion calling for RNA-Seq samples, utilizing the STAR-Fusion algorithm. This requires input of a genome resource library, in accordance with the original STAR-Fusion tool, and outputs candidate fusion transcripts.", + "keywords": ["fusion", "starfusion", "rna"], + "tools": [ + { + "parabricks": { + "description": "NVIDIA Clara Parabricks GPU-accelerated genomics tools", + "homepage": "https://www.nvidia.com/en-us/clara/genomics/", + "documentation": "https://docs.nvidia.com/clara/parabricks/latest/index.html", + "licence": ["https://docs.nvidia.com/clara/parabricks/latest/eula.html"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "chimeric_junction": { + "type": "file", + "description": "Path to the Chimeric.out.junction file produced by STAR", + "pattern": "*/Chimeric.out.junction", + "ontologies": [] + } + } + ], + [ + { + "meta1": { + "type": "map", + "description": "Groovy Map containing genome lib dir information\n" + } + }, + { + "genome_lib_dir": { + "type": "directory", + "description": "Path to a genome resource library directory. The indexing required to run STAR should be completed by the user beforehand.", + "pattern": "*", + "ontologies": [] + } + } + ] + ], + "output": { + "fusions": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fusion_predictions.tsv": { + "type": "file", + "description": "Fusion events from STAR-fusion", + "pattern": "fusion_predictions.tsv" + } + } + ] + ], + "abridged": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fusion_predictions.abridged.tsv": { + "type": "file", + "description": "Abridged version of fusion events from STAR-fusion", + "pattern": "fusion_predictions.abridged.tsv" + } + } + ] + ], + "versions_parabricks": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "parabricks": { + "type": "string", + "description": "The tool name" + } + }, + { + "pbrun version | grep -m1 '^pbrun:' | sed 's/^pbrun:[[:space:]]*//'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "parabricks": { + "type": "string", + "description": "The tool name" + } + }, + { + "pbrun version | grep -m1 '^pbrun:' | sed 's/^pbrun:[[:space:]]*//'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@gburnett-nvidia"], + "maintainers": ["@gburnett-nvidia"] } - ] - }, - "authors": [ - "@prototaxites" - ], - "maintainers": [ - "@prototaxites" - ] - }, - "pipelines": [ - { - "name": "mag", - "version": "5.4.2" - } - ] - }, - { - "name": "metamaps_classify", - "path": "modules/nf-core/metamaps/classify/meta.yml", - "type": "module", - "meta": { - "name": "metamaps_classify", - "description": "Strain-level metagenomic assignment", - "keywords": [ - "metamaps", - "long reads", - "metagenomics", - "taxonomy" - ], - "tools": [ - { - "metamaps": { - "description": "MetaMaps is a tool for long-read metagenomic analysis", - "homepage": "https://github.com/DiltheyLab/MetaMaps", - "documentation": "https://github.com/DiltheyLab/MetaMaps/blob/master/README.md", - "tool_dev_url": "https://github.com/DiltheyLab/MetaMaps", - "doi": "10.1038/s41467-019-10934-2", - "licence": [ - "Public Domain" - ], - "identifier": "biotools:metamaps" + }, + { + "name": "parabricks_starfusion_build", + "path": "modules/nf-core/parabricks/starfusion_build/meta.yml", + "type": "module", + "meta": { + "name": "parabricks_starfusion_build", + "description": "Download STAR-fusion genome resource required to run STAR-Fusion caller", + "keywords": ["download", "starfusion", "build"], + "tools": [ + { + "star-fusion": { + "description": "Fusion calling algorithm for RNAseq data", + "homepage": "https://github.com/STAR-Fusion/", + "documentation": "https://github.com/STAR-Fusion/STAR-Fusion/wiki/installing-star-fusion", + "tool_dev_url": "https://github.com/STAR-Fusion/STAR-Fusion", + "doi": "10.1186/s13059-019-1842-9", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Metadata map", + "required": true + } + }, + { + "fasta": { + "type": "file", + "description": "Input FASTA file", + "pattern": "*.{fa,fasta}", + "required": true, + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Second metadata map", + "required": true + } + }, + { + "gtf": { + "type": "file", + "description": "Input GTF (Gene Transfer Format) file", + "pattern": "*.gtf", + "required": true, + "ontologies": [ + { + "edam": "http://edamontology.org/format_2306" + } + ] + } + } + ], + { + "fusion_annot_lib": { + "type": "file", + "description": "Fusion annotation library file containing known fusion genes", + "required": true, + "ontologies": [ + { + "edam": "http://edamontology.org/topic_0203" + } + ] + } + }, + { + "dfam_species": { + "type": "string", + "description": "Dfam species name" + } + }, + { + "pfam_url": { + "type": "file", + "description": "Pfam URL" + } + }, + { + "dfam_urls": { + "type": "file", + "description": "Dfam URLs" + } + }, + { + "annot_filter_url": { + "type": "file", + "description": "Annotation filter URL" + } + } + ], + "output": { + "reference": [ + [ + { + "meta": { + "type": "map", + "description": "Metadata map" + } + }, + { + "${prefix}_genome_lib_build_dir": { + "type": "directory", + "description": "Genome library build directory", + "pattern": "*_genome_lib_build_dir" + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@praveenraj2018", "@martings", "@alanmmobbs93", "@delfiterradas", "@sofiromano"], + "maintainers": ["@praveenraj2018"] } - 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"keywords": [ - "metagenomics", - "classification", - "fastq", - "bam", - "fasta" - ], - "tools": [ - { - "metaphlan3": { - "description": "Identify clades (phyla to species) present in the metagenome obtained from a microbiome sample and their relative abundance", - "homepage": "https://huttenhower.sph.harvard.edu/metaphlan/", - "documentation": "https://github.com/biobakery/MetaPhlAn", - "doi": "10.7554/eLife.65088", - "licence": [ - "MIT License" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "Metaphlan 3.0 can classify the metagenome from a variety of input data types, including FASTQ files (single-end and paired-end), FASTA, bowtie2-produced SAM files (produced from alignments to the MetaPHlAn marker database) and intermediate bowtie2 alignment files (bowtie2out)", - "pattern": "*.{fastq.gz, fasta, fasta.gz, sam, bowtie2out.txt}", - "ontologies": [] - } - } - ], - { - "metaphlan_db": { - "type": "file", - "description": "Directory containing pre-downloaded and uncompressed MetaPhlAn3 database downloaded from: http://cmprod1.cibio.unitn.it/biobakery3/metaphlan_databases/.\nNote that you will also need to specify `--index` and the database version name (e.g. 'mpa_v31_CHOCOPhlAn_201901') in your module.conf ext.args for METAPHLAN3_METAPHLAN3!\n", - "pattern": "*/", - "ontologies": [] - } - } - ], - "output": { - "profile": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_profile.txt": { - "type": "file", - "description": "Tab-separated output file of the predicted taxon relative abundances", - "pattern": "*.{txt}", - "ontologies": [] - } - } - ] - ], - "biom": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.biom": { - "type": "file", - "description": "General-use format for representing biological sample by observation contingency tables", - "pattern": "*.{biom}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3746" - } - ] - } - } - ] - ], - "bt2out": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bowtie2out.txt": { - "type": "file", - "description": "Bowtie2 output file", - "pattern": "*.{bowtie2out.txt}", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@MGordon09" - ], - "maintainers": [ - "@MGordon09" - ] - } - }, - { - "name": "metaphlan_makedb", - "path": "modules/nf-core/metaphlan/makedb/meta.yml", - "type": "module", - "meta": { - "name": "metaphlan_makedb", - "description": "Build MetaPhlAn database for taxonomic profiling.", - "keywords": [ - "metaphlan", - "index", - "database", - "metagenomics" - ], - "tools": [ - { - "metaphlan": { - "description": "Identify clades (phyla to species) present in the metagenome obtained from a microbiome sample and their relative abundance", - "homepage": "https://huttenhower.sph.harvard.edu/metaphlan/", - "documentation": "https://github.com/biobakery/MetaPhlAn", - "doi": "10.7554/eLife.65088", - "licence": [ - "MIT License" - ], - "identifier": "biotools:metaphlan" - } - } - ], - "output": { - "db": [ - { - "metaphlan_db_latest": { - "type": "directory", - "description": "Output directory containing the indexed METAPHLAN database", - "pattern": "*/" - } - } - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } + }, + { + "name": "paragraph_idxdepth", + "path": "modules/nf-core/paragraph/idxdepth/meta.yml", + "type": "module", + "meta": { + "name": "paragraph_idxdepth", + "description": "Determines the depth in a BAM/CRAM file", + "keywords": ["bam", "cram", "depth", "paragraph"], + "tools": [ + { + "paragraph": { + "description": "Graph realignment tools for structural variants", + "homepage": "https://github.com/Illumina/paragraph", + "documentation": "https://github.com/Illumina/paragraph", + "tool_dev_url": "https://github.com/Illumina/paragraph", + "doi": "10.1101/635011", + "licence": ["Apache License 2.0"], + "identifier": "biotools:Paragraph" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM file", + "pattern": "*.{bam,cram}", + "ontologies": [] + } + }, + { + "input_index": { + "type": "file", + "description": "Index of the BAM/CRAM file", + "pattern": "*.{bai,crai}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing information for the fasta\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference genome FASTA", + "pattern": "*.{fasta,fna,fa}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing information for the fasta_fai\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta_fai": { + "type": "file", + "description": "Index of the reference genome FASTA", + "pattern": "*.fai", + "ontologies": [] + } + } + ] + ], + "output": { + "depth": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.json": { + "type": "file", + "description": "A JSON file containing depth, depth variance, read length and other parameters", + "pattern": "*.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "binned_depth": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "A TSV file containing the binned normalized depth. Can only be calculated for CRAM files", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@nvnieuwk"], + "maintainers": ["@nvnieuwk"] } - ] - }, - "authors": [ - "@LilyAnderssonLee" - ], - "maintainers": [ - "@LilyAnderssonLee" - ] - } - }, - { - "name": "metaphlan_mergemetaphlantables", - "path": "modules/nf-core/metaphlan/mergemetaphlantables/meta.yml", - "type": "module", - "meta": { - "name": "metaphlan_mergemetaphlantables", - "description": "Merges output abundance tables from MetaPhlAn4", - "keywords": [ - "metagenomics", - "classification", - "merge", - "table", - "profiles" - ], - "tools": [ - { - "metaphlan4": { - "description": "Identify clades (phyla to species) present in the metagenome obtained from a microbiome sample and their relative abundance", - "homepage": "https://huttenhower.sph.harvard.edu/metaphlan/", - "documentation": "https://github.com/biobakery/MetaPhlAn", - "doi": "10.1038/s41587-023-01688-w", - "licence": [ - "MIT License" - ], - "identifier": "biotools:metaphlan" + }, + { + "name": "paragraph_multigrmpy", + "path": "modules/nf-core/paragraph/multigrmpy/meta.yml", + "type": "module", + "meta": { + "name": "paragraph_multigrmpy", + "description": "Genotype structural variants using paragraph and grmpy", + "keywords": ["vcf", "json", "structural variants", "graphs", "genotyping"], + "tools": [ + { + "paragraph": { + "description": "Graph realignment tools for structural variants", + "homepage": "https://github.com/Illumina/paragraph", + "documentation": "https://github.com/Illumina/paragraph", + "tool_dev_url": "https://github.com/Illumina/paragraph", + "doi": "10.1101/635011", + "licence": ["Apache License 2.0"], + "identifier": "biotools:Paragraph" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "variants": { + "type": "file", + "description": "A VCF or JSON file containing called structural variants", + "pattern": "*.{vcf,json}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + }, + { + "variants_index": { + "type": "file", + "description": "The index for the VCF file", + "pattern": "*.tbi", + "ontologies": [] + } + }, + { + "reads": { + "type": "file", + "description": "BAM or CRAM file(s) to genotype against. These should be specified inside the `manifest`", + "pattern": "*.{bam,cram}", + "ontologies": [] + } + }, + { + "reads_index": { + "type": "file", + "description": "The index/indices for the BAM/CRAM file(s)", + "pattern": "*.{bai,crai}", + "ontologies": [] + } + }, + { + "manifest": { + "type": "file", + "description": "A tab separated file containing information on the BAM/CRAM files.\nThis information can be generated using paragraph/idxdepth.\nMore information can be found here: https://github.com/Illumina/paragraph#sample-manifest\n", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information for the FASTA file\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The reference FASTA file used to generate the VCF and BAM/CRAM files", + "pattern": "*.{fa,fasta,fna}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information for the FASTA index file\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta_fai": { + "type": "file", + "description": "The index of the reference FASTA file", + "pattern": "*.fai", + "ontologies": [] + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "The genotyped VCF file in BGZIP format", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "json": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.json.gz": { + "type": "file", + "description": "The genotyped JSON file in GZIP format", + "pattern": "*.json.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@nvnieuwk"], + "maintainers": ["@nvnieuwk"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "profiles": { - "type": "file", - "description": "List of per-sample MetaPhlAn4 taxonomic abundance tables", - "pattern": "*", - "ontologies": [] - } + }, + { + "name": "paragraph_vcf2paragraph", + "path": "modules/nf-core/paragraph/vcf2paragraph/meta.yml", + "type": "module", + "meta": { + "name": "paragraph_vcf2paragraph", + "description": "Convert a VCF file to a JSON graph", + "keywords": ["vcf", "json", "structural_variants"], + "tools": [ + { + "paragraph": { + "description": "Graph realignment tools for structural variants", + "homepage": "https://github.com/Illumina/paragraph", + "documentation": "https://github.com/Illumina/paragraph", + "tool_dev_url": "https://github.com/Illumina/paragraph", + "doi": "10.1101/635011", + "licence": ["Apache License 2.0"], + "identifier": "biotools:Paragraph" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "The VCF/BCF file", + "pattern": "*.{vcf,bcf}(.gz)?", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference genome VCF was generated against", + "pattern": "*.{fasta,fna,fa}", + "ontologies": [] + } + } + ] + ], + "output": { + "graph": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.json.gz": { + "type": "file", + "description": "The created graph in BGZIP format", + "pattern": "*.json.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@nvnieuwk"], + "maintainers": ["@nvnieuwk"] } - ] - ], - "output": { - "txt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.txt": { - "type": "file", - "description": "Combined MetaPhlAn4 table", - "pattern": "*.txt", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } + }, + { + "name": "paraphase", + "path": "modules/nf-core/paraphase/meta.yml", + "type": "module", + "meta": { + "name": "paraphase", + "description": "HiFi-based caller for highly homologous genes", + "keywords": ["paraphase", "long-read", "HiFi"], + "tools": [ + { + "paraphase": { + "description": "HiFi-based caller for highly homologous genes", + "homepage": "https://github.com/PacificBiosciences/paraphase", + "documentation": "https://github.com/PacificBiosciences/paraphase", + "tool_dev_url": "https://github.com/PacificBiosciences/paraphase", + "doi": "10.1016/j.ajhg.2023.01.001", + "licence": ["BSD-3-clause-Clear"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:true ]`\n" + } + }, + { + "bam": { + "type": "file", + "description": "Sorted BAM file", + "pattern": "*.bam", + "ontologies": [] + } + }, + { + "bai": { + "type": "file", + "description": "Index of BAM file", + "pattern": "*.bai", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The reference fasta file", + "pattern": "*.fasta", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing config information\ne.g. [ id:'config' ]\n" + } + }, + { + "config": { + "type": "file", + "description": "Config file", + "pattern": "*.yaml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + ], + "output": { + "json": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:true ]`\n" + } + }, + { + "*.paraphase.json": { + "type": "file", + "description": "Summary of haplotype and variant calls", + "pattern": "*.paraphase.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:true ]`\n" + } + }, + { + "*.paraphase.bam": { + "type": "file", + "description": "(re)aligned BAM file", + "pattern": "*.paraphase.bam", + "ontologies": [] + } + } + ] + ], + "bai": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:true ]`\n" + } + }, + { + "*.paraphase.bam.bai": { + "type": "file", + "description": "Index of (re)aligned BAM file", + "pattern": "*.paraphase.bam.bai", + "ontologies": [] + } + } + ] + ], + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:true ]`\n" + } + }, + { + "${prefix}_paraphase_vcfs/*.vcf.gz": { + "type": "file", + "description": "compressed VCF file(s) per gene", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "vcf_index": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:true ]`\n" + } + }, + { + "${prefix}_paraphase_vcfs/*.vcf.gz.{csi,tbi}": { + "type": "file", + "description": "compressed VCF file index", + "pattern": "*.vcf.gz.{tbi,csi}", + "ontologies": [] + } + } + ] + ], + "versions_minimap2": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "minimap2": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "minimap2 --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_paraphase": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "paraphase": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "paraphase --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_samtools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "samtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "samtools version | sed '1!d;s/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "minimap2": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "minimap2 --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "paraphase": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "paraphase --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "samtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "samtools version | sed '1!d;s/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@fellen31"], + "maintainers": ["@fellen31"] } - ] - }, - "authors": [ - "@jfy133", - "@LilyAnderssonLee" - ], - "maintainers": [ - "@jfy133", - "@LilyAnderssonLee" - ] - }, - "pipelines": [ - { - "name": "taxprofiler", - "version": "2.0.0" - } - ] - }, - { - "name": "metaphlan_metaphlan", - "path": "modules/nf-core/metaphlan/metaphlan/meta.yml", - "type": "module", - "meta": { - "name": "metaphlan_metaphlan", - "description": "MetaPhlAn is a tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.", - "keywords": [ - "metagenomics", - "classification", - "fastq", - "fasta", - "sam" - ], - "tools": [ - { - "metaphlan": { - "description": "Identify clades (phyla to species) present in the metagenome obtained from a microbiome sample and their relative abundance", - "homepage": "https://huttenhower.sph.harvard.edu/metaphlan/", - "documentation": "https://github.com/biobakery/MetaPhlAn", - "doi": "10.1038/s41587-023-01688-w", - "licence": [ - "MIT License" - ], - "identifier": "biotools:metaphlan" + }, + { + "name": "paraphrase", + "path": "modules/nf-core/paraphrase/meta.yml", + "type": "module", + "meta": { + "name": "paraphrase", + "description": "Parse and annotate paraphrase JSONs", + "keywords": ["long-read", "paraphrase", "annotate"], + "tools": [ + { + "paraphrase": { + "description": "Paraphase JSON parser", + "homepage": "https://github.com/Clinical-Genomics/paraphrase", + "documentation": "https://github.com/Clinical-Genomics/paraphrase/README.md", + "tool_dev_url": "https://github.com/Clinical-Genomics/paraphrase", + "licence": ["MIT"] + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information. e.g. `[ id:'sample1']`" + } + }, + { + "jsons": { + "type": "file", + "description": "One or more JSON files from paraphase", + "pattern": "*.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + }, + { + "samples": { + "type": "list", + "description": "Sample names corresponding to the JSON files. Must be in the same order as the JSON files." + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information." + } + }, + { + "yaml": { + "type": "file", + "description": "YAML file containing rules for annotation", + "pattern": "*.yaml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3473" + } + ] + } + } + ], + { + "tsv_output": { + "type": "boolean", + "description": "Whether to output in TSV format instead of JSON. Default is false (JSON output)." + } + } + ], + "output": { + "json": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information. e.g. `[ id:'sample1']`" + } + }, + { + "*.json": { + "type": "file", + "description": "Annotated output in JSON format", + "pattern": "*.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information. e.g. `[ id:'sample1']`" + } + }, + { + "*.tsv": { + "type": "file", + "description": "Annotated output in TSV format", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_paraphrase": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "paraphrase": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "paraphrase --version | sed 's/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "paraphrase": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "paraphrase --version | sed 's/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@fellen31"], + "maintainers": ["@fellen31"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + }, + { + "name": "parsesdrf_convert", + "path": "modules/nf-core/parsesdrf/convert/meta.yml", + "type": "module", + "meta": { + "name": "parsesdrf_convert", + "description": "Convert an SDRF (Sample and Data Relationship Format) file into a\npipeline-specific samplesheet/configuration using the `parse_sdrf\nconvert-` subcommands of the sdrf-pipelines package. The chosen\n`format` selects the subcommand; the module owns the output filenames and\nemits one tuple per supported format (mhcquant, openms, maxquant, msstats,\nnormalyzerde, diann).\n", + "keywords": [ + "sdrf", + "sdrf-pipelines", + "samplesheet", + "proteomics", + "immunopeptidomics", + "mhcquant", + "openms", + "maxquant", + "msstats", + "normalyzerde", + "diann", + "metadata" + ], + "tools": [ + { + "sdrf-pipelines": { + "description": "A set of tools to validate and convert SDRF files for proteomics pipelines.", + "homepage": "https://github.com/bigbio/sdrf-pipelines", + "documentation": "https://github.com/bigbio/sdrf-pipelines", + "tool_dev_url": "https://github.com/bigbio/sdrf-pipelines", + "doi": "10.1021/acs.jproteome.1c00505", + "licence": ["Apache-2.0"], + "identifier": "biotools:sdrf-pipelines" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample/run information\ne.g. `[ id:'PXD009752' ]`\n" + } + }, + { + "sdrf": { + "type": "file", + "description": "SDRF file describing the experimental design and sample metadata.", + "pattern": "*.{tsv,sdrf.tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, + { + "fasta": { + "type": "file", + "description": "Protein database FASTA. Required when `format == 'maxquant'`\n(passed to `-f`); pass `[]` otherwise.\n", + "pattern": "*.{fasta,fa,fasta.gz,fa.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + }, + { + "raw_folder": { + "type": "string", + "description": "Directory prefix embedded as a literal string into the\n`` block of the generated MaxQuant `mqpar.xml`; must\nresolve on the host that later runs MaxQuant. Required when\n`format == 'maxquant'`; pass `''` otherwise.\n" + } + } + ], + { + "format": { + "type": "string", + "description": "Target converter. One of: `mhcquant`, `openms`, `maxquant`,\n`msstats`, `normalyzerde`, `diann`. Selects the\n`parse_sdrf convert-` subcommand.\n" + } + } + ], + "output": { + "mhcquant": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample/run information" + } + }, + { + "${prefix}_samplesheet.tsv": { + "type": "file", + "description": "MHCquant samplesheet TSV (`-os`).", + "pattern": "*_samplesheet.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, + { + "${prefix}_presets.tsv": { + "type": "file", + "description": "MHCquant search-preset TSV (`-op`).", + "pattern": "*_presets.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "openms": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample/run information" + } + }, + { + "${prefix}_samplesheet.tsv": { + "type": "file", + "description": "OpenMS samplesheet TSV (renamed from `openms.tsv`).", + "pattern": "*_samplesheet.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, + { + "${prefix}_experimental_design.tsv": { + "type": "file", + "description": "OpenMS experimental design TSV.", + "pattern": "*_experimental_design.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "maxquant": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample/run information" + } + }, + { + "${prefix}.xml": { + "type": "file", + "description": "MaxQuant `mqpar.xml` (`-o1`).", + "pattern": "*.xml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2332" + } + ] + } + }, + { + "${prefix}_design.txt": { + "type": "file", + "description": "MaxQuant experimental design TXT (`-o2`).", + "pattern": "*_design.txt", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "msstats": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample/run information" + } + }, + { + "${prefix}.csv": { + "type": "file", + "description": "MSstats annotation CSV (`-o`).", + "pattern": "*.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "normalyzerde": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample/run information" + } + }, + { + "${prefix}_design.csv": { + "type": "file", + "description": "NormalyzerDE design CSV (`-o`).", + "pattern": "*_design.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + }, + { + "${prefix}_comparisons.csv": { + "type": "file", + "description": "NormalyzerDE comparisons CSV (`-oc`).", + "pattern": "*_comparisons.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "diann": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample/run information" + } + }, + { + "${prefix}.cfg": { + "type": "file", + "description": "DIA-NN config (renamed from `diann_config.cfg`).", + "pattern": "*.cfg", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + }, + { + "${prefix}_design.tsv": { + "type": "file", + "description": "DIA-NN experimental design TSV (renamed from `diann_design.tsv`).", + "pattern": "*_design.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_sdrfpipelines": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "sdrf-pipelines": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "parse_sdrf --version | cut -d ' ' -f 2": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "sdrf-pipelines": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "parse_sdrf --version | cut -d ' ' -f 2": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@jonasscheid"], + "maintainers": ["@jonasscheid"] }, - { - "input": { - "type": "file", - "description": "Metaphlan can classify the metagenome from a variety of input data types, including FASTQ files (single-end and paired-end), FASTA, bowtie2-produced SAM files (produced from alignments to the MetaPHlAn marker database) and intermediate bowtie2 alignment files (bowtie2out)", - "pattern": "*.{fastq.gz, fasta, fasta.gz, sam, bowtie2out.txt}", - "ontologies": [] - } - } - ], - { - "metaphlan_db_latest": { - "type": "file", - "description": "Directory containing pre-downloaded and uncompressed MetaPhlAn database downloaded from: http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/.\nNote that you will also need to specify `--index` and the database version name (e.g. 'mpa_vJan21_TOY_CHOCOPhlAnSGB_202103') in your module.conf ext.args for METAPHLAN_METAPHLAN!\n", - "pattern": "*/", - "ontologies": [] - } - }, - { - "save_samfile": { - "type": "boolean", - "description": "Whether to save the SAM file produced by MetaPhlAn of read alignments to MetaPhlAn database gene sequences\n" - } - } - ], - "output": { - "profile": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_profile.txt": { - "type": "file", - "description": "Tab-separated output file of the predicted taxon relative abundances", - "pattern": "*.{txt}", - "ontologies": [] - } - } - ] - ], - "biom": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.biom": { - "type": "file", - "description": "General-use format for representing biological sample by observation contingency tables", - "pattern": "*.{biom}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3746" - } - ] - } - } - ] - ], - "bt2out": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bowtie2out.txt": { - "type": "file", - "description": "Intermediate Bowtie2 output produced from mapping the metagenome against the MetaPHlAn marker database ( not compatible with `bowtie2out` files generated with MetaPhlAn versions below 3 )", - "pattern": "*.{bowtie2out.txt}", - "ontologies": [] - } - } - ] - ], - "sam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.sam": { - "type": "file", - "description": "SAM file produced by MetaPPhlAn of read alignments to MetaPhlAn database gene sequences", - "pattern": "*.{sam}", - "ontologies": [] - } - } + "pipelines": [ + { + "name": "mhcquant", + "version": "3.2.0" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] }, - "authors": [ - "@MGordon09", - "@LilyAnderssonLee" - ], - "maintainers": [ - "@MGordon09", - "@LilyAnderssonLee" - ] - }, - "pipelines": [ { - "name": "funcprofiler", - "version": "dev" + "name": "parsnp", + "path": "modules/nf-core/parsnp/meta.yml", + "type": "module", + "meta": { + "name": "parsnp", + "description": "Parsnp is a command-line-tool for efficient microbial core genome alignment and SNP detection.", + "keywords": ["alignment", "bacteria", "phylogeny", "microbial genomics", "core genome", "SNP"], + "tools": [ + { + "parsnp": { + "description": "Parsnp is a command-line-tool for efficient microbial core genome alignment and SNP detection.", + "homepage": "https://harvest.readthedocs.io/en/latest/content/parsnp/tutorial.html", + "documentation": "https://harvest.readthedocs.io/en/latest/content/parsnp/tutorial.html", + "tool_dev_url": "https://github.com/marbl/parsnp", + "doi": "10.1093/bioinformatics/btae311", + "licence": ["custom; see https://raw.githubusercontent.com/marbl/parsnp/master/LICENSE"], + "identifier": "biotools:parsnp" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "genomes": { + "type": "directory", + "description": "Directory containing genome assemblies in FASTA format to be aligned" + } + } + ], + { + "reference": { + "type": "file", + "description": "Reference genome in FASTA format", + "pattern": "*.{fasta,fa,fna}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + "output": { + "xmfa": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.xmfa": { + "type": "file", + "description": "Core-genome multiple sequence alignment in XMFA format", + "pattern": "*.xmfa", + "ontologies": [] + } + } + ] + ], + "ggr": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.ggr": { + "type": "file", + "description": "Compressed binary representation of the alignment generated by the Harvest toolkit, used for visualization with Gingr", + "pattern": "*.ggr", + "ontologies": [] + } + } + ] + ], + "snps_mblocks": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.snps.mblocks": { + "type": "file", + "description": "Core-SNP signature of each sequence in FASTA format, used to generate the phylogeny. Absent when no SNPs are detected.", + "pattern": "*.snps.mblocks", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ] + ], + "tree": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.tree": { + "type": "file", + "description": "Resulting phylogeny in Newick format", + "pattern": "*.tree", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1910" + } + ] + } + } + ] + ], + "partition": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "partition": { + "type": "directory", + "description": "Output directory from partition mode containing results of each partitioned run. Only present when --partition is specified.", + "pattern": "partition" + } + } + ] + ], + "versions_parsnp": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "parsnp": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "parsnp --version 2>/dev/null | tail -n 1 | sed 's/parsnp //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process" + } + }, + { + "parsnp": { + "type": "string", + "description": "The tool name" + } + }, + { + "parsnp --version 2>/dev/null | tail -n 1 | sed 's/parsnp //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@emmcauley"], + "maintainers": ["@emmcauley"] + } }, { - "name": "taxprofiler", - "version": "2.0.0" - } - ] - }, - { - "name": "metaspace_converter", - "path": "modules/nf-core/metaspace/converter/meta.yml", - "type": "module", - "meta": { - "name": "metaspace_converter", - "description": "Export METASPACE datasets to AnnData and SpatialData objects", - "keywords": [ - "anndata", - "spatialdata", - "metabolomics", - "mass spectrometry", - "imaging" - ], - "tools": [ - { - "metaspace_converter": { - "description": "Python package to download and convert datasets from the METASPACE knowledge base to common formats for single-cell and spatial omics analysis", - "homepage": "https://metaspace2020.github.io/metaspace-converter/", - "documentation": "https://metaspace2020.github.io/metaspace-converter/", - "tool_dev_url": "https://github.com/metaspace2020/metaspace-converter", - "licence": [ - "Apache 2.0 license" - ], - "identifier": "biotools:metaspace" - } - } - ], - "input": [ - { - "ds_id": { - "type": "string", - "description": "METASPACE dataset identifier to retrieve and convert to AnnData and SpatialData formats." - } - }, - { - "database_name_": { - "type": "string", - "description": "Name of the metabolite annotation database to use (e.g., HMDB)" - } - }, - { - "database_version_": { - "type": "string", - "description": "Version of the annotation database to use (e.g., v4)" - } - }, - { - "fdr_": { - "type": "string", - "description": "False Discovery Rate threshold for filtering metabolite annotations.", - "pattern": "^(0(\\.[0-9]+)?|1(\\.0+)?)$" - } - }, - { - "use_tic_": { - "type": "string", - "description": "Controls whether intensity values are scaled by the total ion count per pixel.\n", - "pattern": "^(true|false)$" - } - }, - { - "metadata_as_obs_": { - "type": "string", - "description": "Whether to store metadata in the obs dataframe instead of uns.\n", - "pattern": "^(true|false)$" - } - } - ], - "output": { - "adata_object": [ - { - "AnnData_${ds_id}.h5ad": { - "type": "file", - "description": "AnnData object in .h5ad format. Obs are single pixels and vars are metabolites", - "ontologies": [] - } - } - ], - "sdata_object": [ - { - "SpatialData_${ds_id}.zarr": { - "type": "directory", - "description": "SpatialData format in .zarr format" - } - } - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@bisho2122" - ], - "maintainers": [ - "@bisho2122" - ] - } - }, - { - "name": "metaspace_download", - "path": "modules/nf-core/metaspace/download/meta.yml", - "type": "module", - "meta": { - "name": "metaspace_download", - "description": "A module to download dataset results from the METASPACE platform and save them as CSV files, using a containerized Python script. Inputs are provided via a CSV file or a list of datasets, with results saved to a specified output directory.", - "keywords": [ - "metaspace", - "metabolite annotation", - "data-download", - "csv" - ], - "tools": [ - { - "metaspace2020": { - "description": "Python package providing programmatic access to the METASPACE platform", - "homepage": "https://metaspace2020.readthedocs.io", - "documentation": "https://metaspace2020.readthedocs.io", - "tool_dev_url": "https://github.com/metaspace2020/metaspace/tree/master/metaspace/python-client", - "licence": [ - "Apache-2.0 license" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "dataset_id": { - "type": "string", - "description": "The ID of the dataset to process.\nThe ID is the last part of the dataset URL.\nFor example, in the URL `https://metaspace2020.org/dataset/2022-08-05_17h28m56s`,\nthe `dataset_id` is `2022-08-05_17h28m56s`.\n", - "optional": false - } - }, - { - "database": { - "type": "string", - "description": "The database to download the dataset from (default: 'HMDB').\nIf not provided, all dataset will be included.\n", - "optional": true - } - }, - { - "version": { - "type": "string", - "description": "The version of the database to download the dataset from (default: 'v4').\nIf not provided, all versions will be included.\n", - "optional": true - } - } - ] - ], - "output": { - "results": [ - { - "${dataset_id}_*.csv": { - "type": "file", - "description": "CSV file containing the downloaded dataset results, saved to the directory specified by the output parameter.\nFilename format is '{dataset_id}_*.csv'.\n", - "pattern": "*.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752:latest" - }, - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ], - "log": [ - { - "emit:": { - "type": "string", - "description": "The standard output (stdout) of the script, containing log messages.\nYou can print the last log to see the download progress of all the datasets.\nExample:\n METASPACE_DOWNLOAD.out.log.view { \"${it.split('\\n').last().trim()}\" }\nIt will print the last log message of the script.\nFor Example:\n \"❌ {dataset_id} Dataset not found or inaccessible. Skipping this dataset.\"\n \"❌ {dataset_id} could not find database: {database}\"\n \"❌ {dataset_id} has no annotation data in database: {database}.\"\n \"⚠️ {dataset_id} has multiple {database} version. All the version saved to {filename}\"\n \"✅ {dataset_id} with {database} database are saved to {filename}\"\n \"✅ {dataset_id} with all database are saved to {filename}\"\n" - } - } - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "YAML file containing the versions of the tools used in the pipeline.\nThis file is automatically generated by the pipeline and should not be modified.\n", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - }, - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@Dewey-Wang" - ], - "maintainers": [ - "@Dewey-Wang" - ] - } - }, - { - "name": "metator_pipeline", - "path": "modules/nf-core/metator/pipeline/meta.yml", - "type": "module", - "meta": { - "name": "metator_pipeline", - "description": "Metagenomic Tridimensional Organisation-based Reassembly - A set of scripts that streamlines the processing and binning of metagenomic metaHiC datasets.", - 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"*.fa.gz", - "ontologies": [ + }, + { + "name": "pbccs", + "path": "modules/nf-core/pbccs/meta.yml", + "type": "module", + "meta": { + "name": "pbccs", + "description": "Pacbio ccs - Generate Highly Accurate Single-Molecule Consensus Reads", + "keywords": ["ccs", "pacbio", "isoseq", "subreads"], + "tools": [ + { + "pbccs": { + "description": "pbccs - Generate Highly Accurate Single-Molecule Consensus Reads (HiFi Reads)", + "homepage": "https://github.com/PacificBiosciences/pbbioconda", + "documentation": "https://ccs.how/", + "tool_dev_url": "https://github.com/PacificBiosciences/ccs", + "licence": ["BSD-3-Clause-Clear"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\nid: id of the split file\n" + } + }, + { + "bam": { + "type": "file", + "description": "Raw subreads bam", + "pattern": "*.subreads.bam", + "ontologies": [] + } + }, + { + "pbi": { + "type": "file", + "description": "Pacbio BAM 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"meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.chunk*.bam.pbi": { + "type": "file", + "description": "PacBio Index of CCS sequences", + "pattern": "*.pbi", + "ontologies": [] + } + } + ] + ], + "report_txt": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.report.txt": { + "type": "file", + "description": "CCS report in text format", + "pattern": "*.report.txt", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + } + ] + ], + "report_json": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.report.json": { + "type": "file", + "description": "CCS report in JSON format", + "pattern": "*.report.json", + "ontologies": [ + { + "edam": 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], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing database information\ne.g. [ id:'test']\n" - } + }, + { + "name": "pbtk_pbmerge", + "path": "modules/nf-core/pbtk/pbmerge/meta.yml", + "type": "module", + "meta": { + "name": "pbtk_pbmerge", + "description": "Simple tool which merges several PacBio BAM files together", + "keywords": ["pbtk", "pbmerge", "genomics", "pacbio", "bam"], + "tools": [ + { + "pbtk": { + "description": "pbtk - PacBio BAM toolkit", + "homepage": "https://github.com/PacificBiosciences/pbtk", + "documentation": "https://github.com/PacificBiosciences/pbtk#usage", + "tool_dev_url": "https://github.com/PacificBiosciences/pbtk", + "doi": "no DOI available", + "licence": ["BSD-3-clause-Clear"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "bams": { + "type": "file", + "description": "PacBio BAM files", + "pattern": "*.bam", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + } + ] + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "The merged PacBio BAM file", + "pattern": "*.bam", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + } + ] + ], + "pbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.pbi": { + "type": "file", + "description": "BAM Pacbio index file", + "pattern": "*.bam.pbi", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@haidyi"], + "maintainers": ["@haidyi"] }, - { - "db": { - "type": "file", - "description": "A database formatted for MIDAS", - "pattern": "*.{db}", - "ontologies": [] - } - } - ], - { - "mode": { - "type": "string", - "description": "The mode to run MIDAS is", - "pattern": "*" - } - } - ], - "output": { - "results": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/*": { - "type": "file", - "description": "A directory of results from MIDAS run", - "pattern": "*", - "ontologies": [] - } - } + "pipelines": [ + { + "name": "pacsomatic", + "version": "dev" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@rpetit3" - ], - "maintainers": [ - "@rpetit3" - ] - } - }, - { - "name": "mifaser", - "path": "modules/nf-core/mifaser/meta.yml", - "type": "module", - "meta": { - "name": "mifaser", - "description": "Functional annotation of metagenomic reads by assigning enzyme commission (EC) numbers", - "keywords": [ - "metagenomics", - "functional annotation", - "EC numbers", - "fastq" - ], - "tools": [ - { - "mifaser": { - "description": "mi-faser: microsecond functional annotation of sequences, a massive scalability upgrade", - "homepage": "https://sourceforge.net/projects/mifaser/", - "documentation": "https://sourceforge.net/projects/mifaser/", - "tool_dev_url": "https://sourceforge.net/projects/mifaser/", - "doi": "10.1093/nar/gkx1209", - "licence": [ - "NPOSL-3.0" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:true ]`\n" - } + }, + { + "name": "pcgr_getref", + "path": "modules/nf-core/pcgr/getref/meta.yml", + "type": "module", + "meta": { + "name": "pcgr_getref", + "description": "Get reference to run Personal Cancer Genome Reporter (PCGR)", + "keywords": ["cancer", "reference", "pcgr", "mtb"], + "tools": [ + { + "pcgr": { + "description": "The Personal Cancer Genome Reporter (PCGR) is a stand-alone software package for functional annotation and translation of individual tumor genomes for precision cancer medicine", + "homepage": "https://sigven.github.io/pcgr/index.html", + "documentation": "https://sigven.github.io/pcgr/articles/running.html", + "tool_dev_url": "https://github.com/sigven/pcgr/", + "doi": "10.1093/bioinformatics/btx817", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "bundleversion": { + "type": "string", + "description": "PCGR reference data bundle version", + "pattern": "*[0-9]*", + "ontologies": [] + } + }, + { + "genome": { + "type": "string", + "description": "PCGR reference genome version", + "pattern": "grch37|grch38", + "ontologies": [] + } + } + ] + ], + "output": { + "pcgrref": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${bundleversion}": { + "type": "directory", + "description": "PCGR reference data directory", + "pattern": "{bundleversion}/", + "ontologies": [] + } + } + ] + ], + "versions_curl": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "curl": { + "type": "string", + "description": "The tool name" + } + }, + { + "curl --version | head -1 | cut -d ' ' -f 2": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ], + "versions_gzip": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "gzip": { + "type": "string", + "description": "The tool name" + } + }, + { + "gzip --version | head -1 | cut -d ' ' -f 2": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ], + "versions_tar": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "tar": { + "type": "string", + "description": "The tool name" + } + }, + { + "tar --version | head -1 | cut -d ' ' -f 4": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "curl": { + "type": "string", + "description": "The tool name" + } + }, + { + "curl --version | head -1 | cut -d ' ' -f 2": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "gzip": { + "type": "string", + "description": "The tool name" + } + }, + { + "gzip --version | head -1 | cut -d ' ' -f 2": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "tar": { + "type": "string", + "description": "The tool name" + } + }, + { + "tar --version | head -1 | cut -d ' ' -f 4": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@famosab"], + "maintainers": ["@famosab"] }, - { - "reads": { - "type": "file", - "description": "Single-end or paired-end FASTQ files. Use meta.single_end to indicate input type.\n", - "pattern": "*.{fastq,fastq.gz,fq,fq.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ], - { - "db": { - "type": "directory", - "description": "Path to the mi-faser database folder" - } - } - ], - "output": { - "multi_ec": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*multi_ec.tsv": { - "type": "file", - "description": "TSV file with multi-EC functional assignments per read", - "pattern": "*multi_ec.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "analysis": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*analysis.tsv": { - "type": "file", - "description": "TSV file with per-sample functional analysis summary", - "pattern": "*analysis.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "ec_counts": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*ec_count.tsv": { - "type": "file", - "description": "TSV file with EC number counts", - "pattern": "*ec_count.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_mifaser": [ - [ - { - "${task.process}": { - "type": "string", - "description": "Process name" - } - }, - { - "mi-faser": { - "type": "string", - "description": "Tool name" - } - }, - { - "mifaser --version 2>&1 | sed 's/* v//'": { - "type": "eval", - "description": "mifaser version string" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "Process name" - } - }, - { - "mi-faser": { - "type": "string", - "description": "Tool name" - } - }, - { - "mifaser --version 2>&1 | sed 's/* v//'": { - "type": "eval", - "description": "mifaser version string" - } - } + "pipelines": [ + { + "name": "variantprioritization", + "version": "1.0.0" + } ] - ] - }, - "authors": [ - "@nickp60" - ], - "maintainers": [ - "@nickp60" - ] - }, - "pipelines": [ - { - "name": "funcprofiler", - "version": "dev" - } - ] - }, - { - "name": "mindagap_duplicatefinder", - "path": "modules/nf-core/mindagap/duplicatefinder/meta.yml", - "type": "module", - "meta": { - "name": "MINDAGAP_DUPLICATEFINDER", - "description": "marks duplicate spots along gridline edges.", - "keywords": [ - "imaging", - "resolve_bioscience", - "spatial_transcriptomics" - ], - "tools": [ - { - "mindagap": { - "description": "Takes a single panorama image and fills the empty grid lines with neighbour-weighted values.", - "homepage": "https://github.com/ViriatoII/MindaGap/blob/main/README.md", - "documentation": "https://github.com/ViriatoII/MindaGap/blob/main/README.md", - "tool_dev_url": "https://github.com/ViriatoII/MindaGap", - "licence": [ - "BSD 3-clause License" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "spot_table": { - "type": "file", - "description": "tsv file containing one spot per row with order x,y,z,gene without column header.", - "pattern": "*.{tsv,txt}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "output": { - "marked_dups_spots": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*markedDups.txt": { - "type": "file", - "description": "tab-separated text file containing one spot per row, with duplicated spots labeled with \"Duplicated\" in their gene column.", - "pattern": "*.{markedDups.txt}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1964" - } - ] - } - } - ] - ], - "versions_mindagap": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "mindagap": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "mindagap.py test -v": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "mindagap": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "mindagap.py test -v": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@FloWuenne" - ], - "maintainers": [ - "@FloWuenne" - ] - }, - "pipelines": [ - { - "name": "molkart", - "version": "1.2.0" - } - ] - }, - { - "name": "mindagap_mindagap", - "path": "modules/nf-core/mindagap/mindagap/meta.yml", - "type": "module", - "meta": { - "name": "mindagap_mindagap", - "description": "Takes a single panorama image and fills the empty grid lines with neighbour-weighted values.", - "keywords": [ - "imaging", - "resolve_bioscience", - "spatial_transcriptomics" - ], - "tools": [ - { - "mindagap": { - "description": "Mindagap is a collection of tools to process multiplexed FISH data, such as produced by Resolve Biosciences Molecular Cartography.", - "homepage": "https://github.com/ViriatoII/MindaGap", - "documentation": "https://github.com/ViriatoII/MindaGap/blob/main/README.md", - "tool_dev_url": "https://github.com/ViriatoII/MindaGap", - "licence": [ - "BSD-3-Clause license" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "panorama": { - "type": "file", - "description": "A tiff file containing gridlines as produced by Molecular Cartography imaging.", - "pattern": "*.{tif,tiff}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3591" - } - ] - } - } - ] - ], - "output": { - "tiff": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.{tif,tiff}": { - "type": "file", - "description": "A tiff file with gridlines filled based on consecutive gaussian blurring.", - "pattern": "*.{tiff}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3591" - } - ] - } - } - ] - ], - "versions_mindagap": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "mindagap": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "mindagap.py test -v": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "mindagap": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "mindagap.py test -v": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@ViriatoII", - "@flowuenne" - ], - "maintainers": [ - "@ViriatoII", - "@flowuenne" - ] - }, - "pipelines": [ - { - "name": "molkart", - "version": "1.2.0" - } - ] - }, - { - "name": "minia", - "path": "modules/nf-core/minia/meta.yml", - "type": "module", - "meta": { - "name": "minia", - "description": "Minia is a short-read assembler based on a de Bruijn graph", - "keywords": [ - "assembler", - "short-read", - "de Bruijn" - ], - "tools": [ - { - "minia": { - "description": "Minia is a short-read assembler based on a de Bruijn graph, capable of assembling\na human genome on a desktop computer in a day. The output of Minia is a set of contigs.\n", - "homepage": "https://github.com/GATB/minia", - "documentation": "https://github.com/GATB/minia", - "licence": [ - "AGPL-3.0-or-later" - ], - "identifier": "biotools:minia" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "Input reads in FastQ format", - "pattern": "*.{fastq.gz, fastq}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "output": { - "contigs": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.contigs.fa.gz": { - "type": "file", - "description": "The assembled contigs", - "pattern": "*.contigs.fa.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "unitigs": [ - [ - { - "meta": { - "type": "map", - 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By defaults peddy uses hg19/GRCh37, \"--sites hg38\" can be specified in the process argument or a custom file following syntax https://github.com/brentp/peddy/blob/master/peddy/GRCH37.sites can be provided", + "pattern": "*.sites", + "ontologies": [] + } + } + ] + ], + "output": { + "vs_html": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.vs.html": { + "type": "file", + "description": "HTML file comparison between reported and inferred sex", + "pattern": "*.vs.html", + "ontologies": [] + } + } + ] + ], + "html": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.html": { + "type": "file", + "description": "HTML report", + "pattern": "*.html", + "ontologies": [] + } + } + ] + ], + "ped": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.peddy.ped": { + "type": "file", + "description": "Inferred PED file", + "pattern": "*.peddy.ped", + "ontologies": [] + } + } + ] + ], + "het_check_png": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.het_check.png": { + "type": "file", + "description": "PNG file containing heterozygosity check.\nRate of het calls, allele-balance at het calls,\nmean and median depth, and a PCA projection onto thousand\ngenomes.\n", + "pattern": "*.het_check.png", + "ontologies": [] + } + } + ] + ], + "ped_check_png": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.ped_check.png": { + "type": "file", + "description": "PNG file containing pedigree check between reported\nand inferred sex\n", + "pattern": "*.het_check.png", + "ontologies": [] + } + } + ] + ], + "sex_check_png": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.sex_check.png": { + "type": "file", + "description": "PNG file with sex check performs a comparison\nbetween the sex reported in the ped file and that\ninferred from the genotypes on the non-PAR regions\nof the X chromosome.\n", + "pattern": "*.sex_check.png", + "ontologies": [] + } + } + ] + ], + "het_check_csv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.het_check.csv": { + "type": "file", + "description": "CSV file containing heterozygosity check.\nRate of het calls, allele-balance at het calls,\nmean and median depth, and a PCA projection onto thousand\ngenomes.\n", + "pattern": "*.het_check.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "ped_check_csv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.ped_check.csv": { + "type": "file", + "description": "CSV file containing pedigree check between reported\nand inferred sex\n", + "pattern": "*.het_check.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "sex_check_csv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.sex_check.csv": { + "type": "file", + "description": "CSV file with sex check performs a comparison\nbetween the sex reported in the ped file and that\ninferred from the genotypes on the non-PAR regions\nof the X chromosome.\n", + "pattern": "*.sex_check.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "ped_check_rel_difference_csv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.ped_check.rel-difference.csv": { + "type": "file", + "description": "CSV file with the comparison between inferred and given relatedness\n", + "pattern": "*.ped_check.rel-difference.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "versions_peddy": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "peddy": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "peddy --version | sed 's/peddy, version //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "peddy": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "peddy --version | sed 's/peddy, version //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@rannick"], + "maintainers": ["@rannick"] }, - { - "region": { - "type": "string", - "description": "Region to perform imputation", - "pattern": "(chr)?\\d*:\\d*-\\d*" - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + "pipelines": [ + { + "name": "raredisease", + "version": "3.0.0" } - }, - { - "*.{bcf,sav,vcf.gz,vcf,ubcf,usav}": { - "type": "file", - "description": "Imputed variants file", - "pattern": "*.{bcf,sav,vcf.gz,vcf,ubcf,usav}", - "ontologies": [ + ] + }, + { + "name": "peka", + "path": "modules/nf-core/peka/meta.yml", + "type": "module", + "meta": { + "name": "peka", + "description": "Runs PEKA CLIP peak k-mer analysis", + "keywords": ["motif", "CLIP", "iCLIP", "genomics", "k-mer"], + "tools": [ + { + "peka": { + "description": "Positionally-enriched k-mer analysis (PEKA) is a software package for identifying enriched protein-RNA binding motifs from CLIP datasets", + "homepage": "https://github.com/ulelab/peka", + "documentation": "https://github.com/ulelab/peka", + "tool_dev_url": "https://github.com/ulelab/peka", + "doi": "10.1186/s13059-022-02755-2", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "peaks": { + "type": "file", + "description": "BED file of peak regions", + "pattern": "*.{bed,bed.gz}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "crosslinks": { + "type": "file", + "description": "BED file of crosslinks", + "pattern": "*.{bed,bed.gz}", + "ontologies": [] + } + } + ], + { + "fasta": { + "type": "file", + "description": "Genome reference sequence used", + "pattern": "*.{fa,fasta}", + "ontologies": [] + } + }, { - "edam": "http://edamontology.org/format_3016" + "fai": { + "type": "file", + "description": "FAI file corresponding to the reference sequence", + "pattern": "*.{fai}", + "ontologies": [] + } }, { - "edam": "http://edamontology.org/format_3020" + "gtf": { + "type": "file", + "description": "A segmented GTF used to annotate peaks", + "pattern": "*.{gtf}", + "ontologies": [] + } } - ] - } - } - ] - ], - "versions_minimac4": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "minimac4": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "minimac4 --version |& sed '1!d ; s/minimac v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "minimac4": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "minimac4 --version |& sed '1!d ; s/minimac v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@LouisLeNezet" - ], - "maintainers": [ - "@LouisLeNezet" - ] - }, - "pipelines": [ - { - "name": "phaseimpute", - "version": "1.1.0" - } - ] - }, - { - "name": "minimap2_align", - "path": "modules/nf-core/minimap2/align/meta.yml", - "type": "module", - "meta": { - "name": "minimap2_align", - "description": "A versatile pairwise aligner for genomic and spliced nucleotide sequences", - "keywords": [ - "align", - "fasta", - "fastq", - "genome", - "paf", - "reference" - ], - "tools": [ - { - "minimap2": { - "description": "A versatile pairwise aligner for genomic and spliced nucleotide sequences.\n", - "homepage": "https://github.com/lh3/minimap2", - "documentation": "https://github.com/lh3/minimap2#uguide", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FASTA or FASTQ files of size 1 and 2 for single-end\nand paired-end data, respectively.\n", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test_ref']\n" - } - }, - { - "reference": { - "type": "file", - "description": "Reference database in FASTA format.\n", - "ontologies": [] - } - } - ], - { - "bam_format": { - "type": "boolean", - "description": "Specify that output should be in BAM format" - } - }, - { - "bam_index_extension": { - "type": "string", - "description": "BAM alignment index extension (e.g. \"bai\")" - } - }, - { - "cigar_paf_format": { - "type": "boolean", - "description": "Specify that output CIGAR should be in PAF format" - } - }, - { - "cigar_bam": { - "type": "boolean", - "description": "Write CIGAR with >65535 ops at the CG tag. This is recommended when\ndoing XYZ (https://github.com/lh3/minimap2#working-with-65535-cigar-operations)\n" + ], + "output": { + "cluster": [ + [ + { + "meta": { + "type": "file", + "description": "TSV file of summed occurrence distributions of k-mers within defined clusters", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, + { + "*mer_cluster_distribution*": { + "type": "file", + "description": "TSV file of summed occurrence distributions of k-mers within defined clusters", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "distribution": [ + [ + { + "meta": { + "type": "file", + "description": "TSV file of summed occurrence distributions of k-mers within defined clusters", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, + { + "*mer_distribution*": { + "type": "file", + "description": "TSV file with calculated PEKA score and occurrence distribution for all possible k-mers", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "rtxn": [ + [ + { + "meta": { + "type": "file", + "description": "TSV file of summed occurrence distributions of k-mers within defined clusters", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, + { + "*rtxn*": { + "type": "file", + "description": "rtxn file", + "pattern": "*rtxn*", + "ontologies": [] + } + } + ] + ], + "pdf": [ + [ + { + "meta": { + "type": "file", + "description": "TSV file of summed occurrence distributions of k-mers within defined clusters", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, + { + "*.pdf": { + "type": "file", + "description": "PDF file with graphs showing k-mer occurrence distributions around thresholded crosslink sites", + "pattern": "*.pdf", + "ontologies": [] + } + } + ] + ], + "tsites": [ + [ + { + "meta": { + "type": "file", + "description": "TSV file of summed occurrence distributions of k-mers within defined clusters", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, + { + "*thresholded_sites*.bed.gz": { + "type": "file", + "description": "BED file of thresholded sites", + "pattern": "*thresholded_sites*.bed.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "oxn": [ + [ + { + "meta": { + "type": "file", + "description": "TSV file of summed occurrence distributions of k-mers within defined clusters", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, + { + "*oxn*.bed.gz": { + "type": "file", + "description": "BED file of oxn sites", + "pattern": "*oxn*.bed.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "clust": [ + [ + { + "meta": { + "type": "file", + "description": "TSV file of summed occurrence distributions of k-mers within defined clusters", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, + { + "*_clusters.csv": { + "type": "file", + "description": "CSV file of clusters", + "pattern": "*_clusters.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@kkuret", "@codeprimate123", "@chris-cheshire", "@charlotteanne"], + "maintainers": ["@kkuret", "@codeprimate123", "@chris-cheshire", "@charlotteanne"] } - } - ], - "output": { - "paf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.paf": { - "type": "file", - "description": "Alignment in PAF format", - "pattern": "*.paf", - "ontologies": [] - } - } - ] - ], - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "Alignment in BAM format", - "pattern": "*.bam", - "ontologies": [] - } - } - ] - ], - "index": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bam.${bam_index_extension}": { - "type": "file", - "description": "BAM alignment index", - "pattern": "*.bam.*", - "ontologies": [] - } - } - ] - ], - "versions_minimap2": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process name" - } - }, - { - "minimap2": { - "type": "string", - "description": "The tool name" - } - }, - { - "minimap2 --version": { - "type": "eval", - "description": "The tool version" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process name" - } - }, - { - "minimap2": { - "type": "string", - "description": "The tool name" - } - }, - { - "minimap2 --version": { - "type": "eval", - "description": "The tool version" - } - } - ] - ] }, - "authors": [ - "@heuermh", - "@sofstam", - "@sateeshperi", - "@jfy133", - "@fellen31" - ], - "maintainers": [ - "@heuermh", - "@sofstam", - "@sateeshperi", - "@jfy133", - "@fellen31" - ] - }, - "pipelines": [ { - "name": "abotyper", - "version": "dev" + "name": "perbase", + "path": "modules/nf-core/perbase/meta.yml", + "type": "module", + "meta": { + "name": "perbase", + "description": "Per-base metrics on BAM/CRAM files.", + "keywords": ["bam", "cram", "depth"], + "tools": [ + { + "perbase": { + "description": "Per-base metrics on BAM/CRAM files.", + "homepage": "https://github.com/sstadick/perbase", + "documentation": "https://github.com/sstadick/perbase", + "tool_dev_url": "https://github.com/sstadick/perbase", + "doi": "10.21105/joss.09774", + "licence": ["MIT"], + "identifier": "biotools:perbase" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "bam": { + "type": "file", + "description": "Sorted BAM/CRAM file", + "pattern": "*.{bam,cram}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_25722" + }, + { + "edam": "http://edamontology.org/format_3462" + } + ] + } + }, + { + "index": { + "type": "file", + "description": "BAI/CRAI file", + "pattern": "*.{bai,crai}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3327" + } + ] + } + }, + { + "bed": { + "type": "file", + "description": "bed file containing regions of interest, where only bases from the given regions will be reported", + "pattern": "*.{bed}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3003" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference fasta (optional)", + "pattern": "*.{fasta,fa}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + }, + { + "fai": { + "type": "file", + "description": "FAI file (optional)", + "pattern": "*.{fai}", + "ontologies": [] + } + } + ] + ], + "output": { + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.tsv.gz": { + "type": "file", + "description": "TSV file", + "pattern": "*.{tsv.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_perbase": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "perbase": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "perbase --version |& sed \"1!d ; s/perbase //\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "perbase": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "perbase --version |& sed \"1!d ; s/perbase //\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@camlloyd"], + "maintainers": ["@camlloyd"] + } }, { - "name": "bacass", - "version": "2.6.0" + "name": "percolator", + "path": "modules/nf-core/percolator/meta.yml", + "type": "module", + "meta": { + "name": "percolator", + "description": "Rescore peptide-spectrum matches and estimate false discovery rates using the Percolator semi-supervised learning algorithm.", + "keywords": [ + "proteomics", + "spectrum identification", + "psm", + "peptide", + "protein", + "rescoring", + "false discovery rate", + "features" + ], + "tools": [ + { + "percolator": { + "description": "Semi-supervised learning for peptide identification from shotgun proteomics datasets.", + "homepage": "http://percolator.ms", + "documentation": "http://percolator.ms", + "tool_dev_url": "https://github.com/percolator/percolator", + "doi": "10.1038/nmeth1113", + "licence": ["Apache-2.0"], + "identifier": "biotools:percolator" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" + } + }, + { + "peptide_identification": { + "type": "file", + "description": "peptide identifications as PIN (Percolator input) file", + "pattern": "*.pin", + "ontologies": [] + } + } + ] + ], + "output": { + "pout_xml": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" + } + }, + { + "${prefix}.pout.xml": { + "type": "file", + "description": "Percolator output in XML format containing all PSM-level results", + "pattern": "*.pout.xml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2332" + } + ] + } + } + ] + ], + "pout_pepxml": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" + } + }, + { + "${prefix}.pep.xml": { + "type": "file", + "description": "Percolator output in pepXML format", + "pattern": "*.pep.xml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3655" + } + ] + } + } + ] + ], + "features_pin": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" + } + }, + { + "${prefix}.features.pin": { + "type": "file", + "description": "Tab-separated file with rescored features (PIN format)", + "pattern": "*.features.pin", + "ontologies": [] + } + } + ] + ], + "weights": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" + } + }, + { + "${prefix}.weights.tsv": { + "type": "file", + "description": "TSV file containing the final feature weights", + "pattern": "*.weights.tsv", + "ontologies": [] + } + } + ] + ], + "target_peptides": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" + } + }, + { + "${prefix}.pep.target.pout": { + "type": "file", + "description": "Target peptide-level results in tab separated format (pout)", + "pattern": "*.pep.target.pout", + "ontologies": [] + } + } + ] + ], + "decoy_peptides": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" + } + }, + { + "${prefix}.pep.decoy.pout": { + "type": "file", + "description": "Decoy peptide-level results in tab separated format (pout)", + "pattern": "*.pep.decoy.pout", + "ontologies": [] + } + } + ] + ], + "target_psms": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" + } + }, + { + "${prefix}.psm.target.pout": { + "type": "file", + "description": "Target PSM-level results in tab separated format (pout)", + "pattern": "*.psm.target.pout", + "ontologies": [] + } + } + ] + ], + "decoy_psms": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" + } + }, + { + "${prefix}.psm.decoy.pout": { + "type": "file", + "description": "Decoy PSM-level results in tab separated format (pout)", + "pattern": "*.psm.decoy.pout", + "ontologies": [] + } + } + ] + ], + "target_proteins": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" + } + }, + { + "${prefix}.protein.target.pout": { + "type": "file", + "description": "Target protein-level results in tab separated format (pout)", + "pattern": "*.protein.target.pout", + "ontologies": [] + } + } + ] + ], + "decoy_proteins": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" + } + }, + { + "${prefix}.protein.decoy.pout": { + "type": "file", + "description": "Decoy protein-level results in tab separated format (pout)", + "pattern": "*.protein.decoy.pout", + "ontologies": [] + } + } + ] + ], + "versions_percolator": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "percolator": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "percolator --help 2>&1 | head -1 | sed \"s;Percolator version \\([^,]*\\),.*;\\1;\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "percolator": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "percolator --help 2>&1 | head -1 | sed \"s;Percolator version \\([^,]*\\),.*;\\1;\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@julianu"], + "maintainers": ["@julianu"] + }, + "pipelines": [ + { + "name": "mspepid", + "version": "dev" + } + ] }, { - "name": "circdna", - "version": "1.1.0" + "name": "phantompeakqualtools", + "path": "modules/nf-core/phantompeakqualtools/meta.yml", + "type": "module", + "meta": { + "name": "phantompeakqualtools", + "description": "\"This package computes informative enrichment and quality measures\nfor ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used\nto obtain robust estimates of the predominant fragment length or\ncharacteristic tag shift values in these assays.\"\n", + "keywords": ["ChIP-Seq", "QC", "phantom peaks"], + "tools": [ + { + "phantompeakqualtools": { + "description": "\"This package computes informative enrichment and quality measures\nfor ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used\nto obtain robust estimates of the predominant fragment length or\ncharacteristic tag shift values in these assays.\"\n", + "documentation": "https://github.com/kundajelab/phantompeakqualtools", + "tool_dev_url": "https://github.com/kundajelab/phantompeakqualtools", + "doi": "10.1101/gr.136184.111", + "licence": ["BSD-3-clause"], + "identifier": "biotools:phantompeakqualtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}", + "ontologies": [] + } + } + ] + ], + "output": { + "spp": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.out": { + "type": "file", + "description": "A ChIP-Seq Processing Pipeline file containing\npeakshift/phantomPeak results\n", + "pattern": "*.{out}", + "ontologies": [] + } + } + ] + ], + "pdf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.pdf": { + "type": "file", + "description": "A pdf containing save cross-correlation plots", + "pattern": "*.{pdf}", + "ontologies": [] + } + } + ] + ], + "rdata": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.Rdata": { + "type": "file", + "description": "Rdata file containing the R session", + "pattern": "*.{Rdata}", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@drpatelh", "@edmundmiller", "@JoseEspinosa"], + "maintainers": ["@drpatelh", "@edmundmiller", "@JoseEspinosa"] + }, + "pipelines": [ + { + "name": "chipseq", + "version": "2.1.0" + } + ] }, { - "name": "crisprseq", - "version": "2.3.0" + "name": "pharmcat_matcher", + "path": "modules/nf-core/pharmcat/matcher/meta.yml", + "type": "module", + "meta": { + "name": "pharmcat_matcher", + "description": "The Named Allele Matcher is responsible for calling diplotypes from variant call data.\nWhile it is designed to be used in the PharmCAT pipeline, it can also be run independently.\nThe Named Allele Matcher does not currently support structural variants, including gene copy\nnumber. If structural variants are detected in the VCF data, it will be ignored and a warning\nwill be issued.\nIf it detects more than the expected number of alleles in the GT column of the VCF, only the\nfirst two alleles will be used and a warning will be issued. On haploid chromosomes, only\nthe first allele will be used.\n", + "keywords": ["vcf", "pharmcat", "matcher", "PGx"], + "tools": [ + { + "pharmcat": { + "description": "\"PharmCAT (Pharmacogenomics Clinical Annotation Tool) is a bioinformatics\ntool that analyzes genetic variants to predict drug response and tailor medical\ntreatment to an individual patient’s genetic profile.\"\n", + "homepage": "https://pharmcat.clinpgx.org/", + "documentation": "https://pharmcat.clinpgx.org/", + "tool_dev_url": "https://github.com/PharmGKB/PharmCAT", + "doi": "10.1002/cpt.928", + "licence": ["MPL-2.0"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', name:'test_sample' ]`\n" + } + }, + { + "vcf": { + "type": "file", + "description": "The vcf file to be inspected", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + }, + { + "index": { + "type": "file", + "description": "The tbi/csi file to be inspected", + "pattern": "*.{tbi,csi}", + "ontologies": [] + } + } + ], + { + "genes": { + "type": "list", + "description": "List of genes to be processed" + } + } + ], + "output": { + "matcher_json": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', name:'test_sample' ]`\n" + } + }, + { + "*.match.json": { + "type": "file", + "description": "Json output from the matcher module of PharmCAT", + "pattern": "*.match.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "matcher_html": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', name:'test_sample' ]`\n" + } + }, + { + "*.match.html": { + "type": "file", + "description": "HTML output from the matcher module of PharmCAT", + "pattern": "*.match.html", + "ontologies": [] + } + } + ] + ], + "versions_pharmcat": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "pharmcat": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pharmcat --version | cut -f2 -d ' '": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "pharmcat": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pharmcat --version | cut -f2 -d ' '": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@ramsainanduri"], + "maintainers": ["@ramsainanduri"] + } }, { - "name": "evexplorer", - "version": "dev" + "name": "pharmcat_phenotyper", + "path": "modules/nf-core/pharmcat/phenotyper/meta.yml", + "type": "module", + "meta": { + "name": "pharmcat_phenotyper", + "description": "The PharmCAT Phenotyper is a core module of the Pharmacogenomics Clinical Annotation Tool\nthat translates patient diplotypes into specific, actionable metabolizer phenotypes\n(e.g., Poor Metabolizer). It operates by analyzing the JSON output from the Named\nAllele Matcher, mapping these results to established clinical guidelines (such as\nCPIC) to predict drug response.\n", + "keywords": ["vcf", "pharmcat", "phenotyper", "PGx"], + "tools": [ + { + "pharmcat": { + "description": "\"PharmCAT (Pharmacogenomics Clinical Annotation Tool) is a bioinformatics\ntool that analyzes genetic variants to predict drug response and tailor medical\ntreatment to an individual patient’s genetic profile.\"\n", + "homepage": "https://pharmcat.clinpgx.org/", + "documentation": "https://pharmcat.clinpgx.org/", + "tool_dev_url": "https://github.com/PharmGKB/PharmCAT", + "doi": "10.1002/cpt.928", + "licence": ["MPL-2.0"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', name:'test_sample' ]`\n" + } + }, + { + "match_json": { + "type": "file", + "description": "The Json output from the matcher module of pharmcat", + "pattern": "*.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + }, + { + "outside_match_tsv": { + "type": "file", + "description": "Tab seperated file containing diplotypes calls from other callers", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "output": { + "phenotyper_json": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', name:'test_sample' ]`\n" + } + }, + { + "*.phenotype.json": { + "type": "file", + "description": "Json output from the phenotyper module of PharmCAT", + "pattern": "*.phenotype.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "versions_pharmcat": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "pharmcat": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pharmcat --version | cut -f2 -d ' '": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "pharmcat": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pharmcat --version | cut -f2 -d ' '": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@ramsainanduri"], + "maintainers": ["@ramsainanduri"] + } }, { - "name": "genomeassembler", - "version": "1.1.0" + "name": "pharmcat_reporter", + "path": "modules/nf-core/pharmcat/reporter/meta.yml", + "type": "module", + "meta": { + "name": "pharmcat_reporter", + "description": "The Reporter module is responsible for generating a report with genotype-specific\nexpert-reviewed drug prescribing recommendations for clinical decision support.\n", + "keywords": ["pharmcat", "report", "PGx"], + "tools": [ + { + "pharmcat": { + "description": "\"PharmCAT (Pharmacogenomics Clinical Annotation Tool) is a bioinformatics\ntool that analyzes genetic variants to predict drug response and tailor medical\ntreatment to an individual patient’s genetic profile.\"\n", + "homepage": "https://pharmcat.clinpgx.org/", + "documentation": "https://pharmcat.clinpgx.org/", + "tool_dev_url": "https://github.com/PharmGKB/PharmCAT", + "doi": "10.1002/cpt.928", + "licence": ["MPL-2.0"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', name:'test_sample' ]`\n" + } + }, + { + "phenotypes": { + "type": "file", + "description": "The vcf file to be inspected", + "pattern": "*.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "output": { + "report_json": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', name:'test_sample' ]`\n" + } + }, + { + "*.report.json": { + "type": "file", + "description": "Json output from the reporter module of PharmCAT", + "pattern": "*.report.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "report_html": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', name:'test_sample' ]`\n" + } + }, + { + "*.report.html": { + "type": "file", + "description": "HTML output from the reporter module of PharmCAT", + "pattern": "*.report.html", + "ontologies": [] + } + } + ] + ], + "report_tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', name:'test_sample' ]`\n" + } + }, + { + "*.report.tsv": { + "type": "file", + "description": "Tab separated output from the reporter module of PharmCAT", + "pattern": "*.report.tsv", + "ontologies": [] + } + } + ] + ], + "versions_pharmcat": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "pharmcat": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pharmcat --version | cut -f2 -d ' '": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "pharmcat": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pharmcat --version | cut -f2 -d ' '": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@ramsainanduri"], + "maintainers": ["@ramsainanduri"] + } }, { - "name": "isoseq", - "version": "2.0.0" + "name": "pharmcat_vcfpreprocessor", + "path": "modules/nf-core/pharmcat/vcfpreprocessor/meta.yml", + "type": "module", + "meta": { + "name": "pharmcat_vcfpreprocessor", + "description": "The PharmCAT VCF Preprocessor is a script that can pre-process VCF files for PharmCAT to make sure the VCF file complies with PharmCAT's VCF Requirements", + "keywords": ["preprocessing", "vcf", "phamrcat"], + "tools": [ + { + "pharmcat": { + "description": "PharmCAT (Pharmacogenomics Clinical Annotation Tool) is a bioinformatics tool that analyzes genetic variants to predict drug response and tailor medical treatment to an individual patient’s genetic profile. ", + "homepage": "https://pharmcat.clinpgx.org/", + "documentation": "https://pharmcat.clinpgx.org/", + "tool_dev_url": "https://github.com/PharmGKB/PharmCAT", + "doi": "10.1002/cpt.928", + "licence": ["MPL-2.0"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', name:'test_sample' ]`\n" + } + }, + { + "vcf_gz": { + "type": "file", + "description": "The vcf file to be inspected", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + }, + { + "vcf_index": { + "type": "file", + "description": "The tbi/csi file to be inspected", + "pattern": "*.{tbi,csi}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Genome fasta file", + "pattern": "*.{fa,fasta,fa.gz,fasta.gz}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Genome index file", + "pattern": "*.{fai,fai.gz}", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" + } + }, + { + "pharmcat_positions": { + "type": "file", + "description": "Pharmcat positions vcf", + "pattern": "*.vcf.{gz,bgz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + }, + { + "pharmcat_positions_index": { + "type": "file", + "description": "Pharmcat positions vcf index file", + "pattern": "*.{tbi,csi}", + "ontologies": [] + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" + } + }, + { + "pharmcat_uniallelic_positions": { + "type": "file", + "description": "Pharmcat uniallelic positions vcf", + "pattern": "*.vcf.{gz,bgz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + }, + { + "pharmcat_uniallelic_positions_index": { + "type": "file", + "description": "Pharmcat uniallelic positions vcf index file", + "pattern": "*.{tbi,csi}", + "ontologies": [] + } + } + ] + ], + "output": { + "preprocessed_vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', name:'test_sample' ]`\n" + } + }, + { + "*.preprocessed.vcf.bgz": { + "type": "file", + "description": "Preprocessed vcf file", + "pattern": "*.preprocessed.vcf.bgz", + "ontologies": [] + } + } + ] + ], + "missing_pgx_var": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', name:'test_sample' ]`\n" + } + }, + { + "*.missing_pgx_var.vcf": { + "type": "file", + "description": "Missing position in PGX VCF file", + "pattern": "*.missing_pgx_var.vcf", + "ontologies": [] + } + } + ] + ], + "versions_pharmcat_vcf_preprocessor": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "pharmcat_vcf_preprocessor": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pharmcat_vcf_preprocessor --version | cut -f4 -d ' '": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "pharmcat_vcf_preprocessor": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pharmcat_vcf_preprocessor --version | cut -f4 -d ' '": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@ramsainanduri"], + "maintainers": ["@ramsainanduri"] + } }, { - "name": "mag", - "version": "5.4.2" + "name": "pharokka_installdatabases", + "path": "modules/nf-core/pharokka/installdatabases/meta.yml", + "type": "module", + "meta": { + "name": "pharokka_installdatabases", + "description": "Install databases necessary for Pharokka's functional analysis", + "keywords": ["pharokka", "prokka", "bakta", "phage", "function", "install", "database"], + "tools": [ + { + "pharokka": { + "description": "Fast Phage Annotation Program", + "homepage": "https://pharokka.readthedocs.io", + "documentation": "https://pharokka.readthedocs.io", + "tool_dev_url": "https://github.com/gbouras13/pharokka", + "doi": "10.1093/bioinformatics/btac776", + "licence": ["MIT"], + "identifier": "biotools:pharokka" + } + } + ], + "output": { + "pharokka_db": [ + { + "${prefix}/": { + "type": "directory", + "description": "Directory pointing to Pharokka's database", + "pattern": "${prefix}/" + } + } + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@CarsonJM"], + "maintainers": ["@CarsonJM"] + }, + "pipelines": [ + { + "name": "phageannotator", + "version": "dev" + } + ] }, { - "name": "methylong", - "version": "2.0.0" + "name": "pharokka_pharokka", + "path": "modules/nf-core/pharokka/pharokka/meta.yml", + "type": "module", + "meta": { + "name": "pharokka_pharokka", + "description": "Functional annotation of phages", + "keywords": ["pharokka", "phage", "function", "prokka", "bakta"], + "tools": [ + { + "pharokka": { + "description": "Fast Phage Annotation Program", + "homepage": "https://pharokka.readthedocs.io", + "documentation": "https://pharokka.readthedocs.io", + "tool_dev_url": "https://github.com/gbouras13/pharokka", + "doi": "10.1093/bioinformatics/btac776", + "licence": ["MIT"], + "identifier": "biotools:pharokka" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "phage_fasta": { + "type": "file", + "description": "A FASTA file containing phage sequence(s)", + "pattern": "*.{fasta,fna,fa}", + "ontologies": [] + } + } + ], + { + "pharokka_db": { + "type": "file", + "description": "Directory containing Pharokka's database", + "ontologies": [] + } + } + ], + "output": { + "cds_final_merged_output": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}_pharokka/${prefix}_cds_final_merged_output.tsv": { + "type": "file", + "description": "A file containing the final merged output of CDSs", + "pattern": "*_cds_final_merged_output.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "cds_functions": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}_pharokka/${prefix}_cds_functions.tsv": { + "type": "file", + "description": "A file that includes count of CDSs, tRNAs, CRISPRs, tmRNAs, and PHROG functions assigned to CDSs", + "pattern": "*_cds_functions.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "length_gc_cds_density": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}_pharokka/${prefix}_length_gc_cds_density.tsv": { + "type": "file", + "description": "A file containing the length, GC content, and CDS density of the phage genome", + "pattern": "*_length_gc_cds_density.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "card": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}_pharokka/${prefix}_top_hits_card.tsv": { + "type": "file", + "description": "OPTIONAL - A file containing any CARD database hits", + "pattern": "*top_hits_card.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "vfdb": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}_pharokka/${prefix}_top_hits_vfdb.tsv": { + "type": "file", + "description": "OPTIONAL - A file containing any VFDB database hits", + "pattern": "*top_hits_vfdb.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "mash": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}_pharokka/${prefix}_top_hits_mash_inphared.tsv": { + "type": "file", + "description": "OPTIONAL - File containing top hits to INPHARED database", + "pattern": "*_top_hits_mash_inphared.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "reoriented": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}_pharokka/${prefix}_genome_terminase_reoriented.fasta": { + "type": "file", + "description": "OPTIONAL - FASTA file reoriented to start with the large terminase subunit", + "pattern": "*_genome_terminase_reoriented.fasta", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@CarsonJM"], + "maintainers": ["@CarsonJM"] + }, + "pipelines": [ + { + "name": "phageannotator", + "version": "dev" + } + ] }, { - "name": "radseq", - "version": "dev" + "name": "phenoimager2mc", + "path": "modules/nf-core/phenoimager2mc/meta.yml", + "type": "module", + "meta": { + "name": "phenoimager2mc", + "description": "Formatting PhenoImager TIFF output files into stacked and normalized OME-TIFF files per cycle, compatible as ASHLAR and MCMICRO input.", + "keywords": ["imaging", "registration", "ome-tif", "Staging", "MCMICRO"], + "tools": [ + { + "phenoimager2mc": { + "description": "PhenoImager output conversion into a stacked and normalized OME-TIFF file per cycle.", + "homepage": "https://github.com/SchapiroLabor/phenoimager2mc", + "documentation": "https://github.com/SchapiroLabor/phenoimager2mc/README.md", + "tool_dev_url": "https://github.com/SchapiroLabor/phenoimager2mc", + "licence": ["GPL-2.0 license"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "tiles": { + "type": "list", + "description": "Folder or list with TIFF files of one cycle from PhenoImager" + } + } + ] + ], + "output": { + "tif": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.tif": { + "type": "file", + "description": "One output .tif file containing concatenated tiles of the cycle.", + "pattern": "*.{tif,tiff}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3591" + } + ] + } + } + ] + ], + "versions_phenoimager2mc": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "phenoimager2mc": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "phenoimager2mc --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_python": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "python": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python --version | sed -e \"s/Python //g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_ome_types": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "ome_types": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python -m pip show ome_types | sed -n \"s/Version: //p\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "phenoimager2mc": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "phenoimager2mc --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "python": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python --version | sed -e \"s/Python //g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "ome_types": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python -m pip show ome_types | sed -n \"s/Version: //p\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@chiarasch", "@kbestak"], + "maintainers": ["@chiarasch"] + } }, { - "name": "scnanoseq", - "version": "1.2.2" + "name": "phispy", + "path": "modules/nf-core/phispy/meta.yml", + "type": "module", + "meta": { + "name": "phispy", + "description": "Predict prophages in bacterial genomes", + "keywords": ["genomics", "virus", "phage", "prophage", "annotation", "identification"], + "tools": [ + { + "phispy": { + "description": "Prophage finder using multiple metrics", + "homepage": "https://github.com/linsalrob/PhiSpy/blob/master/README.md", + "documentation": "https://github.com/linsalrob/PhiSpy/blob/master/README.md", + "tool_dev_url": "https://github.com/linsalrob/PhiSpy/", + "doi": "10.1093/nar/gks406", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "gbk": { + "type": "file", + "description": "Genome file in .gbk or .gbff format.", + "pattern": "*.{gbk,gbff}", + "ontologies": [] + } + } + ] + ], + "output": { + "coordinates": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.tsv": { + "type": "file", + "description": "Coordinates of each prophage identified in the genome,\nand their att sites (if found).\n", + "pattern": "*.{tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "gbk": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.gb*": { + "type": "file", + "description": "A duplicate GenBank record that is the same as the input record,\nbut we have inserted the prophage information, including att\nsites into the record.\n", + "pattern": "*.{gbk,gbff}", + "ontologies": [] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.log": { + "type": "file", + "description": "File containing the PhiSpy execution log", + "pattern": "*.{log}", + "ontologies": [] + } + } + ] + ], + "information": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}_prophage_information.tsv": { + "type": "file", + "description": "File containing all the genes of the genome, one per line.\nThe tenth column describes how likely the gene is a phage gene.\n", + "pattern": "*.{tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "bacteria_fasta": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}_bacteria.fasta": { + "type": "file", + "description": "Genome with prophage regions masked with N.", + "pattern": "*.{fasta}", + "ontologies": [] + } + } + ] + ], + "bacteria_gbk": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}_bacteria.gbk": { + "type": "file", + "description": "Genome sequences identified as bacterial.", + "pattern": "*.{gbk}", + "ontologies": [] + } + } + ] + ], + "phage_fasta": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}_phage.fasta": { + "type": "file", + "description": "Phage sequences extracted from the genome.", + "pattern": "*.{fasta}", + "ontologies": [] + } + } + ] + ], + "phage_gbk": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}_phage.gbk": { + "type": "file", + "description": "Phage sequences extracted from the genome.", + "pattern": "*.{gbk}", + "ontologies": [] + } + } + ] + ], + "prophage_gff": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}_prophage.gff3": { + "type": "file", + "description": "Prophage information in GFF3 format.", + "pattern": "*.{gff3}", + "ontologies": [] + } + } + ] + ], + "prophage_tbl": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}_prophage.tbl": { + "type": "file", + "description": "File containing prophage number and its location in the genome.\n", + "pattern": "*.{tbl}", + "ontologies": [] + } + } + ] + ], + "prophage_tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}_prophage.tsv": { + "type": "file", + "description": "A file containing simpler version of the coordinates file,\nwith only prophage number, contig, start and stop.\n", + "pattern": "*.{tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@jvfe"], + "maintainers": ["@jvfe"] + } }, { - "name": "taxprofiler", - "version": "2.0.0" + "name": "phyloflash", + "path": "modules/nf-core/phyloflash/meta.yml", + "type": "module", + "meta": { + "name": "phyloflash", + "description": "phyloFlash is a pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.", + "keywords": ["metagenomics", "illumina datasets", "phylogenetic composition"], + "tools": [ + { + "phyloflash": { + "description": "phyloFlash is a pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.", + "homepage": "https://hrgv.github.io/phyloFlash/", + "documentation": "https://hrgv.github.io/phyloFlash/usage.html", + "tool_dev_url": "https://github.com/HRGV/phyloFlash", + "doi": "10.1128/mSystems.00920-20", + "licence": ["GPL v3"], + "identifier": "biotools:phyloflash" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "Channel containing single or paired-end reads", + "pattern": "*.{fastq.gz,fq.gz}", + "ontologies": [] + } + } + ], + { + "silva_db": { + "type": "directory", + "description": "Folder containing SILVA database" + } + }, + { + "univec_db": { + "type": "directory", + "description": "Folder containing UniVec database", + "pattern": "UniVec" + } + } + ], + "output": { + "results": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${meta.id}*/*": { + "type": "directory", + "description": "Folder containing the results of phyloFlash analysis", + "pattern": "${prefix}*" + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@abhi18av"], + "maintainers": ["@abhi18av"] + } }, { - "name": "viralmetagenome", - "version": "1.1.1" - } - ] - }, - { - "name": "minimap2_index", - "path": "modules/nf-core/minimap2/index/meta.yml", - "type": "module", - "meta": { - "name": "minimap2_index", - "description": "Provides fasta index required by minimap2 alignment.", - "keywords": [ - "index", - "fasta", - "reference" - ], - "tools": [ - { - "minimap2": { - "description": "A versatile pairwise aligner for genomic and spliced nucleotide sequences.\n", - "homepage": "https://github.com/lh3/minimap2", - "documentation": "https://github.com/lh3/minimap2#uguide", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + "name": "picard_addorreplacereadgroups", + "path": "modules/nf-core/picard/addorreplacereadgroups/meta.yml", + "type": "module", + "meta": { + "name": "picard_addorreplacereadgroups", + "description": "Assigns all the reads in a file to a single new read-group", + "keywords": ["add", "replace", "read-group", "picard"], + "tools": [ + { + "picard": { + "description": "A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS)\ndata and formats such as SAM/BAM/CRAM and VCF.\n", + "homepage": "https://broadinstitute.github.io/picard/", + "documentation": "https://gatk.broadinstitute.org/hc/en-us/articles/360037226472-AddOrReplaceReadGroups-Picard-", + "tool_dev_url": "https://github.com/broadinstitute/picard", + "licence": ["MIT"], + "identifier": "biotools:picard_tools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "Sequence reads file, can be SAM/BAM/CRAM format", + "pattern": "*.{bam,cram,sam}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference genome file", + "pattern": "*.{fasta,fa,fasta.gz,fa.gz}", + "ontologies": [] + } + }, + { + "fai": { + "type": "file", + "description": "Reference genome index file", + "pattern": "*.{fai,fasta.fai,fa.fai,fasta.gz.fai,fa.gz.fai}", + "ontologies": [] + } + } + ] + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Output BAM file", + "pattern": "*.{bam}", + "ontologies": [] + } + } + ] + ], + "bai": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bai": { + "type": "file", + "description": "An optional BAM index file", + "pattern": "*.{bai}", + "ontologies": [] + } + } + ] + ], + "cram": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.cram": { + "type": "file", + "description": "Output CRAM file", + "pattern": "*.{cram}", + "ontologies": [] + } + } + ] + ], + "versions_picard": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "picard": { + "type": "string", + "description": "The tool name" + } + }, + { + "picard AddOrReplaceReadGroups --version 2>&1 | sed -n 's/.*Version://p'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "picard": { + "type": "string", + "description": "The tool name" + } + }, + { + "picard AddOrReplaceReadGroups --version 2>&1 | sed -n 's/.*Version://p'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@sateeshperi", "@mjcipriano", "@hseabolt", "@cmatKhan", "@muffato"], + "maintainers": ["@sateeshperi", "@mjcipriano", "@hseabolt", "@cmatKhan", "@muffato"] }, - { - "fasta": { - "type": "file", - "description": "Reference database in FASTA format.\n", - "ontologies": [] - } - } - ] - ], - "output": { - "index": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.mmi": { - "type": "file", - "description": "Minimap2 fasta index.", - "pattern": "*.mmi", - "ontologies": [] - } - } - ] - ], - "versions_minimap2": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "minimap2": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "minimap2 --version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "minimap2": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "minimap2 --version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "methylseq", + "version": "4.2.0" + }, + { + "name": "pathogensurveillance", + "version": "1.1.0" + }, + { + "name": "raredisease", + "version": "3.0.0" + } ] - ] }, - "authors": [ - "@yuukiiwa", - "@drpatelh" - ], - "maintainers": [ - "@yuukiiwa", - "@drpatelh" - ] - }, - "pipelines": [ { - "name": "crisprseq", - "version": "2.3.0" + "name": "picard_bedtointervallist", + "path": "modules/nf-core/picard/bedtointervallist/meta.yml", + "type": "module", + "meta": { + "name": "picard_bedtointervallist", + "description": "Creates an interval list from a bed file and a reference dict", + "keywords": ["bed", "interval list", "picard", "convert"], + "tools": [ + { + "gatk4": { + "description": "Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools\nwith a primary focus on variant discovery and genotyping. Its powerful processing engine\nand high-performance computing features make it capable of taking on projects of any size.\n", + "homepage": "https://gatk.broadinstitute.org/hc/en-us", + "documentation": "https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s", + "doi": "10.1158/1538-7445.AM2017-3590", + "licence": ["Apache-2.0"], + "identifier": "biotools:picard_tools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "bed": { + "type": "file", + "description": "Input bed file", + "pattern": "*.bed", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome']\n" + } + }, + { + "dict": { + "type": "file", + "description": "Sequence dictionary", + "pattern": "*.dict", + "ontologies": [] + } + } + ] + ], + "output": { + "intervallist": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "*.intervallist": { + "type": "file", + "description": "gatk interval list file", + "pattern": "*.intervallist", + "ontologies": [] + } + } + ] + ], + "versions_picard": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "picard": { + "type": "string", + "description": "The tool name" + } + }, + { + "picard BedToIntervalList --version 2>&1 | sed -n 's/.*Version://p'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "picard": { + "type": "string", + "description": "The tool name" + } + }, + { + "picard BedToIntervalList --version 2>&1 | sed -n 's/.*Version://p'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@kevinmenden", "@matthdsm"], + "maintainers": ["@kevinmenden", "@matthdsm"] + }, + "pipelines": [ + { + "name": "methylseq", + "version": "4.2.0" + } + ] }, { - "name": "evexplorer", - "version": "dev" + "name": "picard_cleansam", + "path": "modules/nf-core/picard/cleansam/meta.yml", + "type": "module", + "meta": { + "name": "picard_cleansam", + "description": "Cleans the provided BAM, soft-clipping beyond-end-of-reference alignments and setting MAPQ to 0 for unmapped reads", + "keywords": ["clean", "bam", "picard", "sam", "clipping"], + "tools": [ + { + "picard": { + "description": "A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS)\ndata and formats such as SAM/BAM/CRAM and VCF.\n", + "homepage": "https://broadinstitute.github.io/picard/", + "documentation": "https://gatk.broadinstitute.org/hc/en-us/articles/360036491452-CleanSam-Picard-", + "tool_dev_url": "https://github.com/broadinstitute/picard", + "licence": ["MIT"], + "identifier": "biotools:picard_tools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file", + "pattern": "*.{bam}", + "ontologies": [] + } + } + ] + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Cleaned BAM file", + "pattern": "*.{bam}", + "ontologies": [] + } + } + ] + ], + "versions_picard": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "picard": { + "type": "string", + "description": "The tool name" + } + }, + { + "picard CleanSam --version 2>&1 | sed -n 's/.*Version://p'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "picard": { + "type": "string", + "description": "The tool name" + } + }, + { + "picard CleanSam --version 2>&1 | sed -n 's/.*Version://p'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@sateeshperi", "@mjcipriano", "@hseabolt"], + "maintainers": ["@sateeshperi", "@mjcipriano", "@hseabolt"] + } }, { - "name": "mag", - "version": "5.4.2" + "name": "picard_collectalignmentsummarymetrics", + "path": "modules/nf-core/picard/collectalignmentsummarymetrics/meta.yml", + "type": "module", + "meta": { + "name": "picard_collectalignmentsummarymetrics", + "description": "Collect metrics about the alignment summary of a paired-end library.", + "keywords": ["metrics", "alignment", "statistics", "bam"], + "tools": [ + { + "picard": { + "description": "Java tools for working with NGS data in the BAM format", + "homepage": "https://broadinstitute.github.io/picard/", + "documentation": "https://broadinstitute.github.io/picard/", + "tool_dev_url": "https://github.com/broadinstitute/picard", + "licence": ["MIT"], + "identifier": "biotools:picard_tools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Fasta file", + "pattern": "*.{fasta}", + "ontologies": [] + } + } + ] + ], + "output": { + "metrics": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "Standard alignment summary metrics", + "pattern": "*.txt", + "ontologies": [] + } + } + ] + ], + "versions_picard": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "picard": { + "type": "string", + "description": "The tool name" + } + }, + { + "picard CollectAlignmentSummaryMetrics --version 2>&1 | sed -n 's/.*Version://p'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "picard": { + "type": "string", + "description": "The tool name" + } + }, + { + "picard CollectAlignmentSummaryMetrics --version 2>&1 | sed -n 's/.*Version://p'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@mikefeixu", "@FerriolCalvet"], + "maintainers": ["@mikefeixu"] + } }, { - "name": "radseq", - "version": "dev" + "name": "picard_collecthsmetrics", + "path": "modules/nf-core/picard/collecthsmetrics/meta.yml", + "type": "module", + "meta": { + "name": "picard_collecthsmetrics", + "description": "Collects hybrid-selection (HS) metrics for a SAM or BAM file.", + "keywords": ["alignment", "metrics", "statistics", "insert", "hybrid-selection", "quality", "bam"], + "tools": [ + { + "picard": { + "description": "A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS)\ndata and formats such as SAM/BAM/CRAM and VCF.\n", + "homepage": "https://broadinstitute.github.io/picard/", + "documentation": "https://broadinstitute.github.io/picard/", + "tool_dev_url": "https://github.com/broadinstitute/picard/", + "licence": ["MIT"], + "identifier": "biotools:picard_tools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "An aligned BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}", + "ontologies": [] + } + }, + { + "bai": { + "type": "file", + "description": "Optional aligned BAM/CRAM/SAM file index", + "pattern": "*.{bai,crai,sai}", + "ontologies": [] + } + }, + { + "bait_intervals": { + "type": "file", + "description": "An interval file that contains the locations of the baits used.", + "pattern": "*.{interval_list,bed,bed.gz}", + "ontologies": [] + } + }, + { + "target_intervals": { + "type": "file", + "description": "An interval file that contains the locations of the targets.", + "pattern": "*.{interval_list,bed,bed.gz}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "ref": { + "type": "file", + "description": "A reference file to calculate dropout metrics measuring reduced representation of reads.\nOptional input.\n", + "pattern": "*.{fa,fa.gz,fasta,fasta.gz,fna,fna.gz}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "ref_fai": { + "type": "file", + "description": "Index of reference file. Only needed when reference is supplied.", + "pattern": "*.fai", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "ref_dict": { + "type": "file", + "description": "Sequence dictionary of FASTA file. Only needed when bed interval lists are supplied.", + "pattern": "*.dict", + "ontologies": [] + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "ref_gzi": { + "type": "file", + "description": "Index of reference file. Only needed when gzipped reference is supplied.", + "pattern": "*.gzi", + "ontologies": [] + } + } + ] + ], + "output": { + "metrics": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_metrics": { + "type": "file", + "description": "Alignment metrics files generated by picard", + "pattern": "*_{metrics}", + "ontologies": [] + } + } + ] + ], + "versions_picard": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "picard": { + "type": "string", + "description": "The tool name" + } + }, + { + "picard CollectHsMetrics --version 2>&1 | sed -n 's/.*Version://p'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "picard": { + "type": "string", + "description": "The tool name" + } + }, + { + "picard CollectHsMetrics --version 2>&1 | sed -n 's/.*Version://p'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@projectoriented", "@matthdsm"], + "maintainers": ["@projectoriented", "@matthdsm"] + }, + "pipelines": [ + { + "name": "methylseq", + "version": "4.2.0" + }, + { + "name": "raredisease", + "version": "3.0.0" + }, + { + "name": "seqinspector", + "version": "1.0.1" + }, + { + "name": "variantcatalogue", + "version": "dev" + } + ] }, { - "name": "scnanoseq", - "version": "1.2.2" + "name": "picard_collectinsertsizemetrics", + "path": "modules/nf-core/picard/collectinsertsizemetrics/meta.yml", + "type": "module", + "meta": { + "name": "picard_collectinsertsizemetrics", + "description": "Collect metrics about the insert size distribution of a paired-end library.", + "keywords": ["metrics", "alignment", "insert", "statistics", "bam"], + "tools": [ + { + "picard": { + "description": "Java tools for working with NGS data in the BAM format", + "homepage": "https://broadinstitute.github.io/picard/", + "documentation": "https://broadinstitute.github.io/picard/", + "tool_dev_url": "https://github.com/broadinstitute/picard", + "licence": ["MIT"], + "identifier": "biotools:picard_tools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}", + "ontologies": [] + } + } + ] + ], + "output": { + "metrics": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "Values used by Picard to generate the insert size histograms", + "pattern": "*.txt", + "ontologies": [] + } + } + ] + ], + "histogram": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.pdf": { + "type": "file", + "description": "Insert size histogram in PDF format", + "pattern": "*.pdf", + "ontologies": [] + } + } + ] + ], + "versions_picard": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "picard": { + "type": "string", + "description": "The tool name" + } + }, + { + "picard CollectInsertSizeMetrics --version 2>&1 | sed -n 's/.*Version://p'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "picard": { + "type": "string", + "description": "The tool name" + } + }, + { + "picard CollectInsertSizeMetrics --version 2>&1 | sed -n 's/.*Version://p'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@FerriolCalvet"], + "maintainers": ["@FerriolCalvet"] + }, + "pipelines": [ + { + "name": "rnafusion", + "version": "4.1.2" + } + ] }, { - "name": "taxprofiler", - "version": "2.0.0" + "name": "picard_collectmultiplemetrics", + "path": "modules/nf-core/picard/collectmultiplemetrics/meta.yml", + "type": "module", + "meta": { + "name": "picard_collectmultiplemetrics", + "description": "Collect multiple metrics from a BAM file", + "keywords": ["alignment", "metrics", "statistics", "insert", "quality", "bam"], + "tools": [ + { + "picard": { + "description": "A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS)\ndata and formats such as SAM/BAM/CRAM and VCF.\n", + "homepage": "https://broadinstitute.github.io/picard/", + "documentation": "https://broadinstitute.github.io/picard/", + "licence": ["MIT"], + "identifier": "biotools:picard_tools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "SAM/BAM/CRAM file", + "pattern": "*.{sam,bam,cram}", + "ontologies": [] + } + }, + { + "bai": { + "type": "file", + "description": "Optional SAM/BAM/CRAM file index", + "pattern": "*.{sai,bai,crai}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome']\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Genome fasta file", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome']\n" + } + }, + { + "fai": { + "type": "file", + "description": "Index of FASTA file. Only needed when fasta is supplied.", + "pattern": "*.fai", + "ontologies": [] + } + } + ] + ], + "output": { + "metrics": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_metrics": { + "type": "file", + "description": "Alignment metrics files generated by picard", + "pattern": "*_{metrics}", + "ontologies": [] + } + } + ] + ], + "pdf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.pdf": { + "type": "file", + "description": "PDF plots of metrics", + "pattern": "*.{pdf}", + "ontologies": [] + } + } + ] + ], + "versions_picard": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "picard": { + "type": "string", + "description": "The tool name" + } + }, + { + "picard CollectMultipleMetrics --version 2>&1 | sed -n 's/.*Version://p'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "picard": { + "type": "string", + "description": "The tool name" + } + }, + { + "picard CollectMultipleMetrics --version 2>&1 | sed -n 's/.*Version://p'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@drpatelh"], + "maintainers": ["@drpatelh"] + }, + "pipelines": [ + { + "name": "atacseq", + "version": "2.1.2" + }, + { + "name": "callingcards", + "version": "1.0.0" + }, + { + "name": "chipseq", + "version": "2.1.0" + }, + { + "name": "raredisease", + "version": "3.0.0" + }, + { + "name": "seqinspector", + "version": "1.0.1" + }, + { + "name": "ssds", + "version": "dev" + }, + { + "name": "viralmetagenome", + "version": "1.1.1" + }, + { + "name": "viralrecon", + "version": "3.0.0" + } + ] }, { - "name": "viralmetagenome", - "version": "1.1.1" - } - ] - }, - { - "name": "miniprot_align", - "path": "modules/nf-core/miniprot/align/meta.yml", - "type": "module", - "meta": { - "name": "miniprot_align", - "description": "A versatile pairwise aligner for genomic and spliced nucleotide sequences", - "keywords": [ - "align", - "fasta", - "protein", - "genome", - "paf", - "gff" - ], - "tools": [ - { - "miniprot": { - "description": "A versatile pairwise aligner for genomic and protein sequences.\n", - "homepage": "https://github.com/lh3/miniprot", - "documentation": "https://github.com/lh3/miniprot", - "licence": [ - "MIT" - ], - "identifier": "biotools:miniprot" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + "name": "picard_collectrnaseqmetrics", + "path": "modules/nf-core/picard/collectrnaseqmetrics/meta.yml", + "type": "module", + "meta": { + "name": "picard_collectrnaseqmetrics", + "description": "Collect metrics from a RNAseq BAM file", + "keywords": ["rna", "bam", "metrics", "alignment", "statistics", "quality"], + "tools": [ + { + "picard": { + "description": "A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS)\ndata and formats such as SAM/BAM/CRAM and VCF.\n", + "homepage": "https://broadinstitute.github.io/picard/", + "documentation": "https://broadinstitute.github.io/picard/", + "tool_dev_url": "https://github.com/broadinstitute/picard", + "licence": ["MIT"], + "identifier": "biotools:picard_tools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false, strandedness:true ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/SAM file", + "pattern": "*.{bam,sam}", + "ontologies": [] + } + } + ], + { + "ref_flat": { + "type": "file", + "description": "Genome ref_flat file", + "ontologies": [] + } + }, + { + "fasta": { + "type": "file", + "description": "Genome fasta file", + "ontologies": [] + } + }, + { + "rrna_intervals": { + "type": "file", + "description": "Interval file of ribosomal RNA regions", + "ontologies": [] + } + } + ], + "output": { + "metrics": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.rna_metrics": { + "type": "file", + "description": "RNA alignment metrics files generated by picard", + "pattern": "*.rna_metrics", + "ontologies": [] + } + } + ] + ], + "pdf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.pdf": { + "type": "file", + "description": "Plot normalized position vs. coverage in a pdf file generated by picard", + "ontologies": [] + } + } + ] + ], + "versions_picard": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "picard": { + "type": "string", + "description": "The tool name" + } + }, + { + "picard CollectRnaSeqMetrics --version 2>&1 | sed -n 's/.*Version://p'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "picard": { + "type": "string", + "description": "The tool name" + } + }, + { + "picard CollectRnaSeqMetrics --version 2>&1 | sed -n 's/.*Version://p'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@anoronh4"], + "maintainers": ["@anoronh4"] }, - { - "pep": { - "type": "file", - "description": "a fasta file contains one or multiple protein sequences", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\n" - } - }, - { - "ref": { - "type": "file", - "description": "Reference database in FASTA format or miniprot index format.", - "ontologies": [] - } - } - ] - ], - "output": { - "paf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.paf": { - "type": "file", - "description": "Alignment in PAF format", - "pattern": "*.paf", - "ontologies": [] - } - } - ] - ], - "gff": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.gff": { - "type": "file", - "description": "Alignment in gff format", - "pattern": "*.gff", - "ontologies": [] - } - } - ] - ], - "versions_miniprot": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "miniprot": { - "type": "string", - "description": "The tool name" - } - }, - { - "miniprot --version": { - "type": "eval", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "miniprot": { - "type": "string", - "description": "The tool name" - } - }, - { - "miniprot --version": { - "type": "eval", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@yumisims", - "@muffato" - ], - "maintainers": [ - "@yumisims", - "@muffato" - ] - } - }, - { - "name": "miniprot_index", - "path": "modules/nf-core/miniprot/index/meta.yml", - "type": "module", - "meta": { - "name": "miniprot_index", - "description": "Provides fasta index required by miniprot alignment.", - "keywords": [ - "index", - "fasta", - "genome", - "reference" - ], - "tools": [ - { - "miniprot": { - "description": "A versatile pairwise aligner for genomic and protein sequences.\n", - "homepage": "https://github.com/lh3/miniprot", - "documentation": "https://github.com/lh3/miniprot", - "licence": [ - "MIT" - ], - "identifier": "biotools:miniprot" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference database in FASTA format.\n", - "ontologies": [] - } - } - ] - ], - "output": { - "index": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.mpi": { - "type": "file", - "description": "miniprot fasta index.", - "pattern": "*.mpi", - 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"description": "miRanda is an algorithm for finding genomic targets for microRNAs", - "keywords": [ - "microrna", - "mirna", - "target prediction" - ], - "tools": [ - { - "miranda": { - "description": "An algorithm for finding genomic targets for microRNAs", - "homepage": "https://cbio.mskcc.org/miRNA2003/miranda.html", - "documentation": "https://cbio.mskcc.org/miRNA2003/miranda.html", - "doi": "10.1186/gb-2003-5-1-r1", - "licence": [ - "GNU Public License" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "query": { - "type": "file", - "description": "FASTA file containing the microRNA query sequences", - "pattern": "*.{fa,fasta}", - "ontologies": [] - } - } - ], - { - "mirbase": { - "type": "file", - "description": "FASTA file containing the sequence(s) to be scanned", - "pattern": "*.{fa,fasta}", - "ontologies": [] - } - } - ], - "output": { - "txt": [ - 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"keywords": [ - "mirdeep2", - "mapper", - "RNA sequencing" - ], - "tools": [ - { - "mirdeep2": { - "description": "miRDeep2 Mapper (`mapper.pl`) is part of the miRDeep2 suite. It collapses identical reads, maps them to a reference genome, and outputs both collapsed FASTA and ARF files for downstream miRNA detection and analysis.\n", - "homepage": "https://www.mdc-berlin.de/content/mirdeep2-documentation", - "documentation": "https://www.mdc-berlin.de/content/mirdeep2-documentation", - "tool_dev_url": "https://github.com/rajewsky-lab/mirdeep2", - "doi": "10.1093/nar/gkn491", - "licence": [ - "GPL V3" - ], - "identifier": "biotools:mirdeep2" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information, e.g. `[ id:'sample1', single_end:false ]`" - } - }, - { - "reads": { - "type": "file", - "description": "File containing the raw sequencing reads that need to be collapsed and mapped to a reference genome.", - "pattern": "*.fa", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing information about the genome index." - } - }, - { - "index": { - "type": "file", - "description": "Path to the genome index file used for mapping the reads to the genome.", - "pattern": "*", - "ontologies": [] - } - } - ] - ], - "output": { - "outputs": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information, e.g. `[ id:'sample1', single_end:false ]`" - } - }, - { - "*.fa": { - "type": "file", - "description": "Collapsed reads in FASTA format.", - "pattern": "*.fa", - "ontologies": [] - } - }, - { - "*.arf": { - "type": "file", - "description": "Alignment Read Format (ARF) file containing the mapping of reads to the genome.", - "pattern": "*.arf", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions for tracking.", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@atrigila" - ], - "maintainers": [ - "@atrigila" - ] - }, - "pipelines": [ - { - "name": "smrnaseq", - "version": "2.4.1" - } - ] - }, - { - "name": "mirdeep2_mirdeep2", - "path": "modules/nf-core/mirdeep2/mirdeep2/meta.yml", - "type": "module", - "meta": { - "name": "mirdeep2_mirdeep2", - "description": "miRDeep2 is a tool for identifying known and novel miRNAs in deep sequencing data by analyzing sequenced RNAs. It integrates the mapping of sequencing reads to the genome and predicts miRNA precursors and mature miRNAs.\n", - "keywords": [ - "mirdeep2", - "miRNA", - "RNA sequencing" - ], - "tools": [ - { - "mirdeep2": { - "description": "miRDeep2 is a tool that discovers microRNA genes by analyzing sequenced RNAs.\nIt includes three main scripts: `miRDeep2.pl`, `mapper.pl`, and `quantifier.pl` for comprehensive miRNA detection and quantification.\n", - "homepage": "https://www.mdc-berlin.de/content/mirdeep2-documentation", - "documentation": "https://www.mdc-berlin.de/content/mirdeep2-documentation", - "tool_dev_url": "https://github.com/rajewsky-lab/mirdeep2", - "doi": "10.1093/nar/gkn491", - "licence": [ - "GPL V3" - ], - "identifier": "biotools:mirdeep2" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information, e.g. `[ id:'sample1', single_end:false ]`" - } - }, - { - "processed_reads": { - "type": "file", - "description": "FASTA file containing the processed sequencing reads.", - 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"description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "hairpin": { - "type": "file", - "description": "Hairpin file", - "pattern": "*.{fa,fasta}", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "gtf": { - "type": "file", - "description": "GTF file", - "pattern": "*.{gtf}", - "ontologies": [] - } - }, - { - "species": { - "type": "string", - "description": "Species name of the GTF file" - } - } - ] - ], - "output": { - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "counts/*.tsv": { - "type": "file", - "description": "TSV file", - "pattern": "*.{tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions": [ - { - 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Each sample is characterized by profiling sequencing quality, read length, sequencing depth and miRNA complexity and also the amounts of miRNAs versus undesirable sequences (derived from tRNAs, rRNAs and sequencing artifacts). In addition to these routine quality control (QC) analyses, miRTrace can accurately and sensitively resolve taxonomic origins of small RNA-Seq data based on the composition of clade-specific miRNAs. This feature can be used to detect cross-clade contaminations in typical lab settings. 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Each row consists of the following columns \"FASTQ file path, id, adapter, PHRED-ASCII-offset\".", - "ontologies": [] - } - } - ], - { - "mirtrace_species": { - "type": "string", - "description": "Target species in microRNA sequencing data (miRbase encoding, e.g. “hsa” for Homo sapiens)" - } - } - ], - "output": { - "html": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.html": { - "type": "file", - "description": "HTML file", - "pattern": "*.{html}", - "ontologies": [] - } - } - ] - ], - "json": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.json": { - "type": "file", - "description": "JSON file", - "pattern": "*.{json}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "TSV file", - "pattern": "*.{tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "all_fa": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "qc_passed_reads.all.collapsed/*.{fa,fasta}": { - "type": "file", - "description": "QC-passed reads in FASTA file. Identical reads are collapsed. Entries are sorted by abundance.", - "pattern": "*.{fa,fasta}", - "ontologies": [] - } - } - ] - ], - "rnatype_unknown_fa": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "qc_passed_reads.rnatype_unknown.collapsed/*.{fa,fasta}": { - "type": "file", - "description": "Unknown RNA type QC-passed reads in FASTA file. Identical reads are collapsed. 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} - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + }, + { + "name": "picard_collectwgsmetrics", + "path": "modules/nf-core/picard/collectwgsmetrics/meta.yml", + "type": "module", + "meta": { + "name": "picard_collectwgsmetrics", + "description": "Collect metrics about coverage and performance of whole genome sequencing (WGS) experiments.", + "keywords": ["alignment", "metrics", "statistics", "quality", "bam"], + "tools": [ + { + "picard": { + "description": "A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS)\ndata and formats such as SAM/BAM/CRAM and VCF.\n", + "homepage": "https://broadinstitute.github.io/picard/", + "documentation": "https://broadinstitute.github.io/picard/", + "licence": ["MIT"], + "identifier": "biotools:picard_tools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "Aligned reads file", + "pattern": "*.{bam, cram}", + "ontologies": [] + } + }, + { + "bai": { + "type": "file", + "description": "(Optional) Aligned reads file index", + "pattern": "*.{bai,crai}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Genome fasta file", + "pattern": "*.{fa,fasta,fna}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Genome fasta file index", + "pattern": "*.{fai}", + "ontologies": [] + } + } + ], + { + "intervallist": { + "type": "file", + "description": "Picard Interval List. Defines which contigs to include. Can be generated from a BED file with GATK BedToIntervalList.", + "ontologies": [] + } + } + ], + "output": { + "metrics": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_metrics": { + "type": "file", + "description": "Alignment metrics files generated by picard", + "pattern": "*_{metrics}", + "ontologies": [] + } + } + ] + ], + "versions_picard": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "picard": { + "type": "string", + "description": "The tool name" + } + }, + { + "picard CollectWgsMetrics --version 2>&1 | sed -n 's/.*Version://p'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "picard": { + "type": "string", + "description": "The tool name" + } + }, + { + "picard CollectWgsMetrics --version 2>&1 | sed -n 's/.*Version://p'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@drpatelh", "@flowuenne", "@lassefolkersen", "@ramprasadn"], + "maintainers": ["@drpatelh", "@flowuenne", "@lassefolkersen", "@ramprasadn"] }, - { - "species": { - "type": "string", - "description": "Latin name of the species for which a mitochondrial genome should be fetched", - "pattern": "[A-Z]?[a-z]* [a-z]*" - } - } - ] - ], - "output": { - "reference": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.fasta": { - "type": "file", - "description": "Downloaded mitochondrial genome in Fasta format", - "pattern": "*.{fasta,fa}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - }, - { - "*.gb": { - "type": "file", - "description": "Downloaded mitochondrial genome in Genbank format", - "pattern": "*.gb", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1936" - } - ] - } - } - ] - ], - "versions_mitohifi": [ - [ - { - "${task.process}": { - "type": "string", - "description": "Name of the process" - } - }, - { - "mitohifi": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "echo 3.2.3": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "Name of the process" - } - }, - { - "mitohifi": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "echo 3.2.3": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "raredisease", + "version": "3.0.0" + }, + { + "name": "rnafusion", + "version": "4.1.2" + }, + { + "name": "variantcatalogue", + "version": "dev" + } ] - ] - }, - "authors": [ - "@verku" - ], - "maintainers": [ - "@verku" - ] - } - }, - { - "name": "mitohifi_mitohifi", - "path": "modules/nf-core/mitohifi/mitohifi/meta.yml", - "type": "module", - "meta": { - "name": "MITOHIFI_MITOHIFI", - "description": "A python workflow that assembles mitogenomes from Pacbio HiFi reads", - "keywords": [ - "mitochondrion", - "chloroplast", - "PacBio" - ], - "tools": [ - { - "mitohifi.py": { - "description": "A python workflow that assembles mitogenomes from Pacbio HiFi reads", - "homepage": "https://github.com/marcelauliano/MitoHiFi", - "documentation": "https://github.com/marcelauliano/MitoHiFi", - "tool_dev_url": "https://github.com/marcelauliano/MitoHiFi", - "doi": "10.1101/2022.12.23.521667", - "licence": [ - "MIT" - ], - "identifier": "biotools:mitohifi" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "Path to PacBio HiFi reads or fasta contigs", - "pattern": "*.{fa,fa.gz,fasta,fasta.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "ref_fa": { - "type": "file", - "description": "Reference mitochondrial genome to align reads or contigs against", - "pattern": "*.{fa,fasta}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } + }, + { + "name": "picard_createsequencedictionary", + "path": "modules/nf-core/picard/createsequencedictionary/meta.yml", + "type": "module", + "meta": { + "name": "picard_createsequencedictionary", + "description": "Creates a sequence dictionary for a reference sequence.", + "keywords": ["sequence", "dictionary", "picard"], + "tools": [ + { + "picard": { + "description": "Creates a sequence dictionary file (with \".dict\" extension) from a reference sequence provided in FASTA format, which is required by many processing and analysis tools. The output file contains a header but no SAMRecords, and the header contains only sequence records.\n", + "homepage": "https://broadinstitute.github.io/picard/", + "documentation": "https://gatk.broadinstitute.org/hc/en-us/articles/360036712531-CreateSequenceDictionary-Picard-", + "tool_dev_url": "https://github.com/broadinstitute/picard", + "licence": ["MIT"], + "identifier": "biotools:picard_tools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The reference fasta file", + "pattern": "*.fasta", + "ontologies": [] + } + } + ] + ], + "output": { + "reference_dict": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.dict": { + "type": "file", + "description": "picard dictionary file", + "pattern": "*.{dict}", + "ontologies": [] + } + } + ] + ], + "versions_picard": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "picard": { + "type": "string", + "description": "The tool name" + } + }, + { + "picard CreateSequenceDictionary --version 2>&1 | sed -n 's/.*Version://p'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "picard": { + "type": "string", + "description": "The tool name" + } + }, + { + "picard CreateSequenceDictionary --version 2>&1 | sed -n 's/.*Version://p'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@sateeshperi", "@mjcipriano", "@hseabolt"], + "maintainers": ["@sateeshperi", "@mjcipriano", "@hseabolt"] }, - { - "ref_gb": { - "type": "file", - "description": "Reference mitochondrial genome annotation", - "pattern": "*.{gb}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1936" - } - ] - } - } - ], - { - "input_mode": { - "type": "string", - "description": "Specifies type of input - reads or contigs", - "pattern": "{reads,contigs}" - } - }, - { - "mito_code": { - "type": "integer", - "description": "Integer reference number of mitochondrial genetic code - see\nhttps://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details.\n" - } - } - ], - "output": { - "fasta": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "final_mitogenome.fasta": { - "type": "file", - "description": "Fasta file containing final chosen mitochondrial sequence", - "pattern": "final_mitogenome.fasta", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ], - "stats": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "contigs_stats.tsv": { - "type": "file", - "description": "Statistics of all identified mitochondrial contigs", - "pattern": "contigs_stats.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "gb": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "final_mitogenome.gb": { - "type": "file", - "description": "GB annotation file of final chosen mitochondrial sequence,\nif Mitofinder mode was used for annotation.\n", - "pattern": "final_mitogenome.gb", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1936" - } - ] - } - } - ] - ], - "gff": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "final_mitogenome.gff": { - "type": "file", - "description": "GB annotation file of final chosen mitochondrial sequence,\nif Mitos mode was used for annotation.\n", - "pattern": "final_mitogenome.gff", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1975" - } - ] - } - } - ] - ], - "all_potential_contigs": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "all_potential_contigs.fa": { - "type": "file", - "description": "Fasta file containing sequences of all potential mitogenome contigs", - "pattern": "all_potential_contigs.fa", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ], - "contigs_annotations": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "contigs_annotations.png": { - "type": "file", - "description": "Graphical representation of annotated genes and tRNAs", - "pattern": "contigs_annotations.png", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3603" - } - ] - } - } - ] - ], - "contigs_circularization": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "contigs_circularization/": { - "type": "directory", - "description": "Contains circularization reports", - "pattern": "contigs_circularization/" - } - } - ] - ], - "contigs_filtering": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "contigs_filtering/": { - "type": "directory", - "description": "Contains files with initial blast matches", - "pattern": "contigs_filtering/" - } - } - ] - ], - "coverage_mapping": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "coverage_mapping/": { - "type": "directory", - "description": "Contains statistics on coverage mapping", - "pattern": "coverage_mapping/" - } - } - ] - ], - "coverage_plot": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "coverage_plot.png": { - "type": "file", - "description": "Read coverage plot for mitochondrial contigs", - "pattern": "coverage_plot.png", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3603" - } - ] - } - } - ] - ], - "final_mitogenome_annotation": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "final_mitogenome.annotation.png": { - "type": "file", - "description": "Graphical representation of annotated genes for the final\nmitogenome contig\n", - "pattern": "final_mitogenome.annotation.png", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3603" - } - ] - } - } - ] - ], - "final_mitogenome_choice": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "final_mitogenome_choice/": { - "type": "directory", - "description": "Files with potential contigs clusterings and alignments", - "pattern": "final_mitogenome_choice/" - } - } - ] - ], - "final_mitogenome_coverage": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "final_mitogenome.coverage.png": { - "type": "file", - "description": "Graphical representation of reads coverage plot for the\nfinal mitogenome contig\n", - "pattern": "final_mitogenome.coverage.png", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3603" - } - ] - } - } - ] - ], - "potential_contigs": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "potential_contigs/": { - "type": "directory", - "description": "Files with sequences and annotations of the potential contigs", - "pattern": "potential_contigs/" - } - } - ] - ], - "reads_mapping_and_assembly": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads_mapping_and_assembly/": { - "type": "directory", - "description": "Read mapping files for run from the raw reads", - "pattern": "reads_mapping_and_assembly/" - } - } - ] - ], - "shared_genes": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "shared_genes.tsv": { - "type": "directory", - "description": "Report on genes shared with the reference genome", - "pattern": "shared_genes.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.log": { - "type": "directory", - "description": "Log file describing Mitohifi run", - "pattern": "*.log", - "ontologies": [ - { - "edam": "http://edamontology.org/data_3671" - } - ] - } - } - ] - ], - "all_files": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*": { - "type": "file", - "description": "All files output by Mitohifi in a single channel.", - "ontologies": [] - } - } - ] - ], - "versions_mitohifi": [ - [ - { - "${task.process}": { - "type": "string", - "description": "Name of the process" - } - }, - { - "mitohifi": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "echo 3.2.3": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "Name of the process" - } - }, - { - "mitohifi": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "echo 3.2.3": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "methylseq", + "version": "4.2.0" + }, + { + "name": "pathogensurveillance", + "version": "1.1.0" + }, + { + "name": "seqinspector", + "version": "1.0.1" + }, + { + "name": "variantbenchmarking", + "version": "1.5.0" + } ] - ] - }, - "authors": [ - "@ksenia-krasheninnikova", - "@prototaxites" - ], - "maintainers": [ - "@ksenia-krasheninnikova" - ] - } - }, - { - "name": "mitorsaw_haplotype", - "path": "modules/nf-core/mitorsaw/haplotype/meta.yml", - "type": "module", - "meta": { - "name": "mitorsaw_haplotype", - "description": "Mitorsaw analyses mitochondrial variants and identifies heteroplasmy and homoplasmy", - "keywords": [ - "heteroplasmy", - "homoplasmy", - "mitochondrial", - "mitorsaw", - "haplotype" - ], - "tools": [ - { - "mitorsaw": { - "description": "A tool for mitochondrial analysis for HiFi sequencing data", - "homepage": "https://github.com/PacificBiosciences/mitorsaw", - "documentation": "https://github.com/PacificBiosciences/mitorsaw/tree/main/docs", - "tool_dev_url": "https://github.com/PacificBiosciences/mitorsaw", - "licence": [ - "Pacific Biosciences Software License Agreement" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM file", - "pattern": "*.bam", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - }, - { - "bai": { - "type": "file", - "description": "BAM index file", - "pattern": "*.bai", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3327" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. `[ id:'genome' ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome in FASTA format", - "pattern": "*.{fa,fasta}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - }, - { - "fai": { - "type": "file", - "description": "Reference genome index file", - "pattern": "*.fai", - "ontologies": [] - } - } - ], - { - "include_hap_stats": { - "type": "boolean", - "description": "Whether to include haplotype statistics output file", - "default": false - } - }, - { - "include_debug_output": { - "type": "boolean", - "description": "Whether to generate debug output files", - "default": false + }, + { + "name": "picard_crosscheckfingerprints", + "path": "modules/nf-core/picard/crosscheckfingerprints/meta.yml", + "type": "module", + "meta": { + "name": "picard_crosscheckfingerprints", + "description": "Checks that all data in the set of input files appear to come from the same individual", + "keywords": ["alignment", "metrics", "statistics", "fingerprint", "bam"], + "tools": [ + { + "picard": { + "description": "A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS)\ndata and formats such as SAM/BAM/CRAM and VCF.\n", + "homepage": "https://broadinstitute.github.io/picard/", + "documentation": "https://broadinstitute.github.io/picard/", + "tool_dev_url": "https://github.com/broadinstitute/picard/", + "licence": ["MIT"], + "identifier": "biotools:picard_tools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input1": { + "type": "file", + "description": "List containing 1 or more bam/vcf files or a file containing filepaths", + "pattern": "*.{bam,vcf,vcf.gz,txt,fofn}", + "ontologies": [] + } + }, + { + "input1_index": { + "type": "file", + "description": "List containing 1 or more bam/vcf files indexes", + "pattern": "*.{bai,csi,crai,tbi}", + "ontologies": [] + } + }, + { + "input2": { + "type": "file", + "description": "Optional list containing 1 or more bam/vcf files or a file containing filepaths", + "pattern": "*.{bam,vcf,vcf.gz,txt,fofn}", + "ontologies": [] + } + }, + { + "input2_index": { + "type": "file", + "description": "List containing 1 or more bam/vcf files indexes", + "pattern": "*.{bai,csi,crai,tbi}", + "ontologies": [] + } + }, + { + "haplotype_map": { + "type": "file", + "description": "Haplotype map file", + "pattern": "*.{txt,vcf,vcf.gz}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference genome file", + "pattern": "*.{fasta,fa,fasta.gz,fa.gz}", + "ontologies": [] + } + } + ] + ], + "output": { + "crosscheck_metrics": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.crosscheck_metrics.txt": { + "type": "file", + "description": "Metrics created by crosscheckfingerprints", + "pattern": "*.{crosscheck_metrics.txt}", + "ontologies": [] + } + } + ] + ], + "versions_picard": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "picard": { + "type": "string", + "description": "The tool name" + } + }, + { + "picard CrosscheckFingerprints --version 2>&1 | sed -n 's/.*Version://p'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "picard": { + "type": "string", + "description": "The tool name" + } + }, + { + "picard CrosscheckFingerprints --version 2>&1 | sed -n 's/.*Version://p'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@matthdsm"], + "maintainers": ["@matthdsm"] } - } - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample1' ]\n" - } - }, - { - "*${prefix}.vcf.gz": { - "type": "file", - "description": "Compressed VCF file containing haplotype information", - "pattern": "*.vcf.gz", - "ontologies": [ + }, + { + "name": "picard_extractfingerprint", + "path": "modules/nf-core/picard/extractfingerprint/meta.yml", + "type": "module", + "meta": { + "name": "picard_extractfingerprint", + "description": "Computes/Extracts the fingerprint genotype likelihoods from the supplied file. It is given as a list of PLs at the fingerprinting sites.", + "keywords": ["picard", "extract", "fingerprint", "bam"], + "tools": [ + { + "picard": { + "description": "A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS)\ndata and formats such as SAM/BAM/CRAM and VCF.\n", + "homepage": "https://broadinstitute.github.io/picard/", + "documentation": "https://broadinstitute.github.io/picard/", + "tool_dev_url": "https://github.com/broadinstitute/picard/", + "licence": ["MIT"], + "identifier": "biotools:picard_tools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "file", + "description": "Input SAM/BAM/CRAM file\n", + "ontologies": [] + } + }, + { + "bam": { + "type": "file", + "description": "BAM file", + "pattern": "*.{bam}", + "ontologies": [] + } + }, + { + "bai": { + "type": "file", + "description": "BAM index file", + "pattern": "*.{bai}", + "ontologies": [] + } + } + ], + { + "haplotype_map": { + "type": "file", + "description": "A file of haplotype information. The file lists a set of SNPs, optionally arranged in high-LD blocks, to be used for fingerprinting.\nSee https://software.broadinstitute.org/gatk/documentation/article?id=9526 for details.\n", + "pattern": "*.{txt,vcf,vcf.gz}", + "ontologies": [] + } + }, + { + "fasta": { + "type": "file", + "description": "Reference sequence file", + "pattern": "*.{fasta,fna,fa}", + "ontologies": [] + } + }, { - "edam": "http://edamontology.org/format_3016" + "fasta_fai": { + "type": "file", + "description": "Reference sequence index file", + "pattern": "*.{fai}", + "ontologies": [] + } }, { - "edam": "http://edamontology.org/format_3989" + "sequence_dictionary": { + "type": "file", + "description": "Reference sequence dictionary file", + "ontologies": [] + } } - ] - } - } - ] - ], - "tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample1' ]\n" - } - }, - { - "*${prefix}.vcf.gz.tbi": { - "type": "file", - "description": "Index file for the compressed VCF file", - "pattern": "*.vcf.gz.tbi", - "ontologies": [] - } - } - ] - ], - "stats": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample1' ]\n" - } - }, - { - "${prefix}.json": { - "type": "file", - "description": "Mitorsaw statistics in JSON format", - "pattern": "*.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "coverage_stats": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample1' ]\n" - } - }, - { - "${prefix}_debug/coverage_stats.json": { - "type": "file", - "description": "Coverage statistics in JSON format", - "pattern": "coverage_stats.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "sequences_chrM": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample1' ]\n" - } - }, - { - "${prefix}_debug/sequences_chrM.fa": { - "type": "file", - "description": "Haplotype sequences in FASTA format", - "pattern": "sequences_chrM.fa", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ], - "custom_alignments_bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample1' ]\n" - } - }, - { - "${prefix}_debug/mito_igv_custom/custom_alignments.bam": { - "type": "file", - "description": "Custom alignments in BAM format", - "pattern": "custom_alignments.bam", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - } - ] - ], - "custom_alignments_bai": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample1' ]\n" - } - }, - { - "${prefix}_debug/mito_igv_custom/custom_alignments.bam.bai": { - "type": "file", - "description": "Custom alignments index file", - "pattern": "custom_alignments.bam.bai", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3327" - } - ] - } - } - ] - ], - "igv_session": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample1' ]\n" - } - }, - { - "${prefix}_debug/mito_igv_custom/custom_igv_session.xml": { - "type": "file", - "description": "IGV session file in XML format", - "pattern": "custom_igv_session.xml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2332" - } - ] - } - } - ] - ], - "custom_ref_fa": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample1' ]\n" - } - }, - { - "${prefix}_debug/mito_igv_custom/custom_reference.fa": { - "type": "file", - "description": "Custom reference genome in FASTA format", - "pattern": "custom_reference.fa", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ], - "custom_ref_fai": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample1' ]\n" - } - }, - { - "${prefix}_debug/mito_igv_custom/custom_reference.fa.fai": { - "type": "file", - "description": "Custom reference genome index file", - "pattern": "custom_reference.fa.fai", - "ontologies": [] - } - } - ] - ], - "custom_regions": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample1' ]\n" - } - }, - { - "${prefix}_debug/mito_igv_custom/custom_regions.bed": { - "type": "file", - "description": "Custom regions in BED format", - "pattern": "custom_regions.bed", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3003" - } - ] - } - } - ] - ], - "versions_mitorsaw": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "mitorsaw": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "mitorsaw --version | sed 's/mitorsaw //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "mitorsaw": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "mitorsaw --version | sed 's/mitorsaw //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@eliottBo" - ], - "maintainers": [ - "@eliottBo" - ] - } - }, - { - "name": "mlst", - "path": "modules/nf-core/mlst/meta.yml", - "type": "module", - "meta": { - "name": "mlst", - "description": "Run Torsten Seemann's classic MLST on a genome assembly", - "keywords": [ - "mlst", - "typing", - "bacteria", - "assembly" - ], - "tools": [ - { - "mlst": { - "description": "Scan contig files against PubMLST typing schemes", - "homepage": "https://github.com/tseemann/mlst", - "licence": [ - "GPL v2" - ], - "identifier": "biotools:mlst" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Assembly fasta file", - "pattern": "*.{fasta,fa,fna}", - "ontologies": [] - } - } - ] - ], - "output": { - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "MLST calls in tsv format", - "pattern": "*.{tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_mlst": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "mlst": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "mlst --version 2>&1 | sed \"s/mlst //\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "mlst": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "mlst --version 2>&1 | sed \"s/mlst //\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@lskatz", - "@tseemann" - ], - "maintainers": [ - "@lskatz", - "@tseemann" - ] - } - }, - { - "name": "mmseqs_cluster", - "path": "modules/nf-core/mmseqs/cluster/meta.yml", - "type": "module", - "meta": { - "name": "mmseqs_cluster", - "description": "Cluster sequences using MMSeqs2 cluster.", - "keywords": [ - "protein sequence", - "databases", - "clustering", - "searching", - "indexing", - "mmseqs2" - ], - "tools": [ - { - "mmseqs": { - "description": "MMseqs2: ultra fast and sensitive sequence search and clustering suite", - "homepage": "https://github.com/soedinglab/MMseqs2", - "documentation": "https://mmseqs.com/latest/userguide.pdf", - "tool_dev_url": "https://github.com/soedinglab/MMseqs2", - "doi": "10.1093/bioinformatics/btw006", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:mmseqs" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "db_input": { - "type": "file", - "description": "Input database", - "ontologies": [] - } + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "VCF file", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.vcf.gz.tbi": { + "type": "file", + "description": "Tabix index file", + "pattern": "*.vcf.gz.tbi", + "ontologies": [] + } + } + ] + ], + "versions_picard": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "picard": { + "type": "string", + "description": "The tool name" + } + }, + { + "picard ExtractFingerprint --version 2>&1 | sed -n 's/.*Version://p'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "picard": { + "type": "string", + "description": "The tool name" + } + }, + { + "picard ExtractFingerprint --version 2>&1 | sed -n 's/.*Version://p'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@adamrtalbot", "@mauro-saporita"], + "maintainers": ["@adamrtalbot", "@mauro-saporita"] } - ] - ], - "output": { - "db_cluster": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "${prefix}/": { - "type": "file", - "description": "a clustered MMseqs2 database used for clustering", - "ontologies": [] - } - } - ] - ], - "versions_mmseqs": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "mmseqs": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "mmseqs version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "mmseqs": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "mmseqs version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] }, - "authors": [ - "@Joon-Klaps" - ], - "maintainers": [ - "@Joon-Klaps" - ] - }, - "pipelines": [ { - "name": "proteinfamilies", - "version": "2.3.0" + "name": "picard_fastqtosam", + "path": "modules/nf-core/picard/fastqtosam/meta.yml", + "type": "module", + "meta": { + "name": "picard_fastqtosam", + "description": "Converts a FASTQ file to an unaligned BAM or SAM file.", + "keywords": ["fastq", "unaligned", "bam"], + "tools": [ + { + "picard": { + "description": "A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS)\ndata and formats such as SAM/BAM/CRAM and VCF.\n", + "homepage": "https://broadinstitute.github.io/picard/", + "documentation": "https://gatk.broadinstitute.org/hc/en-us/articles/360036510672-FastqToSam-Picard-", + "tool_dev_url": "https://github.com/broadinstitute/picard", + "licence": ["MIT"], + "identifier": "biotools:picard_tools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", + "ontologies": [] + } + } + ] + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Unaligned bam file", + "pattern": "*.{bam}", + "ontologies": [] + } + } + ] + ], + "versions_picard": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "picard": { + "type": "string", + "description": "The tool name" + } + }, + { + "picard FastqToSam --version 2>&1 | sed -n 's/.*Version://p'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "picard": { + "type": "string", + "description": "The tool name" + } + }, + { + "picard FastqToSam --version 2>&1 | sed -n 's/.*Version://p'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@matthdsm"], + "maintainers": ["@matthdsm"] + } }, { - "name": "viralmetagenome", - "version": "1.1.1" - } - ] - }, - { - "name": "mmseqs_createdb", - "path": "modules/nf-core/mmseqs/createdb/meta.yml", - "type": "module", - "meta": { - "name": "mmseqs_createdb", - "description": "Create an MMseqs database from an existing FASTA/Q file", - "keywords": [ - "protein sequence", - "databases", - "clustering", - "searching", - "indexing", - "mmseqs2" - ], - "tools": [ - { - "mmseqs": { - "description": "MMseqs2: ultra fast and sensitive sequence search and clustering suite", - "homepage": "https://github.com/soedinglab/MMseqs2", - "documentation": "https://mmseqs.com/latest/userguide.pdf", - "tool_dev_url": "https://github.com/soedinglab/MMseqs2", - "doi": "10.1093/bioinformatics/btw006", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:mmseqs" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } + "name": "picard_filtersamreads", + "path": "modules/nf-core/picard/filtersamreads/meta.yml", + "type": "module", + "meta": { + "name": "picard_filtersamreads", + "description": "Filters SAM/BAM files to include/exclude either aligned/unaligned reads or based on a read list", + "keywords": ["bam", "filter", "picard", "sam"], + "tools": [ + { + "picard": { + "description": "A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS)\ndata and formats such as SAM/BAM/CRAM and VCF.\n", + "homepage": "https://broadinstitute.github.io/picard/", + "documentation": "https://broadinstitute.github.io/picard/", + "tool_dev_url": "https://github.com/broadinstitute/picard", + "licence": ["MIT"], + "identifier": "biotools:picard_tools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "List of BAM files. If filtering without read list must be sorted by queryname with picard sortsam", + "pattern": "*.{bam}", + "ontologies": [] + } + }, + { + "readlist": { + "type": "file", + "description": "Optional text file containing reads IDs to include or exclude", + "ontologies": [] + } + } + ], + { + "filter": { + "type": "string", + "description": "Picard filter type", + "pattern": "includeAligned|excludeAligned|includeReadList|excludeReadList" + } + } + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Filtered BAM file", + "pattern": "*.{bam}", + "ontologies": [] + } + } + ] + ], + "versions_picard": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "picard": { + "type": "string", + "description": "The tool name" + } + }, + { + "picard FilterSamReads --version 2>&1 | sed -n 's/.*Version://p'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "picard": { + "type": "string", + "description": "The tool name" + } + }, + { + "picard FilterSamReads --version 2>&1 | sed -n 's/.*Version://p'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@jfy133"], + "maintainers": ["@jfy133"] }, - { - "sequence": { - "type": "file", - "description": "Input sequences in FASTA/Q (zipped or unzipped) format to parse into an mmseqs database", - "pattern": "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,fastq,fastq.gz,fq,fq.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "output": { - "db": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "${prefix}/": { - "type": "directory", - "description": "The created MMseqs2 database" - } - } - ] - ], - "versions_mmseqs": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "mmseqs": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "mmseqs version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "mmseqs": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "mmseqs version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "rnadnavar", + "version": "dev" + } ] - ] }, - "authors": [ - "@Joon-Klaps" - ], - "maintainers": [ - "@Joon-Klaps", - "@vagkaratzas" - ] - }, - "pipelines": [ { - "name": "funcscan", - "version": "3.0.0" - }, - { - "name": "proteinfamilies", - "version": "2.3.0" + "name": "picard_fixmateinformation", + "path": "modules/nf-core/picard/fixmateinformation/meta.yml", + "type": "module", + "meta": { + "name": "picard_fixmateinformation", + "description": "Verify mate-pair information between mates and fix if needed", + "keywords": ["mate-pair", "picard", "bam", "sam"], + "tools": [ + { + "picard": { + "description": "A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS)\ndata and formats such as SAM/BAM/CRAM and VCF.\n", + "homepage": "https://broadinstitute.github.io/picard/", + "documentation": "https://gatk.broadinstitute.org/hc/en-us/articles/360036713471-FixMateInformation-Picard-", + "tool_dev_url": "https://github.com/broadinstitute/picard", + "licence": ["MIT"], + "identifier": "biotools:picard_tools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file", + "pattern": "*.{bam}", + "ontologies": [] + } + } + ] + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "mate-pair verified BAM file", + "pattern": "*.{bam}", + "ontologies": [] + } + } + ] + ], + "versions_picard": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "picard": { + "type": "string", + "description": "The tool name" + } + }, + { + "picard FixMateInformation --version 2>&1 | sed -n 's/.*Version://p'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "picard": { + "type": "string", + "description": "The tool name" + } + }, + { + "picard FixMateInformation --version 2>&1 | sed -n 's/.*Version://p'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@sateeshperi", "@mjcipriano", "@hseabolt"], + "maintainers": ["@sateeshperi", "@mjcipriano", "@hseabolt"] + } }, { - "name": "viralmetagenome", - "version": "1.1.1" - } - ] - }, - { - "name": "mmseqs_createindex", - "path": "modules/nf-core/mmseqs/createindex/meta.yml", - "type": "module", - "meta": { - "name": "mmseqs_createindex", - "description": "Creates sequence index for mmseqs database", - "keywords": [ - "protein sequence", - "databases", - "clustering", - "searching", - "indexing" - ], - "tools": [ - { - "mmseqs": { - "description": "MMseqs2: ultra fast and sensitive sequence search and clustering suite", - "homepage": "https://github.com/soedinglab/MMseqs2", - "documentation": "https://mmseqs.com/latest/userguide.pdf", - "tool_dev_url": "https://github.com/soedinglab/MMseqs2", - "doi": "10.1093/bioinformatics/btw006", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:mmseqs" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } + "name": "picard_liftovervcf", + "path": "modules/nf-core/picard/liftovervcf/meta.yml", + "type": "module", + "meta": { + "name": "picard_liftovervcf", + "description": "Lifts over a VCF file from one reference build to another.", + "keywords": ["vcf", "picard", "liftovervcf"], + "tools": [ + { + "picard": { + "description": "Move annotations from one assembly to another", + "homepage": "https://gatk.broadinstitute.org/hc/en-us/articles/360037060932-LiftoverVcf-Picard", + "documentation": "https://gatk.broadinstitute.org/hc/en-us/articles/360037060932-LiftoverVcf-Picard", + "tool_dev_url": "https://github.com/broadinstitute/picard", + "licence": ["MIT"], + "identifier": "biotools:picard_tools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]" + } + }, + { + "input_vcf": { + "type": "file", + "description": "VCF file", + "pattern": "*.{vcf,vcf.gz}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "dict": { + "type": "file", + "description": "dictionary for fasta file", + "pattern": "*.{dict}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "fasta file", + "pattern": "*.fasta", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "chain": { + "type": "file", + "description": "The liftover chain file", + "ontologies": [] + } + } + ] + ], + "output": { + "vcf_lifted": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]" + } + }, + { + "*.lifted.vcf.gz": { + "type": "file", + "description": "VCF file containing successfully lifted variants", + "pattern": "*.{lifted.vcf.gz}", + "ontologies": [] + } + } + ] + ], + "vcf_unlifted": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]" + } + }, + { + "*.unlifted.vcf.gz": { + "type": "file", + "description": "VCF file containing unsuccessfully lifted variants", + "pattern": "*.{unlifted.vcf.gz}", + "ontologies": [] + } + } + ] + ], + "versions_picard": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "picard": { + "type": "string", + "description": "The tool name" + } + }, + { + "picard LiftoverVcf --version 2>&1 | sed -n 's/.*Version://p'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "picard": { + "type": "string", + "description": "The tool name" + } + }, + { + "picard LiftoverVcf --version 2>&1 | sed -n 's/.*Version://p'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@lucpen", "@ramprasadn"], + "maintainers": ["@lucpen", "@ramprasadn"] }, - { - "db": { - "type": "directory", - "description": "Directory containing the DB to be indexed\n", - "pattern": "*" - } - } - ] - ], - "output": { - "db_indexed": [ - [ - { - "meta": { - "type": "directory", - "description": "Directory containing the DB and the generated indexes\n", - "pattern": "*" - } - }, - { - "db": { - "type": "directory", - "description": "Directory containing the DB and the generated indexes\n", - "pattern": "*" - } - } - ] - ], - "versions_mmseqs": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "mmseqs": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "mmseqs version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "mmseqs": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "mmseqs version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "raredisease", + "version": "3.0.0" + }, + { + "name": "variantbenchmarking", + "version": "1.5.0" + } ] - ] - }, - "authors": [ - "@JoseEspinosa" - ], - "maintainers": [ - "@JoseEspinosa" - ] - }, - "pipelines": [ - { - "name": "proteinfold", - "version": "2.0.0" - } - ] - }, - { - "name": "mmseqs_createtaxdb", - "path": "modules/nf-core/mmseqs/createtaxdb/meta.yml", - "type": "module", - "meta": { - "name": "mmseqs_createtaxdb", - "description": "Adds taxonomy information to an existing MMseqs2 database", - "keywords": [ - "protein sequence", - "databases", - "clustering", - "searching", - "taxonomy" - ], - "tools": [ - { - "mmseqs": { - "description": "MMseqs2: ultra fast and sensitive sequence search and clustering suite", - "homepage": "https://github.com/soedinglab/MMseqs2", - "documentation": "https://mmseqs.com/latest/userguide.pdf", - "tool_dev_url": "https://github.com/soedinglab/MMseqs2", - "doi": "10.1093/bioinformatics/btw006", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:mmseqs" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "db": { - "type": "directory", - "description": "Directory containing the MMseqs2 database\n", - "pattern": "*" - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "taxdump_dir": { - "type": "directory", - "description": "Directory containing NCBI taxonomy dump files (names.dmp, nodes.dmp, merged.dmp).\nIf not provided, the module will attempt to download them from NCBI\n", - "pattern": "*" - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } + }, + { + "name": "picard_markduplicates", + "path": "modules/nf-core/picard/markduplicates/meta.yml", + "type": "module", + "meta": { + "name": "picard_markduplicates", + "description": "Locate and tag duplicate reads in a BAM file", + "keywords": ["markduplicates", "pcr", "duplicates", "bam", "sam", "cram"], + "tools": [ + { + "picard": { + "description": "A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS)\ndata and formats such as SAM/BAM/CRAM and VCF.\n", + "homepage": "https://broadinstitute.github.io/picard/", + "documentation": "https://broadinstitute.github.io/picard/", + "licence": ["MIT"], + "identifier": "biotools:picard_tools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "Sequence reads file, can be SAM/BAM/CRAM format", + "pattern": "*.{bam,cram,sam}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference genome fasta file, required for CRAM input", + "pattern": "*.{fasta,fa}", + "ontologies": [] + } + }, + { + "fai": { + "type": "file", + "description": "Reference genome fasta index", + "pattern": "*.{fai}", + "ontologies": [] + } + } + ] + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "BAM file with duplicate reads marked/removed", + "pattern": "*.{bam}", + "ontologies": [] + } + } + ] + ], + "bai": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bai": { + "type": "file", + "description": "An optional BAM index file. If desired, --CREATE_INDEX must be passed as a flag", + "pattern": "*.{bai}", + "ontologies": [] + } + } + ] + ], + "cram": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.cram": { + "type": "file", + "description": "Output CRAM file", + "pattern": "*.{cram}", + "ontologies": [] + } + } + ] + ], + "metrics": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.metrics.txt": { + "type": "file", + "description": "Duplicate metrics file generated by picard", + "pattern": "*.{metrics.txt}", + "ontologies": [] + } + } + ] + ], + "versions_picard": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "picard": { + "type": "string", + "description": "The tool name" + } + }, + { + "picard MarkDuplicates --version 2>&1 | sed -n 's/.*Version://p'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "picard": { + "type": "string", + "description": "The tool name" + } + }, + { + "picard MarkDuplicates --version 2>&1 | sed -n 's/.*Version://p'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@drpatelh", "@projectoriented", "@ramprasadn"], + "maintainers": ["@drpatelh", "@projectoriented", "@ramprasadn"] }, - { - "tax_mapping_file": { - "type": "file", - "description": "File mapping sequence IDs to taxonomy IDs.\nIf not provided, the module will attempt to download the Uniprot id mapping file\n", - "pattern": "*", - "ontologies": [] - } - } - ] - ], - "output": { - "db_with_taxonomy": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "db": { - "type": "directory", - "description": "Directory containing the database with added taxonomy information\n", - "pattern": "*" - } - } - ] - ], - "versions_mmseqs": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "mmseqs": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "mmseqs | grep 'Version' | sed 's/MMseqs2 Version: //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "mmseqs": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "mmseqs | grep 'Version' | sed 's/MMseqs2 Version: //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "atacseq", + "version": "2.1.2" + }, + { + "name": "chipseq", + "version": "2.1.0" + }, + { + "name": "circdna", + "version": "1.1.0" + }, + { + "name": "cutandrun", + "version": "3.2.2" + }, + { + "name": "methylseq", + "version": "4.2.0" + }, + { + "name": "pathogensurveillance", + "version": "1.1.0" + }, + { + "name": "raredisease", + "version": "3.0.0" + }, + { + "name": "rnaseq", + "version": "3.26.0" + }, + { + "name": "rnavar", + "version": "1.2.3" + }, + { + "name": "sammyseq", + "version": "dev" + }, + { + "name": "scnanoseq", + "version": "1.2.2" + }, + { + "name": "ssds", + "version": "dev" + }, + { + "name": "viralmetagenome", + "version": "1.1.1" + }, + { + "name": "viralrecon", + "version": "3.0.0" + } ] - ] - }, - "authors": [ - "@dialvarezs" - ], - "maintainers": [ - "@dialvarezs" - ] - } - }, - { - "name": "mmseqs_createtsv", - "path": "modules/nf-core/mmseqs/createtsv/meta.yml", - "type": "module", - "meta": { - "name": "mmseqs_createtsv", - "description": "Create a tsv file from a query and a target database as well as the result database", - "keywords": [ - "protein sequence", - "databases", - "clustering", - "searching", - "indexing", - "mmseqs2", - "tsv" - ], - "tools": [ - { - "mmseqs": { - "description": "MMseqs2: ultra fast and sensitive sequence search and clustering suite", - "homepage": "https://github.com/soedinglab/MMseqs2", - "documentation": "https://mmseqs.com/latest/userguide.pdf", - "tool_dev_url": "https://github.com/soedinglab/MMseqs2", - "doi": "10.1093/bioinformatics/btw006", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:mmseqs" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "db_result": { - "type": "directory", - "description": "an MMseqs2 database with result data" - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "db_query": { - "type": "directory", - "description": "an MMseqs2 database with query data" - } + }, + { + "name": "picard_meanqualitybycycle", + "path": "modules/nf-core/picard/meanqualitybycycle/meta.yml", + "type": "module", + "meta": { + "name": "picard_meanqualitybycycle", + "description": "Collect metrics about the mean quality by cycle of a paired-end library.", + "keywords": ["metrics", "alignment", "mean", "statistics", "bam"], + "tools": [ + { + "picard": { + "description": "Java tools for working with NGS data in the BAM format", + "homepage": "https://broadinstitute.github.io/picard/", + "documentation": "https://broadinstitute.github.io/picard/", + "tool_dev_url": "https://github.com/broadinstitute/picard", + "licence": ["MIT"], + "identifier": "biotools:picard_tools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}", + "ontologies": [] + } + } + ] + ], + "output": { + "metrics": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "Values used by Picard to generate chart.", + "pattern": "*.txt", + "ontologies": [] + } + } + ] + ], + "pdf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.pdf": { + "type": "file", + "description": "Chart in PDF format", + "pattern": "*.pdf", + "ontologies": [] + } + } + ] + ], + "versions_picard": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "picard": { + "type": "string", + "description": "The tool name" + } + }, + { + "picard MeanQualityByCycle --version 2>&1 | sed -n 's/.*Version://p'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "picard": { + "type": "string", + "description": "The tool name" + } + }, + { + "picard MeanQualityByCycle --version 2>&1 | sed -n 's/.*Version://p'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@mikefeixu", "@FerriolCalvet"], + "maintainers": ["@mikefeixu"] } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } + }, + { + "name": "picard_mergesamfiles", + "path": "modules/nf-core/picard/mergesamfiles/meta.yml", + "type": "module", + "meta": { + "name": "picard_mergesamfiles", + "description": "Merges multiple BAM files into a single file", + "keywords": ["merge", "alignment", "bam", "sam"], + "tools": [ + { + "picard": { + "description": "A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS)\ndata and formats such as SAM/BAM/CRAM and VCF.\n", + "homepage": "https://broadinstitute.github.io/picard/", + "documentation": "https://broadinstitute.github.io/picard/", + "licence": ["MIT"], + "identifier": "biotools:picard_tools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bams": { + "type": "list", + "description": "List of input BAM files to be merged", + "pattern": "*.{bam}" + } + } + ] + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Merged BAM file", + "pattern": "*.{bam}", + "ontologies": [] + } + } + ] + ], + "versions_picard": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "picard": { + "type": "string", + "description": "The tool name" + } + }, + { + "picard MergeSamFiles --version 2>&1 | sed -n 's/.*Version://p'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "picard": { + "type": "string", + "description": "The tool name" + } + }, + { + "picard MergeSamFiles --version 2>&1 | sed -n 's/.*Version://p'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@drpatelh"], + "maintainers": ["@drpatelh"] }, - { - "db_target": { - "type": "directory", - "description": "an MMseqs2 database with target data" - } - } - ] - ], - "output": { - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "The resulting tsv file created using the query, target and result MMseqs databases", - "pattern": "*.{tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_mmseqs": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "mmseqs": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "mmseqs version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "mmseqs": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "mmseqs version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "atacseq", + "version": "2.1.2" + }, + { + "name": "chipseq", + "version": "2.1.0" + } ] - ] }, - "authors": [ - "@Joon-Klaps" - ], - "maintainers": [ - "@Joon-Klaps" - ] - }, - "pipelines": [ { - "name": "funcscan", - "version": "3.0.0" + "name": "picard_positionbaseddownsamplesam", + "path": "modules/nf-core/picard/positionbaseddownsamplesam/meta.yml", + "type": "module", + "meta": { + "name": "picard_positionbaseddownsamplesam", + "description": "Samples a SAM/BAM/CRAM file using flowcell position information for the best approximation of having sequenced fewer reads", + "keywords": ["sample", "bam", "sam", "cram"], + "tools": [ + { + "picard": { + "description": "A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS)\ndata and formats such as SAM/BAM/CRAM and VCF.\n", + "homepage": "https://broadinstitute.github.io/picard/", + "documentation": "https://broadinstitute.github.io/picard/", + "licence": ["MIT"], + "identifier": "biotools:picard_tools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file", + "pattern": "*.{bam,cram,sam}", + "ontologies": [] + } + }, + { + "fraction": { + "type": "float", + "description": "Fraction of reads to downsample to" + } + } + ] + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.ds*.bam": { + "type": "file", + "description": "A downsampled BAM file", + "pattern": "*.{bam}", + "ontologies": [] + } + } + ] + ], + "bai": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.ds*.bai": { + "type": "file", + "description": "An optional BAM index file. If desired, --CREATE_INDEX must be passed as a flag", + "pattern": "*.{bai}", + "ontologies": [] + } + } + ] + ], + "num_reads": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "ACTUAL_NUM_READS": { + "type": "integer", + "description": "The actual number of downsampled reads" + } + } + ] + ], + "versions_picard": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "picard": { + "type": "string", + "description": "The tool name" + } + }, + { + "picard PositionBasedDownsampleSam --version 2>&1 | sed -n 's/.*Version://p'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "picard": { + "type": "string", + "description": "The tool name" + } + }, + { + "picard PositionBasedDownsampleSam --version 2>&1 | sed -n 's/.*Version://p'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@bwlang"] + } }, { - "name": "proteinfamilies", - "version": "2.3.0" + "name": "picard_renamesampleinvcf", + "path": "modules/nf-core/picard/renamesampleinvcf/meta.yml", + "type": "module", + "meta": { + "name": "picard_renamesampleinvcf", + "description": "changes name of sample in the vcf file", + "keywords": ["picard", "picard/renamesampleinvcf", "vcf"], + "tools": [ + { + "picard": { + "description": "A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS)\ndata and formats such as SAM/BAM/CRAM and VCF.\n", + "homepage": "https://broadinstitute.github.io/picard/", + "documentation": "https://broadinstitute.github.io/picard/", + "tool_dev_url": "https://github.com/broadinstitute/picard", + "licence": ["MIT"], + "identifier": "biotools:picard_tools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF file", + "pattern": "*.{vcf,vcf.gz}", + "ontologies": [] + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "VCF file", + "pattern": "*.{vcf,vcf.gz}", + "ontologies": [] + } + } + ] + ], + "versions_picard": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "picard": { + "type": "string", + "description": "The tool name" + } + }, + { + "picard RenameSampleInVcf --version 2>&1 | sed -n 's/.*Version://p'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "picard": { + "type": "string", + "description": "The tool name" + } + }, + { + "picard RenameSampleInVcf --version 2>&1 | sed -n 's/.*Version://p'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@Lucpen"], + "maintainers": ["@Lucpen"] + }, + "pipelines": [ + { + "name": "raredisease", + "version": "3.0.0" + } + ] }, { - "name": "viralmetagenome", - "version": "1.1.1" - } - ] - }, - { - "name": "mmseqs_databases", - "path": "modules/nf-core/mmseqs/databases/meta.yml", - "type": "module", - "meta": { - "name": "mmseqs_databases", - "description": "Download an mmseqs-formatted database", - "keywords": [ - "database", - "indexing", - "clustering", - "searching" - ], - "tools": [ - { - "mmseqs": { - "description": "MMseqs2: ultra fast and sensitive sequence search and clustering suite", - "homepage": "https://github.com/soedinglab/MMseqs2", - "documentation": "https://mmseqs.com/latest/userguide.pdf", - "tool_dev_url": "https://github.com/soedinglab/MMseqs2", - "doi": "10.1093/bioinformatics/btw006", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:mmseqs" - } - } - ], - "input": [ - { - "database": { - "type": "string", - "description": "Database available through the mmseqs2 databases interface - see https://github.com/soedinglab/MMseqs2/wiki#downloading-databases for details" - } - } - ], - "output": { - "database": [ - { - "${prefix}/": { - "type": "directory", - "description": "Directory containing processed mmseqs database" - } + "name": "picard_scatterintervalsbyns", + "path": "modules/nf-core/picard/scatterintervalsbyns/meta.yml", + "type": "module", + "meta": { + "name": "picard_scatterintervalsbyns", + "description": "Writes an interval list created by splitting a reference at Ns.A Program for breaking up a reference into intervals of alternating regions of N and ACGT bases", + "keywords": ["interval_list", "scatter", "regions"], + "tools": [ + { + "picard": { + "description": "A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS)\ndata and formats such as SAM/BAM/CRAM and VCF.\n", + "homepage": "https://broadinstitute.github.io/picard/", + "documentation": "https://broadinstitute.github.io/picard/", + "tool_dev_url": "https://github.com/broadinstitute/picard", + "licence": ["MIT"], + "identifier": "biotools:picard_tools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing fasta information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Fasta file to derive the intervals from", + "pattern": "*.{fasta,fa,fna}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing fai information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Index of the fasta file", + "pattern": "*.fai", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing dictionary information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "dict": { + "type": "file", + "description": "Sequence dictionary of the fasta file", + "pattern": "*.dict", + "ontologies": [] + } + } + ] + ], + "output": { + "intervals": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.interval_list": { + "type": "file", + "description": "The scattered intervals", + "pattern": "*.interval_list", + "ontologies": [] + } + } + ] + ], + "versions_picard": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "picard": { + "type": "string", + "description": "The tool name" + } + }, + { + "picard ScatterIntervalsByNs --version 2>&1 | sed -n 's/.*Version://p'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "picard": { + "type": "string", + "description": "The tool name" + } + }, + { + "picard ScatterIntervalsByNs --version 2>&1 | sed -n 's/.*Version://p'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@nvnieuwk"], + "maintainers": ["@nvnieuwk"] } - ], - "versions_mmseqs": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "mmseqs": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "mmseqs version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "mmseqs": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "mmseqs version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] }, - "authors": [ - "@prototaxites" - ], - "maintainers": [ - "@prototaxites" - ] - }, - "pipelines": [ { - "name": "funcscan", - "version": "3.0.0" + "name": "picard_setnmmdanduqtags", + "path": "modules/nf-core/picard/setnmmdanduqtags/meta.yml", + "type": "module", + "meta": { + "name": "picard_setnmmdanduqtags", + "description": "This tool takes in a coordinate-sorted SAM or BAM and calculatesthe NM, MD, and UQ tags by comparing with the reference.", + "keywords": ["bam", "uq", "nm", "md"], + "tools": [ + { + "picard": { + "description": "Java tools for working with NGS data in the BAM format", + "homepage": "https://broadinstitute.github.io/picard/", + "documentation": "https://broadinstitute.github.io/picard/", + "tool_dev_url": "https://github.com/broadinstitute/picard", + "licence": ["MIT"], + "identifier": "biotools:picard_tools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "bam": { + "type": "file", + "description": "Sorted BAM/SAM file", + "pattern": "*.{bam,sam}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + }, + { + "edam": "http://edamontology.org/format_2573" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "reference": { + "type": "file", + "description": "Reference fasta file", + "pattern": "*.{fasta,fa}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ] + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Sorted BAM file", + "pattern": "*.bam", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + } + ] + ], + "bai": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.bai": { + "type": "file", + "description": "BAM indexing file", + "pattern": "*.bai", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3327" + } + ] + } + } + ] + ], + "versions_picard": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "picard": { + "type": "string", + "description": "The tool name" + } + }, + { + "picard SetNmMdAndUqTags --version 2>&1 | sed -n 's/.*Version://p'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "picard": { + "type": "string", + "description": "The tool name" + } + }, + { + "picard SetNmMdAndUqTags --version 2>&1 | sed -n 's/.*Version://p'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@anoronh4"], + "maintainers": ["@anoronh4"] + } }, { - "name": "mag", - "version": "5.4.2" - } - ] - }, - { - "name": "mmseqs_easycluster", - "path": "modules/nf-core/mmseqs/easycluster/meta.yml", - "type": "module", - "meta": { - "name": "mmseqs_easycluster", - "description": "Cluster sequences using MMSeqs2 easy cluster.", - "keywords": [ - "protein sequence", - "databases", - "clustering", - "searching", - "mmseqs2" - ], - "tools": [ - { - "mmseqs": { - "description": "MMseqs2: ultra fast and sensitive sequence search and clustering suite", - "homepage": "https://github.com/soedinglab/MMseqs2", - "documentation": "https://mmseqs.com/latest/userguide.pdf", - "tool_dev_url": "https://github.com/soedinglab/MMseqs2", - "doi": "10.1093/bioinformatics/btw006", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:mmseqs" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "sequence": { - "type": "file", - "description": "Input sequence file in FASTA/FASTQ format for clustering", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1920" - } - ] - } - } - ] - ], - "output": { - "representatives": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*rep_seq.fasta": { - "type": "file", - "description": "a fasta file containing the cluster representatives", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ], - "fasta": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*all_seqs.fasta": { - "type": "file", - "description": "a fasta-like file per cluster", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ], - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "an adjacency list file containing the clusters", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_mmseqs": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "mmseqs": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "mmseqs version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "mmseqs": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "mmseqs version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@Joon-Klaps" - ], - "maintainers": [ - "@Joon-Klaps" - ] - } - }, - { - "name": "mmseqs_easysearch", - "path": "modules/nf-core/mmseqs/easysearch/meta.yml", - "type": "module", - "meta": { - "name": "mmseqs_easysearch", - "description": "Searches for the sequences of a fasta file in a database using MMseqs2", - "keywords": [ - "protein sequence", - "databases", - "searching", - "mmseqs2" - ], - "tools": [ - { - "mmseqs": { - "description": "MMseqs2: ultra fast and sensitive sequence search and clustering suite", - "homepage": "https://github.com/soedinglab/MMseqs2", - "documentation": "https://mmseqs.com/latest/userguide.pdf", - "tool_dev_url": "https://github.com/soedinglab/MMseqs2", - "doi": "10.1093/bioinformatics/btw006", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:mmseqs" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing input fasta file information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Fasta file", - "pattern": "*.{fa,fasta}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing database information\ne.g. `[ id:'test' ]`\n" - } + "name": "picard_sortsam", + "path": "modules/nf-core/picard/sortsam/meta.yml", + "type": "module", + "meta": { + "name": "picard_sortsam", + "description": "Sorts BAM/SAM files based on a variety of picard specific criteria", + "keywords": ["sort", "bam", "sam", "picard"], + "tools": [ + { + "picard": { + "description": "A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS)\ndata and formats such as SAM/BAM/CRAM and VCF.\n", + "homepage": "https://broadinstitute.github.io/picard/", + "documentation": "https://broadinstitute.github.io/picard/", + "licence": ["MIT"], + "identifier": "biotools:picard_tools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,sam}", + "ontologies": [] + } + } + ], + { + "sort_order": { + "type": "string", + "description": "Picard sort order type", + "pattern": "unsorted|queryname|coordinate|duplicate|unknown" + } + } + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Sorted BAM/CRAM/SAM file", + "pattern": "*.{bam}", + "ontologies": [] + } + } + ] + ], + "versions_picard": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "picard": { + "type": "string", + "description": "The tool name" + } + }, + { + "picard SortSam --version 2>&1 | sed -n 's/.*Version://p'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "picard": { + "type": "string", + "description": "The tool name" + } + }, + { + "picard SortSam --version 2>&1 | sed -n 's/.*Version://p'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@jfy133"], + "maintainers": ["@jfy133"] }, - { - "db_target": { - "type": "directory", - "description": "an MMseqs2 database with target data, e.g. uniref90" - } - } - ] - ], - "output": { - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing input fasta file information\ne.g. `[ id:'test']`\n" - } - }, - { - "${prefix}.tsv": { - "type": "file", - "description": "tsv file with the results of the search", - "pattern": "*.{tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_mmseqs": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "mmseqs": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "mmseqs version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "mmseqs": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "mmseqs version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "pathogensurveillance", + "version": "1.1.0" + }, + { + "name": "ssds", + "version": "dev" + } ] - ] - }, - "authors": [ - "@luisas" - ], - "maintainers": [ - "@luisas" - ] - }, - "pipelines": [ - { - "name": "viralmetagenome", - "version": "1.1.1" - } - ] - }, - { - "name": "mmseqs_linclust", - "path": "modules/nf-core/mmseqs/linclust/meta.yml", - "type": "module", - "meta": { - "name": "mmseqs_linclust", - "description": "Cluster sequences in linear time using MMSeqs2 linclust.", - "keywords": [ - "protein sequence", - "databases", - "clustering", - "searching", - "indexing", - "mmseqs2" - ], - "tools": [ - { - "mmseqs": { - "description": "MMseqs2: ultra fast and sensitive sequence search and clustering suite", - "homepage": "https://github.com/soedinglab/MMseqs2", - "documentation": "https://mmseqs.com/latest/userguide.pdf", - "tool_dev_url": "https://github.com/soedinglab/MMseqs2", - "doi": "10.1093/bioinformatics/btw006", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:mmseqs" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } + }, + { + "name": "picard_sortvcf", + "path": "modules/nf-core/picard/sortvcf/meta.yml", + "type": "module", + "meta": { + "name": "picard_sortvcf", + "description": "Sorts vcf files", + "keywords": ["sort", "vcf", "sortvcf"], + "tools": [ + { + "picard": { + "description": "Java tools for working with NGS data in the BAM/CRAM/SAM and VCF format", + "homepage": "https://broadinstitute.github.io/picard/", + "documentation": "https://broadinstitute.github.io/picard/command-line-overview.html#SortVcf", + "licence": ["MIT"], + "identifier": "biotools:picard_tools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF file", + "pattern": "*.{vcf,vcf.gz}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference genome fasta file", + "pattern": "*.{fasta,fa}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "dict": { + "type": "file", + "description": "Reference genome dictionary file", + "pattern": "*.{dict}", + "ontologies": [] + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_sorted.vcf.gz": { + "type": "file", + "description": "Sorted VCF file", + "pattern": "*.{vcf}", + "ontologies": [] + } + } + ] + ], + "versions_picard": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "picard": { + "type": "string", + "description": "The tool name" + } + }, + { + "picard SortVcf --version 2>&1 | sed -n 's/.*Version://p'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "picard": { + "type": "string", + "description": "The tool name" + } + }, + { + "picard SortVcf --version 2>&1 | sed -n 's/.*Version://p'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@ramprasadn"], + "maintainers": ["@ramprasadn"] }, - { - "db_input": { - "type": "file", - "description": "Input database", - "ontologies": [] - } - } - ] - ], - "output": { - "db_cluster": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "${prefix}/": { - "type": "directory", - "description": "a clustered MMseqs2 database" - } - } - ] - ], - "versions_mmseqs": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "mmseqs": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "mmseqs version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "mmseqs": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "mmseqs version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "raredisease", + "version": "3.0.0" + } ] - ] }, - "authors": [ - "@vagkaratzas" - ], - "maintainers": [ - "@vagkaratzas" - ] - }, - "pipelines": [ { - "name": "proteinfamilies", - "version": "2.3.0" + "name": "picard_splitsambynumberofreads", + "path": "modules/nf-core/picard/splitsambynumberofreads/meta.yml", + "type": "module", + "meta": { + "name": "picard_splitsambynumberofreads", + "description": "Splits a SAM/BAM/CRAM file to multiple files. This tool splits the input query-grouped SAM/BAM/CRAM file into multiple files while maintaining the sort order. This can be used to split a large unmapped input in order to parallelize alignment.", + "keywords": ["split", "parallel", "bam", "subset", "downsample", "sam", "cram"], + "tools": [ + { + "picard": { + "description": "Splits a SAM or BAM file to multiple BAMs by number of reads.", + "homepage": "https://gatk.broadinstitute.org/hc/en-us/articles/360037064232-SplitSamByNumberOfReads-Picard", + "documentation": "https://gatk.broadinstitute.org/hc/en-us/articles/360037064232-SplitSamByNumberOfReads-Picard", + "tool_dev_url": "https://github.com/broadinstitute/picard", + "licence": ["MIT"], + "identifier": "biotools:picard_tools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/SAM/CRAM file", + "pattern": "*.{bam,sam,cram}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + }, + { + "edam": "http://edamontology.org/format_2573" + }, + { + "edam": "http://edamontology.org/format_3462" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference fasta (optional - only required for CRAM input)", + "pattern": "*.{fasta,fa}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + }, + { + "fai": { + "type": "file", + "description": "FAI file (optional - only required for CRAM input)", + "pattern": "*.{fai}" + } + } + ], + { + "split_to_N_reads": { + "type": "integer", + "description": "Split to have approximately N reads per output file, e.g. `4000000`.\nThe actual number of reads per output file will vary by no more than the number of output files * (the maximum number of reads with the same queryname - 1).\nIncompatible with `split_to_N_files`\n" + } + }, + { + "split_to_N_files": { + "type": "integer", + "description": "Split to N files, e.g. `3`.\n`Incompatible with split_to_N_files`\n" + } + }, + { + "arguments_file": { + "type": "file", + "description": "optional Picard arguments file", + "pattern": "*.{txt,list,args,arguments}" + } + } + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "picardsplit/*.{bam,sam,cram}": { + "type": "file", + "description": "Split BAM files", + "pattern": "*.{bam,sam,cram}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + } + ] + ], + "versions_picard": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "picard": { + "type": "string", + "description": "The tool name" + } + }, + { + "picard SplitSamByNumberOfReads --version 2>&1 | sed -n 's/.*Version://p'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "picard": { + "type": "string", + "description": "The tool name" + } + }, + { + "picard SplitSamByNumberOfReads --version 2>&1 | sed -n 's/.*Version://p'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@Y-Pei"], + "maintainers": ["@Y-Pei"] + } }, { - "name": "viralmetagenome", - "version": "1.1.1" - } - ] - }, - { - "name": "mmseqs_makepaddedseqdb", - "path": "modules/nf-core/mmseqs/makepaddedseqdb/meta.yml", - "type": "module", - "meta": { - "name": "mmseqs_makepaddedseqdb", - "description": "Create an MMseqs padded database from an existing MMseqs database", - "keywords": [ - "protein sequence", - "databases", - "clustering", - "searching", - "indexing", - "mmseqs2" - ], - "tools": [ - { - "mmseqs": { - "description": "MMseqs2: ultra fast and sensitive sequence search and clustering suite", - "homepage": "https://github.com/soedinglab/MMseqs2", - "documentation": "https://mmseqs.com/latest/userguide.pdf", - "tool_dev_url": "https://github.com/soedinglab/MMseqs2", - "doi": "10.1093/bioinformatics/btw006", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:mmseqs" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "db_in": { - "type": "directory", - "description": "Input of existing MMseqs database" - } - } - ] - ], - "output": { - "db_padded": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "${prefix}/": { - "type": "directory", - "description": "The padded MMseqs2 database" - } - } - ] - ], - "versions_mmseqs": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "mmseqs": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "mmseqs version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "mmseqs": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "mmseqs version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@nbtm-sh" - ], - "maintainers": [ - "@nbtm-sh" - ] - } - }, - { - "name": "mmseqs_search", - "path": "modules/nf-core/mmseqs/search/meta.yml", - "type": "module", - "meta": { - "name": "mmseqs_search", - "description": "Search and calculate a score for similar sequences in a query and a target database.", - "keywords": [ - "protein sequence", - "databases", - "clustering", - "searching", - "indexing", - "mmseqs2" - ], - "tools": [ - { - "mmseqs": { - "description": "MMseqs2: ultra fast and sensitive sequence search and clustering suite", - "homepage": "https://github.com/soedinglab/MMseqs2", - "documentation": "https://mmseqs.com/latest/userguide.pdf", - "tool_dev_url": "https://github.com/soedinglab/MMseqs2", - "doi": "10.1093/bioinformatics/btw006", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:mmseqs" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "db_query": { - "type": "file", - "description": "Query database", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "db_target": { - "type": "file", - "description": "Target database", - "ontologies": [] - } - } - ] - ], - "output": { - "db_search": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "${prefix}/": { - "type": "directory", - "description": "an MMseqs2 database with search results" - } - } - ] - ], - "versions_mmseqs": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "mmseqs": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "mmseqs version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "mmseqs": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "mmseqs version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@Joon-Klaps" - ], - "maintainers": [ - "@Joon-Klaps" - ] - } - }, - { - "name": "mmseqs_taxonomy", - "path": "modules/nf-core/mmseqs/taxonomy/meta.yml", - "type": "module", - "meta": { - "name": "mmseqs_taxonomy", - "description": "Computes the lowest common ancestor by identifying the query sequence homologs against the target database.", - "keywords": [ - "protein sequence", - "nucleotide sequence", - "databases", - "taxonomy", - "homologs", - "mmseqs2" - ], - "tools": [ - { - "mmseqs": { - "description": "MMseqs2: ultra fast and sensitive sequence search and clustering suite", - "homepage": "https://github.com/soedinglab/MMseqs2", - 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"https://github.com/broadinstitute/pilon", + "doi": "10.1371/journal.pone.0112963", + "licence": ["GPL-2.0-or-later"], + "identifier": "biotools:pilon" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information for the fasta\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA of the input genome", + "pattern": "*.{fasta}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information for the bam file\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file of reads aligned to the input genome", + "pattern": "*.{bam}", + "ontologies": [] + } + }, + { + "bai": { + "type": "file", + "description": "BAI file (BAM index) of BAM reads aligned to the input genome", + "pattern": "*.{bai}", + "ontologies": [] + } + } + ], + { + "pilon_mode": { + "type": "string", + "description": "Indicates the type of bam file used (frags for paired-end sequencing of DNA fragments, such as Illumina paired-end reads of fragment size <1000bp, jumps for paired sequencing data of larger insert size, such as Illumina mate pair libraries, typically of insert size >1000bp, unpaired for unpaired sequencing reads, bam will automatically classify the BAM as one of the three types above (version 1.17 and higher).", + "enum": ["frags", "jumps", "unpaired", "bam"] + } + } + ], + "output": { + "improved_assembly": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fasta": { + "type": "file", + "description": "fasta file, improved assembly", + "pattern": "*.{fasta}", + "ontologies": [] + } + } + ] + ], + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { 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"description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.wig": { + "type": "file", + "description": "files that may be viewed in genome browsers such as IGV, GenomeView, and other applications that support these formats", + "pattern": "*.{wig}", + "ontologies": [] + } + } + ] + ], + "versions_pilon": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "pilon": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pilon --version | sed 's/^.*version //; s/ .*\\$//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "pilon": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pilon --version | sed 's/^.*version //; s/ 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"methylong", - "version": "2.0.0" - } - ] - }, - { - "name": "molkartgarage_clahe", - "path": "modules/nf-core/molkartgarage/clahe/meta.yml", - "type": "module", - "meta": { - "name": "molkartgarage_clahe", - "description": "Contrast-limited adjusted histogram equalization (CLAHE) on single-channel tif images.", - "keywords": [ - "clahe", - "image_processing", - "imaging", - "correction" - ], - "tools": [ - { - "molkartgarage": { - "description": "One-stop-shop for scripts and tools for processing data for molkart and spatial omics pipelines.", - "homepage": "https://github.com/SchapiroLabor/molkart-local/tree/main", - "documentation": "https://github.com/SchapiroLabor/molkart-local/tree/main", - "tool_dev_url": "https://github.com/SchapiroLabor/molkart-local/blob/main/scripts/molkart_clahe.py", - "licence": [ - "MIT" - ], - "identifier": "" + }, + { + "name": "pindel_pindel", + "path": "modules/nf-core/pindel/pindel/meta.yml", + "type": "module", + "meta": { + "name": "pindel_pindel", + "description": "Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data", + "keywords": ["deletions", "insertions", "tandem duplications"], + "tools": [ + { + "pindel": { + "description": "Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data", + "homepage": "https://gmt.genome.wustl.edu/packages/pindel/", + "documentation": "https://gmt.genome.wustl.edu/packages/pindel/user-manual.html", + "licence": ["GPL v3"], + "identifier": "biotools:pindel" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information, insert_size is either determined using Picard/CollectInsertSizeMetrics\nor a sensible default - setting ext.args2 to either in modules.conf\ne.g. [ id:'test', single_end:false, insert_size:500 ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file", + "pattern": "*.bam", + "ontologies": [] + } + }, + { + "bai": { + "type": "file", + "description": "BAM index file", + "pattern": "*.bai", + "ontologies": [] + } + } + ], + { + "fasta": { + "type": "file", + "description": "Input reference genome fasta file", + "ontologies": [] + } + }, + { + "fai": { + "type": "file", + "description": "Input reference genome fasta index file", + "ontologies": [] + } + }, + { + "bed": { + "type": "file", + "description": "BED file containing regions of interest", + "ontologies": [] + } + } + ], + "output": { + "bp": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_BP": { + "type": "file", + "description": "File containing breakpoints", + "pattern": "*_{BP}", + "ontologies": [] + } + } + ] + ], + "cem": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_CloseEndMapped": { + "type": "file", + "description": "File containing close end reads", + "pattern": "*_{CloseEndMapped}", + "ontologies": [] + } + } + ] + ], + "del": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_D": { + "type": "file", + "description": "File containing deletions", + "pattern": "*_{D}", + "ontologies": [] + } + } + ] + ], + "dd": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_DD": { + "type": "file", + "description": "File containing dispersed duplications", + "pattern": "*_{DD}", + "ontologies": [] + } + } + ] + ], + "int_final": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_INT_final": { + "type": "file", + "description": "int file", + "pattern": "*_INT_final", + "ontologies": [] + } + } + ] + ], + "inv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_INV": { + "type": "file", + "description": "File containing inversions", + "pattern": "*_{INV}", + "ontologies": [] + } + } + ] + ], + "li": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_LI": { + "type": "file", + "description": "File containing long insertions", + "pattern": "*_{LI}", + "ontologies": [] + } + } + ] + ], + "rp": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_RP": { + "type": "file", + 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containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bams": { + "type": "file", + "description": "One or more BAM files", + "pattern": "*.{bam}", + "ontologies": [] + } + }, + { + "bais": { + "type": "file", + "description": "Corresponding BAM file indexes", + "pattern": "*.bam.bai", + "ontologies": [] + } + } + ], + { + "assay_type": { + "type": "string", + "description": "Assay type" + } + } + ], + "output": { + "divergent_TREs": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_divergent_peaks.bed": { + "type": "file", + "description": "Divergent TREs", + "pattern": "*_divergent_peaks.bed", + "optional": true, + "ontologies": [] + } + } + ] + ], + "bidirectional_TREs": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_bidirectional_peaks.bed": { + "type": "file", + "description": "Divergent TREs and convergent TREs", + "pattern": "*_bidirectional_peaks.bed", + "optional": true, + "ontologies": [] + } + } + ] + ], + "unidirectional_TREs": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_unidirectional_peaks.bed": { + "type": "file", + "description": "Unidirectional TREs, maybe lncRNAs transcribed from enhancers (e-lncRNAs)", + "pattern": "*_unidirectional_peaks.bed", + "optional": true, + "ontologies": [] + } + } + ] + ], + "peakcalling_log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "peakcalling_*.log": { + "type": "file", + "description": "Peakcalling log for debugging purposes", + "pattern": "peakcalling_*.log", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@edmundmiller"], + "maintainers": ["@edmundmiller"] }, - { - "image": { - "type": "file", - "description": "Single-channel tiff file to be corrected.", - "pattern": "*.{tif,tiff}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3591" - } - ] - } - } - ] - ], - "output": { - "img_clahe": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } - }, - { - "*.tiff": { - "type": "file", - "description": "CLAHE corrected tiff file.", - "pattern": "*.{tiff}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3591" - } - ] - } - } - ] - ], - "versions_clahe": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "clahe": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python /local/scripts/molkart_clahe.py --version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_scikitimage": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "scikit-image": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python -c 'import skimage; print(skimage.__version__)'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "clahe": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python /local/scripts/molkart_clahe.py --version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "scikit-image": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python -c 'import skimage; print(skimage.__version__)'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "nascent", + "version": "2.3.0" + } ] - ] - }, - "authors": [ - "@kbestak" - ], - "maintainers": [ - "@kbestak" - ] - } - }, - { - "name": "mosdepth", - "path": "modules/nf-core/mosdepth/meta.yml", - "type": "module", - "meta": { - "name": "mosdepth", - "description": "Calculates genome-wide sequencing coverage.", - "keywords": [ - "mosdepth", - "bam", - "cram", - "coverage" - ], - "tools": [ - { - "mosdepth": { - "description": "Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing.\n", - "documentation": "https://github.com/brentp/mosdepth", - "doi": "10.1093/bioinformatics/btx699", - "licence": [ - "MIT" - ], - "identifier": "biotools:mosdepth" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "Input BAM/CRAM file", - "pattern": "*.{bam,cram}", - "ontologies": [] - } - }, - { - "bai": { - "type": "file", - "description": "Index for BAM/CRAM file", - "pattern": "*.{bai,crai}", - "ontologies": [] - } - }, - { - "bed": { - "type": "file", - "description": "BED file with intersected intervals", - "pattern": "*.{bed}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing bed information\ne.g. [ id:'test' ]\n" - } + }, + { + "name": "pirate", + "path": "modules/nf-core/pirate/meta.yml", + "type": "module", + "meta": { + "name": "pirate", + "description": "Pangenome toolbox for bacterial genomes", + "keywords": ["gff", "pan-genome", "alignment"], + "tools": [ + { + "pirate": { + "description": "Pangenome analysis and threshold evaluation toolbox", + "homepage": "https://github.com/SionBayliss/PIRATE", + "documentation": "https://github.com/SionBayliss/PIRATE/wiki", + "tool_dev_url": "https://github.com/SionBayliss/PIRATE", + "doi": "10.1093/gigascience/giz119", + "licence": ["GPL v3"], + "identifier": "biotools:PIRATE" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "gff": { + "type": "file", + "description": "A set of GFF3 formatted files", + "pattern": "*.{gff}", + "ontologies": [] + } + } + ] + ], + "output": { + "results": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}_results/*": { + "type": "directory", + "description": "Directory containing PIRATE result files", + "pattern": "*/*" + } + } + ] + ], + "aln": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}_results/core_alignment.fasta": { + "type": "file", + "description": "Core-genome alignment produced by PIRATE (Optional)", + "pattern": "*.{fasta}", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@rpetit3", "@zachary-foster"], + "maintainers": ["@rpetit3"] }, - { - "fasta": { - "type": "file", - "description": "Reference genome FASTA file", - "pattern": "*.{fa,fasta}", - "ontologies": [] - } - } - ], - { - "quantize_labels": { - "type": "list", - "description": "List of labels for quantized coverage bins, e.g. [ \"NO_COVERAGE\", \"LOW_COVERAGE\", \"MEDIUM_COVERAGE\", \"HIGH_COVERAGE\" ]\nThe first value will be assigned to the `MOSDEPTH_Q0` environment variable, the second to `MOSDEPTH_Q1`, and so on.\nThese can then be used in the `--quantize` option of mosdepth to assign labels to quantized coverage bins.\n" - } - } - ], - "output": { - "global_txt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.global.dist.txt": { - "type": "file", - "description": "Text file with global cumulative coverage distribution", - "pattern": "*.{global.dist.txt}", - "ontologies": [] - } - } - ] - ], - "summary_txt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.summary.txt": { - "type": "file", - "description": "Text file with summary mean depths per chromosome and regions", - "pattern": "*.{summary.txt}", - "ontologies": [] - } - } - ] - ], - "regions_txt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.region.dist.txt": { - "type": "file", - "description": "Text file with region cumulative coverage distribution", - "pattern": "*.{region.dist.txt}", - "ontologies": [] - } - } - ] - ], - "per_base_d4": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.per-base.d4": { - "type": "file", - "description": "D4 file with per-base coverage", - "pattern": "*.{per-base.d4}", - "ontologies": [] - } - } - ] - ], - "per_base_bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.per-base.bed.gz": { - "type": "file", - "description": "BED file with per-base coverage", - "pattern": "*.{per-base.bed.gz}", - "ontologies": [] - } - } - ] - ], - "per_base_csi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.per-base.bed.gz.csi": { - "type": "file", - "description": "Index file for BED file with per-base coverage", - "pattern": "*.{per-base.bed.gz.csi}", - "ontologies": [] - } - } - ] - ], - "regions_bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.regions.bed.gz": { - "type": "file", - "description": "BED file with per-region coverage", - "pattern": "*.{regions.bed.gz}", - "ontologies": [] - } - } - ] - ], - "regions_csi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.regions.bed.gz.csi": { - "type": "file", - "description": "Index file for BED file with per-region coverage", - "pattern": "*.{regions.bed.gz.csi}", - "ontologies": [] - } - } - ] - ], - "quantized_bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.quantized.bed.gz": { - "type": "file", - "description": "BED file with binned coverage", - "pattern": "*.{quantized.bed.gz}", - "ontologies": [] - } - } - ] - ], - "quantized_csi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.quantized.bed.gz.csi": { - "type": "file", - "description": "Index file for BED file with binned coverage", - "pattern": "*.{quantized.bed.gz.csi}", - "ontologies": [] - } - } - ] - ], - "thresholds_bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.thresholds.bed.gz": { - "type": "file", - "description": "BED file with the number of bases in each region that are covered at or above each threshold", - "pattern": "*.{thresholds.bed.gz}", - "ontologies": [] - } - } - ] - ], - "thresholds_csi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.thresholds.bed.gz.csi": { - "type": "file", - "description": "Index file for BED file with threshold coverage", - "pattern": "*.{thresholds.bed.gz.csi}", - "ontologies": [] - } - } - ] - ], - "versions_mosdepth": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "mosdepth": { - "type": "string", - "description": "The tool name" - } - }, - { - "mosdepth --version | sed 's/mosdepth //g'": { - "type": "eval", - "description": "The command used to generate the version of the tool" - } - } - ] - ], - "versions_gzip": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "gzip": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gzip -V 2>&1 | sed 's/gzip \\([0-9.]*\\).*/\\1/;q'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "mosdepth": { - "type": "string", - "description": "The tool name" - } - }, - { - "mosdepth --version | sed 's/mosdepth //g'": { - "type": "eval", - "description": "The command used to generate the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "gzip": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gzip -V 2>&1 | sed 's/gzip \\([0-9.]*\\).*/\\1/;q'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "pathogensurveillance", + "version": "1.1.0" + } ] - ] }, - "authors": [ - "@joseespinosa", - "@drpatelh", - "@ramprasadn", - "@matthdsm" - ], - "maintainers": [ - "@joseespinosa", - "@ramprasadn", - "@matthdsm" - ] - }, - "pipelines": [ { - "name": "createpanelrefs", - "version": "dev" + "name": "plasmidfinder", + "path": "modules/nf-core/plasmidfinder/meta.yml", + "type": "module", + "meta": { + "name": "plasmidfinder", + "description": "Identify plasmids in bacterial sequences and assemblies", + "keywords": ["fasta", "fastq", "plasmid"], + "tools": [ + { + "plasmidfinder": { + "description": "PlasmidFinder allows identification of plasmids in total or partial sequenced isolates of bacteria.", + "homepage": "https://cge.cbs.dtu.dk/services/PlasmidFinder/", + "documentation": "https://bitbucket.org/genomicepidemiology/plasmidfinder", + "tool_dev_url": "https://bitbucket.org/genomicepidemiology/plasmidfinder", + "doi": "10.1128/AAC.02412-14", + "licence": ["Apache-2.0"], + "identifier": "biotools:PlasmidFinder" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input FASTA or FASTQ formatted genome sequences", + "pattern": "*.{fastq.gz,fq.gz,fastq.gz,fna.gz,fa.gz}", + "ontologies": [] + } + } + ] + ], + "output": { + "json": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.json": { + "type": "file", + "description": "The results from analysis in JSON format", + "pattern": "*.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "txt": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "The summary of results from analysis", + "pattern": "*.txt", + "ontologies": [] + } + } + ] + ], + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "The results from analysis in TSV format", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "genome_seq": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*-hit_in_genome_seq.fsa": { + "type": "file", + "description": "FASTA of sequences in the input with a hit", + "pattern": "*-hit_in_genome_seq.fsa", + "ontologies": [] + } + } + ] + ], + "plasmid_seq": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*-plasmid_seqs.fsa": { + "type": "file", + "description": "FASTA of plasmid sequences with a hit against the input", + "pattern": "*-plasmid_seqs.fsa", + "ontologies": [] + } + } + ] + ], + "versions_plasmidfinder": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "plasmidfinder": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "2.1.6": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "plasmidfinder": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "2.1.6": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@eit-maxlcummins", "@rpetit3"], + "maintainers": ["@rpetit3"] + } }, { - "name": "genomicrelatedness", - "version": "dev" + "name": "plasmidid", + "path": "modules/nf-core/plasmidid/meta.yml", + "type": "module", + "meta": { + "name": "plasmidid", + "description": "assembles bacterial plasmids", + "keywords": ["assembly", "plasmid", "bacterial"], + "tools": [ + { + "plasmidid": { + "description": "Pipeline for plasmid identification and reconstruction", + "homepage": "https://github.com/BU-ISCIII/plasmidID/wiki", + "documentation": "https://github.com/BU-ISCIII/plasmidID#readme", + "tool_dev_url": "https://github.com/BU-ISCIII/plasmidID", + "licence": ["GPL v3"], + "identifier": "biotools:plasmidid" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "scaffold": { + "type": "file", + "description": "Fasta file containing scaffold\n", + "ontologies": [] + } + } + ], + { + "fasta": { + "type": "file", + "description": "FASTA reference file", + "pattern": "*.{fasta,fa}", + "ontologies": [] + } + } + ], + "output": { + "html": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/*final_results.html": { + "type": "file", + "description": "html file with results rendered", + "pattern": "*.{html}", + "ontologies": [] + } + } + ] + ], + "tab": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/*final_results.tab": { + "type": "file", + "description": "Results in a tabular file", + "pattern": "*.{tab}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "images": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/images/": { + "type": "directory", + "description": "Directory containing the images produced by plasmidid", + "pattern": "images" + } + } + ] + ], + "logs": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/logs/": { + "type": "directory", + "description": "Directory containing the logs produced by plasmidid", + "pattern": "logs" + } + } + ] + ], + "data": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/data/": { + "type": "directory", + "description": "Directory containing the data produced by plasmidid", + "pattern": "data" + } + } + ] + ], + "database": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/database/": { + "type": "directory", + "description": "Directory containing the database produced by plasmidid", + "pattern": "database" + } + } + ] + ], + "fasta_files": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/fasta_files/": { + "type": "directory", + "description": "Directory containing the fasta files produced by plasmidid", + "pattern": "fasta_files" + } + } + ] + ], + "kmer": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/kmer/": { + "type": "directory", + "description": "Directory containing the kmer files produced by plasmidid", + "pattern": "database" + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@joseespinosa", "@drpatelh"], + "maintainers": ["@joseespinosa", "@drpatelh"] + }, + "pipelines": [ + { + "name": "viralrecon", + "version": "3.0.0" + } + ] }, { - "name": "pacsomatic", - "version": "dev" + "name": "plastid_make_wiggle", + "path": "modules/nf-core/plastid/make_wiggle/meta.yml", + "type": "module", + "meta": { + "name": "plastid_make_wiggle", + "description": "Create wiggle or bedGraph files from alignment files after applying a read mapping rule (e.g. to map ribosome-protected footprints at their P-sites), for visualization in a genome browser", + "keywords": ["genomics", "riboseq", "psite", "wiggle", "bedgraph"], + "tools": [ + { + "plastid": { + "description": "Nucleotide-resolution analysis of next-generation sequencing and genomics data", + "homepage": 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Use 'fiveprime_variable' with p_offsets file to map reads to P-sites.\n", + "enum": ["fiveprime", "threeprime", "center", "fiveprime_variable"] + } + } + ], + "output": { + "tracks": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.{wig,bedgraph}": { + "type": "file", + "description": "wig/bedgraph tracks for forward and reverse strands", + "pattern": "*.{wig,bedgraph}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3005" + }, + { + "edam": "http://edamontology.org/format_3583" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@suhrig"], + "maintainers": ["@suhrig"] + } }, { - "name": "raredisease", - "version": "3.0.0" + "name": "plastid_metagene_generate", + "path": "modules/nf-core/plastid/metagene_generate/meta.yml", + "type": "module", + "meta": { + "name": "plastid_metagene_generate", + "description": "Compute a metagene profile of read alignments, counts, or quantitative data over one or more regions of interest, optionally applying a mapping rule", + "keywords": ["genomics", "riboseq", "psite"], + "tools": [ + { + "plastid": { + "description": "Nucleotide-resolution analysis of next-generation sequencing and genomics data", + "homepage": "https://github.com/joshuagryphon/plastid", + "documentation": "https://plastid.readthedocs.io/en/latest/", + "tool_dev_url": "https://github.com/joshuagryphon/plastid", + "doi": "10.1186/s12864-016-3278-x", + "licence": ["BSD-3-clause"], + "identifier": "biotools:plastid" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Map containing reference information for the reference genome annotation file\ne.g. `[ id:'Ensembl human v.111' ]`\n" + } + }, + { + "annotation": { + "type": "file", + "description": "annotation file of reference genome (BED, bigBed, GTF, GFF3)", + "pattern": "*.{bed,bigbed,gtf,gff3}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3003" + }, + { + "edam": "http://edamontology.org/format_3004" + }, + { + "edam": "http://edamontology.org/format_2306" + }, + { + "edam": "http://edamontology.org/format_1975" + } + ] + } + } + ] + ], + "output": { + "rois_txt": [ + [ + { + "meta": { + "type": "map", + "description": "Map containing reference information for the reference genome annotation file\ne.g. `[ id:'Ensembl human v.111' ]`\n" + } + }, + { + "*_rois.txt": { + "type": "file", + "description": "Tab-delimited text file describing the maximal spanning window for each gene", + "pattern": "*_rois.txt", + "ontologies": [] + } + } + ] + ], + "rois_bed": [ + [ + { + "meta": { + "type": "map", + "description": "Map containing reference information for the reference genome annotation file\ne.g. `[ id:'Ensembl human v.111' ]`\n" + } + }, + { + "*_rois.bed": { + "type": "file", + "description": "Maximal spanning windows in BED format for visualization in a genome\nbrowser. The thickly-rendered portion of a window indicates its landmark.\n", + "pattern": "*_rois.bed", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3003" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@suhrig"], + "maintainers": ["@suhrig"] + } }, { - "name": "rnadnavar", - "version": "dev" + "name": "plastid_psite", + "path": "modules/nf-core/plastid/psite/meta.yml", + "type": "module", + "meta": { + "name": "plastid_psite", + "description": "Estimate position of ribosomal P-site within ribosome profiling read alignments as a function of read length", + "keywords": ["genomics", "riboseq", "psite"], + "tools": [ + { + "plastid": { + "description": "Nucleotide-resolution analysis of next-generation sequencing and genomics data", + "homepage": "https://github.com/joshuagryphon/plastid", + "documentation": "https://plastid.readthedocs.io/en/latest/", + "tool_dev_url": "https://github.com/joshuagryphon/plastid", + "doi": "10.1186/s12864-016-3278-x", + "licence": ["BSD-3-clause"], + "identifier": "biotools:plastid" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "bam": { + "type": "file", + "description": "Genome BAM file", + "pattern": "*.bam", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + }, + { + "bam_index": { + "type": "file", + "description": "Genome BAM index file", + "pattern": "*.bai", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3327" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Map containing reference information for the reference genome GTF file\ne.g. `[ id:'Ensembl human v.111' ]`\n" + } + }, + { + "rois_txt": { + "type": "file", + "description": "Tab-delimited text file describing the maximal spanning\nwindow for each gene (output from plastid_metagene_generate)\n", + "pattern": "*.txt", + "ontologies": [] + } + } + ] + ], + "output": { + "metagene_profiles": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*_metagene_profiles.txt": { + "type": "file", + "description": "Matrix containing metagene profile for each read length", + "pattern": "*_metagene_profiles.txt", + "ontologies": [] + } + } + ] + ], + "p_offsets_png": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*_p_offsets.png": { + "type": "file", + "description": "Graphical illustration of metagene profiles", + "pattern": "*_p_offsets.png", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3603" + } + ] + } + } + ] + ], + "p_offsets": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*_p_offsets.txt": { + "type": "file", + "description": "Selected p-site offset for each read length", + "pattern": "*_p_offsets.txt", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@suhrig"], + "maintainers": ["@suhrig"] + } }, { - 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"name": "variantcatalogue", - "version": "dev" + "name": "plink2_filter", + "path": "modules/nf-core/plink2/filter/meta.yml", + "type": "module", + "meta": { + "name": "plink2_filter", + "description": "Filters plink bfiles or pfiles with filters such as maf or var", + "keywords": ["plink2", "filter", "samples", "variants", "missingness", "qualty"], + "tools": [ + { + "plink2": { + "description": "Whole genome association analysis toolset, designed to perform a range\nof basic, large-scale analyses in a computationally efficient manner\n", + "homepage": "http://www.cog-genomics.org/plink/2.0/", + "documentation": "http://www.cog-genomics.org/plink/2.0/general_usage", + "doi": "10.1186/s13742-015-0047-8", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "plink_genotype_file": { + "type": "file", + "description": "PLINK binary genotype table file or PLINK 2 binary genotype table file", + "pattern": "*.{bed,pgen}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3003" + } + ] + } + }, + { + "plink_variant_file": { + "type": "file", + "description": "PLINK extended MAP file or PLINK 2 variant information file", + "pattern": "*.{bim,pvar}", + "ontologies": [] + } + }, + { + "plink_sample_file": { + "type": "file", + "description": "PLINK sample information file or PLINK 2 sample information file", + "pattern": "*.{fam,psam}", + "ontologies": [] + } + } + ] + ], + "output": { + "bim": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bim": { + "type": "file", + "description": "PLINK extended map file", + "pattern": "*.bim", + "ontologies": [] + } + } + ] + ], + "bed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "PLINK binary allelic genotype table", + "pattern": "*.bed", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3003" + } + ] + } + } + ] + ], + "fam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fam": { + "type": "file", + "description": "PLINK sample information file", + "pattern": "*.fam", + "ontologies": [] + } + } + ] + ], + "pgen": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.pgen": { + "type": "file", + "description": "PLINK 2 binary genotype table", + "pattern": "*.pgen", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3003" + } + ] + } + } + ] + ], + "psam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.psam": { + "type": "file", + "description": "PLINK 2 sample information file", + "pattern": "*.psam", + "ontologies": [] + } + } + ] + ], + "pvar": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.pvar": { + "type": "file", + "description": "PLINK 2 variant information file", + "pattern": "*.pvar", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@jodennehy"], + "maintainers": ["@jodennehy"] + } }, { - 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"name": "viralrecon", - "version": "3.0.0" - } - ] - }, - { - "name": "motus_downloaddb", - "path": "modules/nf-core/motus/downloaddb/meta.yml", - "type": "module", - "meta": { - "name": "motus_downloaddb", - "description": "Download the mOTUs database", - "keywords": [ - "classify", - "metagenomics", - "fastq", - "taxonomic profiling", - "database", - "download" - ], - "tools": [ - { - "motus": { - "description": "The mOTU profiler is a computational tool that estimates relative taxonomic abundance of known and currently unknown microbial community members using metagenomic shotgun sequencing data.", - "documentation": "https://github.com/motu-tool/mOTUs/wiki", - "tool_dev_url": "https://github.com/motu-tool/mOTUs", - "doi": "10.1186/s40168-022-01410-z", - "licence": [ - "GPL v3" - ], - "identifier": "" - } - } - ], - "input": [ - { - "motus_downloaddb_script": { - "type": "file", - "description": "The script to download the mOTUs database", - "ontologies": [] - } - } - ], - "output": { - "db": [ - { - "db_mOTU/": { - "type": "directory", - "description": "The mOTUs database directory", - "pattern": "db_mOTU" - } - } - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@jianhong" - ], - "maintainers": [ - "@jianhong" - ] - } - }, - { - "name": "motus_merge", - "path": "modules/nf-core/motus/merge/meta.yml", - "type": "module", - "meta": { - "name": "motus_merge", - "description": "Taxonomic meta-omics profiling using universal marker genes", - "keywords": [ - "classify", - "metagenomics", - "fastq", - "taxonomic profiling", - "merging", - "merge", - "otu table" - ], - "tools": [ - { - "motus": { - "description": "Marker gene-based OTU (mOTU) profiling", - "homepage": "https://motu-tool.org/", - "documentation": "https://github.com/motu-tool/mOTUs/wiki", - "tool_dev_url": "https://github.com/motu-tool/mOTUs", - 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} - ] - } - } - ], - "output": { - "txt": [ - [ - { - "meta": { - "type": "file", - "description": "OTU table in txt format, if BIOM format not requested", - "pattern": "*.txt", - "ontologies": [] - } - }, - { - "*.txt": { - "type": "file", - "description": "OTU table in txt format, if BIOM format not requested", - "pattern": "*.txt", - "ontologies": [] - } - } - ] - ], - "biom": [ - [ - { - "meta": { - "type": "file", - "description": "OTU table in txt format, if BIOM format not requested", - "pattern": "*.txt", - "ontologies": [] - } - }, - { - "*.biom": { - "type": "file", - "description": "OTU table in biom format, if BIOM format requested", - "pattern": "*.biom", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3746" - } - ] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - 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"ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@jianhong" - ], - "maintainers": [ - "@jianhong" - ] - }, - "pipelines": [ - { - "name": "taxprofiler", - "version": "2.0.0" - } - ] - }, - { - "name": "msisensor2_msi", - "path": "modules/nf-core/msisensor2/msi/meta.yml", - "type": "module", - "meta": { - "name": "msisensor2_msi", - "description": "msisensor2 detection of MSI regions.", - "keywords": [ - "msi", - "microsatellite", - "microsatellite instability", - "tumor", - "cfDNA" - ], - "tools": [ - { - "msisensor2": { - "description": "MSIsensor2 is a novel algorithm based machine learning, featuring a large upgrade in the microsatellite instability (MSI) detection for tumor only sequencing data, including Cell-Free DNA (cfDNA), Formalin-Fixed Paraffin-Embedded(FFPE) and other sample types. 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], - "identifier": "biotools:msisensor" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "normal_bam": { - "type": "file", - "description": "Coordinate sorted BAM/CRAM/SAM file from normal tissue", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } - }, - { - "normal_bai": { - "type": "file", - "description": "Index for coordinate sorted BAM/CRAM/SAM file from normal tissue", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } - }, - { - "tumor_bam": { - "type": "file", - "description": "Coordinate sorted BAM/CRAM/SAM file from tumor tissue", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } - }, - { - "tumor_bai": { - "type": "file", - "description": "Index for coordinate sorted BAM/CRAM/SAM file from tumor tissue", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } - }, - { - "metascan": { - "type": "file", - "description": "metascan file", - "ontologies": [] - } - }, - { - "homopolymers": { - "type": "file", - "description": "Output file from MSIsensor scan module", - "pattern": "*.msisensor_scan.tab", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "output": { - "output": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}": { - "type": "file", - "description": "Output file from MSIsensor msi module", - "ontologies": [] - } - } - ] - ], - "output_dis": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}_dis": { - "type": "file", - "description": "Output file from MSIsensor module", - "ontologies": [] - } - } - ] - ], - "output_germline": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}_germline": { - "type": "file", - "description": "Output file from MSIsensor module", - "ontologies": [] - } - } - ] - ], - "output_somatic": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}_somatic": { - "type": "file", - "description": "Output file from MSIsensor module", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@kevbrick" - ], - "maintainers": [ - "@kevbrick" - ] - } - }, - { - "name": "msisensor_scan", - "path": "modules/nf-core/msisensor/scan/meta.yml", - "type": "module", - "meta": { - "name": "msisensor_scan", - "description": "Scan a reference genome to get microsatellite & homopolymer information", - "deprecated": true, - "keywords": [ - "homoploymer", - "microsatellite", - "MSI" - ], - "tools": [ - { - "msisensor": { - "description": "MSIsensor is a C++ program to detect replication slippage variants at microsatellite regions, and differentiate them as somatic or germline.", - "homepage": "https://github.com/ding-lab/msisensor", - "doi": "10.1093/bioinformatics/btt755", - "licence": [ - "MIT" - ], - "identifier": "biotools:msisensor" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA file", - "pattern": "*.{fa,fasta}", - "ontologies": [] - } - } - ] - ], - "output": { - "txt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tab": { - "type": "file", - "description": "MSIsensor scan output file of homopolymers & minisatellites", - "pattern": "*.msisensor_scan.txt", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@kevbrick" - ], - "maintainers": [ - "@kevbrick" - ] - } - }, - { - "name": "msisensorpro_msisomatic", - "path": "modules/nf-core/msisensorpro/msisomatic/meta.yml", - "type": "module", - "meta": { - "name": "msisensorpro_msisomatic", - "description": "MSIsensor-pro evaluates Microsatellite Instability (MSI) for cancer patients with next generation sequencing data. It accepts the whole genome sequencing, whole exome sequencing and target region (panel) sequencing data as input", - "keywords": [ - "micro-satellite-scan", - "msisensor-pro", - "msi", - "somatic" - ], - "tools": [ - { - "msisensorpro": { - "description": "Microsatellite Instability (MSI) detection using high-throughput sequencing data.", - "homepage": "https://github.com/xjtu-omics/msisensor-pro", - "documentation": "https://github.com/xjtu-omics/msisensor-pro/wiki", - "tool_dev_url": "https://github.com/xjtu-omics/msisensor-pro", - "doi": "10.1016/j.gpb.2020.02.001", - "licence": [ - "Custom Licence" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "normal": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } - }, - { - "normal_index": { - "type": "file", - "description": "BAM/CRAM/SAM index file", - "pattern": "*.{bai,crai,sai}", - "ontologies": [] - } - }, - { - "tumor": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } - }, - { - "tumor_index": { - "type": "file", - "description": "BAM/CRAM/SAM index file", - "pattern": "*.{bai,crai,sai}", - "ontologies": [] - } - }, - { - "intervals": { - "type": "file", - "description": "bed file containing interval information, optional", - "pattern": "*.{bed}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing genome information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome", - "pattern": "*.{fasta}", - "ontologies": [] - } - } - ], - { - "msisensor_scan": { - "type": "file", - "description": "Output from msisensor-pro/scan, containing list of msi regions", - "pattern": "*.list", - "ontologies": [] - } - } - ], - "output": { - "output_report": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}": { - "type": "file", - "description": "File containing final report with all detected microsatellites, unstable somatic microsatellites, msi score", - "ontologies": [] - } - } - ] - ], - "output_dis": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}_dis": { - "type": "file", - "description": "File containing distribution results", - "ontologies": [] - } - } - ] - ], - "output_germline": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}_germline": { - "type": "file", - "description": "File containing germline results", - "ontologies": [] - } - } - ] - ], - "output_somatic": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}_somatic": { - "type": "file", - "description": "File containing somatic results", - "ontologies": [] - } - } - ] - ], - "versions_msisensorpro": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "msisensor-pro": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "msisensor-pro --version 2>&1 | sed -nE 's/Version:\\s*//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "msisensor-pro": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "msisensor-pro --version 2>&1 | sed -nE 's/Version:\\s*//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@FriederikeHanssen" - ], - "maintainers": [ - "@FriederikeHanssen" - ] - }, - "pipelines": [ - { - "name": "sarek", - "version": "3.8.1" - } - ] - }, - { - "name": "msisensorpro_pro", - "path": "modules/nf-core/msisensorpro/pro/meta.yml", - "type": "module", - "meta": { - "name": "msisensorpro_pro", - "description": "MSIsensor-pro/pro is a tool used to evaluate MSI using single (tumor) sample sequencing data", - "keywords": [ - "msisensor-pro", - "pro", - "micro-satellite" - ], - "tools": [ - { - "msisensorpro": { - "description": "Microsatellite Instability (MSI) detection using high-throughput sequencing data.", - "homepage": "https://github.com/xjtu-omics/msisensor-pro", - "documentation": "https://github.com/xjtu-omics/msisensor-pro/wiki", - "tool_dev_url": "https://github.com/xjtu-omics/msisensor-pro", - "doi": "10.1016/j.gpb.2020.02.001", - "licence": [ - "Custom Licence" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "input": { - "type": "file", - "description": "sorted BAM/CRAM file", - "pattern": "*.{bam,cram}", - "ontologies": [] - } - }, - { - "index": { - "type": "file", - "description": "index file for input", - "pattern": "*.{bai,crai}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "list": { - "type": "file", - "description": "micro-satellite list", - "pattern": "*.{list}", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "reference genome used to create micro-satellite list", - "pattern": "*.{fasta}", - "ontologies": [] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "fai": { - "type": "file", - "description": "index file for reference fasta", - "pattern": "*.{fai}", - "ontologies": [] - } - } - ] - ], - "output": { - "summary_msi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "${prefix}": { - "type": "file", - "description": "txt file containing summary of results", - "ontologies": [] - } - } - ] - ], - "all_msi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "${prefix}_all": { - "type": "file", - "description": "txt file containing all results", - "ontologies": [] - } - } - ] - ], - "dis_msi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "${prefix}_dis": { - "type": "file", - "description": "txt file containing the allele length distribution", - "ontologies": [] - } - } - ] - ], - "unstable_msi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "${prefix}_unstable": { - "type": "file", - "description": "txt file containing unstable micro-satellite sites", - "ontologies": [] - } - } - ] - ], - "versions_msisensorpro": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "msisensor-pro": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "msisensor-pro --version 2>&1 | sed -nE 's/Version:\\s*//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "msisensor-pro": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "msisensor-pro --version 2>&1 | sed -nE 's/Version:\\s*//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@Tuur-ds" - ], - "maintainers": [ - "@Tuur-ds" - ] - } - }, - { - "name": "msisensorpro_scan", - "path": "modules/nf-core/msisensorpro/scan/meta.yml", - "type": "module", - "meta": { - "name": "msisensorpro_scan", - "description": "MSIsensor-pro evaluates Microsatellite Instability (MSI) for cancer patients with next generation sequencing data. It accepts the whole genome sequencing, whole exome sequencing and target region (panel) sequencing data as input", - "keywords": [ - "micro-satellite-scan", - "msisensor-pro", - "scan" - ], - "tools": [ - { - "msisensorpro": { - "description": "Microsatellite Instability (MSI) detection using high-throughput sequencing data.", - "homepage": "https://github.com/xjtu-omics/msisensor-pro", - "documentation": "https://github.com/xjtu-omics/msisensor-pro/wiki", - "tool_dev_url": "https://github.com/xjtu-omics/msisensor-pro", - "doi": "10.1016/j.gpb.2020.02.001", - "licence": [ - "Custom Licence" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome", - "pattern": "*.{fasta}", - "ontologies": [] - } - } - ] - ], - "output": { - "list": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.list": { - "type": "file", - "description": "File containing microsatellite list", - "pattern": "*.{list}", - "ontologies": [] - } - } - ] - ], - "versions_msisensorpro": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "msisensor-pro": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "msisensor-pro --version 2>&1 | sed -nE 's/Version:\\s*//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "msisensor-pro": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "msisensor-pro --version 2>&1 | sed -nE 's/Version:\\s*//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@FriederikeHanssen" - ], - "maintainers": [ - "@FriederikeHanssen" - ] - }, - "pipelines": [ - { - "name": "references", - "version": "0.1" }, { - "name": "sarek", - "version": "3.8.1" - } - ] - }, - { - "name": "mtmalign_align", - "path": "modules/nf-core/mtmalign/align/meta.yml", - "type": "module", - "meta": { - "name": "mtmalign_align", - "description": "Aligns protein structures using mTM-align", - "keywords": [ - "alignment", - "MSA", - "genomics", - "structure" - ], - "tools": [ - { - "mTM-align": { - "description": "Algorithm for structural multiple sequence alignments", - "homepage": "http://yanglab.nankai.edu.cn/mTM-align/", - "documentation": "http://yanglab.nankai.edu.cn/mTM-align/help/", - "tool_dev_url": "http://yanglab.nankai.edu.cn/mTM-align/", - "doi": "10.1093/bioinformatics/btx828", - "licence": [ - "None" - ], - "identifier": "" - } - }, - { - "pigz": { - "description": "Parallel implementation of the gzip algorithm.", - "homepage": "https://zlib.net/pigz/", - "documentation": "https://zlib.net/pigz/pigz.pdf", - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" - } - }, - { - "pdbs": { - "type": "file", - "description": "Input protein structures in PDB format. Files may be gzipped or uncompressed. They should contain exactly one chain!", - "pattern": "*.{pdb}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1476" - }, - { - "edam": "http://edamontology.org/format_1477" - } - ] - } - } - ], - { - "compress": { - "type": "boolean", - "description": "Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded." - } - } - ], - "output": { - "alignment": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" - } - }, - { - "${prefix}.aln${compress ? '.gz' : ''}": { - "type": "file", - "description": "Alignment in FASTA format. May be gzipped or uncompressed.", - "pattern": "*.aln{.gz,}", - "ontologies": [ + "name": "plink2_indeppairwise", + "path": "modules/nf-core/plink2/indeppairwise/meta.yml", + "type": "module", + "meta": { + "name": "plink2_indeppairwise", + "description": "Produce pruned set of variants in approximatelinkage equilibrium", + "keywords": ["plink2", "linkage equilibrium", "pruning"], + "tools": [ + { + "plink2": { + "description": "Whole genome association analysis toolset, designed to perform a range\nof basic, large-scale analyses in a computationally efficient manner\n", + "homepage": "http://www.cog-genomics.org/plink/2.0/", + "documentation": "http://www.cog-genomics.org/plink/2.0/general_usage", + "doi": "10.1186/s13742-015-0047-8", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "plink_genotype_file": { + "type": "file", + "description": "PLINK binary genotype table file or PLINK 2 binary genotype table file", + "pattern": "*.{bed,pgen}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3003" + } + ] + } + }, + { + "plink_variant_file": { + "type": "file", + "description": "PLINK extended MAP file or PLINK 2 variant information file", + "pattern": "*.{bim,pvar}", + "ontologies": [] + } + }, + { + "plink_sample_file": { + "type": "file", + "description": "PLINK sample information file or PLINK 2 sample information file", + "pattern": "*.{fam,psam}", + "ontologies": [] + } + } + ], { - "edam": "http://edamontology.org/format_2554" + "win": { + "type": "integer", + "description": "Window size in variant count or kilobase (if the 'kb' modifier is present) units, a variant count to shift the window at the end of each step, and a variance inflation factor (VIF) threshold.", + "pattern": "*.{}" + } }, { - "edam": "http://edamontology.org/format_1921" + "step": { + "type": "integer", + "description": "Variant count to shift the window at the end of each step.", + "pattern": "*.{}" + } }, { - "edam": "http://edamontology.org/format_1984" + "r2": { + "type": "float", + "description": "R squared threshold", + "pattern": "*.{}" + } } - ] - } - } - ] - ], - "structure": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" - } - }, - { - "${prefix}.pdb${compress ? '.gz' : ''}": { - "type": "file", - "description": "Overlaid structures in PDB format. May be gzipped or uncompressed.", - "pattern": "${prefix}.pdb{.gz,}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1476" - } - ] - } - } - ] - ], - "versions_mtmalign": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "mtm-align": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "mtm-align -h | sed -n \"s/.*Version \\([0-9]*\\).*/\\1/p\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_pigz": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pigz": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pigz --version 2>&1 | sed \"s/^.*pigz[[:space:]]*//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "mtm-align": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "mtm-align -h | sed -n \"s/.*Version \\([0-9]*\\).*/\\1/p\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pigz": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pigz --version 2>&1 | sed \"s/^.*pigz[[:space:]]*//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@lrauschning" - ], - "maintainers": [ - "@lrauschning" - ] - }, - "pipelines": [ - { - "name": "multiplesequencealign", - "version": "1.1.1" - } - ] - }, - { - "name": "mtnucratio", - "path": "modules/nf-core/mtnucratio/meta.yml", - "type": "module", - "meta": { - "name": "mtnucratio", - "description": "A small Java tool to calculate ratios between MT and nuclear sequencing reads in a given BAM file.", - "keywords": [ - "mtnucratio", - "ratio", - "reads", - "bam", - "mitochondrial to nuclear ratio", - "mitochondria", - "statistics" - ], - "tools": [ - { - "mtnucratio": { - "description": "A small tool to determine MT to Nuclear ratios for NGS data.", - "homepage": "https://github.com/apeltzer/MTNucRatioCalculator", - "documentation": "https://github.com/apeltzer/MTNucRatioCalculator", - "tool_dev_url": "https://github.com/apeltzer/MTNucRatioCalculator", - "doi": "10.1186/s13059-016-0918-z", - "licence": [ - "GPL v3" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "(coordinate) sorted BAM/SAM file", - "pattern": "*.{bam,sam}", - "ontologies": [] - } - } - ], - { - "mt_id": { - "type": "string", - "description": "Identifier of the contig/chromosome of interest (e.g. chromosome, contig) as in the aligned against reference FASTA file, e.g. mt or chrMT for mitochondria" - } - } - ], - "output": { - "mtnucratio": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.mtnucratio": { - "type": "file", - "description": "Text file containing metrics (mtreads, mt_cov_avg, nucreads, nuc_cov_avg, mt_nuc_ratio)", - "pattern": "*.mtnucratio", - "ontologies": [] - } - } - ] - ], - "json": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.json": { - "type": "file", - "description": "JSON file, containing metadata map with sample name, tool name and version, and metrics as in txt file", - "pattern": "*.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@louperelo" - ], - "maintainers": [ - "@louperelo" - ] - } - }, - { - "name": "mudskipper_bulk", - "path": "modules/nf-core/mudskipper/bulk/meta.yml", - "type": "module", - "meta": { - "name": "mudskipper_bulk", - "description": "Convert genomic BAM/SAM files to transcriptomic BAM/RAD files.", - "keywords": [ - "bam", - "transcriptome", - "transcriptomic", - "mudskipper", - "sam", - "rad" - ], - "tools": [ - { - "mudskipper": { - "description": "mudskipper is a tool for converting genomic BAM/SAM files to transcriptomic BAM/RAD files.", - "homepage": "https://github.com/OceanGenomics/mudskipper", - "documentation": "https://github.com/OceanGenomics/mudskipper", - "tool_dev_url": "https://github.com/OceanGenomics/mudskipper", - "licence": [ - "BSD 3-clause" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "Name-Sorted BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } - } - ], - { - "index": { - "type": "directory", - "description": "Annotation index created by mudskipper/index" - } - }, - { - "gtf": { - "type": "file", - "description": "Annotation file", - "pattern": "*.{gtf,gff,gff3}", - "ontologies": [] - } - }, - { - "rad": { - "type": "string", - "description": "File type" - } - } - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "${prefix}.bam": { - "type": "file", - "description": "Sorted BAM file", - "pattern": "*.bam", - "ontologies": [] - } - } - ] - ], - "rad": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "${prefix}.rad": { - "type": "file", - "description": "RAD file", - "pattern": "*.rad", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@anoronh4" - ] - } - }, - { - "name": "mudskipper_index", - "path": "modules/nf-core/mudskipper/index/meta.yml", - "type": "module", - "meta": { - "name": "mudskipper_index", - "description": "Build and store a gtf index, which is useful for converting genomic BAM/SAM files to transcriptomic BAM/SAM files.", - "keywords": [ - "bam", - "transcriptome", - "transcriptomic", - "index", - "mudskipper", - "sam" - ], - "tools": [ - { - "mudskipper": { - "description": "mudskipper is a tool for converting genomic BAM/SAM files to transcriptomic BAM/RAD files.", - "homepage": "https://github.com/OceanGenomics/mudskipper", - "documentation": "https://github.com/OceanGenomics/mudskipper", - "tool_dev_url": "https://github.com/OceanGenomics/mudskipper", - "licence": [ - "BSD 3-clause" - ], - "identifier": "" - } - } - ], - "input": [ - { - "gtf": { - "type": "file", - "description": "Transcript annotation file.", - "pattern": "*.{gtf,gff,gff3}", - "ontologies": [] - } - } - ], - "output": { - "index": [ - { - "index/": { - "type": "directory", - "description": "Mudskipper index for running mudskipper conversion tools", - "pattern": "*/" - } - } - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@anoronh4" - ] - } - }, - { - "name": "multiqc", - "path": "modules/nf-core/multiqc/meta.yml", - "type": "module", - "meta": { - "name": "multiqc", - "description": "Aggregate results from bioinformatics analyses across many samples into a single report", - "keywords": [ - "QC", - "bioinformatics tools", - "Beautiful stand-alone HTML report" - ], - "tools": [ - { - "multiqc": { - "description": "MultiQC searches a given directory for analysis logs and compiles a HTML report.\nIt's a general use tool, perfect for summarising the output from numerous bioinformatics tools.\n", - "homepage": "https://multiqc.info/", - "documentation": "https://multiqc.info/docs/", - "licence": [ - "GPL-3.0-or-later" - ], - "identifier": "biotools:multiqc" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample1', single_end:false ]\n" - } - }, - { - "multiqc_files": { - "type": "file", - "description": "List of reports / files recognised by MultiQC, for example the html and zip output of FastQC\n", - "ontologies": [] - } - }, - { - "multiqc_config": { - "type": "file", - "description": "Optional config yml for MultiQC", - "pattern": "*.{yml,yaml}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - }, - { - "multiqc_logo": { - "type": "file", - "description": "Optional logo file for MultiQC", - "pattern": "*.{png}", - "ontologies": [] - } - }, - { - "replace_names": { - "type": "file", - "description": "Optional two-column sample renaming file. First column a set of\npatterns, second column a set of corresponding replacements. Passed via\nMultiQC's `--replace-names` option.\n", - "pattern": "*.{tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - }, - { - "sample_names": { - "type": "file", - "description": "Optional TSV file with headers, passed to the MultiQC --sample_names\nargument.\n", - "pattern": "*.{tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "output": { - "report": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample1', single_end:false ]\n" - } - }, - { - "*.html": { - "type": "file", - "description": "MultiQC report file", - "pattern": ".html", - "ontologies": [] - } - } - ] - ], - "data": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample1', single_end:false ]\n" - } - }, - { - "*_data": { - "type": "directory", - "description": "MultiQC data dir", - "pattern": "multiqc_data" - } - } - ] - ], - "plots": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample1', single_end:false ]\n" - } - }, - { - "*_plots": { - "type": "file", - "description": "Plots created by MultiQC", - "pattern": "*_plots", - "ontologies": [] - } - } - ] - ], - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "multiqc": { - "type": "string", - "description": "The tool name" - } - }, - { - "multiqc --version | sed \"s/.* //g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@abhi18av", - "@bunop", - "@drpatelh", - "@jfy133" - ], - "maintainers": [ - "@abhi18av", - "@bunop", - "@drpatelh", - "@jfy133" - ], - "containers": { - "conda": { - "linux/amd64": { - "lock_file": "modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-839587b417d23042_1.txt" - }, - "linux/arm64": { - "lock_file": "modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-3e45d17b40a576b4_1.txt" - } - }, - "docker": { - "linux/amd64": { - "name": "community.wave.seqera.io/library/multiqc:1.35--839587b417d23042", - "build_id": "bd-839587b417d23042_1", - "scan_id": "sc-f87d7a31551c029f_1" - }, - "linux/arm64": { - "name": "community.wave.seqera.io/library/multiqc:1.35--3e45d17b40a576b4", - "build_id": "bd-3e45d17b40a576b4_1", - "scan_id": "sc-1d0cf4ed1a4b61e0_1" - } - }, - "singularity": { - "linux/amd64": { - "name": "oras://community.wave.seqera.io/library/multiqc:1.35--cb7458fda84d6393", - "build_id": "bd-cb7458fda84d6393_1", - "https": "https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/12/1297c0f5075c19486da167ebf1b6136907d6b5339697b87b29fda335221785b3/data" - }, - "linux/arm64": { - "name": "oras://community.wave.seqera.io/library/multiqc:1.35--f79e87603d312ac0", - "build_id": "bd-f79e87603d312ac0_1", - "https": "https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c0/c007304153702edc622f1a76b41505e7fca65c7145e5b8b2ddce62a5c59af207/data" + ], + "output": { + "prune_in": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.prune.in": { + "type": "file", + "description": "Variants in linkage equilibrium", + "pattern": "*.prune.in", + "ontologies": [] + } + } + ] + ], + "prune_out": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.prune.out": { + "type": "file", + "description": "Excluded variants", + "pattern": "*.prune.out", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@tdkaliki"], + "maintainers": ["@tdkaliki"] } - } - } - }, - "pipelines": [ - { - "name": "abotyper", - "version": "dev" - }, - { - "name": "airrflow", - "version": "5.0.0" }, { - "name": "alleleexpression", - "version": "dev" + "name": "plink2_pca", + "path": "modules/nf-core/plink2/pca/meta.yml", + "type": "module", + "meta": { + "name": "plink2_pca", + "description": "Perform PCA analysis using PLINK", + "keywords": ["plink2", "pca", "plink2_pca"], + "tools": [ + { + "plink2": { + "description": "Whole genome association analysis toolset, designed to perform a range\nof basic, large-scale analyses in a computationally efficient manner\n", + "homepage": "http://www.cog-genomics.org/plink/2.0/", + "documentation": "http://www.cog-genomics.org/plink/2.0/general_usage", + "doi": "10.1186/s13742-015-0047-8", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "npcs": { + "type": "integer", + "description": "Number of PCs to compute" + } + }, + { + "use_approx": { + "type": "boolean", + "description": "If true, use the approximate method" + } + }, + { + "pgen": { + "type": "file", + "description": "PLINK 2 binary genotype table", + "pattern": "*.{pgen}", + "ontologies": [] + } + }, + { + "psam": { + "type": "file", + "description": "PLINK 2 sample information file", + "pattern": "*.{psam}", + "ontologies": [] + } + }, + { + "pvar": { + "type": "file", + "description": "PLINK 2 variant information file", + "pattern": "*.{pvar}", + "ontologies": [] + } + } + ] + ], + "output": { + "evecfile": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\n", + "pattern": "*.eigenvec" + } + }, + { + "*.eigenvec": { + "type": "map", + "description": "Groovy Map containing sample information\n", + "pattern": "*.eigenvec" + } + } + ] + ], + "evfile": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\n", + "pattern": "*.eigenvec" + } + }, + { + "*.eigenval": { + "type": "map", + "description": "Groovy Map containing sample information\n", + "pattern": "*.eigenval" + } + } + ] + ], + "logfile": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\n", + "pattern": "*.eigenvec" + } + }, + { + "*.log": { + "type": "map", + "description": "Groovy Map containing sample information\n", + "pattern": "*.log" + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing the version of the program\n", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@bruno-ariano"], + "maintainers": ["@bruno-ariano"] + } }, { - "name": "ampliseq", - "version": "2.17.0" + "name": "plink2_remove", + "path": "modules/nf-core/plink2/remove/meta.yml", + "type": "module", + "meta": { + "name": "plink2_remove", + "description": "Remove samples from a plink2 dataset", + "keywords": ["plink2", "remove samples", "population genomics"], + "tools": [ + { + "plink2": { + "description": "Whole genome association analysis toolset, designed to perform a range\nof basic, large-scale analyses in a computationally efficient manner\n", + "homepage": "http://www.cog-genomics.org/plink/2.0/", + "documentation": "http://www.cog-genomics.org/plink/2.0/general_usage", + "doi": "10.1186/s13742-015-0047-8", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "plink_genotype_file": { + "type": "file", + "description": "PLINK binary genotype table file or PLINK 2 binary genotype table file", + "pattern": "*.{bed,pgen}", + "ontologies": [] + } + }, + { + "plink_variant_file": { + "type": "file", + "description": "PLINK extended MAP file or PLINK 2 variant information file", + "pattern": "*.{bim,pvar}", + "ontologies": [] + } + }, + { + "plink_sample_file": { + "type": "file", + "description": "PLINK sample information file or PLINK 2 sample information file", + "pattern": "*.{fam,psam}", + "ontologies": [] + } + } + ], + { + "sample_exclude_list": { + "type": "file", + "description": "List of samples to exclude", + "ontologies": [ + { + "edam": "http://edamontology.org/data_0971" + } + ] + } + } + ], + "output": { + "remove_bim": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.bim": { + "type": "file", + "description": "PLINK extended MAP file", + "pattern": "*.bim", + "ontologies": [] + } + } + ] + ], + "remove_bed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "PLINK binary genotype table file", + "pattern": "*.bed", + "ontologies": [] + } + } + ] + ], + "remove_fam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.fam": { + "type": "file", + "description": "PLINK sample information file", + "pattern": "*.fam", + "ontologies": [] + } + } + ] + ], + "remove_pgen": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.pgen": { + "type": "file", + "description": "PLINK 2 binary genotype table file", + "pattern": "*.{pgen}", + "ontologies": [] + } + } + ] + ], + "remove_psam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.psam": { + "type": "file", + "description": "PLINK 2 sample information file", + "pattern": "*.{psam}", + "ontologies": [] + } + } + ] + ], + "remove_pvar": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.pvar": { + "type": "file", + "description": "PLINK 2 variant information file", + "pattern": "*.{pvar}", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@RuthEberhardt"], + "maintainers": ["@RuthEberhardt"] + } }, { - "name": "bacass", - "version": "2.6.0" + "name": "plink2_score", + "path": "modules/nf-core/plink2/score/meta.yml", + "type": "module", + "meta": { + "name": "plink2_score", + "description": "Apply a scoring system to each sample in a plink 2 fileset", + "keywords": ["plink2", "score", "scoring"], + "tools": [ + { + "plink2": { + "description": "Whole genome association analysis toolset, designed to perform a range\nof basic, large-scale analyses in a computationally efficient manner\n", + "homepage": "http://www.cog-genomics.org/plink/2.0/", + "documentation": "http://www.cog-genomics.org/plink/2.0/general_usage", + "doi": "10.1186/s13742-015-0047-8", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "pgen": { + "type": "file", + "description": "PLINK 2 binary genotype table", + "pattern": "*.{pgen}", + "ontologies": [] + } + }, + { + "psam": { + "type": "file", + "description": "PLINK 2 sample information file", + "pattern": "*.{psam}", + "ontologies": [] + } + }, + { + "pvar": { + "type": "file", + "description": "PLINK 2 variant information file", + "pattern": "*.{pvar}", + "ontologies": [] + } + } + ], + { + "scorefile": { + "type": "file", + "description": "A text file containing variant identifiers and weights", + "pattern": "*.{scores,txt,scorefile}", + "ontologies": [] + } + } + ], + "output": { + "score": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.sscore": { + "type": "file", + "description": "A text file containing sample scores, in plink 2 .sscore format", + "pattern": "*.{sscore}", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@nebfield"], + "maintainers": ["@nebfield"] + } }, { - "name": "bamtofastq", - "version": "2.2.1" + "name": "plink2_vcf", + "path": "modules/nf-core/plink2/vcf/meta.yml", + "type": "module", + "meta": { + "name": "plink2_vcf", + "description": "Import variant genetic data using plink2", + "keywords": ["plink2", "import", "variant genetic"], + "tools": [ + { + "plink2": { + "description": "Whole genome association analysis toolset, designed to perform a range\nof basic, large-scale analyses in a computationally efficient manner\n", + "homepage": "http://www.cog-genomics.org/plink/2.0/", + "documentation": "http://www.cog-genomics.org/plink/2.0/general_usage", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "Variant calling file (vcf)", + "pattern": "*.{vcf}, *.{vcf.gz}", + "ontologies": [] + } + } + ] + ], + "output": { + "pgen": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.pgen": { + "type": "file", + "description": "PLINK 2 binary genotype table", + "pattern": "*.{pgen}", + "ontologies": [] + } + } + ] + ], + "psam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.psam": { + "type": "file", + "description": "PLINK 2 sample information file", + "pattern": "*.{psam}", + "ontologies": [] + } + } + ] + ], + "pvar": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.pvar": { + "type": "file", + "description": "PLINK 2 variant information file", + "pattern": "*.{pvar.zst}", + "ontologies": [] + } + } + ] + ], + "pvar_zst": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.pvar.zst": { + "type": "file", + "description": "PLINK 2 variant information zst file", + "pattern": "*.pvar.zst", + "ontologies": [ + { + "edam": "http://edamontology.org/format_4006" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@nebfield"], + "maintainers": ["@nebfield"] + } }, { - "name": "callingcards", - "version": "1.0.0" + "name": "plink2_vcf2bgen", + "path": "modules/nf-core/plink2/vcf2bgen/meta.yml", + "type": "module", + "meta": { + "name": "plink2_vcf2bgen", + "description": "Convert from VCF file to BGEN file version 1.2 format preserving dosages.", + "keywords": ["plink2", "bgen file", "vcf file", "genotype dosages"], + "tools": [ + { + "plink2": { + "description": "Whole genome association analysis toolset, designed to perform a range\nof basic, large-scale analyses in a computationally efficient manner\n", + "homepage": "http://www.cog-genomics.org/plink/2.0/", + "documentation": "http://www.cog-genomics.org/plink/2.0/general_usage", + "doi": "10.1186/s13742-015-0047-8", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "vcf": { + "type": "file", + "description": "A vcf or vcf.gz file with genetic variants", + "pattern": "*.{vcf,vcf.gz}", + "ontologies": [] + } + }, + { + "dosage_field": { + "type": "string", + "description": "The FORMAT field that contains the dosage information. Set to DS to when a dosage field is not present." + } + }, + { + "bgen_reffirst": { + "type": "boolean", + "description": "Set true to write BGEN file with ref-first flag. With this option the first allele in the BGEN correspond to the REF allele." + } + }, + { + "sample_name_mode": { + "type": "string", + "description": "Option to use to set IID/FID in the BGEN file. Allowed values are double-id, const-fid , or id-delim ." + } + } + ] + ], + "output": { + "bgen_file": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.bgen": { + "type": "file", + "description": "BGEN file version 1.2", + "pattern": "*.bgen", + "ontologies": [] + } + } + ] + ], + "sample_file": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.sample": { + "type": "file", + "description": "Sample file defining samples in the BGEN", + "pattern": "*.sample", + "ontologies": [] + } + } + ] + ], + "log_file": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.log": { + "type": "file", + "description": "Log file generated by plink2 with information on the process applied", + "pattern": "*.log", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@edg1983"], + "maintainers": ["@edg1983"] + } }, { - "name": "cellpainting", - "version": "dev" + "name": "plink_bcf", + "path": "modules/nf-core/plink/bcf/meta.yml", + "type": "module", + "meta": { + "name": "plink_bcf", + "description": "Analyses binary variant call format (BCF) files using plink", + "keywords": ["plink", "bcf", "bed", "bim", "fam"], + "tools": [ + { + "plink": { + "description": "Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.", + "homepage": "https://www.cog-genomics.org/plink", + "documentation": "https://www.cog-genomics.org/plink/1.9/data#", + "tool_dev_url": "https://www.cog-genomics.org/plink/1.9/dev", + "licence": ["GPL"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bcf": { + "type": "file", + "description": "Binary variant call format file (bcf)", + "pattern": "*.{bcf}", + "ontologies": [] + } + } + ] + ], + "output": { + "bed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "PLINK binary biallelic genotype table", + "pattern": "*.{bed}", + "ontologies": [] + } + } + ] + ], + "bim": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bim": { + "type": "file", + "description": "PLINK extended MAP file", + "pattern": "*.{bim}", + "ontologies": [] + } + } + ] + ], + "fam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fam": { + "type": "file", + "description": "PLINK sample information file", + "pattern": "*.{fam}", + "ontologies": [] + } + } + ] + ], + "versions_plink": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "plink": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "plink --version 2>&1 | sed 's/^PLINK v//;s/ .*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@atrigila"], + "maintainers": ["@atrigila"], + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "plink": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "plink --version 2>&1 | sed 's/^PLINK v//;s/ .*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + } + } + }, + { + "name": "plink_epistasis", + "path": "modules/nf-core/plink/epistasis/meta.yml", + "type": "module", + "meta": { + "name": "plink_epistasis", + "description": "Epistasis in PLINK, analyzing how the effects of one gene depend on the presence of others.", + "keywords": ["interactions", "variants", "regression"], + "tools": [ + { + "plink": { + "description": "Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.", + "homepage": "https://www.cog-genomics.org/plink", + "documentation": "https://www.cog-genomics.org/plink/1.9/data#recode", + "tool_dev_url": "https://www.cog-genomics.org/plink/1.9/dev", + "licence": ["GPL"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\nmeta is associated to the PLINK native file input\n" + } + }, + { + "bed": { + "type": "file", + "description": "PLINK binary biallelic genotype table file", + "pattern": "*.{bed}", + "ontologies": [] + } + }, + { + "bim": { + "type": "file", + "description": "PLINK extended MAP file", + "pattern": "*.{bim}", + "ontologies": [] + } + }, + { + "fam": { + "type": "file", + "description": "PLINK sample information file", + "pattern": "*.{fam}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information,\ne.g. [ id:'test', single_end:false ]\nmeta2 is associated to VCF file input\n" + } + }, + { + "vcf": { + "type": "file", + "description": "Variant calling file (vcf)", + "pattern": "*.{vcf}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information,\ne.g. [ id:'test', single_end:false ]\nmeta3 is associated to BCF file input\n" + } + }, + { + "bcf": { + "type": "file", + "description": "PLINK variant information + sample ID + genotype call binary file", + "pattern": "*.{bcf}", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing sample information,\ne.g. [ id:'test', single_end:false ]\nmeta4 is associated to phenotype file input\n" + } + }, + { + "phe": { + "type": "file", + "description": "PLINK file containing phenotype information. This phenotype information can be read from the third column with the --pheno option or from a specific column with the --pheno-name option.", + "pattern": "*.{phe}", + "ontologies": [] + } + } + ] + ], + "output": { + "epi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.epi.cc": { + "type": "file", + "description": "PLINK epistasis file", + "pattern": "*.{epi.cc}", + "ontologies": [] + } + } + ] + ], + "episummary": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.epi.cc.summary": { + "type": "file", + "description": "PLINK epistasis summary file", + "pattern": "*.{epi.cc.summary}", + "ontologies": [] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.log": { + "type": "file", + "description": "PLINK epistasis log file", + "pattern": "*.{log}", + "ontologies": [] + } + } + ] + ], + "nosex": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.nosex": { + "type": "file", + "description": "Ambiguous sex ID file", + "pattern": "*.{nosex}", + "ontologies": [] + } + } + ] + ], + "versions_plink": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "plink": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "plink --version 2>&1 | sed 's/^PLINK v//;s/ .*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@davidebag"], + "maintainers": ["@davidebag"], + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "plink": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "plink --version 2>&1 | sed 's/^PLINK v//;s/ .*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + } + } + }, + { + "name": "plink_exclude", + "path": "modules/nf-core/plink/exclude/meta.yml", + "type": "module", + "meta": { + "name": "plink_exclude", + "description": "Exclude variant identifiers from plink bfiles", + "keywords": ["exclude", "plink", "variant identifiers"], + "tools": [ + { + "plink": { + "description": "Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.", + "homepage": "https://www.cog-genomics.org/plink", + "licence": ["GPL"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bed": { + "type": "file", + "description": "PLINK binary biallelic genotype table", + "pattern": "*.{bed}", + "ontologies": [] + } + }, + { + "bim": { + "type": "file", + "description": "PLINK extended MAP file", + "pattern": "*.{bim}", + "ontologies": [] + } + }, + { + "fam": { + "type": "file", + "description": "PLINK sample information file", + "pattern": "*.{fam}", + "ontologies": [] + } + }, + { + "variants": { + "type": "file", + "description": "A text file containing variant identifiers to remove (one per line)", + "pattern": "*.{txt}", + "ontologies": [] + } + } + ] + ], + "output": { + "bed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "PLINK binary biallelic genotype table file", + "pattern": "*.{bed}", + "ontologies": [] + } + } + ] + ], + "bim": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bim": { + "type": "file", + "description": "PLINK extended MAP file", + "pattern": "*.{bim}", + "ontologies": [] + } + } + ] + ], + "fam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fam": { + "type": "file", + "description": "PLINK sample information file", + "pattern": "*.{fam}", + "ontologies": [] + } + } + ] + ], + "versions_plink": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "plink": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "plink --version 2>&1 | sed 's/^PLINK v//;s/ .*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@atrigila"], + "maintainers": ["@atrigila"], + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "plink": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "plink --version 2>&1 | sed 's/^PLINK v//;s/ .*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + } + } + }, + { + "name": "plink_extract", + "path": "modules/nf-core/plink/extract/meta.yml", + "type": "module", + "meta": { + "name": "plink_extract", + "description": "Subset plink bfiles with a text file of variant identifiers", + "keywords": ["extract", "plink", "subset", "bfiles"], + "tools": [ + { + "plink": { + "description": "Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.", + "homepage": "https://www.cog-genomics.org/plink", + "licence": ["GPL"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bed": { + "type": "file", + "description": "PLINK binary biallelic genotype table", + "pattern": "*.{bed}", + "ontologies": [] + } + }, + { + "bim": { + "type": "file", + "description": "PLINK extended MAP file", + "pattern": "*.{bim}", + "ontologies": [] + } + }, + { + "fam": { + "type": "file", + "description": "PLINK sample information file", + "pattern": "*.{fam}", + "ontologies": [] + } + }, + { + "variants": { + "type": "file", + "description": "A text file containing variant identifiers to keep (one per line)", + "pattern": "*.{keep}", + "ontologies": [] + } + } + ] + ], + "output": { + "bed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "PLINK binary biallelic genotype table", 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Produced with the option --allow-no-sex", + "pattern": "*.{nosex}", + "ontologies": [] + } + } + ] + ], + "versions_plink": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "plink": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "plink --version 2>&1 | sed 's/^PLINK v//;s/ .*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@LorenzoS96"], + "maintainers": ["@LorenzoS96"], + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "plink": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "plink --version 2>&1 | sed 's/^PLINK v//;s/ .*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + } + }, + "pipelines": [ + { + "name": "gwas", + "version": "dev" + } 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At each step, all variants in the current window with VIF exceeding the threshold are removed." + } + } + ], + "output": { + "prunein": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.prune.in": { + "type": "file", + "description": "File with IDs of pruned subset of markers that are in approximate linkage equilibrium with each other", + "pattern": "*.{prune.in}", + "ontologies": [] + } + } + ] + ], + "pruneout": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.prune.out": { + "type": "file", + "description": "File with IDs of excluded variants", + "pattern": "*.{prune.out}", + "ontologies": [] + } + } + ] + ], + "versions_plink": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "plink": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "plink --version 2>&1 | sed 's/^PLINK v//;s/ .*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@atrigila"], + "maintainers": ["@atrigila"], + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "plink": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "plink --version 2>&1 | sed 's/^PLINK v//;s/ .*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + } + } + }, + { + "name": "plink_indeppairwise", + "path": "modules/nf-core/plink/indeppairwise/meta.yml", + "type": "module", + "meta": { + "name": "plink_indeppairwise", + "description": "Produce a pruned subset of markers that are in approximate linkage equilibrium with each other. Pairs of variants in the current window with squared correlation greater than the threshold are noted and variants are greedily pruned from the window until no such pairs remain.", + "keywords": ["plink", "indep pairwise", "variant pruning", "bim", "fam"], + "tools": [ + { + "plink": { + "description": "Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.", + "homepage": "https://www.cog-genomics.org/plink", + "documentation": "https://www.cog-genomics.org/plink/1.9/data", + "tool_dev_url": "https://www.cog-genomics.org/plink/1.9/dev", + "licence": ["GPL"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bed": { + "type": "file", + "description": "PLINK binary biallelic genotype table file", + "pattern": "*.{bed}", + "ontologies": [] + } + }, + { + "bim": { + "type": "file", + "description": "PLINK extended MAP file", + "pattern": "*.{bim}", + "ontologies": [] + } + }, + { + "fam": { + "type": "file", + "description": "PLINK sample information file", + "pattern": "*.{fam}", + "ontologies": [] + } + } + ], + { + "window_size": { + "type": "string", + "description": "Window size in variant count or kilobase (if the 'kb' modifier is present) units, a variant count to shift the window at the end of each step, and a variance inflation factor (VIF) threshold." + } + }, + { + "variant_count": { + "type": "string", + "description": "Variant count to shift the window at the end of each step." + } + }, + { + "r2_threshold": { + "type": "string", + "description": "Pairwise r2 threshold. At each step, pairs of variants in the current window with squared correlation greater than the threshold are noted, and variants are greedily pruned from the window until no such pairs remain" + } + } + ], + "output": { + "prunein": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.prune.in": { + "type": "file", + "description": "File with IDs of pruned subset of markers that are in approximate linkage equilibrium with each other", + "pattern": "*.{prune.in}", + "ontologies": [] + } + } + ] + ], + "pruneout": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.prune.out": { + "type": "file", + "description": "File with IDs of excluded variants", + "pattern": "*.{prune.out}", + "ontologies": [] + } + } + ] + ], + "versions_plink": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "plink": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "plink --version 2>&1 | sed 's/^PLINK v//;s/ .*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@atrigila"], + "maintainers": ["@atrigila"], + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "plink": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "plink --version 2>&1 | sed 's/^PLINK v//;s/ .*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + } + } + }, + { + "name": "plink_ld", + "path": "modules/nf-core/plink/ld/meta.yml", + "type": "module", + "meta": { + "name": "plink_ld", + "description": "LD analysis in PLINK examines genetic variant associations within populations", + "keywords": ["genetics", "associations", "variants"], + "tools": [ + { + "plink": { + "description": "Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.", + "homepage": "https://www.cog-genomics.org/plink", + "documentation": "https://www.cog-genomics.org/plink/1.9/data#recode", + "tool_dev_url": "https://www.cog-genomics.org/plink/1.9/dev", + "licence": ["GPL"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\nmeta is associated to PLINK native files input\n" + } + }, + { + "bed": { + "type": "file", + "description": "PLINK binary biallelic genotype table file", + "pattern": "*.{bed}", + "ontologies": [] + } + }, + { + "bim": { + "type": "file", + "description": "PLINK extended MAP file", + "pattern": "*.{bim}", + "ontologies": [] + } + }, + { + "fam": { + "type": "file", + "description": "PLINK sample information file", + "pattern": "*.{fam}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\nmeta2 is associated to VCF files input\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF format input file", + "pattern": "*.{vcf} | *{vcf.gz}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\nmeta is associated to BCF files input\n" + } + }, + { + "bcf": { + "type": "file", + "description": "BCF format input file", + "pattern": "*.{bcf}", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\nmeta is associated to randomly selected snp files input\n" + } + }, + { + "snpfile": { + "type": "file", + "description": "randomly selected snp identifiers, used to calculate linkage disequilibrium", + "pattern": "*.{txt}", + "ontologies": [] + } + } + ] + ], + "output": { + "ld": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.ld": { + "type": "file", + "description": "The output of a linkage disequilibrium analysis in PLINK typically includes a table showing variant pairs and their associated LD values, often expressed as R².\n", + "ontologies": [] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.log": { + "type": "file", + "description": "Log file of the ld process\n", + "ontologies": [] + } + } + ] + ], + "nosex": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.nosex": { + "type": "file", + "description": "Ambiguous sex ID file\n", + "ontologies": [] + } + } + ] + ], + "versions_plink": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "plink": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "plink --version 2>&1 | sed 's/^PLINK v//;s/ .*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@davidebag"], + "maintainers": ["@davidebag"], + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "plink": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "plink --version 2>&1 | sed 's/^PLINK v//;s/ .*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + } + } + }, + { + "name": "plink_recode", + "path": "modules/nf-core/plink/recode/meta.yml", + "type": "module", + "meta": { + "name": "plink_recode", + "description": "Recodes plink bfiles into a new text fileset applying different modifiers", + "keywords": ["recode", "bfiles", "plink", "whole genome association"], + "tools": [ + { + "plink": { + "description": "Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.", + "homepage": "https://www.cog-genomics.org/plink", + "documentation": "https://www.cog-genomics.org/plink/1.9/data#recode", + "tool_dev_url": "https://www.cog-genomics.org/plink/1.9/dev", + "licence": ["GPL"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bed": { + "type": "file", + "description": "PLINK binary biallelic genotype table file", + "pattern": "*.{bed}", + "ontologies": [] + } + }, + { + "bim": { + "type": "file", + "description": "PLINK extended MAP file", + "pattern": "*.{bim}", + "ontologies": [] + } + }, + { + "fam": { + "type": "file", + "description": "PLINK sample information file", + "pattern": "*.{fam}", + "ontologies": [] + } + } + ] + ], + "output": { + "ped": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.ped": { + "type": "file", + "description": "PLINK/MERLIN/Haploview text pedigree + genotype table file. Produced by the default \"--recode\" or by \"--recode 12\".", + "pattern": "*.{ped}", + "ontologies": [] + } + } + ] + ], + "map": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.map": { + "type": "file", + "description": "PLINK text fileset variant information file. Produced by the default \"--recode\" or by \"--recode 12\".", + "pattern": "*.{map}", + "ontologies": [] + } + } + ] + ], + "txt": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "Text file. Produced by \"--recode 23\". Can only be used in a file with only one sample.", + "pattern": "*.{txt}", + "ontologies": [] + } + } + ] + ], + "raw": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.raw": { + "type": "file", + "description": "Additive + dominant component file. Produced by \"--recode AD\" or \"--recode A\".", + "pattern": "*.{raw}", + "ontologies": [] + } + } + ] + ], + "traw": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.traw": { + "type": "file", + "description": "Variant-major additive component file. Produced by \"--recode A-transpose\".", + "pattern": "*.{traw}", + "ontologies": [] + } + } + ] + ], + "beagledat": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.beagle.dat": { + "type": "file", + "description": "BEAGLE file", + "pattern": "*.{beagle.dat}", + "ontologies": [] + } + } + ] + ], + "chrdat": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.chr-*.dat": { + "type": "file", + "description": "chr file", + "pattern": "*.{chr-*.dat}", + "ontologies": [] + } + } + ] + ], + "chrmap": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + ".*chr-*.map": { + "type": "file", + "description": "chr map file", + "pattern": "*.{chr-*.map}", + "ontologies": [] + } + } + ] + ], + "geno": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.recode.geno.txt": { + "type": "file", + "description": "BIMBAM genotype file. Produced by \"--recode bimbam\".", + "pattern": "*.{recode.geno.txt}", + "ontologies": [] + } + } + ] + ], + "pheno": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.recode.pheno.txt": { + "type": "file", + "description": "BIMBAM phenotype file. Produced by \"--recode bimbam\".", + "pattern": "*.{recode.pheno.txt}", + "ontologies": [] + } + } + ] + ], + "pos": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.recode.pos.txt": { + "type": "file", + "description": "BIMBAM variant position file. Produced by \"--recode bimbam\".", + "pattern": "*.{recode.pos.txt}", + "ontologies": [] + } + } + ] + ], + "phase": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.recode.phase.inp": { + "type": "file", + "description": "fastPHASE format. Produced by \"--recode fastphase\".", + "pattern": "*.{recode.phase.inp}", + "ontologies": [] + } + } + ] + ], + "info": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.info": { + "type": "file", + "description": "Haploview map file. Produced by \"--recode HV\".", + "pattern": "*.{info}", + "ontologies": [] + } + } + ] + ], + "lgen": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.lgen": { + "type": "file", + "description": "PLINK long-format genotype file. Produced by \"--recode lgen\".", + "pattern": "*.{lgen}", + "ontologies": [] + } + } + ] + ], + "list": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.list": { + "type": "file", + "description": "Genotype list file. Produced by \"--recode list\".", + "pattern": "*.{list}", + "ontologies": [] + } + } + ] + ], + "gen": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.gen": { + "type": "file", + "description": "Oxford genotype file format. Produced by \"--recode oxford\".", + "pattern": "*.{gen}", + "ontologies": [] + } + } + ] + ], + "gengz": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.gen.gz": { + "type": "file", + "description": "Compressed Oxford genotype file format", + "pattern": "*.{gen.gz}", + "ontologies": [] + } + } + ] + ], + "sample": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.sample": { + "type": "file", + "description": "Oxford sample information file. Produced by \"--recode oxford\".", + "pattern": "*.{sample}", + "ontologies": [] + } + } + ] + ], + "rlist": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.rlist": { + "type": "file", + "description": "Rare genotype list file. Produced by \"--recode rlist\".", + "pattern": "*.{rlist}", + "ontologies": [] + } + } + ] + ], + "strctin": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.strct_in": { + "type": "file", + "description": "Structure-format file. Produced by \"--recode structure\".", + "pattern": "*.{strct_in}", + "ontologies": [] + } + } + ] + ], + "tped": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tped": { + "type": "file", + "description": "Transposed text PED file. Produced by \"--recode transpose\".", + "pattern": "*.{tped}", + "ontologies": [] + } + } + ] + ], + "tfam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tfam": { + "type": "file", + "description": "Transposed text FAM file. Produced by \"--recode transpose\".", + "pattern": "*.{tfam}", + "ontologies": [] + } + } + ] + ], + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf": { + "type": "file", + "description": "Variant calling file (VCF). Produced by \"--recode vcf\".", + "pattern": "*.{vcf}", + "ontologies": [] + } + } + ] + ], + "vcfgz": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "Compressed variant calling file (VCF). Produced by \"--recode vcf bgz\".", + "pattern": "*.{vcf.gz}", + "ontologies": [] + } + } + ] + ], + "versions_plink": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "plink": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "plink --version 2>&1 | sed 's/^PLINK v//;s/ .*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@atrigila"], + "maintainers": ["@atrigila"], + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "plink": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "plink --version 2>&1 | sed 's/^PLINK v//;s/ .*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + } + } + }, + { + "name": "plink_vcf", + "path": "modules/nf-core/plink/vcf/meta.yml", + "type": "module", + "meta": { + "name": "plink_vcf", + "description": "Analyses variant calling files using plink", + "keywords": ["plink", "vcf", "variant", "call"], + "tools": [ + { + "plink": { + "description": "Whole genome association analysis toolset, designed to perform a range\nof basic, large-scale analyses in a computationally efficient manner\n", + "homepage": "https://www.cog-genomics.org/plink", + "tool_dev_url": "https://www.cog-genomics.org/plink/1.9/dev", + "licence": ["GPL"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "Variant calling file (vcf)", + "pattern": "*.{vcf}", + "ontologies": [] + } + } + ] + ], + "output": { + "bed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "PLINK binary biallelic genotype table", + "pattern": "*.{bed}", + "ontologies": [] + } + } + ] + ], + "bim": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bim": { + "type": "file", + "description": "PLINK extended MAP file", + "pattern": "*.{bim}", + "ontologies": [] + } + } + ] + ], + "fam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fam": { + "type": "file", + "description": "PLINK sample information file", + "pattern": "*.{fam}", + "ontologies": [] + } + } + ] + ], + "versions_plink": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "plink": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "plink --version 2>&1 | sed 's/^PLINK v//;s/ .*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@Mxrcon", "@abhi18av"], + "maintainers": ["@Mxrcon", "@abhi18av"], + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "plink": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "plink --version 2>&1 | sed 's/^PLINK v//;s/ .*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + } + }, + "pipelines": [ + { + "name": "gwas", + "version": "dev" + } + ] }, { - "name": "circrna", - "version": "dev" + "name": "plotsr", + "path": "modules/nf-core/plotsr/meta.yml", + "type": "module", + "meta": { + "name": "plotsr", + "description": "Plotsr generates high-quality visualisation of synteny and structural rearrangements between multiple genomes.", + "keywords": ["genomics", "synteny", "rearrangements", "chromosome"], + "tools": [ + { + "plotsr": { + "description": "Visualiser for structural annotations between multiple genomes", + "homepage": "https://github.com/schneebergerlab/plotsr", + "documentation": "https://github.com/schneebergerlab/plotsr", + "tool_dev_url": "https://github.com/schneebergerlab/plotsr", + "doi": "10.1093/bioinformatics/btac196", + "licence": ["MIT"], + "identifier": "biotools:plotsr" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "syri": { + "type": "file", + "description": "Structural annotation mappings (syri.out) identified by SyRI", + "pattern": "*syri.out", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "fastas": { + "type": "list", + "description": "Fasta files in the sequence specified by the `genomes` file", + "pattern": "*.{fasta,fa,fsa,faa}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "genomes": { + "type": "string", + "description": "A genomes.txt file including the header: #file\tname\ttags\nand Fasta file names, title for the plot and plotsr configuration tags. As example is:\n#file name tags\ngenome.fasta test lw:1.5\ngenome2.fasta reference lw:1.5\n", + "pattern": "*.txt" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "bedpe": { + "type": "file", + "description": "Structural annotation mappings in BEDPE format", + "pattern": "*.bedpe", + "ontologies": [] + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "markers": { + "type": "file", + "description": "File containing path to markers", + "pattern": "*.bed", + "ontologies": [] + } + } + ], + [ + { + "meta6": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "tracks": { + "type": "file", + "description": "File listing paths and details for all tracks to be plotted", + "pattern": "*.txt", + "ontologies": [] + } + } + ], + [ + { + "meta7": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "chrord": { + "type": "file", + "description": "File containing reference (first genome) chromosome IDs in the order in which they are to be plotted.\nFile requires one chromosome ID per line. Not compatible with --chr\n", + "pattern": "*.txt", + "ontologies": [] + } + } + ], + [ + { + "meta8": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "chrname": { + "type": "file", + "description": "File containing reference (first genome) chromosome names to be used in the plot.\nFile needs to be a TSV with the chromosome ID in first column and chromosome name in the second.\n", + "pattern": "*.txt", + "ontologies": [] + } + } + ] + ], + "output": { + "png": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.png": { + "type": "file", + "description": "Synteny plot", + "pattern": "*.png", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@GallVp"], + "maintainers": ["@GallVp"] + } }, { - "name": "coproid", - "version": "2.0.1" + "name": "pmdtools_filter", + "path": "modules/nf-core/pmdtools/filter/meta.yml", + "type": "module", + "meta": { + "name": "pmdtools_filter", + "description": "pmdtools command to filter ancient DNA molecules from others", + "keywords": ["pmdtools", "aDNA", "filter", "damage"], + "tools": [ + { + "pmdtools": { + "description": "Compute postmortem damage patterns and decontaminate ancient genomes", + "homepage": "https://github.com/pontussk/PMDtools", + "documentation": "https://github.com/pontussk/PMDtools", + "tool_dev_url": "https://github.com/pontussk/PMDtools", + "doi": "10.1073/pnas.1318934111", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file", + "pattern": "*.bam", + "ontologies": [] + } + }, + { + "bai": { + "type": "file", + "description": "BAM index file", + "pattern": "*.bai", + "ontologies": [] + } + } + ], + { + "threshold": { + "type": "float", + "description": "Post-mortem damage score threshold" + } + }, + { + "reference": { + "type": "file", + "description": "FASTA file", + "pattern": "*.{fa,fasta}", + "ontologies": [] + } + } + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Filtered BAM file", + "pattern": "*.bam", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@alexandregilardet"], + "maintainers": ["@alexandregilardet"] + } }, { - "name": "createpanelrefs", - "version": "dev" - }, - { - "name": "createtaxdb", - "version": "3.0.0" - }, - { - "name": "crisprseq", - "version": "2.3.0" - }, - { - "name": "dartseq", - "version": "dev" - }, - { - "name": "datasync", - "version": "dev" + "name": "pneumocat", + "path": "modules/nf-core/pneumocat/meta.yml", + "type": "module", + "meta": { + "name": "pneumocat", + "description": "Determine Streptococcus pneumoniae serotype from Illumina paired-end reads", + "keywords": ["fastq", "serotype", "Streptococcus pneumoniae"], + "tools": [ + { + "pneumocat": { + "description": "PneumoCaT (Pneumococcal Capsular Typing) uses a two-step step approach to assign capsular type to S.pneumoniae genomic data (Illumina)", + "homepage": "https://github.com/ukhsa-collaboration/PneumoCaT", + "documentation": "https://github.com/ukhsa-collaboration/PneumoCaT", + "tool_dev_url": "https://github.com/ukhsa-collaboration/PneumoCaT", + "doi": "10.7717/peerj.2477", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "Input Illunina paired-end FASTQ files", + "pattern": "*.{fq.gz,fastq.gz}", + "ontologies": [] + } + } + ] + ], + "output": { + "xml": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.xml": { + "type": "file", + "description": "The predicted serotype in XML format", + "pattern": "*.xml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2332" + } + ] + } + } + ] + ], + "txt": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "A detailed description of the predicted serotype", + "pattern": "*.txt", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@rpetit3"], + "maintainers": ["@rpetit3"] + } }, { - "name": "deepmutscan", - "version": "dev" + "name": "polypolish_polish", + "path": "modules/nf-core/polypolish/polish/meta.yml", + "type": "module", + "meta": { + "name": "polypolish_polish", + "description": "Polishing genome assemblies with short reads.", + "keywords": ["assembly polishing", "genome polishing", "ont"], + "tools": [ + { + "polypolish": { + "description": "Polishing genome assemblies with short reads.", + "homepage": "https://github.com/rrwick/Polypolish", + "documentation": "https://github.com/rrwick/Polypolish/wiki", + "tool_dev_url": "https://github.com/rrwick/Polypolish", + "doi": "10.1099/mgen.0.001254", + "licence": ["GPL3"], + "identifier": "biotools:polypolish" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA file with draft assembly of ONT data", + "pattern": "*.{fasta,fna,fa,fas}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "sam": { + "type": "file", + "description": "List of SAM files of short reads mapped against the FASTA input file", + "pattern": "*.sam", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2573" + } + ] + } + } + ], + { + "save_debug": { + "type": "boolean", + "description": "Turn debug output on", + "pattern": "true|false" + } + } + ], + "output": { + "fasta": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.fasta": { + "type": "file", + "description": "FASTA file with polished draft assembly", + "pattern": "*.{fasta,fna,fa,fas}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ] + ], + "debug": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "File with debug base information", + "pattern": "*.txt", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@ktrappe"], + "maintainers": ["@ktrappe"] + } }, { - "name": "demo", - "version": "1.1.0" + "name": "poolsnp", + "path": "modules/nf-core/poolsnp/meta.yml", + "type": "module", + "meta": { + "name": "poolsnp", + "description": "PoolSNP is a heuristic SNP caller, which uses an MPILEUP file and a reference genome in FASTA format as inputs.", + "keywords": ["poolseq", "mpileup", "variant-calling"], + "tools": [ + { + "poolsnp": { + "description": "PoolSNP is a heuristic SNP caller, which uses an MPILEUP file and a reference genome in FASTA format as inputs.", + "homepage": "https://github.com/capoony/PoolSNP", + "documentation": "https://github.com/capoony/PoolSNP/blob/master/README.md", + "licence": ["Apache-2.0"], + "args_id": "$args", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information.\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "mpileup": { + "type": "file", + "description": "MPILEUP file. This file contains the base calls and alignment information\nfor each position in the reference genome.\nIt is used as input for variant calling and other downstream analyses.\n", + "pattern": "*.mpileup", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information.\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "reference": { + "type": "file", + "description": "Reference genome in FASTA format.\nMay NOT contain any special characters such as \"/|,:\"\n", + "pattern": "*.{fasta,fa}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information.\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "max_cov": { + "type": "float", + "description": "Maximum coverage is calculated for every library and chromosomal arm\nas the percentile of a coverage distribution,\ne.g. max-cov=0.98 will only consider positions within the 98% coverage percentile\nfor a given sample and chromosomal arm.\nNote: Provide `max_cov` or `max_cov_file` but not both.\nRead more: https://github.com/capoony/PoolSNP\n" + } + }, + { + "max_cov_file": { + "type": "file", + "description": "File containing the maximum coverage thresholds for all chromosomal arms and libraries.\nThis file needs to be tab-delimited with two columns:\n1. Chromosomal name\n2. Comma-separated list of coverage thresholds for each sample in the mpileup file.\ne.g. `2L 100,100,100,200,200` would mean a threshold of 100 for the first three samples\nand 200 for the last two samples on chromosomal arm 2L.\nNote: Provide `max_cov` or `max_cov_file` but not both.\nRead more: https://github.com/capoony/PoolSNP\n", + "ontologies": [] + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "Gzipped VCF file containing allele counts and frequencies for every position and library", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "max_cov": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*cov-*.txt": { + "type": "file", + "description": "File containing the maximum coverage thresholds for all chromosomal arms and libraries", + "pattern": "*cov-*.txt", + "ontologies": [] + } + } + ] + ], + "bad_sites": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*BS.txt.gz": { + "type": "file", + "description": "File containing a list of sites (variable and invariable) that did not pass the SNP calling criteria", + "pattern": "*BS.txt.gz", + "optional": true, + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@abhilesh"], + "maintainers": ["@abhilesh"] + } }, { - "name": "demultiplex", - "version": "1.7.1" + "name": "popscle_demuxlet", + "path": "modules/nf-core/popscle/demuxlet/meta.yml", + "type": "module", + "meta": { + "name": "popscle_demuxlet", + "description": "Software to deconvolute sample identity and identify multiplets when multiple samples are pooled by barcoded single cell sequencing and external genotyping data for each sample is available.", + "keywords": ["popscle", "demultiplexing", "genotype-based deconvoltion", "single cell"], + "tools": [ + { + "popscle": { + "description": "A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and auxiliary tools", + "homepage": "https://github.com/statgen/popscle", + "documentation": "https://github.com/statgen/popscle", + "tool_dev_url": "https://github.com/statgen/popscle", + "doi": "10.1038/nbt.4042", + "licence": ["Apache-2.0"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "plp_prefix": { + "type": "string", + "description": "Prefix of pileup files (CEL,VAR and PLP) produced by popscle/dsc_pileup." + } + }, + { + "bam": { + "type": "file", + "description": "Input SAM/BAM/CRAM file without running popscle/dsc_pileup, must be sorted by coordinates and indexed.", + "pattern": "*.{bam,cram,sam}", + "ontologies": [] + } + }, + { + "donor_genotype": { + "type": "file", + "description": "Input VCF/BCF file, containing the individual genotypes (GT), posterior probability (GP), or genotype likelihood (PL) to assign each barcode to a specific sample (or a pair of samples) in the VCF file.", + "pattern": "*.{vcf,bcf}", + "ontologies": [] + } + } + ] + ], + "output": { + "demuxlet_result": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "*.best": { + "type": "file", + "description": "Result of demuxlet containing the best guess of the sample identity, with detailed statistics to reach to the best guess.", + "pattern": "*.best", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@mari-ga", "@maxozo", "@wxicu", "@Zethson"], + "maintainers": ["@mari-ga", "@maxozo", "@wxicu", "@Zethson"] + } }, { - "name": "denovotranscript", - "version": "1.2.1" + "name": "popscle_dscpileup", + "path": "modules/nf-core/popscle/dscpileup/meta.yml", + "type": "module", + "meta": { + "name": "popscle_dscpileup", + "description": "Software to pileup reads and corresponding base quality for each overlapping SNPs and each barcode.", + "keywords": ["popscle", "demultiplexing", "genotype-based deconvoltion", "single cell", "pile up"], + "tools": [ + { + "popscle": { + "description": "A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and auxiliary tools", + "homepage": "https://github.com/statgen/popscle", + "documentation": "https://github.com/statgen/popscle", + "tool_dev_url": "https://github.com/statgen/popscle", + "doi": "10.1038/nbt.4042", + "licence": ["Apache-2.0"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "bam": { + "type": "file", + "description": "Input SAM/BAM/CRAM file produced by the standard 10x sequencing platform, or any other barcoded single cell RNA-seq.", + "pattern": "*.{bam,cram,sam}", + "ontologies": [] + } + }, + { + "vcf": { + "type": "file", + "description": "Input VCF/BCF file files containing (AC) and (AN) from referenced population (e.g. 1000g).", + "pattern": "*.{vcf,bcf}", + "ontologies": [] + } + } + ] + ], + "output": { + "cel": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "*.cel.gz": { + "type": "file", + "description": "Contains the relation between numerated barcode ID and barcode and the number of SNP and number of UMI for each barcoded droplet.", + "pattern": "*.cel.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "plp": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "*.plp.gz": { + "type": "file", + "description": "Contains the overlapping SNP and the corresponding read and base quality for each barcode ID.", + "pattern": "*.plp.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "var": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "*.var.gz": { + "type": "file", + "description": "Contains the position, reference allele and allele frequency for each SNP.", + "pattern": "*.var.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "umi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "*.umi.gz": { + "type": "file", + "description": "Contains the position covered by each umi.", + "pattern": "*.umi.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@mari-ga", "@maxozo", "@wxicu", "@Zethson"], + "maintainers": ["@mari-ga", "@maxozo", "@wxicu", "@Zethson"] + } }, { - "name": "detaxizer", - "version": "1.3.0" + "name": "popscle_freemuxlet", + "path": "modules/nf-core/popscle/freemuxlet/meta.yml", + "type": "module", + "meta": { + "name": "popscle_freemuxlet", + "description": "Software to deconvolute sample identity and identify multiplets when multiple samples are pooled by barcoded single cell sequencing and external genotyping data for each sample is not available.", + "keywords": ["popscle", "demultiplexing", "genotype-based deconvoltion", "single cell"], + "tools": [ + { + "popscle": { + "description": "A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and auxiliary tools", + "homepage": "https://github.com/statgen/popscle", + "documentation": "https://github.com/statgen/popscle", + "tool_dev_url": "https://github.com/statgen/popscle", + "doi": "10.1038/nbt.4042", + "licence": ["Apache-2.0"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "plp": { + "type": "directory", + "description": "Directory contains pileup files (CEL,VAR and PLP) produced by popscle/dsc_pileup." + } + }, + { + "n_sample": { + "type": "integer", + "description": "Number of samples multiplexed together." + } + } + ] + ], + "output": { + "result": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.clust1.samples.gz": { + "type": "file", + "description": "Output file contains the best guess of the sample identity, with detailed statistics to reach to the best guess.", + "pattern": "*.clust1.samples.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.clust1.vcf.gz": { + "type": "file", + "description": "Output vcf file for each sample inferred and clustered from freemuxlet.", + "pattern": "*.clust1.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "lmix": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.lmix": { + "type": "file", + "description": "Output file contains basic statistics for each barcode.", + "pattern": "*.lmix", + "ontologies": [] + } + } + ] + ], + "singlet_result": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.clust0.samples.gz": { + "type": "file", + "description": "Optional output file contains the best sample identity assuming all droplets are singlets when writing auxiliary output files is turned on.", + "pattern": "*.clust0.samples.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "singlet_vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.clust0.vcf.gz": { + "type": "file", + "description": "Optional output vcf file for each sample inferred and clustered from freemuxlet assuming all droplets are singlets when writing auxiliary output files is turned on.", + "pattern": "*.clust0.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@wxicu"], + "maintainers": ["@wxicu"] + } }, { - "name": "diseasemodulediscovery", - "version": "dev" + "name": "porechop_abi", + "path": "modules/nf-core/porechop/abi/meta.yml", + "type": "module", + "meta": { + "name": "porechop_abi", + "description": "Extension of Porechop whose purpose is to process adapter sequences in ONT reads.", + "keywords": ["porechop_abi", "adapter", "nanopore"], + "tools": [ + { + "porechop_abi": { + "description": "Extension of Porechop whose purpose is to process adapter sequences in ONT reads.", + "homepage": "https://github.com/bonsai-team/Porechop_ABI", + "documentation": "https://github.com/bonsai-team/Porechop_ABI", + "tool_dev_url": "https://github.com/bonsai-team/Porechop_ABI", + "doi": "10.1101/2022.07.07.499093", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "fastq/fastq.gz file", + "pattern": "*.{fastq,fastq.gz,fq,fq.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ], + { + "custom_adapters": { + "type": "file", + "description": "Text file containing custom adapters", + "ontologies": [] + } + } + ], + "output": { + "reads": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fastq.gz": { + "type": "file", + "description": "Adapter-trimmed fastq.gz file", + "pattern": "*.fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "Log file containing stdout information", + "pattern": "*.log", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@sofstam", "LilyAnderssonLee"], + "maintainers": ["@sofstam", "LilyAnderssonLee"] + }, + "pipelines": [ + { + "name": "mag", + "version": "5.4.2" + }, + { + "name": "taxprofiler", + "version": "2.0.0" + } + ] }, { - "name": "drop", - "version": "1.0.0" + "name": "porechop_porechop", + "path": "modules/nf-core/porechop/porechop/meta.yml", + "type": "module", + "meta": { + "name": "porechop_porechop", + "description": "Adapter removal and demultiplexing of Oxford Nanopore reads", + "keywords": ["adapter", "nanopore", "demultiplexing"], + "tools": [ + { + "porechop": { + "description": "Adapter removal and demultiplexing of Oxford Nanopore reads", + "homepage": "https://github.com/rrwick/Porechop", + "documentation": "https://github.com/rrwick/Porechop", + "tool_dev_url": "https://github.com/rrwick/Porechop", + "doi": "10.1099/mgen.0.000132", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "fastq/fastq.gz file", + "pattern": "*.{fastq,fastq.gz,fq,fq.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ] + ], + "output": { + "reads": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fastq.gz": { + "type": "file", + "description": "Demultiplexed and/or adapter-trimmed fastq.gz file", + "pattern": "*.{fastq.gz}", + "ontologies": [] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "Log file containing stdout information", + "pattern": "*.log", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": [ + "@ggabernet", + "@jasmezz", + "@d4straub", + "@LaurenceKuhl", + "@SusiJo", + "@jonasscheid", + "@jonoave", + "@GokceOGUZ", + "@jfy133" + ], + "maintainers": [ + "@ggabernet", + "@jasmezz", + "@d4straub", + "@LaurenceKuhl", + "@SusiJo", + "@jonasscheid", + "@jonoave", + "@GokceOGUZ", + "@jfy133" + ] + }, + "pipelines": [ + { + "name": "bacass", + "version": "2.6.0" + }, + { + "name": "genomeassembler", + "version": "1.1.0" + }, + { + "name": "mag", + "version": "5.4.2" + }, + { + "name": "methylong", + "version": "2.0.0" + }, + { + "name": "taxprofiler", + "version": "2.0.0" + } + ] }, { - "name": "epitopeprediction", - "version": "3.1.0" + "name": "portcullis_full", + "path": "modules/nf-core/portcullis/full/meta.yml", + "type": "module", + "meta": { + "name": "portcullis_full", + "description": "Run all Portcullis steps in one go", + "keywords": ["rnaseq", "genome", "splice", "junction"], + "tools": [ + { + "portcullis": { + "description": "Portcullis is a tool that filters out invalid splice junctions from RNA-seq alignment data. It accepts BAM files from various RNA-seq mappers, analyzes splice junctions and removes likely false positives, outputting filtered results in multiple formats for downstream analysis.", + "homepage": "https://portcullis.readthedocs.io/en/latest/index.html", + "documentation": "https://portcullis.readthedocs.io/en/latest/using.html", + "doi": "10.1101/217620", + "license": ["GPL-3.0"], + "identifier": "biotools:portcullis" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information about the sample\ne.g. [ id:'sample1', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "RNA-seq-aligned and sorted BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + }, + { + "edam": "http://edamontology.org/format_2573" + }, + { + "edam": "http://edamontology.org/format_3462" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing information about the sample\ne.g. [ id:'sample1', single_end:false ]\n" + } + }, + { + "bed": { + "type": "file", + "description": "Input reference annotation of junctions in BED format", + "pattern": "*.bed", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3003" + } + ] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing information about the sample\ne.g. [ id:'sample1', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input genome reference fasta file", + "pattern": "*.{fa,fasta}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1332" + } + ] + } + } + ] + ], + "output": { + "pass_junctions_bed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample1', single_end:false ]\n" + } + }, + { + "*.pass.junctions.bed": { + "type": "file", + "description": "Filtered splice junction coordinates in BED format, containing genomic coordinates of valid splice junctions after filtering out false positives\n", + "pattern": "*.pass.junctions.bed", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3003" + } + ] + } + } + ] + ], + "pass_junctions_tab": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample1', single_end:false ]\n" + } + }, + { + "*.pass.junctions.tab": { + "type": "file", + "description": "Tabular representation of filtered splice junctions with additional metrics including junction scores, read support, and filtering decision data\n", + "pattern": "*.pass.junctions.tab", + "ontologies": [ + { + "eadam": "http://edamontology.org/format_3475" + }, + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample1', single_end:false ]\n" + } + }, + { + "*.portcullis.log": { + "type": "file", + "description": "Log file containing Portcullis execution details, processing steps, and filtering statistics", + "pattern": "*.log", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + } + ] + ], + "intron_gff": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample1', single_end:false ]\n" + } + }, + { + "*.intron.gff3": { + "type": "file", + "description": "Output intron-based junctions in GFF format.\n", + "pattern": "*.intron.gff3", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1975" + } + ] + } + } + ] + ], + "exon_gff": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample1', single_end:false ]\n" + } + }, + { + "*.exon.gff3": { + "type": "file", + "description": "Output exon-based junctions in GFF format.\n", + "pattern": "*.exon.gff3", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1975" + } + ] + } + } + ] + ], + "spliced_bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample1', single_end:false ]\n" + } + }, + { + "*.spliced.bam": { + "type": "file", + "description": "BAM file after filtering original BAM file by removing alignments associated with bad junctions\n", + "pattern": "*.spliced.bam", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + } + ] + ], + "spliced_bai": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample1', single_end:false ]\n" + } + }, + { + "*.spliced.bam.bai": { + "type": "file", + "description": "Index of the output BAM file\n", + "pattern": "*spliced.bam.bai", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3327" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@jblancoheredia"], + "maintainer": ["@jblancoheredia", "@anoronh4"] + } }, { - "name": "evexplorer", - "version": "dev" + "name": "portello", + "path": "modules/nf-core/portello/meta.yml", + "type": "module", + "meta": { + "name": "portello", + "description": "Transfer HiFi read mappings from their own assembly contigs to a standard reference", + "keywords": ["assembly", "transfer", "pacbio", "genomics"], + "tools": [ + { + "portello": { + "description": "Method to transfer HiFi read mappings from de novo assembly to reference", + "homepage": "https://github.com/PacificBiosciences/portello", + "documentation": "https://github.com/PacificBiosciences/portello", + "tool_dev_url": "https://github.com/PacificBiosciences/portello", + "licence": [ + "Pacific Biosciences Software License (https://github.com/PacificBiosciences/portello/blob/main/LICENSE.md)" + ], + "identifier": "biotools:portello" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "asm_to_ref_bam": { + "type": "file", + "description": "Assembly contig to reference genome alignment file in BAM/CRAM format", + "pattern": "*.{bam,cram}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + }, + { + "edam": "http://edamontology.org/format_2573" + } + ] + } + }, + { + "asm_to_ref_bai": { + "type": "file", + "description": "BAM/CRAM index file", + "pattern": "*.{bam.bai,cram.crai}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + }, + { + "edam": "http://edamontology.org/format_2573" + } + ] + } + }, + { + "read_to_asm_bam": { + "type": "file", + "description": "Read to assembly alignment file in BAM/CRAM format", + "pattern": "*.{bam,cram}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + }, + { + "edam": "http://edamontology.org/format_2573" + } + ] + } + }, + { + "read_to_asm_bai": { + "type": "file", + "description": "BAM/CRAM/SAM index file", + "pattern": "*.{bam,cram}.bai", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + }, + { + "edam": "http://edamontology.org/format_2573" + } + ] + } + }, + { + "ref_fasta": { + "type": "file", + "description": "Reference genome FASTA file", + "pattern": "*.fa*", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + }, + { + "assembly_mode": { + "type": "string", + "description": "The assembly mode used for the input BAM files", + "enum": ["fully-phased", "partially-phased"] + } + }, + { + "output_vcf": { + "type": "boolean", + "description": "Whether to output phased variant calls in VCF format" + } + } + ] + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map 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"http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.vcf.gz.tbi": { + "type": "file", + "description": "VCF index file", + "pattern": "*.{vcf.gz.tbi}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3616" + } + ] + } + } + ] + ], + "versions_portello": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "portello": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "portello --version | sed -e 's/portello //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "portello": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "portello --version | sed -e 's/portello //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@sofiademmou"], + "maintainers": ["@sofiademmou"] + } }, { - "name": "fastqrepair", - "version": "1.0.0" + "name": "preseq_ccurve", + "path": "modules/nf-core/preseq/ccurve/meta.yml", + "type": "module", + "meta": { + "name": "preseq_ccurve", + "description": "Software for predicting library complexity and genome coverage in high-throughput sequencing", + "keywords": ["preseq", "library", "complexity"], + "tools": [ + { + "preseq": { + "description": "Software for predicting library complexity and genome coverage in high-throughput sequencing", + "homepage": "http://smithlabresearch.org/software/preseq/", + "documentation": "http://smithlabresearch.org/wp-content/uploads/manual.pdf", + "tool_dev_url": "https://github.com/smithlabcode/preseq", + "licence": ["GPL"], + "identifier": "biotools:preseq" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}", + "ontologies": [] + } + } + ] + ], + "output": { + "c_curve": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.c_curve.txt": { + "type": "file", + "description": "Preseq c_curve output file", + "pattern": "*.{c_curve.txt}", + "ontologies": [] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "Log file containing stderr produced by Preseq", + "pattern": "*.{log}", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@drpatelh", "@edmundmiller"], + "maintainers": ["@drpatelh", "@edmundmiller"] + }, + "pipelines": [ + { + "name": "callingcards", + "version": "1.0.0" + }, + { + "name": "genomicrelatedness", + "version": "dev" + }, + { + "name": "nascent", + "version": "2.3.0" + } + ] }, { - "name": "fastquorum", - "version": "1.2.0" + "name": "preseq_lcextrap", + "path": "modules/nf-core/preseq/lcextrap/meta.yml", + "type": "module", + "meta": { + "name": "preseq_lcextrap", + "description": "Software for predicting library complexity and genome coverage in high-throughput sequencing", + "keywords": ["preseq", "library", "complexity"], + "tools": [ + { + "preseq": { + "description": "Software for predicting library complexity and genome coverage in high-throughput sequencing", + "homepage": "http://smithlabresearch.org/software/preseq/", + "documentation": "http://smithlabresearch.org/wp-content/uploads/manual.pdf", + "tool_dev_url": "https://github.com/smithlabcode/preseq", + "licence": ["GPL"], + "identifier": "biotools:preseq" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}", + "ontologies": [] + } + } + ] + ], + "output": { + "lc_extrap": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.lc_extrap.txt": { + "type": "file", + "description": "File containing output of Preseq lcextrap", + "pattern": "*.{lc_extrap.txt}", + "ontologies": [] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "Log file containing stderr produced by Preseq", + "pattern": "*.{log}", + "ontologies": [] + } + } + ] + ], + "versions_preseq": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "preseq": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "preseq 2>&1 | sed -n 's/.*Version: \\(.*\\)/\\1/p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "preseq": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "preseq 2>&1 | sed -n 's/.*Version: \\(.*\\)/\\1/p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@drpatelh", "@edmundmiller"], + "maintainers": ["@drpatelh", "@edmundmiller"] + }, + "pipelines": [ + { + "name": "atacseq", + "version": "2.1.2" + }, + { + "name": "chipseq", + "version": "2.1.0" + }, + { + "name": "cutandrun", + "version": "3.2.2" + }, + { + "name": "genomicrelatedness", + "version": "dev" + }, + { + "name": "methylseq", + "version": "4.2.0" + }, + { + "name": "nascent", + "version": "2.3.0" + }, + { + "name": "rnaseq", + "version": "3.26.0" + } + ] }, { - "name": "funcprofiler", - "version": "dev" + "name": "president", + "path": "modules/nf-core/president/meta.yml", + "type": "module", + "meta": { + "name": "president", + "description": "Calculate pairwise nucleotide identity with respect to a reference sequence", + "keywords": ["fasta", "genome", "qc", "nucleotides"], + "tools": [ + { + "president": { + "description": "Calculate pairwise nucleotide identity with respect to a reference sequence", + "homepage": "https://github.com/rki-mf1/president", + "documentation": "https://github.com/rki-mf1/president", + "tool_dev_url": "https://github.com/rki-mf1/president", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information, e.g. [ id:'test', single_end:false ]" + } + }, + { + "fasta": { + "type": "file", + "description": "One fasta file or a list of multiple fasta files to perform president on. Has to be uncompressed!", + "pattern": "*.{fasta,fas,fa,fna,ffn,faa,mpfa,frn}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing information about the reference genome" + } + }, + { + "reference": { + "type": "file", + "description": "Fasta of a reference genome. Has to be uncompressed!", + "pattern": "*.{fasta,fas,fa,fna,ffn,faa,mpfa,frn}", + "ontologies": [] + } + } + ], + { + "compress": { + "type": "boolean", + "description": "Set to \"true\" if fasta output should be compressed" + } + } + ], + "output": { + "valid_fasta": [ + [ + { + "meta": { + "type": "file", + "description": "Fasta file containing sequences which passed the qc (\"valid.fasta\"). If true is set on the \"compress\" input value, the file is gz-compressed.", + "pattern": "*.{fasta.gz, fasta}", + "ontologies": [] + } + }, + { + "${prefix}_valid.fasta*": { + "type": "file", + "description": "Fasta file containing sequences which passed the qc (\"valid.fasta\"). If true is set on the \"compress\" input value, the file is gz-compressed.", + "pattern": "*.{fasta.gz, fasta}", + "ontologies": [] + } + } + ] + ], + "invalid_fasta": [ + [ + { + "meta": { + "type": "file", + "description": "Fasta file containing sequences which passed the qc (\"valid.fasta\"). If true is set on the \"compress\" input value, the file is gz-compressed.", + "pattern": "*.{fasta.gz, fasta}", + "ontologies": [] + } + }, + { + "${prefix}_invalid.fasta*": { + "type": "file", + "description": "Fasta file containing sequences which didn't pass the qc (\"invalid.fasta\"). If true is set on the \"compress\" input value, the files are gz-compressed.", + "pattern": "*_invalid.{fasta.gz, fasta}", + "ontologies": [] + } + } + ] + ], + "report": [ + [ + { + "meta": { + "type": "file", + "description": "Fasta file containing sequences which passed the qc (\"valid.fasta\"). If true is set on the \"compress\" input value, the file is gz-compressed.", + "pattern": "*.{fasta.gz, fasta}", + "ontologies": [] + } + }, + { + "*.tsv": { + "type": "file", + "description": "Report with some information for every sample, like statistic values. See docs for details", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "file", + "description": "Fasta file containing sequences which passed the qc (\"valid.fasta\"). If true is set on the \"compress\" input value, the file is gz-compressed.", + "pattern": "*.{fasta.gz, fasta}", + "ontologies": [] + } + }, + { + "*.log": { + "type": "file", + "description": "Log file of president", + "pattern": "*.log", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@paulwolk"], + "maintainers": ["@paulwolk", "@gallvp"] + } }, { - "name": "funcscan", - "version": "3.0.0" + "name": "presto_filterseq", + "path": "modules/nf-core/presto/filterseq/meta.yml", + "type": "module", + "meta": { + "name": "presto_filterseq", + "description": "Filter reads by quality score.", + "keywords": ["immcantation", "airrseq", "genomics", "immunoinformatics"], + "tools": [ + { + "presto": { + "description": "A bioinformatics toolkit for processing high-throughput lymphocyte receptor sequencing data.", + "homepage": "https://immcantation.readthedocs.io", + "documentation": "https://presto.readthedocs.io", + "tool_dev_url": "https://bitbucket.org/kleinstein/presto", + "doi": "10.1093/bioinformatics/btu138", + "licence": ["AGPL v3"], + "identifier": "biotools:presto-measure" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "reads": { + "type": "file", + "description": "fastq file", + "pattern": "*.{fastq}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ] + ], + "output": { + "reads": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*_quality-pass.fastq": { + "type": "file", + "description": "filtered fastq file", + "pattern": "*.{fastq}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ] + ], + "logs": [ + { + "*_command_log.txt": { + "type": "file", + "description": "command logs", + "pattern": "*.txt", + "ontologies": [] + } + } + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ], + "log_tab": [ + { + "*.tab": { + "type": "file", + "description": "parsed log table", + "pattern": "*.tab", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + }, + "authors": ["@ggabernet"] + } }, { - "name": "genomeannotator", - "version": "dev" + "name": "pretextmap", + "path": "modules/nf-core/pretextmap/meta.yml", + "type": "module", + "meta": { + "name": "pretextmap", + "description": "converts sam/bam/cram/pairs into genome contact map", + "keywords": ["contact", "bam", "map"], + "tools": [ + { + "pretextmap": { + "description": "Paired REad TEXTure Mapper. Converts SAM formatted read pairs into genome contact maps.", + "homepage": "https://github.com/wtsi-hpag/PretextMap", + "documentation": "https://github.com/wtsi-hpag/PretextMap/blob/master/README.md", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM/SAM file or pairs formatted reads file", + "pattern": "*.{bam,cram,sam,pairs.gz}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference sequence file", + "pattern": "*.{fasta,fna,fa}", + "ontologies": [] + } + }, + { + "fai": { + "type": "file", + "description": "Reference sequence index file", + "pattern": "*.{fai}", + "ontologies": [] + } + } + ] + ], + "output": { + "pretext": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.pretext": { + "type": "file", + "description": "pretext map", + "pattern": "*.pretext", + "ontologies": [] + } + } + ] + ], + "versions_pretextmap": [ + [ + { + "${task.process}": { + "type": "string", + "description": "Name of the process" + } + }, + { + "PretextMap": { + "type": "string", + "description": "Name of the tool" + } + }, + { + "PretextMap | sed \"/Version/!d; s/.*Version //\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_samtools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "Name of the process" + } + }, + { + "samtools": { + "type": "string", + "description": "Name of the tool" + } + }, + { + "samtools --version | sed \"1!d; s/samtools //\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "Name of the process" + } + }, + { + "PretextMap": { + "type": "string", + "description": "Name of the tool" + } + }, + { + "PretextMap | sed \"/Version/!d; s/.*Version //\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "Name of the process" + } + }, + { + "samtools": { + "type": "string", + "description": "Name of the tool" + } + }, + { + "samtools --version | sed \"1!d; s/samtools //\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@marrip", "@getrudeln"], + "maintainers": ["@marrip", "@getrudeln"] + } }, { - "name": "genomeqc", - "version": "dev" + "name": "pretextsnapshot", + "path": "modules/nf-core/pretextsnapshot/meta.yml", + "type": "module", + "meta": { + "name": "pretextsnapshot", + "description": "A module to generate images from Pretext contact maps.", + "keywords": ["pretext", "image", "hic", "png", "jpg", "bmp", "contact maps"], + "tools": [ + { + "pretextsnapshot": { + "description": "Commandline image generator for Pretext Hi-C genome contact maps.", + "homepage": "https://github.com/wtsi-hpag/PretextSnapshot", + "tool_dev_url": "https://github.com/wtsi-hpag/PretextSnapshot", + "licence": ["https://github.com/wtsi-hpag/PretextSnapshot/blob/master/LICENSE"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "pretext_map": { + "type": "file", + "description": "pretext hic map", + "pattern": "*.pretext", + "ontologies": [] + } + }, + { + "order_file": { + "type": "file", + "description": "Custom ordering of scaffolds in pretext snapshot output.\nThis is a single column file of scaffold names\n" + } + } + ] + ], + "output": { + "image": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{jpeg,png,bmp}": { + "type": "file", + "description": "image of a hic contact map", + "pattern": "*.{jpeg,png,bmp}", + "ontologies": [] + } + } + ] + ], + "versions_pretextsnapshot": [ + [ + { + "${task.process}": { + "type": "string", + "description": "Name of the process" + } + }, + { + "PretextSnapshot": { + "type": "string", + "description": "Name of the tool" + } + }, + { + "PretextSnapshot --version | sed 's/^.*PretextSnapshot Version //g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "PretextSnapshot": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "PretextSnapshot --version | sed 's/^.*PretextSnapshot Version //g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@epaule"], + "maintainers": ["@epaule", "@DLBPointon"] + } }, { - "name": "genomeskim", - "version": "dev" + "name": "pridepy_downloadfile", + "path": "modules/nf-core/pridepy/downloadfile/meta.yml", + "type": "module", + "meta": { + "name": "pridepy_downloadfile", + "description": "Download a single file from the PRIDE Archive by name using pridepy.", + "keywords": ["pride", "download", "proteomics", "mass spectrometry"], + "tools": [ + { + "pridepy": { + "description": "Python client library and command-line tool to access PRIDE Archive data\nprogrammatically, including downloading files from public proteomics datasets.\n", + "homepage": "https://github.com/PRIDE-Archive/pridepy", + "documentation": "https://github.com/PRIDE-Archive/pridepy", + "tool_dev_url": "https://github.com/PRIDE-Archive/pridepy", + "licence": ["Apache-2.0"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "file_name": { + "type": "string", + "description": "Name of the file to download from the PRIDE Archive dataset" + } + }, + { + "pride_accession": { + "type": "string", + "description": "PRIDE Archive project accession (e.g. PXD000001) identifying the dataset" + } + } + ] + ], + "output": { + "file": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${file_name}": { + "type": "file", + "description": "The file downloaded from the PRIDE Archive", + "pattern": "*" + } + } + ] + ], + "versions_pridepy": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "pridepy": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python -c \"from importlib.metadata import version; print(version('pridepy'))\"": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "pridepy": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python -c \"from importlib.metadata import version; print(version('pridepy'))\"": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@jonasscheid"], + "maintainers": ["@jonasscheid"] + } }, { - "name": "genomicrelatedness", - "version": "dev" + "name": "pridepy_fetchsdrf", + "path": "modules/nf-core/pridepy/fetchsdrf/meta.yml", + "type": "module", + "meta": { + "name": "pridepy_fetchsdrf", + "description": "Fetch an SDRF file from the PRIDE Archive for a given project accession.", + "keywords": ["pride", "sdrf", "proteomics", "download", "metadata"], + "tools": [ + { + "pridepy": { + "description": "Python client library to access PRIDE Archive data programmatically,\nincluding downloading files and metadata for public proteomics datasets.\n", + "homepage": "https://github.com/PRIDE-Archive/pridepy", + "documentation": "https://github.com/PRIDE-Archive/pridepy", + "tool_dev_url": "https://github.com/PRIDE-Archive/pridepy", + "licence": ["Apache-2.0"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'PXD004684' ]`\n" + } + }, + { + "pride_id": { + "type": "string", + "description": "PRIDE Archive project accession (e.g. PXD004684)" + } + } + ] + ], + "output": { + "sdrf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'PXD004684' ]`\n" + } + }, + { + "${prefix}.sdrf.tsv": { + "type": "file", + "description": "SDRF (Sample and Data Relationship Format) file describing the experimental design of the PRIDE project", + "pattern": "*.sdrf.tsv" + } + } + ] + ], + "versions_pridepy": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "pridepy": { + "type": "string", + "description": "The tool name" + } + }, + { + "python -c \"from importlib.metadata import version; print(version('pridepy'))\"": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "pridepy": { + "type": "string", + "description": "The tool name" + } + }, + { + "python -c \"from importlib.metadata import version; print(version('pridepy'))\"": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@jonasscheid"], + "maintainers": ["@jonasscheid"] + }, + "pipelines": [ + { + "name": "mhcquant", + "version": "3.2.0" + } + ] }, { - "name": "gwas", - "version": "dev" + "name": "primerprospector_analyzeprimers", + "path": "modules/nf-core/primerprospector/analyzeprimers/meta.yml", + "type": "module", + "meta": { + "name": "primerprospector_analyzeprimers", + "description": "Score PCR primers for binding to target sequences", + "keywords": ["primer design", "pcr", "fasta", "sequence analysis", "primer scoring"], + "tools": [ + { + "primerprospector": { + "description": "Primer Prospector is a pipeline of programs to design and analyze PCR primers.", + "homepage": "https://pprospector.sourceforge.net/", + "documentation": "https://pprospector.sourceforge.net/scripts/analyze_primers.html", + "tool_dev_url": "https://sourceforge.net/p/pprospector/code/", + "doi": "10.1093/bioinformatics/btr087", + "licence": ["GPL"], + "args_id": "$args", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information. Mandatory.\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Target FASTA file or files to score primers against. Mandatory.", + "pattern": "*.{fasta,fa,fna}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + }, + { + "primers": { + "type": "file", + "description": "Tab-delimited primers file containing primer names and sequences. Optional\nwhen primer name and sequence are supplied with task.ext.args.\n", + "pattern": "*.{txt,tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "output": { + "hits": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_hits.txt": { + "type": "file", + "description": "Primer hit detail files, including mismatches, gaps, positions, and weighted scores. One file is produced per primer.", + "pattern": "*_hits.txt", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "plots": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.ps": { + "type": "file", + "description": "PostScript summary plots of primer mismatch and weighted score information. One file is produced per primer.", + "pattern": "*.ps", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + } + ] + ], + "versions_primerprospector": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "primerprospector": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "analyze_primers.py --version 2>&1 | grep -Eo '[0-9]+(\\.[0-9]+)+' | tail -n 1": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "primerprospector": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "analyze_primers.py --version 2>&1 | grep -Eo '[0-9]+(\\.[0-9]+)+' | tail -n 1": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@vagkaratzas"], + "maintainers": ["@vagkaratzas"] + } }, { - "name": "hgtseq", - "version": "1.1.0" + "name": "prinseqplusplus", + "path": "modules/nf-core/prinseqplusplus/meta.yml", + "type": "module", + "meta": { + "name": "prinseqplusplus", + "description": "PRINSEQ++ is a C++ implementation of the prinseq-lite.pl program. It can be used to filter, reformat or trim genomic and metagenomic sequence data", + "keywords": ["fastq", "fasta", "filter", "trim"], + "tools": [ + { + "prinseqplusplus": { + "description": "PRINSEQ++ - Multi-threaded C++ sequence cleaning", + "homepage": "https://github.com/Adrian-Cantu/PRINSEQ-plus-plus", + "documentation": "https://github.com/Adrian-Cantu/PRINSEQ-plus-plus", + "tool_dev_url": "https://github.com/Adrian-Cantu/PRINSEQ-plus-plus", + "doi": "10.7287/peerj.preprints.27553v1", + "licence": ["GPL v2"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end\ndata, respectively.\n", + "ontologies": [] + } + } + ] + ], + "output": { + "good_reads": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_good_out*.fastq.gz": { + "type": "file", + "description": "Reads passing filter(s) in gzipped FASTQ format", + "pattern": "*_good_out_{R1,R2}.fastq.gz", + "ontologies": [] + } + } + ] + ], + "single_reads": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_single_out*.fastq.gz": { + "type": "file", + "description": "Single reads without the pair passing filter(s) in gzipped FASTQ format\n", + "pattern": "*_single_out_{R1,R2}.fastq.gz", + "ontologies": [] + } + } + ] + ], + "bad_reads": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_bad_out*.fastq.gz": { + "type": "file", + "description": "Reads without not passing filter(s) in gzipped FASTQ format\n", + "pattern": "*_bad_out_{R1,R2}.fastq.gz", + "ontologies": [] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "Verbose level 2 STDOUT information in a log file\n", + "pattern": "*.log", + "ontologies": [] + } + } + ] + ], + "versions_prinseqplusplus": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "prinseqplusplus": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "prinseq++ --version | cut -f 2 -d ' '": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "prinseqplusplus": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "prinseq++ --version | cut -f 2 -d ' '": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@jfy133"], + "maintainers": ["@jfy133"] + }, + "pipelines": [ + { + "name": "taxprofiler", + "version": "2.0.0" + }, + { + "name": "viralmetagenome", + "version": "1.1.1" + } + ] }, { - "name": "hicar", - "version": "1.0.0" + "name": "prodigal", + "path": "modules/nf-core/prodigal/meta.yml", + "type": "module", + "meta": { + "name": "prodigal", + "description": "Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program", + "keywords": ["prokaryotes", "gene finding", "microbial"], + "tools": [ + { + "prodigal": { + "description": "Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program", + "homepage": "https://github.com/hyattpd/Prodigal", + "documentation": "https://github.com/hyattpd/prodigal/wiki", + "tool_dev_url": "https://github.com/hyattpd/Prodigal", + "doi": "10.1186/1471-2105-11-119", + "licence": ["GPL v3"], + "identifier": "biotools:prodigal" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "genome": { + "type": "file", + "description": "fasta/fasta.gz file", + "ontologies": [] + } + } + ], + { + "output_format": { + "type": "string", + "description": "Output format (\"gbk\"/\"gff\"/\"sqn\"/\"sco\")" + } + } + ], + "output": { + "gene_annotations": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.${output_format}.gz": { + "type": "file", + "description": "gene annotations in output_format given as input", + "pattern": "*.{output_format}", + "ontologies": [] + } + } + ] + ], + "nucleotide_fasta": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.fna.gz": { + "type": "file", + "description": "nucleotide sequences file", + "pattern": "*.{fna}", + "ontologies": [] + } + } + ] + ], + "amino_acid_fasta": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.faa.gz": { + "type": "file", + "description": "protein translations file", + "pattern": "*.{faa}", + "ontologies": [] + } + } + ] + ], + "all_gene_annotations": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}_all.txt.gz": { + "type": "file", + "description": "complete starts file", + "pattern": "*.{_all.txt}", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@grst"], + "maintainers": ["@grst"] + }, + "pipelines": [ + { + "name": "funcscan", + "version": "3.0.0" + }, + { + "name": "mag", + "version": "5.4.2" + }, + { + "name": "metapep", + "version": "1.0.0" + }, + { + "name": "metatdenovo", + "version": "1.3.0" + } + ] }, { - "name": "hlatyping", - "version": "2.2.0" + "name": "prokka", + "path": "modules/nf-core/prokka/meta.yml", + "type": "module", + "meta": { + "name": "prokka", + "description": "Whole genome annotation of small genomes (bacterial, archeal, viral)", + "keywords": ["annotation", "fasta", "prokka"], + "tools": [ + { + "prokka": { + "description": "Rapid annotation of prokaryotic genomes", + "homepage": "https://github.com/tseemann/prokka", + "doi": "10.1093/bioinformatics/btu153", + "licence": ["GPL v2"], + "identifier": "biotools:prokka" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA file to be annotated. Has to contain at least a non-empty string dummy value.\n", + "ontologies": [] + } + } + ], + { + "proteins": { + "type": "file", + "description": "FASTA file of trusted proteins to first annotate from (optional)", + "ontologies": [] + } + }, + { + "prodigal_tf": { + "type": "file", + "description": "Training file to use for Prodigal (optional)", + "ontologies": [] + } + } + ], + "output": { + "gff": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/*.gff": { + "type": "file", + "description": "annotation in GFF3 format, containing both sequences and annotations", + "pattern": "*.{gff}", + "ontologies": [] + } + } + ] + ], + "gbk": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/*.gbk": { + "type": "file", + "description": "annotation in GenBank format, containing both sequences and annotations", + "pattern": "*.{gbk}", + "ontologies": [] + } + } + ] + ], + "fna": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/*.fna": { + "type": "file", + "description": "nucleotide FASTA file of the input contig sequences", + "pattern": "*.{fna}", + "ontologies": [] + } + } + ] + ], + "faa": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/*.faa": { + "type": "file", + "description": "protein FASTA file of the translated CDS sequences", + "pattern": "*.{faa}", + "ontologies": [] + } + } + ] + ], + "ffn": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/*.ffn": { + "type": "file", + "description": "nucleotide FASTA file of all the prediction transcripts (CDS, rRNA, tRNA, tmRNA, misc_RNA)", + "pattern": "*.{ffn}", + "ontologies": [] + } + } + ] + ], + "sqn": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/*.sqn": { + "type": "file", + "description": "an ASN1 format \"Sequin\" file for submission to Genbank", + "pattern": "*.{sqn}", + "ontologies": [] + } + } + ] + ], + "fsa": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/*.fsa": { + "type": "file", + "description": "nucleotide FASTA file of the input contig sequences, used by \"tbl2asn\" to create the .sqn file", + "pattern": "*.{fsa}", + "ontologies": [] + } + } + ] + ], + "tbl": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/*.tbl": { + "type": "file", + "description": "feature Table file, used by \"tbl2asn\" to create the .sqn file", + "pattern": "*.{tbl}", + "ontologies": [] + } + } + ] + ], + "err": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/*.err": { + "type": "file", + "description": "unacceptable annotations - the NCBI discrepancy report.", + "pattern": "*.{err}", + "ontologies": [] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/*.log": { + "type": "file", + "description": "contains all the output that Prokka produced during its run", + "pattern": "*.{log}", + "ontologies": [] + } + } + ] + ], + "txt": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/*.txt": { + "type": "file", + "description": "statistics relating to the annotated features found", + "pattern": "*.{txt}", + "ontologies": [] + } + } + ] + ], + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/*.tsv": { + "type": "file", + "description": "tab-separated file of all features (locus_tag,ftype,len_bp,gene,EC_number,COG,product)", + "pattern": "*.{tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_prokka": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "prokka": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "prokka --version 2>&1 | sed 's/^.*prokka //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "prokka": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "prokka --version 2>&1 | sed 's/^.*prokka //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@rpetit3"], + "maintainers": ["@rpetit3"] + }, + "pipelines": [ + { + "name": "bacass", + "version": "2.6.0" + }, + { + "name": "funcscan", + "version": "3.0.0" + }, + { + "name": "mag", + "version": "5.4.2" + }, + { + "name": "magmap", + "version": "1.0.0" + }, + { + "name": "metatdenovo", + "version": "1.3.0" + }, + { + "name": "viralmetagenome", + "version": "1.1.1" + } + ] }, { - "name": "isoseq", - "version": "2.0.0" + "name": "proovframe_fix", + "path": "modules/nf-core/proovframe/fix/meta.yml", + "type": "module", + "meta": { + "name": "proovframe_fix", + "description": "frame-shift correction for long read (meta)genomics - fix frameshifts in reads", + "keywords": ["frame-shift correction", "long-read sequencing", "sequence analysis"], + "tools": [ + { + "proovframe": { + "description": "frame-shift correction for long read (meta)genomics", + "homepage": "https://github.com/thackl/proovframe", + "documentation": "https://github.com/thackl/proovframe", + "tool_dev_url": "https://github.com/thackl/proovframe", + "doi": "10.1101/2021.08.23.457338", + "licence": ["MIT"], + "identifier": "biotools:proovframe" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "fa": { + "type": "file", + "description": "A FASTA file containing a database of guide protein sequences", + "pattern": "*.{faa,fasta,fa}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "tsv": { + "type": "file", + "description": "Output TSV file from proovframe/map with the frameshift-aware protein to read alignments from proovframe/map", + "pattern": "*.{tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "output": { + "out_fa": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.fa": { + "type": "file", + "description": "Result FASTA with fixed frameshift reads", + "pattern": "*.{fa}", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@mcarbajo", "@vagkaratzas"], + "maintainers": ["@vagkaratzas", "@Ge94"] + } }, { - "name": "liverctanalysis", - "version": "dev" + "name": "proovframe_map", + "path": "modules/nf-core/proovframe/map/meta.yml", + "type": "module", + "meta": { + "name": "proovframe_map", + "description": "frame-shift correction for long read (meta)genomics - maps proteins to reads", + "keywords": ["frame-shift correction", "long-read sequencing", "sequence analysis"], + "tools": [ + { + "proovframe": { + "description": "frame-shift correction for long read (meta)genomics", + "homepage": "https://github.com/thackl/proovframe", + "documentation": "https://github.com/thackl/proovframe", + "tool_dev_url": "https://github.com/thackl/proovframe", + "doi": "10.1101/2021.08.23.457338", + "licence": ["MIT"], + "identifier": "biotools:proovframe" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "A FASTA fna file containing raw read nucleotide sequences", + "pattern": "*.{fasta,fa}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "faa": { + "type": "file", + "description": "A proteome fasta file to create a database of guide protein sequences from", + "pattern": "*.{faa,fasta,fa}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "db": { + "type": "file", + "description": "A previously generated diamond database of guide protein sequences", + "pattern": "*.{dmnd}", + "ontologies": [] + } + } + ] + ], + "output": { + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "Output TSV file with the frameshift-aware protein to read alignments", + "pattern": "*.{tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@manuelcarbajo", "@MGS-sails", "@vagkaratzas"], + "maintainers": ["@vagkaratzas", "@Ge94"] + } }, { - "name": "lncpipe", - "version": "dev" + "name": "propr_grea", + "path": "modules/nf-core/propr/grea/meta.yml", + "type": "module", + "meta": { + "name": "propr_grea", + "description": "Perform Gene Ratio Enrichment Analysis", + "keywords": [ + "propr", + "grea", + "logratio", + "differential expression", + "functional enrichment", + "functional analysis" + ], + "tools": [ + { + "grea": { + "description": "Gene Ratio Enrichment Analysis", + "homepage": "https://github.com/tpq/propr", + "documentation": "https://rdrr.io/cran/propr/man/propr.html", + "tool_dev_url": "https://github.com/tpq/propr", + "doi": "10.2202/1544-6115.1175", + "licence": ["GPL-2"], + "identifier": "biotools:propr" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing data information.\nThis can be used at the workflow level to pass optional parameters to the module.\n[id: 'test', ...]\n" + } + }, + { + "adjacency": { + "type": "file", + "description": "Adjacency matrix representing the graph connections (ie. 1 for edges, 0 otherwise).\nThis can be the adjacency matrix output from gene ratio approaches like propr/propd.\n", + "pattern": "*.{csv,tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + }, + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing data information.\nThis can be used at the workflow level to pass optional parameters to the module.\n[id: 'test', ...]\n" + } + }, + { + "gmt": { + "type": "file", + "description": "A tab delimited file format that describes gene sets. The first column is the\nconcept id (eg. GO term, pathway, etc), the second column is the concept description, and the\nrest are nodes (eg. genes) that is associated to the given concept.\n", + "pattern": "*.{gmt}", + "ontologies": [] + } + } + ] + ], + "output": { + "results": [ + [ + { + "meta": { + "type": "file", + "description": "Groovy Map containing sample information.\nThis can be used at the workflow level to pass optional parameters to the module.\n[id: 'test', ...]\n", + "ontologies": [] + } + }, + { + "*.grea.tsv": { + "type": "file", + "description": "Output file containing the information about the tested concepts (ie. gene sets)\nand enrichment statistics.\n", + "pattern": "*.grea.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ], + "session_info": [ + { + "*.R_sessionInfo.log": { + "type": "file", + "description": "dump of R SessionInfo", + "pattern": "*.R_sessionInfo.log", + "ontologies": [] + } + } + ] + }, + "authors": ["@caraiz2001", "@suzannejin"], + "maintainers": ["@caraiz2001", "@suzannejin"] + } }, { - "name": "lsmquant", - "version": "1.0.0" + "name": "propr_logratio", + "path": "modules/nf-core/propr/logratio/meta.yml", + "type": "module", + "meta": { + "name": "propr_logratio", + "description": "Transform the data matrix using centered logratio transformation (CLR) or additive logratio transformation (ALR)", + "keywords": ["alr", "clr", "logratio", "boxcox", "transformation", "propr"], + "tools": [ + { + "propr": { + "description": "Logratio methods for omics data", + "homepage": "https://github.com/tpq/propr", + "documentation": "https://rdrr.io/cran/propr/man/propr.html", + "tool_dev_url": "https://github.com/tpq/propr", + "doi": "10.1038/s41598-017-16520-0", + "licence": ["GPL-2"], + "identifier": "biotools:propr" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing additional information.\nmeta.id can be used to name the output files.\n[id: 'test', ...]\n" + } + }, + { + "count": { + "type": "file", + "description": "Count matrix, where rows = variables or genes, columns = samples or cells.\nThis matrix should not contain zeros. Otherwise, they will be first replaced by the minimum value.\nYou may want to handle the zeros with a different method beforehand.\n", + "pattern": "*.{csv,tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + }, + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "output": { + "logratio": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing additional information.\nmeta.id can be used to name the output files.\n[id: 'test', ...]\n" + } + }, + { + "*.logratio.tsv": { + "type": "file", + "description": "ALR/CLR transformed data matrix. With rows = variables or genes, columns = samples or cells.", + "pattern": "*.logratio.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "session_info": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing additional information.\nmeta.id can be used to name the output files.\n[id: 'test', ...]\n" + } + }, + { + "*.R_sessionInfo.log": { + "type": "file", + "description": "dump of R SessionInfo", + "pattern": "*.R_sessionInfo.log", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@suzannejin", "@oprana22"], + "maintainers": ["@suzannejin", "@oprana22"] + } }, { - "name": "mag", - "version": "5.4.2" + "name": "propr_propd", + "path": "modules/nf-core/propr/propd/meta.yml", + "type": "module", + "meta": { + "name": "propr_propd", + "description": "Perform differential proportionality analysis", + "keywords": ["differential", "proportionality", "logratio", "expression", "propr", "propd"], + "tools": [ + { + "propr": { + "description": "Logratio methods for omics data", + "homepage": "https://github.com/tpq/propr", + "documentation": "https://rdrr.io/cran/propr/man/propr.html", + "tool_dev_url": "https://github.com/tpq/propr", + "doi": "10.1038/s41598-017-16520-0", + "licence": ["GPL-2"], + "identifier": "biotools:propr" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing contrast information. This can be used at the\nworkflow level to pass optional parameters to the module, e.g.\n[ id:'contrast1', blocking:'patient' ] passed in as ext.args like:\n'--blocking_variable $meta.blocking'.\n" + } + }, + { + "contrast_variable": { + "type": "string", + "description": "The column in the sample sheet that should be used to define groups for\ncomparison\n" + } + }, + { + "reference": { + "type": "string", + "description": "The value within the contrast_variable column of the sample sheet that\nshould be used to derive the reference samples\n" + } + }, + { + "target": { + "type": "string", + "description": "The value within the contrast_variable column of the sample sheet that\nshould be used to derive the target samples\n" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy map containing study-wide metadata related to the sample sheet\nand matrix\n" + } + }, + { + "samplesheet": { + "type": "file", + "description": "CSV or TSV format sample sheet with sample metadata\n", + "ontologies": [] + } + }, + { + "counts": { + "type": "file", + "description": "Raw TSV or CSV format expression matrix as output from the nf-core\nRNA-seq workflow\n", + "ontologies": [] + } + } + ] + ], + "output": { + "results_genewise": [ + [ + { + "meta": { + "type": "file", + "description": "TSV-format table of genes associated with differential expression\ninformation as compiled from the propd results\n", + "pattern": "*.propd.genewise.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, + { + "*.propd.genewise.tsv": { + "type": "file", + "description": "TSV-format table of genes associated with differential expression\ninformation as compiled from the propd results\n", + "pattern": "*.propd.genewise.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "genewise_plot": [ + [ + { + "meta": { + "type": "file", + "description": "TSV-format table of genes associated with differential expression\ninformation as compiled from the propd results\n", + "pattern": "*.propd.genewise.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, + { + "*.propd.genewise.png": { + "type": "file", + "description": "PNG-format plot of accumulated between group variance vs median log\nfold change. Genes with high between group variance and high log fold\nchange are likely to be differentially expressed.\n", + "pattern": "*.propd.genewise.png", + "ontologies": [] + } + } + ] + ], + "rdata": [ + [ + { + "meta": { + "type": "file", + "description": "TSV-format table of genes associated with differential expression\ninformation as compiled from the propd results\n", + "pattern": "*.propd.genewise.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, + { + "*.propd.rds": { + "type": "file", + "description": "(Optional) R data containing propd object\n", + "pattern": "*.propd.rds", + "ontologies": [] + } + } + ] + ], + "results_pairwise": [ + [ + { + "meta": { + "type": "file", + "description": "TSV-format table of genes associated with differential expression\ninformation as compiled from the propd results\n", + "pattern": "*.propd.genewise.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, + { + "*.propd.pairwise.tsv": { + "type": "file", + "description": "(Optional) TSV-format table of the native propd pairwise results. This\ntable contains the differential proportionality values associated to\neach pair of genes.\n", + "pattern": "*.propd.pairwise.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "results_pairwise_filtered": [ + [ + { + "meta": { + "type": "file", + "description": "TSV-format table of genes associated with differential expression\ninformation as compiled from the propd results\n", + "pattern": "*.propd.genewise.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, + { + "*.propd.pairwise_filtered.tsv": { + "type": "file", + "description": "(Optional) TSV-format table of the filtered propd pairwise results. This\ntable contains the pairs of genes with significant differential\nproportionality values.\n", + "pattern": "*.propd.pairwise_filtered.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "adjacency": [ + [ + { + "meta": { + "type": "file", + "description": "TSV-format table of genes associated with differential expression\ninformation as compiled from the propd results\n", + "pattern": "*.propd.genewise.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, + { + "*.propd.adjacency.csv": { + "type": "file", + "description": "(Optional) CSV-format table of the adjacency matrix defining a graph, with\nedges (1) associated to pairs of genes that are significantly differentially\nproportional.\n", + "pattern": "*.propd.adjacency.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "fdr": [ + [ + { + "meta": { + "type": "file", + "description": "TSV-format table of genes associated with differential expression\ninformation as compiled from the propd results\n", + "pattern": "*.propd.genewise.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, + { + "*.propd.fdr.tsv": { + "type": "file", + "description": "(Optional) TSV-format table of FDR values. When permutation tests is performed,\nthis table is generated with the FDR values calculated by the permutation tests.\nThis is a more conservative test than the default BH method, but more\ncomputationally expensive.\n", + "pattern": "*.propd.fdr.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "session_info": [ + { + "*.R_sessionInfo.log": { + "type": "file", + "description": "dump of R SessionInfo", + "pattern": "*.R_sessionInfo.log", + "ontologies": [] + } + } + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "topics": { + "versions": [ + { + "versions.yml": { + "type": "string", + "description": "The name of the process" + } + } + ] + }, + "authors": ["@suzannejin", "@caraiz2001"], + "maintainers": ["@suzannejin"] + } }, { - "name": "magmap", - "version": "1.0.0" + "name": "propr_propr", + "path": "modules/nf-core/propr/propr/meta.yml", + "type": "module", + "meta": { + "name": "propr_propr", + "description": "Perform logratio-based correlation analysis -> get proportionality & basis shrinkage partial correlation coefficients.\nOne can also compute standard correlation coefficients, if required.\n", + "keywords": ["coexpression", "correlation", "proportionality", "logratio", "propr", "corpcor"], + "tools": [ + { + "propr": { + "description": "Logratio methods for omics data", + "homepage": "https://github.com/tpq/propr", + "documentation": "https://rdrr.io/cran/propr/man/propr.html", + "tool_dev_url": "https://github.com/tpq/propr", + "doi": "10.1038/s41598-017-16520-0", + "licence": ["GPL-2"], + "identifier": "biotools:propr" + } + }, + { + "corpcor": { + "description": "Efficient Estimation of Covariance and (Partial) Correlation", + "homepage": "https://cran.r-project.org/web/packages/corpcor/index.html", + "documentation": "https://cran.r-project.org/web/packages/corpcor/corpcor.pdf", + "doi": "10.2202/1544-6115.1175", + "licence": ["GPL >=3"], + "identifier": "biotools:propr" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information.\nThis can be used at the workflow level to pass optional parameters to the module.\n[id: 'test', ...]\n" + } + }, + { + "count": { + "type": "file", + "description": "Count matrix, where rows = variables or genes, columns = samples or cells.\nThis matrix should not contain zeros. Otherwise, they will be replaced by the minimum number.\nIt is recommended to handle the zeros beforehand with the method of preference.\n", + "pattern": "*.{csv,tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + }, + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "output": { + "propr": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information.\nThis can be used at the workflow level to pass optional parameters to the module.\n[id: 'test', ...]\n" + } + }, + { + "*.propr.rds": { + "type": "file", + "description": "R propr object", + "pattern": "*.propr.rds", + "ontologies": [] + } + } + ] + ], + "matrix": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information.\nThis can be used at the workflow level to pass optional parameters to the module.\n[id: 'test', ...]\n" + } + }, + { + "*.propr.tsv": { + "type": "file", + "description": "Coefficient matrix", + "pattern": "*.propr.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "fdr": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information.\nThis can be used at the workflow level to pass optional parameters to the module.\n[id: 'test', ...]\n" + } + }, + { + "*.fdr.tsv": { + "type": "file", + "description": "(optional) propr fdr table", + "pattern": "*.fdr.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "adj": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information.\nThis can be used at the workflow level to pass optional parameters to the module.\n[id: 'test', ...]\n" + } + }, + { + "*.adj.csv": { + "type": "file", + "description": "(optional) propr adjacency table", + "pattern": "*.adj.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "warnings": [ + { + "*.warnings.log": { + "type": "file", + "description": "Warnings", + "pattern": "*.warnings.log", + "ontologies": [] + } + } + ], + "session_info": [ + { + "*.R_sessionInfo.log": { + "type": "file", + "description": "dump of R SessionInfo", + "pattern": "*.R_sessionInfo.log", + "ontologies": [] + } + } + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@suzannejin"] + } }, { - "name": "marsseq", - "version": "1.0.3" + "name": "proseg_proseg", + "path": "modules/nf-core/proseg/proseg/meta.yml", + "type": "module", + "meta": { + "name": "proseg", + "description": "Proseg (probabilistic segmentation) is a cell segmentation method for in situ spatial transcriptomics.", + "keywords": ["segmentation", "spatial", "transcriptomics"], + "tools": [ + { + "proseg": { + "description": "Proseg (probabilistic segmentation) is a cell segmentation method for in situ spatial transcriptomics.", + "homepage": "https://github.com/dcjones/proseg", + "documentation": "https://github.com/dcjones/proseg", + "tool_dev_url": "https://github.com/dcjones/proseg", + "doi": "10.1038/s41592-025-02697-0", + "licence": ["GPLv3"] + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "transcripts": { + "type": "file", + "description": "Transcript ids, genes, revised positions, assignment probability, etc.", + "pattern": "*transcript-metadata.{csv.gz,csv,parquet}" + } + } + ], + { + "mode": { + "type": "string", + "description": "Proseg preset mode", + "enum": ["xenium", "merfish", "cosmx"] + } + }, + [ + { + "transcript_metadata_fmt": { + "type": "string", + "description": "Format of the transcript metadata file", + "enum": ["csv", "csv.gz", "parquet"] + } + }, + { + "cell_metadata_fmt": { + "type": "file", + "description": "Format of the cell metadata file", + "enum": ["csv", "csv.gz", "parquet"] + } + }, + { + "expected_counts_fmt": { + "type": "file", + "description": "Format of the expected counts file", + "enum": ["csv", "csv.gz", "parquet"] + } + } + ] + ], + "output": { + "transcript_metadata": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*transcript-metadata.{csv,csv.gz,parquet}": { + "type": "file", + "description": "Transcript ids, genes, revised positions, assignment probability, etc.", + "pattern": "*transcript-metadata.{csv.gz,csv,parquet}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "union_cell_polygons": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*cell-polygons-union.geojson.gz": { + "type": "file", + "description": "Union cell polygons", + "pattern": "*cell-polygons-union.geojson.gz" + } + } + ] + ], + "cell_polygons": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*cell-polygons.geojson.gz": { + "type": "file", + "description": "Cell polygons file", + "pattern": "*cell-polygons.geojson.gz" + } + } + ] + ], + "cell_metadata": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*cell-metadata.{csv,csv.gz,parquet}": { + "type": "file", + "description": "Cell metadata file", + "pattern": "*cell-metadata.{csv.gz,csv,parquet}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "cell_polygons_layers": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*cell-polygons-layers.geojson.gz": { + "type": "file", + "description": "Cell polygon layers file", + "pattern": "*cell-polygons-layers.geojson.gz" + } + } + ] + ], + "expected_counts": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*expected-counts.{csv,csv.gz,parquet}": { + "type": "file", + "description": "Expected transcript counts file", + "pattern": "*expected-counts.{csv.gz,csv,parquet}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "maxpost_counts": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*maxpost-counts.{csv,csv.gz,parquet}": { + "type": "file", + "description": "point estimate of counts per cell", + "pattern": "*maxpost-counts.{csv.gz,csv,parquet}", + "optional": true, + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "output_rates": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*output-rates.{csv,csv.gz,parquet}": { + "type": "file", + "description": "Estimated poisson expression rates for each cell", + "pattern": "*output-rates.{csv.gz,csv,parquet}", + "optional": true, + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "cell_hulls": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*cell-hulls.{csv,csv.gz,parquet}": { + "type": "file", + "description": "Cell convex hulls", + "pattern": "*cell-hulls.{csv.gz,csv,parquet}", + "optional": true, + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "gene_metadata": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*gene-metadata.{csv,csv.gz,parquet}": { + "type": "file", + "description": "gene metadata", + "pattern": "*gene-metadata.{csv.gz,csv,parquet}", + "optional": true, + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "metagene_rates": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*metagene-rates.{csv,csv.gz,parquet}": { + "type": "file", + "description": "metagene rates", + "pattern": "*metagene-rates.{csv.gz,csv,parquet}", + "optional": true, + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "metagene_loadings": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*metagene-loadings.{csv,csv.gz,parquet}": { + "type": "file", + "description": "metagene loadings", + "pattern": "*metagene-loadings.{csv.gz,csv,parquet}", + "optional": true, + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "cell_voxels": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*cell-voxels.{csv,csv.gz,parquet}": { + "type": "file", + "description": "table of each voxel in each cell", + "pattern": "*cell-voxels.{csv.gz,csv,parquet}", + "optional": true, + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@derrik-gratz"], + "maintainers": ["@derrik-gratz"] + } }, { - "name": "mcmicro", - "version": "dev" - }, - { - "name": "metaboigniter", - "version": "2.0.1" - }, - { - "name": "metapep", - "version": "1.0.0" - }, - { - "name": "metatdenovo", - "version": "1.3.0" - }, - { - "name": "methylarray", - "version": "dev" - }, - { - "name": "methylong", - "version": "2.0.0" - }, - { - "name": "methylseq", - "version": "4.2.0" - }, - { - "name": "mhcquant", - "version": "3.2.0" - }, - { - "name": "mitodetect", - "version": "dev" + "name": "proseg_proseg_to_baysor", + "path": "modules/nf-core/proseg/proseg_to_baysor/meta.yml", + "type": "module", + "meta": { + "name": "proseg_to_baysor", + "description": "Convert proseg outputs to baysor format for import to Xenium explorer", + "keywords": ["segmentation", "spatial", "transcriptomics"], + "tools": [ + { + "proseg": { + "description": "Proseg (probabilistic segmentation) is a cell segmentation method for in situ spatial transcriptomics.", + "homepage": "https://github.com/dcjones/proseg", + "documentation": "https://github.com/dcjones/proseg", + "tool_dev_url": "https://github.com/dcjones/proseg", + "doi": "10.1038/s41592-025-02697-0", + "licence": ["GPLv3"] + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "transcript_metadata": { + "type": "file", + "description": "Transcript ids, genes, revised positions, assignment probability, etc.", + "pattern": "*transcript-metadata.csv.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "cell_polygons": { + "type": "file", + "description": "Path to the cell polygons file.", + "pattern": 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} + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@derrik-gratz"], + "maintainers": ["@derrik-gratz"] + } }, { - "name": "molkart", - "version": "1.2.0" + "name": "proteinortho", + "path": "modules/nf-core/proteinortho/meta.yml", + "type": "module", + "meta": { + "name": "proteinortho", + "description": "Proteinortho is a tool to detect orthologous genes within different species.", + "keywords": [ + "orthology", + "co-orthology", + "homology", + "sequence similarity", + "spectral clustering", + "comparative genomics", + "genomics" + ], + "tools": [ + { + "proteinortho": { + "description": "Proteinortho is a tool to detect orthologous genes within different species.", + "homepage": "https://gitlab.com/paulklemm_PHD/proteinortho", + "documentation": 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N.B. as reported in https://www.bioconductor.org/packages/devel/bioc/vignettes/PureCN/inst/doc/Quick.html, it is advised to provide a normal panel (VCF format) to precompute mapping bias for faster runtimes.", + "keywords": [ + "copy number alteration calling", + "normal database", + "panel of normals", + "hybrid capture sequencing", + "targeted sequencing", + "DNA sequencing" + ], + "tools": [ + { + "purecn": { + "description": "Copy number calling and SNV classification using targeted short read sequencing", + "homepage": "https://bioconductor.org/packages/release/bioc/html/PureCN.html", + "documentation": "https://bioconductor.org/packages/release/bioc/html/PureCN.html", + "tool_dev_url": "https://github.com/lima1/PureCN", + "doi": "10.1186/s13029-016-0060-z", + "licence": ["Artistic-2.0"], + "args_id": "$args", + "identifier": "biotools:purecn" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "coverage_files": { + "type": "file", + "description": "Coverage files from normal samples", + "pattern": "*.txt.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + }, + { + "normal_vcf": { + "type": "file", + "description": "Normal panel in VCF format, used to precompute mapping bias\nfor faster runtimes. Optional.\n", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + }, + { + "normal_vcf_tbi": { + "type": "file", + "description": "Normal panel in VCF format", + "pattern": "*.vcf.gz.tbi", + "ontologies": [] + } + } + ], + { + "genome": { + "type": "string", + "description": "Genome build" + } + }, + { + "assay": { + "type": "string", + "description": "Assay name" + } + } + ], + "output": { + "rds": [ + [ + { + "meta": { + "type": "file", + "description": "File containing the generated panel of normals", + "pattern": "normalDB*.rds", + "ontologies": [] + } + }, + { + "normalDB*.rds": { + "type": "file", + "description": "File containing the generated panel of normals", + "pattern": "normalDB*.rds", + "ontologies": [] + } + } + ] + ], + "png": [ + [ + { + "meta": { + "type": "file", + "description": "File containing the generated panel of normals", + "pattern": "normalDB*.rds", + "ontologies": [] + } + }, + { + "interval_weights*.png": { + "type": "file", + "description": "Plot of interval weights calculated from the panel of normals", + "pattern": "interval_weights*.png", + "ontologies": [] + } + } + ] + ], + "bias_rds": [ + [ + { + "meta": { + "type": "file", + "description": "File containing the generated panel of normals", + "pattern": "normalDB*.rds", + "ontologies": [] + } + }, + { + "mapping_bias*.rds": { + "type": "file", + "description": "Calculated mapping bias from the normal files", + "pattern": "mapping_bias*.rds", + "ontologies": [] + } + } + ] + ], + "bias_bed": [ + [ + { + "meta": { + "type": "file", + "description": "File containing the generated panel of normals", + "pattern": "normalDB*.rds", + "ontologies": [] + } + }, + { + "mapping_bias_hq_sites*.bed": { + "type": "file", + "description": "Calculated mapping bias sites from the normal files", + "pattern": "mapping_bias_hq_sites*.bed", + "ontologies": [] + } + } + ] + ], + "low_cov_bed": [ + [ + { + "meta": { + "type": "file", + "description": "File containing the generated panel of normals", + "pattern": "normalDB*.rds", + "ontologies": [] + } + }, + { + "low_coverage_targets*.bed": { + "type": "file", + "description": "BED with possibly low coverage targets identified, only\ngenerated if there are low coverage targets\n", + "pattern": "low_coverage_targets*.bed", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@aldosr", "@lbeltrame"], + "maintainers": ["@aldosr", "@lbeltrame"] + } }, { - "name": "omicsgenetraitassociation", - "version": "dev" + "name": "purecn_run", + "path": "modules/nf-core/purecn/run/meta.yml", + "type": "module", + "meta": { + "name": "purecn_run", + "description": "Run PureCN workflow to normalize, segment and determine purity and ploidy", + "keywords": [ + "copy number alteration calling", + "hybrid capture sequencing", + "targeted sequencing", + "DNA sequencing" + ], + "tools": [ + { + "purecn": { + "description": "Copy number calling and SNV classification using targeted short read sequencing", + "homepage": "https://bioconductor.org/packages/release/bioc/html/PureCN.html", + "documentation": "https://bioconductor.org/packages/release/bioc/html/PureCN.html", + "tool_dev_url": "https://github.com/lima1/PureCN", + "doi": "10.1186/s13029-016-0060-z", + "license": ["Artistic-2.0"], + "args_id": "$args", + "identifier": "biotools:purecn" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "intervals": { + "type": "file", + "description": "BED file of target intervals, generated from IntervalFile.R\n", + "pattern": "{*.bed,*.txt}", + "ontologies": [] + } + }, + { + "coverage": { + "type": "file", + "description": "Coverage file generated from Coverage.R", + "pattern": "*.txt", + "ontologies": [] + } + }, + { + "vcf": { + "type": "file", + "description": "VCF containing variant calls", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ], + { + "normal_db": { + "type": "file", + "description": "Normal panel database", + "ontologies": [] + } + }, + { + "mapping_bias": { + "type": "file", + "description": "Mapping bias file generated with normal panel", + "ontologies": [] + } + }, + { + "genome": { + "type": "string", + "description": "Genome build" + } + } + ], + "output": { + "pdf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.pdf": { + "type": "file", + "description": "PDF file containing copy number plots\n", + "pattern": "*.pdf", + "ontologies": [] + } + } + ] + ], + "local_optima_pdf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*_local_optima.pdf": { + "type": "file", + "description": "PDF file containing local optima plots\n", + "pattern": "*_local_optima.pdf", + "ontologies": [] + } + } + ] + ], + "seg": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*_dnacopy.seg": { + "type": "file", + "description": "Tab-delimited file containing segmentation results\n", + "pattern": "*_dnacopy.seg", + "ontologies": [] + } + } + ] + ], + "csv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "${prefix}.csv": { + "type": "file", + "description": "Tab-delimited file containing sample purity, ploidy\nand flags information\n", + "pattern": "${prefix}.csv", + "ontologies": [] + } + } + ] + ], + "genes_csv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*_genes.csv": { + "type": "file", + "description": "CSV file containing gene copy number calls. Optional\n", + "pattern": "*_genes.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "amplification_pvalues_csv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*_amplification_pvalues.csv": { + "type": "file", + "description": "CSV file containing amplification p-values. Optional\n", + "pattern": "*_amplification_pvalues.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "vcf_gz": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "GZipped VCF file containing SNV calls. Optional\n", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "variants_csv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*_variants.csv": { + "type": "file", + "description": "CSV file containing SNV calls. Optional\n", + "pattern": "*_variants.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "loh_csv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*_loh.csv": { + "type": "file", + "description": "CSV file containing LOH calls. Optional\n", + "pattern": "*_loh.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "chr_pdf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*_chromosomes.pdf": { + "type": "file", + "description": "PDF file containing chromosome plots. Optional\n", + "pattern": "*_chromosomes.pdf", + "ontologies": [] + } + } + ] + ], + "segmentation_pdf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*_segmentation.pdf": { + "type": "file", + "description": "PDF file containing segmentation plots. Optional\n", + "pattern": "*_segmentation.pdf", + "ontologies": [] + } + } + ] + ], + "multisample_seg": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*_multisample.seg": { + "type": "file", + "description": "multisample segmentation results", + "pattern": "*_multisample.seg", + "ontologies": [] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "Log file of the analysis", + "pattern": "*.log", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@aldosr", "@lbeltrame"], + "maintainers": ["@aldosr", "@lbeltrame"] + } }, { - "name": "pacsomatic", - "version": "dev" + "name": "purgedups_calcuts", + "path": "modules/nf-core/purgedups/calcuts/meta.yml", + "type": "module", + "meta": { + "name": "purgedups_calcuts", + "description": "Calculate coverage cutoffs to determine when to purge duplicated sequence.", + "keywords": ["coverage", "cutoff", "purge duplications"], + "tools": [ + { + "purgedups": { + "description": "Purge_dups is a package used to purge haplotigs and overlaps in an assembly based on read depth", + "homepage": "https://github.com/dfguan/purge_dups", + "documentation": "https://github.com/dfguan/purge_dups", + "tool_dev_url": "https://github.com/dfguan/purge_dups", + "doi": "10.1093/bioinformatics/btaa025", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "stat": { + "type": "file", + "description": "Histogram of coverage", + "pattern": "*.stat", + "ontologies": [] + } + } + ] + ], + "output": { + "cutoff": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.cutoffs": { + "type": "file", + "description": "Cutoff file", + "pattern": "*.cutoffs", + "ontologies": [] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.calcuts.log": { + "type": "file", + "description": "Log file", + "pattern": ".calcuts.log", + "ontologies": [] + } + } + ] + ], + "versions_purgedups": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "purge_dups": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "1.2.6": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "purge_dups": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "1.2.6": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@mahesh-panchal"], + "maintainers": ["@mahesh-panchal"] + } }, { - "name": "pacvar", - "version": "1.0.1" + "name": "purgedups_getseqs", + "path": "modules/nf-core/purgedups/getseqs/meta.yml", + "type": "module", + "meta": { + "name": "purgedups_getseqs", + "description": "Separates out sequences purged of falsely duplicated sequences.", + "keywords": ["haplotype purging", "duplicate purging", "false duplications", "assembly curation"], + "tools": [ + { + "purgedups": { + "description": "Purge_dups is a package used to purge haplotigs and overlaps in an assembly based on read depth", + "homepage": "https://github.com/dfguan/purge_dups", + "documentation": "https://github.com/dfguan/purge_dups", + "tool_dev_url": "https://github.com/dfguan/purge_dups", + "doi": "10.1093/bioinformatics/btaa025", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "assembly": { + "type": "file", + "description": "Draft assembly in fasta format", + "pattern": "*.fasta", + "ontologies": [] + } + }, + { + "bed": { + "type": "file", + "description": "Bed file listing duplicated sequences, produced by PURGEDUPS_PURGEDUPS", + "pattern": "*.bed", + "ontologies": [] + } + } + ] + ], + "output": { + "haplotigs": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.hap.fa": { + "type": "file", + "description": "Fasta file containing purged haplotigs", + "pattern": "*.hap.fa", + "ontologies": [] + } + } + ] + ], + "purged": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.purged.fa": { + "type": "file", + "description": "Fasta file purged of duplicated haplotigs", + "pattern": "*.purged.fa", + "ontologies": [] + } + } + ] + ], + "versions_purgedups": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "purge_dups": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "1.2.6": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "purge_dups": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "1.2.6": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@mahesh-panchal"], + "maintainers": ["@mahesh-panchal"] + } }, { - "name": "pairgenomealign", - "version": "2.2.3" + "name": "purgedups_histplot", + "path": "modules/nf-core/purgedups/histplot/meta.yml", + "type": "module", + "meta": { + "name": "purgedups_histplot", + "description": "Plots the read coverage from a purge dups statistics file and cutoffs.", + "keywords": ["Read coverage histogram", "Duplication purging", "Read depth"], + "tools": [ + { + "purgedups": { + "description": "Purge_dups is a package used to purge haplotigs and overlaps in an assembly based on read depth", + "homepage": "https://github.com/dfguan/purge_dups", + "documentation": "https://github.com/dfguan/purge_dups", + "tool_dev_url": "https://github.com/dfguan/purge_dups", + "doi": "10.1093/bioinformatics/btaa025", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "statfile": { + "type": "file", + "description": "A Purge dups statistic file", + "pattern": "*.stat", + "ontologies": [] + } + }, + { + "cutoff": { + "type": "file", + "description": "A Purge dups cutoff file", + "pattern": "*.cutoffs", + "ontologies": [] + } + } + ] + ], + "output": { + "png": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.png": { + "type": "file", + "description": "A png file of the read depth coverage.", + "pattern": "*.png", + "ontologies": [] + } + } + ] + ], + "versions_purgedups": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "purge_dups": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "1.2.6": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "purge_dups": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "1.2.6": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@mahesh-panchal"], + "maintainers": ["@mahesh-panchal"] + } }, { - "name": "pangenome", - "version": "1.1.3" + "name": "purgedups_pbcstat", + "path": "modules/nf-core/purgedups/pbcstat/meta.yml", + "type": "module", + "meta": { + "name": "purgedups_pbcstat", + "description": "Create read depth histogram and base-level read depth for an assembly based on pacbio data", + "keywords": ["sort", "genome assembly", "purge duplications", "read depth"], + "tools": [ + { + "purgedups": { + "description": "Purge_dups is a package used to purge haplotigs and overlaps in an assembly based on read depth", + "homepage": "https://github.com/dfguan/purge_dups", + "documentation": "https://github.com/dfguan/purge_dups", + "tool_dev_url": "https://github.com/dfguan/purge_dups", + "doi": "10.1093/bioinformatics/btaa025", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "paf_alignment": { + "type": "file", + "description": "PAF alignment file", + "pattern": "*.paf", + "ontologies": [] + } + } + ] + ], + "output": { + "stat": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.PB.stat": { + "type": "file", + "description": "PacBio Statistic file", + "pattern": "*.PB.stat", + "ontologies": [] + } + } + ] + ], + "basecov": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.PB.base.cov": { + "type": "file", + "description": "PacBio Base coverage file", + "pattern": "*.PB.base.cov", + "ontologies": [] + } + } + ] + ], + "versions_purgedups": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "purge_dups": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "1.2.6": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "purge_dups": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "1.2.6": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@mahesh-panchal"], + "maintainers": ["@mahesh-panchal"] + } }, { - 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"name": "quantms", - "version": "1.2.0" + "name": "pygenprop_info", + "path": "modules/nf-core/pygenprop/info/meta.yml", + "type": "module", + "meta": { + "name": "pygenprop_info", + "description": "Display a summary of the contents of a Micromeda file, including the number of samples,\ngenome property assignments, step assignments, InterProScan matches, and protein sequences.\n", + "keywords": [ + "genome properties", + "functional annotation", + "interproscan", + "pathway analysis", + "micromeda", + "summary" + ], + "tools": [ + { + "pygenprop": { + "description": "A python library for programmatic usage of EBI InterPro Genome Properties.", + "homepage": "https://github.com/Micromeda/pygenprop", + "documentation": "https://pygenprop.readthedocs.io/en/latest/", + "tool_dev_url": "https://github.com/Micromeda/pygenprop", + "licence": ["Apache-2.0"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "meda": { + "type": "file", + "description": "Micromeda SQLite database containing Genome Properties assignments\n(output of pygenprop build)\n", + "pattern": "*.micro", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3621" + } + ] + } + } + ] + ], + "output": { + "info": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.info": { + "type": "file", + "description": "Plain-text summary report of the Micromeda file contents, including counts of\nsamples, genome property assignments, step assignments, InterProScan matches,\nand protein sequences\n", + "pattern": "*.info", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + } + ] + ], + "versions_pygenprop": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "pygenprop": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "\"1.1\"": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_python": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "python": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python -V | sed \"s/Python //g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "pygenprop": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "\"1.1\"": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "python": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python -V | sed \"s/Python //g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@vagkaratzas"], + "maintainers": ["@vagkaratzas"] + } }, { - "name": "radseq", - "version": "dev" + "name": "pypgx_computecontrolstatistics", + "path": "modules/nf-core/pypgx/computecontrolstatistics/meta.yml", + "type": "module", + "meta": { + "name": "pypgx_computecontrolstatistics", + "description": "Compute summary statistics for control gene from BAM files.", + "keywords": ["pypgx", "pharmacogenetics", "controlstatistics"], + "tools": [ + { + "pypgx": { + "description": "A Python package for pharmacogenomics research", + "homepage": "https://pypgx.readthedocs.io/en/latest/", + "documentation": "https://pypgx.readthedocs.io/en/latest/", + "tool_dev_url": "https://github.com/sbslee/pypgx", + "doi": "10.1371/journal.pone.0272129", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "bam": { + "type": "file", + "description": "Sorted BAM file", + "pattern": "*.{bam}", + "ontologies": [] + } + }, + { + "bai": { + "type": "file", + "description": "BAM index file", + "pattern": "*.{bai}", + "ontologies": [] + } + } + ], + { + "control_gene": { + "type": "string", + "description": "Gene to use as control gene", + "pattern": "{VDR,EGFR,RYR1}" + } + } + ], + "output": { + "control_stats": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n", + "pattern": "*.{zip}" + } + }, + { + "*.zip": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n", + "pattern": "*.{zip}" + } + } + ] + ], + "versions_pypgx": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "pypgx": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pypgx -v 2>&1 | grep -oE \"[0-9]+\\.[0-9]+\\.[0-9]+\" | head -1": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "pypgx": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pypgx -v 2>&1 | grep -oE \"[0-9]+\\.[0-9]+\\.[0-9]+\" | head -1": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@jorisvansteenbrugge"], + "maintainers": ["@jorisvansteenbrugge"] + } }, { - "name": "rangeland", - "version": "1.0.0" + "name": "pypgx_createinputvcf", + "path": "modules/nf-core/pypgx/createinputvcf/meta.yml", + "type": "module", + "meta": { + "name": "pypgx_createinputvcf", + "description": "Call SNVs/indels from BAM files for all target genes.", + "keywords": ["pypgx", "Pharmacogenetics", "variants"], + "tools": [ + { + "pypgx": { + "description": "A Python package for pharmacogenomics research", + "homepage": "https://pypgx.readthedocs.io/en/latest/", + "documentation": "https://pypgx.readthedocs.io/en/latest/", + "tool_dev_url": "https://github.com/sbslee/pypgx", + "doi": "10.1371/journal.pone.0272129", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [id: 'test']\n" + } + }, + { + "bam": { + "type": "file", + "description": "Input BAM file", + "pattern": "*.{bam}", + "ontologies": [] + } + }, + { + "bai": { + "type": "file", + "description": "Input BAM index file", + "pattern": "*.{bam.bai}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [id: 'test']\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference genome file", + "pattern": "*.{fasta,fa,fna,fasta.gz,fa.gz,fna.gz}", + "ontologies": [] + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [id: 'test']\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "VCF file containing called SNVs/indels", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [id: 'test']\n" + } + }, + { + "*.vcf.gz.tbi": { + "type": "file", + "description": "File containing the VCF tabix index", + "pattern": "*.vcf.gz.tbi", + "ontologies": [] + } + } + ] + ], + "versions_pypgx": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "pypgx": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pypgx -v 2>&1 | grep -oE \"[0-9]+\\.[0-9]+\\.[0-9]+\" | head -1": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "pypgx": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pypgx -v 2>&1 | grep -oE \"[0-9]+\\.[0-9]+\\.[0-9]+\" | head -1": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@jorisvansteenbrugge"], + "maintainers": ["@jorisvansteenbrugge"] + } }, { - "name": "raredisease", - "version": "3.0.0" + "name": "pypgx_preparedepthofcoverage", + "path": "modules/nf-core/pypgx/preparedepthofcoverage/meta.yml", + "type": "module", + "meta": { + "name": "pypgx_preparedepthofcoverage", + "description": "Prepare a depth of coverage file for all target genes with SV from BAM files.", + "keywords": ["Pharmacogenetics", "pypgx", "SV"], + "tools": [ + { + "pypgx": { + "description": "A Python package for pharmacogenomics research", + "homepage": "https://pypgx.readthedocs.io/en/latest/", + "documentation": "https://pypgx.readthedocs.io/en/latest/", + "tool_dev_url": "https://github.com/sbslee/pypgx", + "doi": "10.1371/journal.pone.0272129", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "bam": { + "type": "file", + "description": "Input BAM file", + "pattern": "*.{bam}", + "ontologies": [] + } + }, + { + "bai": { + "type": "file", + "description": "Input BAM index file", + "pattern": "*.{bam.bai}", + "ontologies": [] + } + } + ] + ], + "output": { + "coverage": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n", + "pattern": "*.{zip}" + } + }, + { + "*.zip": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n", + "pattern": "*.{zip}" + } + } + ] + ], + "versions_pypgx": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "pypgx": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pypgx -v 2>&1 | grep -oE \"[0-9]+\\.[0-9]+\\.[0-9]+\" | head -1": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "pypgx": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pypgx -v 2>&1 | grep -oE \"[0-9]+\\.[0-9]+\\.[0-9]+\" | head -1": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@jorisvansteenbrugge"], + "maintainers": ["@jorisvansteenbrugge"] + } }, { - "name": "readsimulator", - "version": "1.0.1" + "name": "pypgx_runngspipeline", + "path": "modules/nf-core/pypgx/runngspipeline/meta.yml", + "type": "module", + "meta": { + "name": "pypgx_runngspipeline", + "description": "PyPGx pharmacogenomics genotyping pipeline for NGS data.", + "keywords": ["pypgx", "pharmacogenetics", "genotyping"], + "tools": [ + { + "pypgx": { + "description": "A Python package for pharmacogenomics research", + "homepage": "https://pypgx.readthedocs.io/en/latest/", + "documentation": "https://pypgx.readthedocs.io/en/latest/", + "tool_dev_url": "https://github.com/sbslee/pypgx", + "doi": "10.1371/journal.pone.0272129", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`.\n" + } + }, + { + "vcf": { + "type": "file", + "description": "BGZIP compressed VCF file with SNVs/indels. Output of pypgx/createinputvcf.", + "pattern": "*.{vcf.gz}", + "ontologies": [] + } + }, + { + "tbi": { + "type": "file", + "description": "VCF tabix index.", + "pattern": "*.{vcf.gz.tbi}", + "ontologies": [] + } + }, + { + "coverage": { + "type": "file", + "description": "ZIP compressed file with depth of coverage information. Output of pypgx/preparedepthofcoverage. Coverage information is only required when running the module on a pharmacogene with known structural variants.", + "pattern": "*.{zip}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3987" + } + ] + } + }, + { + "control_stats": { + "type": "file", + "description": "ZIP compressed file with control statistics. Output of pypgx/computecontrolstatistics. Control statistics are only required when running the module on a pharmacogene with known structural variants.", + "ontologies": [] + } + }, + { + "pgx_gene": { + "type": "string", + "description": "Pharmacogene to genotype/phenotype. A list of supported genes is available in the pypgx documentation \"https://pypgx.readthedocs.io/en/latest/genes.html\"" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`.\n" + } + }, + { + "resource_bundle": { + "type": "directory", + "description": "Path to the pypgx resource bundle (https://github.com/sbslee/pypgx-bundle)." + } + } + ] + ], + "output": { + "results": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*pypgx_output/results.zip": { + "type": "file", + "description": "Main output file of the pipeline in ZIP format, containing a table with star-alleles per sample and CNV calls where applicable.", + "ontologies": [] + } + } + ] + ], + "cnv_calls": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*pypgx_output/cnv-calls.zip": { + "type": "file", + "description": "Optional output file in ZIP format, containing CNV calls per sample.", + "ontologies": [] + } + } + ] + ], + "consolidated_variants": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*pypgx_output/consolidated-variants.zip": { + "type": "file", + "description": "Output file in ZIP format, containing a consolidated (and phased) VCF file.", + "ontologies": [] + } + } + ] + ], + "versions_pypgx": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "pypgx": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pypgx -v 2>&1 | grep -oE \"[0-9]+\\.[0-9]+\\.[0-9]+\" | head -1": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "pypgx": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pypgx -v 2>&1 | grep -oE \"[0-9]+\\.[0-9]+\\.[0-9]+\" | head -1": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@jorisvansteenbrugge"], + "maintainers": ["@jorisvansteenbrugge"] + } }, { - "name": "references", - "version": "0.1" + "name": "pypolca_run", + "path": "modules/nf-core/pypolca/run/meta.yml", + "type": "module", + "meta": { + "name": "pypolca_run", + "description": "Short read polisher for long read assemblies", + "keywords": ["polish", "python", "genomics"], + "tools": [ + { + "pypolca": { + "description": "Standalone Python re-implementation of the POLCA polisher from MaSuRCA", + "homepage": "https://github.com/gbouras13/pypolca", + "documentation": "https://github.com/gbouras13/pypolca?tab=readme-ov-file#usage", + "doi": "10.1099/mgen.0.001254", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of short reads for assembly polishing. Length 1 for single-end and 2 for paired-end", + "pattern": "*.{fastq,fq}.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "contigs": { + "type": "file", + "description": "Genome assembly from long reads", + "pattern": "*.{fa,fasta,fna}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ] + ], + "output": { + "polished": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}/*_corrected.fasta": { + "type": "file", + "description": "Polished assembly", + "pattern": "*.{fasta}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ] + ], + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}/*.vcf": { + "type": "file", + "description": "variant calls", + "pattern": "*.vcf", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + } + ] + } + } + ] + ], + "report": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}/*.report": { + "type": "file", + "description": "Pypolca report", + "pattern": "*.report", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + } + ] + ], + "versions_pypolca": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "pypolca": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pypolca --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "pypolca": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pypolca --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@dwells-eit"], + "maintainers": ["@dwells-eit"] + } }, { - "name": "reportho", - "version": "1.1.0" + "name": "pyrodigal", + "path": "modules/nf-core/pyrodigal/meta.yml", + "type": "module", + "meta": { + "name": "pyrodigal", + "description": "Pyrodigal is a Python module that provides bindings to Prodigal, a fast, reliable protein-coding gene prediction for prokaryotic genomes.", + "keywords": ["sort", "annotation", "prediction", "prokaryote"], + "tools": [ + { + "pyrodigal": { + "description": "Pyrodigal is a Python module that provides bindings to Prodigal (ORF finder for microbial sequences) using Cython.", + "homepage": "https://pyrodigal.readthedocs.org/", + "documentation": "https://pyrodigal.readthedocs.org/", + "tool_dev_url": "https://github.com/althonos/pyrodigal/", + "doi": "10.21105/joss.04296", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA file", + "pattern": "*.{fasta.gz,fa.gz,fna.gz}", + "ontologies": [] + } + } + ], + { + "output_format": { + "type": "string", + "description": "Output format", + "pattern": "{gbk,gff}" + } + } + ], + "output": { + "annotations": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.${output_format}.gz": { + "type": "file", + "description": "Gene annotations. The file format is specified via input channel \"output_format\".", + "pattern": "*.{gbk,gff}.gz", + "ontologies": [] + } + } + ] + ], + "fna": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fna.gz": { + "type": "file", + "description": "nucleotide sequences file", + "pattern": "*.{fna.gz}", + "ontologies": [] + } + } + ] + ], + "faa": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.faa.gz": { + "type": "file", + "description": "protein translations file", + "pattern": "*.{faa.gz}", + "ontologies": [] + } + } + ] + ], + "score": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.score.gz": { + "type": "file", + "description": "all potential genes (with scores)", + "pattern": "*.{score.gz}", + "ontologies": [] + } + } + ] + ], + "versions_pyrodigal": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "pyrodigal": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pyrodigal --version |& sed 's/pyrodigal v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "pyrodigal": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pyrodigal --version |& sed 's/pyrodigal v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@louperelo"], + "maintainers": ["@louperelo"] + }, + "pipelines": [ + { + "name": "funcscan", + "version": "3.0.0" + } + ] }, { - "name": "ribomsqc", - "version": "1.0.0" + "name": "qcat", + "path": "modules/nf-core/qcat/meta.yml", + "type": "module", + "meta": { + "name": "qcat", + "description": "Demultiplexer for Nanopore samples", + "keywords": ["demultiplex", "nanopore", "sample"], + "tools": [ + { + "qcat": { + "description": "A demultiplexer for Nanopore samples\n", + "homepage": "https://github.com/nanoporetech/qcat", + "documentation": "https://github.com/nanoporetech/qcat#qcat", + "licence": ["MPL-2.0"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "Non-demultiplexed fastq files\n", + "ontologies": [] + } + } + ], + { + "barcode_kit": { + "type": "string", + "description": "Barcode kit used for demultiplexing" + } + } + ], + "output": { + "reads": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fastq/*.fastq.gz": { + "type": "file", + "description": "Demultiplexed fastq samples", + "pattern": "*.fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@yuukiiwa", "@drpatelh"], + "maintainers": ["@yuukiiwa", "@drpatelh"] + } }, { - "name": "riboseq", - "version": "1.2.0" + "name": "qcatch", + "path": "modules/nf-core/qcatch/meta.yml", + "type": "module", + "meta": { + "name": "qcatch", + "description": "Cell-filtering and QC reporting tool for alevin-fry quantification results", + "keywords": ["single-cell", "quality control", "alevin-fry", "cell filtering", "QC report"], + "tools": [ + { + "qcatch": { + "description": "QCatch is a quality control and cell filtering tool designed for single-cell RNA-seq data processed by alevin-fry.\nIt generates comprehensive QC reports and filtered count matrices.\n", + "homepage": "https://github.com/COMBINE-lab/QCatch", + "licence": ["BSD-3-Clause"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "chemistry": { + "type": "string", + "description": "Chemistry type for the single-cell experiment, which determines the partition range for the empty_drops step.\nSupported values: '10X_3p_v2', '10X_3p_v3', '10X_3p_v4', '10X_5p_v3', '10X_3p_LT', '10X_HT'.\nIf using a standard 10X chemistry and quantification was performed with simpleaf (v0.19.5 or later),\nQCatch will try to infer the correct chemistry from the metadata.\n" + } + }, + { + "quant_dir": { + "type": "directory", + "description": "Directory containing alevin-fry quantification results (af_quant output from simpleaf quant).\nMust contain the quantification matrix and associated metadata files.\n", + "ontologies": [] + } + } + ] + ], + "output": { + "report": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.html": { + "type": "file", + "description": "HTML QC report generated by QCatch containing visualizations and metrics\n", + "pattern": "*.html", + "ontologies": [] + } + } + ] + ], + "filtered_h5ad": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_filtered_quants.h5ad": { + "type": "file", + "description": "Filtered quantification matrix in h5ad format (AnnData)\n", + "pattern": "*_filtered_quants.h5ad", + "ontologies": [] + } + } + ] + ], + "metrics_summary": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_metrics_summary.csv": { + "type": "file", + "description": "CSV file containing summary metrics from QC analysis\n", + "pattern": "*_metrics_summary.csv", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions\n", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@wzheng0520", "@dongzehe"], + "maintainers": ["@wzheng0520", "@dongzehe"] + } }, { - "name": "rnadnavar", - "version": "dev" + "name": "qsv_cat", + "path": "modules/nf-core/qsv/cat/meta.yml", + "type": "module", + "meta": { + "name": "qsv_cat", + "description": "Concatenate two or more CSV (or TSV) tables into a single table", + "keywords": ["concatenate", "tsv", "csv"], + "tools": [ + { + "csvtk": { + "description": "Blazing-fast Data-Wrangling toolkit", + "homepage": "https://qsv.dathere.com", + "documentation": "https://github.com/dathere/qsv", + "tool_dev_url": "https://github.com/dathere/qsv", + "licence": ["MIT", "UNLICENSE"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "csv": { + "type": "file", + "description": "CSV/TSV formatted files", + "pattern": "*.{csv,tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + }, + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + { + "mode": { + "type": "string", + "description": "Concatenation mode (rows, columns or rowskey)", + "pattern": "^(rows|columns|rowskey)$" + } + }, + { + "out_format": { + "type": "string", + "description": "Output format (.csv for comma delimiter, .ssv for semicolon, and .tsv or .tab for tab)", + "pattern": "^(csv|ssv|tsv|tab)$" + } + }, + { + "skip_input_format_check": { + "type": "boolean", + "description": "Skip input format check (by default QSV checks input format based on file extension)" + } + } + ], + "output": { + "csv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "${prefix}.${out_format}": { + "type": "file", + "description": "Concatenated CSV/TSV file", + "pattern": "*.{csv,tsv,tab,ssv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + }, + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_qsv": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "qsv": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "qsv --version | cut -d' ' -f2 | cut -d'-' -f1": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "qsv": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "qsv --version | cut -d' ' -f2 | cut -d'-' -f1": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@dialvarezs"], + "maintainers": ["@dialvarezs"] + }, + "pipelines": [ + { + "name": "mag", + "version": "5.4.2" + } + ] }, { - 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"name": "rnaseq", - "version": "3.26.0" + "name": "qualimap_bamqccram", + "path": "modules/nf-core/qualimap/bamqccram/meta.yml", + "type": "module", + "meta": { + "name": "qualimap_bamqccram", + "description": "Evaluate alignment data", + "keywords": ["quality control", "qc", "bam"], + "tools": [ + { + "qualimap": { + "description": "Qualimap 2 is a platform-independent application written in\nJava and R that provides both a Graphical User Interface and\na command-line interface to facilitate the quality control of\nalignment sequencing data and its derivatives like feature counts.\n", + "homepage": "http://qualimap.bioinfo.cipf.es/", + "documentation": "http://qualimap.conesalab.org/doc_html/index.html", + "doi": "10.1093/bioinformatics/bts503", + "licence": ["GPL-2.0-only"], + "identifier": "biotools:qualimap" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "cram": { + "type": "file", + "description": "Input cram file", + "pattern": "*.{cram}", + "ontologies": [] + } + }, + { + "crai": { + "type": "file", + "description": "Index file for cram file", + "pattern": "*.{crai}", + "ontologies": [] + } + } + ], + { + "gff": { + "type": "file", + "description": "Feature file with regions of interest", + "pattern": "*.{gff,gtf,bed}", + "ontologies": [] + } + }, + { + "fasta": { + "type": "file", + "description": "Reference file of cram file", + "pattern": "*.{fasta,fa,fna}", + "ontologies": [] + } + }, + { + "fasta_fai": { + "type": "file", + "description": "Index file for reference file", + "pattern": "*.{fai}", + "ontologies": [] + } + } + ], + "output": { + "results": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}": { + "type": "directory", + "description": "Qualimap results dir", + "pattern": "*/*" + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@FriederikeHanssen"], + "maintainers": ["@FriederikeHanssen"] + }, + "pipelines": [ + { + "name": "methylseq", + "version": "4.2.0" + } + ] }, { - 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File is tab separated with no header, one row per SNP, with col 1 = chromosome, col 2 = physical position (sorted from smallest to largest), col 3 = reference base, col 4 = alternate base. Bases are capitalized.", + "pattern": "*.{txt}", + "ontologies": [] + } + }, + { + "phasefile": { + "type": "file", + "description": "(Optional) File with truth phasing results. Supersedes genfile if both options given. File has a header row with a name for each sample, matching what is found in the bam file. Each subject is then a tab separated column, with 0 = ref and 1 = alt, separated by a vertical bar |, e.g. 0|0 or 0|1. Note therefore this file has one more row than posfile which has no header.", + "pattern": "*.{txt}", + "ontologies": [] + } + }, + { + "genfile": { + "type": "file", + "description": "(Optional) Path to gen file with high coverage results. Empty for no genfile. 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Each subject is then a tab seperated column, with 0 = hom ref, 1 = het, 2 = hom alt and NA indicating missing genotype, with rows corresponding to rows of the posfile. Note therefore this file has one more row than posfile which has no header [default \"\"]", + "pattern": "*.{txt}", + "ontologies": [] + } + }, + { + "chr": { + "type": "string", + "description": "(Mandatory) What chromosome to run. Should match BAM headers." + } + }, + { + "regions_start": { + "type": "integer", + "description": "(Mandatory) When running imputation, where to start from. The 1-based position x is kept if regionStart <= x <= regionEnd." + } + }, + { + "regions_end": { + "type": "integer", + "description": "(Mandatory) When running imputation, where to stop." + } + }, + { + "ngen": { + "type": "integer", + "description": "Number of generations since founding or mixing. Note that the algorithm is relatively robust to this. Use nGen = 4 * Ne / K if unsure." + } + }, + { + "buffer": { + "type": "integer", + "description": "Buffer of region to perform imputation over. So imputation is run form regionStart-buffer to regionEnd+buffer, and reported for regionStart to regionEnd, including the bases of regionStart and regionEnd." + } + }, + { + "genetic_map": { + "type": "file", + "description": "(Optional) File with genetic map information, a file with 3 white-space delimited entries giving position (1-based), genetic rate map in cM/Mbp, and genetic map in cM. If no file included, rate is based on physical distance and expected rate (expRate).", + "pattern": "*.{txt,map}{,gz}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "(Optional) File with reference genome.", + "pattern": "*.{fa,fasta}", + "ontologies": [] + } + }, + { + "fasta_fai": { + "type": "file", + "description": "(Optional) File with reference genome index.", + "pattern": "*.{fai}", + "ontologies": [] + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "VCF file with both SNP annotation information and per-sample genotype information.", + "pattern": "*.{vcf.gz}", + "ontologies": [] + } + } + ] + ], + "tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz.tbi": { + "type": "file", + "description": "TBI file of the VCF.", + "pattern": "*.{vcf.gz.tbi}", + "ontologies": [] + } + } + ] + ], + "rdata": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "RData": { + "type": "directory", + "description": "Folder of RData objects generated during the imputation process.\n", + "pattern": "RData" + } + } + ] + ], + "plots": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "plots": { + "type": "directory", + "description": "Folder of plots generated during the imputation process.\n", + "pattern": "plots" + } + } + ] + ], + "versions_r_quilt": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "r-quilt": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "Rscript -e \"cat(as.character(packageVersion('QUILT')))\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_r_base": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "r-base": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "R --version | sed \"1!d; s/.*version //; s/ .*//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "r-quilt": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "Rscript -e \"cat(as.character(packageVersion('QUILT')))\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "r-base": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "R --version | sed \"1!d; s/.*version //; s/ .*//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@atrigila"], + "maintainers": ["@atrigila"] + } }, { - "name": "seqsubmit", - "version": "dev" + "name": "racon", + "path": "modules/nf-core/racon/meta.yml", + "type": "module", + "meta": { + "name": "racon", + "description": "Consensus module for raw de novo DNA assembly of long uncorrected reads", + "keywords": ["assembly", "pacbio", "nanopore", "polish"], + "tools": [ + { + "racon": { + "description": "Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads.", + "homepage": "https://github.com/lbcb-sci/racon", + "documentation": "https://github.com/lbcb-sci/racon", + "tool_dev_url": "https://github.com/lbcb-sci/racon", + "doi": "10.1101/gr.214270.116", + "licence": ["MIT"], + "identifier": "biotools:Racon" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files. Racon expects single end reads", + "pattern": "*.{fastq,fastq.gz,fq,fq.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + }, + { + "assembly": { + "type": "file", + "description": "Genome assembly to be improved", + "pattern": "*.{fasta,fa}", + "ontologies": [] + } + }, + { + "paf": { + "type": "file", + "description": "Alignment in PAF format", + "pattern": "*.paf", + "ontologies": [] + } + } + ] + ], + "output": { + "improved_assembly": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_assembly_consensus.fasta.gz": { + "type": "file", + "description": "Improved genome assembly", + "pattern": "*_assembly_consensus.fasta.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "versions_racon": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "racon": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "racon --version 2>&1 | sed \"s/^.*v//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "racon": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "racon --version 2>&1 | sed \"s/^.*v//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@avantonder"], + "maintainers": ["@avantonder"] + }, + "pipelines": [ + { + "name": "bacass", + "version": "2.6.0" + }, + { + "name": "crisprseq", + "version": "2.3.0" + } + ] }, { - "name": "smrnaseq", - "version": "2.4.1" + "name": "ragtag_patch", + "path": "modules/nf-core/ragtag/patch/meta.yml", + "type": "module", + "meta": { + "name": "ragtag_patch", + "description": "Homology-based assembly patching: Make continuous joins and fill gaps in 'target.fa' using sequences from 'query.fa'", + "keywords": ["assembly", "consensus", "ragtag", "patch"], + "tools": [ + { + "ragtag": { + "description": "Fast reference-guided genome assembly scaffolding", + "homepage": "https://github.com/malonge/RagTag/wiki", + "documentation": "https://github.com/malonge/RagTag/wiki", + "tool_dev_url": "https://github.com/malonge/RagTag", + "doi": "10.1186/s13059-022-02823-7", + "licence": ["MIT"], + "identifier": "biotools:ragtag" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "target": { + "type": "file", + "description": "Target assembly", + "pattern": "*.{fasta,fasta.gz}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "query": { + "type": "file", + "description": "Query assembly", + "pattern": "*.{fasta,fasta.gz}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "exclude": { + "type": "file", + "description": "list of target sequences to ignore", + "pattern": "*.txt", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "skip": { + "type": "file", + "description": "list of query sequences to ignore", + "pattern": "*.txt", + "ontologies": [] + } + } + ] + ], + "output": { + "patch_fasta": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.patch.fasta": { + "type": "file", + "description": "FASTA file containing the patched assembly", + "pattern": "*.patch.fasta", + "ontologies": [] + } + } + ] + ], + "patch_agp": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.patch.agp": { + "type": "file", + "description": "AGP file defining how ragtag.patch.fasta is built", + "pattern": "*.patch.agp", + "ontologies": [] + } + } + ] + ], + "patch_components_fasta": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.comps.fasta": { + "type": "file", + "description": "The split target assembly and the renamed query assembly combined into one FASTA file. This file contains all components in ragtag.patch.agp", + "pattern": "*.comps.fasta", + "ontologies": [] + } + } + ] + ], + "assembly_alignments": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.ragtag.patch.asm.*": { + "type": "file", + "description": "Assembly alignment files", + "pattern": "*.ragtag.patch.asm.*", + "ontologies": [] + } + } + ] + ], + "target_splits_agp": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.ctg.agp": { + "type": "file", + "description": "An AGP file defining how the target assembly was split at gaps", + "pattern": "*.ctg.agp", + "ontologies": [] + } + } + ] + ], + "target_splits_fasta": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.ctg.fasta": { + "type": "file", + "description": "FASTA file containing the target assembly split at gaps", + "pattern": "*.ctg.fasta", + "ontologies": [] + } + } + ] + ], + "qry_rename_agp": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.rename.agp": { + "type": "file", + "description": "An AGP file defining the new names for query sequences", + "pattern": "*.rename.agp", + "ontologies": [] + } + } + ] + ], + "qry_rename_fasta": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.rename.fasta": { + "type": "file", + "description": "A FASTA file with the original query sequence, but with new names", + "pattern": "*.rename.fasta", + "ontologies": [] + } + } + ] + ], + "stderr": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.patch.err": { + "type": "file", + "description": "Standard error logging for all external RagTag commands", + "pattern": "*.patch.err", + "ontologies": [] + } + } + ] + ], + "versions_ragtag": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "ragtag": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "ragtag.py -v | sed 's/v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "ragtag": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "ragtag.py -v | sed 's/v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@nschan"], + "maintainers": ["@nschan"] + }, + "pipelines": [ + { + "name": "genomeassembler", + "version": "1.1.0" + } + ] }, { - "name": "spatialvi", - "version": "dev" + "name": "ragtag_scaffold", + "path": "modules/nf-core/ragtag/scaffold/meta.yml", + "type": "module", + "meta": { + "name": "ragtag_scaffold", + "description": "Scaffolding is the process of ordering and orienting draft assembly (query)\nsequences into longer sequences. Gaps (stretches of \"N\" characters) are placed\nbetween adjacent query sequences to indicate the presence of unknown sequence.\nRagTag uses whole-genome alignments to a reference assembly to scaffold query sequences.\nRagTag does not alter input query sequence in any way and only orders and orients sequences, joining them with gaps.\n", + "keywords": ["scaffolding", "ragtag", "assembly", "genome"], + "tools": [ + { + "ragtag": { + "description": "Fast reference-guided genome assembly scaffolding", + "homepage": "https://github.com/malonge/RagTag/wiki", + "documentation": "https://github.com/malonge/RagTag/wiki", + "tool_dev_url": "https://github.com/malonge/RagTag", + "doi": "10.1186/s13059-022-02823-7", + "licence": ["MIT"], + "identifier": "biotools:ragtag" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "assembly": { + "type": "file", + "description": "Assembly to be scaffolded", + "pattern": "*.{fasta,fasta.gz,fa,fa.gz}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "reference": { + "type": "file", + "description": "Reference assembly", + "pattern": "*.{fasta,fasta.gz,fa,fa.gz}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "exclude": { + "type": "file", + "description": "list of target sequences to ignore", + "pattern": "*.txt", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "skip": { + "type": "file", + "description": "list of query sequences to leave unplaced", + "pattern": "*.txt", + "ontologies": [] + } + }, + { + "hard_skip": { + "type": "file", + "description": "list of query headers to leave unplaced and exclude from 'chr0' ('-C')", + "pattern": "*.txt", + "ontologies": [] + } + } + ] + ], + "output": { + "corrected_assembly": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.fasta": { + "type": "file", + "description": "FASTA file containing the patched assembly", + "pattern": "*.fasta", + "ontologies": [] + } + } + ] + ], + "corrected_agp": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.agp": { + "type": "file", + "description": "agp file defining how corrected_assembly is built", + "pattern": "*.agp", + "ontologies": [] + } + } + ] + ], + "corrected_stats": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.stats": { + "type": "file", + "description": "Statistics on the scaffold", + "pattern": "*.stats", + "ontologies": [] + } + } + ] + ], + "versions_ragtag": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "ragtag": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "ragtag.py -v | sed 's/v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "ragtag": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "ragtag.py -v | sed 's/v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@nschan"], + "maintainers": ["@nschan"] + }, + "pipelines": [ + { + "name": "genomeassembler", + "version": "1.1.0" + } + ] }, { - "name": "spatialxe", - "version": "dev" + "name": "rapidnj", + "path": "modules/nf-core/rapidnj/meta.yml", + "type": "module", + "meta": { + "name": "rapidnj", + "description": "Produces a Newick format phylogeny from a multiple sequence alignment using a Neighbour-Joining algorithm. Capable of bacterial genome size alignments.", + "keywords": ["phylogeny", "newick", "neighbour-joining"], + "tools": [ + { + "rapidnj": { + "description": "RapidNJ is an algorithmic engineered implementation of canonical neighbour-joining. It uses an efficient search heuristic to speed-up the core computations of the neighbour-joining method that enables RapidNJ to outperform other state-of-the-art neighbour-joining implementations.", + "homepage": "https://birc.au.dk/software/rapidnj", + "documentation": "https://birc.au.dk/software/rapidnj", + "tool_dev_url": "https://github.com/somme89/rapidNJ", + "doi": "10.1007/978-3-540-87361-7_10", + "licence": ["GPL v2"], + "identifier": "biotools:rapidnj" + } + } + ], + "input": [ + { + "alignment": { + "type": "file", + "description": "A FASTA format multiple sequence alignment file", + "pattern": "*.{fasta,fas,fa,mfa}", + "ontologies": [] + } + } + ], + "output": { + "stockholm_alignment": [ + { + "*.sth": { + "type": "file", + "description": "An alignment in Stockholm format", + "pattern": "*.{sth}", + "ontologies": [] + } + } + ], + "phylogeny": [ + { + "*.tre": { + "type": "file", + "description": "A phylogeny in Newick format", + "pattern": "*.{tre}", + "ontologies": [] + } + } + ], + "versions_rapidnj": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "rapidnj": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "echo 2.3.2": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_biopython": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "biopython": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python -c \"import Bio; print(Bio.__version__)\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "rapidnj": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "echo 2.3.2": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "biopython": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python -c \"import Bio; print(Bio.__version__)\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@aunderwo", "@avantonder"], + "maintainers": ["@aunderwo", "@avantonder"] + } }, { - "name": "ssds", - "version": "dev" + "name": "rastair_call", + "path": "modules/nf-core/rastair/call/meta.yml", + "type": "module", + "meta": { + "name": "rastair_call", + "description": "Assess positive C->T conversion as a readout for methylation on a genome-wide basis", + "keywords": ["methylation", "rastair", "C->T conversion", "bisulphite", "bisulfite", "bam", "mCtoT"], + "tools": [ + { + "rastair": { + "description": "A tool for rapid genome-wide assessment of positive C->T conversion as a readout for methylation.\n", + "homepage": "https://bitbucket.org/bsblabludwig/rastair/src/master/", + "documentation": "https://bitbucket.org/bsblabludwig/rastair/src/master/README.md", + "licence": ["GPL-3.0"] + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM file", + "pattern": "*.{bam,cram}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bai": { + "type": "file", + "description": "BAM/CRAM index file", + "pattern": "*.{bai,crai}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input genome fasta file", + "pattern": "*.{fasta,fa}" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "FASTA index file", + "pattern": "*.fai" + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "parsed_trim_OT": { + "type": "string", + "description": "Number of nucleotides to trim from Original Top (OT) reads." + } + } + ], + [ + { + "meta6": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "parsed_trim_OB": { + "type": "string", + "description": "Number of nucleotides to trim from Original Bottom (OB) reads." + } + } + ] + ], + "output": { + "txt": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.rastair_call.txt": { + "type": "file", + "description": "Text file from Rastair call containing C->T conversion metrics", + "pattern": "*.rastair_call.txt" + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@eduard-casas"], + "maintainers": ["@eduard-casas"] + }, + "pipelines": [ + { + "name": "methylseq", + "version": "4.2.0" + } + ] }, { - 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"name": "viralintegration", - "version": "0.1.1" + "name": "raw2ometiff", + "path": "modules/nf-core/raw2ometiff/meta.yml", + "type": "module", + "meta": { + "name": "raw2ometiff", + "description": "write your description here", + "keywords": ["ome", "tiff", "imaging"], + "tools": [ + { + "raw2ometiff": { + "description": "Java application to convert a directory of tiles to an OME-TIFF pyramid.", + "homepage": "https://github.com/glencoesoftware/raw2ometiff", + "documentation": "https://github.com/glencoesoftware/raw2ometiff", + "tool_dev_url": "https://github.com/glencoesoftware/raw2ometiff", + "licence": ["GPL-2.0"], + "identifier": "biotools:raw2ometiff" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "zarr_dir": { + "type": "directory", + "description": "Tile directory must contain a full pyramid in a Zarr container.", + "pattern": "*.{zarr}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3915" + } + ] + } + } + ] + ], + "output": { + "ometiff": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "*.ome.tiff": { + "type": "file", + "description": "OME-TIFF pyramid", + "pattern": "*.ome.tiff", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3727" + } + ] + } + } + ] + ], + "versions_raw2ometiff": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "raw2ometiff": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "raw2ometiff --version |& sed -n \"1s/Version = //p\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_bioformats": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bioformats": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "raw2ometiff --version |& sed -n \"2s/Bio-Formats version = //p\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "raw2ometiff": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "raw2ometiff --version |& sed -n \"1s/Version = //p\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bioformats": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "raw2ometiff --version |& sed -n \"2s/Bio-Formats version = //p\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@CaroAMN"], + "maintainers": ["@CaroAMN"] + } }, { - "name": "viralmetagenome", - "version": "1.1.1" + "name": "raxmlng", + "path": "modules/nf-core/raxmlng/meta.yml", + "type": "module", + "meta": { + "name": "raxmlng", + "description": "RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion.", + "keywords": ["phylogeny", "newick", "maximum likelihood"], + "tools": [ + { + "raxmlng": { + "description": "RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion.", + "homepage": "https://github.com/amkozlov/raxml-ng", + "documentation": "https://github.com/amkozlov/raxml-ng/wiki", + "tool_dev_url": "https://github.com/amkozlov/raxml-ng", + "doi": "10.1093/bioinformatics/btz305", + "license": ["GPL v2-or-later"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information (e.g. [ id:'sample1' ])" + } + }, + { + "alignment": { + "type": "file", + "description": "A FASTA format multiple sequence alignment file", + "pattern": "*.{fasta,fas,fa,mfa}", + "ontologies": [] + } + }, + { + "model": { + "type": "string", + "description": "The substitution model to use for the phylogenetic inference" + } + } + ] + ], + "output": { + "phylogeny": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information", + "pattern": "*.{raxml.bestTree}" + } + }, + { + "*.raxml.bestTree": { + "type": "file", + "description": "A phylogeny in Newick format", + "pattern": "*.{raxml.bestTree}", + "ontologies": [] + } + } + ] + ], + "phylogeny_bootstrapped": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information", + "pattern": "*.{raxml.bestTree}" + } + }, + { + "*.raxml.bootstraps": { + "type": "file", + "description": "A phylogeny in Newick format with bootstrap values", + "pattern": "*.{raxml.bootstraps}", + "optional": true, + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@avantonder", "@aunderwo"], + "maintainers": ["@avantonder", "@aunderwo"] + } }, { - "name": "viralrecon", - "version": "3.0.0" - } - ] - }, - { - "name": "multiqc_sav", - "path": "modules/nf-core/multiqc_sav/meta.yml", - "type": "module", - "meta": { - "name": "multiqc_sav", - "description": "Aggregate results from bioinformatics analyses across many samples into a single report, with support for multiqc_sav plugin", - "keywords": [ - "QC", - "bioinformatics tools", - "Beautiful stand-alone HTML report", - "Illumina", - "Sequencing Analysis Viewer", - "SAV" - ], - "tools": [ - { - "multiqc": { - "description": "MultiQC searches a given directory for analysis logs and compiles a HTML report.\nIt's a general use tool, perfect for summarising the output from numerous bioinformatics tools.\n", - "homepage": "https://multiqc.info/", - "documentation": "https://multiqc.info/docs/", - "licence": [ - "GPL-3.0-or-later" - ], - "identifier": "biotools:multiqc" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample1', single_end:false ]\n" - } - }, - { - "runinfo_xml": { - "type": "file", - "description": "Illumina RunInfo.xml file", - "pattern": "RunInfo.xml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2332" - } - ] - } - }, - { - "interop_bin": { - "type": "file", - "description": "Illumina InterOp binary files", - "pattern": "InterOp/*.bin", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2333" - } - ] - } - }, - { - "extra_multiqc_files": { - "type": "file", - "description": "List of reports / files rec ognised by MultiQC, for example the html and zip output of FastQC\n", - "ontologies": [] - } - }, - { - "multiqc_config": { - "type": "file", - "description": "Optional config yml for MultiQC", - "pattern": "*.{yml,yaml}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - }, - { - "extra_multiqc_config": { - "type": "file", - "description": "Second optional config yml for MultiQC. Will override common sections in multiqc_config.", - "pattern": "*.{yml,yaml}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - }, - { - "multiqc_logo": { - "type": "file", - "description": "Optional logo file for MultiQC", - "pattern": "*.{png}", - "ontologies": [] - } - }, - { - "replace_names": { - "type": "file", - "description": "Optional two-column sample renaming file. First column a set of\npatterns, second column a set of corresponding replacements. Passed via\nMultiQC's `--replace-names` option.\n", - "pattern": "*.{tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - }, - { - "sample_names": { - "type": "file", - "description": "Optional TSV file with headers, passed to the MultiQC --sample_names\nargument.\n", - "pattern": "*.{tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "output": { - "report": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample1', single_end:false ]\n" - } - }, - { - "*.html": { - "type": "file", - "description": "MultiQC report file", - "pattern": ".html", - "ontologies": [] - } - } - ] - ], - "data": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample1', single_end:false ]\n" - } - }, - { - "*_data": { - "type": "directory", - "description": "MultiQC data dir", - "pattern": "multiqc_data" - } - } - ] - ], - "plots": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample1', single_end:false ]\n" - } - }, - { - "*_plots": { - "type": "file", - "description": "Plots created by MultiQC", - "pattern": "*_data", - "ontologies": [] - } - } - ] - ], - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "multiqc": { - "type": "string", - "description": "The tool name" - } - }, - { - "multiqc --version | sed \"s/.* //g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_multiqc_sav": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "multiqc_sav": { - "type": "string", - "description": "The tool name" - } - }, - { - "python -c \"import multiqc_sav; print(multiqc_sav.__version__)\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_interop": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "interop": { - "type": "string", - "description": "The tool name" - } - }, - { - "python -c \"import interop; print(interop.__version__)\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@matthdsm", - "@delfiterradas" - ], - "maintainers": [ - "@matthdsm" - ] - } - }, - { - "name": "multiqcsav", - "path": "modules/nf-core/multiqcsav/meta.yml", - "type": "module", - "meta": { - "name": "multiqcsav", - "description": "Aggregate results from bioinformatics analyses across many samples into a single report, with support for multiqc_sav plugin", - "keywords": [ - "QC", - "bioinformatics tools", - "Beautiful stand-alone HTML report", - "Illumina", - "Sequencing Analysis Viewer", - "SAV" - ], - "tools": [ - { - "multiqc": { - "description": "MultiQC searches a given directory for analysis logs and compiles a HTML report.\nIt's a general use tool, perfect for summarising the output from numerous bioinformatics tools.\n", - "homepage": "https://multiqc.info/", - "documentation": "https://multiqc.info/docs/", - "licence": [ - "GPL-3.0-or-later" - ], - "identifier": "biotools:multiqc" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample1', single_end:false ]\n" - } - }, - { - "xml": { - "type": "file", - "description": "xml files from an Illumina sequencing run", - "pattern": "*.xml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2332" - } - ] - } - }, - { - "interop_bin": { - "type": "file", - "description": "Illumina InterOp binary files", - "pattern": "InterOp/*.bin", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2333" - } - ] - } - }, - { - "extra_multiqc_files": { - "type": "file", - "description": "List of reports / files recognised by MultiQC, for example the html and zip output of FastQC\n", - "ontologies": [] - } - }, - { - "multiqc_config": { - "type": "file", - "description": "Optional config yml for MultiQC", - "pattern": "*.{yml,yaml}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - }, - { - "multiqc_logo": { - "type": "file", - "description": "Optional logo file for MultiQC", - "pattern": "*.{png}", - "ontologies": [] - } - }, - { - "replace_names": { - "type": "file", - "description": "Optional two-column sample renaming file. First column a set of\npatterns, second column a set of corresponding replacements. Passed via\nMultiQC's `--replace-names` option.\n", - "pattern": "*.{tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } + "name": "rbt_vcfsplit", + "path": "modules/nf-core/rbt/vcfsplit/meta.yml", + "type": "module", + "meta": { + "name": "rbt_vcfsplit", + "description": "A tool for splitting VCF/BCF files into N equal chunks, including BND support", + "keywords": ["genomics", "splitting", "VCF", "BCF", "variants"], + "tools": [ + { + "rust-bio-tools": { + "description": "A growing collection of fast and secure command line utilities for dealing with NGS data implemented on top of Rust-Bio.", + "homepage": "https://github.com/rust-bio/rust-bio-tools", + "documentation": "https://github.com/rust-bio/rust-bio-tools", + "tool_dev_url": "https://github.com/rust-bio/rust-bio-tools", + "doi": "no DOI available", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF file with variants to be split", + "pattern": "*.{vcf,bcf,vcf.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + }, + { + "edam": "http://edamontology.org/format_3020" + } + ] + } + } + ], + { + "numchunks": { + "type": "integer", + "description": "Number of chunks to split the VCF file into. The default is 15." + } + } + ], + "output": { + "bcfchunks": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.bcf": { + "type": "file", + "description": "Chunks of the input VCF file, split into `numchunks` equal parts.", + "pattern": "*.bcf", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3020" + } + ] + } + } + ] + ], + "versions_rbt": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "rbt": { + "type": "string", + "description": "The tool name" + } + }, + { + "rbt --version | grep -oE '[0-9]+(\\.[0-9]+)+' | head -n 1": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "rbt": { + "type": "string", + "description": "The tool name" + } + }, + { + "rbt --version | grep -oE '[0-9]+(\\.[0-9]+)+' | head -n 1": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@famosab"], + "maintainers": ["@famosab"] }, - { - "sample_names": { - "type": "file", - "description": "Optional TSV file with headers, passed to the MultiQC --sample_names\nargument.\n", - "pattern": "*.{tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "output": { - "report": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample1', single_end:false ]\n" - } - }, - { - "*.html": { - "type": "file", - "description": "MultiQC report file", - "pattern": ".html", - "ontologies": [] - } - } - ] - ], - "data": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample1', single_end:false ]\n" - } - }, - { - "*_data": { - "type": "directory", - "description": "MultiQC data dir", - "pattern": "multiqc_data" - } - } - ] - ], - "plots": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample1', single_end:false ]\n" - } - }, - { - "*_plots": { - "type": "file", - "description": "Plots created by MultiQC", - "pattern": "*_data", - "ontologies": [] - } - } - ] - ], - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "multiqc": { - "type": "string", - "description": "The tool name" - } - }, - { - "multiqc --version | sed \"s/.* //g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "sarek", + "version": "3.8.1" + } ] - ], - "versions_interop": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "interop": { - "type": "string", - "description": "The tool name" - } - }, - { - "python -c \"import interop; print(interop.__version__)\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_multiqcsav": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "multiqcsav": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python -c \"import multiqc_sav; print(multiqc_sav.__version__)\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@matthdsm", - "@delfiterradas" - ], - "maintainers": [ - "@matthdsm" - ], - "containers": { - "conda": { - "linux/amd64": { - "lock_file": "modules/nf-core/multiqcsav/.conda-lock/linux_amd64-bd-d497f2c0ee14021c_1.txt" - }, - "linux/arm64": { - "lock_file": "modules/nf-core/multiqcsav/.conda-lock/linux_arm64-bd-63d3faa1f4fa1fa6_1.txt" - } - }, - "docker": { - "linux/amd64": { - "name": "community.wave.seqera.io/library/multiqc_multiqc_sav_pip_interop:d497f2c0ee14021c", - "build_id": "bd-d497f2c0ee14021c_1", - "scan_id": "sc-872ef428e7dd759e_1" - }, - "linux/arm64": { - "name": "community.wave.seqera.io/library/multiqc_multiqc_sav_pip_interop:63d3faa1f4fa1fa6", - "build_id": "bd-63d3faa1f4fa1fa6_1", - "scan_id": "sc-d2c09f2fb4caa3ad_1" - } - }, - "singularity": { - "linux/amd64": { - "name": "oras://community.wave.seqera.io/library/multiqc_multiqc_sav_pip_interop:f4f70d0f966edec3", - "build_id": "bd-f4f70d0f966edec3_1", - "https": "https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/80/80a772836e24ece3afc4eb53f6584a311000842e6323b8e725d37fd88b566768/data" - }, - "linux/arm64": { - "name": "oras://community.wave.seqera.io/library/multiqc_multiqc_sav_pip_interop:8285dbf19c66f011", - "build_id": "bd-8285dbf19c66f011_1", - "https": "https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/20/20f8e844c2df1a8893ac3897249bf3166752c17c41822271c12a51821b13c685/data" - } - } - } - }, - "pipelines": [ + }, { - "name": "demultiplex", - "version": "1.7.1" - } - ] - }, - { - "name": "multiseqdemux", - "path": "modules/nf-core/multiseqdemux/meta.yml", - "type": "module", - "meta": { - "name": "multiseqdemux", - "description": "Identify singlets, doublets and negative cells from multiplexing experiments. Annotate singlets by tags.", - "keywords": [ - "demultiplexing", - "hashing-based deconvolution", - "single-cell" - ], - "tools": [ - { - "multiseqdemux": { - "description": "MULTIseqDemux is the demultiplexing module of Seurat, which demultiplex samples based on data from cell hashing.", - "homepage": "https://satijalab.org/seurat/reference/multiseqdemux", - "documentation": "https://satijalab.org/seurat/reference/multiseqdemux", - "tool_dev_url": "https://github.com/satijalab/seurat", - "doi": "10.1038/s41592-019-0433-8", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "seurat_object": { - "type": "file", - "description": "A `.rds` file containing the seurat object. Assumes that the hash tag oligo (HTO) data has been added and normalized.\n", - "ontologies": [] - } - }, - { - "assay": { - "type": "string", - "description": "Name of the Hashtag assay, usually called \"HTO\" by default. Use the custom name if the assay has been named differently.\n" - } - } - ] - ], - "output": { - "params": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*_params_multiseqdemux.csv": { - "type": "file", - "description": "The used parameters to call MULTIseqDemux in the R-Script.", - "pattern": "_params_multiseqdemux.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "results": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*_res_multiseqdemux.csv": { - "type": "file", - "description": "Resuls of MULTIseqDemux.", - "pattern": "_res_multiseqdemux.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "rds": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*_multiseqdemux.rds": { - "type": "file", - "description": "SeuratObject saved as RDS.", - "pattern": "_multiseqdemux.rds", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@LuisHeinzlmeier" - ], - "maintainers": [ - "@LuisHeinzlmeier" - ] - } - }, - { - "name": "multivcfanalyzer", - "path": "modules/nf-core/multivcfanalyzer/meta.yml", - "type": "module", - "meta": { - "name": "multivcfanalyzer", - "description": "SNP table generator from GATK UnifiedGenotyper with functionality geared for aDNA", - "keywords": [ - "vcf", - "ancient DNA", - "aDNA", - "SNP", - "GATK UnifiedGenotyper", - "SNP table" - ], - "tools": [ - { - "multivcfanalyzer": { - "description": "MultiVCFAnalyzer is a VCF file post-processing tool tailored for aDNA. License on Github repository.", - "homepage": "https://github.com/alexherbig/MultiVCFAnalyzer", - "documentation": "https://github.com/alexherbig/MultiVCFAnalyzer", - "tool_dev_url": "https://github.com/alexherbig/MultiVCFAnalyzer", - "doi": "10.1038/nature13591", - "licence": [ - "GPL >=3" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "vcfs": { - "type": "file", - "description": "One or a list of gzipped or uncompressed VCF file", - "pattern": "*.vcf", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome VCF was generated against", - "pattern": "*.{fasta,fna,fa}", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "snpeff_results": { - "type": "file", - "description": "Results from snpEff in txt format (Optional)", - "pattern": "*.txt", - "ontologies": [] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "gff": { - "type": "file", - "description": "GFF file corresponding to reference genome fasta (Optional)", - "pattern": "*.gff", - "ontologies": [] - } - } - ], - { - "allele_freqs": { - "type": "boolean", - "description": "Whether to include the percentage of reads a given allele is\npresent in in the SNP table.\n" + "name": "regenie_step1", + "path": "modules/nf-core/regenie/step1/meta.yml", + "type": "module", + "meta": { + "name": "regenie_step1", + "description": "Run REGENIE step 1 to fit whole-genome regression models and emit LOCO predictions", + "keywords": ["regenie", "gwas", "association", "burden test", "genomics"], + "tools": [ + { + "regenie": { + "description": "Regenie is a C++ program for whole genome regression modelling of large genome-wide association studies (GWAS).", + "homepage": "https://rgcgithub.github.io/regenie/", + "documentation": "https://rgcgithub.github.io/regenie/options/", + "tool_dev_url": "https://github.com/rgcgithub/regenie", + "doi": "10.1038/s41588-021-00870-7", + "licence": ["MIT"], + "identifier": "biotools:regenie" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing genotype information\nKeep only the genotype analysis identifier in this map\nREGENIE consumes the staged basename of `plink_genotype_file` as the `--bed` or `--pgen` prefix, so the `.bed/.bim/.fam` or `.pgen/.pvar/.psam` files must share one basename\ne.g. `[ id:'cohort' ]`\n" + } + }, + { + "plink_genotype_file": { + "type": "file", + "description": "PLINK primary genotype file in BED or PGEN format", + "pattern": "*.{bed,pgen}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3003" + } + ] + } + }, + { + "plink_variant_file": { + "type": "file", + "description": "PLINK variant metadata file in BIM or PVAR format", + "pattern": "*.{bim,pvar,zst}", + "ontologies": [] + } + }, + { + "plink_sample_file": { + "type": "file", + "description": "PLINK sample metadata file in FAM or PSAM format", + "pattern": "*.{fam,psam}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing genotype/sample information associated with the phenotype file input\nKeep only the shared genotype/sample identifier in this map\ne.g. `[ id:'plink_simulated' ]`\n" + } + }, + { + "pheno": { + "type": "file", + "description": "Phenotype file passed to `--phenoFile`", + "pattern": "*.{phe,pheno,txt,tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing genotype/sample information associated with the covariate input\ne.g. `[ id:'plink_simulated' ]`\n" + } + }, + { + "covar": { + "type": "file", + "optional": true, + "description": "Optional covariate file passed to `--covarFile`; provide `[]` when absent", + "pattern": "*.{covar,cov,txt,tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + { + "bsize": { + "type": "integer", + "description": "Optional block size passed to `--bsize`; pass `[]` to use the module default of `1000`" + } + } + ], + "output": { + "predictions": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing genotype/sample information\ne.g. `[ id:'plink_simulated' ]`\n" + } + }, + { + "*_pred.list": { + "type": "file", + "description": "REGENIE prediction list file", + "pattern": "*_pred.list", + "ontologies": [] + } + } + ] + ], + "loco": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing genotype/sample information\ne.g. `[ id:'plink_simulated' ]`\n" + } + }, + { + "*.loco.gz": { + "type": "file", + "description": "REGENIE LOCO prediction files", + "pattern": "*.loco.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3987" + } + ] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing genotype information\ne.g. `[ id:'plink_simulated' ]`\n" + } + }, + { + "*.log": { + "type": "file", + "description": "REGENIE step 1 log file", + "pattern": "*.log", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + } + ] + ], + "versions_regenie": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "regenie": { + "type": "string", + "description": "The tool name" + } + }, + { + "regenie --version 2>&1 | sed -n \"1{s/^v//;s/\\.gz$//;p}\"": { + "type": "eval", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "regenie": { + "type": "string", + "description": "The tool name" + } + }, + { + "regenie --version 2>&1 | sed -n \"1{s/^v//;s/\\.gz$//;p}\"": { + "type": "eval", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@lyh970817"], + "maintainers": ["@lyh970817"], + "containers": { + "conda": { + "linux_amd64": { + "lock_file": "modules/nf-core/regenie/step1/.conda-lock/linux_amd64-bd-5d361f9fcb2f85cf_1.txt" + } + }, + "docker": { + "linux_amd64": { + "build_id": "bd-5d361f9fcb2f85cf_1", + "name": "community.wave.seqera.io/library/regenie:4.1.2--5d361f9fcb2f85cf", + "scanId": "sc-cc9eb5ed5eb381dd_2" + } + }, + "singularity": { + "linux_amd64": { + "build_id": "bd-7c121fb4ecd57890_1", + "name": "oras://community.wave.seqera.io/library/regenie:4.1.2--7c121fb4ecd57890", + "https": "https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/7a/7a05bf71ea09adc5ebf9f0c656c9b326c0f16ba8e4966914972e58313469a466/data" + } + } + } } - }, - { - "genotype_quality": { - "type": "integer", - "description": "Minimum GATK genotyping threshold threshold of which a SNP call\nfalling under is 'discarded'\n" + }, + { + "name": "regtools_junctionsextract", + "path": "modules/nf-core/regtools/junctionsextract/meta.yml", + "type": "module", + "meta": { + "name": "regtools_junctionsextract", + "description": "Extract exon-exon junctions from an RNAseq BAM file. The output is a BED file in the BED12 format.", + "keywords": ["regtools", "leafcutter", "RNA-seq", "splicing"], + "tools": [ + { + "regtools": { + "description": "RegTools is a set of tools that integrate DNA-seq and RNA-seq data to help interpret mutations in a regulatory and splicing context.", + "homepage": "https://regtools.readthedocs.io/en/latest/", + "documentation": "https://regtools.readthedocs.io/en/latest/#usage", + "tool_dev_url": "https://github.com/griffithlab/regtools", + "licence": ["MIT"], + "identifier": "biotools:regtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "bam": { + "type": "file", + "description": "Sorted BAM file", + "pattern": "*.{bam}", + "ontologies": [] + } + }, + { + "bai": { + "type": "file", + "description": "Index to sorted BAM file", + "pattern": "*.{bai}", + "ontologies": [] + } + } + ], + { + "strand_specificity": { + "type": "string", + "description": "Strand specificity of the RNA-seq library preparation.\nOptions are 'XS', use XS tags provided by aligner; 'RF', first-strand; 'FR', second-strand.\n", + "enum": ["XS", "RF", "FR"] + } + } + ], + "output": { + "junc": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.junc": { + "type": "file", + "description": "BED12 file containing exon-exon \"regtools_junctionsextract\"\n", + "pattern": "*.{junc}", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@abartlett004"], + "maintainers": ["@abartlett004"] } - }, - { - "coverage": { - "type": "integer", - "description": "Minimum number of a reads that a position must be covered by to be\nreported\n" + }, + { + "name": "repeatmasker_repeatmasker", + "path": "modules/nf-core/repeatmasker/repeatmasker/meta.yml", + "type": "module", + "meta": { + "name": "repeatmasker_repeatmasker", + "description": "Screening DNA sequences for interspersed repeats and low complexity DNA sequences\n", + "keywords": ["genome", "annotation", "repeat", "mask"], + "tools": [ + { + "repeatmasker": { + "description": "RepeatMasker is a program that screens DNA sequences for interspersed\nrepeats and low complexity DNA sequences\n", + "homepage": "https://www.repeatmasker.org/", + "documentation": "https://www.repeatmasker.org/webrepeatmaskerhelp.html", + "tool_dev_url": "https://github.com/rmhubley/RepeatMasker", + "licence": ["Open Software License v. 2.1"], + "identifier": "biotools:repeatmasker" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Genome assembly", + "pattern": "*.{fasta,fa,fas,fsa,faa,fna}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + { + "lib": { + "type": "file", + "description": "Custom library (e.g. from another species)", + "pattern": "*.{fasta,fa,fas,fsa,faa,fna}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + "output": { + "masked": [ + [ + { + "meta": { + "type": "file", + "description": "Masked fasta", + "pattern": "*.{masked}", + "ontologies": [] + } + }, + { + "${prefix}.masked": { + "type": "file", + "description": "Masked fasta", + "pattern": "*.{masked}", + "ontologies": [] + } + } + ] + ], + "out": [ + [ + { + "meta": { + "type": "file", + "description": "Masked fasta", + "pattern": "*.{masked}", + "ontologies": [] + } + }, + { + "${prefix}.out": { + "type": "file", + "description": "Out file", + "pattern": "*.{out}", + "ontologies": [] + } + } + ] + ], + "tbl": [ + [ + { + "meta": { + "type": "file", + "description": "Masked fasta", + "pattern": "*.{masked}", + "ontologies": [] + } + }, + { + "${prefix}.tbl": { + "type": "file", + "description": "tbl file", + "pattern": "*.{tbl}", + "ontologies": [] + } + } + ] + ], + "gff": [ + [ + { + "meta": { + "type": "file", + "description": "Masked fasta", + "pattern": "*.{masked}", + "ontologies": [] + } + }, + { + "${prefix}.gff": { + "type": "file", + "description": "GFF file", + "pattern": "*.{gff}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2305" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@kherronism", "@gallvp"], + "maintainers": ["@kherronism", "@gallvp"] } - }, - { - "homozygous_freq": { - "type": "integer", - "description": "Fraction of reads a base must have to be called 'homozygous'" + }, + { + "name": "repeatmasker_rmouttogff3", + "path": "modules/nf-core/repeatmasker/rmouttogff3/meta.yml", + "type": "module", + "meta": { + "name": "repeatmasker_rmouttogff3", + "description": "A utility script to assist to convert old RepeatMasker *.out files to version 3 gff files.", + "keywords": ["sort", "repeatmasker", "genomics"], + "tools": [ + { + "repeatmasker": { + "description": "RepeatMasker is a program that screens DNA sequences for interspersed\nrepeats and low complexity DNA sequences\n", + "homepage": "https://www.repeatmasker.org/", + "documentation": "https://www.repeatmasker.org/webrepeatmaskerhelp.html", + "tool_dev_url": "https://github.com/rmhubley/RepeatMasker", + "licence": ["Open Software License v. 2.1"], + "identifier": "biotools:repeatmasker" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "out": { + "type": "file", + "description": "RepeatMasker out file", + "pattern": "*.{out}", + "ontologies": [] + } + } + ] + ], + "output": { + "gff3": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.gff3": { + "type": "file", + "description": "Sorted BAM/CRAM/SAM file", + "pattern": "*.{gff3}", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@GallVp"], + "maintainers": ["@GallVp"] } - }, - { - "heterozygous_freq": { - "type": "integer", - "description": "Fraction of which whereby if a call falls above this value, and lower\nthan the homozygous threshold, a base will be called 'heterozygous'.\n" + }, + { + "name": "repeatmodeler_builddatabase", + "path": "modules/nf-core/repeatmodeler/builddatabase/meta.yml", + "type": "module", + "meta": { + "name": "repeatmodeler_builddatabase", + "description": "Create a database for RepeatModeler", + "keywords": ["genomics", "fasta", "repeat"], + "tools": [ + { + "repeatmodeler": { + "description": "RepeatModeler is a de-novo repeat family identification and modeling package.", + "homepage": "https://github.com/Dfam-consortium/RepeatModeler", + "documentation": "https://github.com/Dfam-consortium/RepeatModeler", + "tool_dev_url": "https://github.com/Dfam-consortium/RepeatModeler", + "licence": ["Open Software License v2.1"], + "identifier": "biotools:repeatmodeler" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Fasta file", + "pattern": "*.{fasta,fsa,fa}", + "ontologies": [] + } + } + ] + ], + "output": { + "db": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}.*": { + "type": "file", + "description": "Database files for repeatmodeler", + "pattern": "`${prefix}.*`", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@GallVp"], + "maintainers": ["@GallVp"] } - }, - [ - { - "meta5": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "gff_exclude": { - "type": "file", - "description": "file listing positions that will be 'filtered' (i.e. ignored)\n(Optional)\n", - "pattern": "*.vcf", - "ontologies": [] - } + }, + { + "name": "repeatmodeler_repeatmodeler", + "path": "modules/nf-core/repeatmodeler/repeatmodeler/meta.yml", + "type": "module", + "meta": { + "name": "repeatmodeler_repeatmodeler", + "description": "Performs de novo transposable element (TE) family identification with RepeatModeler", + "keywords": ["genomics", "fasta", "repeat", "transposable element"], + "tools": [ + { + "repeatmodeler": { + "description": "RepeatModeler is a de-novo repeat family identification and modeling package.", + "homepage": "https://github.com/Dfam-consortium/RepeatModeler", + "documentation": "https://github.com/Dfam-consortium/RepeatModeler", + "tool_dev_url": "https://github.com/Dfam-consortium/RepeatModeler", + "licence": ["Open Software License v2.1"], + "identifier": "biotools:repeatmodeler" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "db": { + "type": "file", + "description": "RepeatModeler database files generated with REPEATMODELER_BUILDDATABASE", + "pattern": "*", + "ontologies": [] + } + } + ] + ], + "output": { + "fasta": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.fa": { + "type": "file", + "description": "Consensus repeat sequences", + "pattern": "*.fa", + "ontologies": [] + } + } + ] + ], + "stk": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.stk": { + "type": "file", + "description": "Seed alignments", + "pattern": "*.stk", + "ontologies": [] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.log": { + "type": "file", + "description": "A summarized log of the run", + "pattern": "*.log", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@GallVp"], + "maintainers": ["@GallVp"] } - ] - ], - "output": { - "full_alignment": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*fullAlignment.fasta.gz": { - "type": "file", - "description": "Fasta a fasta file of all positions contained in the VCF files i.e. including ref calls", - "pattern": ".fasta.gz", - "ontologies": [ + }, + { + "name": "resfinder_run", + "path": "modules/nf-core/resfinder/run/meta.yml", + "type": "module", + "meta": { + "name": "resfinder_run", + "description": "ResFinder identifies acquired antimicrobial resistance genes in total or partial sequenced isolates of bacteria", + "keywords": ["blastn", "kma", "microbes", "resfinder", "resistance genes"], + "tools": [ + { + "resfinder": { + "description": "ResFinder identifies acquired antimicrobial resistance genes in total or partial sequenced isolates of bacteria", + "homepage": "https://bitbucket.org/genomicepidemiology/resfinder.git/src", + "documentation": "https://bitbucket.org/genomicepidemiology/resfinder/src/master/README.md", + "tool_dev_url": "https://bitbucket.org/genomicepidemiology/resfinder.git/src", + "doi": "10.1099/mgen.0.000748", + "licence": ["APACHE-2.0"], + "identifier": "biotools:resfinder" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "fastq": { + "type": "file", + "description": "fastq file(s)", + "pattern": "*.{fastq,fq}{.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + }, + { + "fasta": { + "type": "file", + "description": "fasta file", + "pattern": "*.{fa,fna}", + "ontologies": [] + } + } + ], { - "edam": "http://edamontology.org/format_3615" + "db_point": { + "type": "directory", + "description": "database directory containing known point mutations" + } }, { - "edam": "http://edamontology.org/format_3989" + "db_res": { + "type": "directory", + "description": "database directory containing known resistance genes" + } } - ] - } - } - ] - ], - "info_txt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*info.txt": { - "type": "file", - "description": "Information about the run", - "pattern": ".txt", - "ontologies": [] - } - } - ] - ], - "snp_alignment": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*snpAlignment.fasta.gz": { - "type": "file", - "description": "A fasta file of just SNP positions with samples only", - "pattern": ".fasta.gz", - "ontologies": [ + ], + "output": { + "json": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.json": { + "type": "file", + "description": "CGE standardized json file", + "pattern": "*.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "disinfinder_kma": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "disinfinder_kma": { + "type": "directory", + "description": "directory holding kma results", + "pattern": "disinfinder_kma" + } + } + ] + ], + "pheno_table_species": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "pheno_table_species.txt": { + "type": "file", + "description": "table with species specific AMR phenotypes", + "pattern": "pheno_table_species.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "pheno_table": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "pheno_table.txt": { + "type": "file", + "description": "table with all AMR phenotypes", + "pattern": "pheno_table.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "pointfinder_kma": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "pointfinder_kma": { + "type": "directory", + "description": "directory holding kma results", + "pattern": "pointfinder_kma" + } + } + ] + ], + "pointfinder_prediction": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "PointFinder_prediction.txt": { + "type": "file", + "description": "tab separated table; 1 is given to a predicted resistance against an antibiotic class, 0 is given to not resistance detected", + "pattern": "PointFinder_prediction.txt", + "ontologies": [] + } + } + ] + ], + "pointfinder_results": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "PointFinder_results.txt": { + "type": "file", + "description": "tab separated table with predicted point mutations leading to antibiotic resistance", + "pattern": "PointFinder_results.txt", + "ontologies": [] + } + } + ] + ], + "pointfinder_table": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "PointFinder_table.txt": { + "type": "file", + "description": "predicted point mutations grouped into genes to which they belong", + "pattern": "PointFinder_table.txt", + "ontologies": [] + } + } + ] + ], + "resfinder_hit_in_genome_seq": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "ResFinder_Hit_in_genome_seq.fsa": { + "type": "file", + "description": "fasta sequence of resistance gene hits found in the input data (query)", + "pattern": "ResFinder_Hit_in_genome_seq.fsa", + "ontologies": [] + } + } + ] + ], + "resfinder_blast": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "resfinder_blast": { + "type": "directory", + "description": "directory holding blast results", + "pattern": "resfinder_kma" + } + } + ] + ], + "resfinder_kma": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "resfinder_kma": { + "type": "directory", + "description": "directory holding kma results", + "pattern": "resfinder_kma" + } + } + ] + ], + "resfinder_resistance_gene_seq": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "ResFinder_Resistance_gene_seq.fsa": { + "type": "file", + "description": "fasta sequence of resistance gene hits found in the database (reference)", + "pattern": "ResFinder_Resistance_gene_seq.fsa", + "ontologies": [] + } + } + ] + ], + "resfinder_results_table": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "ResFinder_results_table.txt": { + "type": "file", + "description": "predicted resistance genes grouped by antibiotic class", + "pattern": "ResFinder_results_table.txt", + "ontologies": [] + } + } + ] + ], + "resfinder_results_tab": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "ResFinder_results_tab.txt": { + "type": "file", + "description": "tab separated table with predicted resistance genes", + "pattern": "ResFinder_results_tab.txt", + "ontologies": [] + } + } + ] + ], + "resfinder_results": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "ResFinder_results.txt": { + "type": "file", + "description": "predicted resistance genes grouped by antibiotic class and hit alignments to reference resistance genes", + "pattern": "ResFinder_results.txt", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@marrip"], + "maintainers": ["@marrip"] + } + }, + { + "name": "rgi_bwt", + "path": "modules/nf-core/rgi/bwt/meta.yml", + "type": "module", + "meta": { + "name": "rgi_bwt", + "description": "Predict antibiotic resistance from protein or nucleotide data", + "keywords": ["bacteria", "fasta", "antibiotic resistance"], + "tools": [ + { + "rgi": { + "description": "This tool provides a preliminary annotation of your DNA sequence(s) based upon the data available in The Comprehensive Antibiotic Resistance Database (CARD). Hits to genes tagged with Antibiotic Resistance ontology terms will be highlighted. As CARD expands to include more pathogens, genomes, plasmids, and ontology terms this tool will grow increasingly powerful in providing first-pass detection of antibiotic resistance associated genes. See license at CARD website.", + "homepage": "https://card.mcmaster.ca", + "documentation": "https://github.com/arpcard/rgi", + "tool_dev_url": "https://github.com/arpcard/rgi", + "doi": "10.1093/nar/gkz935", + "licence": ["https://card.mcmaster.ca/about"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "Single-end or paired-end nucleotide sequences in FASTQ or FASTA format", + "pattern": "*.{fastq,fastq.gz,fq,fq.gz,fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ], { - "edam": "http://edamontology.org/format_3615" + "card": { + "type": "directory", + "description": "Directory containing the CARD database. This is expected to be the unarchived but otherwise unaltered download folder (see RGI documentation for download instructions).", + "pattern": "*/" + } }, { - "edam": "http://edamontology.org/format_3989" + "wildcard": { + "type": "directory", + "description": "Directory containing the WildCARD database (optional). This is expected to be the unarchived but otherwise unaltered download folder (see RGI documentation for download instructions).", + "pattern": "*/" + } } - ] + ], + "output": { + "json": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.json": { + "type": "file", + "description": "JSON formatted file with RGI results", + "pattern": "*.{json}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "Tab-delimited file with RGI results", + "pattern": "*.{txt}", + "ontologies": [] + } + } + ] + ], + "tmp": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "temp/": { + "type": "directory", + "description": "Directory containing various intermediate files", + "pattern": "temp/" + } + } + ] + ], + "versions_rgi": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "rgi": { + "type": "string", + "description": "The tool name" + } + }, + { + "rgi main --version": { + "type": "string", + "description": "The version string returned by the command" + } + } + ] + ], + "versions_db": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "rgi-database": { + "type": "string", + "description": "The tool name" + } + }, + { + "echo \\$DB_VERSION": { + "type": "string", + "description": "The CARD database version string" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "rgi": { + "type": "string", + "description": "The tool name" + } + }, + { + "rgi main --version": { + "type": "string", + "description": "Command used to collect the version" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "rgi-database": { + "type": "string", + "description": "The tool name" + } + }, + { + "echo \\$DB_VERSION": { + "type": "string", + "description": "Command used to collect the version" + } + } + ] + ] + }, + "authors": ["@vinisalazar"], + "maintainers": ["@nickp60", "@vinisalazar"] + }, + "pipelines": [ + { + "name": "funcprofiler", + "version": "dev" } - } ] - ], - "snp_genome_alignment": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" + }, + { + "name": "rgi_cardannotation", + "path": "modules/nf-core/rgi/cardannotation/meta.yml", + "type": "module", + "meta": { + "name": "rgi_cardannotation", + "description": "Preprocess the CARD database for RGI to predict antibiotic resistance from protein or nucleotide data", + "keywords": ["bacteria", "fasta", "antibiotic resistance"], + "tools": [ + { + "rgi": { + "description": "This module preprocesses the downloaded Comprehensive Antibiotic Resistance Database (CARD) which can then be used as input for RGI.", + "homepage": "https://card.mcmaster.ca", + "documentation": "https://github.com/arpcard/rgi", + "tool_dev_url": "https://github.com/arpcard/rgi", + "doi": "10.1093/nar/gkz935", + "licence": ["https://card.mcmaster.ca/about"], + "identifier": "" + } + } + ], + "input": [ + { + "card": { + "type": "directory", + "description": "Directory containing the CARD database", + "pattern": "*/" + } + } + ], + "output": { + "db": [ + { + "card_database_processed": { + "type": "directory", + "description": "Directory containing the processed CARD database files", + "pattern": "*/" + } + } + ], + "tool_version": [ + { + "RGI_VERSION": { + "type": "string", + "description": "The version of the tool in string format (useful for downstream tools such as hAMRronization)" + } + } + ], + "db_version": [ + { + "DB_VERSION": { + "type": "string", + "description": "The version of the used database in string format (useful for downstream tools such as hAMRronization)" + } + } + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@rpetit3", "@jfy133", "@jasmezz"], + "maintainers": ["@rpetit3", "@jfy133", "@jasmezz"] + }, + "pipelines": [ + { + "name": "funcscan", + "version": "3.0.0" } - }, - { - "*snpAlignmentIncludingRefGenome.fasta.gz": { - "type": "file", - "description": "A fasta file of just SNP positions with reference genome", - "pattern": ".fasta.gz", - "ontologies": [ + ] + }, + { + "name": "rgi_main", + "path": "modules/nf-core/rgi/main/meta.yml", + "type": "module", + "meta": { + "name": "rgi_main", + "description": "Predict antibiotic resistance from protein or nucleotide data", + "keywords": ["bacteria", "fasta", "antibiotic resistance"], + "tools": [ + { + "rgi": { + "description": "This tool provides a preliminary annotation of your DNA sequence(s) based upon the data available in The Comprehensive Antibiotic Resistance Database (CARD). Hits to genes tagged with Antibiotic Resistance ontology terms will be highlighted. As CARD expands to include more pathogens, genomes, plasmids, and ontology terms this tool will grow increasingly powerful in providing first-pass detection of antibiotic resistance associated genes. See license at CARD website", + "homepage": "https://card.mcmaster.ca", + "documentation": "https://github.com/arpcard/rgi", + "tool_dev_url": "https://github.com/arpcard/rgi", + "doi": "10.1093/nar/gkz935", + "licence": ["https://card.mcmaster.ca/about"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Nucleotide or protein sequences in FASTA format", + "pattern": "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}", + "ontologies": [] + } + } + ], { - "edam": "http://edamontology.org/format_3615" + "card": { + "type": "directory", + "description": "Directory containing the CARD database. This is expected to be the unarchived but otherwise unaltered download folder (see RGI documentation for download instructions).", + "pattern": "*/" + } }, { - "edam": "http://edamontology.org/format_3989" + "wildcard": { + "type": "directory", + "description": "Directory containing the WildCARD database (optional). This is expected to be the unarchived but otherwise unaltered download folder (see RGI documentation for download instructions).", + "pattern": "*/" + } } - ] + ], + "output": { + "json": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.json": { + "type": "file", + "description": "JSON formatted file with RGI results", + "pattern": "*.{json}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "Tab-delimited file with RGI results", + "pattern": "*.{txt}", + "ontologies": [] + } + } + ] + ], + "tmp": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "temp/": { + "type": "directory", + "description": "Directory containing various intermediate files", + "pattern": "temp/" + } + } + ] + ], + "tool_version": [ + { + "RGI_VERSION": { + "type": "string", + "description": "The version of the tool in string format (useful for downstream tools such as hAMRronization)" + } + } + ], + "db_version": [ + { + "DB_VERSION": { + "type": "string", + "description": "The version of the used database in string format (useful for downstream tools such as hAMRronization)" + } + } + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@rpetit3", "@jfy133", "@jasmezz"], + "maintainers": ["@rpetit3", "@jfy133", "@jasmezz"] + }, + "pipelines": [ + { + "name": "funcscan", + "version": "3.0.0" } - } - ] - ], - "snpstatistics": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*snpStatistics.tsv": { - "type": "file", - "description": "Some basic statistics about the SNP calls of each sample", - "pattern": ".tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "snptable": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*snpTable.tsv": { - "type": "file", - "description": "Basic SNP table of combined positions taken from each VCF file", - "pattern": ".tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "snptable_snpeff": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*snpTableForSnpEff.tsv": { - "type": "file", - "description": "Input file for SnpEff", - "pattern": ".tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "snptable_uncertainty": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*snpTableWithUncertaintyCalls.tsv": { - "type": "file", - "description": "Same as above, but with lower case characters indicating uncertain calls", - "pattern": ".tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "structure_genotypes": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*structureGenotypes.tsv": { - "type": "file", - "description": "Input file for STRUCTURE", - "pattern": ".tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "structure_genotypes_nomissing": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*structureGenotypes_noMissingData-Columns.tsv": { - "type": "file", - "description": "Alternate input file for STRUCTURE", - "pattern": ".tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } ] - ], - "json": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*MultiVCFAnalyzer.json": { - "type": "file", - "description": "Summary statistics in MultiQC JSON format", - "pattern": ".json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "versions_multivcfanalyzer": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "multivcfanalyzer": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "multivcfanalyzer -h | head -n 1 | cut -f 3 -d \" \"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_tabix": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "tabix": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "tabix -h 2>&1 | grep Version | cut -f 2 -d \" \"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "multivcfanalyzer": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "multivcfanalyzer -h | head -n 1 | cut -f 3 -d \" \"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "tabix": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "tabix -h 2>&1 | grep Version | cut -f 2 -d \" \"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@jfy133" - ], - "maintainers": [ - "@jfy133", - "@TCLamnidis" - ] - } - }, - { - "name": "mummer", - "path": "modules/nf-core/mummer/meta.yml", - "type": "module", - "meta": { - "name": "mummer", - "description": "MUMmer is a system for rapidly aligning entire genomes", - "keywords": [ - "align", - "genome", - "fasta" - ], - "tools": [ - { - "mummer": { - "description": "MUMmer is a system for rapidly aligning entire genomes", - "homepage": "http://mummer.sourceforge.net/", - "documentation": "http://mummer.sourceforge.net/", - "tool_dev_url": "http://mummer.sourceforge.net/", - "doi": "10.1186/gb-2004-5-2-r12", - "licence": [ - "The Artistic License" - ], - "identifier": "biotools:mummer" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "ref": { - "type": "file", - "description": "FASTA file of the reference sequence", - "pattern": "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}", - "ontologies": [] - } + }, + { + "name": "rhocall_annotate", + "path": "modules/nf-core/rhocall/annotate/meta.yml", + "type": "module", + "meta": { + "name": "rhocall_annotate", + "description": "Markup VCF file using rho-calls.", + "keywords": ["roh", "rhocall", "runs_of_homozygosity"], + "tools": [ + { + "rhocall": { + "description": "Call regions of homozygosity and make tentative UPD calls.", + "homepage": "https://github.com/dnil/rhocall", + "documentation": "https://github.com/dnil/rhocall", + "tool_dev_url": "https://github.com/dnil", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "vcf file", + "pattern": "*.{vcf,vcf.gz}", + "ontologies": [] + } + }, + { + "tbi": { + "type": "file", + "description": "vcf index file", + "pattern": "*.{tbi}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "roh": { + "type": "file", + "description": "Bcftools roh style TSV file with CHR,POS,AZ,QUAL", + "pattern": "*.{roh}", + "ontologies": [] + } + } + ], + { + "bed": { + "type": "file", + "description": "BED file with AZ windows.", + "pattern": "*.{bed}", + "ontologies": [] + } + } + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_rhocall.vcf": { + "type": "file", + "description": "vcf file", + "pattern": "*.{vcf,vcf.gz}", + "ontologies": [] + } + } + ] + ], + "versions_rhocall": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "rhocall": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "rhocall --version | sed 's/rhocall, version //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "rhocall": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "rhocall --version | sed 's/rhocall, version //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@ramprasadn"], + "maintainers": ["@ramprasadn"] }, - { - "query": { - "type": "file", - "description": "FASTA file of the query sequence", - "pattern": "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}", - "ontologies": [] - } - } - ] - ], - "output": { - "coords": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.coords": { - "type": "file", - "description": "File containing coordinates of matches between reference and query sequence", - "pattern": "*.coords", - "ontologies": [] - } - } - ] - ], - "versions_mummer": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "mummer": { - "type": "string", - "description": "The tool name" - } - }, - { - "3.23": { - "type": "string", - "description": "The version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "mummer": { - "type": "string", - "description": "The tool name" - } - }, - { - "3.23": { - "type": "string", - "description": "The version of the tool" - } - } + "pipelines": [ + { + "name": "raredisease", + "version": "3.0.0" + } ] - ] - }, - "authors": [ - "@mjcipriano", - "@sateeshperi" - ], - "maintainers": [ - "@mjcipriano", - "@sateeshperi" - ] - } - }, - { - "name": "muscle", - "path": "modules/nf-core/muscle/meta.yml", - "type": "module", - "meta": { - "name": "muscle", - "description": "MUSCLE is a program for creating multiple alignments of amino acid or nucleotide sequences. A range of options are provided that give you the choice of optimizing accuracy, speed, or some compromise between the two", - "keywords": [ - "msa", - "multiple sequence alignment", - "phylogeny" - ], - "tools": [ - { - "muscle": { - "description": "MUSCLE is a multiple sequence alignment tool with high accuracy and throughput", - "homepage": "https://www.drive5.com/muscle", - "documentation": "http://www.drive5.com/muscle/muscle.html#_Toc81224840", - "doi": "10.1093/nar/gkh340", - "licence": [ - "http://www.drive5.com/muscle/manual/license.html" - ], - "identifier": "biotools:muscle" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } + }, + { + "name": "rhocall_viz", + "path": "modules/nf-core/rhocall/viz/meta.yml", + "type": "module", + "meta": { + "name": "rhocall_viz", + "description": "Call regions of homozygosity and make tentative UPD calls", + "keywords": ["roh", "bcftools", "runs_of_homozygosity"], + "tools": [ + { + "rhocall": { + "description": "Call regions of homozygosity and make tentative UPD calls.", + "homepage": "https://github.com/dnil/rhocall", + "documentation": "https://github.com/dnil/rhocall", + "tool_dev_url": "https://github.com/dnil", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF file", + "pattern": "*.{vcf}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "roh": { + "type": "file", + "description": "Input RHO file produced from rhocall", + "pattern": "*.{roh}", + "ontologies": [] + } + } + ] + ], + "output": { + "bed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}/${prefix}.bed": { + "type": "file", + "description": "Bed file containing roh calls", + "pattern": "*.{bed}", + "ontologies": [] + } + } + ] + ], + "wig": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}/${prefix}.wig": { + "type": "file", + "description": "Wig file containing roh calls", + "pattern": "*.{wig}", + "ontologies": [] + } + } + ] + ], + "versions_rhocall": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "rhocall": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "rhocall --version | sed 's/rhocall, version //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "rhocall": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "rhocall --version | sed 's/rhocall, version //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@ramprasadn"], + "maintainers": ["@ramprasadn"] }, - { - "fasta": { - "type": "file", - "description": "Input sequences for alignment must be in FASTA format", - "pattern": "*.{fasta,fa,fna}", - "ontologies": [] - } - } - ] - ], - "output": { - "aligned_fasta": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*.afa": { - "type": "file", - "description": "Multiple sequence alignment produced in FASTA format", - "pattern": "*.{afa}", - "ontologies": [] - } - } - ] - ], - "phyi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*.phyi": { - "type": "file", - "description": "Multiple sequence alignment produced in PHYLIP interleaved format", - "pattern": "*.{phyi}", - "ontologies": [] - } - } - ] - ], - "phys": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*.phys": { - "type": "file", - "description": "Multiple sequence alignment produced in PHYLIP sequential format", - "pattern": "*.{phys}", - "ontologies": [] - } - } - ] - ], - "clustalw": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*.clw": { - "type": "file", - "description": "Multiple sequence alignment produced in ClustalW format without base/residue numbering", - "pattern": "*.{clw}", - "ontologies": [] - } - } - ] - ], - "html": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*.html": { - "type": "file", - "description": "Multiple sequence alignment produced in HTML format", - "pattern": "*.{html}", - "ontologies": [] - } - } - ] - ], - "msf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*.msf": { - "type": "file", - "description": "GCG Multiple Sequence File (MSF) alignment format (similar to CLUSTALW)", - "pattern": "*.{msf}", - "ontologies": [] - } - } - ] - ], - "tree": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*.tree": { - "type": "file", - "description": "NJ or UPGMA tree in Newick format produced from a multiple sequence alignment", - "pattern": "*.{tree}", - "ontologies": [] - } - } + "pipelines": [ + { + "name": "raredisease", + "version": "3.0.0" + } ] - ], - "log": [ - { - "*.log": { - "type": "file", - "description": "Log file of MUSCLE run", - "pattern": "*{.log}", - "ontologies": [] - } - } - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@MGordon" - ], - "maintainers": [ - "@MGordon" - ] - } - }, - { - "name": "muscle5_super5", - "path": "modules/nf-core/muscle5/super5/meta.yml", - "type": "module", - "meta": { - "name": "muscle5_super5", - "description": "Muscle is a program for creating multiple alignments of amino acid or nucleotide sequences. This particular module uses the super5 algorithm for very big alignments. 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], - { - "compress": { - "type": "boolean", - "description": "Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded." + }, + { + "name": "ribocode_ribocode", + "path": "modules/nf-core/ribocode/ribocode/meta.yml", + "type": "module", + "meta": { + "name": "ribocode_ribocode", + "description": "Call ORFs with RiboCode from Ribo-Seq data", + "keywords": ["ribo-seq", "ribosome profiling", "orf calling"], + "tools": [ + { + "ribocode": { + "description": "A package for detecting the actively translated ORFs using ribosome-profiling data", + "homepage": "https://github.com/xryanglab/RiboCode", + "documentation": "https://github.com/xryanglab/RiboCode", + "tool_dev_url": "https://github.com/xryanglab/RiboCode", + "doi": "10.1093/nar/gky179", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "Sorted BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing annotation information\ne.g. [ id:'genome' ]\n" + } + }, + { + "annotation": { + "type": "directory", + "description": "Directory containing RiboCode annotation files from ribocode/prepare", + "pattern": "annotation" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing config information\ne.g. [ id:'config' ]\n" + } + }, + { + "config": { + "type": "file", + "description": "RiboCode configuration file containing P-site offsets from ribocode/metaplots", + "pattern": "*_config.txt", + "ontologies": [] + } + } + ] + ], + "output": { + "orf_txt": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.txt": { + "type": "file", + "description": "Text file containing all detected ORFs with detailed information", + "pattern": "*.txt", + "ontologies": [] + } + } + ] + ], + "orf_txt_collapsed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}_collapsed.txt": { + "type": "file", + "description": "Text file containing collapsed ORFs (merged isoforms)", + "pattern": "*_collapsed.txt", + "ontologies": [] + } + } + ] + ], + "orf_pdf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_ORFs_category.pdf": { + "type": "file", + "description": "PDF file with ORF category distribution plots", + "pattern": "*_ORFs_category.pdf", + "ontologies": [] + } + } + ] + ], + "psites_hd5": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_psites.hd5": { + "type": "file", + "description": "HDF5 file containing P-site positions", + "pattern": "*_psites.hd5", + "ontologies": [] + } + } + ] + ], + "versions_ribocode": [ + [ + { + "${task.process}": { + "type": "string", + "description": "Name of the process" + } + }, + { + "ribocode": { + "type": "string", + "description": "Name of the tool" + } + }, + { + "RiboCode --version 2>&1": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "Name of the process" + } + }, + { + "ribocode": { + "type": "string", + "description": "Name of the tool" + } + }, + { + "RiboCode --version 2>&1": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@JackCurragh"] } - } - ], - "output": { - "alignment": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*.aln{.gz,}": { - "type": "file", - "description": "Multiple sequence alignment produced in gzipped FASTA format. 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Note: the accuracy reduces for reads shorter than 40\n", + "pattern": "integer >= 1" + } } - ] + ], + "output": { + "fastq": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.nonrna*.fastq.gz": { + "type": "file", + "description": "rRNA depleted FastQ files", + "pattern": "*.nonrna*.fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.log": { + "type": "file", + "description": "Log file from RiboDetector", + "pattern": "*.log", + "ontologies": [] + } + } + ] + ], + "versions_ribodetector": [ + [ + { + "${task.process}": { + "type": "string", + "description": "Name of the process" + } + }, + { + "ribodetector": { + "type": "string", + "description": "Name of the tool" + } + }, + { + "ribodetector --version | sed \"s/ribodetector //\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_cuda": [ + [ + { + "${task.process}": { + "type": "string", + "description": "Name of the process" + } + }, + { + "cuda": { + "type": "string", + "description": "Name of the runtime" + } + }, + { + "python -c \"import torch; print(torch.version.cuda or 'no CUDA available')\"": { + "type": "eval", + "description": "CUDA version bundled with the task's pytorch build, or `no CUDA available` on the non-GPU path" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "Name of the process" + } + }, + { + "ribodetector": { + "type": "string", + "description": "Name of the tool" + } + }, + { + "ribodetector --version | sed \"s/ribodetector //\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "Name of the process" + } + }, + { + "cuda": { + "type": "string", + "description": "Name of the runtime" + } + }, + { + "python -c \"import torch; print(torch.version.cuda or 'no CUDA available')\"": { + "type": "eval", + "description": "CUDA version bundled with the task's pytorch build, or `no CUDA available` on the non-GPU path" + } + } + ] + ] + }, + "authors": ["@maxibor"], + "maintainers": ["@maxibor"] + }, + "pipelines": [ + { + "name": "rnaseq", + "version": "3.26.0" } - 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} - }, - { - "muscle -version | head -n 1 | cut -d \" \" -f 2 | sed \"s/.linux64//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pigz": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pigz --version 2>&1 | sed \"s/^.*pigz[[:space:]]*//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } ] - ] - }, - "authors": [ - "@alessiovignoli", - "@JoseEspinosa" - ], - "maintainers": [ - "@alessiovignoli", - "@JoseEspinosa", - "@lrauschning" - ] - }, - "pipelines": [ - { - "name": "multiplesequencealign", - "version": "1.1.1" - } - ] - }, - { - "name": "muse_call", - "path": "modules/nf-core/muse/call/meta.yml", - "type": "module", - "meta": { - "name": "muse_call", - "description": "pre-filtering and calculating position-specific summary statistics using the Markov substitution model", - "keywords": [ - "variant calling", - "somatic", - "wgs", - "wxs", - "vcf" - ], - "tools": [ - { - "MuSE": { - "description": "Somatic point mutation caller based on Markov substitution model for molecular evolution", - "homepage": "https://bioinformatics.mdanderson.org/public-software/muse/", - "documentation": "https://github.com/wwylab/MuSE", - "tool_dev_url": "https://github.com/wwylab/MuSE", - "doi": "10.1101/gr.278456.123", - "licence": [ - "https://github.com/danielfan/MuSE/blob/master/LICENSE" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "tumor_bam": { - "type": "file", - "description": "Sorted tumor BAM file", - "pattern": "*.bam", - "ontologies": [] - } - }, - { - "tumor_bai": { - "type": "file", - "description": "Index file for the tumor BAM file", - "pattern": "*.bai", - "ontologies": [] - } - }, - { - "normal_bam": { - "type": "file", - "description": "Sorted matched normal BAM file", - "pattern": "*.bam", - "ontologies": [] - } - }, - { - "normal_bai": { - "type": "file", - "description": "Index file for the normal BAM file", - "pattern": "*.bai", - "ontologies": [] - } + }, + { + "name": "ribotish_predict", + "path": "modules/nf-core/ribotish/predict/meta.yml", + "type": "module", + "meta": { + "name": "ribotish_predict", + "description": "Quality control of riboseq bam data", + "keywords": ["riboseq", "predict", "bam"], + "tools": [ + { + "ribotish": { + "description": "Ribo TIS Hunter (Ribo-TISH) identifies translation activities using ribosome profiling data.", + "homepage": "https://github.com/zhpn1024/ribotish", + "documentation": "https://github.com/zhpn1024/ribotish", + "tool_dev_url": "https://github.com/zhpn1024/ribotish", + "doi": "10.1038/s41467-017-01981-8", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing riboseq sample information\ne.g. `[ id:'sample1', single_end:false ]\n" + } + }, + { + "bam_ribo": { + "type": "file", + "description": "Sorted riboseq BAM file(s)", + "pattern": "*.{bam}", + "ontologies": [] + } + }, + { + "bai_ribo": { + "type": "file", + "description": "Index for sorted riboseq bam file(s)", + "pattern": "*.{bai}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing TI-Seq sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "bam_ti": { + "type": "file", + "description": "Sorted TI-Seq BAM file(s)", + "pattern": "*.{bam}", + "ontologies": [] + } + }, + { + "bai_ti": { + "type": "file", + "description": "Index for sorted TI-Seq BAM file(s)", + "pattern": "*.{bai}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. `[ id:'Ensembl human v.111' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Fasta-format sequence file for reference sequences used in the bam file\n", + "pattern": "*.gtf", + "ontologies": [] + } + }, + { + "gtf": { + "type": "file", + "description": "GTF-format annotation file for reference sequences used in the bam file\n", + "pattern": "*.gtf", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing information on candidate ORFs\n" + } + }, + { + "candidate_orfs": { + "type": "file", + "description": "3-column (transIDstarttstop) candidate ORFs file\n", + "pattern": "*.txt", + "ontologies": [] + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing information on riboseq P-site offset parameter\nfiles\n" + } + }, + { + "para_ribo": { + "type": "file", + "description": "Input P-site offset parameter files for riboseq bam files\n", + "pattern": "*.py", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3996" + } + ] + } + } + ], + [ + { + "meta6": { + "type": "map", + "description": "Groovy Map containing information on TI-seq P-site offset parameter\nfiles\n" + } + }, + { + "para_ti": { + "type": "file", + "description": "Input P-site offset parameter files for TI-seq bam files\n", + "pattern": "*.py", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3996" + } + ] + } + } + ], + [ + { + "meta7": { + "type": "map", + "description": "Groovy Map containing reference information for the secondary\nannotation file\n" + } + }, + { + "reference_gtf": { + "type": "file", + "description": "Optional secondary GTF annotation passed to ribotish as\n`-a ` (e.g. a MANE/RefSeq overlay applied on\ntop of the primary GTF). Pass `[]` to omit.\n", + "pattern": "*.gtf", + "ontologies": [] + } + } + ] + ], + "output": { + "predictions": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*_pred.txt": { + "type": "file", + "description": "txt file all possible ORF results that fit the thresholds\n", + "pattern": "*.{txt}", + "ontologies": [] + } + } + ] + ], + "all": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*_all.txt": { + "type": "file", + "description": "txt file similar to the predictions but do not use FDR (q-value) cutoff\n", + "pattern": "*.{txt}", + "ontologies": [] + } + } + ] + ], + "transprofile": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*_transprofile.py": { + "type": "file", + "description": "Output RPF P-site profile for each transcript. The profile data is in\npython dict format, recording non-zero read counts at different\npositions on transcript.\n", + "pattern": "*.{py}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3996" + } + ] + } + } + ] + ], + "versions_ribotish": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "ribotish": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "ribotish --version | sed 's/ribotish //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "ribotish": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "ribotish --version | sed 's/ribotish //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@pinin4fjords"], + "maintainers": ["@pinin4fjords"] }, - { - "reference": { - "type": "file", - "description": "reference genome file", - "pattern": ".fasta", - "ontologies": [] - } - } - ] - ], - "output": { - "txt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.MuSE.txt": { - "type": "file", - "description": "position-specific summary statistics", - "pattern": "*.MuSE.txt", - "ontologies": [] - } - } - ] - ], - "versions_muse": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "muse": { - "type": "string", - "description": "The tool name" - } - }, - { - "MuSE --version | sed -e 's/MuSE, version //g' | sed -e 's/MuSE v//g'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "muse": { - "type": "string", - "description": "The tool name" - } - }, - { - "MuSE --version | sed -e 's/MuSE, version //g' | sed -e 's/MuSE v//g'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } + "pipelines": [ + { + "name": "riboseq", + "version": "1.2.0" + } ] - ] - }, - "authors": [ - "@famosab" - ], - "maintainers": [ - "@famosab" - ] - }, - "pipelines": [ - { - "name": "sarek", - "version": "3.8.1" - } - ] - }, - { - "name": "muse_sump", - "path": "modules/nf-core/muse/sump/meta.yml", - "type": "module", - "meta": { - "name": "muse_sump", - "description": "Computes tier-based cutoffs from a sample-specific error model which is generated by muse/call and reports the finalized variants", - "keywords": [ - "variant calling", - "somatic", - "wgs", - "wxs", - "vcf" - ], - "tools": [ - { - "MuSE": { - "description": "Somatic point mutation caller based on Markov substitution model for molecular evolution", - "homepage": "https://bioinformatics.mdanderson.org/public-software/muse/", - "documentation": "https://github.com/wwylab/MuSE", - "tool_dev_url": "https://github.com/wwylab/MuSE", - "doi": "10.1101/gr.278456.123", - "licence": [ - "https://github.com/danielfan/MuSE/blob/master/LICENSE" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "muse_call_txt": { - "type": "file", - "description": "single input file generated by 'MuSE call'", - "pattern": "*.MuSE.txt", - "ontologies": [] - } - }, - { - "ref_vcf": { - "type": "file", - "description": "dbSNP vcf file that should be bgzip compressed, tabix indexed and\nbased on the same reference genome used in 'MuSE call'\n", - "pattern": ".vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } + }, + { + "name": "ribotish_quality", + "path": "modules/nf-core/ribotish/quality/meta.yml", + "type": "module", + "meta": { + "name": "ribotish_quality", + "description": "Quality control of riboseq bam data", + "keywords": ["riboseq", "quality", "bam"], + "tools": [ + { + "ribotish": { + "description": "Ribo TIS Hunter (Ribo-TISH) identifies translation activities using ribosome profiling data.", + "homepage": "https://github.com/zhpn1024/ribotish", + "documentation": "https://github.com/zhpn1024/ribotish", + "tool_dev_url": "https://github.com/zhpn1024/ribotish", + "doi": "10.1038/s41467-017-01981-8", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "bam": { + "type": "file", + "description": "Sorted BAM/CRAM/SAM file", + "pattern": "*.{bam}", + "ontologies": [] + } + }, + { + "bai": { + "type": "file", + "description": "Index for sorted BAM/CRAM/SAM file", + "pattern": "*.{bai}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. `[ id:'Ensembl human v.111' ]`\n" + } + }, + { + "gtf": { + "type": "file", + "description": "GTF-format annotation file for reference sequences used in the bam file\n", + "pattern": "*.gtf", + "ontologies": [] + } + } + ] + ], + "output": { + "distribution": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "file containing distribution", + "pattern": "*.{txt}", + "ontologies": [] + } + } + ] + ], + "pdf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.pdf": { + "type": "file", + "description": "Pdf figure file is plot of all the distributions and illustration of\nquality and P-site offset\n", + "pattern": "*.{pdf}", + "ontologies": [] + } + } + ] + ], + "offset": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.para.py": { + "type": "file", + "description": "This file saves P-site offsets for different reads lengths in python\ncode dict format, and can be used in further analysis\n", + "pattern": "*.{para.py}", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@pinin4fjords"], + "maintainers": ["@pinin4fjords"] }, - { - "ref_vcf_tbi": { - "type": "file", - "description": "Tabix index for the dbSNP vcf file", - "pattern": ".vcf.gz.tbi", - "ontologies": [] - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.vcf.gz": { - "type": "map", - "description": "bgzipped vcf file with called variants", - "pattern": "*.vcf.gz" - } - } - ] - ], - "tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.vcf.gz.tbi": { - "type": "map", - "description": "tabix index of bgzipped vcf file with called variants", - "pattern": "*.vcf.gz.tbi" - } - } - ] - ], - "versions_muse": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "muse": { - "type": "string", - "description": "The tool name" - } - }, - { - "MuSE --version | sed -e 's/MuSE, version //g' | sed -e 's/MuSE v//g'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ], - "versions_bgzip": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bgzip": { - "type": "string", - "description": "The tool name" - } - }, - { - "bgzip --version | sed -n 's/bgzip (htslib) \\([0-9.]*\\)/\\1/p'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "muse": { - "type": "string", - "description": "The tool name" - } - }, - { - "MuSE --version | sed -e 's/MuSE, version //g' | sed -e 's/MuSE v//g'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bgzip": { - "type": "string", - "description": "The tool name" - } - }, - { - "bgzip --version | sed -n 's/bgzip (htslib) \\([0-9.]*\\)/\\1/p'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } + "pipelines": [ + { + "name": "riboseq", + "version": "1.2.0" + } ] - ] - }, - "authors": [ - "@famosab" - ], - "maintainers": [ - "@famosab" - ] - }, - "pipelines": [ - { - "name": "sarek", - "version": "3.8.1" - } - ] - }, - { - "name": "mygene", - "path": "modules/nf-core/mygene/meta.yml", - "type": "module", - "meta": { - "name": "mygene", - "description": "Fetch the GO concepts for a list of genes", - "keywords": [ - "mygene", - "go", - "annotation" - ], - "tools": [ - { - "mygene": { - "description": "A python wrapper to query/retrieve gene annotation data from Mygene.info.", - "homepage": "https://mygene.info/", - "documentation": "https://docs.mygene.info/projects/mygene-py/en/latest/", - "tool_dev_url": "https://github.com/biothings/mygene.py", - "doi": "10.1093/nar/gks1114", - "licence": [ - "Apache-2.0" - ], - "identifier": "biotools:mygene" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } + }, + { + "name": "ribotricer_detectorfs", + "path": "modules/nf-core/ribotricer/detectorfs/meta.yml", + "type": "module", + "meta": { + "name": "ribotricer_detectorfs", + "description": "Accurate detection of short and long active ORFs using Ribo-seq data", + "keywords": ["riboseq", "orf", "genomics"], + "tools": [ + { + "ribotricer": { + "description": "Python package to detect translating ORF from Ribo-seq data", + "homepage": "https://github.com/smithlabcode/ribotricer", + "documentation": "https://github.com/smithlabcode/ribotricer", + "tool_dev_url": "https://github.com/smithlabcode/ribotricer", + "doi": "10.1093/bioinformatics/btz878", + "licence": ["GNU General Public v3 (GPL v3)"], + "identifier": "biotools:ribotricer" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Map containing riboseq sample information\ne.g. `[ id:'sample1', single_end:false, strandedness: 'single' ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}", + "ontologies": [] + } + }, + { + "bai": { + "type": "file", + "description": "Index for sorted BAM/CRAM/SAM file", + "pattern": "*.{bai}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Map containing reference information for the candidate ORFs\ne.g. `[ id:'Ensembl human v.111' ]`\n" + } + }, + { + "candidate_orfs": { + "type": "file", + "description": "TSV file with candidate ORFs from 'ribotricer prepareorfs'", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "output": { + "protocol": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing riboseq sample information\ne.g. `[ id:'sample1', single_end:false ]\n" + } + }, + { + "*_protocol.txt": { + "type": "file", + "description": "txt file containing inferred protocol if it was inferred (not supplied as input)", + "pattern": "*_protocol.txt", + "ontologies": [] + } + } + ] + ], + "bam_summary": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing riboseq sample information\ne.g. `[ id:'sample1', single_end:false ]\n" + } + }, + { + "*_bam_summary.txt": { + "type": "file", + "description": "Text summary of reads found in the BAM", + "pattern": "*_bam_summary.txt", + "ontologies": [] + } + } + ] + ], + "read_length_dist": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing riboseq sample information\ne.g. `[ id:'sample1', single_end:false ]\n" + } + }, + { + "*_read_length_dist.pdf": { + "type": "file", + "description": "PDF-format read length distribution as quality control", + "pattern": "*_read_length_dist.pdf", + "ontologies": [] + } + } + ] + ], + "metagene_profile_5p": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing riboseq sample information\ne.g. `[ id:'sample1', single_end:false ]\n" + } + }, + { + "*_metagene_profiles_5p.tsv": { + "type": "file", + "description": "Metagene profile aligning with the start codon", + "pattern": "*_metagene_profiles_5p.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "metagene_profile_3p": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing riboseq sample information\ne.g. `[ id:'sample1', single_end:false ]\n" + } + }, + { + "*_metagene_profiles_3p.tsv": { + "type": "file", + "description": "Metagene profile aligning with the stop codon", + "pattern": "*_metagene_profiles_3p.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "metagene_plots": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing riboseq sample information\ne.g. `[ id:'sample1', single_end:false ]\n" + } + }, + { + "*_metagene_plots.pdf": { + "type": "file", + "description": "Metagene plots for quality control", + "pattern": "*_metagene_plots.pdf", + "ontologies": [] + } + } + ] + ], + "psite_offsets": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing riboseq sample information\ne.g. `[ id:'sample1', single_end:false ]\n" + } + }, + { + "*_psite_offsets.txt": { + "type": "file", + "description": "\"If the P-site offsets are not provided, txt file containing the\nderived relative offsets\"\n", + "pattern": "*_psite_offsets.txt", + "ontologies": [] + } + } + ] + ], + "pos_wig": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing riboseq sample information\ne.g. `[ id:'sample1', single_end:false ]\n" + } + }, + { + "*_pos.wig": { + "type": "file", + "description": "Positive strand WIG file for visualization in Genome Browser", + "pattern": "*_pos.wig", + "ontologies": [] + } + } + ] + ], + "neg_wig": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing riboseq sample information\ne.g. `[ id:'sample1', single_end:false ]\n" + } + }, + { + "*_neg.wig": { + "type": "file", + "description": "Negative strand WIG file for visualization in Genome Browser", + "pattern": "*_neg.wig", + "ontologies": [] + } + } + ] + ], + "orfs": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing riboseq sample information\ne.g. `[ id:'sample1', single_end:false ]\n" + } + }, + { + "*_translating_ORFs.tsv": { + "type": "file", + "description": "\"TSV with ORFs assessed as translating in this BAM file. You can output\nall ORFs regardless of the translation status with option --report_all\"\n", + "pattern": "*_translating_ORFs.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@pinin4fjords"], + "maintainers": ["@pinin4fjords"] }, - { - "gene_list": { - "type": "file", - "description": "A tsv/csv file that contains a list of gene ids in one of the columns. By default, the column name should be \"gene_id\", but this can be changed by using \"--columname gene_id\" in ext.args.", - "pattern": "*.{csv,tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - }, - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "output": { - "gmt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.gmt": { - "type": "file", - "description": "Each row contains the GO id, a description, and a list of gene ids.\n", - "pattern": "*.gmt", - "ontologies": [] - } - } - ] - ], - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "(optional) A tsv file with the following columns:\nquery, mygene_id, go_id, go_term, go_evidence, go_category, symbol, name, taxid\n", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_mygene": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "mygene": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "3.2.2": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "mygene": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "3.2.2": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "riboseq", + "version": "1.2.0" + } ] - ] - }, - "authors": [ - "@suzannejin" - ], - "maintainers": [ - "@suzannejin" - ] - } - }, - { - "name": "mykrobe_predict", - "path": "modules/nf-core/mykrobe/predict/meta.yml", - "type": "module", - "meta": { - "name": "mykrobe_predict", - "description": "AMR predictions for supported species", - "keywords": [ - "fastq", - "bam", - "antimicrobial resistance" - ], - "tools": [ - { - "mykrobe": { - "description": "Antibiotic resistance prediction in minutes", - "homepage": "http://www.mykrobe.com/", - "documentation": "https://github.com/Mykrobe-tools/mykrobe/wiki", - "tool_dev_url": "https://github.com/Mykrobe-tools/mykrobe", - "doi": "10.1038/ncomms10063", - "licence": [ - "MIT" - ], - "identifier": "biotools:Mykrobe" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + }, + { + "name": "ribotricer_prepareorfs", + "path": "modules/nf-core/ribotricer/prepareorfs/meta.yml", + "type": "module", + "meta": { + "name": "ribotricer_prepareorfs", + "description": "Accurate detection of short and long active ORFs using Ribo-seq data", + "keywords": ["riboseq", "orf", "genomics"], + "tools": [ + { + "ribotricer": { + "description": "Python package to detect translating ORF from Ribo-seq data", + "homepage": "https://github.com/smithlabcode/ribotricer", + "documentation": "https://github.com/smithlabcode/ribotricer", + "tool_dev_url": "https://github.com/smithlabcode/ribotricer", + "doi": "10.1093/bioinformatics/btz878", + "licence": ["GNU General Public v3 (GPL v3)"], + "identifier": "biotools:ribotricer" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. `[ id:'Ensembl human v.111' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Fasta-format sequence file for reference sequences used in the bam file\n", + "pattern": "*.gtf", + "ontologies": [] + } + }, + { + "gtf": { + "type": "file", + "description": "GTF-format annotation file for reference sequences used in the bam file\n", + "pattern": "*.gtf", + "ontologies": [] + } + } + ] + ], + "output": { + "candidate_orfs": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. `[ id:'Ensembl human v.111' ]`\n" + } + }, + { + "*_candidate_orfs.tsv": { + "type": "file", + "description": "TSV file with candidate ORFs", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@pinin4fjords"], + "maintainers": ["@pinin4fjords"] }, - { - "seqs": { - "type": "file", - "description": "BAM or FASTQ file", - "pattern": "*.{bam,fastq.gz,fq.gz}", - "ontologies": [] - } - } - ], - { - "species": { - "type": "string", - "description": "Species to make AMR prediction against", - "pattern": "*" - } - } - ], - "output": { - "csv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.csv": { - "type": "file", - "description": "AMR predictions in CSV format", - "pattern": "*.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "json": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.json": { - "type": "file", - "description": "AMR predictions in JSON format", - "pattern": "*.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } + "pipelines": [ + { + "name": "riboseq", + "version": "1.2.0" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - 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"Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } + }, + { + "name": "ribowaltz", + "path": "modules/nf-core/ribowaltz/meta.yml", + "type": "module", + "meta": { + "name": "ribowaltz", + "description": "Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data", + "keywords": ["riboseq", "psite", "genomics"], + "tools": [ + { + "ribowaltz": { + "description": "Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data.", + "homepage": "https://github.com/LabTranslationalArchitectomics/riboWaltz", + "documentation": "https://github.com/LabTranslationalArchitectomics/riboWaltz", + "tool_dev_url": "https://github.com/LabTranslationalArchitectomics/riboWaltz", + "doi": "10.1371/journal.pcbi.1006169", + "licence": ["MIT"], + "identifier": "biotools:ribowaltz" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "bam": { + "type": "file", + "description": "Transcriptome BAM file", + "pattern": "*.{bam}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Map containing reference information for the reference genome GTF file\ne.g. `[ id:'Ensembl human v.111' ]`\n" + } + }, + { + "gtf": { + "type": "file", + "description": "GTF file of reference genome", + "pattern": "*.{gtf.gz,gtf}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Map containing reference information for the reference genome FASTA file\ne.g. `[ id:'Ensembl human v.111' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA file of reference genome", + "pattern": "*.{fasta,fa,fasta.gz,fa.gz}", + "ontologies": [] + } + } + ] + ], + "output": { + "best_offset": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.best_offset.txt": { + "type": "file", + "description": "Text file with the extremity used for the offset correction step and the best offset for each sample (optional, in case no offsets could be determined, usually because no reads pass filtering criteria)", + "pattern": "*.best_offset.txt", + "ontologies": [] + } + } + ] + ], + "offset": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.psite_offset.tsv{,.gz}": { + "type": "file", + "description": "TSV file containing P-site offsets for each read length (optional, in case no offsets could be determined, usually because no reads pass filtering criteria)", + "pattern": "*.psite_offset.tsv.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "offset_plot": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "offset_plot/*": { + "type": "file", + "description": "P-site offset plots for each read length (optional)", + "pattern": "offset_plot/*", + "ontologies": [] + } + } + ] + ], + "psites": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.psite.tsv{,.gz}": { + "type": "file", + "description": "TSV file containing P-site transcriptomic coordinates and information for each alignment (optional)", + "pattern": "*.psite.tsv.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "codon_coverage_rpf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.codon_coverage_rpf.tsv{,.gz}": { + "type": "file", + "description": "TSV file with codon-level RPF coverage for each transcript (optional)", + "pattern": "*.codon_coverage_rpf.tsv.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "codon_coverage_psite": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.codon_coverage_psite.tsv{,.gz}": { + "type": "file", + "description": "TSV file with codon-level P-site coverage for each transcript (optional)", + "pattern": "*.codon_coverage_psite.tsv.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "cds_coverage": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.cds_coverage_psite.tsv{,.gz}": { + "type": "file", + "description": "TSV file with CDS P-site in-frame counts for each transcript (optional)", + "pattern": "*.cds_coverage_psite.tsv.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "cds_window_coverage": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*nt_coverage_psite.tsv{,.gz}": { + "type": "file", + "description": "TSV file with CDS P-site in-frame counts for each transcript, excluding P-sites within defined distances to start and stop codons (defined by passing --exclude_start and --exclude_stop with the number of nucleotides) (optional)", + "pattern": "*nt_coverage_psite.tsv.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "ribowaltz_qc": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "ribowaltz_qc/*.pdf": { + "type": "file", + "description": "riboWaltz diagnostic plots (optional)", + "pattern": "ribowaltz_qc/*", + "ontologies": [] + } + } + ] + ], + "ribowaltz_qc_data": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "ribowaltz_qc/*.tsv": { + "type": "file", + "description": "TSV files containing data underlying riboWaltz QC plots including read length distribution, read length bins for P-site offset identification, ends heatmap, codon usage, P-site region distribution, frame distribution, frame distribution stratified by read length, and metaprofile P-site frequency around start/stop codons (optional)", + "pattern": "ribowaltz_qc/*.tsv", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@iraiosub"], + "maintainers": ["@iraiosub"] }, - { - "reads": { - "type": "file", - "description": "Input long reads in FASTQ or FASTA format (FASTQ preferred for base quality information)", - "pattern": "*.{fastq,fq,fastq.gz,fq.gz,fasta,fa,fasta.gz,fa.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - }, - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ], - "output": { - "results": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "${prefix}": { - "type": "directory", - "description": "Directory containing all myloasm output files and folders", - "pattern": "*" - } - } - ] - ], - "contigs": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "${prefix}/assembly_primary.fa": { - "type": "file", - "description": "Primary assembly contigs in FASTA format", - "pattern": "assembly_primary.fa", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ], - "gfa": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "${prefix}/final_contig_graph.gfa": { - "type": "file", - "description": "Final contig graph in GFA format", - "pattern": "final_contig_graph.gfa", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3975" - } - ] - } - } - ] - ], - "contigs_alt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "${prefix}/alternate_assemblies/assembly_alternate.fa": { - "type": "file", - "description": "Alternative assembly contigs in FASTA format", - "pattern": "assembly_alternate.fa", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ], - "contigs_dup": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "${prefix}/alternate_assemblies/duplicated_contigs.fa": { - "type": "file", - "description": "Duplicated contigs in FASTA format", - "pattern": "duplicated_contigs.fa", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ], - "mapping": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "${prefix}/3-mapping/map_to_unitigs.paf.gz": { - "type": "file", - "description": "Mapping of reads to unitigs in PAF format (compressed)", - "pattern": "map_to_unitigs.paf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "${prefix}/*.log": { - "type": "file", - 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{ + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "gff": { + "type": "file", + "description": "A set of GFF3 formatted files", + "pattern": "*.{gff}", + "ontologies": [] + } + } + ] + ], + "output": { + "results": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "results/*": { + "type": "directory", + "description": "Directory containing Roary result files", + "pattern": "*/*" + } + } + ] + ], + "aln": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "results/*.aln": { + "type": "file", + "description": "Core-genome alignment produced by Roary (Optional)", + "pattern": "*.{aln}", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File 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"meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "Input reads for quantification (FASTQ files or BAM file for --alignments mode)", + "pattern": "*.{fastq.gz,bam}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + }, + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + } + ], + { + "index": { + "type": "file", + "description": "RSEM index", + "pattern": "rsem/*", + "ontologies": [] + } + } + ], + "output": { + "counts_gene": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.genes.results": { + "type": "file", + "description": "Expression counts on gene level", + "pattern": "*.genes.results", + "ontologies": [] + } + } + ] + ], + "counts_transcript": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.isoforms.results": { + "type": "file", + "description": "Expression counts on transcript level", + "pattern": "*.isoforms.results", + "ontologies": [] + } + } + ] + ], + "stat": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.stat": { + "type": "file", + "description": "RSEM statistics", + "pattern": "*.stat", + "ontologies": [] + } + } + ] + ], + "logs": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.log": { + "type": "file", + "description": "RSEM logs", + "pattern": "*.log", + "ontologies": [] + } + } + ] + ], + "versions_rsem": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "rsem": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "rsem-calculate-expression --version | sed 's/Current version: RSEM v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_star": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "star": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "STAR --version | sed -e \"s/STAR_//g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "bam_star": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.STAR.genome.bam": { + "type": "file", + "description": "BAM file generated by STAR (optional)", + "pattern": "*.STAR.genome.bam", + "ontologies": [] + } + } + ] + ], + "bam_genome": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}.genome.bam": { + "type": "file", + "description": "Genome BAM file (optional)", + "pattern": "*.genome.bam", + "ontologies": [] + } + } + ] + ], + "bam_transcript": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}.transcript.bam": { + "type": "file", + "description": "Transcript BAM file (optional)", + "pattern": "*.transcript.bam", + "ontologies": [] + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "rsem": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "rsem-calculate-expression --version | sed 's/Current version: RSEM v//'": { + "type": "eval", + "description": "The expression to 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"pattern": "*.ali" - } - } + "pipelines": [ + { + "name": "rnaseq", + "version": "3.26.0" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@vagkaratzas" - ], - "maintainers": [ - "@vagkaratzas" - ] - } - }, - { - "name": "nanocomp", - "path": "modules/nf-core/nanocomp/meta.yml", - "type": "module", - "meta": { - "name": "nanocomp", - "description": "Compare multiple runs of long read sequencing data and alignments", - "keywords": [ - "bam", - "fasta", - "fastq", - "qc", - "nanopore" - ], - "tools": [ - { - "nanocomp": { - "description": "Compare multiple runs of long read sequencing data and alignments", - "homepage": "https://github.com/wdecoster/nanocomp", - "documentation": "https://github.com/wdecoster/nanocomp", - "licence": [ - "MIT License" - ], - "identifier": "biotools:nanocomp" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false]" - } + }, + { + "name": "rsem_preparereference", + "path": "modules/nf-core/rsem/preparereference/meta.yml", + "type": "module", + "meta": { + "name": "rsem_preparereference", + "description": "Prepare a reference genome for RSEM", + "keywords": ["rsem", "genome", "index"], + "tools": [ + { + "rseqc": { + "description": "RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome\n", + "homepage": "https://github.com/deweylab/RSEM", + "documentation": "https://github.com/deweylab/RSEM", + "doi": "10.1186/1471-2105-12-323", + "licence": ["GPL-3.0-or-later"], + "identifier": "biotools:rsem" + } + } + ], + "input": [ + { + "fasta": { + "type": "file", + "description": "The Fasta file of the reference genome", + "pattern": "*.{fasta,fa}", + "ontologies": [] + } + }, + { + "gtf": { + "type": "file", + "description": "The GTF file of the reference genome", + "pattern": "*.gtf", + "ontologies": [] + } + } + ], + "output": { + "index": [ + { + "rsem": { + "type": "directory", + "description": "RSEM index directory", + "pattern": "rsem" + } + } + ], + "transcript_fasta": [ + { + "*transcripts.fa": { + "type": "file", + "description": "Fasta file of transcripts", + "pattern": "rsem/*transcripts.fa", + "ontologies": [] + } + } + ], + "versions_rsem": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "rsem": { + "type": "string", + "description": "The tool name" + } + }, + { + "rsem-calculate-expression --version | sed -e \"s/Current version: RSEM v//g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_star": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "star": { + "type": "string", + "description": "The tool name" + } + }, + { + "STAR --version | sed -e \"s/STAR_//g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "rsem": { + "type": "string", + "description": "The tool name" + } + }, + { + "rsem-calculate-expression --version | sed -e \"s/Current version: RSEM v//g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "star": { + "type": "string", + "description": "The tool name" + } + }, + { + "STAR --version | sed -e \"s/STAR_//g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@drpatelh", "@kevinmenden"], + "maintainers": ["@drpatelh", "@kevinmenden"] }, - 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It is used to evaluate called CNV regions for agreement with a baseline CNV set.", + "keywords": ["benchmarking", "vcf", "rtg-tools", "cnv-eval", "copy-number-variants"], + "tools": [ + { + "rtgtools": { + "description": "RealTimeGenomics Tools -- Utilities for accurate VCF comparison and manipulation.", + "homepage": "https://www.realtimegenomics.com/products/rtg-tools", + "documentation": "https://cdn.jsdelivr.net/gh/RealTimeGenomics/rtg-tools@master/installer/resources/tools/RTGOperationsManual.pdf", + "tool_dev_url": "https://github.com/RealTimeGenomics/rtg-tools", + "licence": ["BSD-2-clause"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "query_vcf": { + "type": "file", + "description": "A VCF with called CNV variants to benchmark against the baseline. Records must contain INFO END and INFO SVTYPE (DUP or DEL).", + "pattern": "*.{vcf,vcf.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + } + ] + } + }, + { + "query_vcf_tbi": { + "type": "file", + "description": "The index of the VCF file with called variants", + "pattern": "*.{vcf.gz.tbi,vcf.tbi}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3616" + } + ] + } + }, + { + "truth_vcf": { + "type": "file", + "description": "A baseline VCF containing expected CNV calls. Records must contain INFO END and INFO SVTYPE (DUP or DEL).", + "pattern": "*.{vcf,vcf.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + } + ] + } + }, + { + "truth_vcf_tbi": { + "type": "file", + "description": "The index of the baseline VCF to compare against", + "pattern": "*.{vcf.gz.tbi,vcf.tbi}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3616" + } + ] + } + }, + { + "evaluation_regions_bed": { + "type": "file", + "description": "A BED file containing the regions of interest for evaluation (required). Regions are intersected with truth and calls VCFs to obtain CNV regions.", + "pattern": "*.bed", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3003" + } + ] + } + } + ] + ], + "output": { + "baseline_bed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.baseline.bed.gz": { + "type": "file", + "description": "A BED file containing truth CNV regions with TP/FN status, SVTYPE, and the span of the original truth VCF record", + "pattern": "*.baseline.bed.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3003" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "calls_bed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.calls.bed.gz": { + "type": "file", + "description": "A BED file containing called CNV regions with TP/FP status, SVTYPE, the span of the original calls VCF record, and the score value", + "pattern": "*.calls.bed.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3003" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "weighted_roc": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.weighted_roc.tsv.gz": { + "type": "file", + "description": "TSV file containing weighted ROC data that can be plotted with rocplot", + "pattern": "*.weighted_roc.tsv.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "summary": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.summary.txt": { + "type": "file", + "description": "A TXT file containing the summary statistics of the evaluation", + "pattern": "*.summary.txt", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1964" + } + ] + } + } + ] + ], + "versions_rtgtools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "rtgtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "rtg version | sed 's/Product: RTG Tools //; q'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "rtgtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "rtg version | sed 's/Product: RTG Tools //; q'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@SevaNur"], + "maintainers": ["@SevaNur"] }, - { - "ontreads": { - "type": "file", - "description": "Compressed or uncompressed nanopore reads in fasta or fastq formats.", - "pattern": "*.{fa,fna,faa,fasta,fq,fastq}{,.gz,.bz2,.xz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ], - { - "output_format": { - "type": "string", - "description": "Specifies the output format. One of these formats: fasta, fastq; fasta.gz, fastq.gz; fasta.bz2, fastq.bz2; fasta.lzma, fastq.lzma." - } - } - ], - "output": { - "stats": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.{stats,json}": { - "type": "file", - "description": "Summary report of reads statistics.", - "pattern": "*.{stats,json}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "reads": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "${prefix}.${output_format}": { - "type": "file", - "description": "Filtered reads.", - "pattern": "*.{fasta,fastq}{,.gz,.bz2,.lzma}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "versions_nanoq": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "nanoq": { - "type": "string", - "description": "The tool name" - } - }, - { - "nanoq --version | sed -e 's/nanoq //g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "nanoq": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "nanoq --version | sed -e 's/nanoq //g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "variantbenchmarking", + "version": "1.5.0" + } ] - ] }, - "authors": [ - "@LilyAnderssonLee" - ], - "maintainers": [ - "@LilyAnderssonLee" - ] - }, - "pipelines": [ { - "name": "mag", - "version": "5.4.2" + "name": "rtgtools_format", + "path": "modules/nf-core/rtgtools/format/meta.yml", + "type": "module", + "meta": { + "name": "rtgtools_format", + "description": "Converts the contents of sequence data files (FASTA/FASTQ/SAM/BAM) into the RTG Sequence Data File (SDF) format.", + "keywords": ["rtg", "fasta", "fastq", "bam", "sam"], + "tools": [ + { + "rtgtools": { + "description": "RealTimeGenomics Tools -- Utilities for accurate VCF comparison and manipulation", + "homepage": "https://www.realtimegenomics.com/products/rtg-tools", + "documentation": "https://cdn.jsdelivr.net/gh/RealTimeGenomics/rtg-tools@master/installer/resources/tools/RTGOperationsManual.pdf", + "tool_dev_url": "https://github.com/RealTimeGenomics/rtg-tools", + "licence": ["BSD"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input1": { + "type": "file", + "description": "FASTA, FASTQ, BAM or SAM file. This should be the left input file when using paired end FASTQ/FASTA data", + "pattern": "*.{fasta,fa,fna,fastq,fastq.gz,fq,fq.gz,bam,sam}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + }, + { + "input2": { + "type": "file", + "description": "The right input file when using paired end FASTQ/FASTA data", + "pattern": "*.{fasta,fa,fna,fastq,fastq.gz,fq,fq.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + }, + { + "sam_rg": { + "type": "file", + "description": "A file containing a single readgroup header as a SAM header. This can also be supplied as a string in `task.ext.args` as `--sam-rg `.", + "pattern": "*.{txt,sam}", + "ontologies": [] + } + } + ] + ], + "output": { + "sdf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.sdf": { + "type": "directory", + "description": "The sequence dictionary format folder created from the input file(s)", + "pattern": "*.sdf" + } + } + ] + ], + "versions_rtgtools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "rtgtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "rtg version | head -n 1 | sed 's/Product: RTG Tools //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "rtgtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "rtg version | head -n 1 | sed 's/Product: RTG Tools //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@nvnieuwk"], + "maintainers": ["@nvnieuwk"] + }, + "pipelines": [ + { + "name": "raredisease", + "version": "3.0.0" + }, + { + "name": "variantbenchmarking", + "version": "1.5.0" + } + ] }, { - "name": "taxprofiler", - "version": "2.0.0" - } - ] - }, - { - "name": "narfmap_align", - "path": "modules/nf-core/narfmap/align/meta.yml", - "type": "module", - "meta": { - "name": "narfmap_align", - "description": "Performs fastq alignment to a reference using NARFMAP", - "keywords": [ - "alignment", - "map", - "fastq", - "bam", - "sam" - ], - "tools": [ - { - "narfmap": { - "description": "narfmap is a fork of the Dragen mapper/aligner Open Source Software.", - "homepage": "https://github.com/bioinformaticsorphanage/NARFMAP", - "documentation": "https://github.com/bioinformaticsorphanage/NARFMAP/blob/main/doc/usage.md#basic-command-line-usage", - "tool_dev_url": "https://github.com/bioinformaticsorphanage/NARFMAP", - "licence": [ - "GPL v3" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "hashmap": { - "type": "file", - "description": "NARFMAP hash table", - "pattern": "Directory containing NARFMAP hash table *.{cmp,.bin,.txt}", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome in FASTA format", - "pattern": "*.{fasta,fa,fna}", - "ontologies": [] - } + "name": "rtgtools_pedfilter", + "path": "modules/nf-core/rtgtools/pedfilter/meta.yml", + "type": "module", + "meta": { + "name": "rtgtools_pedfilter", + "description": "Converts a PED file to VCF headers", + "keywords": ["rtgtools", "pedfilter", "vcf", "ped"], + "tools": [ + { + "rtgtools": { + "description": "RealTimeGenomics Tools -- Utilities for accurate VCF comparison and manipulation", + "homepage": "https://www.realtimegenomics.com/products/rtg-tools", + "documentation": "https://cdn.jsdelivr.net/gh/RealTimeGenomics/rtg-tools@master/installer/resources/tools/RTGOperationsManual.pdf", + "tool_dev_url": "https://github.com/RealTimeGenomics/rtg-tools", + "licence": ["BSD"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "The input file, can be either a PED or a VCF file", + "pattern": "*.{vcf,vcf.gz,ped}", + "ontologies": [] + } + } + ] + ], + "output": { + "output": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{vcf.gz,ped}": { + "type": "file", + "description": "The output file, can be either a filtered PED file\nor a VCF file containing the PED headers (needs --vcf as argument)\n", + "pattern": "*.{vcf.gz,ped}", + "ontologies": [] + } + } + ] + ], + "versions_rtgtools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "rtgtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "rtg version | sed 's/Product: RTG Tools //; q'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "rtgtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "rtg version | sed 's/Product: RTG Tools //; q'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@nvnieuwk"], + "maintainers": ["@nvnieuwk"] } - ], - { - "sort_bam": { - "type": "boolean", - "description": "Sort the BAM file after alignment" + }, + { + "name": "rtgtools_rocplot", + "path": "modules/nf-core/rtgtools/rocplot/meta.yml", + "type": "module", + "meta": { + "name": "rtgtools_rocplot", + "description": "Plot ROC curves from vcfeval ROC data files, either to an image, or an interactive GUI. The interactive GUI isn't possible for nextflow.", + "keywords": ["rtgtools", "rocplot", "validation", "vcf"], + "tools": [ + { + "rtgtools": { + "description": "RealTimeGenomics Tools -- Utilities for accurate VCF comparison and manipulation", + "homepage": "https://www.realtimegenomics.com/products/rtg-tools", + "documentation": "https://cdn.jsdelivr.net/gh/RealTimeGenomics/rtg-tools@master/installer/resources/tools/RTGOperationsManual.pdf", + "tool_dev_url": "https://github.com/RealTimeGenomics/rtg-tools", + "licence": ["BSD"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "Input TSV ROC files created with RTGTOOLS_VCFEVAL", + "pattern": "*.tsv.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "output": { + "png": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.png": { + "type": "file", + "description": "The resulting rocplot in PNG format", + "pattern": "*.png", + "ontologies": [] + } + } + ] + ], + "svg": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.svg": { + "type": "file", + "description": "The resulting rocplot in SVG format", + "pattern": "*.svg", + "ontologies": [] + } + } + ] + ], + "versions_rtgtools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "rtgtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "rtg version | sed 's/Product: RTG Tools //; q'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "rtgtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "rtg version | sed 's/Product: RTG Tools //; q'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@nvnieuwk"], + "maintainers": ["@nvnieuwk"] } - } - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "file", - "description": "Output BAM file containing read alignments", - "pattern": "*.{bam}", - "ontologies": [] - } - }, - { - "*.bam": { - "type": "file", - "description": "Output BAM file containing read alignments", - "pattern": "*.{bam}", - "ontologies": [] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "file", - "description": "Output BAM file containing read alignments", - "pattern": "*.{bam}", - "ontologies": [] - } - }, - { - "*.log": { - "type": "file", - "description": "Log file of NARFMAP run", - "pattern": "*{.log}", - "ontologies": [] - } - } - ] - ], - "versions_narfmap": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "narfmap": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "dragen-os --version 2>&1": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_samtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_pigz": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pigz": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pigz --version 2>&1 | sed 's/pigz //g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "narfmap": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "dragen-os --version 2>&1": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pigz": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pigz --version 2>&1 | sed 's/pigz //g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + }, + { + "name": "rtgtools_svdecompose", + "path": "modules/nf-core/rtgtools/svdecompose/meta.yml", + "type": "module", + "meta": { + "name": "rtgtools_svdecompose", + "description": "The svdecompose tool of RTG tools. 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{ + "type": "file", + "description": "YAML file containing versions of tools used in the module", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "topics": { + "versions": [ + { + "versions.yml": { + "type": "string", + "description": "The name of the process" + } + } + ] + }, + "authors": ["@mribeirodantas"], + "maintainers": ["@mribeirodantas"] } - }, - { - "groups": { - "type": "string", - "description": "NCBI taxonomic groups to download. Can be a comma-separated list. Options are ['all', 'archaea', 'bacteria', 'fungi', 'invertebrate', 'metagenomes', 'plant', 'protozoa', 'vertebrate_mammalian', 'vertebrate_other', 'viral']" + }, + { + "name": "rundbcan_cazymeannotation", + "path": "modules/nf-core/rundbcan/cazymeannotation/meta.yml", + "type": "module", + "meta": { + "name": "rundbcan_cazymeannotation", + "description": "CAZyme annotation module for the dbcan pipeline. This module is used to annotate carbohydrate-active enzymes (CAZymes) from genomic data using the dbCAN annotation tool.", + "keywords": ["dbCAN", "download", "CAZyme", "CAZyme gene Cluster", "genomes"], + "tools": [ + { + "dbcan": { + "description": "Standalone version of dbCAN annotation tool for automated CAZyme annotation.", + "homepage": "https://bcb.unl.edu/dbCAN2/", + "documentation": "https://run-dbcan.readthedocs.io/en/latest/", + "tool_dev_url": "https://github.com/bcb-unl/run_dbcan", + "doi": "10.1093/nar/gkad328", + "licence": ["GPL v3-or-later"], + "identifier": "biotools:dbcan" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "input_raw_data": { + "type": "file", + "description": "FASTA file for protein sequences.", + "pattern": "*.{fasta,fa,faa}", + "ontologies": [ + { + "edam": "http://edamontology.org/data_2044" + }, + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + { + "dbcan_db": { + "type": "directory", + "description": "Path to the dbCAN database directory." + } + } + ], + "output": { + "cazyme_annotation": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "${prefix}_overview.tsv": { + "type": "file", + "description": "TSV file containing the results of dbCAN CAZyme annotation.\n", + "ontologies": [] + } + } + ] + ], + "dbcanhmm_results": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "${prefix}_dbCAN_hmm_results.tsv": { + "type": "file", + "description": "TSV file containing the detailed dbCAN HMM results for CAZyme annotation.\n", + "ontologies": [] + } + } + ] + ], + "dbcansub_results": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "${prefix}_dbCANsub_hmm_results.tsv": { + "type": "file", + "description": "TSV file containing the detailed dbCAN subfamily results for CAZyme annotation.\n", + "ontologies": [] + } + } + ] + ], + "dbcandiamond_results": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "${prefix}_diamond.out": { + "type": "file", + "description": "TSV file containing the detailed dbCAN diamond results for CAZyme annotation.\n", + "ontologies": [] + } + } + ] + ], + "versions_rundbcan": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "rundbcan": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "run_dbcan version | sed 's/dbCAN version: //g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "rundbcan": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "run_dbcan version | sed 's/dbCAN version: //g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@Xinpeng021001"], + "maintainers": ["@Xinpeng021001"] } - } - ], - "output": { - "gbk": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_genomic.gbff.gz": { - "type": "file", - "description": "GenBank format of the genomic sequence(s) in the assembly", - "pattern": "*_genomic.gbff.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "fna": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_genomic.fna.gz": { - "type": "file", - "description": "FASTA format of the genomic sequence(s) in the assembly.", - "pattern": "*_genomic.fna.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "rm": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_rm.out.gz": { - "type": "file", - "description": "RepeatMasker output for eukaryotes.", - "pattern": "*_rm.out.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "features": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_feature_table.txt.gz": { - "type": "file", - "description": "Tab-delimited text file reporting locations and attributes for a subset of annotated features", - "pattern": "*_feature_table.txt.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "gff": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_genomic.gff.gz": { - "type": "file", - "description": "Annotation of the genomic sequence(s) in GFF3 format", - "pattern": "*_genomic.gff.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "faa": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_protein.faa.gz": { - "type": "file", - "description": "FASTA format of the accessioned protein products annotated on the genome assembly.", - "pattern": "*_protein.faa.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "gpff": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_protein.gpff.gz": { - "type": "file", - "description": "GenPept format of the accessioned protein products annotated on the genome assembly.", - "pattern": "*_protein.gpff.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "wgs_gbk": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_wgsmaster.gbff.gz": { - "type": "file", - "description": "GenBank flat file format of the WGS master for the assembly", - "pattern": "*_wgsmaster.gbff.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "cds": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_cds_from_genomic.fna.gz": { - "type": "file", - "description": "FASTA format of the nucleotide sequences corresponding to all CDS features annotated on the assembly", - "pattern": "*_cds_from_genomic.fna.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "rna": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_rna.fna.gz": { - "type": "file", - "description": "FASTA format of accessioned RNA products annotated on the genome assembly", - "pattern": "*_rna.fna.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "rna_fna": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_rna_from_genomic.fna.gz": { - "type": "file", - "description": "FASTA format of the nucleotide sequences corresponding to all RNA features annotated on the assembly", - "pattern": "*_rna_from_genomic.fna.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "report": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_assembly_report.txt": { - "type": "file", - "description": "Tab-delimited text file reporting the name, role and sequence accession.version for objects in the assembly", - "pattern": "*_assembly_report.txt", - "ontologies": [] - } - } - ] - ], - "stats": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_assembly_stats.txt": { - "type": "file", - "description": "Tab-delimited text file reporting statistics for the assembly", - "pattern": "*_assembly_stats.txt", - "ontologies": [] - } - } - ] - ], - "versions_ncbigenomedownload": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process name" - } - }, - { - "ncbigenomedownload": { - "type": "string", - "description": "The tool name" - } - }, - { - "ncbi-genome-download --version": { - "type": "eval", - "description": "The tool version" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process name" - } - }, - { - "ncbigenomedownload": { - "type": "string", - "description": "The tool name" - } - }, - { - "ncbi-genome-download --version": { - "type": "eval", - "description": "The tool version" - } - } - ] - ] }, - "authors": [ - "@rpetit3" - ], - "maintainers": [ - "@rpetit3" - ] - }, - "pipelines": [ { - "name": "genomeqc", - "version": "dev" + "name": "rundbcan_database", + "path": "modules/nf-core/rundbcan/database/meta.yml", + "type": "module", + "meta": { + "name": "rundbcan_database", + "description": "command from run_dbcan to prepare the database for dbCAN annotation.", + "keywords": ["dbCAN", "download", "CAZyme", "CAZyme gene Cluster", "genomes"], + "tools": [ + { + "run_dbcan": { + "description": "Standalone version of dbCAN annotation tool for automated CAZyme annotation.", + "homepage": "https://bcb.unl.edu/dbCAN2/", + "documentation": "https://run-dbcan.readthedocs.io/en/latest/", + "tool_dev_url": "https://github.com/bcb-unl/run_dbcan", + "doi": "10.1093/nar/gkad328", + "licence": ["GPL v3-or-later"], + "identifier": "biotools:dbcan" + } + } + ], + "input": [], + "output": { + "dbcan_db": [ + { + "dbcan_db": { + "type": "directory", + "description": "Download directory for dbCAN databases", + "pattern": "dbcan_db" + } + } + ], + "versions_rundbcan": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "rundbcan": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "run_dbcan version | sed 's/dbCAN version: //g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "rundbcan": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "run_dbcan version | sed 's/dbCAN version: //g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@Xinpeng021001"], + "maintainers": ["@Xinpeng021001"] + } }, { - "name": "readsimulator", - "version": "1.0.1" - } - ] - }, - { - "name": "ncbitools_vecscreen", - "path": "modules/nf-core/ncbitools/vecscreen/meta.yml", - "type": "module", - "meta": { - "name": "NCBITOOLS_VECSCREEN", - "description": "NCBI tool for detecting vector contamination in nucleic acid sequences. This tool is older than NCBI's FCS-adaptor, which is for the same purpose", - "keywords": [ - "assembly", - "genomics", - "quality control", - "contamination", - "vector", - "NCBI" - ], - "tools": [ - { - "ncbitools": { - "description": "\"NCBI libraries for biology applications (text-based utilities)\"\n", - "homepage": "https://www.ncbi.nlm.nih.gov/tools/vecscreen/", - "documentation": "https://www.ncbi.nlm.nih.gov/tools/vecscreen/interpretation/", - "tool_dev_url": "https://www.ncbi.nlm.nih.gov/tools/vecscreen/", - "licence": [ - "The Open Database License" - ], - "identifier": "" + "name": "rundbcan_easycgc", + "path": "modules/nf-core/rundbcan/easycgc/meta.yml", + "type": "module", + "meta": { + "name": "rundbcan_easycgc", + "description": "CGC annotation module for the dbcan pipeline. This module is used to annotate carbohydrate-active enzymes (CAZymes) from genomic data using the dbCAN annotation tool.", + "keywords": ["dbCAN", "download", "CAZyme", "CAZyme gene Cluster", "genomes"], + "tools": [ + { + "dbcan": { + "description": "Standalone version of dbCAN annotation tool for automated CAZyme annotation.", + "homepage": "https://bcb.unl.edu/dbCAN2/", + "documentation": "https://run-dbcan.readthedocs.io/en/latest/", + "tool_dev_url": "https://github.com/bcb-unl/run_dbcan", + "doi": "10.1093/nar/gkad328", + "licence": ["GPL v3-or-later"], + "identifier": "biotools:dbcan" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "input_raw_data": { + "type": "file", + "description": "FASTA file for protein sequences.", + "pattern": "*.{fasta,fa,faa}", + "ontologies": [ + { + "edam": "http://edamontology.org/data_2044" + }, + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "input_gff": { + "type": "file", + "description": "GFF file for protein sequences.", + "ontologies": [] + } + }, + { + "gff_type": { + "type": "string", + "description": "Type of GFF file. Options are `NCBI_prok`, `JGI`, `NCBI_euk`, and `prodigal`. This is used to parse the GFF file correctly.\n" + } + } + ], + { + "dbcan_db": { + "type": "directory", + "description": "Path to the dbCAN database directory." + } + } + ], + "output": { + "cazyme_annotation": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "${prefix}_overview.tsv": { + "type": "file", + "description": "TSV file containing the results of dbCAN CAZyme annotation.\n", + "ontologies": [] + } + } + ] + ], + "dbcanhmm_results": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "${prefix}_dbCAN_hmm_results.tsv": { + "type": "file", + "description": "TSV file containing the detailed dbCAN HMM results for CAZyme annotation.\n", + "ontologies": [] + } + } + ] + ], + "dbcansub_results": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "${prefix}_dbCANsub_hmm_results.tsv": { + "type": "file", + "description": "TSV file containing the detailed dbCAN subfamily results for CAZyme annotation.\n", + "ontologies": [] + } + } + ] + ], + "dbcandiamond_results": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "${prefix}_diamond.out": { + "type": "file", + "description": "TSV file containing the detailed dbCAN diamond results for CAZyme annotation.\n", + "ontologies": [] + } + } + ] + ], + "cgc_gff": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "${prefix}_cgc.gff": { + "type": "file", + "description": "GFF file containing the CAZyme gene clusters (CGC) identified by dbCAN. This file is generated from the dbCAN annotation and contains the locations of CAZyme gene clusters in the genome.\n", + "ontologies": [] + } + } + ] + ], + "cgc_standard_out": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "${prefix}_cgc_standard_out.tsv": { + "type": "file", + "description": "Standard output file from dbCAN for CAZyme gene clusters (CGC) in a tabular format. This file summarizes the CAZyme gene clusters identified in the genome.\n", + "ontologies": [] + } + } + ] + ], + "diamond_out_tc": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "${prefix}_diamond.out.tc": { + "type": "file", + "description": "TSV file containing the diamond output for transporter annotation.\n", + "ontologies": [] + } + } + ] + ], + "tf_hmm_results": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "${prefix}_TF_hmm_results.tsv": { + "type": "file", + "description": "TSV file containing the results of Transcription factor.\n", + "ontologies": [] + } + } + ] + ], + "stp_hmm_results": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "${prefix}_STP_hmm_results.tsv": { + "type": "file", + "description": "TSV file containing the results of signaling transduction proteins (STP) annotation.\n", + "ontologies": [] + } + } + ] + ], + "versions_rundbcan": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "rundbcan": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "run_dbcan version | sed 's/dbCAN version: //g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "rundbcan": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "run_dbcan version | sed 's/dbCAN version: //g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@Xinpeng021001"], + "maintainers": ["@Xinpeng021001"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', taxid:'6973' ]\n" - } - }, - { - "fasta_file": { - "type": "file", - "description": "FASTA file that will be screened for contaminants", - "ontologies": [] - } + }, + { + "name": "rundbcan_easysubstrate", + "path": "modules/nf-core/rundbcan/easysubstrate/meta.yml", + "type": "module", + "meta": { + "name": "rundbcan_easysubstrate", + "description": "Substrate annotation module for the dbcan pipeline. This module is used to annotate carbohydrate-active enzymes (CAZymes) from genomic data using the dbCAN annotation tool.", + "keywords": ["dbCAN", "download", "CAZyme", "CAZyme gene Cluster", "genomes"], + "tools": [ + { + "dbcan": { + "description": "Standalone version of dbCAN annotation tool for automated CAZyme annotation.", + "homepage": "https://bcb.unl.edu/dbCAN2/", + "documentation": "https://run-dbcan.readthedocs.io/en/latest/", + "tool_dev_url": "https://github.com/bcb-unl/run_dbcan", + "doi": "10.1093/nar/gkad328", + "licence": ["GPL v3-or-later"], + "identifier": "biotools:dbcan" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "input_raw_data": { + "type": "file", + "description": "FASTA file for protein sequences.", + "pattern": "*.{fasta,fa,faa}", + "ontologies": [ + { + "edam": "http://edamontology.org/data_2044" + }, + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "input_gff": { + "type": "file", + "description": "GFF file for protein sequences.", + "ontologies": [] + } + }, + { + "gff_type": { + "type": "string", + "description": "Type of GFF file. Options are `NCBI_prok`, `JGI`, `NCBI_euk`, and `prodigal`. This is used to parse the GFF file correctly.\n" + } + } + ], + { + "dbcan_db": { + "type": "directory", + "description": "Path to the dbCAN database directory." + } + } + ], + "output": { + "cazyme_annotation": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "${prefix}_overview.tsv": { + "type": "file", + "description": "TSV file containing the results of dbCAN CAZyme annotation.\n", + "ontologies": [] + } + } + ] + ], + "dbcanhmm_results": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "${prefix}_dbCAN_hmm_results.tsv": { + "type": "file", + "description": "TSV file containing the detailed dbCAN HMM results for CAZyme annotation.\n", + "ontologies": [] + } + } + ] + ], + "dbcansub_results": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "${prefix}_dbCANsub_hmm_results.tsv": { + "type": "file", + "description": "TSV file containing the detailed dbCAN subfamily results for CAZyme annotation.\n", + "ontologies": [] + } + } + ] + ], + "dbcandiamond_results": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "${prefix}_diamond.out": { + "type": "file", + "description": "TSV file containing the detailed dbCAN diamond results for CAZyme annotation.\n", + "ontologies": [] + } + } + ] + ], + "cgc_gff": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "${prefix}_cgc.gff": { + "type": "file", + "description": "GFF file containing the CAZyme gene clusters (CGC) identified by dbCAN. This file is generated from the dbCAN annotation and contains the locations of CAZyme gene clusters in the genome.\n", + "ontologies": [] + } + } + ] + ], + "cgc_standard_out": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "${prefix}_cgc_standard_out.tsv": { + "type": "file", + "description": "Standard output file from dbCAN for CAZyme gene clusters (CGC) in a tabular format. This file summarizes the CAZyme gene clusters identified in the genome.\n", + "ontologies": [] + } + } + ] + ], + "diamond_out_tc": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "${prefix}_diamond.out.tc": { + "type": "file", + "description": "TSV file containing the diamond output for transporter annotation.\n", + "ontologies": [] + } + } + ] + ], + "tf_hmm_results": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "${prefix}_TF_hmm_results.tsv": { + "type": "file", + "description": "TSV file containing the results of Transcription factor.\n", + "ontologies": [] + } + } + ] + ], + "stp_hmm_results": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "${prefix}_STP_hmm_results.tsv": { + "type": "file", + "description": "TSV file containing the results of signaling transduction proteins (STP) annotation.\n", + "ontologies": [] + } + } + ] + ], + "total_cgc_info": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "${prefix}_total_cgc_info.tsv": { + "type": "file", + "description": "TSV file summarizing the total additional genes in the genome.\n", + "ontologies": [] + } + } + ] + ], + "substrate_prediction": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "${prefix}_substrate_prediction.tsv": { + "type": "file", + "description": "TSV file containing the substrate predictions based on the CGC annotations from dbCAN.\n", + "ontologies": [] + } + } + ] + ], + "synteny_pdf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "${prefix}_synteny_pdf/": { + "type": "directory", + "description": "Directory containing the synteny plots in PDF format for the CAZyme gene clusters (CGC) identified by dbCAN. This directory will contain one or more PDF files showing the syntenic regions of the CGC in the genome.\n" + } + } + ] + ], + "versions_rundbcan": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "rundbcan": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "run_dbcan version | sed 's/dbCAN version: //g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "rundbcan": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "run_dbcan version | sed 's/dbCAN version: //g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@Xinpeng021001"], + "maintainers": ["@Xinpeng021001"] } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } + }, + { + "name": "rustqc", + "path": "modules/nf-core/rustqc/meta.yml", + "type": "module", + "meta": { + "name": "rustqc", + "description": "All-in-one RNA-seq post-alignment QC replacing dupRadar, featureCounts biotype QC, RSeQC, Preseq, Qualimap, and SAMtools stats", + "keywords": [ + "rnaseq", + "quality control", + "qc", + "bam", + "dupradar", + "featurecounts", + "rseqc", + "preseq", + "qualimap", + "samtools" + ], + "tools": [ + { + "rustqc": { + "description": "RustQC is a high-performance, Rust-based tool that replaces multiple\npost-alignment RNA-seq QC tools in a single pass over the BAM file.\nIt produces output compatible with MultiQC for dupRadar, featureCounts\nbiotype QC, RSeQC (bam_stat, infer_experiment, read_distribution,\nread_duplication, junction_annotation, junction_saturation,\ninner_distance, TIN), Preseq, Qualimap, and SAMtools\n(flagstat, idxstats, stats).\n", + "homepage": "https://seqeralabs.github.io/RustQC/", + "documentation": "https://seqeralabs.github.io/RustQC/", + "tool_dev_url": "https://github.com/seqeralabs/rustqc", + "licence": ["GPL-3.0-or-later"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "Sorted BAM file", + "pattern": "*.{bam}", + "ontologies": [] + } + }, + { + "bai": { + "type": "file", + "description": "BAM index file", + "pattern": "*.{bai}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "gtf": { + "type": "file", + "description": "GTF annotation file", + "pattern": "*.{gtf}", + "ontologies": [] + } + } + ] + ], + "output": { + "dupradar": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/dupradar/*": { + "type": "file", + "description": "dupRadar-compatible duplication rate plots and tables", + "pattern": "${prefix}/dupradar/*", + "ontologies": [] + } + } + ] + ], + "featurecounts": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/featurecounts/*": { + "type": "file", + "description": "featureCounts-compatible biotype quantification files", + "pattern": "${prefix}/featurecounts/*", + "ontologies": [] + } + } + ] + ], + "preseq": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/preseq/*": { + "type": "file", + "description": "Preseq-compatible library complexity extrapolation", + "pattern": "${prefix}/preseq/*", + "ontologies": [] + } + } + ] + ], + "samtools": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/samtools/*": { + "type": "file", + "description": "SAMtools flagstat, idxstats, and stats output", + "pattern": "${prefix}/samtools/*", + "ontologies": [] + } + } + ] + ], + "rseqc": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/rseqc/**": { + "type": "file", + "description": "RSeQC-compatible outputs (bam_stat, infer_experiment, read_distribution, read_duplication, junction_annotation, junction_saturation, inner_distance, TIN)", + "pattern": "${prefix}/rseqc/**", + "ontologies": [] + } + } + ] + ], + "qualimap": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/qualimap/**": { + "type": "file", + "description": "Qualimap RNA-seq QC report and raw data", + "pattern": "${prefix}/qualimap/**", + "ontologies": [] + } + } + ] + ], + "versions_rustqc": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "rustqc": { + "type": "string", + "description": "The tool name" + } + }, + { + "rustqc --version 2>&1 | sed -n '1s/rustqc //; 1s/ .*//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "rustqc": { + "type": "string", + "description": "The tool name" + } + }, + { + "rustqc --version 2>&1 | sed -n '1s/rustqc //; 1s/ .*//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@ewels", "@pinin4fjords"], + "maintainers": ["@ewels", "@pinin4fjords"], + "containers": { + "docker": { + "linux/amd64": { + "name": "community.wave.seqera.io/library/rustqc:0.2.1--00df1502b490e005", + "build_id": "bd-00df1502b490e005_1" + } + }, + "singularity": { + "linux/amd64": { + "name": "oras://community.wave.seqera.io/library/rustqc:0.2.1--3982097e14c103d4", + "build_id": "bd-3982097e14c103d4_1", + "https": "https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/2a/2a8a0514855c54307399fd0f664c2685e76c8cc07631e767c1e37c575b18d59f/data" + } + } + } }, - { - "adapters_database_directory": { - "type": "directory", - "description": "Directory containing the adapters database" - } - } - ] - ], - "output": { - "vecscreen_output": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', taxid:'9606' ]\n" - } - }, - { - "${prefix}.vecscreen.out": { - "type": "file", - "description": "VecScreen report 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This can be in different formats depending on the value of the optional -f parameter. 0 = HTML format, with alignments. 1 = HTML format, no alignments. 2 = Text list, with alignments. 3 = Text list, no alignments. default = 0", - "pattern": "*.vecscreen.out", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@eeaunin" - ] - } - }, - { - "name": "nextclade_datasetget", - "path": "modules/nf-core/nextclade/datasetget/meta.yml", - "type": "module", - "meta": { - "name": "nextclade_datasetget", - "description": "Get dataset for SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks (C++ implementation)", - "keywords": [ - "nextclade", - "variant", - "consensus" - ], - "tools": [ - { - "nextclade": { - "description": "SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks", - "homepage": "https://github.com/nextstrain/nextclade", - "documentation": "https://github.com/nextstrain/nextclade", - "tool_dev_url": "https://github.com/nextstrain/nextclade", - "licence": [ - "MIT" - ], - "identifier": "biotools:nextclade" - } - } - ], - "input": [ - { - "dataset": { - "type": "string", - "description": "Name of dataset to retrieve. A list of available datasets can be obtained using the nextclade dataset list command.", - "pattern": ".+" - } - }, - { - "tag": { - "type": "string", - "description": "Version tag of the dataset to download. A list of available datasets can be obtained using the nextclade dataset list command.", - "pattern": ".+" - } - } - ], - "output": { - "dataset": [ - { - "$prefix": { - "type": "directory", - "description": "Directory containing the dataset" - } - } - ], - "versions_nextclade": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "nextclade": { - "type": "string", - "description": "The tool name" - } - }, - { - "nextclade --version 2>&1 | sed 's/.*nextclade \\([^ ]*\\).*/\\1/'": { - "type": "eval", - "description": "The version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "nextclade": { - "type": "string", - "description": "The tool name" - } - }, - { - "nextclade --version 2>&1 | sed 's/.*nextclade \\([^ ]*\\).*/\\1/'": { - "type": "eval", - "description": "The version of the tool" - } - } + "pipelines": [ + { + "name": "rnaseq", + "version": "3.26.0" + } ] - ] - }, - "authors": [ - "@antunderwood", - "@drpatelh" - ], - "maintainers": [ - "@antunderwood", - "@drpatelh" - ], - "updated on 2024.08.27": [ - "@nmshahir" - ] - }, - "pipelines": [ - { - "name": "viralrecon", - "version": "3.0.0" - } - ] - }, - { - "name": "nextclade_run", - "path": "modules/nf-core/nextclade/run/meta.yml", - "type": "module", - "meta": { - "name": "nextclade_run", - "description": "SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks (C++ implementation)", - "keywords": [ - "nextclade", - "variant", - "consensus" - ], - "tools": [ - { - "nextclade": { - "description": "SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks", - "homepage": "https://github.com/nextstrain/nextclade", - "documentation": "https://github.com/nextstrain/nextclade", - "tool_dev_url": "https://github.com/nextstrain/nextclade", - "licence": [ - "MIT" - ], - "identifier": "biotools:nextclade" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + }, + { + "name": "s4pred_runmodel", + "path": "modules/nf-core/s4pred/runmodel/meta.yml", + "type": "module", + "meta": { + "name": "s4pred_runmodel", + "description": "Prediction of a protein's secondary structure from its amino acid sequence", + "keywords": ["protein", "secondary structure", "prediction"], + "tools": [ + { + "s4pred": { + "description": "Accurate prediction of a protein's secondary structure from its amino acid sequence", + "homepage": "https://github.com/psipred/s4pred", + "documentation": "https://github.com/psipred/s4pred", + "tool_dev_url": "https://github.com/psipred/s4pred", + "doi": "10.1093/bioinformatics/btab491", + "licence": ["GPL v3-or-later"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "protein FASTA file containing one or more amino acid sequences to predict their respective secondary structures", + "pattern": "*.{fasta,fa,fas,fna,faa}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ] + ], + "output": { + "preds": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}": { + "type": "directory", + "description": "A folder with all the prediction outputs", + "pattern": "${prefix}" + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@vagkaratzas"], + "maintainers": ["@vagkaratzas"] }, - 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"ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@rpetit3" - ], - "maintainers": [ - "@rpetit3" - ] - } - }, - { - "name": "ngmerge", - "path": "modules/nf-core/ngmerge/meta.yml", - "type": "module", - "meta": { - "name": "ngmerge", - "description": "Merging paired-end reads and removing sequencing adapters.", - "keywords": [ - "sort", - "reads merging", - "merge mate pairs" - ], - "tools": [ - { - "ngmerge": { - "description": "Merging paired-end reads and removing sequencing adapters.", - "homepage": "https://github.com/jsh58/NGmerge", - "documentation": "https://github.com/jsh58/NGmerge", - "tool_dev_url": "https://github.com/jsh58/NGmerge", - "doi": "10.1186/s12859-018-2579-2", - "licence": [ - "MIT" - ], - "identifier": "" + }, + { + "name": "salsa2", + "path": "modules/nf-core/salsa2/meta.yml", + "type": "module", + "meta": { + "name": "salsa2", + "description": "SALSA, A tool to scaffold long read assemblies with HiC", + "keywords": ["assembly", "hi-c", "scaffolding", "long reads", "salsa", "salsa2"], + "tools": [ + { + "salsa2": { + "description": "Salsa is a tool to scaffold long read assemblies with Hi-C.", + "homepage": "https://github.com/marbl/SALSA", + "documentation": "https://github.com/marbl/SALSA", + "tool_dev_url": "https://github.com/marbl/SALSA", + "doi": "10.1186/s12864-017-3879-z", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Fasta file of assembly. Headers must not contain ':'", + "pattern": "*.{fa, fasta}", + "ontologies": [] + } + }, + { + "index": { + "type": "file", + "description": "Fasta index file of assembly containing the length of contigs.", + "pattern": "*.{fa.fai, fasta.fai}", + "ontologies": [] + } + } + ], + { + "bed": { + "type": "file", + "description": "BED file of alignments sorted by read names, e.g., from HiC-Pro", + "pattern": "*.{bed}", + "ontologies": [] + } + }, + { + "gfa": { + "type": "file", + "description": "GFA file of the assembly graph", + "ontologies": [] + } + }, + { + "dup": { + "type": "file", + "description": "File containing the duplicated contigs", + "ontologies": [] + } + }, + { + "filter_bed": { + "type": "file", + "description": "BED file of the filtered alignments", + "pattern": "*.{bed}", + "ontologies": [] + } + } + ], + "output": { + "fasta": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_scaffolds_FINAL.fasta": { + "type": "file", + "description": "Sequences for the scaffolds generated by the algorithm", + "pattern": "*_scaffolds_FINAL.fasta", + "ontologies": [] + } + } + ] + ], + "agp": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_scaffolds_FINAL.agp": { + "type": "file", + "description": "AGP style output for the scaffolds describing the assignment, orientation and ordering of contigs along the scaffolds", + "pattern": "*_scaffolds_FINAL.agp", + "ontologies": [] + } + } + ] + ], + "agp_original_coordinates": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*/*scaffolds_FINAL.original-coordinates.agp": { + "type": "file", + "description": "Secondary output AGP file with names and coordinates matching the original input assembly (optional)", + "pattern": "*scaffolds_FINAL.original-coordinates.agp", + "ontologies": [] + } + } + ] + ], + "versions_salsa2": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "salsa2": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "2.3": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "salsa2": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "2.3": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@scorreard"], + "maintainers": ["@scorreard"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } + }, + { + "name": "saltshaker_call", + "path": "modules/nf-core/saltshaker/call/meta.yml", + "type": "module", + "meta": { + "name": "saltshaker_call", + "description": "mtDNA deletion and duplication calling downstream of mitosalt", + "keywords": ["saltshaker", "mitosalt", "mtDNA", "structural-variant calling"], + "tools": [ + { + "saltshaker": { + "description": "A Python package for classifying and visualizing mitochondrial structural variants from MitoSAlt pipeline output.", + "homepage": "https://github.com/aksenia/saltshaker", + "documentation": "https://github.com/aksenia/saltshaker/tree/main/saltshaker/docs" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "breakpoint": { + "type": "file", + "description": "breakpoint file from mitosalt", + "pattern": "*.{breakpoint}", + "ontologies": [] + } + }, + { + "cluster": { + "type": "file", + "description": "cluster file from mitosalt", + "pattern": "*.{cluster}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'fasta' ]\n" + } + }, + { + "mtfasta": { + "type": "file", + "description": "Reference mitochondrial genome in FASTA format", + "pattern": "*.{fasta,fa}", + "ontologies": [] + } + } + ], + { + "flank": { + "type": "integer", + "description": "Basepairs flanking a deletion" + } + }, + { + "heteroplasmy_limit": { + "type": "float", + "description": "Minimum heteroplasmy level to report a deletion/duplication" + } + }, + { + "mito_length": { + "type": "integer", + "description": "Length of the mitochondrial genome" + } + }, + { + "heavy_strand_origin_start": { + "type": "integer", + "description": "Start position of the heavy strand origin of replication" + } + }, + { + "heavy_strand_origin_end": { + "type": "integer", + "description": "End position of the heavy strand origin of replication" + } + }, + { + "light_strand_origin_start": { + "type": "integer", + "description": "Start position of the light strand origin of replication" + } + }, + { + "light_strand_origin_end": { + "type": "integer", + "description": "End position of the light strand origin of replication" + } + } + ], + "output": { + "call": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_call_metadata.tsv": { + "type": "file", + "description": "tsv with variant call metadata to be used in saltshaker_classify", + "pattern": "*_call_metadata.tsv", + "ontologies": [] + } + } + ] + ], + "versions_saltshaker": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "saltshaker": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "1.0.0": { + "type": "string", + "description": "Hardcoded version of saltshaker used in the module" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "saltshaker": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "1.0.0": { + "type": "string", + "description": "Hardcoded version of saltshaker used in the module" + } + } + ] + ] + }, + "authors": ["@ieduba"], + "maintainers": ["@ieduba"] }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 2; i.e., paired-end data.\n", - "pattern": "*.{fa,fasta,fastq,fq,fa.gz,fasta.gz,fastq.gz,fq.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "output": { - "merged_reads": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*.merged.fq.gz": { - "type": "file", - "description": "fastq file merged reads", - "pattern": "*.{fa,fasta,fastq,fq,fa.gz,fasta.gz,fastq.gz,fq.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "unstitched_read1": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*_1.fastq.gz": { - "type": "file", - "description": "fastq file unstitched read 1", - "pattern": "*.{fa,fasta,fastq,fq,fa.gz,fasta.gz,fastq.gz,fq.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "unstitched_read2": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*_2.fastq.gz": { - "type": "file", - "description": "fastq file unstitched read 2", - "pattern": "*.{fa,fasta,fastq,fq,fa.gz,fasta.gz,fastq.gz,fq.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } + "pipelines": [ + { + "name": "raredisease", + "version": "3.0.0" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@charlotteanne", - "@jsh58" - ], - "maintainers": [ - "@charlotteanne", - "@jsh58" - ] - } - }, - { - "name": "ngsbits_bedannotategc", - "path": "modules/nf-core/ngsbits/bedannotategc/meta.yml", - "type": "module", - "meta": { - "name": "ngsbits_bedannotategc", - "description": "Annotates GC content fraction to regions in a BED file.", - "keywords": [ - "gc", - "bed", - "regions" - ], - "tools": [ - { - "ngsbits": { - "description": "Short-read sequencing tools", - "homepage": "https://github.com/imgag/ngs-bits", - "documentation": "https://github.com/imgag/ngs-bits", - "tool_dev_url": "https://github.com/imgag/ngs-bits", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "bed": { - "type": "file", - "description": "Input BED file containing regions to annotate", - "pattern": "*.bed", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference fasta information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference FASTA to use", - "pattern": "*.{fasta,fa,fna}", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference fasta information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } + }, + { + "name": "saltshaker_classify", + "path": "modules/nf-core/saltshaker/classify/meta.yml", + "type": "module", + "meta": { + "name": "saltshaker_classify", + "description": "mtDNA deletion and duplication classification downstream of mitosalt", + "keywords": ["saltshaker", "mitosalt", "mtDNA", "structural-variant calling"], + "tools": [ + { + "saltshaker": { + "description": "A Python package for classifying and visualizing mitochondrial structural variants from MitoSAlt pipeline output.", + "homepage": "https://github.com/aksenia/saltshaker", + "documentation": "https://github.com/aksenia/saltshaker/tree/main/saltshaker/docs" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "call": { + "type": "file", + "description": "call metadata file from saltshaker_call", + "pattern": "*_call_metadata.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/operation_3227" + }, + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + { + "mito_name": { + "type": "string", + "description": "Name of the mitochondrial chromosome" + } + } + ], + "output": { + "classify": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_classify_metadata.tsv": { + "type": "file", + "description": "tsv with classified call metadata to be used in saltshaker_plot", + "pattern": "*_classify_metadata.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/operation_3225" + }, + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "txt": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_classify.txt": { + "type": "file", + "description": "txt file with case classification", + "pattern": "*_classify.txt", + "ontologies": [ + { + "edam": "http://edamontology.org/operation_3225" + }, + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + } + ] + ], + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*saltshaker.vcf": { + "type": "file", + "description": "vcf file with classified calls", + "pattern": "*saltshaker.vcf", + "ontologies": [ + { + "edam": "http://edamontology.org/operation_3225" + }, + { + "edam": "http://edamontology.org/format_3016" + } + ] + } + } + ] + ], + "versions_saltshaker": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "saltshaker": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "1.0.1": { + "type": "string", + "description": "Hardcoded version of saltshaker used in the module" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "saltshaker": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "1.0.1": { + "type": "string", + "description": "Hardcoded version of saltshaker used in the module" + } + } + ] + ] + }, + "authors": ["@ieduba"], + "maintainers": ["@ieduba"] }, - { - "fai": { - "type": "file", - "description": "The index file from the reference FASTA", - "pattern": "*.fai", - "ontologies": [] - } - } - ] - ], - "output": { - "output": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.bed": { - "type": "file", - "description": "Annotated BED file with GC content fraction", - "pattern": "*.bed", - "ontologies": [] - } - } + "pipelines": [ + { + "name": "raredisease", + "version": "3.0.0" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@nvnieuwk" - ], - "maintainers": [ - "@nvnieuwk" - ] - } - }, - { - "name": "ngsbits_bedcoverage", - "path": "modules/nf-core/ngsbits/bedcoverage/meta.yml", - "type": "module", - "meta": { - "name": "ngsbits_bedcoverage", - "description": "Annotates a BED file with the average coverage of the regions from one or several BAM/CRAM file(s).", - "keywords": [ - "bed", - "coverage", - "regions" - ], - "tools": [ - { - "ngsbits": { - "description": "Short-read sequencing tools", - "homepage": "https://github.com/imgag/ngs-bits", - "documentation": "https://github.com/imgag/ngs-bits", - "tool_dev_url": "https://github.com/imgag/ngs-bits", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "reads": { - "type": "file", - "description": "Input BAM/CRAM/SAM file(s), can be one file or a list of files", - "pattern": "*.{bam,cram,sam}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_25722" - }, - { - "edam": "http://edamontology.org/format_2573" - }, - { - "edam": "http://edamontology.org/format_3462" - } - ] - } - }, - { - "reads_index": { - "type": "file", - "description": "The index file(s) from the input BAM/CRAM/SAM file(s)", - "pattern": "*.{bai,crai}", - "ontologies": [] - } - }, - { - "bed": { - "type": "file", - "description": "Input BED file containing regions to annotate", - "pattern": "*.bed", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference fasta information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference FASTA to use (mandatory when CRAM files are used, otherwise optional)", - "pattern": "*.{fasta,fa,fna}", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference fasta information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } + }, + { + "name": "saltshaker_plot", + "path": "modules/nf-core/saltshaker/plot/meta.yml", + "type": "module", + "meta": { + "name": "saltshaker_plot", + "description": "mtDNA deletion and duplication plotting downstream of mitosalt", + "keywords": ["saltshaker", "mitosalt", "mtDNA", "structural-variant calling"], + "tools": [ + { + "saltshaker": { + "description": "A Python package for classifying and visualizing mitochondrial structural variants from MitoSAlt pipeline output.", + "homepage": "https://github.com/aksenia/saltshaker", + "documentation": "https://github.com/aksenia/saltshaker/tree/main/saltshaker/docs" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "classify": { + "type": "file", + "description": "classify metadata file from saltshaker_classify", + "pattern": "*_classify_metadata.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/operation_3225" + }, + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "output": { + "plot": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*saltshaker.png": { + "type": "file", + "description": "png file with saltshaker plot", + "pattern": "*saltshaker.png", + "ontologies": [ + { + "edam": "http://edamontology.org/operation_0337" + }, + { + "edam": "http://edamontology.org/format_3603" + } + ] + } + } + ] + ], + "versions_saltshaker": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "saltshaker": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "1.0.0": { + "type": "string", + "description": "Hardcoded version of saltshaker used in the module" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "saltshaker": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "1.0.0": { + "type": "string", + "description": "Hardcoded version of saltshaker used in the module" + } + } + ] + ] + }, + "authors": ["@ieduba"], + "maintainers": ["@ieduba"] }, - { - "fai": { - "type": "file", - "description": "The index file from the reference FASTA", - "pattern": "*.fai", - "ontologies": [] - } - } - ] - ], - "output": { - "bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.bed": { - "type": "file", - "description": "Output BED file with average coverage of the regions", - "pattern": "*.bed", - "ontologies": [] - } - } + "pipelines": [ + { + "name": "raredisease", + "version": "3.0.0" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@nvnieuwk" - ], - "maintainers": [ - "@nvnieuwk" - ] - } - }, - { - "name": "ngsbits_samplegender", - "path": "modules/nf-core/ngsbits/samplegender/meta.yml", - "type": "module", - "meta": { - "name": "ngsbits_samplegender", - "description": "Determines the gender of a sample from the BAM/CRAM file.", - "keywords": [ - "gender", - "cram", - "bam", - "short reads" - ], - "tools": [ - { - "ngsbits": { - "description": "Short-read sequencing tools", - "homepage": "https://github.com/imgag/ngs-bits", - "documentation": "https://github.com/imgag/ngs-bits", - "tool_dev_url": "https://github.com/imgag/ngs-bits", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "One or more BAM/CRAM files to determine the gender of", - "pattern": "*.{bam,cram}", - "ontologies": [] - } - }, - { - "bai": { - "type": "file", - "description": "The index file(s) from the input BAM/CRAM file(s)", - "pattern": "*.{bai,crai}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference fasta information\ne.g. [ id:'test' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference FASTA to use (mandatory when CRAM files are used)", - "pattern": "*.{fasta,fa,fna}", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference fasta information\ne.g. [ id:'test' ]\n" - } + }, + { + "name": "sam2lca_analyze", + "path": "modules/nf-core/sam2lca/analyze/meta.yml", + "type": "module", + "meta": { + "name": "sam2lca_analyze", + "description": "Calling lowest common ancestors from multi-mapped reads in SAM/BAM/CRAM files", + "keywords": ["LCA", "alignment", "bam", "metagenomics", "Ancestor", "multimapper"], + "tools": [ + { + "sam2lca": { + "description": "Lowest Common Ancestor on SAM/BAM/CRAM alignment files", + "homepage": "https://github.com/maxibor/sam2lca", + "documentation": "https://sam2lca.readthedocs.io", + "doi": "10.21105/joss.04360", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}", + "ontologies": [] + } + }, + { + "bai": { + "type": "file", + "description": "BAM/CRAM/SAM index", + "pattern": "*.{bai,.crai}", + "ontologies": [] + } + } + ], + { + "database": { + "type": "file", + "description": "Directory containing the sam2lca database", + "pattern": "*", + "ontologies": [] + } + } + ], + "output": { + "csv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.csv": { + "type": "file", + "description": "CSV file containing the sam2lca results", + "pattern": "*.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "json": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.json": { + "type": "file", + "description": "JSON file containing the sam2lca results", + "pattern": "*.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Optional sorted BAM/CRAM/SAM file annotated with LCA taxonomic information", + "pattern": "*.bam", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@maxibor"], + "maintainers": ["@maxibor"] }, - { - "fai": { - "type": "file", - "description": "The index file from the reference FASTA", - "pattern": "*.fai", - "ontologies": [] - } - } - ], - { - "method": { - "type": "string", - "description": "The method to use to define the gender (possibilities are 'xy', 'hetx' and 'sry')", - "pattern": "(xy|hetx|sry)" - } - } - ], - "output": { - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "An output TSV file containing the results of the gender prediction", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_ngsbits": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "ngsbits": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "SampleGender --version 2>&1 | sed 's/SampleGender //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "ngsbits": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "SampleGender --version 2>&1 | sed 's/SampleGender //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "coproid", + "version": "2.0.1" + } ] - ] - }, - "authors": [ - "@nvnieuwk" - ], - "maintainers": [ - "@nvnieuwk" - ] - }, - "pipelines": [ - { - "name": "raredisease", - "version": "3.0.0" - } - ] - }, - { - "name": "ngsbits_updhunter", - "path": "modules/nf-core/ngsbits/updhunter/meta.yml", - "type": "module", - "meta": { - "name": "ngsbits_updhunter", - "description": "UPD detection from trio variant data.", - "keywords": [ - "upd", - "vcf", - "genomics" - ], - "tools": [ - { - "ngsbits": { - "description": "Short-read sequencing tools", - "homepage": "https://github.com/imgag/ngs-bits", - "documentation": "https://github.com/imgag/ngs-bits", - "tool_dev_url": "https://github.com/imgag/ngs-bits", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "vcf": { - "type": "file", - "description": "vcf file", - "pattern": "*.vcf{,.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - } - ] - } + }, + { + "name": "sambamba_depth", + "path": "modules/nf-core/sambamba/depth/meta.yml", + "type": "module", + "meta": { + "name": "sambamba_depth", + "description": "Outputs a coverage file from bam files", + "keywords": ["depth", "coverage", "sambamba"], + "tools": [ + { + "sambamba": { + "description": "Tools for working with SAM/BAM data", + "homepage": "https://lomereiter.github.io/sambamba/docs/sambamba-view.html", + "documentation": "https://lomereiter.github.io/sambamba/docs/sambamba-view.html", + "tool_dev_url": "https://github.com/biod/sambamba", + "doi": "10.1093/bioinformatics/btv098", + "licence": ["GPL v2"], + "identifier": "biotools:sambamba" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file", + "pattern": "*.{bam}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + }, + { + "bai": { + "type": "file", + "description": "BAI file", + "pattern": "*.{bai}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing regions information\n" + } + }, + { + "bed": { + "type": "file", + "description": "bed file", + "pattern": "*.{bed}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3003" + } + ] + } + } + ], + { + "mode": { + "type": "string", + "description": "Analysis mode can be region, window, base", + "pattern": "region|window|base" + } + } + ], + "output": { + "bed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.bed": { + "type": "file", + "description": "bed file", + "pattern": "*.bed", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3586" + } + ] + } + } + ] + ], + "versions_sambamba": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "sambamba": { + "type": "string", + "description": "The tool name" + } + }, + { + "sambamba --version 2>&1 | grep -oPm1 'sambamba \\\\K[0-9.]+'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "sambamba": { + "type": "string", + "description": "The tool name" + } + }, + { + "sambamba --version 2>&1 | grep -oPm1 'sambamba \\\\K[0-9.]+'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@peterpru"], + "maintainers": ["@peterpru"] }, - { - "bed": { - "type": "file", - "description": "bed file with regions to exclude", - "pattern": "*.bed", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3003" - } - ] - } - } - ] - ], - "output": { - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "TSV file containing the detected UPDs", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "igv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.igv": { - "type": "file", - "description": "IGV file containing informative variants", - "pattern": "*.igv", - "ontologies": [] - } - } + "pipelines": [ + { + "name": "raredisease", + "version": "3.0.0" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@matthdsm" - ], - "maintainers": [ - "@matthdsm" - ] - } - }, - { - "name": "ngscheckmate_fastq", - "path": "modules/nf-core/ngscheckmate/fastq/meta.yml", - "type": "module", - "meta": { - "name": "ngscheckmate_fastq", - "description": "Determining whether sequencing data comes from the same individual by using SNP matching. This module generates vaf files for individual fastq file(s), ready for the vafncm module.", - "keywords": [ - "ngscheckmate", - "matching", - "snp", - "qc" - ], - "tools": [ - { - "ngscheckmate": { - "description": "NGSCheckMate is a software package for identifying next generation sequencing (NGS) data files from the same individual, including matching between DNA and RNA.", - "homepage": "https://github.com/parklab/NGSCheckMate", - "documentation": "https://github.com/parklab/NGSCheckMate", - "tool_dev_url": "https://github.com/parklab/NGSCheckMate", - "doi": "10.1093/nar/gkx193", - "licence": [ - "MIT" - ], - "identifier": "biotools:ngscheckmate" + }, + { + "name": "sambamba_flagstat", + "path": "modules/nf-core/sambamba/flagstat/meta.yml", + "type": "module", + "meta": { + "name": "sambamba_flagstat", + "description": "Outputs some statistics drawn from read flags.", + "keywords": ["stats", "flagstat", "sambamba"], + "tools": [ + { + "sambamba": { + "description": "Tools for working with SAM/BAM data", + "homepage": "https://lomereiter.github.io/sambamba/docs/sambamba-view.html", + "documentation": "https://lomereiter.github.io/sambamba/docs/sambamba-view.html", + "tool_dev_url": "https://github.com/biod/sambamba", + "licence": ["GPL v2"], + "identifier": "biotools:sambamba" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file", + "pattern": "*.{bam}", + "ontologies": [] + } + } + ] + ], + "output": { + "stats": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.stats": { + "type": "file", + "description": "Stats file", + "pattern": "*.{stats}", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@kubranarci"], + "maintainers": ["@kubranarci"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information about the fastq files\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "reads": { - "type": "file", - "description": "Raw fastq files for one sample, single or paired end.", - "pattern": "*.{fastq.gz}", - "ontologies": [] - } + }, + { + "name": "sambamba_markdup", + "path": "modules/nf-core/sambamba/markdup/meta.yml", + "type": "module", + "meta": { + "name": "sambamba_markdup", + "description": "find and mark duplicate reads in BAM file", + "keywords": ["markduplicates", "duplicates", "bam"], + "tools": [ + { + "sambamba": { + "description": "process your BAM data faster!", + "homepage": "https://lomereiter.github.io/sambamba/docs/sambamba-view.html", + "documentation": "https://lomereiter.github.io/sambamba/docs/sambamba-view.html", + "tool_dev_url": "https://github.com/biod/sambamba", + "licence": ["GPL v2"], + "identifier": "biotools:sambamba" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}", + "ontologies": [] + } + } + ] + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Sorted BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}", + "ontologies": [] + } + } + ] + ], + "bai": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bai": { + "type": "file", + "description": "An optional BAM index file.", + "pattern": "*.{bai}", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@BioInf2305"], + "maintainers": ["@BioInf2305"] } - ], - [ - { - "meta2": { - "type": "file", - "description": "Groovy Map containing sample information about the NGSCheckMate SNP pt file\ne.g. `[ id:'test', single_end:false ]`\n", - "ontologies": [] - } - }, - { - "snp_pt": { - "type": "file", - "description": "PT file containing SNP data, generated by ngscheckmate/patterngenerator. For human data, use the files from NGSCheckMate's github repository.", - "pattern": "*.{pt}", - "ontologies": [] - } - } - ] - ], - "output": { - "vaf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*.vaf": { - "type": "file", - "description": "Text file containing reference/alt allele depth for each SNP position contained in the PT file.", - "pattern": "*.{vaf}", - "ontologies": [] - } - } - ] - ], - "versions_ngscheckmate": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "ngscheckmate": { - "type": "string", - "description": "The tool name" - } - }, - { - "ncm.py --help | sed '7!d;s/.* v//g'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "ngscheckmate": { - "type": "string", - "description": "The tool name" - } - }, - { - "ncm.py --help | sed '7!d;s/.* v//g'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@sppearce" - ], - "maintainers": [ - "@sppearce" - ] - } - }, - { - "name": "ngscheckmate_ncm", - "path": "modules/nf-core/ngscheckmate/ncm/meta.yml", - "type": "module", - "meta": { - "name": "ngscheckmate_ncm", - "description": "Determining whether sequencing data comes from the same individual by using SNP matching. Designed for humans on vcf or bam files.", - "keywords": [ - "ngscheckmate", - "matching", - "snp" - ], - "tools": [ - { - "ngscheckmate": { - "description": "NGSCheckMate is a software package for identifying next generation sequencing (NGS) data files from the same individual, including matching between DNA and RNA.", - "homepage": "https://github.com/parklab/NGSCheckMate", - "documentation": "https://github.com/parklab/NGSCheckMate", - "tool_dev_url": "https://github.com/parklab/NGSCheckMate", - "doi": "10.1093/nar/gkx193", - "licence": [ - "MIT" - ], - "identifier": "biotools:ngscheckmate" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "files": { - "type": "file", - "description": "VCF or BAM files for each sample, in a merged channel (possibly gzipped). BAM files require an index too.", - "pattern": "*.{vcf,vcf.gz,bam,bai}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing SNP information\ne.g. [ id:'test' ]\n" - } - }, - { - "snp_bed": { - "type": "file", - "description": "BED file containing the SNPs to analyse", - "pattern": "*.{bed}", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference fasta index information\ne.g. [ id:'test' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "fasta file for the genome, only used in the bam mode", - "pattern": "*.{fasta}", - "ontologies": [] - } - }, - { - "fai": { - "type": "file", - "description": "fasta index file for the genome, only used in the bam mode", - "pattern": "*.{fai}", - "ontologies": [] - } - } - ] - ], - "output": { - "corr_matrix": [ - [ - { - "meta": { - "type": "file", - "description": "A text file containing the correlation matrix between each sample", - "pattern": "*corr_matrix.txt", - "ontologies": [] - } - }, - { - "*_corr_matrix.txt": { - "type": "file", - "description": "A text file containing the correlation matrix between each sample", - "pattern": "*corr_matrix.txt", - "ontologies": [] - } - } - ] - ], - "matched": [ - [ - { - "meta": { - "type": "file", - "description": "A text file containing the correlation matrix between each sample", - "pattern": "*corr_matrix.txt", - "ontologies": [] - } - }, - { - "*_matched.txt": { - "type": "file", - "description": "A txt file containing only the samples that match with each other", - "pattern": "*matched.txt", - "ontologies": [] - } - } - ] - ], - "all": [ - [ - { - "meta": { - "type": "file", - "description": "A text file containing the correlation matrix between each sample", - "pattern": "*corr_matrix.txt", - "ontologies": [] - } - }, - { - "*_all.txt": { - "type": "file", - "description": "A txt file containing all the sample comparisons, whether they match or not", - "pattern": "*all.txt", - "ontologies": [] - } - } - ] - ], - "pdf": [ - [ - { - "meta": { - "type": "file", - "description": "A text file containing the correlation matrix between each sample", - "pattern": "*corr_matrix.txt", - "ontologies": [] - } - }, - { - "*.pdf": { - "type": "file", - "description": "A pdf containing a dendrogram showing how the samples match up", - "pattern": "*.{pdf}", - "ontologies": [] - } - } - ] - ], - "vcf": [ - [ - { - "meta": { - "type": "file", - "description": "A text file containing the correlation matrix between each sample", - "pattern": "*corr_matrix.txt", - "ontologies": [] - } - }, - { - "*.vcf": { - "type": "file", - "description": "If ran in bam mode, vcf files for each sample giving the SNP calls used", - "pattern": "*.vcf", - "ontologies": [] - } - } - ] - ], - "versions_ngscheckmate": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "ngscheckmate": { - "type": "string", - "description": "The tool name" - } - }, - { - "ncm.py --help | sed '7!d;s/.* v//g'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "ngscheckmate": { - "type": "string", - "description": "The tool name" - } - }, - { - "ncm.py --help | sed '7!d;s/.* v//g'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@sppearce" - ], - "maintainers": [ - "@sppearce" - ] - }, - "pipelines": [ - { - "name": "sarek", - "version": "3.8.1" - } - ] - }, - { - "name": "ngscheckmate_patterngenerator", - "path": "modules/nf-core/ngscheckmate/patterngenerator/meta.yml", - "type": "module", - "meta": { - "name": "ngscheckmate_patterngenerator", - "description": "Determining whether sequencing data comes from the same individual by using SNP matching. This module generates PT files from a bed file containing individual positions.", - "keywords": [ - "ngscheckmate", - "matching", - "snp", - "qc" - ], - "tools": [ - { - "ngscheckmate": { - "description": "NGSCheckMate is a software package for identifying next generation sequencing (NGS) data files from the same individual, including matching between DNA and RNA.", - "homepage": "https://github.com/parklab/NGSCheckMate", - "documentation": "https://github.com/parklab/NGSCheckMate", - "tool_dev_url": "https://github.com/parklab/NGSCheckMate", - "doi": "10.1093/nar/gkx193", - "licence": [ - "MIT" - ], - "identifier": "biotools:ngscheckmate" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information about the bed file\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "bed": { - "type": "file", - "description": "BED file containing population-level SNPs to use", - "pattern": "*.bed", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information about the fasta genome\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Genome fasta file", - "pattern": "*.fasta", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } + }, + { + "name": "samblaster", + "path": "modules/nf-core/samblaster/meta.yml", + "type": "module", + "meta": { + "name": "samblaster", + "description": "This module combines samtools and samblaster in order to use\nsamblaster capability to filter or tag SAM files, with the advantage\nof maintaining both input and output in BAM format.\nSamblaster input must contain a sequence header: for this reason it has been piped\nwith the \"samtools view -h\" command.\nAdditional desired arguments for samtools can be passed using:\noptions.args2 for the input bam file\noptions.args3 for the output bam file\n", + "keywords": ["sort", "duplicate marking", "bam"], + "tools": [ + { + "samblaster": { + "description": "samblaster is a fast and flexible program for marking duplicates in read-id grouped paired-end SAM files.\nIt can also optionally output discordant read pairs and/or split read mappings to separate SAM files,\nand/or unmapped/clipped reads to a separate FASTQ file.\nBy default, samblaster reads SAM input from stdin and writes SAM to stdout.\n", + "documentation": "https://github.com/GregoryFaust/samblaster", + "tool_dev_url": "https://github.com/GregoryFaust/samblaster", + "doi": "10.1093/bioinformatics/btu314", + "licence": ["MIT"], + "identifier": "biotools:samblaster" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file", + "pattern": "*.bam", + "ontologies": [] + } + } + ] + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Tagged or filtered BAM file", + "pattern": "*.bam", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@lescai"], + "maintainers": ["@lescai", "@gallvp"] }, - { - "bowtie_index": { - "type": "directory", - "description": "Folder of Bowtie genome index files" - } - } - ] - ], - "output": { - "pt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*.pt": { - "type": "file", - "description": "Generated binary pattern file, containing FASTQ strings to match from within raw data", - "pattern": "*.pt", - "ontologies": [] - } - } - ] - ], - "versions_ngscheckmate": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "ngscheckmate": { - "type": "string", - "description": "The tool name" - } - }, - { - "ncm.py --help | sed '7!d;s/.* v//g'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "ngscheckmate": { - "type": "string", - "description": "The tool name" - } - }, - { - "ncm.py --help | sed '7!d;s/.* v//g'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } + "pipelines": [ + { + "name": "rnadnavar", + "version": "dev" + } ] - ] - }, - "authors": [ - "@sppearce" - ], - "maintainers": [ - "@sppearce" - ] - } - }, - { - "name": "ngscheckmate_vafncm", - "path": "modules/nf-core/ngscheckmate/vafncm/meta.yml", - "type": "module", - "meta": { - "name": "ngscheckmate_vafncm", - "description": "Determining whether sequencing data comes from the same individual by using SNP matching. This module generates PT files from a bed file containing individual positions.", - "keywords": [ - "ngscheckmate", - "matching", - "snp", - "qc" - ], - "tools": [ - { - "ngscheckmate": { - "description": "NGSCheckMate is a software package for identifying next generation sequencing (NGS) data files from the same individual, including matching between DNA and RNA.", - "homepage": "https://github.com/parklab/NGSCheckMate", - "documentation": "https://github.com/parklab/NGSCheckMate", - "tool_dev_url": "https://github.com/parklab/NGSCheckMate", - "doi": "10.1093/nar/gkx193", - "licence": [ - "MIT" - ], - "identifier": "biotools:ngscheckmate" + }, + { + "name": "samclip", + "path": "modules/nf-core/samclip/meta.yml", + "type": "module", + "meta": { + "name": "samclip", + "description": "Filters SAM/BAM/CRAM files for soft and hard clipped alignments", + "keywords": ["soft-clipped reads", "hard-clipped reads", "clipping", "genomics", "sam", "bam", "cram"], + "tools": [ + { + "samclip": { + "description": "Filters SAM file for soft and hard clipped alignments", + "homepage": "https://github.com/tseemann/samclip", + "documentation": "https://github.com/tseemann/samclip", + "tool_dev_url": "https://github.com/tseemann/samclip", + "doi": "no DOI available", + "licence": ["GPL v3"], + "identifier": "biotools:samclip" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file", + "pattern": "*.bam", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing fasta reference information\ne.g. `[ id:'ref' ]`\n" + } + }, + { + "reference": { + "type": "file", + "description": "reference FASTA file\n", + "pattern": "*.{fasta,fa,fasta.gz,fa.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + }, + { + "reference_index": { + "type": "file", + "description": "reference FASTA file index\n", + "pattern": "*.fai", + "ontologies": [] + } + } + ] + ], + "output": { + "reads": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information. e.g. `[ id:'sample1']`" + } + }, + { + "*.{bam,cram}": { + "type": "file", + "description": "Filtered BAM/CRAM file", + "pattern": "*.{bam,cram}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + }, + { + "edam": "http://edamontology.org/format_3462" + } + ] + } + } + ] + ], + "versions_samclip": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "samclip": { + "type": "string", + "description": "The tool name" + } + }, + { + "samclip --version | sed 's/^.*samclip //g'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ], + "versions_samtools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "samtools": { + "type": "string", + "description": "The tool name" + } + }, + { + "samtools version | sed '1!d;s/.* //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "samclip": { + "type": "string", + "description": "The tool name" + } + }, + { + "samclip --version | sed 's/^.*samclip //g'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "samtools": { + "type": "string", + "description": "The tool name" + } + }, + { + "samtools version | sed '1!d;s/.* //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@emmcauley"], + "maintainers": ["@emmcauley"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information about the combined set of files\ne.g. `[ id:'combined' ]`\n" - } - }, - { - "vafs": { - "type": "file", - "description": "Text files containing information about reference/alternate allele depths for the SNP positions, generated by ngscheckmate/fastq", - "pattern": "*.{vaf}", - "ontologies": [] - } + }, + { + "name": "samplesheetparser_info", + "path": "modules/nf-core/samplesheetparser/info/meta.yml", + "type": "module", + "meta": { + "name": "samplesheetparser_info", + "description": "Display a structured JSON summary of an Illumina SampleSheet.csv (V1 or V2)\nincluding format version, sample count, lanes, index type, read lengths,\nadapter sequences, experiment name, and instrument platform.\nUseful for logging run metadata or conditional branching in pipelines.\n", + "keywords": ["illumina", "samplesheet", "metadata", "bclconvert", "bcl2fastq", "genomics"], + "tools": [ + { + "samplesheet-parser": { + "description": "Format-agnostic parser for Illumina SampleSheet.csv files.\nSupports IEM V1 (bcl2fastq) and BCLConvert V2 with auto-detection,\nbidirectional conversion, index validation, and Hamming distance checking.\n", + "homepage": "https://github.com/chaitanyakasaraneni/samplesheet-parser", + "documentation": "https://illumina-samplesheet.readthedocs.io", + "tool_dev_url": "https://github.com/chaitanyakasaraneni/samplesheet-parser", + "doi": "10.5281/zenodo.18989694", + "licence": ["Apache-2.0"], + "identifier": "biotools:samplesheet-parser" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information.\nUse [ id:'run_id' ] to identify the sheet.\n" + } + }, + { + "samplesheet": { + "type": "file", + "description": "Illumina SampleSheet.csv (V1 or V2 format, auto-detected)", + "pattern": "*.{csv,CSV}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "output": { + "json": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.info.json": { + "type": "file", + "description": "JSON summary with file, format, sample_count, lanes, index_type,\nread_lengths, adapters, experiment_name, and instrument fields.\n", + "pattern": "*.info.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "versions_samplesheetparser": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "samplesheet-parser": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "samplesheet --version | sed 's/samplesheet-parser //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "samplesheet-parser": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "samplesheet --version | sed 's/samplesheet-parser //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@chaitanyakasaraneni"], + "maintainers": ["@chaitanyakasaraneni"] } - ] - ], - "output": { - "pdf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information about the combined set of files\ne.g. `[ id:'combined' ]`\n" - } - }, - { - "*.pdf": { - "type": "file", - "description": "A pdf containing a dendrogram showing how the samples match up.| Note due to a bug in the R script used by the tool this is not produced when only two samples are given.", - "pattern": "*.{pdf}", - "ontologies": [] - } - } - ] - ], - "corr_matrix": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information about the combined set of files\ne.g. `[ id:'combined' ]`\n" - } - }, - { - "*_corr_matrix.txt": { - "type": "file", - "description": "A text file containing the correlation matrix between each sample", - "pattern": "*corr_matrix.txt", - "ontologies": [] - } - } - ] - ], - "all": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information about the combined set of files\ne.g. `[ id:'combined' ]`\n" - } - }, - { - "*_all.txt": { - "type": "file", - "description": "A txt file containing all the sample comparisons, whether they match or not", - "pattern": "*all.txt", - "ontologies": [] - } - } - ] - ], - "matched": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information about the combined set of files\ne.g. `[ id:'combined' ]`\n" - } - }, - { - "*_matched.txt": { - "type": "file", - "description": "A txt file containing only the samples that match with each other", - "pattern": "*matched.txt", - "ontologies": [] - } - } - ] - ], - "versions_ngscheckmate": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "ngscheckmate": { - "type": "string", - "description": "The tool name" - } - }, - { - "ncm.py --help | sed '7!d;s/.* v//g'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "ngscheckmate": { - "type": "string", - "description": "The tool name" - } - }, - { - "ncm.py --help | sed '7!d;s/.* v//g'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@sppearce" - ], - "maintainers": [ - "@sppearce" - ] - } - }, - { - "name": "nonpareil_curve", - "path": "modules/nf-core/nonpareil/curve/meta.yml", - "type": "module", - "meta": { - "name": "nonpareil_curve", - "description": "Visualise metagenome redundancy curve in PNG format from a single Nonpareil npo file", - "keywords": [ - "metagenomics", - "statistics", - "coverage", - "complexity", - "redundancy", - "diversity", - "visualisation" - ], - "tools": [ - { - "nonpareil": { - "description": "Estimate average coverage and create curves for metagenomic datasets", - "homepage": "https://github.com/lmrodriguezr/nonpareil", - "documentation": "https://nonpareil.readthedocs.io/en/latest/", - "tool_dev_url": "https://github.com/lmrodriguezr/nonpareil", - "doi": "10.1128/msystems.00039-", - "licence": [ - "Artistic License 2.0" - ], - "identifier": "biotools:nonpareil" + }, + { + "name": "samplesheetparser_validate", + "path": "modules/nf-core/samplesheetparser/validate/meta.yml", + "type": "module", + "meta": { + "name": "samplesheetparser_validate", + "description": "Validate an Illumina SampleSheet.csv (V1 or V2) for index, adapter, and\nstructural issues. Format is auto-detected. Exits 0 if valid, 1 if errors\nare found — causing the pipeline to fail early with a clear message rather\nthan discovering demultiplexing problems downstream.\n", + "keywords": [ + "illumina", + "samplesheet", + "validation", + "demultiplexing", + "bclconvert", + "bcl2fastq", + "genomics" + ], + "tools": [ + { + "samplesheet-parser": { + "description": "Format-agnostic parser for Illumina SampleSheet.csv files.\nSupports IEM V1 (bcl2fastq) and BCLConvert V2 with auto-detection,\nbidirectional conversion, index validation, and Hamming distance checking.\n", + "homepage": "https://github.com/chaitanyakasaraneni/samplesheet-parser", + "documentation": "https://illumina-samplesheet.readthedocs.io", + "tool_dev_url": "https://github.com/chaitanyakasaraneni/samplesheet-parser", + "doi": "10.5281/zenodo.18989694", + "licence": ["Apache-2.0"], + "identifier": "biotools:samplesheet-parser" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information.\nUse [ id:'run_id' ] to identify the sheet.\n" + } + }, + { + "samplesheet": { + "type": "file", + "description": "Illumina SampleSheet.csv (V1 or V2 format)", + "pattern": "*.{csv,CSV}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "output": { + "json": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.validation.json": { + "type": "file", + "description": "Structured JSON validation report with is_valid, errors, warnings,\nand min_hamming_distance fields.\n", + "pattern": "*.validation.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "versions_samplesheetparser": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "samplesheet-parser": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "samplesheet --version | sed 's/samplesheet-parser //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "samplesheet-parser": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "samplesheet --version | sed 's/samplesheet-parser //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@chaitanyakasaraneni"], + "maintainers": ["@chaitanyakasaraneni"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } + }, + { + "name": "samshee", + "path": "modules/nf-core/samshee/meta.yml", + "type": "module", + "meta": { + "name": "samshee", + "description": "Module to validate illumina® Sample Sheet v2 files.", + "keywords": ["samplesheet", "illumina", "bclconvert", "bcl2fastq"], + "tools": [ + { + "samshee": { + "description": "A schema-agnostic parser and writer for illumina® sample sheets v2 and similar documents.", + "homepage": "https://github.com/lit-regensburg/samshee", + "documentation": "https://github.com/lit-regensburg/samshee/blob/main/README.md", + "tool_dev_url": "https://github.com/lit-regensburg/samshee", + "licence": ["MIT license"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', lane:1 ]\n" + } + }, + { + "samplesheet": { + "type": "file", + "description": "illumina v2 samplesheet", + "pattern": "*.{csv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ], + { + "file_schema_validator": { + "type": "string", + "description": "Optional JSON file used additional samplesheet validation settings" + } + } + ], + "output": { + "samplesheet": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', lane:1 ]\n" + } + }, + { + "*_formatted.csv": { + "type": "file", + "description": "illumina v2 samplesheet", + "ontologies": [] + } + } + ] + ], + "versions_samshee": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "samshee": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "0.2.13": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_python": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "python": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python --version | sed -e \"s/Python //g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "samshee": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "0.2.13": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "python": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python --version | sed -e \"s/Python //g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@nschcolnicov"], + "maintainers": ["@nschcolnicov"] }, - { - "npo": { - "type": "file", - "description": "Single npo redundancy summary file from nonpareil itself", - "pattern": "*.npo", - "ontologies": [] - } - } - ] - ], - "output": { - "png": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*.png": { - "type": "file", - "description": "PNG file of the Nonpareil curve", - "pattern": "*.png", - "ontologies": [] - } - } + "pipelines": [ + { + "name": "demultiplex", + "version": "1.7.1" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } + }, + { + "name": "samtools_addreplacerg", + "path": "modules/nf-core/samtools/addreplacerg/meta.yml", + "type": "module", + "meta": { + "name": "samtools_addreplacerg", + "description": "Adds or replaces read group (RG) tags in BAM/CRAM/SAM files", + "keywords": ["addreplacerg", "bam", "sam", "cram"], + "tools": [ + { + "samtools": { + "description": "Tools for dealing with SAM, BAM and CRAM files", + "homepage": "http://www.htslib.org", + "documentation": "https://www.htslib.org/doc/samtools-addreplacerg.html", + "tool_dev_url": "https://github.com/samtools/samtools", + "doi": "10.1093/bioinformatics/btp352", + "licence": ["MIT"], + "identifier": "biotools:samtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}", + "ontologies": [] + } + }, + { + "index": { + "type": "file", + "description": "BAM/CRAM/SAM index file", + "pattern": "*.{bai,csi,crai}", + "ontologies": [] + } + }, + { + "read_group": { + "type": "string", + "description": "Read group line to add or replace", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference file the CRAM was created with (optional)", + "pattern": "*.{fasta,fa}", + "ontologies": [] + } + }, + { + "fai": { + "type": "file", + "description": "Index of the reference file the CRAM was created with (optional)", + "pattern": "*.fai", + "ontologies": [] + } + }, + { + "gzi": { + "type": "file", + "description": "Index of the compressed reference file the CRAM was created with (optional)", + "pattern": "*.gzi", + "ontologies": [] + } + } + ] + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.bam": { + "type": "file", + "description": "BAM file with updated RG tags", + "pattern": "${prefix}.bam", + "ontologies": [] + } + } + ] + ], + "cram": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.cram": { + "type": "file", + "description": "CRAM file with updated RG tags", + "pattern": "${prefix}.cram", + "ontologies": [] + } + } + ] + ], + "sam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.sam": { + "type": "file", + "description": "SAM file with updated RG tags", + "pattern": "${prefix}.sam", + "ontologies": [] + } + } + ] + ], + "bai": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.bam.bai": { + "type": "file", + "description": "BAM index file", + "pattern": "${prefix}.bam.bai", + "ontologies": [] + } + } + ] + ], + "csi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.bam.csi": { + "type": "file", + "description": "BAM CSI index file", + "pattern": "${prefix}.bam.csi", + "ontologies": [] + } + } + ] + ], + "crai": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.cram.crai": { + "type": "file", + "description": "CRAM index file", + "pattern": "${prefix}.cram.crai", + "ontologies": [] + } + } + ] + ], + "versions_samtools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "samtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "samtools version | sed '1!d;s/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "samtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "samtools version | sed '1!d;s/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@sainsachiko"], + "maintainers": ["@sainsachiko"] } - ] - }, - "authors": [ - "@jfy133" - ], - "maintainers": [ - "@jfy133" - ] - }, - "pipelines": [ - { - "name": "taxprofiler", - "version": "2.0.0" - } - ] - }, - { - "name": "nonpareil_nonpareil", - "path": "modules/nf-core/nonpareil/nonpareil/meta.yml", - "type": "module", - "meta": { - "name": "nonpareil_nonpareil", - "description": "Calculate metagenome redundancy curve from FASTQ files", - "keywords": [ - "metagenomics", - "statistics", - "coverage", - "redundancy", - "diversity", - "complexity" - ], - "tools": [ - { - "nonpareil": { - "description": "Estimate average coverage and create curves for metagenomic datasets", - "homepage": "https://github.com/lmrodriguezr/nonpareil", - "documentation": "https://nonpareil.readthedocs.io/en/latest/", - "tool_dev_url": "https://github.com/lmrodriguezr/nonpareil", - "doi": "10.1128/msystems.00039-", - "licence": [ - "Artistic License 2.0" - ], - "identifier": "biotools:nonpareil" + }, + { + "name": "samtools_ampliconclip", + "path": "modules/nf-core/samtools/ampliconclip/meta.yml", + "type": "module", + "meta": { + "name": "samtools_ampliconclip", + "description": "Clips read alignments where they match BED file defined regions", + "keywords": ["amplicon", "clipping", "ampliconclip", "samtools"], + "tools": [ + { + "samtools": { + "description": "SAMtools is a set of utilities for interacting with and post-processing\nshort DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.\nThese files are generated as output by short read aligners like BWA.\n", + "homepage": "http://www.htslib.org/", + "documentation": "http://www.htslib.org/doc/samtools.html", + "doi": "10.1093/bioinformatics/btp352", + "licence": ["MIT"], + "identifier": "biotools:samtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}", + "ontologies": [] + } + } + ], + { + "bed": { + "type": "file", + "description": "BED file of regions to be removed (e.g. amplicon primers)", + "pattern": "*.{bed}", + "ontologies": [] + } + }, + { + "save_cliprejects": { + "type": "boolean", + "description": "Save filtered reads to a file" + } + }, + { + "save_clipstats": { + "type": "boolean", + "description": "Save clipping stats to a file" + } + } + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.clipallowed.bam": { + "type": "file", + "description": "Clipped reads BAM file", + "pattern": "*.{bam}", + "ontologies": [] + } + } + ] + ], + "stats": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.clipstats.txt": { + "type": "file", + "description": "Clipping statistics text file", + "pattern": "*.{clipstats.txt}", + "ontologies": [] + } + } + ] + ], + "rejects_bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.cliprejects.bam": { + "type": "file", + "description": "Filtered reads BAM file", + "pattern": "*.{cliprejects.bam}", + "ontologies": [] + } + } + ] + ], + "versions_samtools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "samtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "samtools version | sed '1!d;s/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "samtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "samtools version | sed '1!d;s/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@bjohnnyd"], + "maintainers": ["@bjohnnyd", "@matthdsm"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } + }, + { + "name": "samtools_bam2fq", + "path": "modules/nf-core/samtools/bam2fq/meta.yml", + "type": "module", + "meta": { + "name": "samtools_bam2fq", + "description": "The module uses bam2fq method from samtools to\nconvert a SAM, BAM or CRAM file to FASTQ format\n", + "keywords": ["bam2fq", "samtools", "fastq"], + "tools": [ + { + "samtools": { + "description": "Tools for dealing with SAM, BAM and CRAM files", + "documentation": "http://www.htslib.org/doc/1.1/samtools.html", + "licence": ["MIT"], + "identifier": "biotools:samtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "inputbam": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}", + "ontologies": [] + } + } + ], + { + "split": { + "type": "boolean", + "description": "TRUE/FALSE value to indicate if reads should be separated into\n/1, /2 and if present other, or singleton.\nNote: choosing TRUE will generate 4 different files.\nChoosing FALSE will produce a single file, which will be interleaved in case\nthe input contains paired reads.\n" + } + } + ], + "output": { + "reads": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fq.gz": { + "type": "file", + "description": "FASTQ files, which will be either a group of 4 files (read_1, read_2, other and singleton)\nor a single interleaved .fq.gz file if the user chooses not to split the reads.\n", + "pattern": "*.fq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "versions_samtools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "samtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "samtools version | sed '1!d;s/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "samtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "samtools version | sed '1!d;s/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@lescai"], + "maintainers": ["@lescai", "@matthdsm"] }, - { - "reads": { - "type": "file", - "description": "FASTQ or FASTA file (ideally uncompressed, but not required)", - "pattern": "*.{fasta,fna,fas,fa,fastq,fq,fasta.gz,fna.gz,fas.gz,fa.gz,fastq.gz,fq.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ], - { - "format": { - "type": "string", - "description": "File format of input file", - "pattern": "fasta|fastq" - } - }, - { - "mode": { - "type": "string", - "description": "Mode of redundancy estimation", - "pattern": "kmer|alignment" - } - } - ], - "output": { - "npa": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*.npa": { - "type": "file", - "description": "Raw redundancy values", - "pattern": "*.npa", - "ontologies": [] - } - } - ] - ], - "npc": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*.npc": { - "type": "file", - "description": "Mates distribution file", - "pattern": "*.npc", - "ontologies": [] - } - } - ] - ], - "npl": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*.npl": { - "type": "file", - "description": "Log file", - "pattern": "*.npl", - "ontologies": [] - } - } - ] - ], - "npo": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*.npo": { - "type": "file", - "description": "Redundancy summary file", - "pattern": "*.npo", - "ontologies": [] - } - } + "pipelines": [ + { + "name": "rnadnavar", + "version": "dev" + }, + { + "name": "sarek", + "version": "3.8.1" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@jfy133" - ], - "maintainers": [ - "@jfy133" - ] - }, - "pipelines": [ - { - "name": "taxprofiler", - "version": "2.0.0" - } - ] - }, - { - "name": "nonpareil_nonpareilcurvesr", - "path": "modules/nf-core/nonpareil/nonpareilcurvesr/meta.yml", - "type": "module", - "meta": { - "name": "nonpareil_nonpareilcurvesr", - "description": "Generate summary reports with raw data for Nonpareil NPO curves, including MultiQC compatible JSON/TSV files", - "keywords": [ - "metagenomics", - "statistics", - "coverage", - "redundancy", - "diversity", - "complexity", - "multiqc" - ], - "tools": [ - { - "nonpareil": { - "description": "Estimate average coverage and create curves for metagenomic datasets", - "homepage": "https://github.com/lmrodriguezr/nonpareil", - "documentation": "https://nonpareil.readthedocs.io/en/latest/", - "tool_dev_url": "https://github.com/lmrodriguezr/nonpareil", - "doi": "10.1128/msystems.00039-", - "licence": [ - "Artistic License 2.0" - ], - "identifier": "biotools:nonpareil" + }, + { + "name": "samtools_bedcov", + "path": "modules/nf-core/samtools/bedcov/meta.yml", + "type": "module", + "meta": { + "name": "samtools_bedcov", + "description": "reports coverage over regions in a supplied BED file", + "keywords": ["bedcov", "samtools", "coverage", "bed", "bam", "cram", "sam", "regions"], + "tools": [ + { + "samtools": { + "description": "Tools for dealing with SAM, BAM and CRAM files", + "homepage": "http://www.htslib.org/", + "documentation": "http://www.htslib.org/doc/samtools-bedcov.html", + "tool_dev_url": "https://github.com/samtools/samtools", + "doi": "10.1093/bioinformatics/btp352", + "licence": ["MIT"], + "identifier": "biotools:samtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "input": { + "type": "file", + "description": "Sorted BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2573" + }, + { + "edam": "http://edamontology.org/format_2572" + }, + { + "edam": "http://edamontology.org/format_3462" + } + ] + } + }, + { + "input_index": { + "type": "file", + "description": "BAM/CRAM index file", + "pattern": "*.{bai,crai}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3327" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'bed']`\n" + } + }, + { + "bed": { + "type": "file", + "description": "Interval BED file", + "pattern": "*.bed", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3003" + } + ] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference genome file", + "pattern": "*.{fa,fasta}", + "ontologies": [] + } + }, + { + "fasta_index": { + "type": "file", + "description": "Reference genome index file", + "pattern": "*.fai", + "ontologies": [] + } + } + ] + ], + "output": { + "coverage": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "Reports the total read base count (i.e. the sum of per base read depths)\nfor each genomic region specified in the supplied BED file.\nThe regions are output as they appear in the BED file and are 0-based.\nColumns 1-3 are chrom/start/end as per the input BED file, followed by N columns of coverages (for N input BAMs),\nthen (if given -d), N columns of bases-at-depth-X, 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+ } + }, + { + "samtools version | sed '1!d;s/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "samtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "samtools version | sed '1!d;s/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@limrp"] } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'Cladonia_norvegica' ]\n" - } + }, + { + "name": "samtools_depth", + "path": "modules/nf-core/samtools/depth/meta.yml", + "type": "module", + "meta": { + "name": "samtools_depth", + "description": "Computes the depth at each position or region.", + "keywords": ["depth", "samtools", "statistics", "coverage"], + "tools": [ + { + "samtools": { + "description": "Tools for dealing with SAM, BAM and CRAM files; samtools depth – computes the read depth at each position or region", + "homepage": "http://www.htslib.org", + "documentation": "http://www.htslib.org/doc/samtools-depth.html", + "tool_dev_url": "https://github.com/samtools/samtools", + "doi": "10.1093/bioinformatics/btp352", + "licence": ["MIT"], + "identifier": "biotools:samtools" + } + } + ], + "input": [ + [ + { + "meta1": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "sorted BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}", + "ontologies": [] + } + }, + { + "index": { + "type": "file", + "description": "BAM/CRAM index file", + "pattern": "*.{bai,crai}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, 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obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "samtools": { + "type": "string", + "description": "The tool name" + } + }, + { + "samtools version | sed \"1!d;s/.* //\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@louperelo", "@nevinwu"], + "maintainers": ["@louperelo", "@nevinwu", "@matthdsm"] }, - { - "pltd_hmm_files": { - "type": "file", - "description": "HMM profile for plastid gene annotation, with corresponding\n.h3i, h3f, .h3p, .h3m files from hmmpress\n", - "pattern": "*.{fam,h3i,h3f,h3p,h3m}", - "ontologies": [] - } - } - ] - ], - "output": { - "mito_fasta": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*mito.ctg.fasta": { - 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information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*annot_mito.txt": { - "type": "file", - "description": "the MT gene annotation file over all assembled sequences", - "pattern": "*annot_mito.txt", - "ontologies": [] - } - } - ] - ], - "annot_pltd_txt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*annot_pltd.txt": { - "type": "file", - "description": "the PT gene annotation file over all assembled sequences", - "pattern": "*annot_pltd.txt", - "ontologies": [] - } - } - ] - ], - "final_gfa": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*utg.final.gfa": { - "type": "file", - "description": "the GFA file for the final genome assembly", - "pattern": "*utg.final.gfa", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3975" - } - ] - } - } - ] - ], - "initial_gfa": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*utg.gfa": { - "type": "file", - "description": "the GFA file for the initial genome assembly", - "pattern": "*utg.gfa", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3975" - } - ] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.log": { - "type": "file", - "description": "log file describing oatk run", - "pattern": "*.log", - "ontologies": [ - { - "edam": "http://edamontology.org/data_2526" - } - ] - } - } - ] - ], - "versions_oatk": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "oatk": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "oatk --version 2>&1": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "oatk": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "oatk --version 2>&1": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "phaseimpute", + "version": "1.1.0" + } ] - ] - }, - "authors": [ - "@ksenia-krasheninnikova" - ] - } - }, - { - "name": "octopusv_clean", - "path": "modules/nf-core/octopusv/clean/meta.yml", - "type": "module", - "meta": { - "name": "octopusv_clean", - "description": "Clean broken VCF/SVCF files using OctopuSV clean", - "keywords": [ - "vcf", - "sv", - "structural-variants", - "clean", - "harmonization" - ], - "tools": [ - { - "octopusv": { - "description": "End-to-end structural variant post-processing: standardize, merge, compare, and export SVs.", - "homepage": "https://github.com/ylab-hi/OctopuSV", - "documentation": "https://github.com/ylab-hi/OctopuSV", - "tool_dev_url": "https://github.com/ylab-hi/OctopuSV", - "doi": "10.1093/bioinformatics/btaf599", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample1' ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "Input VCF/SVCF file to clean", - "pattern": "*.{vcf,vcf.gz,svcf,svcf.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - }, - { - "edam": "http://edamontology.org/format_3615" - } - ] - } + }, + { + "name": "samtools_dict", + "path": "modules/nf-core/samtools/dict/meta.yml", + "type": "module", + "meta": { + "name": "samtools_dict", + "description": "Create a sequence dictionary file from a FASTA file", + "keywords": ["dict", "fasta", "sequence"], + "tools": [ + { + "samtools": { + "description": "SAMtools is a set of utilities for interacting with and post-processing\nshort DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.\nThese files are generated as output by short read aligners like BWA.\n", + "homepage": "http://www.htslib.org/", + "documentation": "http://www.htslib.org/doc/samtools.html", + "doi": "10.1093/bioinformatics/btp352", + "licence": ["MIT"], + "identifier": "biotools:samtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA file", + "pattern": "*.{fa,fasta}", + "ontologies": [] + } + } + ] + ], + "output": { + "dict": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.dict": { + "type": "file", + "description": "FASTA dictionary file", + "pattern": "*.{dict}", + "ontologies": [] + } + } + ] + ], + "versions_samtools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "samtools": { + "type": "string", + "description": "The tool name" + } + }, + { + "samtools version | sed '1!d;s/.* //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "samtools": { + "type": "string", + "description": "The tool name" + } + }, + { + "samtools version | sed '1!d;s/.* //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@muffato"], + "maintainers": ["@muffato", "@matthdsm"] }, - { - "fasta": { - "type": "file", - "description": "Optional reference FASTA for chromosome harmonization", - "pattern": "*.{fa,fasta}", - "optional": true, - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + "pipelines": [ + { + "name": "fastquorum", + "version": "1.2.0" + }, + { + "name": "oncoanalyser", + "version": "2.3.0" + }, + { + "name": "pacsomatic", + "version": "dev" + }, + { + "name": "pairgenomealign", + "version": "2.2.3" } - }, - { - "*.vcf.gz": { - "type": "file", - "description": "Bgzipped VCF file", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - }, + ] + }, + { + "name": "samtools_faidx", + "path": "modules/nf-core/samtools/faidx/meta.yml", + "type": "module", + "meta": { + "name": "samtools_faidx", + "description": "Index FASTA file, and optionally generate a file of chromosome sizes", + "keywords": ["index", "fasta", "faidx", "chromosome"], + "tools": [ + { + "samtools": { + "description": "SAMtools is a set of utilities for interacting with and post-processing\nshort DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.\nThese files are generated as output by short read aligners like BWA.\n", + "homepage": "http://www.htslib.org/", + "documentation": "http://www.htslib.org/doc/samtools.html", + "doi": "10.1093/bioinformatics/btp352", + "licence": ["MIT"], + "identifier": "biotools:samtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA file", + "pattern": "*.{fa,fasta}", + "ontologies": [] + } + }, + { + "fai": { + "type": "file", + "description": "FASTA index file", + "pattern": "*.{fai}", + "ontologies": [] + } + } + ], { - "edam": "http://edamontology.org/format_3615" + "get_sizes": { + "type": "boolean", + "description": "use cut to get the sizes of the index (true) or not (false)" + } } - ] - } - } - ] - ], - "versions_octopusv": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "octopusv": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python -c \"import importlib.metadata as m; print(m.version('octopusv'))\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "octopusv": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python -c \"import importlib.metadata as m; print(m.version('octopusv'))\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@manascripts" - ], - "maintainers": [ - "@manascripts" - ] - } - }, - { - "name": "octopusv_correct", - "path": "modules/nf-core/octopusv/correct/meta.yml", - "type": "module", - "meta": { - "name": "octopusv_correct", - "description": "Standardize a caller VCF into OctopuSV SVCF format.", - "keywords": [ - "structural", - "variant", - "sv", - "svcf", - "normalize" - ], - "tools": [ - { - "octopusv": { - "description": "End-to-end structural variant post-processing: standardize, merge, compare, and export SVs.", - "homepage": "https://github.com/ylab-hi/OctopuSV", - "documentation": "https://github.com/ylab-hi/OctopuSV", - "tool_dev_url": "https://github.com/ylab-hi/OctopuSV", - "doi": "10.1093/bioinformatics/btaf599", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "vcf": { - "type": "file", - "description": "Structural variant calls in VCF format", - "pattern": "*.{vcf,vcf.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - } - ] - } - } - ] - ], - "output": { - "svcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\n" - } - }, - { - "*.svcf": { - "type": "file", - "description": "Standardized SVCF file", - "pattern": "*.svcf", - "ontologies": [ - { - "edam": "https://github.com/ylab-hi/OctopuSV/blob/main/docs/SVCF_specifications.md" - } - ] - } - } - ] - ], - "versions_octopusv": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "octopusv": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python -c \"import importlib.metadata as m; print(m.version('octopusv'))\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "octopusv": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python -c \"import importlib.metadata as m; print(m.version('octopusv'))\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@manascripts" - ], - "maintainers": [ - "@manascripts" - ] - } - }, - { - "name": "octopusv_merge", - "path": "modules/nf-core/octopusv/merge/meta.yml", - "type": "module", - "meta": { - "name": "octopusv_merge", - "description": "Merge and harmonize structural variant calls from multiple samples.", - "keywords": [ - "structural variants", - "merge", - "genomics", - "svcf" - ], - "tools": [ - { - "octopusv": { - "description": "End-to-end structural variant post-processing: standardize, merge, compare, and export SVs.", - "homepage": "https://github.com/ylab-hi/OctopuSV", - "documentation": "https://github.com/ylab-hi/OctopuSV", - "tool_dev_url": "https://github.com/ylab-hi/octopusV", - "doi": "10.1093/bioinformatics/btaf599", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "svcfs": { - "type": "file", - "description": "List of SVCF files to merge", - "pattern": "*.svcf", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - } - ] - } - }, - { - "strategy_flag": { - "type": "string", - "description": "Merge strategy for octopusv merge. Valid values: union, intersect, specific,\nmin-support, exact-support, max-support, expression. Defaults to union when this flag is empty.\nNOTE: Some flags require additional arguments.\n" - } - } - ] - ], - "output": { - "svcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.svcf": { - "type": "file", - "description": "Sorted VCF file", - "pattern": "*.svcf", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - } - ] - } - } - ] - ], - "upset_plot": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.png": { - "type": "file", - "description": "Upset plot comparing the variants in the input SVCF files (generated with --upsetr-output flag)", - "pattern": "*.png", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3603" - } - ] - } - } - ] - ], - "versions_octopusv": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "octopusv": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python -c \"import importlib.metadata as m; print(m.version('octopusv'))\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "octopusv": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python -c \"import importlib.metadata as m; print(m.version('octopusv'))\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@manascripts" - ], - "maintainers": [ - "@manascripts" - ] - } - }, - { - "name": "octopusv_plot", - "path": "modules/nf-core/octopusv/plot/meta.yml", - "type": "module", - "meta": { - "name": "octopusv_plot", - "description": "Plot structural variant statistics using octopusv stat output", - "keywords": [ - "summary", - "structural variant", - "statistics", - "plot" - ], - "tools": [ - { - "octopusv": { - "description": "End-to-end structural variant post-processing: standardize, merge, compare, and export SVs.", - "homepage": "https://github.com/ylab-hi/OctopuSV", - "documentation": "https://github.com/ylab-hi/OctopuSV", - "tool_dev_url": "https://github.com/ylab-hi/octopusV", - "doi": "10.1093/bioinformatics/btaf599", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "txt": { - "type": "file", - "description": "OctopuSV stats text input", - "pattern": "*.txt", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2330" - } - ] - } - } - ] - ], - "output": { - "sv_sizes_png": [ - [ - { - "meta": { - "type": "map", - "description": "Sample information" - } - }, - { - "${prefix}_sv_sizes.png": { - "type": "file", - "description": "SV sizes plot (PNG)", - "pattern": "*_sv_sizes.png", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3603" - } - ] - } - } - ] - ], - "sv_sizes_svg": [ - [ - { - "meta": { - "type": "map", - "description": "Sample information" - } - }, - { - "${prefix}_sv_sizes.svg": { - "type": "file", - "description": "SV sizes plot (SVG)", - "pattern": "*_sv_sizes.svg", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3604" - } - ] - } - } - ] - ], - "sv_types_png": [ - [ - { - "meta": { - "type": "map", - "description": "Sample information" - } - }, - { - "${prefix}_sv_types.png": { - "type": "file", - "description": "SV types plot (PNG)", - "pattern": "*_sv_types.png", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3603" - } - ] - } - } - ] - ], - "sv_types_svg": [ - [ - { - "meta": { - "type": "map", - "description": "Sample information" - } - }, - { - "${prefix}_sv_types.svg": { - "type": "file", - "description": "SV types plot (SVG)", - "pattern": "*_sv_types.svg", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3604" - } - ] - } - } - ] - ], - "chromosome_distribution_png": [ - [ - { - "meta": { - "type": "map", - "description": "Sample information" - } - }, - { - "${prefix}_chromosome_distribution.png": { - "type": "file", - "description": "Chromosome distribution plot of structural variants (PNG)", - "pattern": "*_chromosome_distribution.png", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3603" - } - ] - } - } - ] - ], - "chromosome_distribution_svg": [ - [ - { - "meta": { - "type": "map", - "description": "Sample information" - } - }, - { - "${prefix}_chromosome_distribution.svg": { - "type": "file", - "description": "Chromosome distribution plot of structural variants (SVG)", - "pattern": "*_chromosome_distribution.svg", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3604" - } - ] - } - } - ] - ], - "versions_octopusv": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "octopusv": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python -c \"import importlib.metadata as m; print(m.version('octopusv'))\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "octopusv": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python -c \"import importlib.metadata as m; print(m.version('octopusv'))\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@manascripts" - ], - "maintainers": [ - "@manascripts" - ] - } - }, - { - "name": "octopusv_svcf2vcf", - "path": "modules/nf-core/octopusv/svcf2vcf/meta.yml", - "type": "module", - "meta": { - "name": "octopusv_svcf2vcf", - "description": "Converts octopusv SVCF files to the standard VCF format", - "keywords": [ - "structural variants", - "svcf2vcf", - "genomics", - "vcf" - ], - "tools": [ - { - "octopusv": { - "description": "End-to-end structural variant post-processing: standardize, merge, compare, and export SVs.", - "homepage": "https://github.com/ylab-hi/OctopuSV", - "documentation": "https://github.com/ylab-hi/OctopuSV", - "tool_dev_url": "https://github.com/ylab-hi/octopusV", - "doi": "10.1093/bioinformatics/btaf599", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } + ], + "output": { + "fa": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{fa,fasta}": { + "type": "file", + "description": "FASTA file", + "pattern": "*.{fa}", + "ontologies": [] + } + } + ] + ], + "sizes": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.sizes": { + "type": "file", + "description": "File containing chromosome lengths", + "pattern": "*.{sizes}", + "ontologies": [] + } + } + ] + ], + "fai": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fai": { + "type": "file", + "description": "FASTA index file", + "pattern": "*.{fai}", + "ontologies": [] + } + } + ] + ], + "gzi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.gzi": { + "type": "file", + "description": "Optional gzip index file for compressed inputs", + "pattern": "*.gzi", + "ontologies": [] + } + } + ] + ], + "versions_samtools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "samtools": { + "type": "string", + "description": "The tool name" + } + }, + { + "samtools version | sed '1!d;s/.* //'": { + "type": "eval", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "samtools": { + "type": "string", + "description": "The tool name" + } + }, + { + "samtools version | sed '1!d;s/.* //'": { + "type": "eval", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@drpatelh", "@ewels", "@phue"], + "maintainers": ["@maxulysse", "@phue", "@matthdsm"] }, - { - "svcf": { - "type": "file", - "description": "SVCF file to convert to a standard VCF file", - "pattern": "*.svcf", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - } - ] - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.vcf": { - "type": "file", - "description": "Sorted VCF file", - "pattern": "*.vcf", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - } - ] - } - } - ] - ], - "versions_octopusv": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "octopusv": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python -c \"import importlib.metadata as m; print(m.version('octopusv'))\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "octopusv": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python -c \"import importlib.metadata as m; print(m.version('octopusv'))\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@manascripts" - ], - "maintainers": [ - "@manascripts" - ] - } - }, - { - "name": "odgi_build", - "path": "modules/nf-core/odgi/build/meta.yml", - "type": "module", - "meta": { - "name": "odgi_build", - "description": "Construct a dynamic succinct variation graph in ODGI format from a GFAv1.", - "keywords": [ - "variation graph", - "pangenome graph", - "gfa", - "graph construction" - ], - "tools": [ - { - "odgi": { - "description": "An optimized dynamic genome/graph implementation", - "homepage": "https://github.com/pangenome/odgi", - "documentation": "https://odgi.readthedocs.io/en/latest/", - "tool_dev_url": "https://github.com/pangenome/odgi", - "doi": "10.1093/bioinformatics/btac308", - "licence": [ - "MIT" - ], - "identifier": "biotools:odgi" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "graph": { - "type": "file", - "description": "Pangenome graph in GFA v1.0 format", - "pattern": "*.{gfa}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3975" - } - ] - } - } - ] - ], - "output": { - "og": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.og": { - "type": "file", - "description": "File containing a pangenome graph in ODGI binary format. Usually ends with '.og'", - "pattern": "*.{og}", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@subwaystation" - ], - "maintainers": [ - "@subwaystation" - ] - }, - "pipelines": [ - { - "name": "pangenome", - "version": "1.1.3" - } - ] - }, - { - "name": "odgi_draw", - "path": "modules/nf-core/odgi/draw/meta.yml", - "type": "module", - "meta": { - "name": "odgi_draw", - "description": "Draw previously-determined 2D layouts of the graph with diverse annotations.", - "keywords": [ - "variation graph", - "pangenome graph", - "gfa", - "graph drawing" - ], - "tools": [ - { - "odgi": { - "description": "An optimized dynamic genome/graph implementation", - "homepage": "https://github.com/pangenome/odgi", - "documentation": "https://odgi.readthedocs.io/en/latest/", - "tool_dev_url": "https://github.com/pangenome/odgi", - "doi": "10.1093/bioinformatics/btac308", - "licence": [ - "MIT" - ], - "identifier": "biotools:odgi" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "graph": { - "type": "file", - "description": "Pangenome graph in GFA v1.0 format or ODGI binary format", - "pattern": "*.{gfa,og}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3975" - } - ] - } - }, - { - "lay": { - "type": "file", - "description": "2D layout from 'odgi layout' in LAY binary format", - "pattern": "*.{lay}", - "ontologies": [] - } - } - ] - ], - "output": { - "png": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.png": { - "type": "file", - "description": "File in PNG format containing a 2D drawing of a pangenome graph", - "pattern": "*.{png}", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@subwaystation" - ], - "maintainers": [ - "@subwaystation" - ] - }, - "pipelines": [ - { - "name": "pangenome", - "version": "1.1.3" - } - ] - }, - { - "name": "odgi_layout", - "path": "modules/nf-core/odgi/layout/meta.yml", - "type": "module", - "meta": { - "name": "odgi_layout", - "description": "Establish 2D layouts of the graph using path-guided stochastic gradient descent. The graph must be sorted and id-compacted.", - "keywords": [ - "variation graph", - "pangenome graph", - "gfa", - "graph layout" - ], - "tools": [ - { - "odgi": { - "description": "An optimized dynamic genome/graph implementation", - "homepage": "https://github.com/pangenome/odgi", - "documentation": "https://odgi.readthedocs.io/en/latest/", - "tool_dev_url": "https://github.com/pangenome/odgi", - "doi": "10.1093/bioinformatics/btac308", - "licence": [ - "MIT" - ], - "identifier": "biotools:odgi" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "graph": { - "type": "file", - "description": "Pangenome graph in GFA v1.0 format or in ODGI binary format", - "pattern": "*.{gfa,og}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3975" - } - ] - } - } - ] - ], - "output": { - "lay": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.lay": { - "type": "file", - "description": "File containing a 2D layout of a pangenome graph in a binary format. Usually ends with '.lay'. Optional output specified by the `--out FILE` argument. Either this or the TSV layout output must be specified.", - "pattern": "*.{lay}", - "ontologies": [] - } - } - ] - ], - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "File containing a 2D layout of a pangenome graph in TSV format. Optional output specified by the `--tsv FILE` argument. Either this or the binary layout output must be specified.", - "pattern": "*.{tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@subwaystation" - ], - "maintainers": [ - "@subwaystation" - ] - }, - "pipelines": [ - { - "name": "pangenome", - "version": "1.1.3" - } - ] - }, - { - "name": "odgi_sort", - "path": "modules/nf-core/odgi/sort/meta.yml", - "type": "module", - "meta": { - "name": "odgi_sort", - "description": "Apply different kind of sorting algorithms to a graph. The most prominent one is the PG-SGD sorting algorithm.", - "keywords": [ - "variation graph", - "pangenome graph", - "gfa", - "graph layout" - ], - "tools": [ - { - "odgi": { - "description": "An optimized dynamic genome/graph implementation", - "homepage": "https://github.com/pangenome/odgi", - "documentation": "https://odgi.readthedocs.io/en/latest/", - "tool_dev_url": "https://github.com/pangenome/odgi", - "doi": "10.1093/bioinformatics/btac308", - "licence": [ - "MIT" - ], - "identifier": "biotools:odgi" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "graph": { - "type": "file", - "description": "Pangenome graph in GFA v1.0 format or in ODGI binary format", - "pattern": "*.{gfa,og}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3975" - } - ] - } - } - ] - ], - "output": { - "sorted_graph": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.og": { - "type": "file", - "description": "1D sorted pangenome graph in ODGI binary format", - "pattern": "*.{og}", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@subwaystation" - ], - "maintainers": [ - "@subwaystation" - ] - }, - "pipelines": [ - { - "name": "pangenome", - "version": "1.1.3" - } - ] - }, - { - "name": "odgi_squeeze", - "path": "modules/nf-core/odgi/squeeze/meta.yml", - "type": "module", - "meta": { - "name": "odgi_squeeze", - "description": "Squeezes multiple graphs in ODGI format into the same file in ODGI format.", - "keywords": [ - "squeeze", - "odgi", - "gfa", - "combine graphs" - ], - "tools": [ - { - "odgi": { - "description": "An optimized dynamic genome/graph implementation", - "homepage": "https://github.com/pangenome/odgi", - "documentation": "https://odgi.readthedocs.io/en/latest/", - "tool_dev_url": "https://github.com/pangenome/odgi", - "doi": "10.1093/bioinformatics/btac308", - "licence": [ - "MIT" - ], - "identifier": "biotools:odgi" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "graphs": { - "type": "file", - "description": "Pangenome graph files in ODGI format.", - "pattern": "*.{og}", - "ontologies": [] - } - } - ] - ], - "output": { - "graph": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.og": { - "type": "file", - "description": "Squeezed pangenome graph in ODGI format.", - "pattern": "*.{og}", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - 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Needs collated input file.", + "pattern": "*_interleaved.fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "singleton": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_singleton.fastq.gz": { + "type": "file", + "description": "Compressed FASTQ file with singleton reads", + "pattern": "*_singleton.fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "other": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_other.fastq.gz": { + "type": "file", + "description": "Compressed FASTQ file with reads with either both READ1 and READ2 flags set or unset", + "pattern": "*_other.fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "versions_samtools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "samtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "samtools version | sed '1!d;s/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "samtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "samtools version | sed '1!d;s/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@priyanka-surana", "@suzannejin"], + "maintainers": ["@priyanka-surana", "@suzannejin", "@matthdsm"] }, - 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}, - { - "openms": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "FileInfo --help 2>&1 | sed -nE 's/^Version: ([0-9.]+).*/\\1/p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@jonasscheid" - ], - "maintainers": [ - "@jonasscheid" - ] - } - }, - { - "name": "openms_textexporter", - "path": "modules/nf-core/openms/textexporter/meta.yml", - "type": "module", - "meta": { - "name": "openms_textexporter", - "description": "Exports various OpenMS XML formats (featureXML, consensusXML, idXML, mzML) to a human-readable text format.", - "keywords": [ - "export", - "openms", - "proteomics", - "text", - "tsv" - ], - "tools": [ - { - "openms": { - "description": "OpenMS is an open-source software C++ library for LC-MS data management and analyses", - "homepage": "https://openms.de", - "documentation": "https://openms.readthedocs.io/en/latest/index.html", - "tool_dev_url": "https://github.com/OpenMS/OpenMS", - 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"tools": [ - { - "openms": { - "description": "OpenMS is an open-source software C++ library for LC-MS data management and analyses", - "homepage": "https://openms.de", - "documentation": "https://openms.readthedocs.io/en/latest/index.html", - "tool_dev_url": "https://github.com/OpenMS/OpenMS", - "doi": "10.1038/s41592-024-02197-7", - "licence": [ - "BSD" - ], - "identifier": "" - } - }, - { - "CometAdapter": { - "description": "Annotates MS/MS spectra using Comet.", - "homepage": "https://openms.de", - "documentation": "https://openms.readthedocs.io/en/latest/index.html", - "identifier": "" - } - }, - { - "Comet": { - "description": "Comet is an open source tandem mass spectrometry (MS/MS) sequence database search tool.", - "homepage": "http://comet-ms.sourceforge.net/", - "documentation": "http://comet-ms.sourceforge.net/", - "identifier": "" + "name": "samtools_fixmate", + "path": "modules/nf-core/samtools/fixmate/meta.yml", + "type": "module", + "meta": { + "name": "samtools_fixmate", + "description": "Samtools fixmate is a tool that can fill in information (insert size, cigar, mapq) about paired end reads onto the corresponding other read. Also has options to remove secondary/unmapped alignments and recalculate whether reads are proper pairs.", + "keywords": ["fixmate", "samtools", "insert size", "repair", "bam", "paired", "read pairs"], + "tools": [ + { + "samtools": { + "description": "SAMtools is a set of utilities for interacting with and post-processing\nshort DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.\nThese files are generated as output by short read aligners like BWA.\n", + "homepage": "http://www.htslib.org/", + "documentation": "http://www.htslib.org/doc/samtools.html", + "tool_dev_url": "https://github.com/samtools/samtools", + "doi": "10.1093/bioinformatics/btp352", + "licence": ["MIT"], + "identifier": "biotools:samtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM/SAM file, must be sorted by name, not coordinate", + "pattern": "*.{bam,cram,sam}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + }, + { + "edam": "http://edamontology.org/format_3462" + }, + { + "edam": "http://edamontology.org/format_2573" + } + ] + } + } + ] + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*.{bam}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + }, + { + "${prefix}.bam": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*.{bam}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + } + ] + ], + "cram": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*.{bam}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + }, + { + "${prefix}.cram": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*.{cram}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3462" + } + ] + } + } + ] + ], + "sam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*.{bam}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + }, + { + "${prefix}.sam": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*.{sam}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2573" + } + ] + } + } + ] + ], + "versions_samtools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "samtools": { + "type": "string", + "description": "The tool name" + } + }, + { + "samtools version | sed '1!d;s/.* //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "samtools": { + "type": "string", + "description": "The tool name" + } + }, + { + "samtools version | sed '1!d;s/.* //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@sppearce"], + "maintainers": ["@sppearce", "@GallVp", "@matthdsm"] } - 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Each input file produces a separate group of pileup columns in the output.", + "keywords": ["mpileup", "bam", "sam", "cram"], + "tools": [ + { + "samtools": { + "description": "SAMtools is a set of utilities for interacting with and post-processing\nshort DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.\nThese files are generated as output by short read aligners like BWA.\n", + "homepage": "http://www.htslib.org/", + "documentation": "http://www.htslib.org/doc/samtools.html", + "doi": "10.1093/bioinformatics/btp352", + "licence": ["MIT"], + "identifier": "biotools:samtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}", + "ontologies": [] + } + }, + { + "index": { + "type": "file", + "description": "CSI/BAI/CRAI file. Optional. Only required when using the '-r' parameter.", + "pattern": "*.{bai,crai,csi}", + "ontologies": [] + } + }, + { + "intervals": { + "type": "file", + "description": "Interval FILE. Optional.", + "pattern": "*.bed", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA reference file. Optional.", + "pattern": "*.{fasta,fa,fna}", + "ontologies": [] + } + }, + { + "fai": { + "type": "file", + "description": "FAI file. Optional. Only required (recommended) when using the '-f' parameter.", + "pattern": "*.{fai}", + "ontologies": [] + } + } + ] + ], + "output": { + "mpileup": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.mpileup.gz": { + "type": "file", + "description": "mpileup file", + "pattern": "*.{mpileup}", + "ontologies": [] + } + } + ] + ], + "versions_samtools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "samtools": { + "type": "string", + "description": "The tool name" + } + }, + { + "samtools version | sed '1!d;s/.* //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "samtools": { + "type": "string", + "description": "The tool name" + } + }, + { + "samtools version | sed '1!d;s/.* //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@drpatelh", "@joseespinosa"], + "maintainers": ["@joseespinosa", "@krannich479", "@matthdsm"] }, - { - "prior_run": { - "type": "directory", - "description": "A folder containing a previous WorkingDirectory from OrthoFinder.\n" - } - } - ] - ], - "output": { - "orthofinder": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "$prefix": { - "type": "directory", - "description": "OrthoFinder output directory" - } - } - ] - ], - "working": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "$prefix/WorkingDirectory": { - "type": "directory", - "description": "OrthoFinder WorkingDirectory (used for the resume function)" - } - } - ] - ], - "versions_orthofinder": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "orthofinder": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "NO_COLOR=1 orthofinder --version | cut -d 'v' -f2 | perl -pe 's/\\e\\[[0-9;]*m//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "orthofinder": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "NO_COLOR=1 orthofinder --version | cut -d 'v' -f2 | perl -pe 's/\\e\\[[0-9;]*m//g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "abotyper", + "version": "dev" + }, + { + "name": "rnadnavar", + "version": "dev" + }, + { + "name": "sarek", + "version": "3.8.1" + } ] - ] - }, - "authors": [ - "@GallVp", - "@chriswyatt1" - ], - "maintainers": [ - "@GallVp", - "@chriswyatt1" - ] - }, - "pipelines": [ - { - "name": "genomeqc", - "version": "dev" - } - ] - }, - { - "name": "osfclient_fetch", - "path": "modules/nf-core/osfclient/fetch/meta.yml", - "type": "module", - "meta": { - "name": "osfclient_fetch", - "description": "A python library and a command-line client for up- and downloading files to and from your Open Science Framework projects", - "keywords": [ - "osf", - "Open Science Framework", - "fetch" - ], - "tools": [ - { - "osfclient": { - "description": "The osfclient is a python library and a command-line client for up- and downloading files to and from your Open Science Framework projects.", - "homepage": "https://osfclient.readthedocs.io/en/latest/", - "documentation": "https://osfclient.readthedocs.io/en/latest/", - "tool_dev_url": "https://github.com/osfclient/osfclient", - "licence": [ - "BSD-3-clause" - ], - "identifier": "" + }, + { + "name": "samtools_quickcheck", + "path": "modules/nf-core/samtools/quickcheck/meta.yml", + "type": "module", + "meta": { + "name": "samtools_quickcheck", + "description": "Quickly check that input files appear to be intact. Checks that beginning of the file contains a valid header (all formats) containing at least one target sequence and then seeks to the end of the file and checks that an end-of-file (EOF) is present and intact (BAM and CRAM only). Alignment records are not checked. The quickcheck module returns a non-zero EXIT_CODE if any input files don't have a valid header or are missing an EOF block. Otherwise EXIT_CODE is zero.", + "keywords": ["check", "quickcheck", "sam", "bam", "cram"], + "tools": [ + { + "samtools": { + "description": "Tools for dealing with SAM, BAM and CRAM files", + "homepage": "https://www.htslib.org/", + "documentation": "https://www.htslib.org/doc/samtools-quickcheck.html", + "tool_dev_url": "https://github.com/samtools/", + "doi": "10.1093/bioinformatics/btp352", + "licence": ["MIT"], + "identifier": "biotools:samtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" + } + }, + { + "bam": { + "type": "file", + "description": "sequence_trace file", + "pattern": "*.{cram,sam,bam}", + "ontologies": [ + { + "edam": "http://edamontology.org/data_0924" + }, + { + "edam": "http://edamontology.org/format_3462" + }, + { + "edam": "http://edamontology.org/format_2573" + }, + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + } + ] + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" + } + }, + { + "bam": { + "type": "file", + "description": "sequence_trace file", + "pattern": "*.{cram,sam,bam}", + "ontologies": [ + { + "edam": "http://edamontology.org/data_0924" + }, + { + "edam": "http://edamontology.org/format_3462" + }, + { + "edam": "http://edamontology.org/format_2573" + }, + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + }, + { + "EXIT_CODE": { + "type": "string", + "description": "Exit code (0 for success, non-zero otherwise) that is the result of the format check.", + "ontologies": [] + } + } + ] + ], + "versions_samtools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "samtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "samtools version | sed '1!d;s/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "samtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "samtools version | sed '1!d;s/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@Krannich479"], + "maintainers": ["@Krannich479", "@matthdsm"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "project_id": { - "type": "string", - "description": "Project ID of the Open Science Framework project to fetch files from" - } + }, + { + "name": "samtools_reheader", + "path": "modules/nf-core/samtools/reheader/meta.yml", + "type": "module", + "meta": { + "name": "samtools_reheader", + "description": "Replace the header in the bam file with the header generated by the command.\nThis command is much faster than replacing the header with a BAM→SAM→BAM conversion.\n", + "keywords": ["reheader", "cram", "bam", "genomics"], + "tools": [ + { + "samtools": { + "description": "SAMtools is a set of utilities for interacting with and post-processing\nshort DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.\nThese files are generated as output by short read aligners like BWA.\n", + "homepage": "http://www.htslib.org/", + "documentation": "http://www.htslib.org/doc/samtools.html", + "doi": "10.1093/bioinformatics/btp352", + "licence": ["MIT"], + "identifier": "biotools:samtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM file to be reheaded", + "pattern": "*.{bam,cram}", + "ontologies": [] + } + }, + { + "bai": { + "type": "file", + "description": "BAM/CRAM index file to be reheaded", + "pattern": "*.{bai,crai,csi}", + "ontologies": [] + } + } + ] + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Reheaded BAM/CRAM file", + "pattern": "*.{bam,cram}", + "ontologies": [] + } + } + ] + ], + "versions_samtools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "samtools": { + "type": "string", + "description": "The tool name" + } + }, + { + "samtools version | sed '1!d;s/.* //'": { + "type": "eval", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "samtools": { + "type": "string", + "description": "The tool name" + } + }, + { + "samtools version | sed '1!d;s/.* //'": { + "type": "eval", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@louislenezet"], + "maintainers": ["@louislenezet", "@matthdsm"] }, - { - "path": { - "type": "string", - "description": "File to fetch from the project" - } - } - ] - ], - "output": { - "download_files": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "${outname}": { - "type": "file", - "description": "Downloaded file", - "pattern": "*", - "ontologies": [] - } - } + "pipelines": [ + { + "name": "phaseimpute", + "version": "1.1.0" + }, + { + "name": "tfactivity", + "version": "dev" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@JacquelineAldridge" - ] - } - }, - { - "name": "paftools_sam2paf", - "path": "modules/nf-core/paftools/sam2paf/meta.yml", - "type": "module", - "meta": { - "name": "paftools_sam2paf", - "description": "A program to convert bam into paf.", - "keywords": [ - "paf", - "bam", - "conversion" - ], - "tools": [ - { - "paftools": { - "description": "A program to manipulate paf files / convert to and from paf.\n", - "homepage": "https://github.com/lh3/minimap2", - "documentation": "https://github.com/lh3/minimap2/blob/master/README.md", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "An input bam file to be converted into paf.", - "ontologies": [] - } - } - ] - ], - "output": { - "paf": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + }, + { + "name": "samtools_samples", + "path": "modules/nf-core/samtools/samples/meta.yml", + "type": "module", + "meta": { + "name": "samtools_samples", + "description": "Write sample names and path to reference genome of an alignment to a text file.\n", + "keywords": ["samples", "bam", "cram", "genomics"], + "tools": [ + { + "samtools": { + "description": "SAMtools is a set of utilities for interacting with and post-processing\nshort DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.\nThese files are generated as output by short read aligners like BWA.\n", + "homepage": "http://www.htslib.org/", + "documentation": "http://www.htslib.org/doc/samtools.html", + "doi": "10.1093/bioinformatics/btp352", + "licence": ["MIT"], + "identifier": "biotools:samtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" + } + }, + { + "bam": { + "type": "file", + "description": "alignment file", + "pattern": "*.{bam,sam,cram}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + }, + { + "edam": "http://edamontology.org/format_2573" + }, + { + "edam": "http://edamontology.org/format_3462" + } + ] + } + }, + { + "bai": { + "type": "file", + "description": "index file for the alignment", + "pattern": "*.{bai,crai}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information." + } + }, + { + "fasta": { + "type": "file", + "description": "reference genome file (optional)", + "pattern": "*.{fasta,fa,fna}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + }, + { + "fai": { + "type": "file", + "description": "index file for the reference genome (optional)", + "pattern": "*.fai" + } + } + ] + ], + "output": { + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" + } + }, + { + "*.tsv": { + "type": "file", + "description": "tab-separated file containing sample names, BAM filename and optionally reference genome path", + "pattern": "*.tsv" + } + } + ] + ], + "versions_samtools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "samtools": { + "type": "string", + "description": "The tool name" + } + }, + { + "samtools version | sed '1!d;s/.* //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "samtools": { + "type": "string", + "description": "The tool name" + } + }, + { + "samtools version | sed '1!d;s/.* //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@Schmytzi"], + "maintainers": ["@Schmytzi", "@matthdsm"] } - ], - "versions_samtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "Name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "Name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_paftools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "Name of the process" - } - }, - { - "paftools": { - "type": "string", - "description": "Name of the tool" - } - }, - { - "paftools.js version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "Name of the process" - } - }, - { - "paftools": { - "type": "string", - "description": "Name of the tool" - } - }, - { - "paftools.js version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "Name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "Name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@DLBPointon" - ], - "maintainers": [ - "@DLBPointon" - ] - } - }, - { - "name": "pairix", - "path": "modules/nf-core/pairix/meta.yml", - "type": "module", - "meta": { - "name": "pairix", - "description": "a tool for indexing and querying on a block-compressed text file\ncontaining pairs of genomic coordinates\n", - "keywords": [ - "index", - "block-compressed", - "pairs" - ], - "tools": [ - { - "pairix": { - "description": "2D indexing on bgzipped text files of paired genomic coordinates", - "homepage": "https://github.com/4dn-dcic/pairix", - "documentation": "https://github.com/4dn-dcic/pairix", - "tool_dev_url": "https://github.com/4dn-dcic/pairix", - "licence": [ - "MIT" - ], - "identifier": "biotools:pairix" + }, + { + "name": "samtools_sormadup", + "path": "modules/nf-core/samtools/sormadup/meta.yml", + "type": "module", + "meta": { + "name": "samtools_sormadup", + "description": "Collate/Fixmate/Sort/Markdup SAM/BAM/CRAM file", + "keywords": ["cat", "collate", "fixmate", "sort", "markduplicates", "bam", "sam", "cram", "multi-tool"], + "tools": [ + { + "samtools_cat": { + "description": "SAMtools is a set of utilities for interacting with and post-processing\nshort DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.\nThese files are generated as output by short read aligners like BWA.\n", + "homepage": "http://www.htslib.org/", + "documentation": "http://www.htslib.org/doc/samtools.html", + "doi": "10.1093/bioinformatics/btp352", + "licence": ["MIT"], + "args_id": "$args", + "identifier": "biotools:samtools" + } + }, + { + "samtools_collate": { + "description": "SAMtools is a set of utilities for interacting with and post-processing\nshort DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.\nThese files are generated as output by short read aligners like BWA.\n", + "homepage": "http://www.htslib.org/", + "documentation": "http://www.htslib.org/doc/samtools.html", + "doi": "10.1093/bioinformatics/btp352", + "licence": ["MIT"], + "args_id": "$args2", + "identifier": "biotools:samtools" + } + }, + { + "samtools_fixmate": { + "description": "SAMtools is a set of utilities for interacting with and post-processing\nshort DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.\nThese files are generated as output by short read aligners like BWA.\n", + "homepage": "http://www.htslib.org/", + "documentation": "http://www.htslib.org/doc/samtools.html", + "doi": "10.1093/bioinformatics/btp352", + "licence": ["MIT"], + "args_id": "$args3", + "identifier": "biotools:samtools" + } + }, + { + "samtools_sort": { + "description": "SAMtools is a set of utilities for interacting with and post-processing\nshort DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.\nThese files are generated as output by short read aligners like BWA.\n", + "homepage": "http://www.htslib.org/", + "documentation": "http://www.htslib.org/doc/samtools.html", + "doi": "10.1093/bioinformatics/btp352", + "licence": ["MIT"], + "args_id": "$args4", + "identifier": "biotools:samtools" + } + }, + { + "samtools_markdup": { + "description": "SAMtools is a set of utilities for interacting with and post-processing\nshort DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.\nThese files are generated as output by short read aligners like BWA.\n", + "homepage": "http://www.htslib.org/", + "documentation": "http://www.htslib.org/doc/samtools.html", + "doi": "10.1093/bioinformatics/btp352", + "licence": ["MIT"], + "args_id": "$args5", + "identifier": "biotools:samtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM/SAM files", + "pattern": "*.{bam,cram,sam}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference genome file", + "pattern": "*.{fasta,fa,fna}", + "ontologies": [] + } + }, + { + "fai": { + "type": "file", + "description": "Reference genome index file", + "pattern": "*.fai", + "ontologies": [] + } + } + ] + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Sorted and duplicate marked BAM file", + "pattern": "*.bam", + "ontologies": [] + } + } + ] + ], + "cram": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.cram": { + "type": "file", + "description": "Sorted and duplicate marked CRAM file", + "pattern": "*.cram", + "ontologies": [] + } + } + ] + ], + "csi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.csi": { + "type": "file", + "description": "Sorted and duplicate marked BAM index file", + "pattern": "*.csi", + "ontologies": [] + } + } + ] + ], + "crai": [ + [ + { + "meta": { + "type": "map", + 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id:'test' ]`\n" + } + }, + { + "${prefix}/copynum.bedgraph": { + "type": "file", + "description": "Copy number BEDGraph file", + "pattern": "*.bedgraph", + "optional": true, + "ontologies": [] + } + } + ] + ], + "copynum_mpack": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "${prefix}/copynum.mpack": { + "type": "file", + "description": "Copy number mpack file", + "pattern": "*.mpack", + "optional": true, + "ontologies": [] + } + } + ] + ], + "debug_breakpoint_clusters": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "${prefix}/debug.breakpoint_clusters.bed": { + "type": "file", + "description": "Debug breakpoint clusters BED file", + "pattern": "*.bed", + "ontologies": [] + } + } + ] + ], + "debug_cluster_refinement": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "${prefix}/debug.cluster.refinement.txt": { + "type": "file", + "description": "Debug cluster refinement text file", + "pattern": "*.txt", + "ontologies": [] + } + } + ] + ], + "discover_settings": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "${prefix}/discover.settings.json": { + "type": "file", + "description": "Discover settings JSON file", + "pattern": "*.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "genome_gclevels": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "${prefix}/genome.gclevels.mpack": { + "type": "file", + "description": "Genome GC levels mpack file", + "pattern": "*.mpack", + "optional": true, + "ontologies": [] + } + } + ] + ], + "max_depth": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "${prefix}/max.depth.bed": { + "type": "file", + "description": "Max depth BED file", + "pattern": "*.bed", + "ontologies": [] + } + } + ] + ], + "run_stats": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "${prefix}/run.stats.json": { + "type": "file", + "description": "Run statistics JSON file", + "pattern": "*.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "sample_gcbias": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "${prefix}/sample.gcbias.mpack": { + "type": "file", + "description": "Sample GC bias mpack file", + "pattern": "*.mpack", + "optional": true, + "ontologies": [] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "${prefix}/sawfish.log": { + "type": "file", + "description": "Sawfish log file", + "pattern": "*.log", + "ontologies": [] + } + } + ] + ], + "depth_mpack": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "${prefix}/depth.mpack": { + "type": "file", + "description": "Depth mpack file", + "pattern": "*.mpack", + "ontologies": [] + } + } + ] + ], + "maf_mpack": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "${prefix}/maf.mpack": { + "type": "file", + "description": "MAF mpack file", + "pattern": "*.mpack", + "optional": true, + "ontologies": [] + } + } + ] + ], + "expected_cn": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "${prefix}/expected.copy.number.bed": { + "type": "file", + "description": "Expected copy number BED file", + "pattern": "*.bed", + "optional": true, + "ontologies": [] + } + } + ] + ], + "discover_dir": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "${prefix}": { + "type": "directory", + "description": "Directory containing all discover output files", + "ontologies": [] + } + } + ] + ], + "versions_sawfish": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "sawfish": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "sawfish --version | sed 's/.* //g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "sawfish": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "sawfish --version | sed 's/.* //g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@padraicc"], + "maintainers": ["@padraicc"] } - ] - ], - "output": { - "pairs": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*pairs.gz": { - "type": "file", - "description": "Merged pairs file", - "pattern": "*.{pairs.gz}", - "ontologies": [] - } - } - ] - ], - "versions_pairtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pairtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pairtools --version | sed 's/.*pairtools.*version //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pairtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pairtools --version | sed 's/.*pairtools.*version //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@nservant" - ], - "maintainers": [ - "@nservant" - ] - } - }, - { - "name": "pairtools_parse", - "path": "modules/nf-core/pairtools/parse/meta.yml", - "type": "module", - "meta": { - "name": "pairtools_parse", - "description": "Find ligation junctions in .sam, make .pairs", - "keywords": [ - "ligation junctions", - "parse", - "pairtools" - ], - "tools": [ - { - "pairtools": { - "description": "CLI tools to process mapped Hi-C data", - "homepage": "http://pairtools.readthedocs.io/", - "documentation": "http://pairtools.readthedocs.io/", - "tool_dev_url": "https://github.com/mirnylab/pairtools", - "licence": [ - "MIT" - ], - "identifier": "" + }, + { + "name": "sawfish_jointcall", + "path": "modules/nf-core/sawfish/jointcall/meta.yml", + "type": "module", + "meta": { + "name": "sawfish_jointcall", + "description": "Joint calling of structural variants from multiple samples using Sawfish", + "keywords": ["sawfish", "structural-variant calling", "joint calling", "CNV calling", "Pacbio"], + "tools": [ + { + "sawfish": { + "description": "Joint structural variant and copy number variant caller for HiFi sequencing data", + "homepage": "https://github.com/PacificBiosciences/sawfish", + "documentation": "https://github.com/PacificBiosciences/sawfish/tree/main/docs", + "doi": "10.1093/bioinformatics/btaf136", + "licence": [ + "Pacific Biosciences Software License (https://github.com/PacificBiosciences/sawfish/blob/main/LICENSE.md)" + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "sample_dirs": { + "type": "directory", + "description": "Sample directories from sawfish discover step", + "pattern": "*_discover_dir/", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'fasta' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference genome in FASTA format", + "pattern": "*.{fasta,fa}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "bams": { + "type": "file", + "description": "Sorted BAM/CRAM file", + "pattern": "*.{bam,cram}", + "ontologies": [] + } + }, + { + "bais": { + "type": "file", + "description": "Index of BAM/CAM file", + "pattern": "*.{bai,crai}", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing additional information\ne.g. [ id:'csv' ]\n" + } + }, + { + "sample_csv": { + "type": "file", + "description": "CSV file listing sample sawfish discover output and the sample bam file used with sawfish discover", + "ontologies": [] + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "*/*_genotyped.sv.vcf.gz": { + "type": "file", + "description": "Joint called variants in compressed VCF format", + "pattern": "*_genotyped.sv.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "*/*_genotyped.sv.vcf.gz.tbi": { + "type": "file", + "description": "Tabix index for the joint called VCF file", + "pattern": "*_genotyped.sv.vcf.gz.tbi", + "ontologies": [] + } + } + ] + ], + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "*/contig.alignment.bam": { + "type": "file", + "description": "Contig alignment BAM file", + "pattern": "*.bam", + "ontologies": [] + } + } + ] + ], + "bam_index": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "*/contig.alignment.bam.csi": { + "type": "file", + "description": "Contig alignment BAM index file", + "pattern": "*.csi", + "ontologies": [] + } + } + ] + ], + "stats": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "*/run.stats.json": { + "type": "file", + "description": "Run statistics JSON file", + "pattern": "*.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "depth_bw": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "*/samples/*/depth.bw": { + "type": "file", + "description": "Sample depth BigWig file", + "pattern": "*.bw", + "ontologies": [] + } + } + ] + ], + "copynum_bedgraph": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "*/samples/*/copynum.bedgraph": { + "type": "file", + "description": "Sample copy number BEDGraph file", + "pattern": "*.bedgraph", + "ontologies": [] + } + } + ] + ], + "gc_bias_corrected_depth_bw": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "*/samples/*/gc_bias_corrected_depth.bw": { + "type": "file", + "description": "Sample GC bias BigWig file", + "pattern": "*.bw", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3006" + } + ] + } + } + ] + ], + "copynum_summary": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "*/samples/*/copynum.summary.json": { + "type": "file", + "description": "Sample copy number summary JSON file", + "pattern": "*.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "maf_bw": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "*/samples/*/maf.bw": { + "type": "file", + "description": "Sample SNV MAF BigWig file", + "pattern": "*.bw", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3006" + } + ] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "*/sawfish.log": { + "type": "file", + "description": "Sawfish log file", + "pattern": "*.log", + "ontologies": [] + } + } + ] + ], + "versions_sawfish": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "sawfish": { + "type": "string", + "description": "The tool name" + } + }, + { + "sawfish --version | sed \"s/.* //g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "sawfish": { + "type": "string", + "description": "The tool name" + } + }, + { + "sawfish --version | sed \"s/.* //g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@padraicc"], + "maintainers": ["@padraicc"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } + }, + { + "name": "scanpy_filter", + "path": "modules/nf-core/scanpy/filter/meta.yml", + "type": "module", + "meta": { + "name": "scanpy_filter", + "description": "Filter cells and genes in single-cell RNA-seq data using Scanpy", + "keywords": ["filter", "quality-control", "scanpy", "single-cell", "preprocessing"], + "tools": [ + { + "scanpy": { + "description": "Single-Cell Analysis in Python", + "homepage": "https://scanpy.readthedocs.io", + "documentation": "https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pp.filter_cells.html", + "tool_dev_url": "https://github.com/scverse/scanpy", + "doi": "10.1186/s13059-017-1382-0", + "licence": ["BSD-3-Clause"] + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "h5ad": { + "type": "file", + "description": "AnnData object in h5ad format", + "pattern": "*.{h5ad}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3590" + } + ] + } + } + ], + [ + { + "min_genes": { + "type": "integer", + "description": "Minimum number of genes expressed per cell" + } + } + ], + [ + { + "min_cells": { + "type": "integer", + "description": "Minimum number of cells expressing each gene" + } + } + ], + [ + { + "min_counts_gene": { + "type": "integer", + "description": "Minimum number of counts per gene" + } + } + ], + [ + { + "min_counts_cell": { + "type": "integer", + "description": "Minimum number of counts per cell" + } + } + ], + [ + { + "max_mito_percentage": { + "type": "integer", + "description": "Maximum percentage of mitochondrial genes per cell" + } + } + ], + [ + { + "symbol_col": { + "type": "string", + "description": "Column name of the gene symbols in the `var` of the AnnData object. Use `index` if the gene symbols are the row names." + } + } + ] + ], + "output": { + "h5ad": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.h5ad": { + "type": "file", + "description": "Filtered AnnData object", + "pattern": "*.h5ad", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3590" + } + ] + } + } + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] + }, + "authors": ["@nictru"], + "maintainers": ["@nictru"] } - ], - { - "chromsizes": { - "type": "file", - "description": "chromosome size file", - "ontologies": [] + }, + { + "name": "scanpy_hashsolo", + "path": "modules/nf-core/scanpy/hashsolo/meta.yml", + "type": "module", + "meta": { + "name": "SCANPY_HASHSOLO", + "description": "Probabilistic demultiplexing of cell hashing data", + "keywords": ["anndata", "single-cell", "hashing", "demultiplexing", "scanpy"], + "tools": [ + { + "scanpy": { + "description": "Single-cell analysis in Python. Scales to >100M cells.", + "homepage": "https://github.com/scverse/scanpy", + "documentation": "https://scanpy.readthedocs.io/en/stable/generated/scanpy.external.pp.hashsolo.html", + "tool_dev_url": "https://github.com/scverse/scanpy", + "doi": "10.1186/s13059-017-1382-0", + "licence": ["BSD-3"], + "identifier": "biotools:scanpy" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "data": { + "type": "file", + "description": "A directory in 10x Genomics format containing `matrix.mtx.gz`, `features.tsv.gz`, `barcodes.tsv.gz` (hashing count matrix), or an AnnData (`.h5ad`) file with hashing counts stored in `.obs`.\n", + "ontologies": [ + { + "edam": "http://edamontology.org/data_3917" + } + ] + } + }, + { + "cell_hashing_columns": { + "type": "list", + "description": "Groovy list (`['hash_1', 'hash_2']`) of `.obs` columns that contain cell hashing counts.\nCan be `[]` if the data is in 10x Genomics format, as the columns are derived from the input.\n" + } + } + ] + ], + "output": { + "assignment": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_assignment_hashsolo.csv": { + "type": "file", + "description": "CSV file containing hashsolo assignment results\n", + "pattern": "*_assignment_hashsolo.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "h5ad": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_hashsolo.h5ad": { + "type": "file", + "description": "Processed AnnData object containing hashsolo results\n", + "pattern": "*_hashsolo.h5ad", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3590" + } + ] + } + } + ] + ], + "params": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n", + "pattern": "*_params_hashsolo.csv" + } + }, + { + "*_params_hashsolo.csv": { + "type": "file", + "description": "CSV file containing parameters used in hashsolo analysis\n", + "pattern": "*_params_hashsolo.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@seohyonkim", "@LuisHeinzlmeier"], + "maintainers": ["@seohyonkim", "@LuisHeinzlmeier"] } - } - ], - "output": { - "pairsam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.pairsam.gz": { - "type": "file", - "description": "parsed pair file", - "pattern": "*.{pairsam.gz}", - "ontologies": [] - } - } - ] - ], - "stat": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.pairsam.stat": { - "type": "file", - "description": "stats of the pairs", - "pattern": "*.{pairsam.stat}", - "ontologies": [] - } - } - ] - ], - "versions_pairtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pairtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pairtools --version | sed 's/.*pairtools.*version //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pairtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pairtools --version | sed 's/.*pairtools.*version //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@jianhong" - ], - "maintainers": [ - "@jianhong" - ] - }, - "pipelines": [ - { - "name": "hicar", - "version": "1.0.0" - } - ] - }, - { - "name": "pairtools_restrict", - "path": "modules/nf-core/pairtools/restrict/meta.yml", - "type": "module", - "meta": { - "name": "pairtools_restrict", - "description": "Assign restriction fragments to pairs", - "keywords": [ - "pairs", - "pairstools", - "restriction fragments" - ], - "tools": [ - { - "pairtools": { - "description": "CLI tools to process mapped Hi-C data", - "homepage": "http://pairtools.readthedocs.io/", - "documentation": "http://pairtools.readthedocs.io/", - 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} - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "pairs": { - "type": "file", - "description": "pairsam file", - "ontologies": [] - } + }, + { + "name": "scramble_clusteranalysis", + "path": "modules/nf-core/scramble/clusteranalysis/meta.yml", + "type": "module", + "meta": { + "name": "scramble_clusteranalysis", + "description": "The Cluster Analysis tool of Scramble analyses and interprets the soft-clipped clusters found by `cluster_identifier`", + "keywords": ["soft-clipped clusters", "scramble", "cluster analysis", "clusteridentifier"], + "tools": [ + { + "scramble": { + "description": "Soft Clipped Read Alignment Mapper", + "homepage": "https://github.com/GeneDx/scramble", + "documentation": "https://github.com/GeneDx/scramble", + "tool_dev_url": "https://github.com/GeneDx/scramble", + "licence": ["CC"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "clusters": { + "type": "file", + "description": "Tab-delimited text file containing soft-clipped clusters. Has to be generated using scramble/clusteridentifier", + "pattern": "*clusters.txt", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing information about the fasta file\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The reference FASTA file (mandatory when using CRAM files)", + "pattern": "*.{fasta,fa}", + "ontologies": [] + } + } + ], + { + "mei_ref": { + "type": "file", + "description": "Optional fasta file containing the MEI reference. This file should only be supplied in special occasions where the default isn't correct", + "pattern": "*.{fasta,fa}", + "ontologies": [] + } + } + ], + "output": { + "meis_tab": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_MEIs.txt": { + "type": "file", + "description": "Tab-delimited text file containing MEI calls", + "pattern": "*_MEIs.txt", + "ontologies": [] + } + } + ] + ], + "dels_tab": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_PredictedDeletions.txt": { + "type": "file", + "description": "Tab-delimited text file containing predicted deletions", + "pattern": "*_PredictedDeletions.txt", + "ontologies": [] + } + } + ] + ], + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf": { + "type": "file", + "description": "A VCF file containing the MEI calls and/or the predicted deletions (depending on the given arguments)", + "pattern": "*.vcf", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@nvnieuwk"], + "maintainers": ["@nvnieuwk"] } - ] - ], - "output": { - "pairs": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.split.pairs.gz": { - "type": "file", - "description": "Duplicates removed pairs", - "pattern": "*.{pairs.gz}", - "ontologies": [] - } - } - ] - ], - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "Output BAM file", - "pattern": "*.bam", - "ontologies": [] - } - } - ] - ], - "versions_pairtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pairtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pairtools --version | sed 's/.*pairtools.*version //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pairtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pairtools --version | sed 's/.*pairtools.*version //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@nservant" - ] - } - }, - { - "name": "pairtools_stats", - "path": "modules/nf-core/pairtools/stats/meta.yml", - "type": "module", - "meta": { - "name": "pairtools_stats", - "description": "Calculate pairs statistics", - "keywords": [ - "stats", - "pairs", - "pairsam" - ], - "tools": [ - { - "pairtools": { - "description": "CLI tools to process mapped Hi-C data", - "homepage": "http://pairtools.readthedocs.io/", - "documentation": "http://pairtools.readthedocs.io/", - "tool_dev_url": "https://github.com/mirnylab/pairtools", - "licence": [ - "MIT" - ], - "identifier": "" + }, + { + "name": "scramble_clusteridentifier", + "path": "modules/nf-core/scramble/clusteridentifier/meta.yml", + "type": "module", + "meta": { + "name": "scramble_clusteridentifier", + "description": "The cluster_identifier tool of Scramble identifies soft clipped clusters", + "keywords": ["bam", "cram", "soft-clipped clusters"], + "tools": [ + { + "scramble": { + "description": "Soft Clipped Read Alignment Mapper", + "homepage": "https://github.com/GeneDx/scramble", + "documentation": "https://github.com/GeneDx/scramble", + "tool_dev_url": "https://github.com/GeneDx/scramble", + "licence": ["CC"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM file", + "pattern": "*.{bam,cram}", + "ontologies": [] + } + }, + { + "input_index": { + "type": "file", + "description": "Index of the BAM/CRAM file", + "pattern": "*.{bai,crai}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing information about the fasta file\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The reference FASTA file (mandatory when using CRAM files)", + "pattern": "*.{fasta,fa}", + "ontologies": [] + } + } + ] + ], + "output": { + "clusters": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.clusters.txt": { + "type": "file", + "description": "Tab-delimited file containing the soft-clipped clusters", + "pattern": "*.clusters.txt", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@nvnieuwk"], + "maintainers": ["@nvnieuwk"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + }, + { + "name": "scvitools_scar", + "path": "modules/nf-core/scvitools/scar/meta.yml", + "type": "module", + "meta": { + "name": "scvitools_scar", + "description": "Module to use scAR to remove ambient RNA from single-cell RNA-seq data", + "keywords": ["single-cell", "scRNA-seq", "ambient RNA removal"], + "tools": [ + { + "scvitools": { + "description": "scvi-tools (single-cell variational inference tools) is a package for end-to-end analysis of single-cell omics data", + "documentation": "https://docs.scvi-tools.org/en/stable/", + "tool_dev_url": "https://github.com/scverse/scvi-tools", + "licence": ["BSD-3-clause"], + "identifier": "" + } + }, + { + "scar": { + "description": "scAR (single-cell Ambient Remover) is a deep learning model for removal of the ambient signals in droplet-based single cell omics.", + "documentation": "https://docs.scvi-tools.org/en/stable/user_guide/models/scar.html", + "tool_dev_url": "https://github.com/Novartis/scar", + "licence": ["Novartis Terms of License"], + "identifier": "biotools:scar" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "filtered": { + "type": "file", + "description": "AnnData file containing filtered data (without empty droplets)", + "pattern": "*.h5ad", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3590" + } + ] + } + }, + { + "unfiltered": { + "type": "file", + "description": "AnnData file containing unfiltered data (with empty droplets)", + "pattern": "*.h5ad", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3590" + } + ] + } + } + ], + { + "input_layer": { + "type": "string", + "description": "Layer to use as input. Defaults to `X`." + } + }, + { + "output_layer": { + "type": "string", + "description": "Layer to save the denoised counts to. Defaults to `scar`." + } + }, + { + "max_epochs": { + "type": "integer", + "description": "Maximum number of epochs to train the model. Defaults to the [heuristic default](https://docs.scvi-tools.org/en/stable/api/reference/scvi.model.get_max_epochs_heuristic.html#scvi.model.get_max_epochs_heuristic)." + } + }, + { + "n_batch": { + "type": "integer", + "description": "Number of batches to use for generating the ambient profile. Defaults to 1. This can be increased to prevent out-of-memory errors." + } + } + ], + "output": { + "h5ad": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.h5ad": { + "type": "file", + "description": "AnnData file containing decontaminated counts as `adata.X`", + "pattern": "*.h5ad", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3590" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software version", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "topics": { + "versions": [ + { + "versions.yml": { + "type": "string", + "description": "The name of the process" + } + } + ] + }, + "authors": ["@nictru"], + "maintainers": ["@nictru"] }, - { - "pairs": { - "type": "file", - "description": "pairs file", - "ontologies": [] - } - } - ] - ], - "output": { - "stats": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.pairs.stat": { - "type": "file", - "description": "Pairs statistics", - "pattern": "*{.pairs.stat}", - "ontologies": [] - } - } - ] - ], - "versions_pairtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pairtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pairtools --version | sed 's/.*pairtools.*version //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pairtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pairtools --version | sed 's/.*pairtools.*version //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "scdownstream", + "version": "dev" + } ] - ] - }, - "authors": [ - "@nservant" - ], - "maintainers": [ - "@nservant" - ] - } - }, - { - "name": "panacus_histgrowth", - "path": "modules/nf-core/panacus/histgrowth/meta.yml", - "type": "module", - "meta": { - "name": "panacus_histgrowth", - "description": "Calculates a coverage histogram from a GFA file and constructs a growth table from this as either a TSV or HTML file", - "keywords": [ - "statistics", - "pangenome", - "graph", - "gfa", - "genomics" - ], - "tools": [ - { - "panacus": { - "description": "panacus is a tool for computing counting statistics for GFA files", - "homepage": "https://github.com/marschall-lab/panacus", - "documentation": "https://github.com/marschall-lab/panacus", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } + }, + { + "name": "scvitools_solo", + "path": "modules/nf-core/scvitools/solo/meta.yml", + "type": "module", + "meta": { + "name": "scvitools_solo", + "description": "Detect doublets in single-cell RNA-Seq data", + "keywords": ["scvi", "solo", "doublets"], + "tools": [ + { + "scvitools": { + "description": "A scalable toolkit for probabilistic modeling applied to single-cell omics data", + "homepage": "https://scvi-tools.org", + "documentation": "https://docs.scvi-tools.org/en/stable/", + "tool_dev_url": "https://github.com/scverse/scvi-tools", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "h5ad": { + "type": "file", + "description": "H5AD anndata object", + "pattern": "*.h5ad", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3590" + } + ] + } + } + ], + { + "batch_key": { + "type": "string", + "description": "Column in adata.obs to use as batch. If not provided, the entire dataset is treated as a single batch." + } + }, + { + "max_epochs": { + "type": "integer", + "description": "Maximum number of epochs to train the model. Defaults to the [heuristic default](https://docs.scvi-tools.org/en/stable/api/reference/scvi.model.get_max_epochs_heuristic.html#scvi.model.get_max_epochs_heuristic)." + } + } + ], + "output": { + "h5ad": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.h5ad": { + "type": "file", + "description": "H5AD anndata object without doublets", + "pattern": "*.h5ad", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3590" + } + ] + } + } + ] + ], + "predictions": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.pkl": { + "type": "file", + "description": "pandas dataframe containing the doublet classification", + "pattern": "*.pkl", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "topics": { + "versions": [ + { + "versions.yml": { + "type": "string", + "description": "The name of the process" + } + } + ] + }, + "authors": ["@LeonHafner"], + "maintainers": ["@LeonHafner"] }, - { - "gfa": { - "type": "file", - "description": "GFA file containing a graph without overlapping nodes", - "pattern": "*.gfa", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3975" - } - ] - } - } - ], - { - "bed_subset": { - "type": "file", - "description": "Optional 1-column TXT-list of paths or 3-/12-column BED file of path coordinates for getting counts by subsetting the graph", - "pattern": "*.{txt, bed}", - "ontologies": [] - } - }, - { - "bed_exclude": { - "type": "file", - "description": "Optional 1-column TXT-list of paths or 3-/12-column BED file of path coordinates for excluding bp/nodes/edges that intersect these paths", - "pattern": "*.{txt, bed}", - "ontologies": [] - } - }, - { - "tsv_groupby": { - "type": "file", - "description": "Optional 2-column TSV file containing path to group mapping according to which counts from different paths get merged", - "pattern": "*.{txt, bed}", - "ontologies": [] - } - } - ], - "output": { - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*.{tsv, html}": { - "type": "file", - "description": "TSV file containing the statistics. Alternatively, the HTML file can be the output", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } + "pipelines": [ + { + "name": "scdownstream", + "version": "dev" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@heringerp" - ], - "maintainers": [ - "@heringerp", - "@subwaystation" - ] - } - }, - { - "name": "panacus_visualize", - "path": "modules/nf-core/panacus/visualize/meta.yml", - "type": "module", - "meta": { - "name": "panacus_visualize", - "description": "Create visualizations from a tsv coverage histogram created with panacus.", - "keywords": [ - "statistics", - "pangenome", - "graph", - "visualization", - "tsv", - "genomics" - ], - "tools": [ - { - "panacus": { - "description": "panacus is a tool for computing counting statistics for GFA files", - "homepage": "https://github.com/marschall-lab/panacus", - "documentation": "https://github.com/marschall-lab/panacus", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } + }, + { + "name": "seacr_callpeak", + "path": "modules/nf-core/seacr/callpeak/meta.yml", + "type": "module", + "meta": { + "name": "seacr_callpeak", + "description": "Call peaks using SEACR on sequenced reads in bedgraph format", + "keywords": ["peak-caller", "peaks", "bedgraph", "cut&tag", "cut&run", "chromatin", "seacr"], + "tools": [ + { + "seacr": { + "description": "SEACR is intended to call peaks and enriched regions from sparse CUT&RUN\nor chromatin profiling data in which background is dominated by \"zeroes\"\n(i.e. regions with no read coverage).\n", + "homepage": "https://github.com/FredHutch/SEACR", + "documentation": "https://github.com/FredHutch/SEACR", + "licence": ["GPL-2.0-only"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bedgraph": { + "type": "file", + "description": "The target bedgraph file from which the peaks will be calculated.\n", + "ontologies": [] + } + }, + { + "ctrlbedgraph": { + "type": "file", + "description": "Control (IgG) data bedgraph file to generate an empirical threshold for peak calling.\n", + "ontologies": [] + } + } + ], + { + "threshold": { + "type": "integer", + "description": "Threshold value used to call peaks if the ctrlbedgraph input is set to []. 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Output from parabricks/fq2bam or gatk4/baserecalibrator.", - "pattern": "*.table", - "ontologies": [] - } + }, + { + "name": "segul_aligntrim", + "path": "modules/nf-core/segul/aligntrim/meta.yml", + "type": "module", + "meta": { + "name": "segul_aligntrim", + "description": "Trim multiple sequence alignments by filtering columns based on missing data proportion or parsimony informative sites using SEGUL.", + "keywords": ["alignment", "trimming", "phylogenomics"], + "tools": [ + { + "segul": { + "description": "An ultrafast and memory efficient tool for phylogenomics", + "homepage": "https://www.segul.app", + "documentation": "https://www.segul.app/docs/cli-usage/align-trim", + "tool_dev_url": "https://github.com/hhandika/segul", + "doi": "10.1111/1755-0998.13964", + "licence": ["MIT"], + "identifier": "biotools:segul" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information.\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "aln": { + "type": "file", + "description": "One or more multiple sequence alignment files. Files with non-standard\nextensions are automatically renamed to .fa for SEGUL compatibility.\n", + "pattern": "*.{fa,fas,fasta,nex,nexus,phy,phylip,aln,alnfaa,clipkit,trimal,msa}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1921" + }, + { + "edam": "http://edamontology.org/format_1929" + }, + { + "edam": "http://edamontology.org/format_1912" + }, + { + "edam": "http://edamontology.org/format_1997" + } + ] + } + } + ] + ], + "output": { + "trimmed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}/trimmed_alignments/*": { + "type": "file", + "description": "Trimmed alignment files.", + "pattern": "*.{fas,nex,phy}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1921" + } + ] + } + } + ] + ], + "summary": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}/trimming_summary.csv": { + "type": "file", + "description": "CSV summary with per-alignment trimming statistics.", + "pattern": "*.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "versions_segul": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "segul": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "segul --version | sed 's/segul //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "segul": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "segul --version | sed 's/segul //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@eparisis"], + "maintainers": ["@eparisis"] } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing sample information.\ne.g. [ id:'test' ]\n" - } + }, + { + "name": "semibin_singleeasybin", + "path": "modules/nf-core/semibin/singleeasybin/meta.yml", + "type": "module", + "meta": { + "name": "semibin_singleeasybin", + "description": "metagenomic binning with self-supervised learning", + "keywords": ["binning", "assembly-binning", "metagenomics"], + "tools": [ + { + "semibin": { + "description": "Metagenomic binning with semi-supervised siamese neural network", + "homepage": "https://github.com/BigDataBiology/SemiBin", + "documentation": "https://semibin.readthedocs.io/en/latest/", + "tool_dev_url": "https://github.com/BigDataBiology/SemiBin", + "doi": "10.1038/s41467-022-29843-y", + "licence": ["MIT"], + "identifier": "biotools:semibin" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Fasta file of the assembled contigs", + "pattern": "*.{fa,fasta,fna,fa.gz,fasta.gz,fna.gz}", + "ontologies": [] + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram}", + "ontologies": [] + } + } + ] + ], + "output": { + "csv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "${prefix}/*.csv": { + "type": "file", + "description": "generated files", + "pattern": "*.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "model": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "${prefix}/*.h5": { + "type": "file", + "description": "model file", + "pattern": "*.h5", + "ontologies": [] + } + } + ] + ], + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "${prefix}/*.tsv": { + "type": "file", + "description": "information of bins", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "output_fasta": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "${prefix}/output_bins/*.fa.gz": { + "type": "file", + "description": "precluster fasta files", + "pattern": "*.fa", + "ontologies": [] + } + } + ] + ], + "versions_semibin": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "SemiBin": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "SemiBin2 --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "SemiBin": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "SemiBin2 --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@BigDataBiology"], + "maintainers": ["@BigDataBiology"] }, - { - "intervals": { - "type": "file", - "description": "intervals", - "ontologies": [] - } - } - ], - [ - { - "meta5": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference fasta - must be unzipped.", - "pattern": "*.fasta", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information.\ne.g. [ id:'test' ]\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "BAM file after applying BQSR.", - "pattern": "*.bam", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - } - ] - ], - "bai": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information.\ne.g. [ id:'test' ]\n" - } - }, - { - "*.bai": { - "type": "file", - "description": "bai index corresponding to output bam file.", - "pattern": "*.bam.bai", - "ontologies": [] - } - } - ] - ], - "versions_parabricks": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "parabricks": { - "type": "string", - "description": "The tool name" - } - }, - { - "pbrun version | grep -m1 '^pbrun:' | sed 's/^pbrun:[[:space:]]*//'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "parabricks": { - "type": "string", - "description": "The tool name" - } - }, - { - "pbrun version | grep -m1 '^pbrun:' | sed 's/^pbrun:[[:space:]]*//'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } + "pipelines": [ + { + "name": "mag", + "version": "5.4.2" + } ] - ] - }, - "authors": [ - "@bsiranosian" - ], - "maintainers": [ - "@bsiranosian", - "@famosab" - ] - } - }, - { - "name": "parabricks_dbsnp", - "path": "modules/nf-core/parabricks/dbsnp/meta.yml", - "type": "module", - "meta": { - "name": "parabricks_dbsnp", - "description": "NVIDIA Clara Parabricks GPU-accelerated variant calls annotation based on dbSNP database", - "keywords": [ - "annotation", - "dbsnp", - "vcf", - "germline" - ], - "tools": [ - { - "parabricks": { - "description": "NVIDIA Clara Parabricks GPU-accelerated genomics tools", - "homepage": "https://www.nvidia.com/en-us/clara/genomics/", - "documentation": "https://docs.nvidia.com/clara/parabricks/latest/index.html", - "licence": [ - "custom" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "vcf_file": { - "type": "file", - "description": "VCF file undergoing annotation.", - "pattern": "*.vcf", - "ontologies": [] - } - }, - { - "dbsnp_file": { - "type": "file", - "description": "dbSNP file required for annotation.", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } + }, + { + "name": "sentieon_applyvarcal", + "path": "modules/nf-core/sentieon/applyvarcal/meta.yml", + "type": "module", + "meta": { + "name": "sentieon_applyvarcal", + "description": "Apply a score cutoff to filter variants based on a recalibration table.\nSentieon's Aplyvarcal performs the second pass in a two-stage process called Variant Quality Score Recalibration (VQSR).\nSpecifically, it applies filtering to the input variants based on the recalibration table produced\nin the previous step VarCal and a target sensitivity value.\nhttps://support.sentieon.com/manual/usages/general/#applyvarcal-algorithm\n", + "keywords": ["sentieon", "applyvarcal", "varcal", "VQSR"], + "tools": [ + { + "sentieon": { + "description": "Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads.\nOur software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.\n", + "homepage": "https://www.sentieon.com/", + "documentation": "https://www.sentieon.com/", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF file to be recalibrated, this should be the same file as used for the first stage VariantRecalibrator.", + "pattern": "*.vcf", + "ontologies": [] + } + }, + { + "vcf_tbi": { + "type": "file", + "description": "tabix index for the input vcf file.", + "pattern": "*.vcf.tbi", + "ontologies": [] + } + }, + { + "recal": { + "type": "file", + "description": "Recalibration file produced when the input vcf was run through VariantRecalibrator in stage 1.", + "pattern": "*.recal", + "ontologies": [] + } + }, + { + "recal_index": { + "type": "file", + "description": "Index file for the recalibration file.", + "pattern": ".recal.idx", + "ontologies": [] + } + }, + { + "tranches": { + "type": "file", + "description": "Tranches file produced when the input vcf was run through VariantRecalibrator in stage 1.", + "pattern": ".tranches", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The reference fasta file", + "pattern": "*.fasta", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "fai": { + "type": "file", + "description": "Index of reference fasta file", + "pattern": "*.fasta.fai", + "ontologies": [] + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "compressed vcf file containing the recalibrated variants.", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "*.tbi": { + "type": "file", + "description": "Index of recalibrated vcf file.", + "pattern": "*vcf.gz.tbi", + "ontologies": [] + } + } + ] + ], + "versions_sentieon": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "sentieon": { + "type": "string", + "description": "The tool name" + } + }, + { + "sentieon driver --version | sed \"s/.*-//g\"": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "sentieon": { + "type": "string", + "description": "The tool name" + } + }, + { + "sentieon driver --version | sed \"s/.*-//g\"": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@assp8200"], + "maintainers": ["@assp8200"] }, - { - "tabix_file": { - "type": "file", - "description": "dbSNP file index.", - "pattern": "*.vcf.gz.tbi", - "ontologies": [] - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*.vcf": { - "type": "file", - "description": "VCF file.", - "pattern": "*{.vcf}", - "ontologies": [] - } - } - ] - ], - "compatible_versions": [ - { - "compatible_versions.yml": { - "type": "file", - "description": "File containing info on compatible CPU-based software versions.", - "pattern": "compatible_versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ], - "versions_parabricks": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "parabricks": { - "type": "string", - "description": "The tool name" - } - }, - { - "pbrun version | grep -m1 '^pbrun:' | sed 's/^pbrun:[[:space:]]*//'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "parabricks": { - "type": "string", - "description": "The tool name" - } - }, - { - "pbrun version | grep -m1 '^pbrun:' | sed 's/^pbrun:[[:space:]]*//'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } + "pipelines": [ + { + "name": "sarek", + "version": "3.8.1" + } ] - ] - }, - "authors": [ - "@Furentsu" - ], - "maintainers": [ - "@famosab" - ] - } - }, - { - "name": "parabricks_deepvariant", - "path": "modules/nf-core/parabricks/deepvariant/meta.yml", - "type": "module", - "meta": { - "name": "parabricks_deepvariant", - "description": "NVIDIA Clara Parabricks GPU-accelerated germline variant calling, replicating deepvariant.", - "keywords": [ - "variant", - "deep variant", - "vcf", - "haplotypecaller", - "germline" - ], - "tools": [ - { - "parabricks": { - "description": "NVIDIA Clara Parabricks GPU-accelerated genomics tools", - "homepage": "https://www.nvidia.com/en-us/clara/genomics/", - "documentation": "https://docs.nvidia.com/clara/parabricks/latest/index.html", - "licence": [ - "custom" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing tumor sample information - id must match read groups for this sample.\n[ id:'test']\n" - } - }, - { - "input": { - "type": "file", - "description": "bam file for sample to be variant called.", - "pattern": "*.bam", - "ontologies": [] - } - }, - { - "input_index": { - "type": "file", - "description": "bai index corresponding to input bam file. Only necessary if intervals are provided.", - "pattern": "*.bai", - "ontologies": [] - } - }, - { - "intervals": { - "type": "file", - "description": "file or files containing genomic intervals for use in base quality score recalibration.", - "pattern": "*.{bed,interval_list,picard,list,intervals}", - "ontologies": [] - } - } - ], - [ - { - "ref_meta": { - "type": "map", - "description": "Groovy Map containing reference information.\n[ id:'test']\n" - } + }, + { + "name": "sentieon_bwaindex", + "path": "modules/nf-core/sentieon/bwaindex/meta.yml", + "type": "module", + "meta": { + "name": "sentieon_bwaindex", + "description": "Create BWA index for reference genome", + "keywords": ["index", "fasta", "genome", "reference", "sentieon"], + "tools": [ + { + "sentieon": { + "description": "Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads.\nOur software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.\n", + "homepage": "https://www.sentieon.com/", + "documentation": "https://www.sentieon.com/", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input genome fasta file", + "ontologies": [] + } + } + ] + ], + "output": { + "index": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bwa": { + "type": "file", + "description": "BWA genome index files", + "pattern": "*.{amb,ann,bwt,pac,sa}", + "ontologies": [] + } + } + ] + ], + "versions_sentieon": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "sentieon": { + "type": "string", + "description": "The tool name" + } + }, + { + "sentieon driver --version | sed \"s/.*-//g\"": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "sentieon": { + "type": "string", + "description": "The tool name" + } + }, + { + "sentieon driver --version | sed \"s/.*-//g\"": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@maxulysse"], + "maintainers": ["@maxulysse"] }, - { - "fasta": { - "type": "file", - "description": "reference fasta - must be unzipped.", - "pattern": "*.fasta", - "ontologies": [] - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information.\ne.g. [ id:'test' ]\n" - } - }, - { - "*.vcf.gz": { - "type": "file", - "description": "vcf file created with deepvariant (does not support .gz for normal vcf), optional", - "pattern": "*.vcf", - "ontologies": [] - } - } - ] - ], - "gvcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information.\ne.g. [ id:'test' ]\n" - } - }, - { - "*.g.vcf.gz": { - "type": "file", - "description": "bgzipped gvcf created with deepvariant, optional", - "pattern": "*.g.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "compatible_versions": [ - { - "compatible_versions.yml": { - "type": "file", - "description": "File containing info on compatible CPU-based software versions.", - "pattern": "compatible_versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ], - "versions_parabricks": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "parabricks": { - "type": "string", - "description": "The tool name" - } - }, - { - "pbrun version | grep -m1 '^pbrun:' | sed 's/^pbrun:[[:space:]]*//'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "parabricks": { - "type": "string", - "description": "The tool name" - } - }, - { - "pbrun version | grep -m1 '^pbrun:' | sed 's/^pbrun:[[:space:]]*//'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } + "pipelines": [ + { + "name": "raredisease", + "version": "3.0.0" + } ] - ] - }, - "authors": [ - "@bsiranosian" - ], - "maintainers": [ - "@famosab" - ] - } - }, - { - "name": "parabricks_fq2bam", - "path": "modules/nf-core/parabricks/fq2bam/meta.yml", - "type": "module", - "meta": { - "name": "parabricks_fq2bam", - "description": "NVIDIA Clara Parabricks GPU-accelerated alignment, sorting, BQSR calculation, and duplicate marking. Note this nf-core module requires files to be copied into the working directory and not symlinked.", - "keywords": [ - "align", - "sort", - "bqsr", - "duplicates" - ], - "tools": [ - { - "parabricks": { - "description": "NVIDIA Clara Parabricks GPU-accelerated genomics tools", - "homepage": "https://www.nvidia.com/en-us/clara/genomics/", - "documentation": "https://docs.nvidia.com/clara/parabricks/latest/index.html", - "licence": [ - "custom" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "fastq.gz files", - "pattern": "*.fastq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - }, - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing fasta information\n" - } - }, - { - "fasta": { - "type": "file", - "description": "reference fasta file - must be unzipped", - "pattern": "*.fasta", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing index information\n" - } - }, - { - "index": { - "type": "file", - "description": "reference BWA index", - "pattern": "*.{amb,ann,bwt,pac,sa}", - "ontologies": [] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing index information\n" - } - }, - { - "intervals": { - "type": "file", - "description": "(optional) file(s) containing genomic intervals for use in base quality score recalibration (BQSR)", - "pattern": "*.{bed,interval_list,picard,list,intervals}", - "ontologies": [] - } - } - ], - [ - { - "meta5": { - "type": "map", - "description": "Groovy Map containing known sites information\n" - } + }, + { + "name": "sentieon_bwamem", + "path": "modules/nf-core/sentieon/bwamem/meta.yml", + "type": "module", + "meta": { + "name": "sentieon_bwamem", + "description": "Performs fastq alignment to a fasta reference using Sentieon's BWA MEM", + "keywords": ["mem", "bwa", "alignment", "map", "fastq", "bam", "sentieon"], + "tools": [ + { + "sentieon": { + "description": "Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads.\nOur software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.\n", + "homepage": "https://www.sentieon.com/", + "documentation": "https://www.sentieon.com/", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "Genome fastq files (single-end or paired-end)", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "index": { + "type": "file", + "description": "BWA genome index files", + "pattern": "*.{amb,ann,bwt,pac,sa}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Genome fasta file", + "pattern": "*.{fa,fasta}", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta_fai": { + "type": "file", + "description": "The index of the FASTA reference.", + "pattern": "*.fai", + "ontologies": [] + } + } + ] + ], + "output": { + "bam_and_bai": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}": { + "type": "file", + "description": "BAM file with corresponding index.", + "pattern": "*.{bam,bai}", + "ontologies": [] + } + }, + { + "${prefix}.{bai,crai}": { + "type": "file", + "description": "BAM file with corresponding index.", + "pattern": "*.{bam,bai}", + "ontologies": [] + } + } + ] + ], + "versions_bwa": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bwa": { + "type": "string", + "description": "The tool name" + } + }, + { + "sentieon bwa 2>&1 | sed -n \"s/^Version: *//p\"": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ], + "versions_sentieon": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "sentieon": { + "type": "string", + "description": "The tool name" + } + }, + { + "sentieon driver --version | sed \"s/.*-//g\"": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bwa": { + "type": "string", + "description": "The tool name" + } + }, + { + "sentieon bwa 2>&1 | sed -n \"s/^Version: *//p\"": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "sentieon": { + "type": "string", + "description": "The tool name" + } + }, + { + "sentieon driver --version | sed \"s/.*-//g\"": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@asp8200"], + "maintainers": ["@asp8200", "@DonFreed"] }, - { - "known_sites": { - "type": "file", - "description": "(optional) known sites file(s) for calculating BQSR. markdups must be true to perform BQSR.", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - }, - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ], - { - "output_fmt": { - "type": "string", - "description": "Output format for the alignment. Options are 'bam' or 'cram'", - "pattern": "{bam,cram}" - } - } - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "Sorted BAM file", - "pattern": "*.bam", - "ontologies": [] - } - } - ] - ], - "bai": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bai": { - "type": "file", - "description": "index corresponding to sorted BAM file", - "pattern": "*.bai", - "ontologies": [] - } - } - ] - ], - "cram": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.cram": { - "type": "file", - "description": "Sorted CRAM file", - "pattern": "*.cram", - "ontologies": [] - } - } - ] - ], - "crai": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.crai": { - "type": "file", - "description": "index corresponding to sorted CRAM file", - "pattern": "*.crai", - "ontologies": [] - } - } - ] - ], - "bqsr_table": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.table": { - "type": "file", - "description": "(optional) table from base quality score recalibration calculation, to be used with parabricks/applybqsr", - "pattern": "*.table", - "ontologies": [] - } - } - ] - ], - "qc_metrics": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_qc_metrics": { - "type": "directory", - "description": "(optional) optional directory of qc metrics", - "pattern": "*_qc_metrics" - } - } - ] - ], - "duplicate_metrics": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.duplicate-metrics.txt": { - "type": "file", - "description": "(optional) metrics calculated from marking duplicates in the bam file", - "pattern": "*.duplicate-metrics.txt", - "ontologies": [] - } - } - ] - ], - "compatible_versions": [ - { - "compatible_versions.yml": { - "type": "file", - "description": "File containing info on compatible CPU-based software versions.", - "pattern": "compatible_versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ], - "versions_parabricks": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "parabricks": { - "type": "string", - "description": "The tool name" - } - }, - { - "pbrun version | grep -m1 '^pbrun:' | sed 's/^pbrun:[[:space:]]*//'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "parabricks": { - "type": "string", - "description": "The tool name" - } - }, - { - "pbrun version | grep -m1 '^pbrun:' | sed 's/^pbrun:[[:space:]]*//'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } + "pipelines": [ + { + "name": "raredisease", + "version": "3.0.0" + }, + { + "name": "sarek", + "version": "3.8.1" + } ] - ] - }, - "authors": [ - "@bsiranosian", - "@adamrtalbot" - ], - "maintainers": [ - "@bsiranosian", - "@adamrtalbot", - "@gallvp", - "@famosab" - ] - }, - "pipelines": [ - { - "name": "sarek", - "version": "3.8.1" - } - ] - }, - { - "name": "parabricks_fq2bammeth", - "path": "modules/nf-core/parabricks/fq2bammeth/meta.yml", - "type": "module", - "meta": { - "name": "parabricks_fq2bammeth", - "description": "NVIDIA Clara Parabricks GPU-accelerated fast, accurate algorithm for mapping methylated DNA sequence reads to a reference genome, performing local alignment, and producing alignment for different parts of the query sequence", - "keywords": [ - "align", - "sort", - "bqsr", - "duplicates", - "bwameth" - ], - "tools": [ - { - "parabricks": { - "description": "NVIDIA Clara Parabricks GPU-accelerated genomics tools", - "homepage": "https://www.nvidia.com/en-us/clara/genomics/", - "documentation": "https://docs.nvidia.com/clara/parabricks/latest/index.html", - "licence": [ - "custom" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "fastq.gz files", - "pattern": "*.fastq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } + }, + { + "name": "sentieon_collectvcmetrics", + "path": "modules/nf-core/sentieon/collectvcmetrics/meta.yml", + "type": "module", + "meta": { + "name": "sentieon_collectvcmetrics", + "description": "Accelerated implementation of the Picard CollectVariantCallingMetrics tool.", + "keywords": ["vcf", "sentieon", "genomics"], + "tools": [ + { + "sentieon": { + "description": "Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads.\nOur software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.\n", + "homepage": "https://www.sentieon.com/", + "documentation": "https://www.sentieon.com/", + "licence": ["Commercial (requires license for use; redistribution allowed)"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "vcf": { + "type": "file", + "description": "Sorted VCF file [required]", + "pattern": "*.vcf", + "ontologies": [] + } + }, + { + "tbi": { + "type": "file", + "description": "VCF index file [required]", + "pattern": "*.vcf{,.gz}.tbi", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "dbsnp": { + "type": "file", + "description": "dbsnp VCF file [required]", + "pattern": "*.vcf{,.gz}", + "ontologies": [] + } + }, + { + "dbsnp_tbi": { + "type": "file", + "description": "dbsnp VCF index file [required]", + "pattern": "*.vcf{,.gz}.tbi", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Genome fasta file [required]", + "pattern": "*.{fa,fasta}", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "fai": { + "type": "file", + "description": "Index of the genome fasta file [required]", + "pattern": "*.fai", + "ontologies": [] + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "interval": { + "type": "file", + "description": "BED file of genome regions to draw coverage from", + "pattern": "*.bed", + "ontologies": [] + } + } + ] + ], + "output": { + "metrics": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.variant_calling_detail_metrics": { + "type": "file", + "description": "Metrics file from VCF\n", + "pattern": "*.variant_calling_detail_metrics", + "ontologies": [] + } + } + ] + ], + "summary": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.variant_calling_summary_metrics": { + "type": "file", + "description": "Summary of VCF metrics\n", + "pattern": "*.collectvcmetrics.txt", + "ontologies": [] + } + } + ] + ], + "versions_sentieon": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "sentieon": { + "type": "string", + "description": "The tool name" + } + }, + { + "sentieon driver --version | sed \"s/.*-//g\"": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "sentieon": { + "type": "string", + "description": "The tool name" + } + }, + { + "sentieon driver --version | sed \"s/.*-//g\"": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@adamrtalbot"], + "maintainers": ["@adamrtalbot"] } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing fasta information\n" - } - }, - { - "fasta": { - "type": "file", - "description": "reference fasta file - must be unzipped", - "pattern": "*.fasta", - "ontologies": [] - } + }, + { + "name": "sentieon_coveragemetrics", + "path": "modules/nf-core/sentieon/coveragemetrics/meta.yml", + "type": "module", + "meta": { + "name": "sentieon_coveragemetrics", + "description": "Accelerated implementation of the GATK DepthOfCoverage tool.", + "keywords": ["coverage", "sentieon", "genomics"], + "tools": [ + { + "sentieon": { + "description": "Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads.\nOur software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.\n", + "homepage": "https://www.sentieon.com/", + "documentation": "https://www.sentieon.com/", + "licence": ["Commercial (requires license for use; redistribution allowed)"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "bam": { + "type": "file", + "description": "Sorted BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}", + "ontologies": [] + } + }, + { + "bai": { + "type": "file", + "description": "BAM/CRAM/SAM file index", + "pattern": "*.{bai,crai}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "interval": { + "type": "file", + "description": "BED file of genome regions to draw coverage from", + "pattern": "*.bed", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Genome fasta file", + "pattern": "*.{fa,fasta}", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "fai": { + "type": "file", + "description": "Index of the genome fasta file", + "pattern": "*.fai", + "ontologies": [] + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "gene_list": { + "type": "file", + "description": "RefSeq file used to aggregate the results", + "pattern": "*", + "ontologies": [] + } + } + ] + ], + "output": { + "per_locus": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}": { + "type": "file", + "description": "The per locus coverage with no partition.", + "pattern": "${sample_id}", + "ontologies": [] + } + } + ] + ], + "sample_summary": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}.${partitions_output}_summary": { + "type": "file", + "description": "The summary for PARTITION_GROUP sample, aggregated over all bases.", + "pattern": "${sample_id}.sample_summary", + "ontologies": [] + } + } + ] + ], + "statistics": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}.${partitions_output}_interval_statistics": { + "type": "file", + "description": "The statistics for PARTITION_GROUP library, aggregated by interval.", + "pattern": "${sample_id}_interval_statistics", + "ontologies": [] + } + } + ] + ], + "coverage_counts": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}.${partitions_output}_cumulative_coverage_counts": { + "type": "file", + "description": "Contains the histogram of loci with depth larger than x.", + "pattern": "${sample_id}_cumulative_coverage_counts", + "ontologies": [] + } + } + ] + ], + "coverage_proportions": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}.${partitions_output}_cumulative_coverage_proportions": { + "type": "file", + "description": "Contains the normalized histogram of loci with depth larger than x.", + "pattern": "${sample_id}_cumulative_coverage_proportions", + "ontologies": [] + } + } + ] + ], + "interval_summary": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}.${partitions_output}_interval_summary": { + "type": "file", + "description": "The summary for PARTITION_GROUP library, aggregated by interval.", + "pattern": "${sample_id}_interval_summary", + "ontologies": [] + } + } + ] + ], + "versions_sentieon": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "sentieon": { + "type": "string", + "description": "The tool name" + } + }, + { + "sentieon driver --version | sed \"s/.*-//g\"": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "sentieon": { + "type": "string", + "description": "The tool name" + } + }, + { + "sentieon driver --version | sed \"s/.*-//g\"": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@adamrtalbot"], + "maintainers": ["@adamrtalbot"] } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing index information\n" - } + }, + { + "name": "sentieon_datametrics", + "path": "modules/nf-core/sentieon/datametrics/meta.yml", + "type": "module", + "meta": { + "name": "sentieon_datametrics", + "description": "Collects multiple quality metrics from a bam file", + "keywords": ["metrics", "bam", "sentieon"], + "tools": [ + { + "sentieon": { + "description": "Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads.\nOur software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.\n", + "homepage": "https://www.sentieon.com/", + "documentation": "https://www.sentieon.com/", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "bam": { + "type": "file", + "description": "Sorted BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}", + "ontologies": [] + } + }, + { + "bai": { + "type": "file", + "description": "Index of th sorted BAM/CRAM/SAM file", + "pattern": "*.{bai,crai,sai}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Genome fasta file", + "pattern": "*.{fa,fasta}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "fai": { + "type": "file", + "description": "Index of the genome fasta file", + "pattern": "*.fai", + "ontologies": [] + } + } + ], + { + "plot_results": { + "type": "boolean", + "description": "Boolean to determine whether plots should be generated", + "pattern": "true or false" + } + } + ], + "output": { + "mq_metrics": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*mq_metrics.txt": { + "type": "file", + "description": "File containing the information about mean base quality score for each sequencing cycle", + "pattern": "*.txt", + "ontologies": [] + } + } + ] + ], + "qd_metrics": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*qd_metrics.txt": { + "type": "file", + "description": "File containing the information about number of bases with a specific base quality score", + "pattern": "*.txt", + "ontologies": [] + } + } + ] + ], + "gc_summary": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*gc_summary.txt": { + "type": "file", + "description": "File containing the information about GC bias in the reference and the sample", + "pattern": "*.txt", + "ontologies": [] + } + } + ] + ], + "gc_metrics": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*gc_metrics.txt": { + "type": "file", + "description": "File containing the information about GC bias in the reference and the sample", + "pattern": "*.txt", + "ontologies": [] + } + } + ] + ], + "aln_metrics": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*aln_metrics.txt": { + "type": "file", + "description": "File containing the statistics about the alignment of the reads", + "pattern": "*.txt", + "ontologies": [] + } + } + ] + ], + "is_metrics": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*is_metrics.txt": { + "type": "file", + "description": "File containing the information about statistical distribution of insert sizes", + "pattern": "*.txt", + "ontologies": [] + } + } + ] + ], + "mq_plot": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*mq_metrics.pdf": { + "type": "file", + "description": "PDF containing plot of mean base quality scores", + "pattern": "*.pdf", + "ontologies": [] + } + } + ] + ], + "qd_plot": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*qd_metrics.pdf": { + "type": "file", + "description": "PDF containing plot of specific base quality score", + "pattern": "*.pdf", + "ontologies": [] + } + } + ] + ], + "is_plot": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*is_metrics.pdf": { + "type": "file", + "description": "PDF containing plot of insert sizes", + "pattern": "*.pdf", + "ontologies": [] + } + } + ] + ], + "gc_plot": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*gc_metrics.pdf": { + "type": "file", + "description": "PDF containing plot of GC bias", + "pattern": "*.pdf", + "ontologies": [] + } + } + ] + ], + "versions_sentieon": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "sentieon": { + "type": "string", + "description": "The tool name" + } + }, + { + "sentieon driver --version | sed \"s/.*-//g\"": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "sentieon": { + "type": "string", + "description": "The tool name" + } + }, + { + "sentieon driver --version | sed \"s/.*-//g\"": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@ramprasadn"], + "maintainers": ["@ramprasadn"] }, - { - "index": { - "type": "file", - "description": "reference BWA index", - "pattern": "*.{amb,ann,bwt,pac,sa}", - "ontologies": [] - } - } - ], - { - "known_sites": { - "type": "file", - "description": "(optional) known sites file(s) for calculating BQSR. markdups must be true to perform BQSR.", - "pattern": "*.vcf.gz", - "ontologies": [ + "pipelines": [ { - "edam": "http://edamontology.org/format_3989" + "name": "raredisease", + "version": "3.0.0" } - ] - } - } - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "Sorted BAM file", - "pattern": "*.bam", - "ontologies": [] - } - } - ] - ], - "bai": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bai": { - "type": "file", - "description": "index corresponding to sorted BAM file", - "pattern": "*.bai", - "ontologies": [] - } - } - ] - ], - "qc_metrics": [ - { - "qc_metrics": { - "type": "directory", - "description": "(optional) optional directory of qc metrics", - "pattern": "qc_metrics" - } - } - ], - "bqsr_table": [ - { - "*.table": { - "type": "file", - "description": "(optional) table from base quality score recalibration calculation, to be used with parabricks/applybqsr", - "pattern": "*.table", - "ontologies": [] - } - } - ], - "duplicate_metrics": [ - { - "duplicate-metrics.txt": { - "type": "file", - "description": "(optional) metrics calculated from marking duplicates in the bam file", - "pattern": "*-duplicate-metrics.txt", - "ontologies": [] - } - } - ], - "versions_parabricks": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "parabricks": { - "type": "string", - "description": "The tool name" - } - }, - { - "pbrun version | grep -m1 '^pbrun:' | sed 's/^pbrun:[[:space:]]*//'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "parabricks": { - "type": "string", - "description": "The tool name" - } - }, - { - "pbrun version | grep -m1 '^pbrun:' | sed 's/^pbrun:[[:space:]]*//'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@sateeshperi" - ], - "maintainers": [ - "@sateeshperi", - "@gallvp" - ] - }, - "pipelines": [ - { - "name": "methylseq", - "version": "4.2.0" - } - ] - }, - { - "name": "parabricks_genotypegvcf", - "path": "modules/nf-core/parabricks/genotypegvcf/meta.yml", - "type": "module", - "meta": { - "name": "parabricks_genotypegvcf", - "description": "NVIDIA Clara Parabricks GPU-accelerated joint genotyping, replicating GATK GenotypeGVCFs", - "keywords": [ - "joint-genotyping", - "gvcf", - "vcf", - "genotypegvcf", - "germline" - ], - "tools": [ - { - "parabricks": { - "description": "NVIDIA Clara Parabricks GPU-accelerated genomics tools", - "homepage": "https://www.nvidia.com/en-us/clara/genomics/", - "documentation": "https://docs.nvidia.com/clara/parabricks/latest/index.html", - "licence": [ - "custom" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "input": { - "type": "file", - "description": "gvcf file for samples to be jointly genotyped.", - "pattern": "*.{g.vcf,g.vcf.gz}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information.\n[ id:'test']\n" - } + }, + { + "name": "sentieon_dedup", + "path": "modules/nf-core/sentieon/dedup/meta.yml", + "type": "module", + "meta": { + "name": "sentieon_dedup", + "description": "Runs the sentieon tool LocusCollector followed by Dedup. LocusCollector collects read information that is used by Dedup which in turn marks or removes duplicate reads.", + "keywords": ["mem", "dedup", "map", "bam", "cram", "sentieon"], + "tools": [ + { + "sentieon": { + "description": "Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads.\nOur software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.\n", + "homepage": "https://www.sentieon.com/", + "documentation": "https://www.sentieon.com/", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file.", + "pattern": "*.bam", + "ontologies": [] + } + }, + { + "bai": { + "type": "file", + "description": "BAI file", + "pattern": "*.bai", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Genome fasta file", + "pattern": "*.{fa,fasta}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta_fai": { + "type": "file", + "description": "The index of the FASTA reference.", + "pattern": "*.fai", + "ontologies": [] + } + } + ] + ], + "output": { + "cram": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.cram": { + "type": "file", + "description": "CRAM file", + "pattern": "*.cram", + "ontologies": [] + } + } + ] + ], + "crai": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.crai": { + "type": "file", + "description": "CRAM index file", + "pattern": "*.crai", + "ontologies": [] + } + } + ] + ], + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "BAM file.", + "pattern": "*.bam", + "ontologies": [] + } + } + ] + ], + "bai": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bai": { + "type": "file", + "description": "BAI file", + "pattern": "*.bai", + "ontologies": [] + } + } + ] + ], + "score": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.score": { + "type": "file", + "description": "The score file indicates which reads LocusCollector finds are likely duplicates.", + "pattern": "*.score", + "ontologies": [] + } + } + ] + ], + "metrics": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.metrics": { + "type": "file", + "description": "Output file containing Dedup metrics incl. histogram data.", + "pattern": "*.metrics", + "ontologies": [] + } + } + ] + ], + "metrics_multiqc_tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.metrics.multiqc.tsv": { + "type": "file", + "description": "Output tsv-file containing Dedup metrics excl. histogram data.", + "pattern": "*.metrics.multiqc.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_sentieon": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "sentieon": { + "type": "string", + "description": "The tool name" + } + }, + { + "sentieon driver --version | sed \"s/.*-//g\"": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "sentieon": { + "type": "string", + "description": "The tool name" + } + }, + { + "sentieon driver --version | sed \"s/.*-//g\"": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@asp8200"], + "maintainers": ["@asp8200"] }, - { - "fasta": { - "type": "file", - "description": "reference fasta - must be unzipped.", - "pattern": "*.fasta", - "ontologies": [] - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "*.vcf": { - "type": "file", - "description": "vcf file after gvcf conversion.", - "pattern": "*.vcf", - "ontologies": [] - } - } - ] - ], - "versions_parabricks": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "parabricks": { - "type": "string", - "description": "The tool name" - } - }, - { - "pbrun version | grep -m1 '^pbrun:' | sed 's/^pbrun:[[:space:]]*//'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "parabricks": { - "type": "string", - "description": "The tool name" - } - }, - { - "pbrun version | grep -m1 '^pbrun:' | sed 's/^pbrun:[[:space:]]*//'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } + "pipelines": [ + { + "name": "raredisease", + "version": "3.0.0" + }, + { + "name": "sarek", + "version": "3.8.1" + } ] - ] - }, - "authors": [ - "@Furentsu", - "@bsiranosian" - ], - "maintainers": [ - "@famosab" - ] - } - }, - { - "name": "parabricks_haplotypecaller", - "path": "modules/nf-core/parabricks/haplotypecaller/meta.yml", - "type": "module", - "meta": { - "name": "parabricks_haplotypecaller", - "description": "NVIDIA Clara Parabricks GPU-accelerated germline variant calling, replicating GATK haplotypecaller.", - "keywords": [ - "variant", - "vcf", - "haplotypecaller", - "germline" - ], - "tools": [ - { - "parabricks": { - "description": "NVIDIA Clara Parabricks GPU-accelerated genomics tools", - "homepage": "https://www.nvidia.com/en-us/clara/genomics/", - "documentation": "https://docs.nvidia.com/clara/parabricks/latest/index.html", - "licence": [ - "custom" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information.\n[ id:'test']\n" - } - }, - { - "input": { - "type": "file", - "description": "bam file for sample to be variant called.", - "pattern": "*.bam", - "ontologies": [] - } - }, - { - "input_index": { - "type": "file", - "description": "(Optional) bai index corresponding to input bam file. Only necessary when using intervals.", - "pattern": "*.bai", - "ontologies": [] - } - }, - { - "intervals": { - "type": "file", - "description": "file or files containing genomic intervals.", - "pattern": "*.{bed,interval_list,picard,list,intervals}", - "ontologies": [] - } - } - ], - [ - { - "ref_meta": { - "type": "map", - "description": "Groovy Map containing reference information.\n[ id:'test']\n" - } + }, + { + "name": "sentieon_dnamodelapply", + "path": "modules/nf-core/sentieon/dnamodelapply/meta.yml", + "type": "module", + "meta": { + "name": "sentieon_dnamodelapply", + "description": "modifies the input VCF file by adding the MLrejected FILTER to the variants", + "keywords": ["dnamodelapply", "vcf", "filter", "sentieon"], + "tools": [ + { + "sentieon": { + "description": "Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads.\nOur software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.\n", + "homepage": "https://www.sentieon.com/", + "documentation": "https://www.sentieon.com/", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "vcf": { + "type": "file", + "description": "INPUT VCF file", + "pattern": "*.{vcf,vcf.gz}", + "ontologies": [] + } + }, + { + "idx": { + "type": "file", + "description": "Index of the input VCF file", + "pattern": "*.{tbi}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Genome fasta file", + "pattern": "*.{fa,fasta}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "fai": { + "type": "file", + "description": "Index of the genome fasta file", + "pattern": "*.fai", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "ml_model": { + "type": "file", + "description": "machine learning model file", + "pattern": "*.model", + "ontologies": [] + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "INPUT VCF file", + "pattern": "*.{vcf,vcf.gz}", + "ontologies": [] + } + } + ] + ], + "tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.vcf.gz.tbi": { + "type": "file", + "description": "Index of the input VCF file", + "pattern": "*.{tbi}", + "ontologies": [] + } + } + ] + ], + "versions_sentieon": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "sentieon": { + "type": "string", + "description": "The tool name" + } + }, + { + "sentieon driver --version | sed \"s/.*-//g\"": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "sentieon": { + "type": "string", + "description": "The tool name" + } + }, + { + "sentieon driver --version | sed \"s/.*-//g\"": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@ramprasadn"], + "maintainers": ["@ramprasadn"] }, - { - "fasta": { - "type": "file", - "description": "reference fasta - must be unzipped.", - "pattern": "*.fasta", - "ontologies": [] - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information.\ne.g. [ id:'test' ]\n" - } - }, - { - "*.vcf": { - "type": "file", - "description": "variant file.", - "pattern": "*.vcf", - "ontologies": [] - } - } - ] - ], - "gvcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information.\ne.g. [ id:'test' ]\n" - } - }, - { - "*.g.vcf.gz": { - "type": "file", - "description": "genomic variant file, gzipped.", - "pattern": "*.g.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "compatible_versions": [ - { - "compatible_versions.yml": { - "type": "file", - "description": "File containing info on compatible CPU-based software versions.", - "pattern": "compatible_versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ], - "versions_parabricks": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "parabricks": { - "type": "string", - "description": "The tool name" - } - }, - { - "pbrun version | grep -m1 '^pbrun:' | sed 's/^pbrun:[[:space:]]*//'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "parabricks": { - "type": "string", - "description": "The tool name" - } - }, - { - "pbrun version | grep -m1 '^pbrun:' | sed 's/^pbrun:[[:space:]]*//'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } + "pipelines": [ + { + "name": "raredisease", + "version": "3.0.0" + }, + { + "name": "sarek", + "version": "3.8.1" + } ] - ] - }, - "authors": [ - "@bsiranosian" - ] - } - }, - { - "name": "parabricks_indexgvcf", - "path": "modules/nf-core/parabricks/indexgvcf/meta.yml", - "type": "module", - "meta": { - "name": "parabricks_indexgvcf", - "description": "NVIDIA Clara Parabricks GPU-accelerated gvcf indexing tool.", - "keywords": [ - "vcf", - "gvcf", - "tbi", - "idx", - "index", - "GPU-accelerated" - ], - "tools": [ - { - "parabricks": { - "description": "NVIDIA Clara Parabricks GPU-accelerated genomics tools", - "homepage": "https://www.nvidia.com/en-us/clara/genomics/", - "documentation": "https://docs.nvidia.com/clara/parabricks/latest/index.html", - "licence": [ - "custom" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing gvcf information\n" - } + }, + { + "name": "sentieon_dnascope", + "path": "modules/nf-core/sentieon/dnascope/meta.yml", + "type": "module", + "meta": { + "name": "sentieon_dnascope", + "description": "DNAscope algorithm performs an improved version of Haplotype variant calling.", + "keywords": ["dnascope", "sentieon", "variant_calling"], + "tools": [ + { + "sentieon": { + "description": "Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads.\nOur software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.\n", + "homepage": "https://www.sentieon.com/", + "documentation": "https://www.sentieon.com/", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file.", + "pattern": "*.bam", + "ontologies": [] + } + }, + { + "bai": { + "type": "file", + "description": "BAI file", + "pattern": "*.bai", + "ontologies": [] + } + }, + { + "intervals": { + "type": "file", + "description": "bed or interval_list file containing interval in the reference that will be used in the analysis", + "pattern": "*.{bed,interval_list}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing meta information for fasta.\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Genome fasta file", + "pattern": "*.{fa,fasta}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing meta information for fasta index.\n" + } + }, + { + "fai": { + "type": "file", + "description": "Index of the genome fasta file", + "pattern": "*.fai", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing meta information for dbsnp.\n" + } + }, + { + "dbsnp": { + "type": "file", + "description": "Single Nucleotide Polymorphism database (dbSNP) file", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing meta information for dbsnp_tbi.\n" + } + }, + { + "dbsnp_tbi": { + "type": "file", + "description": "Index of the Single Nucleotide Polymorphism database (dbSNP) file", + "pattern": "*.vcf.gz.tbi", + "ontologies": [] + } + } + ], + [ + { + "meta6": { + "type": "map", + "description": "Groovy Map containing meta information for machine learning model for Dnascope.\n" + } + }, + { + "ml_model": { + "type": "file", + "description": "machine learning model file", + "pattern": "*.model", + "ontologies": [] + } + } + ], + { + "pcr_indel_model": { + "type": "string", + "description": "Controls the option pcr_indel_model for Dnascope.\nThe possible options are \"NONE\" (used for PCR free samples), and \"HOSTILE\", \"AGGRESSIVE\" and \"CONSERVATIVE\".\nSee Sentieons documentation for further explanation.\n" + } + }, + { + "emit_vcf": { + "type": "string", + "description": "Controls the vcf output from Dnascope.\nPossible options are \"all\", \"confident\" and \"variant\".\nSee Sentieons documentation for further explanation.\n" + } + }, + { + "emit_gvcf": { + "type": "boolean", + "description": "If true, the haplotyper will output a gvcf" + } + } + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.unfiltered.vcf.gz": { + "type": "file", + "description": "Compressed VCF file", + "pattern": "*.unfiltered.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "vcf_tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.unfiltered.vcf.gz.tbi": { + "type": "file", + "description": "Index of VCF file", + "pattern": "*.unfiltered.vcf.gz.tbi", + "ontologies": [] + } + } + ] + ], + "gvcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.g.vcf.gz": { + "type": "file", + "description": "Compressed GVCF file", + "pattern": "*.g.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "gvcf_tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.g.vcf.gz.tbi": { + "type": "file", + "description": "Index of GVCF file", + "pattern": "*.g.vcf.gz.tbi", + "ontologies": [] + } + } + ] + ], + "versions_sentieon": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "sentieon": { + "type": "string", + "description": "The tool name" + } + }, + { + "sentieon driver --version | sed \"s/.*-//g\"": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "sentieon": { + "type": "string", + "description": "The tool name" + } + }, + { + "sentieon driver --version | sed \"s/.*-//g\"": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@ramprasadn"], + "maintainers": ["@ramprasadn"] }, - { - "gvcf": { - "type": "file", - "description": "gvcf file to be indexed", - "pattern": "*.{vcf,vcf.gz}", - "ontologies": [] - } - } - ] - ], - "output": { - "gvcf_index": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing output information\n" - } - }, - { - "*.{idx,tbi}": { - "type": "file", - "description": "Index of the gvcf file", - "pattern": "*.{idx,tbi}", - "ontologies": [] - } - } - ] - ], - "compatible_versions": [ - { - "compatible_versions.yml": { - "type": "file", - "description": "File containing info on compatible CPU-based software versions.", - "pattern": "compatible_versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ], - "versions_parabricks": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "parabricks": { - "type": "string", - "description": "The tool name" - } - }, - { - "pbrun version | grep -m1 '^pbrun:' | sed 's/^pbrun:[[:space:]]*//'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "parabricks": { - "type": "string", - "description": "The tool name" - } - }, - { - "pbrun version | grep -m1 '^pbrun:' | sed 's/^pbrun:[[:space:]]*//'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } + "pipelines": [ + { + "name": "raredisease", + "version": "3.0.0" + }, + { + "name": "sarek", + "version": "3.8.1" + } ] - ] - }, - "authors": [ - "@Furentsu", - "@bsiranosian" - ], - "maintainers": [ - "@famosab" - ] - } - }, - { - "name": "parabricks_minimap2", - "path": "modules/nf-core/parabricks/minimap2/meta.yml", - "type": "module", - "meta": { - "name": "parabricks_minimap2", - "description": "NVIDIA Clara Parabricks GPU-accelerated minimap2 for aligning long read sequences against a large reference database using an accelerated KSW2 to convert FASTQ to BAM/CRAM.", - "keywords": [ - "align", - "sort", - "bqsr", - "duplicates", - "long read" - ], - "tools": [ - { - "parabricks": { - "description": "NVIDIA Clara Parabricks GPU-accelerated genomics tools", - "homepage": "https://www.nvidia.com/en-us/clara/genomics/", - "documentation": "https://docs.nvidia.com/clara/parabricks/latest/index.html", - "licence": [ - "custom" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "Input read file, supported formats - 'fastq', 'fastq.gz', 'fq', 'fq.gz', 'bam'", - "pattern": "^.*\\.(fastq|fastq\\.gz|fq|fq\\.gz|bam)$", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - }, - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing fasta information\n" - } - }, - { - "fasta": { - "type": "file", - "description": "reference fasta file - must be unzipped", - "pattern": "*.fasta", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing index information\n" - } - }, - { - "intervals": { - "type": "file", - "description": "(optional) file(s) containing genomic intervals for use in base quality score recalibration (BQSR)", - "pattern": "*.{bed,interval_list,picard,list,intervals}", - "ontologies": [] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing known sites information\n" - } + }, + { + "name": "sentieon_gvcftyper", + "path": "modules/nf-core/sentieon/gvcftyper/meta.yml", + "type": "module", + "meta": { + "name": "sentieon_gvcftyper", + "description": "Perform joint genotyping on one or more samples pre-called with Sentieon's Haplotyper.\n", + "keywords": ["joint genotyping", "genotype", "gvcf"], + "tools": [ + { + "sentieon": { + "description": "Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads.\nOur software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.\n", + "homepage": "https://www.sentieon.com/", + "documentation": "https://www.sentieon.com/", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "gvcfs": { + "type": "file", + "description": "gVCF(.gz) file\n", + "pattern": "*.{vcf,vcf.gz}", + "ontologies": [] + } + }, + { + "tbis": { + "type": "file", + "description": "index of gvcf file\n", + "pattern": "*.tbi", + "ontologies": [] + } + }, + { + "intervals": { + "type": "file", + "description": "Interval file with the genomic regions included in the library (optional)", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference fasta file", + "pattern": "*.fasta", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Reference fasta index file", + "pattern": "*.fai", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "dbsnp": { + "type": "file", + "description": "dbSNP VCF file", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "dbsnp_tbi": { + "type": "file", + "description": "dbSNP VCF index file", + "pattern": "*.tbi", + "ontologies": [] + } + } + ] + ], + "output": { + "vcf_gz": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "VCF file", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "vcf_gz_tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz.tbi": { + "type": "file", + "description": "VCF index file", + "pattern": "*.vcf.gz.tbi", + "ontologies": [] + } + } + ] + ], + "versions_sentieon": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "sentieon": { + "type": "string", + "description": "The tool name" + } + }, + { + "sentieon driver --version | sed \"s/.*-//g\"": { + "type": "eval", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "sentieon": { + "type": "string", + "description": "The tool name" + } + }, + { + "sentieon driver --version | sed \"s/.*-//g\"": { + "type": "eval", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@asp8200"], + "maintainers": ["@asp8200"] }, - { - "known_sites": { - "type": "file", - "description": "(optional) known sites file(s) for calculating BQSR. markdups must be true to perform BQSR.", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - }, - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ], - { - "output_fmt": { - "type": "string", - "description": "Output format for the alignment. Options are 'bam' or 'cram'", - "pattern": "{bam,cram}" - } - } - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "Sorted BAM file", - "pattern": "*.bam", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - } - ] - ], - "bai": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bai": { - "type": "file", - "description": "index corresponding to sorted BAM file", - "pattern": "*.bai", - "ontologies": [] - } - } - ] - ], - "cram": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.cram": { - "type": "file", - "description": "Sorted CRAM file", - "pattern": "*.cram", - "ontologies": [] - } - } - ] - ], - "crai": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.crai": { - "type": "file", - "description": "index corresponding to sorted CRAM file", - "pattern": "*.crai", - "ontologies": [] - } - } - ] - ], - "bqsr_table": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.table": { - "type": "file", - "description": "(optional) table from base quality score recalibration calculation, to be used with parabricks/applybqsr", - "pattern": "*.table", - "ontologies": [] - } - } - ] - ], - "qc_metrics": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_qc_metrics": { - "type": "directory", - "description": "(optional) optional directory of qc metrics", - "pattern": "*_qc_metrics" - } - } - ] - ], - "duplicate_metrics": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.duplicate-metrics.txt": { - "type": "file", - "description": "(optional) metrics calculated from marking duplicates in the bam file", - "pattern": "*.duplicate-metrics.txt", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2330" - } - ] - } - } - ] - ], - "compatible_versions": [ - { - "compatible_versions.yml": { - "type": "file", - "description": "File containing info on compatible CPU-based software versions.", - "pattern": "compatible_versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ], - "versions_parabricks": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "parabricks": { - "type": "string", - "description": "The tool name" - } - }, - { - "pbrun version | grep -m1 '^pbrun:' | sed 's/^pbrun:[[:space:]]*//'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "parabricks": { - "type": "string", - "description": "The tool name" - } - }, - { - "pbrun version | grep -m1 '^pbrun:' | sed 's/^pbrun:[[:space:]]*//'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } + "pipelines": [ + { + "name": "sarek", + "version": "3.8.1" + } ] - ] - }, - "authors": [ - "@haidyi" - ], - "maintainers": [ - "@haidyi" - ] - } - }, - { - "name": "parabricks_mutectcaller", - "path": "modules/nf-core/parabricks/mutectcaller/meta.yml", - "type": "module", - "meta": { - "name": "parabricks_mutectcaller", - "description": "NVIDIA Clara Parabricks GPU-accelerated somatic variant calling, replicating GATK Mutect2.", - "keywords": [ - "variant", - "vcf", - "mutect2", - "mutect", - "somatic" - ], - "tools": [ - { - "parabricks": { - "description": "NVIDIA Clara Parabricks GPU-accelerated genomics tools", - "homepage": "https://www.nvidia.com/en-us/clara/genomics/", - "documentation": "https://docs.nvidia.com/clara/parabricks/latest/index.html", - "licence": [ - "custom" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information - tumor_id and normal_id must match read groups for the respective samples.\n[ id:'test', tumor_id:'tumor', normal_id:'normal' ]\n" - } - }, - { - "tumor_bam": { - "type": "file", - "description": "bam file for tumor sample.", - "pattern": "*.bam", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - }, - { - "tumor_bam_index": { - "type": "file", - "description": "(Optional) bai index corresponding to tumor bam file. Only required if intervals are provided.", - "pattern": "*.bam.bai", - "ontologies": [] - } - }, - { - "normal_bam": { - "type": "file", - "description": "(Optional) bam file for normal sample in tumor-vs-normal calling.", - "pattern": "*.bam", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - }, - { - "normal_bam_index": { - "type": "file", - "description": "(Optional) bai index corresponding to normal bam file. Only required if intervals are provided.", - "pattern": "*.bam.bai", - "ontologies": [] - } - }, - { - "intervals": { - "type": "file", - "description": "(Optional) file or files containing genomic intervals for use in base quality score recalibration.", - "pattern": "*.{bed,interval_list,picard,list,intervals}", - "ontologies": [] - } - } - ], - [ - { - "ref_meta": { - "type": "map", - "description": "Groovy Map containing reference information\n[ id:'homo_sapiens' ]\n" - } + }, + { + "name": "sentieon_haplotyper", + "path": "modules/nf-core/sentieon/haplotyper/meta.yml", + "type": "module", + "meta": { + "name": "sentieon_haplotyper", + "description": "Runs Sentieon's haplotyper for germline variant calling.", + "keywords": ["sentieon", "haplotypecaller", "haplotype"], + "tools": [ + { + "sentieon": { + "description": "Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads.\nOur software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.\n", + "homepage": "https://www.sentieon.com/", + "documentation": "https://www.sentieon.com/", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM file from alignment", + "pattern": "*.{bam,cram}", + "ontologies": [] + } + }, + { + "input_index": { + "type": "file", + "description": "BAI/CRAI file from alignment", + "pattern": "*.{bai,crai}", + "ontologies": [] + } + }, + { + "intervals": { + "type": "file", + "description": "Bed file with the genomic regions included in the library (optional)", + "ontologies": [] + } + }, + { + "recal_table": { + "type": "file", + "description": "Recalibration table from sentieon/qualcal (optional)", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Genome fasta file", + "pattern": "*.{fa,fasta}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "The index of the FASTA reference.", + "pattern": "*.fai", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "dbsnp": { + "type": "file", + "description": "VCF file containing known sites (optional)", + "ontologies": [] + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "dbsnp_tbi": { + "type": "file", + "description": "VCF index of dbsnp (optional)", + "ontologies": [] + } + } + ], + { + "emit_vcf": { + "type": "string", + "description": "Controls the vcf output from the haplotyper.\nIf emit_vcf is set to \"all\" then the haplotyper will output a vcf generated by the haplotyper in emit-mode \"all\".\nIf emit_vcf is set to \"confident\" then the haplotyper will output a vcf generated by the haplotyper in emit-mode \"confident\".\nIf emit_vcf is set to \"variant\" then the haplotyper will output a vcf generated by the haplotyper in emit_mode \"confident\".\n" + } + }, + { + "emit_gvcf": { + "type": "boolean", + "description": "If true, the haplotyper will output a gvcf" + } + } + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.unfiltered.vcf.gz": { + "type": "file", + "description": "Compressed VCF file", + "pattern": "*.unfiltered.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "vcf_tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.unfiltered.vcf.gz.tbi": { + "type": "file", + "description": "Index of VCF file", + "pattern": "*.unfiltered.vcf.gz.tbi", + "ontologies": [] + } + } + ] + ], + "gvcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.g.vcf.gz": { + "type": "file", + "description": "Compressed GVCF file", + "pattern": "*.g.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "gvcf_tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.g.vcf.gz.tbi": { + "type": "file", + "description": "Index of GVCF file", + "pattern": "*.g.vcf.gz.tbi", + "ontologies": [] + } + } + ] + ], + "versions_sentieon": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "sentieon": { + "type": "string", + "description": "The tool name" + } + }, + { + "sentieon driver --version | sed \"s/.*-//g\"": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "sentieon": { + "type": "string", + "description": "The tool name" + } + }, + { + "sentieon driver --version | sed \"s/.*-//g\"": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@asp8200"], + "maintainers": ["@asp8200"] }, - { - "fasta": { - "type": "file", - "description": "reference fasta - must be unzipped.", - "pattern": "*.fasta", - "ontologies": [] - } - } - ], - { - "panel_of_normals": { - "type": "file", - "description": "(Optional) panel of normals file.", - "pattern": "*.vcf.gz", - "ontologies": [ + "pipelines": [ { - "edam": "http://edamontology.org/format_3989" + "name": "sarek", + "version": "3.8.1" } - ] - } - }, - { - "panel_of_normals_index": { - "type": "file", - "description": "(Optional) tbi index corresponding to panel of normals file.", - "pattern": "*.tbi", - "ontologies": [] - } - } - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.vcf.gz": { - "type": "file", - "description": "Compressed variants file. Will include an annotated vcf file if panel of normals is used.", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "stats": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.vcf.gz.stats": { - "type": "file", - "description": "Variant statistics.", - "pattern": "*.vcf.gz.stats", - "ontologies": [] - } - } - ] - ], - "compatible_versions": [ - { - "compatible_versions.yml": { - "type": "file", - "description": "File containing info on compatible CPU-based software versions.", - "pattern": "compatible_versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ], - "versions_parabricks": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "parabricks": { - "type": "string", - "description": "The tool name" - } - }, - { - "pbrun version | grep -m1 '^pbrun:' | sed 's/^pbrun:[[:space:]]*//'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "parabricks": { - "type": "string", - "description": "The tool name" - } - }, - { - "pbrun version | grep -m1 '^pbrun:' | sed 's/^pbrun:[[:space:]]*//'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } ] - ] - }, - "authors": [ - "@bsiranosian" - ], - "maintainers": [ - "@famosab" - ] - } - }, - { - "name": "parabricks_rnafq2bam", - "path": "modules/nf-core/parabricks/rnafq2bam/meta.yml", - "type": "module", - "meta": { - "name": "parabricks_rnafq2bam", - "description": "This tool is the equivalent of fq2bam for RNA-Seq samples, receiving inputs in FASTQ format, performing alignment with the splice-aware STAR algorithm, optionally marking of duplicate reads, and outputting an aligned BAM file ready for variant and fusion calling.", - "keywords": [ - "align", - "star", - "rna" - ], - "tools": [ - { - "parabricks": { - "description": "NVIDIA Clara Parabricks GPU-accelerated genomics tools", - "homepage": "https://www.nvidia.com/en-us/clara/genomics/", - "documentation": "https://docs.nvidia.com/clara/parabricks/latest/index.html", - "licence": [ - "https://docs.nvidia.com/clara/parabricks/latest/eula.html" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "fastq.gz files", - "pattern": "*.fastq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - }, - { - "edam": "http://edamontology.org/format_1930" - } - ] - } + }, + { + "name": "sentieon_hsmetrics", + "path": "modules/nf-core/sentieon/hsmetrics/meta.yml", + "type": "module", + "meta": { + "name": "sentieon_hsmetrics", + "description": "Collects hybrid-selection (HS) metrics for a SAM or BAM file.", + "keywords": ["metrics", "bam", "sentieon"], + "tools": [ + { + "sentieon": { + "description": "Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads.\nOur software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.\n", + "homepage": "https://www.sentieon.com/", + "documentation": "https://www.sentieon.com/", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + }, + { + "bai": { + "type": "file", + "description": "Index of the BAM/CRAM/SAM file", + "pattern": "*.{bai,crai,sai}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3327" + } + ] + } + }, + { + "bait_intervals": { + "type": "file", + "description": "An interval file that contains the locations of the baits used.", + "pattern": "*.{interval_list,bed,bed.gz}", + "ontologies": [] + } + }, + { + "target_intervals": { + "type": "file", + "description": "An interval file that contains the locations of the targets.", + "pattern": "*.{interval_list,bed,bed.gz}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Genome fasta file", + "pattern": "*.{fa,fasta}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "fai": { + "type": "file", + "description": "Index of the genome fasta file", + "pattern": "*.fai", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3326" + } + ] + } + } + ] + ], + "output": { + "metrics": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "Alignment metrics related to how many reads overlap the target/bait regions.", + "pattern": "*.txt", + "ontologies": [] + } + } + ] + ], + "versions_sentieon": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "sentieon": { + "type": "string", + "description": "The tool name" + } + }, + { + "sentieon driver --version | sed 's/.*-//g'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "sentieon": { + "type": "string", + "description": "The tool name" + } + }, + { + "sentieon driver --version | sed 's/.*-//g'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@sppearce"], + "maintainers": ["@sppearce"] } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing fasta information\n" - } + }, + { + "name": "sentieon_qualcal", + "path": "modules/nf-core/sentieon/qualcal/meta.yml", + "type": "module", + "meta": { + "name": "sentieon_qualcal", + "description": "Generate recalibration table and optionally perform base quality recalibration", + "keywords": ["base quality score recalibration", "bqsr", "sentieon"], + "tools": [ + { + "sentieon": { + "description": "Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads.\nOur software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.\n", + "homepage": "https://www.sentieon.com/", + "documentation": "https://www.sentieon.com/", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM file from alignment", + "pattern": "*.{bam,cram}", + "ontologies": [] + } + }, + { + "input_index": { + "type": "file", + "description": "BAI/CRAI file from alignment", + "pattern": "*.{bai,crai}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The reference fasta file", + "pattern": "*.fasta", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Index of reference fasta file", + "pattern": "*.fasta.fai", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "known_sites": { + "type": "file", + "description": "VCF files with known sites for indels / snps (optional)", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "known_sites_tbi": { + "type": "file", + "description": "Tabix index of the known_sites (optional)", + "pattern": "*.vcf.gz.tbi", + "ontologies": [] + } + } + ], + [ + { + "meta6": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "recalibration_table": { + "type": "file", + "description": "File containing recalibration values (optional)", + "pattern": "*.table", + "ontologies": [] + } + } + ], + { + "generate_recalibrated_bams": { + "type": "boolean", + "description": "If truem, writes recalibrated bams to disc" + } + } + ], + "output": { + "table": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.table": { + "type": "file", + "description": "Pre Recalibration table (optional)", + "pattern": "*.table", + "ontologies": [] + } + } + ] + ], + "table_post": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.table.post": { + "type": "file", + "description": "Post recalibration table (optional)", + "pattern": "*.table.post", + "ontologies": [] + } + } + ] + ], + "recal_alignment": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{cram,bam}": { + "type": "file", + "description": "Recalibrated input files (optional)", + "pattern": "*.{bam,cram}", + "ontologies": [] + } + } + ] + ], + "csv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.csv": { + "type": "file", + "description": "Recalibration results output file used for plotting. (optional)", + "pattern": "*.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "pdf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.pdf": { + "type": "file", + "description": "PDF file containing graphs (optional)", + "pattern": "*.pdf", + "ontologies": [] + } + } + ] + ], + "versions_sentieon": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "sentieon": { + "type": "string", + "description": "The tool name" + } + }, + { + "sentieon driver --version | sed \"s/.*-//g\"": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@FriederikeHanssen"], + "maintainers": ["@FriederikeHanssen"], + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "sentieon": { + "type": "string", + "description": "The tool name" + } + }, + { + "sentieon driver --version | sed \"s/.*-//g\"": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + } + } + }, + { + "name": "sentieon_readwriter", + "path": "modules/nf-core/sentieon/readwriter/meta.yml", + "type": "module", + "meta": { + "name": "sentieon_readwriter", + "description": "Merges BAM files, and/or convert them into cram files. Also, outputs the result of applying the Base Quality Score Recalibration to a file.", + "keywords": ["merge", "convert", "readwriter", "sentieon"], + "tools": [ + { + "sentieon": { + "description": "Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads.\nOur software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.\n", + "homepage": "https://www.sentieon.com/", + "documentation": "https://www.sentieon.com/", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM file.", + "pattern": "*.{bam,cram}", + "ontologies": [] + } + }, + { + "index": { + "type": "file", + "description": "BAI/CRAI file.", + "pattern": "*.{bai,crai}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Genome fasta file", + "pattern": "*.{fa,fasta}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "The index of the FASTA reference.", + "pattern": "*.fai", + "ontologies": [] + } + } + ] + ], + "output": { + "output": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}": { + "type": "file", + "description": "BAM/CRAM file. Depends on how ext.prefix is set. BAM \"ext.prefix = .bam\", CRAM \"ext.prefix = .cram\". Defaults to cram", + "pattern": "*.{bam,cram}", + "ontologies": [] + } + } + ] + ], + "index": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.${index}": { + "type": "file", + "description": "BAM/CRAM index file", + "pattern": "*.{bai,crai}", + "ontologies": [] + } + } + ] + ], + "output_index": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}": { + "type": "file", + "description": "BAM/CRAM file. Depends on how ext.prefix is set. BAM \"ext.prefix = .bam\", CRAM \"ext.prefix = .cram\". Defaults to cram", + "pattern": "*.{bam,cram}", + "ontologies": [] + } + }, + { + "${prefix}.${index}": { + "type": "file", + "description": "BAM/CRAM index file", + "pattern": "*.{bai,crai}", + "ontologies": [] + } + } + ] + ], + "versions_sentieon": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "sentieon": { + "type": "string", + "description": "The tool name" + } + }, + { + "sentieon driver --version | sed \"s/.*-//g\"": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "sentieon": { + "type": "string", + "description": "The tool name" + } + }, + { + "sentieon driver --version | sed \"s/.*-//g\"": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@ramprasadn"], + "maintainers": ["@ramprasadn"] }, - { - "fasta": { - "type": "file", - "description": "reference fasta file - must be unzipped", - "pattern": "*.fasta", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing genome lib dir information\n" - } + "pipelines": [ + { + "name": "raredisease", + "version": "3.0.0" + } + ] + }, + { + "name": "sentieon_rsemcalculateexpression", + "path": "modules/nf-core/sentieon/rsemcalculateexpression/meta.yml", + "type": "module", + "meta": { + "name": "sentieon_rsemcalculateexpression", + "description": "Calculate expression with RSEM", + "keywords": ["rsem", "expression", "quantification", "sentieon"], + "tools": [ + { + "rseqc": { + "description": "RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome\n", + "homepage": "https://github.com/deweylab/RSEM", + "documentation": "https://github.com/deweylab/RSEM", + "doi": "10.1186/1471-2105-12-323", + "licence": ["GPL-3.0-or-later"], + "identifier": "biotools:rsem" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "Input reads for quantification", + "pattern": "*.fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ], + { + "index": { + "type": "file", + "description": "RSEM index", + "pattern": "rsem/*", + "ontologies": [] + } + } + ], + "output": { + "counts_gene": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.genes.results": { + "type": "file", + "description": "Expression counts on gene level", + "pattern": "*.genes.results", + "ontologies": [] + } + } + ] + ], + "counts_transcript": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.isoforms.results": { + "type": "file", + "description": "Expression counts on transcript level", + "pattern": "*.isoforms.results", + "ontologies": [] + } + } + ] + ], + "stat": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.stat": { + "type": "file", + "description": "RSEM statistics", + "pattern": "*.stat", + "ontologies": [] + } + } + ] + ], + "logs": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.log": { + "type": "file", + "description": "RSEM logs", + "pattern": "*.log", + "ontologies": [] + } + } + ] + ], + "bam_star": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.STAR.genome.bam": { + "type": "file", + "description": "BAM file generated by STAR (optional)", + "pattern": "*.STAR.genome.bam", + "ontologies": [] + } + } + ] + ], + "bam_genome": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}.genome.bam": { + "type": "file", + "description": "Genome BAM file (optional)", + "pattern": "*.genome.bam", + "ontologies": [] + } + } + ] + ], + "bam_transcript": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}.transcript.bam": { + "type": "file", + "description": "Transcript BAM file (optional)", + "pattern": "*.transcript.bam", + "ontologies": [] + } + } + ] + ], + "versions_rsem": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "rsem": { + "type": "string", + "description": "The tool name" + } + }, + { + "rsem-calculate-expression --version | sed -e \"s/Current version: RSEM v//g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_star": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "star": { + "type": "string", + "description": "The tool name" + } + }, + { + "STAR --version | sed -e \"s/STAR_//g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_sentieon": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "sentieon": { + "type": "string", + "description": "The tool name" + } + }, + { + "sentieon driver --version 2>&1 | sed -e \"s/sentieon-genomics-//g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "rsem": { + "type": "string", + "description": "The tool name" + } + }, + { + "rsem-calculate-expression --version | sed -e \"s/Current version: RSEM v//g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "star": { + "type": "string", + "description": "The tool name" + } + }, + { + "STAR --version | sed -e \"s/STAR_//g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "sentieon": { + "type": "string", + "description": "The tool name" + } + }, + { + "sentieon driver --version 2>&1 | sed -e \"s/sentieon-genomics-//g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@FriederikeHanssen"], + "maintainers": ["@FriederikeHanssen"] }, - { - "index": { - "type": "directory", - "description": "Path to a genome resource library directory. The indexing required to run STAR should be completed by the user beforehand.", - "pattern": "*", - "ontologies": [] - } - } - ], - { - "qc_metrics": { - "type": "boolean", - "description": "Optionally report QC metrics" - } - }, - { - "mark_duplicates": { - "type": "boolean", - "description": "Optionally mark duplicates" - } - } - ], - "output": { - "log_final": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.Log.final.out": { - "type": "file", - "description": "STAR log final out file", - "pattern": "*Log.final.out", - "ontologies": [] - } - } + "pipelines": [ + { + "name": "rnaseq", + "version": "3.26.0" + } ] - ], - "log_out": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.Log.out": { - "type": "file", - "description": "STAR log out file", - "pattern": "*Log.out", - "ontologies": [] - } - } - ] - ], - "log_progress": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.Log.progress.out": { - "type": "file", - "description": "STAR log progress out file", - "pattern": "*Log.progress.out", - "ontologies": [] - } - } - ] - ], - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.bam": { - "type": "file", - "description": "Output BAM file containing read alignments", - "pattern": "*.{bam}", - "ontologies": [] - } - } - ] - ], - "bai": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.bam.bai": { - "type": "file", - "description": "Output BAM index file", - "pattern": "*.{bam}.{bai}", - "ontologies": [] - } - } - ] - ], - "bam_sorted": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.sortedByCoord.out.bam": { - "type": "file", - "description": "Output BAM file of read alignments sorted by coordinate (optional)", - "pattern": "*.sortedByCoord.out.bam", - "ontologies": [] - } - } - ] - ], - "bam_sorted_aligned": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.Aligned.sortedByCoord.out.bam": { - "type": "file", - "description": "Output BAM file of read alignments sorted by coordinate (optional)", - "pattern": "*.Aligned.sortedByCoord.out.bam", - "ontologies": [] - } - } - ] - ], - "bam_transcript": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*toTranscriptome.out.bam": { - "type": "file", - "description": "Output BAM file of transcriptome alignment (optional)", - "pattern": "*toTranscriptome.out.bam", - "ontologies": [] - } - } - ] - ], - "bam_unsorted": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*Aligned.unsort.out.bam": { - "type": "file", - "description": "Unsorted BAM file of read alignments (optional)", - "pattern": "*Aligned.unsort.out.bam", - "ontologies": [] - } - } - ] - ], - "fastq": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*fastq.gz": { - "type": "file", - "description": "Unmapped FastQ files (optional)", - "pattern": "*fastq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "tab": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tab": { - "type": "file", - "description": "STAR output tab file(s) (optional)", - "pattern": "*.tab", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "spl_junc_tab": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.SJ.out.tab": { - "type": "file", - "description": "STAR output splice junction tab file", - "pattern": "*.SJ.out.tab", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "read_per_gene_tab": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.ReadsPerGene.out.tab": { - "type": "file", - "description": "STAR output read per gene tab file", - "pattern": "*.ReadsPerGene.out.tab", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "junction": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.out.junction": { - "type": "file", - "description": "STAR chimeric junction output file (optional)", - "pattern": "*.out.junction", - "ontologies": [] - } - } - ] - ], - "sam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.out.sam": { - "type": "file", - "description": "STAR output SAM file(s) (optional)", - "pattern": "*.out.sam", - "ontologies": [] - } - } - ] - ], - "wig": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.wig": { - "type": "file", - "description": "STAR output wiggle format file(s) (optional)", - "pattern": "*.wig", - "ontologies": [] - } - } - ] - ], - "bedgraph": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bg": { - "type": "file", - "description": "STAR output bedGraph format file(s) (optional)", - "pattern": "*.bg", - "ontologies": [] - } - } - ] - ], - "qc_metrics": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}_qc_metrics": { - "type": "directory", - "description": "Directory containing QC metrics output by STAR (optional)", - "pattern": "*_qc_metrics", - "ontologies": [] - } - } - ] - ], - "duplicate_metrics": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.duplicate-metrics.txt": { - "type": "file", - "description": "File containing duplicate metrics output by STAR (optional)", - "pattern": "*.duplicate-metrics.txt", - "ontologies": [] - } - } - ] - ], - "versions_parabricks": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "parabricks": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pbrun version 2>&1 | grep -Po '(?<=^pbrun: ).*'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "parabricks": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pbrun version 2>&1 | grep -Po '(?<=^pbrun: ).*'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@gburnett-nvidia" - ], - "maintainers": [ - "@gburnett-nvidia" - ] - }, - "pipelines": [ - { - "name": "rnaseq", - "version": "3.26.0" - } - ] - }, - { - "name": "parabricks_starfusion", - "path": "modules/nf-core/parabricks/starfusion/meta.yml", - "type": "module", - "meta": { - "name": "parabricks_starfusion", - "description": "This tool uses the GPU to perform fusion calling for RNA-Seq samples, utilizing the STAR-Fusion algorithm. This requires input of a genome resource library, in accordance with the original STAR-Fusion tool, and outputs candidate fusion transcripts.", - "keywords": [ - "fusion", - "starfusion", - "rna" - ], - "tools": [ - { - "parabricks": { - "description": "NVIDIA Clara Parabricks GPU-accelerated genomics tools", - "homepage": "https://www.nvidia.com/en-us/clara/genomics/", - "documentation": "https://docs.nvidia.com/clara/parabricks/latest/index.html", - "licence": [ - "https://docs.nvidia.com/clara/parabricks/latest/eula.html" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "chimeric_junction": { - "type": "file", - "description": "Path to the Chimeric.out.junction file produced by STAR", - "pattern": "*/Chimeric.out.junction", - "ontologies": [] - } - } - ], - [ - { - "meta1": { - "type": "map", - "description": "Groovy Map containing genome lib dir information\n" - } - }, - { - "genome_lib_dir": { - "type": "directory", - "description": "Path to a genome resource library directory. The indexing required to run STAR should be completed by the user beforehand.", - "pattern": "*", - "ontologies": [] - } - } - ] - ], - "output": { - "fusions": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fusion_predictions.tsv": { - "type": "file", - "description": "Fusion events from STAR-fusion", - "pattern": "fusion_predictions.tsv" - } - } - ] - ], - "abridged": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fusion_predictions.abridged.tsv": { - "type": "file", - "description": "Abridged version of fusion events from STAR-fusion", - "pattern": "fusion_predictions.abridged.tsv" - } - } - ] - ], - "versions_parabricks": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "parabricks": { - "type": "string", - "description": "The tool name" - } - }, - { - "pbrun version | grep -m1 '^pbrun:' | sed 's/^pbrun:[[:space:]]*//'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "parabricks": { - "type": "string", - "description": "The tool name" - } - }, - { - "pbrun version | grep -m1 '^pbrun:' | sed 's/^pbrun:[[:space:]]*//'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@gburnett-nvidia" - ], - "maintainers": [ - "@gburnett-nvidia" - ] - } - }, - { - "name": "parabricks_starfusion_build", - "path": "modules/nf-core/parabricks/starfusion_build/meta.yml", - "type": "module", - "meta": { - "name": "parabricks_starfusion_build", - "description": "Download STAR-fusion genome resource required to run STAR-Fusion caller", - "keywords": [ - "download", - "starfusion", - "build" - ], - "tools": [ - { - "star-fusion": { - "description": "Fusion calling algorithm for RNAseq data", - "homepage": "https://github.com/STAR-Fusion/", - "documentation": "https://github.com/STAR-Fusion/STAR-Fusion/wiki/installing-star-fusion", - "tool_dev_url": "https://github.com/STAR-Fusion/STAR-Fusion", - "doi": "10.1186/s13059-019-1842-9", - "licence": [ - "GPL v3" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Metadata map", - "required": true - } - }, - { - "fasta": { - "type": "file", - "description": "Input FASTA file", - "pattern": "*.{fa,fasta}", - "required": true, - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Second metadata map", - "required": true - } + }, + { + "name": "sentieon_rsempreparereference", + "path": "modules/nf-core/sentieon/rsempreparereference/meta.yml", + "type": "module", + "meta": { + "name": "sentieon_rsempreparereference", + "description": "Prepare a reference genome for RSEM", + "keywords": ["rsem", "genome", "index", "sentieon"], + "tools": [ + { + "rseqc": { + "description": "RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome\n", + "homepage": "https://github.com/deweylab/RSEM", + "documentation": "https://github.com/deweylab/RSEM", + "doi": "10.1186/1471-2105-12-323", + "licence": ["GPL-3.0-or-later"], + "identifier": "biotools:rsem" + } + } + ], + "input": [ + { + "fasta": { + "type": "file", + "description": "The Fasta file of the reference genome", + "pattern": "*.{fasta,fa}", + "ontologies": [] + } + }, + { + "gtf": { + "type": "file", + "description": "The GTF file of the reference genome", + "pattern": "*.gtf", + "ontologies": [] + } + } + ], + "output": { + "index": [ + { + "rsem": { + "type": "directory", + "description": "RSEM index directory", + "pattern": "rsem" + } + } + ], + "transcript_fasta": [ + { + "*transcripts.fa": { + "type": "file", + "description": "Fasta file of transcripts", + "pattern": "rsem/*transcripts.fa", + "ontologies": [] + } + } + ], + "versions_rsem": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "rsem": { + "type": "string", + "description": "The tool name" + } + }, + { + "rsem-calculate-expression --version | sed -e \"s/Current version: RSEM v//g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_star": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "star": { + "type": "string", + "description": "The tool name" + } + }, + { + "STAR --version | sed -e \"s/STAR_//g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_sentieon": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "sentieon": { + "type": "string", + "description": "The tool name" + } + }, + { + "sentieon driver --version 2>&1 | sed -e \"s/sentieon-genomics-//g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "rsem": { + "type": "string", + "description": "The tool name" + } + }, + { + "rsem-calculate-expression --version | sed -e \"s/Current version: RSEM v//g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "star": { + "type": "string", + "description": "The tool name" + } + }, + { + "STAR --version | sed -e \"s/STAR_//g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "sentieon": { + "type": "string", + "description": "The tool name" + } + }, + { + "sentieon driver --version 2>&1 | sed -e \"s/sentieon-genomics-//g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@FriederikeHanssen"], + "maintainers": ["@FriederikeHanssen"] }, - { - "gtf": { - "type": "file", - "description": "Input GTF (Gene Transfer Format) file", - "pattern": "*.gtf", - "required": true, - "ontologies": [ - { - "edam": "http://edamontology.org/format_2306" - } - ] - } - } - ], - { - "fusion_annot_lib": { - "type": "file", - "description": "Fusion annotation library file containing known fusion genes", - "required": true, - "ontologies": [ + "pipelines": [ { - "edam": "http://edamontology.org/topic_0203" + "name": "rnaseq", + "version": "3.26.0" } - ] - } - }, - { - "dfam_species": { - "type": "string", - "description": "Dfam species name" - } - }, - { - "pfam_url": { - "type": "file", - "description": "Pfam URL" - } - }, - { - "dfam_urls": { - "type": "file", - "description": "Dfam URLs" - } - }, - { - "annot_filter_url": { - "type": "file", - "description": "Annotation filter URL" - } - } - ], - "output": { - "reference": [ - [ - { - "meta": { - "type": "map", - "description": "Metadata map" - } - }, - { - "${prefix}_genome_lib_build_dir": { - "type": "directory", - "description": "Genome library build directory", - "pattern": "*_genome_lib_build_dir" - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@praveenraj2018", - "@martings", - "@alanmmobbs93", - "@delfiterradas", - "@sofiromano" - ], - "maintainers": [ - "@praveenraj2018" - ] - } - }, - { - "name": "parabricks_stargenomegenerate", - "path": "modules/nf-core/parabricks/stargenomegenerate/meta.yml", - "type": "module", - "meta": { - "name": "parabricks_stargenomegenerate", - "description": "This is near identical to the existing star/genomegenerate however it runs on an older version (2.7.2a) that is required for Parabricks compatibility.", - "keywords": [ - "index", - "fasta", - "genome", - "reference" - ], - "tools": [ - { - "star": { - "description": "STAR is a software package for mapping DNA sequences against\na large reference genome, such as the human genome.\n", - "homepage": "https://github.com/alexdobin/STAR", - "manual": "https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf", - "doi": "10.1093/bioinformatics/bts635", - "licence": [ - "MIT" - ], - "identifier": "biotools:star" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Fasta file of the reference genome", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "gtf": { - "type": "file", - "description": "GTF file of the reference genome", - "ontologies": [] - } - } - ] - ], - "output": { - "index": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "star": { - "type": "directory", - "description": "Folder containing the star index files", - "pattern": "star" - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@gburnett-nvidia" - ], - "maintainers": [ - "@gburnett-nvidia" - ] - } - }, - { - "name": "paraclu", - "path": "modules/nf-core/paraclu/meta.yml", - "type": "module", - "meta": { - "name": "paraclu", - "description": "Paraclu finds clusters in data attached to sequences.", - "keywords": [ - "sort", - "cluster", - "bed" - ], - "tools": [ - { - "paraclu": { - "description": "Paraclu finds clusters in data attached to sequences.", - "homepage": "https://gitlab.com/mcfrith/paraclu", - "documentation": "https://gitlab.com/mcfrith/paraclu", - "tool_dev_url": "https://gitlab.com/mcfrith/paraclu", - "licence": [ - "GPL v3-or-later" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bed": { - "type": "file", - "description": "BED file", - "pattern": "*.bed", - "ontologies": [] - } - } - ], - { - "min_cluster": { - "type": "integer", - "description": "Minimum size of cluster", - "pattern": "*.bed" - } - } - ], - "output": { - "bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bed": { - "type": "file", - "description": "clustered BED file", - "pattern": "*.bed", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@mashehu" - ], - "maintainers": [ - "@mashehu" - ] - } - }, - { - "name": "paragraph_idxdepth", - "path": "modules/nf-core/paragraph/idxdepth/meta.yml", - "type": "module", - "meta": { - "name": "paragraph_idxdepth", - "description": "Determines the depth in a BAM/CRAM file", - "keywords": [ - "bam", - "cram", - "depth", - "paragraph" - ], - "tools": [ - { - "paragraph": { - "description": "Graph realignment tools for structural variants", - "homepage": "https://github.com/Illumina/paragraph", - "documentation": "https://github.com/Illumina/paragraph", - "tool_dev_url": "https://github.com/Illumina/paragraph", - "doi": "10.1101/635011", - "licence": [ - "Apache License 2.0" - ], - "identifier": "biotools:Paragraph" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM file", - "pattern": "*.{bam,cram}", - "ontologies": [] - } - }, - { - "input_index": { - "type": "file", - "description": "Index of the BAM/CRAM file", - "pattern": "*.{bai,crai}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing information for the fasta\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome FASTA", - "pattern": "*.{fasta,fna,fa}", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing information for the fasta_fai\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta_fai": { - "type": "file", - "description": "Index of the reference genome FASTA", - "pattern": "*.fai", - "ontologies": [] - } - } - ] - ], - "output": { - "depth": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.json": { - "type": "file", - "description": "A JSON file containing depth, depth variance, read length and other parameters", - "pattern": "*.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "binned_depth": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "A TSV file containing the binned normalized depth. Can only be calculated for CRAM files", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@nvnieuwk" - ], - "maintainers": [ - "@nvnieuwk" - ] - } - }, - { - "name": "paragraph_multigrmpy", - "path": "modules/nf-core/paragraph/multigrmpy/meta.yml", - "type": "module", - "meta": { - "name": "paragraph_multigrmpy", - "description": "Genotype structural variants using paragraph and grmpy", - "keywords": [ - "vcf", - "json", - "structural variants", - "graphs", - "genotyping" - ], - "tools": [ - { - "paragraph": { - "description": "Graph realignment tools for structural variants", - "homepage": "https://github.com/Illumina/paragraph", - "documentation": "https://github.com/Illumina/paragraph", - "tool_dev_url": "https://github.com/Illumina/paragraph", - "doi": "10.1101/635011", - "licence": [ - "Apache License 2.0" - ], - "identifier": "biotools:Paragraph" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "variants": { - "type": "file", - "description": "A VCF or JSON file containing called structural variants", - "pattern": "*.{vcf,json}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - }, - { - "variants_index": { - "type": "file", - "description": "The index for the VCF file", - "pattern": "*.tbi", - "ontologies": [] - } - }, - { - "reads": { - "type": "file", - "description": "BAM or CRAM file(s) to genotype against. These should be specified inside the `manifest`", - "pattern": "*.{bam,cram}", - "ontologies": [] - } - }, - { - "reads_index": { - "type": "file", - "description": "The index/indices for the BAM/CRAM file(s)", - "pattern": "*.{bai,crai}", - "ontologies": [] - } - }, - { - "manifest": { - "type": "file", - "description": "A tab separated file containing information on the BAM/CRAM files.\nThis information can be generated using paragraph/idxdepth.\nMore information can be found here: https://github.com/Illumina/paragraph#sample-manifest\n", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information for the FASTA file\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference FASTA file used to generate the VCF and BAM/CRAM files", - "pattern": "*.{fa,fasta,fna}", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information for the FASTA index file\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta_fai": { - "type": "file", - "description": "The index of the reference FASTA file", - "pattern": "*.fai", - "ontologies": [] - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.vcf.gz": { - "type": "file", - "description": "The genotyped VCF file in BGZIP format", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "json": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.json.gz": { - "type": "file", - "description": "The genotyped JSON file in GZIP format", - "pattern": "*.json.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@nvnieuwk" - ], - "maintainers": [ - "@nvnieuwk" - ] - } - }, - { - "name": "paragraph_vcf2paragraph", - "path": "modules/nf-core/paragraph/vcf2paragraph/meta.yml", - "type": "module", - "meta": { - "name": "paragraph_vcf2paragraph", - "description": "Convert a VCF file to a JSON graph", - "keywords": [ - "vcf", - "json", - "structural_variants" - ], - "tools": [ - { - "paragraph": { - "description": "Graph realignment tools for structural variants", - "homepage": "https://github.com/Illumina/paragraph", - "documentation": "https://github.com/Illumina/paragraph", - "tool_dev_url": "https://github.com/Illumina/paragraph", - "doi": "10.1101/635011", - "licence": [ - "Apache License 2.0" - ], - "identifier": "biotools:Paragraph" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "The VCF/BCF file", - "pattern": "*.{vcf,bcf}(.gz)?", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome VCF was generated against", - "pattern": "*.{fasta,fna,fa}", - "ontologies": [] - } - } - ] - ], - "output": { - "graph": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.json.gz": { - "type": "file", - "description": "The created graph in BGZIP format", - "pattern": "*.json.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@nvnieuwk" - ], - "maintainers": [ - "@nvnieuwk" - ] - } - }, - { - "name": "paraphase", - "path": "modules/nf-core/paraphase/meta.yml", - "type": "module", - "meta": { - "name": "paraphase", - "description": "HiFi-based caller for highly homologous genes", - "keywords": [ - "paraphase", - "long-read", - "HiFi" - ], - "tools": [ - { - "paraphase": { - "description": "HiFi-based caller for highly homologous genes", - "homepage": "https://github.com/PacificBiosciences/paraphase", - "documentation": "https://github.com/PacificBiosciences/paraphase", - "tool_dev_url": "https://github.com/PacificBiosciences/paraphase", - "doi": "10.1016/j.ajhg.2023.01.001", - "licence": [ - "BSD-3-clause-Clear" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:true ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM file", - "pattern": "*.bam", - "ontologies": [] - } - }, - { - "bai": { - "type": "file", - "description": "Index of BAM file", - "pattern": "*.bai", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference fasta file", - "pattern": "*.fasta", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing config information\ne.g. [ id:'config' ]\n" - } - }, - { - "config": { - "type": "file", - "description": "Config file", - "pattern": "*.yaml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - ], - "output": { - "json": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:true ]`\n" - } - }, - { - "*.paraphase.json": { - "type": "file", - "description": "Summary of haplotype and variant calls", - "pattern": "*.paraphase.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:true ]`\n" - } - }, - { - "*.paraphase.bam": { - "type": "file", - "description": "(re)aligned BAM file", - "pattern": "*.paraphase.bam", - "ontologies": [] - } - } - ] - ], - "bai": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:true ]`\n" - } - }, - { - "*.paraphase.bam.bai": { - "type": "file", - "description": "Index of (re)aligned BAM file", - "pattern": "*.paraphase.bam.bai", - "ontologies": [] - } - } - ] - ], - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:true ]`\n" - } - }, - { - "${prefix}_paraphase_vcfs/*.vcf.gz": { - "type": "file", - "description": "compressed VCF file(s) per gene", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "vcf_index": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:true ]`\n" - } - }, - { - "${prefix}_paraphase_vcfs/*.vcf.gz.{csi,tbi}": { - "type": "file", - "description": "compressed VCF file index", - "pattern": "*.vcf.gz.{tbi,csi}", - "ontologies": [] - } - } ] - ], - "versions_minimap2": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "minimap2": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "minimap2 --version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_paraphase": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "paraphase": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "paraphase --version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_samtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "minimap2": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "minimap2 --version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "paraphase": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "paraphase --version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@fellen31" - ], - "maintainers": [ - "@fellen31" - ] - } - }, - { - "name": "paraphrase", - "path": "modules/nf-core/paraphrase/meta.yml", - "type": "module", - "meta": { - "name": "paraphrase", - "description": "Parse and annotate paraphrase JSONs", - "keywords": [ - "long-read", - "paraphrase", - "annotate" - ], - "tools": [ - { - "paraphrase": { - "description": "Paraphase JSON parser", - "homepage": "https://github.com/Clinical-Genomics/paraphrase", - "documentation": "https://github.com/Clinical-Genomics/paraphrase/README.md", - "tool_dev_url": "https://github.com/Clinical-Genomics/paraphrase", - "licence": [ - "MIT" - ] - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information. e.g. `[ id:'sample1']`" - } - }, - { - "jsons": { - "type": "file", - "description": "One or more JSON files from paraphase", - "pattern": "*.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - }, - { - "samples": { - "type": "list", - "description": "Sample names corresponding to the JSON files. Must be in the same order as the JSON files." - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information." - } - }, - { - "yaml": { - "type": "file", - "description": "YAML file containing rules for annotation", - "pattern": "*.yaml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3473" - } - ] - } - } - ], - { - "tsv_output": { - "type": "boolean", - "description": "Whether to output in TSV format instead of JSON. Default is false (JSON output)." - } - } - ], - "output": { - "json": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information. e.g. `[ id:'sample1']`" - } - }, - { - "*.json": { - "type": "file", - "description": "Annotated output in JSON format", - "pattern": "*.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information. e.g. `[ id:'sample1']`" - } - }, - { - "*.tsv": { - "type": "file", - "description": "Annotated output in TSV format", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_paraphrase": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "paraphrase": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "paraphrase --version | sed 's/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "paraphrase": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "paraphrase --version | sed 's/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@fellen31" - ], - "maintainers": [ - "@fellen31" - ] - } - }, - { - "name": "parsesdrf_convert", - "path": "modules/nf-core/parsesdrf/convert/meta.yml", - "type": "module", - "meta": { - "name": "parsesdrf_convert", - "description": "Convert an SDRF (Sample and Data Relationship Format) file into a\npipeline-specific samplesheet/configuration using the `parse_sdrf\nconvert-` subcommands of the sdrf-pipelines package. The chosen\n`format` selects the subcommand; the module owns the output filenames and\nemits one tuple per supported format (mhcquant, openms, maxquant, msstats,\nnormalyzerde, diann).\n", - "keywords": [ - "sdrf", - "sdrf-pipelines", - "samplesheet", - "proteomics", - "immunopeptidomics", - "mhcquant", - "openms", - "maxquant", - "msstats", - "normalyzerde", - "diann", - "metadata" - ], - "tools": [ - { - "sdrf-pipelines": { - "description": "A set of tools to validate and convert SDRF files for proteomics pipelines.", - "homepage": "https://github.com/bigbio/sdrf-pipelines", - "documentation": "https://github.com/bigbio/sdrf-pipelines", - "tool_dev_url": "https://github.com/bigbio/sdrf-pipelines", - "doi": "10.1021/acs.jproteome.1c00505", - "licence": [ - "Apache-2.0" - ], - "identifier": "biotools:sdrf-pipelines" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample/run information\ne.g. `[ id:'PXD009752' ]`\n" - } - }, - { - "sdrf": { - "type": "file", - "description": "SDRF file describing the experimental design and sample metadata.", - "pattern": "*.{tsv,sdrf.tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - }, - { - "fasta": { - "type": "file", - "description": "Protein database FASTA. Required when `format == 'maxquant'`\n(passed to `-f`); pass `[]` otherwise.\n", - "pattern": "*.{fasta,fa,fasta.gz,fa.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - }, - { - "raw_folder": { - "type": "string", - "description": "Directory prefix embedded as a literal string into the\n`` block of the generated MaxQuant `mqpar.xml`; must\nresolve on the host that later runs MaxQuant. Required when\n`format == 'maxquant'`; pass `''` otherwise.\n" - } - } - ], - { - "format": { - "type": "string", - "description": "Target converter. One of: `mhcquant`, `openms`, `maxquant`,\n`msstats`, `normalyzerde`, `diann`. Selects the\n`parse_sdrf convert-` subcommand.\n" - } - } - ], - "output": { - "mhcquant": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample/run information" - } - }, - { - "${prefix}_samplesheet.tsv": { - "type": "file", - "description": "MHCquant samplesheet TSV (`-os`).", - "pattern": "*_samplesheet.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - }, - { - "${prefix}_presets.tsv": { - "type": "file", - "description": "MHCquant search-preset TSV (`-op`).", - "pattern": "*_presets.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "openms": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample/run information" - } - }, - { - "${prefix}_samplesheet.tsv": { - "type": "file", - "description": "OpenMS samplesheet TSV (renamed from `openms.tsv`).", - "pattern": "*_samplesheet.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - }, - { - "${prefix}_experimental_design.tsv": { - "type": "file", - "description": "OpenMS experimental design TSV.", - "pattern": "*_experimental_design.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "maxquant": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample/run information" - } - }, - { - "${prefix}.xml": { - "type": "file", - "description": "MaxQuant `mqpar.xml` (`-o1`).", - "pattern": "*.xml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2332" - } - ] - } - }, - { - "${prefix}_design.txt": { - "type": "file", - "description": "MaxQuant experimental design TXT (`-o2`).", - "pattern": "*_design.txt", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "msstats": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample/run information" - } - }, - { - "${prefix}.csv": { - "type": "file", - "description": "MSstats annotation CSV (`-o`).", - "pattern": "*.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "normalyzerde": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample/run information" - } - }, - { - "${prefix}_design.csv": { - "type": "file", - "description": "NormalyzerDE design CSV (`-o`).", - "pattern": "*_design.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - }, - { - "${prefix}_comparisons.csv": { - "type": "file", - "description": "NormalyzerDE comparisons CSV (`-oc`).", - "pattern": "*_comparisons.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "diann": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample/run information" - } - }, - { - "${prefix}.cfg": { - "type": "file", - "description": "DIA-NN config (renamed from `diann_config.cfg`).", - "pattern": "*.cfg", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2330" - } - ] - } - }, - { - "${prefix}_design.tsv": { - "type": "file", - "description": "DIA-NN experimental design TSV (renamed from `diann_design.tsv`).", - "pattern": "*_design.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_sdrfpipelines": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "sdrf-pipelines": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "parse_sdrf --version | cut -d ' ' -f 2": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "sdrf-pipelines": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "parse_sdrf --version | cut -d ' ' -f 2": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@jonasscheid" - ], - "maintainers": [ - "@jonasscheid" - ] - }, - "pipelines": [ - { - "name": "mhcquant", - "version": "3.2.0" - } - ] - }, - { - "name": "parsnp", - "path": "modules/nf-core/parsnp/meta.yml", - "type": "module", - "meta": { - "name": "parsnp", - "description": "Parsnp is a command-line-tool for efficient microbial core genome alignment and SNP detection.", - "keywords": [ - "alignment", - "bacteria", - "phylogeny", - "microbial genomics", - "core genome", - "SNP" - ], - "tools": [ - { - "parsnp": { - "description": "Parsnp is a command-line-tool for efficient microbial core genome alignment and SNP detection.", - "homepage": "https://harvest.readthedocs.io/en/latest/content/parsnp/tutorial.html", - "documentation": "https://harvest.readthedocs.io/en/latest/content/parsnp/tutorial.html", - "tool_dev_url": "https://github.com/marbl/parsnp", - "doi": "10.1093/bioinformatics/btae311", - "licence": [ - "custom; see https://raw.githubusercontent.com/marbl/parsnp/master/LICENSE" - ], - "identifier": "biotools:parsnp" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } + }, + { + "name": "sentieon_staralign", + "path": "modules/nf-core/sentieon/staralign/meta.yml", + "type": "module", + "meta": { + "name": "sentieon_staralign", + "description": "Align reads to a reference genome using Sentieon STAR", + "keywords": ["align", "fasta", "genome", "reference"], + "tools": [ + { + "sentieon": { + "description": "Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads.\nOur software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.\n", + "homepage": "https://www.sentieon.com/", + "documentation": "https://www.sentieon.com/", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "index": { + "type": "directory", + "description": "STAR genome index", + "pattern": "star" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "gtf": { + "type": "file", + "description": "Annotation GTF file", + "pattern": "*.{gtf}", + "ontologies": [] + } + } + ], + { + "star_ignore_sjdbgtf": { + "type": "boolean", + "description": "Ignore annotation GTF file" + } + } + ], + "output": { + "log_final": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*Log.final.out": { + "type": "file", + "description": "STAR final log file", + "pattern": "*Log.final.out", + "ontologies": [] + } + } + ] + ], + "log_out": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*Log.out": { + "type": "file", + "description": "STAR lot out file", + "pattern": "*Log.out", + "ontologies": [] + } + } + ] + ], + "log_progress": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*Log.progress.out": { + "type": "file", + "description": "STAR log progress file", + "pattern": "*Log.progress.out", + "ontologies": [] + } + } + ] + ], + "versions_star": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "star": { + "type": "string", + "description": "The tool name" + } + }, + { + "sentieon STAR --version | sed -e \"s/STAR_//g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_sentieon": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "sentieon": { + "type": "string", + "description": "The tool name" + } + }, + { + "sentieon driver --version 2>&1 | sed -e \"s/sentieon-genomics-//g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*d.out.bam": { + "type": "file", + "description": "Output BAM file containing read alignments", + "pattern": "*.{bam}", + "ontologies": [] + } + } + ] + ], + "bam_sorted": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.sortedByCoord.out.bam": { + "type": "file", + "description": "Sorted BAM file of read alignments (optional)", + "pattern": "*sortedByCoord.out.bam", + "ontologies": [] + } + } + ] + ], + "bam_sorted_aligned": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.Aligned.sortedByCoord.out.bam": { + "type": "file", + "description": "Sorted BAM file of read alignments (optional)", + "pattern": "*.Aligned.sortedByCoord.out.bam", + "ontologies": [] + } + } + ] + ], + "bam_transcript": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*toTranscriptome.out.bam": { + "type": "file", + "description": "Output BAM file of transcriptome alignment (optional)", + "pattern": "*toTranscriptome.out.bam", + "ontologies": [] + } + } + ] + ], + "bam_unsorted": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*Aligned.unsort.out.bam": { + "type": "file", + "description": "Unsorted BAM file of read alignments (optional)", + "pattern": "*Aligned.unsort.out.bam", + "ontologies": [] + } + } + ] + ], + "fastq": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*fastq.gz": { + "type": "file", + "description": "Unmapped FastQ files (optional)", + "pattern": "*fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "tab": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tab": { + "type": "file", + "description": "STAR output tab file(s) (optional)", + "pattern": "*.tab", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "spl_junc_tab": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.SJ.out.tab": { + "type": "file", + "description": "STAR output splice junction tab file", + "pattern": "*.SJ.out.tab", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "read_per_gene_tab": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.ReadsPerGene.out.tab": { + "type": "file", + "description": "STAR output read per gene tab file", + "pattern": "*.ReadsPerGene.out.tab", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "junction": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.out.junction": { + "type": "file", + "description": "STAR chimeric junction output file (optional)", + "pattern": "*.out.junction", + "ontologies": [] + } + } + ] + ], + "sam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.out.sam": { + "type": "file", + "description": "STAR output SAM file(s) (optional)", + "pattern": "*.out.sam", + "ontologies": [] + } + } + ] + ], + "wig": [ + [ + { + "meta": { + 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"name": "pbmarkdup", - "path": "modules/nf-core/pbmarkdup/meta.yml", - "type": "module", - "meta": { - "name": "pbmarkdup", - "description": "Takes one or multiple sequencing chips of an amplified library as HiFi reads and marks or removes\nduplicates.\n", - "keywords": [ - "markdup", - "bam", - "fastq", - "fasta" - ], - "tools": [ - { - "pbmarkdup": { - "description": "pbmarkdup identifies and marks duplicate reads in PacBio HiFi (CCS) data. It clusters\nhighly similar CCS reads to detect PCR duplicates and flags them in the output files\n(BAM,FASTQ,FASTA) (duplicate bit 0x400), optionally removing duplicates.\n(duplicate bit 0x400), optionally removing duplicates.\n", - "homepage": "https://github.com/PacificBiosciences/pbmarkdup", - "documentation": "https://github.com/PacificBiosciences/pbmarkdup", - "licence": [ - "BSD-3-Clause" - ], - "identifier": "biotools:pbmarkdup" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "input": { - "type": "file", - "description": "Sequencing reads in BAM, FASTQ, or FASTA format.\n", - "pattern": "*.{bam,f*a,/.*f.*\\.gz/}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2546" - }, - { - "edam": "http://edamontology.org/format_1930" - }, - { - "edam": "http://edamontology.org/format_2572" - } - ] - } + }, + { + "name": "sentieon_tnfilter", + "path": "modules/nf-core/sentieon/tnfilter/meta.yml", + "type": "module", + "meta": { + "name": "sentieon_tnfilter", + "description": "Filters the raw output of sentieon/tnhaplotyper2.\n", + "keywords": ["tnfilter", "filter", "sentieon", "tnhaplotyper2", "vcf"], + "tools": [ + { + "sentieon": { + "description": "Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads.\nOur software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.\n", + "homepage": "https://www.sentieon.com/", + "documentation": "https://www.sentieon.com/", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "compressed vcf file from tnhaplotyper2", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + }, + { + "vcf_tbi": { + "type": "file", + "description": "Tabix index of vcf file", + "pattern": "*vcf.gz.tbi", + "ontologies": [] + } + }, + { + "stats": { + "type": "file", + "description": "Stats file that pairs with output vcf file", + "pattern": "*vcf.gz.stats", + "ontologies": [] + } + }, + { + "contamination": { + "type": "file", + "description": "the location and file name of the file containing the contamination information produced by ContaminationModel.", + "pattern": "*.contamination_data.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, + { + "segments": { + "type": "file", + "description": "the location and file name of the file containing the tumor segments information produced by ContaminationModel.", + "pattern": "*.segments", + "ontologies": [] + } + }, + { + "orientation_priors": { + "type": "file", + "description": "the location and file name of the file containing the orientation bias information produced by OrientationBias.", + "pattern": "*.orientation_data.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The reference fasta file", + "pattern": "*.fasta", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Index of reference fasta file", + "pattern": "*.fasta.fai", + "ontologies": [] + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "file", + "description": "file containing filtered tnhaplotyper2 calls.", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "file containing filtered tnhaplotyper2 calls.", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "tbi": [ + [ + { + "meta": { + "type": "file", + "description": "file containing filtered tnhaplotyper2 calls.", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + }, + { + "*.vcf.gz.tbi": { + "type": "file", + "description": "tbi file that pairs with vcf.", + "pattern": "*.vcf.gz.tbi", + "ontologies": [] + } + } + ] + ], + "stats": [ + [ + { + "meta": { + "type": "file", + "description": "file containing filtered tnhaplotyper2 calls.", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + }, + { + "*.vcf.gz.stats": { + "type": "file", + "description": "file containing statistics of the tnfilter run.", + "pattern": "*.stats", + "ontologies": [] + } + } + ] + ], + "versions_sentieon": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "sentieon": { + "type": "string", + "description": "The tool name" + } + }, + { + "sentieon driver --version | sed \"s/.*-//g\"": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "sentieon": { + "type": "string", + "description": "The tool name" + } + }, + { + "sentieon driver --version | sed \"s/.*-//g\"": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@asp8200"] } - ] - ], - "output": { - "markduped": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}.${suffix}": { - "type": "file", - "description": "Markduplicated sequencing reads in the same format as the input file.\n", - "pattern": "*.{bam,f*a,/.*f.*\\.gz/}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2546" - }, + }, + { + "name": "sentieon_tnhaplotyper2", + "path": "modules/nf-core/sentieon/tnhaplotyper2/meta.yml", + "type": "module", + "meta": { + "name": "sentieon_tnhaplotyper2", + "description": "Tnhaplotyper2 performs somatic variant calling on the tumor-normal matched pairs.", + "keywords": ["tnseq", "tnhaplotyper2", "sentieon", "variant_calling"], + "tools": [ + { + "sentieon": { + "description": "Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads.\nOur software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.\n", + "homepage": "https://www.sentieon.com/", + "documentation": "https://www.sentieon.com/", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information.\ne.g. [ id:'test' ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM file(s) from alignment", + "pattern": "*.{bam,cram}", + "ontologies": [] + } + }, + { + "input_index": { + "type": "file", + "description": "BAI/CRAI file(s) from alignment", + "pattern": "*.{bai,crai}", + "ontologies": [] + } + }, + { + "intervals": { + "type": "file", + "description": "Bed file with the genomic regions included in the library (optional)", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" + } + }, + { + "dict": { + "type": "file", + "description": "GATK sequence dictionary", + "pattern": "*.dict", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Genome fasta file", + "pattern": "*.{fa,fasta}", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Index of the genome fasta file", + "pattern": "*.fai", + "ontologies": [] + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" + } + }, + { + "germline_resource": { + "type": "file", + "description": "Population vcf of germline sequencing, containing allele fractions.", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ], + [ + { + "meta6": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" + } + }, + { + "germline_resource_tbi": { + "type": "file", + "description": "Index file for the germline resource.", + "pattern": "*.vcf.gz.tbi", + "ontologies": [] + } + } + ], + [ + { + "meta7": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" + } + }, + { + "panel_of_normals": { + "type": "file", + "description": "vcf file to be used as a panel of normals.", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ], + [ + { + "meta8": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" + } + }, + { + "panel_of_normals_tbi": { + "type": "file", + "description": "Index for the panel of normals.", + "pattern": "*.vcf.gz.tbi", + "ontologies": [] + } + } + ], { - "edam": "http://edamontology.org/format_1930" + "emit_orientation_data": { + "type": "boolean", + "description": "If true, the module will run the sentieon algorithm TNhaplotyper2 followed by the sentieon algorithm OrientationBias." + } }, { - "edam": "http://edamontology.org/format_2572" + "emit_contamination_data": { + "type": "boolean", + "description": "If true, the module will run the sentieon algorithm TNhaplotyper2 followed by the sentieon algorithm ContaminationModel." + } + } + ], + "output": { + "orientation_data": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.orientation_data.tsv": { + "type": "file", + "description": "TSV file from Sentieon's algorithm OrientationBias", + "pattern": "*.orientation_data.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "contamination_data": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.contamination_data.tsv": { + "type": "file", + "description": "TSV file from Sentieon's algorithm ContaminationModel", + "pattern": "*.contamination_data.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "contamination_segments": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.segments": { + "type": "file", + "description": "Tumour segments file from Sentieon's algorithm ContaminationModel", + "pattern": "*.segments", + "ontologies": [] + } + } + ] + ], + "stats": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.stats": { + "type": "file", + "description": "Stats file from Sentieon's algorithm", + "pattern": "*.stats", + "ontologies": [] + } + } + ] + ], + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "VCF file", + "pattern": "*.{vcf.gz}", + "ontologies": [] + } + } + ] + ], + "index": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz.tbi": { + "type": "file", + "description": "Index of the VCF file", + "pattern": "*.vcf.gz.tbi", + "ontologies": [] + } + } + ] + ], + "versions_sentieon": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "sentieon": { + "type": "string", + "description": "The tool name" + } + }, + { + "sentieon driver --version | sed \"s/.*-//g\"": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "sentieon": { + "type": "string", + "description": "The tool name" + } + }, + { + "sentieon driver --version | sed \"s/.*-//g\"": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@asp8200"], + "maintainers": ["@asp8200"] + } + }, + { + "name": "sentieon_tnscope", + "path": "modules/nf-core/sentieon/tnscope/meta.yml", + "type": "module", + "meta": { + "name": "sentieon_tnscope", + "description": "TNscope algorithm performs somatic variant calling on the tumor-normal matched pair or the tumor only data, using a Haplotyper algorithm.", + "keywords": ["tnscope", "sentieon", "variant_calling"], + "tools": [ + { + "sentieon": { + "description": "Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads.\nOur software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.\n", + "homepage": "https://www.sentieon.com/", + "documentation": "https://www.sentieon.com/", + "identifier": "" + } } - ] + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information.\ne.g. [ id:'test' ]\n" + } + }, + { + "input": { + "type": "file", + "description": "One or more BAM or CRAM files.", + "pattern": "*.{bam,cram}", + "ontologies": [] + } + }, + { + "input_index": { + "type": "file", + "description": "Indices for the input files", + "pattern": "*.{bai,crai}", + "ontologies": [] + } + }, + { + "intervals": { + "type": "file", + "description": "bed or interval_list file containing interval in the reference that will be used in the analysis. Only recommended for large WGS data, else the overhead may not be worth the additional parallelisation.", + "pattern": "*.{bed,interval_list}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Genome fasta file", + "pattern": "*.{fa,fasta}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Index of the genome fasta file", + "pattern": "*.fai", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" + } + }, + { + "dbsnp": { + "type": "file", + "description": "Single Nucleotide Polymorphism database (dbSNP) file", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" + } + }, + { + "dbsnp_tbi": { + "type": "file", + "description": "Index of the Single Nucleotide Polymorphism database (dbSNP) file", + "pattern": "*.vcf.gz.tbi", + "ontologies": [] + } + } + ], + [ + { + "meta6": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" + } + }, + { + "pon": { + "type": "file", + "description": "Single Nucleotide Polymorphism database (dbSNP) file", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ], + [ + { + "meta7": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" + } + }, + { + "pon_tbi": { + "type": "file", + "description": "Index of the Single Nucleotide Polymorphism database (dbSNP) file", + "pattern": "*.vcf.gz.tbi", + "ontologies": [] + } + } + ], + [ + { + "meta8": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" + } + }, + { + "cosmic": { + "type": "file", + "description": "Catalogue of Somatic Mutations in Cancer (COSMIC) VCF file.", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ], + [ + { + "meta9": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" + } + }, + { + "cosmic_tbi": { + "type": "file", + "description": "Index of the Catalogue of Somatic Mutations in Cancer (COSMIC) VCF file.", + "pattern": "*.vcf.gz.tbi", + "ontologies": [] + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "VCF file", + "pattern": "*.{vcf.gz}", + "ontologies": [] + } + } + ] + ], + "index": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" + } + }, + { + "*.vcf.gz.tbi": { + "type": "file", + "description": "Index of the VCF file", + "pattern": "*.vcf.gz.tbi", + "ontologies": [] + } + } + ] + ], + "versions_sentieon": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "sentieon": { + "type": "string", + "description": "The tool name" + } + }, + { + "sentieon driver --version | sed \"s/.*-//g\"": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "sentieon": { + "type": "string", + "description": "The tool name" + } + }, + { + "sentieon driver --version | sed \"s/.*-//g\"": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@ramprasadn"], + "maintainers": ["@ramprasadn"] + }, + "pipelines": [ + { + "name": "sarek", + "version": "3.8.1" } - } ] - ], - "dupfile": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${dupfile_name}": { - "type": "file", - "description": "(Optional) File listing duplicate reads (Specify by --dup-file).\n", - "pattern": "*.{bam,f*a,/.*f.*\\.gz/}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2546" + }, + { + "name": "sentieon_varcal", + "path": "modules/nf-core/sentieon/varcal/meta.yml", + "type": "module", + "meta": { + "name": "sentieon_varcal", + "description": "Module for Sentieons VarCal. The VarCal algorithm calculates the Variant Quality Score Recalibration (VQSR).\nVarCal builds a recalibration model for scoring variant quality.\nhttps://support.sentieon.com/manual/usages/general/#varcal-algorithm\n", + "keywords": ["sentieon", "varcal", "variant recalibration"], + "tools": [ + { + "sentieon": { + "description": "Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads.\nOur software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.\n", + "homepage": "https://www.sentieon.com/", + "documentation": "https://www.sentieon.com/", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "input vcf file containing the variants to be recalibrated", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + }, + { + "tbi": { + "type": "file", + "description": "tbi file matching with -vcf", + "pattern": "*.vcf.gz.tbi", + "ontologies": [] + } + } + ], + { + "resource_vcf": { + "type": "file", + "description": "all resource vcf files that are used with the corresponding '--resource' label", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } }, { - "edam": "http://edamontology.org/format_1930" + "resource_tbi": { + "type": "file", + "description": "all resource tbi files that are used with the corresponding '--resource' label", + "pattern": "*.vcf.gz.tbi", + "ontologies": [] + } }, { - "edam": "http://edamontology.org/format_2572" - } - ] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.pbmarkdup.log": { - "type": "file", - "description": "Log file generated by pbmarkdup (if --log-level is specified).\n", - "pattern": "*.pbmarkdup.log", - "ontologies": [] - } - } - ] - ], - "versions_pbmarkdup": [ - [ - { - "${task.process}": { - "type": "string", - "description": "Name of the process" - } - }, - { - "pbmarkdup": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pbmarkdup --version | cut -d' ' -f2": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "Name of the process" - } - }, - { - "pbmarkdup": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pbmarkdup --version | cut -d' ' -f2": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@sainsachiko" - ], - "maintainers": [ - "@sainsachiko" - ] - } - }, - { - "name": "pbmm2_align", - "path": "modules/nf-core/pbmm2/align/meta.yml", - "type": "module", - "meta": { - "name": "pbmm2_align", - "description": "Alignment with PacBio's minimap2 frontend", - "keywords": [ - "align", - "pacbio", - "genomics" - ], - "tools": [ - { - "pbmm2": { - "description": "A minimap2 frontend for PacBio native data formats", - "homepage": "https://github.com/PacificBiosciences/pbmm2", - "documentation": "https://github.com/PacificBiosciences/pbmm2", - "tool_dev_url": "https://github.com/PacificBiosciences/pbmm2", - "licence": [ - "BSD-3-clause-Clear" - ], - "identifier": "biotools:pbmm2" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "fasta file to align bam to", - "pattern": "*.{fasta}", - "ontologies": [] - } - } - ] - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "Sorted BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" + "labels": { + "type": "string", + "description": "necessary arguments for Sentieon's VarCal. Specified to directly match the resources provided. More information can be found at https://support.sentieon.com/manual/usages/general/#varcal-algorithm" + } }, { - "edam": "http://edamontology.org/format_2573" + "fasta": { + "type": "file", + "description": "The reference fasta file", + "pattern": "*.fasta", + "ontologies": [] + } }, { - "edam": "http://edamontology.org/format_3462" + "fai": { + "type": "file", + "description": "Index of reference fasta file", + "pattern": "fasta.fai", + "ontologies": [] + } } - ] + ], + "output": { + "recal": [ + [ + { + "meta": { + "type": "file", + "description": "Output recal file used by ApplyVQSR", + "pattern": "*.recal", + "ontologies": [] + } + }, + { + "*.recal": { + "type": "file", + "description": "Output recal file used by ApplyVQSR", + "pattern": "*.recal", + "ontologies": [] + } + } + ] + ], + "idx": [ + [ + { + "meta": { + "type": "file", + "description": "Output recal file used by ApplyVQSR", + "pattern": "*.recal", + "ontologies": [] + } + }, + { + "*.idx": { + "type": "file", + "description": "Index file for the recal output file", + "pattern": "*.idx", + "ontologies": [] + } + } + ] + ], + "tranches": [ + [ + { + "meta": { + "type": "file", + "description": "Output recal file used by ApplyVQSR", + "pattern": "*.recal", + "ontologies": [] + } + }, + { + "*.tranches": { + "type": "file", + "description": "Output tranches file used by ApplyVQSR", + "pattern": "*.tranches", + "ontologies": [] + } + } + ] + ], + "plots": [ + [ + { + "meta": { + "type": "file", + "description": "Output recal file used by ApplyVQSR", + "pattern": "*.recal", + "ontologies": [] + } + }, + { + "*plots.R": { + "type": "file", + "description": "Optional output rscript file to aid in visualization of the input data and learned model.", + "pattern": "*plots.R", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3999" + } + ] + } + } + ] + ], + "versions_sentieon": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "sentieon": { + "type": "string", + "description": "The tool name" + } + }, + { + "sentieon driver --version | sed \"s/.*-//g\"": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@asp8200"], + "maintainers": ["@asp8200"], + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "sentieon": { + "type": "string", + "description": "The tool name" + } + }, + { + "sentieon driver --version | sed \"s/.*-//g\"": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + } + }, + "pipelines": [ + { + "name": "sarek", + "version": "3.8.1" } - } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@tanyasarkjain" - ], - "maintainers": [ - "@tanyasarkjain" - ] - }, - "pipelines": [ - { - "name": "methylong", - "version": "2.0.0" }, { - "name": "pacsomatic", - "version": "dev" + "name": "sentieon_wgsmetrics", + "path": "modules/nf-core/sentieon/wgsmetrics/meta.yml", + "type": "module", + "meta": { + "name": "sentieon_wgsmetrics", + "description": "Collects whole genome quality metrics from a bam file", + "keywords": ["metrics", "bam", "sentieon"], + "tools": [ + { + "sentieon": { + "description": "Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads.\nOur software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.\n", + "homepage": "https://www.sentieon.com/", + "documentation": "https://www.sentieon.com/", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "bam": { + "type": "file", + "description": "Sorted BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}", + "ontologies": [] + } + }, + { + "bai": { + "type": "file", + "description": "Index of th sorted BAM/CRAM/SAM file", + "pattern": "*.{bai,crai,sai}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Genome fasta file", + "pattern": "*.{fa,fasta}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "fai": { + "type": "file", + "description": "Index of the genome fasta file", + "pattern": "*.fai", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "intervals_list": { + "type": "file", + "description": "intervals", + "ontologies": [] + } + } + ] + ], + "output": { + "wgs_metrics": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "File containing the information about mean base quality score for each sequencing cycle", + "pattern": "*.txt", + "ontologies": [] + } + } + ] + ], + "versions_sentieon": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "sentieon": { + "type": "string", + "description": "The tool name" + } + }, + { + "sentieon driver --version | sed \"s/.*-//g\"": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@ramprasadn"], + "maintainers": ["@ramprasadn"], + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "sentieon": { + "type": "string", + "description": "The tool name" + } + }, + { + "sentieon driver --version | sed \"s/.*-//g\"": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + } + }, + "pipelines": [ + { + "name": "raredisease", + "version": "3.0.0" + } + ] }, { - "name": "pacvar", - "version": "1.0.1" - } - ] - }, - { - "name": "pbptyper", - "path": "modules/nf-core/pbptyper/meta.yml", - "type": "module", - "meta": { - "name": "pbptyper", - "description": "Assign PBP type of Streptococcus pneumoniae assemblies", - "keywords": [ - "bacteria", - "pbp", - "fasta", - "assembly" - ], - "tools": [ - { - "pbptyper": { - "description": "In silico Penicillin Binding Protein (PBP) typer for Streptococcus pneumoniae assemblies", - "homepage": "https://github.com/rpetit3/pbptyper", - "documentation": "https://github.com/rpetit3/pbptyper", - "tool_dev_url": "https://github.com/rpetit3/pbptyper", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + "name": "seq2hla", + "path": "modules/nf-core/seq2hla/meta.yml", + "type": "module", + "meta": { + "name": "seq2hla", + "description": "Precision HLA typing and expression from RNA-seq data using seq2HLA", + "keywords": ["hla", "typing", "rna-seq", "genomics", "immunogenetics"], + "tools": [ + { + "seq2hla": { + "description": "Precision HLA typing and expression from next-generation RNA sequencing data", + "homepage": "https://github.com/TRON-Bioinformatics/seq2HLA", + "documentation": "https://github.com/TRON-Bioinformatics/seq2HLA#readme", + "tool_dev_url": "https://github.com/TRON-Bioinformatics/seq2HLA", + "doi": "10.1186/s13073-015-0240-5", + "licence": ["MIT"], + "identifier": "biotools:seq2HLA" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "reads": { + "type": "file", + "description": "Paired-end FASTQ files for RNA-seq data", + "pattern": "*.{fastq.gz,fq.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ] + ], + "output": { + "class1_genotype_2d": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*ClassI-class.HLAgenotype2digits": { + "type": "file", + "description": "HLA Class I 2-digit genotype results", + "pattern": "*ClassI-class.HLAgenotype2digits", + "ontologies": [] + } + } + ] + ], + "class2_genotype_2d": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*ClassII.HLAgenotype2digits": { + "type": "file", + "description": "HLA Class II 2-digit genotype results", + "pattern": "*ClassII.HLAgenotype2digits", + "ontologies": [] + } + } + ] + ], + "class1_genotype_4d": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*ClassI-class.HLAgenotype4digits": { + "type": "file", + "description": "HLA Class I 4-digit genotype results", + "pattern": "*ClassI-class.HLAgenotype4digits", + "ontologies": [] + } + } + ] + ], + "class2_genotype_4d": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*ClassII.HLAgenotype4digits": { + "type": "file", + "description": "HLA Class II 4-digit genotype results", + "pattern": "*ClassII.HLAgenotype4digits", + "ontologies": [] + } + } + ] + ], + "class1_bowtielog": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*ClassI-class.bowtielog": { + "type": "file", + "description": "HLA Class I Bowtie alignment log", + "pattern": "*ClassI-class.bowtielog", + "ontologies": [] + } + } + ] + ], + "class2_bowtielog": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*ClassII.bowtielog": { + "type": "file", + "description": "HLA Class II Bowtie alignment log", + "pattern": "*ClassII.bowtielog", + "ontologies": [] + } + } + ] + ], + "class1_expression": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', 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], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference plasmid information\ne.g. `[ id:'plasmids' ]`\n" - } + }, + { + "name": "seqkit_seq", + "path": "modules/nf-core/seqkit/seq/meta.yml", + "type": "module", + "meta": { + "name": "seqkit_seq", + "description": "Transforms sequences (extract ID, filter by length, remove gaps, reverse complement...)", + "keywords": ["genomics", "fasta", "fastq", "transform", "filter", "gaps", "complement"], + "tools": [ + { + "seqkit": { + "description": "A cross-platform and ultrafast toolkit for FASTA/Q file manipulation", + "homepage": "https://bioinf.shenwei.me/seqkit/", + "documentation": "https://bioinf.shenwei.me/seqkit/usage/", + "tool_dev_url": "https://github.com/shenwei356/seqkit", + "doi": "10.1371/journal.pone.0163962", + "licence": ["MIT"], + "identifier": "biotools:seqkit" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "fastx": { + "type": "file", + "description": "Input fasta/fastq file", + "pattern": "*.{fsa,fas,fa,fasta,fastq,fq,fsa.gz,fas.gz,fa.gz,fasta.gz,fastq.gz,fq.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ] + ], + "output": { + "fastx": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}.*": { + "type": "file", + "description": "Output fasta/fastq file", + "pattern": "*.{fasta,fasta.gz,fastq,fastq.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ] + ], + "versions_seqkit": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "seqkit": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "seqkit version | sed 's/^.*v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "seqkit": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "seqkit version | sed 's/^.*v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@GallVp"], + "maintainers": ["@GallVp"] }, - 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], - { - "fasta": { - "type": "file", - "description": "Genome reference sequence used", - "pattern": "*.{fa,fasta}", - "ontologies": [] + }, + { + "name": "seqkit_translate", + "path": "modules/nf-core/seqkit/translate/meta.yml", + "type": "module", + "meta": { + "name": "seqkit_translate", + "description": "Translate DNA/RNA to protein sequence", + "keywords": ["seqkit", "translate", "protein"], + "tools": [ + { + "seqkit": { + "description": "A cross-platform and ultrafast toolkit for FASTA/Q file manipulation", + "homepage": "https://bioinf.shenwei.me/seqkit/", + "documentation": "https://bioinf.shenwei.me/seqkit/usage/", + "tool_dev_url": "https://github.com/shenwei356/seqkit", + "doi": "10.1371/journal.pone.0163962", + "licence": ["MIT"], + "identifier": "biotools:seqkit" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "fastx": { + "type": "file", + "description": "Input fasta/fastq file", + "pattern": "*.{fna,fsa,fas,fa,fasta,fastq,fq}[.gz]", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ] + ], + "output": { + "fastx": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}.*": { + "type": "file", + "description": "Translated fasta/fastq file", + "pattern": "*.{fna,fsa,fas,fa,fasta,fastq,fq}[.gz]", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ] + ], + "versions_seqkit": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "seqkit": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "seqkit version | sed 's/^.*v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "seqkit": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "seqkit version | sed 's/^.*v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@delfiterradas"], + "maintainers": ["@delfiterradas"] } - }, - { - "fai": { - "type": "file", - "description": "FAI file corresponding to the reference sequence", - "pattern": "*.{fai}", - "ontologies": [] + }, + { + "name": "seqsero2", + "path": "modules/nf-core/seqsero2/meta.yml", + "type": "module", + "meta": { + "name": "seqsero2", + "description": "Salmonella serotype prediction from reads and assemblies", + "keywords": ["fasta", "fastq", "salmonella", "sertotype"], + "tools": [ + { + "seqsero2": { + "description": "Salmonella serotype prediction from genome sequencing data", + "homepage": "https://github.com/denglab/SeqSero2", + "documentation": "https://github.com/denglab/SeqSero2", + "tool_dev_url": "https://github.com/denglab/SeqSero2", + "doi": "10.1128/AEM.01746-19", + "licence": ["GPL v2"], + "identifier": "biotools:SeqSero2" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "seqs": { + "type": "file", + "description": "FASTQ or FASTA formatted sequences", + "pattern": "*.{fq.gz,fastq.gz,fna.gz,fna,fasta.gz,fasta,fa.gz,fa}", + "ontologies": [] + } + } + ] + ], + "output": { + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "results/*_log.txt": { + "type": "file", + "description": "A log of serotype antigen results", + "pattern": "*_log.txt", + "ontologies": [] + } + } + ] + ], + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "results/*_result.tsv": { + "type": "file", + "description": "Tab-delimited summary of the SeqSero2 results", + "pattern": "*_result.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "txt": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "results/*_result.txt": { + "type": "file", + "description": "Detailed summary of the SeqSero2 results", + "pattern": "*_result.txt", + "ontologies": [] + } + } + ] + ], + "versions_seqsero2": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "seqsero2": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "SeqSero2_package.py --version 2>&1 | sed 's/^.*SeqSero2_package.py //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "seqsero2": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "SeqSero2_package.py --version 2>&1 | sed 's/^.*SeqSero2_package.py //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@rpetit3"], + "maintainers": ["@rpetit3"] } - }, - { - "gtf": { - "type": "file", - "description": "A segmented GTF used to annotate peaks", - "pattern": "*.{gtf}", - "ontologies": [] + }, + { + "name": "seqtk_comp", + "path": "modules/nf-core/seqtk/comp/meta.yml", + "type": "module", + "meta": { + "name": "seqtk_comp", + "description": "Computes sequence statistics from FASTQ or FASTA files", + "keywords": ["seqtk", "comp", "fastx"], + "tools": [ + { + "seqtk_comp": { + "description": "Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format.\nThe seqtk comp command computes base composition, sequence length, and GC content for quality control.\n", + "homepage": "https://github.com/lh3/seqtk", + "documentation": "https://docs.csc.fi/apps/seqtk/", + "tool_dev_url": "https://github.com/lh3/seqtk", + "licence": ["MIT"], + "identifier": "biotools:seqtk" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample1' ]\n" + } + }, + { + "fastx": { + "type": "file", + "description": "A FASTQ or FASTA file", + "pattern": "*.{fastq,fq,fasta,fa,fas,fna}{,.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ] + ], + "output": { + "seqtk_stats": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample1', single_end:false ]\n" + } + }, + { + "*.seqtk_stats.tsv": { + "type": "file", + "description": "The output TSV file summarizing sequence statistics with columns for sequence name, length, counts of A, C, G, T, and N bases, and GC content percentage.\"", + "pattern": "*.seqtk_stats.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_seqtk": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "seqtk": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "seqtk 2>&1 | sed -n 's/^Version: //p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "seqtk": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "seqtk 2>&1 | sed -n 's/^Version: //p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@sainsachiko"], + "maintainers": ["@sainsachiko"] } - } - ], - "output": { - "cluster": [ - [ - { - "meta": { - "type": "file", - "description": "TSV file of summed occurrence distributions of k-mers within defined clusters", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - }, - { - "*mer_cluster_distribution*": { - "type": "file", - "description": "TSV file of summed occurrence distributions of k-mers within defined clusters", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "distribution": [ - [ - { - "meta": { - "type": "file", - "description": "TSV file of summed occurrence distributions of k-mers within defined clusters", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" + }, + { + "name": "seqtk_cutn", + "path": "modules/nf-core/seqtk/cutn/meta.yml", + "type": "module", + "meta": { + "name": "seqtk_cutn", + "description": "Generates a BED file containing genomic locations of lengths of N.", + "keywords": ["cut", "fasta", "seqtk"], + "tools": [ + { + "seqtk": { + "description": "Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. Seqtk mergepe command merges pair-end reads into one interleaved file.", + "homepage": "https://github.com/lh3/seqtk", + "documentation": "https://docs.csc.fi/apps/seqtk/", + "tool_dev_url": "https://github.com/lh3/seqtk", + "licence": ["MIT"], + "identifier": "biotools:seqtk" + } } - ] + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "A single fasta file to be split.", + "pattern": "*.{fasta}", + "ontologies": [] + } + } + ] + ], + "output": { + "bed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "The output bed which summarised locations of cuts", + "pattern": "*.{bed}", + "ontologies": [] + } + } + ] + ], + "versions_seqtk": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "seqtk": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "seqtk 2>&1 | sed -n 's/^Version: //p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "seqtk": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "seqtk 2>&1 | sed -n 's/^Version: //p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@DLBPointon"], + "maintainers": ["@DLBPointon"] + }, + "pipelines": [ + { + "name": "pairgenomealign", + "version": "2.2.3" } - }, - { - "*mer_distribution*": { - "type": "file", - "description": "TSV file with calculated PEKA score and occurrence distribution for all possible k-mers", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" + ] + }, + { + "name": "seqtk_mergepe", + "path": "modules/nf-core/seqtk/mergepe/meta.yml", + "type": "module", + "meta": { + "name": "seqtk_mergepe", + "description": "Interleave pair-end reads from FastQ files", + "keywords": ["interleave", "merge", "fastx"], + "tools": [ + { + "seqtk": { + "description": "Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. Seqtk mergepe command merges pair-end reads into one interleaved file.", + "homepage": "https://github.com/lh3/seqtk", + "documentation": "https://docs.csc.fi/apps/seqtk/", + "tool_dev_url": "https://github.com/lh3/seqtk", + "licence": ["MIT"], + "identifier": "biotools:seqtk" + } } - ] + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,respectively.", + "pattern": "*.{fastq.gz}", + "ontologies": [] + } + } + ] + ], + "output": { + "reads": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fastq.gz": { + "type": "file", + "description": "If single-end reads, the output is the same as the input, 1 FastQ file for each read. If pair-end reads, the read pairs will be interleaved and output as 1 FastQ file for each read pair.", + "pattern": "*.{fastq.gz}", + "ontologies": [] + } + } + ] + ], + "versions_seqtk": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "seqtk": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "seqtk 2>&1 | sed -n 's/^Version: //p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "seqtk": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "seqtk 2>&1 | sed -n 's/^Version: //p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@emnilsson"], + "maintainers": ["@emnilsson"] + }, + "pipelines": [ + { + "name": "mag", + "version": "5.4.2" + }, + { + "name": "metatdenovo", + "version": "1.3.0" } - } - ] - ], - "rtxn": [ - [ - { - "meta": { - "type": "file", - "description": "TSV file of summed occurrence distributions of k-mers within defined clusters", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - }, - { - "*rtxn*": { - "type": "file", - "description": "rtxn file", - "pattern": "*rtxn*", - "ontologies": [] - } - } ] - ], - "pdf": [ - [ - { - "meta": { - "type": "file", - "description": "TSV file of summed occurrence distributions of k-mers within defined clusters", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - }, - { - "*.pdf": { - "type": "file", - "description": "PDF file with graphs showing k-mer occurrence distributions around thresholded crosslink sites", - "pattern": "*.pdf", - "ontologies": [] - } - } - ] - ], - "tsites": [ - [ - { - "meta": { - "type": "file", - "description": "TSV file of summed occurrence distributions of k-mers within defined clusters", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" + }, + { + "name": "seqtk_rename", + "path": "modules/nf-core/seqtk/rename/meta.yml", + "type": "module", + "meta": { + "name": "seqtk_rename", + "description": "Rename sequence names in FASTQ or FASTA files.", + "keywords": ["rename", "fastx", "header"], + "tools": [ + { + "seqtk": { + "description": "Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. The seqtk rename command renames sequence names.", + "homepage": "https://github.com/lh3/seqtk", + "documentation": "https://docs.csc.fi/apps/seqtk/", + "tool_dev_url": "https://github.com/lh3/seqtk", + "licence": ["MIT"], + "identifier": "biotools:seqtk" + } } - ] - } - }, - { - "*thresholded_sites*.bed.gz": { - "type": "file", - "description": "BED file of thresholded sites", - "pattern": "*thresholded_sites*.bed.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "sequences": { + "type": "file", + "description": "A FASTQ or FASTA file", + "pattern": "*.{fastq.gz, fastq, fq, fq.gz, fasta, fastq.gz, fa, fa.gz, fas, fas.gz, fna, fna.gz}", + "ontologies": [] + } + } + ] + ], + "output": { + "sequences": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.gz": { + "type": "file", + "description": "FASTQ/FASTA file containing renamed sequences", + "pattern": "*.{fastq.gz, fasta.gz}", + "ontologies": [] + } + } + ] + ], + "versions_seqtk": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "seqtk": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "seqtk 2>&1 | sed -n 's/^Version: //p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "seqtk": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "seqtk 2>&1 | sed -n 's/^Version: //p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@hseabolt", "@mjcipriano", "@sateeshperi"], + "maintainers": ["@hseabolt", "@mjcipriano", "@sateeshperi"] + } + }, + { + "name": "seqtk_sample", + "path": "modules/nf-core/seqtk/sample/meta.yml", + "type": "module", + "meta": { + "name": "seqtk_sample", + "description": "Subsample reads from FASTQ files", + "keywords": ["sample", "fastx", "reads"], + "tools": [ + { + "seqtk": { + "description": "Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. Seqtk sample command subsamples sequences.", + "homepage": "https://github.com/lh3/seqtk", + "documentation": "https://docs.csc.fi/apps/seqtk/", + "tool_dev_url": "https://github.com/lh3/seqtk", + "licence": ["MIT"], + "identifier": "biotools:seqtk" + } } - ] + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files", + "pattern": "*.{fastq.gz}", + "ontologies": [] + } + }, + { + "sample_size": { + "type": "float", + "description": "Fraction (<1.0) or number (>=1) of reads to sample." + } + } + ] + ], + "output": { + "reads": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fastq.gz": { + "type": "file", + "description": "Subsampled FastQ files", + "pattern": "*.{fastq.gz}", + "ontologies": [] + } + } + ] + ], + "versions_seqtk": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "seqtk": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "seqtk 2>&1 | sed -n 's/^Version: //p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "seqtk": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "seqtk 2>&1 | sed -n 's/^Version: //p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@kaurravneet4123", "@sidorov-si", "@adamrtalbot"], + "maintainers": ["@kaurravneet4123", "@sidorov-si", "@adamrtalbot"] + }, + "pipelines": [ + { + "name": "demultiplex", + "version": "1.7.1" + }, + { + "name": "panoramaseq", + "version": "dev" + }, + { + "name": "pathogensurveillance", + "version": "1.1.0" + }, + { + "name": "raredisease", + "version": "3.0.0" + }, + { + "name": "seqinspector", + "version": "1.0.1" } - } ] - ], - "oxn": [ - [ - { - "meta": { - "type": "file", - "description": "TSV file of summed occurrence distributions of k-mers within defined clusters", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - }, - { - "*oxn*.bed.gz": { - "type": "file", - "description": "BED file of oxn sites", - "pattern": "*oxn*.bed.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" + }, + { + "name": "seqtk_seq", + "path": "modules/nf-core/seqtk/seq/meta.yml", + "type": "module", + "meta": { + "name": "seqtk_seq", + "description": "Common transformation operations on FASTA or FASTQ files.", + "keywords": ["seq", "filter", "transformation"], + "tools": [ + { + "seqtk": { + "description": "Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. The seqtk seq command enables common transformation operations on FASTA or FASTQ files.", + "homepage": "https://github.com/lh3/seqtk", + "documentation": "https://docs.csc.fi/apps/seqtk/", + "tool_dev_url": "https://github.com/lh3/seqtk", + "licence": ["MIT"], + "identifier": "biotools:seqtk" + } } - ] + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "fastx": { + "type": "file", + "description": "A FASTQ or FASTA file", + "pattern": "*.{fastq.gz, fastq, fq, fq.gz, fasta, fastq.gz, fa, fa.gz, fas, fas.gz, fna, fna.gz}", + "ontologies": [] + } + } + ] + ], + "output": { + "fastx": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.gz": { + "type": "file", + "description": "FASTQ/FASTA file containing renamed sequences", + "pattern": "*.{fastq.gz, fasta.gz}", + "ontologies": [] + } + } + ] + ], + "versions_seqtk": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "seqtk": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "seqtk 2>&1 | sed -n 's/^Version: //p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "seqtk": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "seqtk 2>&1 | sed -n 's/^Version: //p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@hseabolt", "@mjcipriano", "@sateeshperi"], + "maintainers": ["@hseabolt", "@mjcipriano", "@sateeshperi"] + }, + "pipelines": [ + { + "name": "crisprseq", + "version": "2.3.0" + }, + { + "name": "metatdenovo", + "version": "1.3.0" + }, + { + "name": "radseq", + "version": "dev" } - } ] - ], - "clust": [ - [ - { - "meta": { - "type": "file", - "description": "TSV file of summed occurrence distributions of k-mers within defined clusters", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" + }, + { + "name": "seqtk_subseq", + "path": "modules/nf-core/seqtk/subseq/meta.yml", + "type": "module", + "meta": { + "name": "seqtk_subseq", + "description": "Select only sequences that match the filtering condition", + "keywords": ["filtering", "selection", "fastx"], + "tools": [ + { + "seqtk": { + "description": "Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format", + "homepage": "https://github.com/lh3/seqtk", + "documentation": "https://docs.csc.fi/apps/seqtk/", + "tool_dev_url": "https://github.com/lh3/seqtk", + "licence": ["MIT"], + "identifier": "biotools:seqtk" + } } - ] - } - }, - { - "*_clusters.csv": { - "type": "file", - "description": "CSV file of clusters", - "pattern": "*_clusters.csv", - "ontologies": [ + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "sequences": { + "type": "file", + "description": "FASTQ/FASTA file", + "pattern": "*.{fq,fq.gz,fa,fa.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ], { - "edam": "http://edamontology.org/format_3752" + "filter_list": { + "type": "file", + "description": "BED file or a text file with a list of sequence names", + "pattern": "*.{bed,lst}", + "ontologies": [] + } } - ] + ], + "output": { + "sequences": [ + [ + { + "meta": { + "type": "file", + "description": "FASTQ/FASTA file", + "pattern": "*.{fq.gz,fa.gz}", + "ontologies": [] + } + }, + { + "*.gz": { + "type": "file", + "description": "FASTQ/FASTA file", + "pattern": "*.{fq.gz,fa.gz}", + "ontologies": [] + } + } + ] + ], + "versions_seqtk": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "seqtk": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "seqtk 2>&1 | sed -n 's/^Version: //p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "seqtk": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "seqtk 2>&1 | sed -n 's/^Version: //p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@sidorov-si"], + "maintainers": ["@sidorov-si"] + }, + "pipelines": [ + { + "name": "ampliseq", + "version": "2.17.0" + }, + { + "name": "phyloplace", + "version": "2.0.0" } - } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@kkuret", - "@codeprimate123", - "@chris-cheshire", - "@charlotteanne" - ], - "maintainers": [ - "@kkuret", - "@codeprimate123", - "@chris-cheshire", - "@charlotteanne" - ] - } - }, - { - "name": "perbase", - "path": "modules/nf-core/perbase/meta.yml", - "type": "module", - "meta": { - "name": "perbase", - "description": "Per-base metrics on BAM/CRAM files.", - "keywords": [ - "bam", - "cram", - "depth" - ], - "tools": [ - { - "perbase": { - "description": "Per-base metrics on BAM/CRAM files.", - "homepage": "https://github.com/sstadick/perbase", - "documentation": "https://github.com/sstadick/perbase", - "tool_dev_url": "https://github.com/sstadick/perbase", - "doi": "10.21105/joss.09774", - "licence": [ - "MIT" - ], - "identifier": "biotools:perbase" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM/CRAM file", - "pattern": "*.{bam,cram}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_25722" - }, - { - "edam": "http://edamontology.org/format_3462" - } - ] - } - }, - { - "index": { - "type": "file", - "description": "BAI/CRAI file", - "pattern": "*.{bai,crai}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3327" - } - ] - } - }, - { - "bed": { - "type": "file", - "description": "bed file containing regions of interest, where only bases from the given regions will be reported", - "pattern": "*.{bed}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3003" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference fasta (optional)", - "pattern": "*.{fasta,fa}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } + }, + { + "name": "seqtk_trim", + "path": "modules/nf-core/seqtk/trim/meta.yml", + "type": "module", + "meta": { + "name": "seqtk_trim", + "description": "Trim low quality bases from FastQ files", + "keywords": ["trimfq", "fastq", "seqtk"], + "tools": [ + { + "seqtk": { + "description": "Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format", + "homepage": "https://github.com/lh3/seqtk", + "documentation": "https://docs.csc.fi/apps/seqtk/", + "tool_dev_url": "https://github.com/lh3/seqtk", + "licence": ["MIT"], + "identifier": "biotools:seqtk" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files", + "pattern": "*.{fastq.gz}", + "ontologies": [] + } + } + ] + ], + "output": { + "reads": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fastq.gz": { + "type": "file", + "description": "Filtered FastQ files", + "pattern": "*.{fastq.gz}", + "ontologies": [] + } + } + ] + ], + "versions_seqtk": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "seqtk": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "seqtk 2>&1 | sed -n 's/^Version: //p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "seqtk": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "seqtk 2>&1 | sed -n 's/^Version: //p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@laramiellindsey"] }, - { - "fai": { - "type": "file", - "description": "FAI file (optional)", - "pattern": "*.{fai}", - "ontologies": [] - } - } - ] - ], - "output": { - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.tsv.gz": { - "type": "file", - "description": "TSV file", - "pattern": "*.{tsv.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_perbase": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "perbase": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "perbase --version |& sed \"1!d ; s/perbase //\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "perbase": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "perbase --version |& sed \"1!d ; s/perbase //\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "demo", + "version": "1.1.0" + } ] - ] - }, - "authors": [ - "@camlloyd" - ], - "maintainers": [ - "@camlloyd" - ] - } - }, - { - "name": "percolator", - "path": "modules/nf-core/percolator/meta.yml", - "type": "module", - "meta": { - "name": "percolator", - "description": "Rescore peptide-spectrum matches and estimate false discovery rates using the Percolator semi-supervised learning algorithm.", - "keywords": [ - "proteomics", - "spectrum identification", - "psm", - "peptide", - "protein", - "rescoring", - "false discovery rate", - "features" - ], - "tools": [ - { - "percolator": { - "description": "Semi-supervised learning for peptide identification from shotgun proteomics datasets.", - "homepage": "http://percolator.ms", - "documentation": "http://percolator.ms", - "tool_dev_url": "https://github.com/percolator/percolator", - "doi": "10.1038/nmeth1113", - "licence": [ - "Apache-2.0" - ], - "identifier": "biotools:percolator" + }, + { + "name": "sequali", + "path": "modules/nf-core/sequali/meta.yml", + "type": "module", + "meta": { + "name": "sequali", + "description": "Sequence quality metrics for FASTQ and uBAM files.", + "keywords": ["quality_control", "qc", "preprocessing"], + "tools": [ + { + "sequali": { + "description": "Fast sequencing quality metrics", + "homepage": "https://github.com/rhpvorderman/sequali", + "documentation": "https://sequali.readthedocs.io/en/latest/", + "tool_dev_url": "https://github.com/rhpvorderman/sequali", + "doi": "10.5281/zenodo.10854010", + "licence": ["AGPL v3-or-later"], + "identifier": "biotools:sequali" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "reads": { + "type": "file", + "description": "Input FASTQ(s) or uBAM file. The format is autodetected and compressed formats are supported.", + "pattern": "*.{fastq,fq,fastq.gz,fq.gz,bam}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ] + ], + "output": { + "html": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.html": { + "type": "file", + "description": "HTML output file.", + "pattern": "*.{html}", + "ontologies": [] + } + } + ] + ], + "json": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.json": { + "type": "file", + "description": "JSON output file.", + "pattern": "*.{json}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "versions_sequali": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "sequali": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "sequali --version |& sed '1!d ; s/sequali //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "sequali": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "sequali --version |& sed '1!d ; s/sequali //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@irliampa", "@DarkoCucin"], + "maintainers": ["@irliampa", "@DarkoCucin"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" - } - }, - { - "peptide_identification": { - "type": "file", - "description": "peptide identifications as PIN (Percolator input) file", - "pattern": "*.pin", - "ontologies": [] - } + }, + { + "name": "sequencetools_pileupcaller", + "path": "modules/nf-core/sequencetools/pileupcaller/meta.yml", + "type": "module", + "meta": { + "name": "sequencetools_pileupcaller", + "description": "PileupCaller is a tool to create genotype calls from bam files using read-sampling methods", + "keywords": [ + "genotyping", + "mpileup", + "random draw", + "pseudohaploid", + "pseudodiploid", + "freqsum", + "plink", + "bed", + "eigenstrat" + ], + "tools": [ + { + "sequencetools": { + "description": "Tools for population genetics on sequencing data", + "homepage": "https://github.com/stschiff/sequenceTools", + "documentation": "https://github.com/stschiff/sequenceTools#readme", + "tool_dev_url": "https://github.com/stschiff/sequenceTools", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "mpileup": { + "type": "file", + "description": "samtools mpileup output.", + "ontologies": [] + } + } + ], + { + "snpfile": { + "type": "file", + "description": "Eigenstrat format .snp file of the sites in the mpileup file to call genotypes on.\nOnly alleles matching the Ref and Alt alleles of the provided snp file will be called.\n", + "ontologies": [] + } + }, + { + "sample_names_fn": { + "type": "file", + "description": "File containing the sample names", + "ontologies": [] + } + } + ], + "output": { + "eigenstrat": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.geno": { + "type": "file", + "description": "A tuple containing the output Eigenstrat-formatted geno, snp and ind files.", + "pattern": "*.{geno,snp,ind}.txt", + "ontologies": [] + } + }, + { + "*.snp": { + "type": "file", + "description": "A tuple containing the output Eigenstrat-formatted geno, snp and ind files.", + "pattern": "*.{geno,snp,ind}.txt", + "ontologies": [] + } + }, + { + "*.ind": { + "type": "file", + "description": "A tuple containing the output Eigenstrat-formatted geno, snp and ind files.", + "pattern": "*.{geno,snp,ind}.txt", + "ontologies": [] + } + } + ] + ], + "plink": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "A tuple containing the output Plink-formatted bed, bim and fam files.", + "pattern": "*.{bed,bim,fam}", + "ontologies": [] + } + }, + { + "*.bim": { + "type": "file", + "description": "A tuple containing the output Plink-formatted bed, bim and fam files.", + "pattern": "*.{bed,bim,fam}", + "ontologies": [] + } + }, + { + "*.fam": { + "type": "file", + "description": "A tuple containing the output Plink-formatted bed, bim and fam files.", + "pattern": "*.{bed,bim,fam}", + "ontologies": [] + } + } + ] + ], + "freqsum": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.freqsum.gz": { + "type": "file", + "description": "The output freqsum-formatted file.", + "pattern": "*.freqsum.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@TCLamnidis"], + "maintainers": ["@TCLamnidis"] } - ] - ], - "output": { - "pout_xml": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" - } - }, - { - "${prefix}.pout.xml": { - "type": "file", - "description": "Percolator output in XML format containing all PSM-level results", - "pattern": "*.pout.xml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2332" - } - ] - } - } - ] - ], - "pout_pepxml": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" - } - }, - { - "${prefix}.pep.xml": { - "type": "file", - "description": "Percolator output in pepXML format", - "pattern": "*.pep.xml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3655" - } - ] - } - } - ] - ], - "features_pin": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" - } - }, - { - "${prefix}.features.pin": { - "type": "file", - "description": "Tab-separated file with rescored features (PIN format)", - "pattern": "*.features.pin", - "ontologies": [] - } - } - ] - ], - "weights": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" - } - }, - { - "${prefix}.weights.tsv": { - "type": "file", - "description": "TSV file containing the final feature weights", - "pattern": "*.weights.tsv", - "ontologies": [] - } - } - ] - ], - "target_peptides": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" - } - }, - { - "${prefix}.pep.target.pout": { - "type": "file", - "description": "Target peptide-level results in tab separated format (pout)", - "pattern": "*.pep.target.pout", - "ontologies": [] - } - } - ] - ], - "decoy_peptides": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" - } - }, - { - "${prefix}.pep.decoy.pout": { - "type": "file", - "description": "Decoy peptide-level results in tab separated format (pout)", - "pattern": "*.pep.decoy.pout", - "ontologies": [] - } - } - ] - ], - "target_psms": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" - } - }, - { - "${prefix}.psm.target.pout": { - "type": "file", - "description": "Target PSM-level results in tab separated format (pout)", - "pattern": "*.psm.target.pout", - "ontologies": [] - } - } - ] - ], - "decoy_psms": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" - } - }, - { - "${prefix}.psm.decoy.pout": { - "type": "file", - "description": "Decoy PSM-level results in tab separated format (pout)", - "pattern": "*.psm.decoy.pout", - "ontologies": [] - } - } - ] - ], - "target_proteins": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" - } - }, - { - "${prefix}.protein.target.pout": { - "type": "file", - "description": "Target protein-level results in tab separated format (pout)", - "pattern": "*.protein.target.pout", - "ontologies": [] - } - } - ] - ], - "decoy_proteins": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" - } - }, - { - "${prefix}.protein.decoy.pout": { - "type": "file", - "description": "Decoy protein-level results in tab separated format (pout)", - "pattern": "*.protein.decoy.pout", - "ontologies": [] - } - } - ] - ], - "versions_percolator": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "percolator": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "percolator --help 2>&1 | head -1 | sed \"s;Percolator version \\([^,]*\\),.*;\\1;\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "percolator": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "percolator --help 2>&1 | head -1 | sed \"s;Percolator version \\([^,]*\\),.*;\\1;\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@julianu" - ], - "maintainers": [ - "@julianu" - ] - }, - "pipelines": [ - { - "name": "mspepid", - "version": "dev" - } - ] - }, - { - "name": "phantompeakqualtools", - "path": "modules/nf-core/phantompeakqualtools/meta.yml", - "type": "module", - "meta": { - "name": "phantompeakqualtools", - "description": "\"This package computes informative enrichment and quality measures\nfor ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used\nto obtain robust estimates of the predominant fragment length or\ncharacteristic tag shift values in these assays.\"\n", - "keywords": [ - "ChIP-Seq", - "QC", - "phantom peaks" - ], - "tools": [ - { - "phantompeakqualtools": { - "description": "\"This package computes informative enrichment and quality measures\nfor ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used\nto obtain robust estimates of the predominant fragment length or\ncharacteristic tag shift values in these assays.\"\n", - "documentation": "https://github.com/kundajelab/phantompeakqualtools", - "tool_dev_url": "https://github.com/kundajelab/phantompeakqualtools", - "doi": "10.1101/gr.136184.111", - "licence": [ - "BSD-3-clause" - ], - "identifier": "biotools:phantompeakqualtools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } - } - ] - ], - "output": { - "spp": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.out": { - "type": "file", - "description": "A ChIP-Seq Processing Pipeline file containing\npeakshift/phantomPeak results\n", - "pattern": "*.{out}", - "ontologies": [] - } - } - ] - ], - "pdf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.pdf": { - "type": "file", - "description": "A pdf containing save cross-correlation plots", - "pattern": "*.{pdf}", - "ontologies": [] - } - } - ] - ], - "rdata": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.Rdata": { - "type": "file", - "description": "Rdata file containing the R session", - "pattern": "*.{Rdata}", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@drpatelh", - "@edmundmiller", - "@JoseEspinosa" - ], - "maintainers": [ - "@drpatelh", - "@edmundmiller", - "@JoseEspinosa" - ] - }, - "pipelines": [ - { - "name": "chipseq", - "version": "2.1.0" - } - ] - }, - { - "name": "pharmcat_matcher", - "path": "modules/nf-core/pharmcat/matcher/meta.yml", - "type": "module", - "meta": { - "name": "pharmcat_matcher", - "description": "The Named Allele Matcher is responsible for calling diplotypes from variant call data.\nWhile it is designed to be used in the PharmCAT pipeline, it can also be run independently.\nThe Named Allele Matcher does not currently support structural variants, including gene copy\nnumber. If structural variants are detected in the VCF data, it will be ignored and a warning\nwill be issued.\nIf it detects more than the expected number of alleles in the GT column of the VCF, only the\nfirst two alleles will be used and a warning will be issued. On haploid chromosomes, only\nthe first allele will be used.\n", - "keywords": [ - "vcf", - "pharmcat", - "matcher", - "PGx" - ], - "tools": [ - { - "pharmcat": { - "description": "\"PharmCAT (Pharmacogenomics Clinical Annotation Tool) is a bioinformatics\ntool that analyzes genetic variants to predict drug response and tailor medical\ntreatment to an individual patient’s genetic profile.\"\n", - "homepage": "https://pharmcat.clinpgx.org/", - "documentation": "https://pharmcat.clinpgx.org/", - "tool_dev_url": "https://github.com/PharmGKB/PharmCAT", - "doi": "10.1002/cpt.928", - "licence": [ - "MPL-2.0" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', name:'test_sample' ]`\n" - } - }, - { - "vcf": { - "type": "file", - "description": "The vcf file to be inspected", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - }, - { - "index": { - "type": "file", - "description": "The tbi/csi file to be inspected", - "pattern": "*.{tbi,csi}", - "ontologies": [] - } - } - ], - { - "genes": { - "type": "list", - "description": "List of genes to be processed" - } - } - ], - "output": { - "matcher_json": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', name:'test_sample' ]`\n" - } - }, - { - "*.match.json": { - "type": "file", - "description": "Json output from the matcher module of PharmCAT", - "pattern": "*.match.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "matcher_html": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', name:'test_sample' ]`\n" - } - }, - { - "*.match.html": { - "type": "file", - "description": "HTML output from the matcher module of PharmCAT", - "pattern": "*.match.html", - "ontologies": [] - } - } - ] - ], - "versions_pharmcat": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pharmcat": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pharmcat --version | cut -f2 -d ' '": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pharmcat": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pharmcat --version | cut -f2 -d ' '": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@ramsainanduri" - ], - "maintainers": [ - "@ramsainanduri" - ] - } - }, - { - "name": "pharmcat_phenotyper", - "path": "modules/nf-core/pharmcat/phenotyper/meta.yml", - "type": "module", - "meta": { - "name": "pharmcat_phenotyper", - "description": "The PharmCAT Phenotyper is a core module of the Pharmacogenomics Clinical Annotation Tool\nthat translates patient diplotypes into specific, actionable metabolizer phenotypes\n(e.g., Poor Metabolizer). It operates by analyzing the JSON output from the Named\nAllele Matcher, mapping these results to established clinical guidelines (such as\nCPIC) to predict drug response.\n", - "keywords": [ - "vcf", - "pharmcat", - "phenotyper", - "PGx" - ], - "tools": [ - { - "pharmcat": { - "description": "\"PharmCAT (Pharmacogenomics Clinical Annotation Tool) is a bioinformatics\ntool that analyzes genetic variants to predict drug response and tailor medical\ntreatment to an individual patient’s genetic profile.\"\n", - "homepage": "https://pharmcat.clinpgx.org/", - "documentation": "https://pharmcat.clinpgx.org/", - "tool_dev_url": "https://github.com/PharmGKB/PharmCAT", - "doi": "10.1002/cpt.928", - "licence": [ - "MPL-2.0" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', name:'test_sample' ]`\n" - } - }, - { - "match_json": { - "type": "file", - "description": "The Json output from the matcher module of pharmcat", - "pattern": "*.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - }, - { - "outside_match_tsv": { - "type": "file", - "description": "Tab seperated file containing diplotypes calls from other callers", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "output": { - "phenotyper_json": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', name:'test_sample' ]`\n" - } - }, - { - "*.phenotype.json": { - "type": "file", - "description": "Json output from the phenotyper module of PharmCAT", - "pattern": "*.phenotype.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "versions_pharmcat": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pharmcat": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pharmcat --version | cut -f2 -d ' '": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pharmcat": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pharmcat --version | cut -f2 -d ' '": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@ramsainanduri" - ], - "maintainers": [ - "@ramsainanduri" - ] - } - }, - { - "name": "pharmcat_reporter", - "path": "modules/nf-core/pharmcat/reporter/meta.yml", - "type": "module", - "meta": { - "name": "pharmcat_reporter", - "description": "The Reporter module is responsible for generating a report with genotype-specific\nexpert-reviewed drug prescribing recommendations for clinical decision support.\n", - "keywords": [ - "pharmcat", - "report", - "PGx" - ], - "tools": [ - { - "pharmcat": { - "description": "\"PharmCAT (Pharmacogenomics Clinical Annotation Tool) is a bioinformatics\ntool that analyzes genetic variants to predict drug response and tailor medical\ntreatment to an individual patient’s genetic profile.\"\n", - "homepage": "https://pharmcat.clinpgx.org/", - "documentation": "https://pharmcat.clinpgx.org/", - "tool_dev_url": "https://github.com/PharmGKB/PharmCAT", - "doi": "10.1002/cpt.928", - "licence": [ - "MPL-2.0" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', name:'test_sample' ]`\n" - } - }, - { - "phenotypes": { - "type": "file", - "description": "The vcf file to be inspected", - "pattern": "*.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "output": { - "report_json": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', name:'test_sample' ]`\n" - } - }, - { - "*.report.json": { - "type": "file", - "description": "Json output from the reporter module of PharmCAT", - "pattern": "*.report.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "report_html": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', name:'test_sample' ]`\n" - } - }, - { - "*.report.html": { - "type": "file", - "description": "HTML output from the reporter module of PharmCAT", - "pattern": "*.report.html", - "ontologies": [] - } - } - ] - ], - "report_tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', name:'test_sample' ]`\n" - } - }, - { - "*.report.tsv": { - "type": "file", - "description": "Tab separated output from the reporter module of PharmCAT", - "pattern": "*.report.tsv", - "ontologies": [] - } - } - ] - ], - "versions_pharmcat": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pharmcat": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pharmcat --version | cut -f2 -d ' '": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pharmcat": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pharmcat --version | cut -f2 -d ' '": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@ramsainanduri" - ], - "maintainers": [ - "@ramsainanduri" - ] - } - }, - { - "name": "pharmcat_vcfpreprocessor", - "path": "modules/nf-core/pharmcat/vcfpreprocessor/meta.yml", - "type": "module", - "meta": { - "name": "pharmcat_vcfpreprocessor", - "description": "The PharmCAT VCF Preprocessor is a script that can pre-process VCF files for PharmCAT to make sure the VCF file complies with PharmCAT's VCF Requirements", - "keywords": [ - "preprocessing", - "vcf", - "phamrcat" - ], - "tools": [ - { - "pharmcat": { - "description": "PharmCAT (Pharmacogenomics Clinical Annotation Tool) is a bioinformatics tool that analyzes genetic variants to predict drug response and tailor medical treatment to an individual patient’s genetic profile. ", - "homepage": "https://pharmcat.clinpgx.org/", - "documentation": "https://pharmcat.clinpgx.org/", - "tool_dev_url": "https://github.com/PharmGKB/PharmCAT", - "doi": "10.1002/cpt.928", - "licence": [ - "MPL-2.0" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', name:'test_sample' ]`\n" - } - }, - { - "vcf_gz": { - "type": "file", - "description": "The vcf file to be inspected", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - }, - { - "vcf_index": { - "type": "file", - "description": "The tbi/csi file to be inspected", - "pattern": "*.{tbi,csi}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Genome fasta file", - "pattern": "*.{fa,fasta,fa.gz,fasta.gz}", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" - } - }, - { - "fai": { - "type": "file", - "description": "Genome index file", - "pattern": "*.{fai,fai.gz}", - "ontologies": [] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" - } - }, - { - "pharmcat_positions": { - "type": "file", - "description": "Pharmcat positions vcf", - "pattern": "*.vcf.{gz,bgz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - }, - { - "pharmcat_positions_index": { - "type": "file", - "description": "Pharmcat positions vcf index file", - "pattern": "*.{tbi,csi}", - "ontologies": [] - } - } - ], - [ - { - "meta5": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" - } - }, - { - "pharmcat_uniallelic_positions": { - "type": "file", - "description": "Pharmcat uniallelic positions vcf", - "pattern": "*.vcf.{gz,bgz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - }, - { - "pharmcat_uniallelic_positions_index": { - "type": "file", - "description": "Pharmcat uniallelic positions vcf index file", - "pattern": "*.{tbi,csi}", - "ontologies": [] - } - } - ] - ], - "output": { - "preprocessed_vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', name:'test_sample' ]`\n" - } - }, - { - "*.preprocessed.vcf.bgz": { - "type": "file", - "description": "Preprocessed vcf file", - "pattern": "*.preprocessed.vcf.bgz", - "ontologies": [] - } - } - ] - ], - "missing_pgx_var": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', name:'test_sample' ]`\n" - } - }, - { - "*.missing_pgx_var.vcf": { - "type": "file", - "description": "Missing position in PGX VCF file", - "pattern": "*.missing_pgx_var.vcf", - "ontologies": [] - } - } - ] - ], - "versions_pharmcat_vcf_preprocessor": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pharmcat_vcf_preprocessor": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pharmcat_vcf_preprocessor --version | cut -f4 -d ' '": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pharmcat_vcf_preprocessor": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pharmcat_vcf_preprocessor --version | cut -f4 -d ' '": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@ramsainanduri" - ], - "maintainers": [ - "@ramsainanduri" - ] - } - }, - { - "name": "pharokka_installdatabases", - "path": "modules/nf-core/pharokka/installdatabases/meta.yml", - "type": "module", - "meta": { - "name": "pharokka_installdatabases", - "description": "Install databases necessary for Pharokka's functional analysis", - "keywords": [ - "pharokka", - "prokka", - "bakta", - "phage", - "function", - "install", - "database" - ], - "tools": [ - { - "pharokka": { - "description": "Fast Phage Annotation Program", - "homepage": "https://pharokka.readthedocs.io", - "documentation": "https://pharokka.readthedocs.io", - "tool_dev_url": "https://github.com/gbouras13/pharokka", - "doi": "10.1093/bioinformatics/btac776", - "licence": [ - "MIT" - ], - "identifier": "biotools:pharokka" - } - } - ], - "output": { - "pharokka_db": [ - { - "${prefix}/": { - "type": "directory", - "description": "Directory pointing to Pharokka's database", - "pattern": "${prefix}/" - } - } - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@CarsonJM" - ], - "maintainers": [ - "@CarsonJM" - ] - }, - "pipelines": [ - { - "name": "phageannotator", - "version": "dev" - } - ] - }, - { - "name": "pharokka_pharokka", - "path": "modules/nf-core/pharokka/pharokka/meta.yml", - "type": "module", - "meta": { - "name": "pharokka_pharokka", - "description": "Functional annotation of phages", - "keywords": [ - "pharokka", - "phage", - "function", - "prokka", - "bakta" - ], - "tools": [ - { - "pharokka": { - "description": "Fast Phage Annotation Program", - "homepage": "https://pharokka.readthedocs.io", - "documentation": "https://pharokka.readthedocs.io", - "tool_dev_url": "https://github.com/gbouras13/pharokka", - "doi": "10.1093/bioinformatics/btac776", - "licence": [ - "MIT" - ], - "identifier": "biotools:pharokka" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "phage_fasta": { - "type": "file", - "description": "A FASTA file containing phage sequence(s)", - "pattern": "*.{fasta,fna,fa}", - "ontologies": [] - } - } - ], - { - "pharokka_db": { - "type": "file", - "description": "Directory containing Pharokka's database", - "ontologies": [] - } - } - ], - "output": { - "cds_final_merged_output": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "${prefix}_pharokka/${prefix}_cds_final_merged_output.tsv": { - "type": "file", - "description": "A file containing the final merged output of CDSs", - "pattern": "*_cds_final_merged_output.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "cds_functions": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "${prefix}_pharokka/${prefix}_cds_functions.tsv": { - "type": "file", - "description": "A file that includes count of CDSs, tRNAs, CRISPRs, tmRNAs, and PHROG functions assigned to CDSs", - "pattern": "*_cds_functions.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "length_gc_cds_density": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "${prefix}_pharokka/${prefix}_length_gc_cds_density.tsv": { - "type": "file", - "description": "A file containing the length, GC content, and CDS density of the phage genome", - "pattern": "*_length_gc_cds_density.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "card": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "${prefix}_pharokka/${prefix}_top_hits_card.tsv": { - "type": "file", - "description": "OPTIONAL - A file containing any CARD database hits", - "pattern": "*top_hits_card.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "vfdb": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "${prefix}_pharokka/${prefix}_top_hits_vfdb.tsv": { - "type": "file", - "description": "OPTIONAL - A file containing any VFDB database hits", - "pattern": "*top_hits_vfdb.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "mash": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "${prefix}_pharokka/${prefix}_top_hits_mash_inphared.tsv": { - "type": "file", - "description": "OPTIONAL - File containing top hits to INPHARED database", - "pattern": "*_top_hits_mash_inphared.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "reoriented": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "${prefix}_pharokka/${prefix}_genome_terminase_reoriented.fasta": { - "type": "file", - "description": "OPTIONAL - FASTA file reoriented to start with the large terminase subunit", - "pattern": "*_genome_terminase_reoriented.fasta", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@CarsonJM" - ], - "maintainers": [ - "@CarsonJM" - ] - }, - "pipelines": [ - { - "name": "phageannotator", - "version": "dev" - } - ] - }, - { - "name": "phenoimager2mc", - "path": "modules/nf-core/phenoimager2mc/meta.yml", - "type": "module", - "meta": { - "name": "phenoimager2mc", - "description": "Formatting PhenoImager TIFF output files into stacked and normalized OME-TIFF files per cycle, compatible as ASHLAR and MCMICRO input.", - "keywords": [ - "imaging", - "registration", - "ome-tif", - "Staging", - "MCMICRO" - ], - "tools": [ - { - "phenoimager2mc": { - "description": "PhenoImager output conversion into a stacked and normalized OME-TIFF file per cycle.", - "homepage": "https://github.com/SchapiroLabor/phenoimager2mc", - "documentation": "https://github.com/SchapiroLabor/phenoimager2mc/README.md", - "tool_dev_url": "https://github.com/SchapiroLabor/phenoimager2mc", - "licence": [ - "GPL-2.0 license" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "tiles": { - "type": "list", - "description": "Folder or list with TIFF files of one cycle from PhenoImager" - } - } - ] - ], - "output": { - "tif": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.tif": { - "type": "file", - "description": "One output .tif file containing concatenated tiles of the cycle.", - "pattern": "*.{tif,tiff}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3591" - } - ] - } - } - ] - ], - "versions_phenoimager2mc": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "phenoimager2mc": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "phenoimager2mc --version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_python": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "python": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python --version | sed -e \"s/Python //g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_ome_types": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "ome_types": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python -m pip show ome_types | sed -n \"s/Version: //p\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "phenoimager2mc": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "phenoimager2mc --version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "python": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python --version | sed -e \"s/Python //g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "ome_types": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python -m pip show ome_types | sed -n \"s/Version: //p\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@chiarasch", - "@kbestak" - ], - "maintainers": [ - "@chiarasch" - ] - } - }, - { - "name": "phispy", - "path": "modules/nf-core/phispy/meta.yml", - "type": "module", - "meta": { - "name": "phispy", - "description": "Predict prophages in bacterial genomes", - "keywords": [ - "genomics", - "virus", - "phage", - "prophage", - "annotation", - "identification" - ], - "tools": [ - { - "phispy": { - "description": "Prophage finder using multiple metrics", - "homepage": "https://github.com/linsalrob/PhiSpy/blob/master/README.md", - "documentation": "https://github.com/linsalrob/PhiSpy/blob/master/README.md", - "tool_dev_url": "https://github.com/linsalrob/PhiSpy/", - "doi": "10.1093/nar/gks406", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "gbk": { - "type": "file", - "description": "Genome file in .gbk or .gbff format.", - "pattern": "*.{gbk,gbff}", - "ontologies": [] - } - } - ] - ], - "output": { - "coordinates": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.tsv": { - "type": "file", - "description": "Coordinates of each prophage identified in the genome,\nand their att sites (if found).\n", - "pattern": "*.{tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "gbk": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.gb*": { - "type": "file", - "description": "A duplicate GenBank record that is the same as the input record,\nbut we have inserted the prophage information, including att\nsites into the record.\n", - "pattern": "*.{gbk,gbff}", - "ontologies": [] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.log": { - "type": "file", - "description": "File containing the PhiSpy execution log", - "pattern": "*.{log}", - "ontologies": [] - } - } - ] - ], - "information": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}_prophage_information.tsv": { - "type": "file", - "description": "File containing all the genes of the genome, one per line.\nThe tenth column describes how likely the gene is a phage gene.\n", - "pattern": "*.{tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "bacteria_fasta": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}_bacteria.fasta": { - "type": "file", - "description": "Genome with prophage regions masked with N.", - "pattern": "*.{fasta}", - "ontologies": [] - } - } - ] - ], - "bacteria_gbk": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}_bacteria.gbk": { - "type": "file", - "description": "Genome sequences identified as bacterial.", - "pattern": "*.{gbk}", - "ontologies": [] - } - } - ] - ], - "phage_fasta": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}_phage.fasta": { - "type": "file", - "description": "Phage sequences extracted from the genome.", - "pattern": "*.{fasta}", - "ontologies": [] - } - } - ] - ], - "phage_gbk": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}_phage.gbk": { - "type": "file", - "description": "Phage sequences extracted from the genome.", - "pattern": "*.{gbk}", - "ontologies": [] - } - } - ] - ], - "prophage_gff": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}_prophage.gff3": { - "type": "file", - "description": "Prophage information in GFF3 format.", - "pattern": "*.{gff3}", - "ontologies": [] - } - } - ] - ], - "prophage_tbl": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}_prophage.tbl": { - "type": "file", - "description": "File containing prophage number and its location in the genome.\n", - "pattern": "*.{tbl}", - "ontologies": [] - } - } - ] - ], - "prophage_tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}_prophage.tsv": { - "type": "file", - "description": "A file containing simpler version of the coordinates file,\nwith only prophage number, contig, start and stop.\n", - "pattern": "*.{tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@jvfe" - ], - "maintainers": [ - "@jvfe" - ] - } - }, - { - "name": "phyloflash", - "path": "modules/nf-core/phyloflash/meta.yml", - "type": "module", - "meta": { - "name": "phyloflash", - "description": "phyloFlash is a pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.", - "keywords": [ - "metagenomics", - "illumina datasets", - "phylogenetic composition" - ], - "tools": [ - { - "phyloflash": { - "description": "phyloFlash is a pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.", - "homepage": "https://hrgv.github.io/phyloFlash/", - "documentation": "https://hrgv.github.io/phyloFlash/usage.html", - "tool_dev_url": "https://github.com/HRGV/phyloFlash", - "doi": "10.1128/mSystems.00920-20", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:phyloflash" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "Channel containing single or paired-end reads", - "pattern": "*.{fastq.gz,fq.gz}", - "ontologies": [] - } - } - ], - { - "silva_db": { - "type": "directory", - "description": "Folder containing SILVA database" - } - }, - { - "univec_db": { - "type": "directory", - "description": "Folder containing UniVec database", - "pattern": "UniVec" - } - } - ], - "output": { - "results": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${meta.id}*/*": { - "type": "directory", - "description": "Folder containing the results of phyloFlash analysis", - "pattern": "${prefix}*" - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@abhi18av" - ], - "maintainers": [ - "@abhi18av" - ] - } - }, - { - "name": "picard_addorreplacereadgroups", - "path": "modules/nf-core/picard/addorreplacereadgroups/meta.yml", - "type": "module", - "meta": { - "name": "picard_addorreplacereadgroups", - "description": "Assigns all the reads in a file to a single new read-group", - "keywords": [ - "add", - "replace", - "read-group", - "picard" - ], - "tools": [ - { - "picard": { - "description": "A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS)\ndata and formats such as SAM/BAM/CRAM and VCF.\n", - "homepage": "https://broadinstitute.github.io/picard/", - "documentation": "https://gatk.broadinstitute.org/hc/en-us/articles/360037226472-AddOrReplaceReadGroups-Picard-", - "tool_dev_url": "https://github.com/broadinstitute/picard", - "licence": [ - "MIT" - ], - "identifier": "biotools:picard_tools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "Sequence reads file, can be SAM/BAM/CRAM format", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome file", - "pattern": "*.{fasta,fa,fasta.gz,fa.gz}", - "ontologies": [] - } - }, - { - "fai": { - "type": "file", - "description": "Reference genome index file", - "pattern": "*.{fai,fasta.fai,fa.fai,fasta.gz.fai,fa.gz.fai}", - "ontologies": [] - } - } - ] - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bam": { - 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"type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "picard": { - "type": "string", - "description": "The tool name" - } - }, - { - "picard AddOrReplaceReadGroups --version 2>&1 | sed -n 's/.*Version://p'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@sateeshperi", - "@mjcipriano", - "@hseabolt", - "@cmatKhan", - "@muffato" - ], - "maintainers": [ - "@sateeshperi", - "@mjcipriano", - "@hseabolt", - "@cmatKhan", - "@muffato" - ] - }, - "pipelines": [ - { - "name": "methylseq", - "version": "4.2.0" - }, - { - "name": "pathogensurveillance", - "version": "1.1.0" - }, - { - "name": "raredisease", - "version": "3.0.0" - } - ] - }, - { - "name": "picard_bedtointervallist", - "path": "modules/nf-core/picard/bedtointervallist/meta.yml", - "type": "module", - "meta": { - "name": "picard_bedtointervallist", - "description": "Creates an interval list from a bed file and a reference dict", - "keywords": [ - "bed", - "interval list", - "picard", - "convert" - ], - "tools": [ - { - "gatk4": { - "description": "Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools\nwith a primary focus on variant discovery and genotyping. Its powerful processing engine\nand high-performance computing features make it capable of taking on projects of any size.\n", - "homepage": "https://gatk.broadinstitute.org/hc/en-us", - "documentation": "https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s", - "doi": "10.1158/1538-7445.AM2017-3590", - "licence": [ - "Apache-2.0" - ], - "identifier": "biotools:picard_tools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "bed": { - "type": "file", - "description": "Input bed file", - "pattern": "*.bed", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome']\n" - } - }, - { - "dict": { - "type": "file", - "description": "Sequence dictionary", - "pattern": "*.dict", - "ontologies": [] - } - } - ] - ], - "output": { - "intervallist": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "*.intervallist": { - "type": "file", - "description": "gatk interval list file", - "pattern": "*.intervallist", - "ontologies": [] - } - } - ] - ], - "versions_picard": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "picard": { - "type": "string", - "description": "The tool name" - } - }, - { - "picard BedToIntervalList --version 2>&1 | sed -n 's/.*Version://p'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "picard": { - "type": "string", - "description": "The tool name" - } - }, - { - "picard BedToIntervalList --version 2>&1 | sed -n 's/.*Version://p'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@kevinmenden", - "@matthdsm" - ], - "maintainers": [ - "@kevinmenden", - "@matthdsm" - ] - }, - "pipelines": [ - { - "name": "methylseq", - "version": "4.2.0" - } - ] - }, - { - "name": "picard_cleansam", - "path": "modules/nf-core/picard/cleansam/meta.yml", - "type": "module", - "meta": { - "name": "picard_cleansam", - "description": "Cleans the provided BAM, soft-clipping beyond-end-of-reference alignments and setting MAPQ to 0 for unmapped reads", - "keywords": [ - "clean", - "bam", - "picard", - "sam", - "clipping" - ], - "tools": [ - { - "picard": { - "description": "A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS)\ndata and formats such as SAM/BAM/CRAM and VCF.\n", - "homepage": "https://broadinstitute.github.io/picard/", - "documentation": "https://gatk.broadinstitute.org/hc/en-us/articles/360036491452-CleanSam-Picard-", - "tool_dev_url": "https://github.com/broadinstitute/picard", - "licence": [ - "MIT" - ], - "identifier": "biotools:picard_tools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file", - "pattern": "*.{bam}", - "ontologies": [] - } - } - ] - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "Cleaned BAM file", - "pattern": "*.{bam}", - "ontologies": [] - } - } - ] - ], - "versions_picard": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "picard": { - "type": "string", - "description": "The tool name" - } - }, - { - "picard CleanSam --version 2>&1 | sed -n 's/.*Version://p'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "picard": { - "type": "string", - "description": "The tool name" - } - }, - { - "picard CleanSam --version 2>&1 | sed -n 's/.*Version://p'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@sateeshperi", - "@mjcipriano", - "@hseabolt" - ], - "maintainers": [ - "@sateeshperi", - "@mjcipriano", - "@hseabolt" - ] - } - }, - { - "name": "picard_collectalignmentsummarymetrics", - "path": "modules/nf-core/picard/collectalignmentsummarymetrics/meta.yml", - "type": "module", - "meta": { - "name": "picard_collectalignmentsummarymetrics", - "description": "Collect metrics about the alignment summary of a paired-end library.", - "keywords": [ - "metrics", - "alignment", - "statistics", - "bam" - ], - "tools": [ - { - "picard": { - "description": "Java tools for working with NGS data in the BAM format", - "homepage": "https://broadinstitute.github.io/picard/", - "documentation": "https://broadinstitute.github.io/picard/", - "tool_dev_url": "https://github.com/broadinstitute/picard", - "licence": [ - "MIT" - ], - "identifier": "biotools:picard_tools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Fasta file", - "pattern": "*.{fasta}", - "ontologies": [] - } - } - ] - ], - "output": { - "metrics": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.txt": { - "type": "file", - "description": "Standard alignment summary metrics", - "pattern": "*.txt", - "ontologies": [] - } - } - ] - ], - "versions_picard": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "picard": { - "type": "string", - "description": "The tool name" - } - }, - { - "picard CollectAlignmentSummaryMetrics --version 2>&1 | sed -n 's/.*Version://p'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "picard": { - "type": "string", - "description": "The tool name" - } - }, - { - "picard CollectAlignmentSummaryMetrics --version 2>&1 | sed -n 's/.*Version://p'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@mikefeixu", - "@FerriolCalvet" - ], - "maintainers": [ - "@mikefeixu" - ] - } - }, - { - "name": "picard_collecthsmetrics", - "path": "modules/nf-core/picard/collecthsmetrics/meta.yml", - "type": "module", - "meta": { - "name": "picard_collecthsmetrics", - "description": "Collects hybrid-selection (HS) metrics for a SAM or BAM file.", - "keywords": [ - "alignment", - "metrics", - "statistics", - "insert", - "hybrid-selection", - "quality", - "bam" - ], - "tools": [ - { - "picard": { - "description": "A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS)\ndata and formats such as SAM/BAM/CRAM and VCF.\n", - "homepage": "https://broadinstitute.github.io/picard/", - "documentation": "https://broadinstitute.github.io/picard/", - "tool_dev_url": "https://github.com/broadinstitute/picard/", - "licence": [ - "MIT" - ], - "identifier": "biotools:picard_tools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "An aligned BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } - }, - { - "bai": { - "type": "file", - "description": "Optional aligned BAM/CRAM/SAM file index", - "pattern": "*.{bai,crai,sai}", - "ontologies": [] - } - }, - { - "bait_intervals": { - "type": "file", - "description": "An interval file that contains the locations of the baits used.", - "pattern": "*.{interval_list,bed,bed.gz}", - "ontologies": [] - } - }, - { - "target_intervals": { - "type": "file", - "description": "An interval file that contains the locations of the targets.", - "pattern": "*.{interval_list,bed,bed.gz}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "ref": { - "type": "file", - "description": "A reference file to calculate dropout metrics measuring reduced representation of reads.\nOptional input.\n", - "pattern": "*.{fa,fa.gz,fasta,fasta.gz,fna,fna.gz}", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "ref_fai": { - "type": "file", - "description": "Index of reference file. Only needed when reference is supplied.", - "pattern": "*.fai", - "ontologies": [] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "ref_dict": { - "type": "file", - "description": "Sequence dictionary of FASTA file. Only needed when bed interval lists are supplied.", - "pattern": "*.dict", - "ontologies": [] - } - } - ], - [ - { - "meta5": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "ref_gzi": { - "type": "file", - "description": "Index of reference file. Only needed when gzipped reference is supplied.", - "pattern": "*.gzi", - "ontologies": [] - } - } - ] - ], - "output": { - "metrics": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_metrics": { - "type": "file", - "description": "Alignment metrics files generated by picard", - "pattern": "*_{metrics}", - "ontologies": [] - } - } - ] - ], - "versions_picard": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "picard": { - "type": "string", - "description": "The tool name" - } - }, - { - "picard CollectHsMetrics --version 2>&1 | sed -n 's/.*Version://p'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "picard": { - "type": "string", - "description": "The tool name" - } - }, - { - "picard CollectHsMetrics --version 2>&1 | sed -n 's/.*Version://p'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@projectoriented", - "@matthdsm" - ], - "maintainers": [ - "@projectoriented", - "@matthdsm" - ] - }, - "pipelines": [ - { - "name": "methylseq", - "version": "4.2.0" }, { - "name": "raredisease", - "version": "3.0.0" + "name": "sequenzautils_bam2seqz", + "path": "modules/nf-core/sequenzautils/bam2seqz/meta.yml", + "type": "module", + "meta": { + "name": "sequenzautils_bam2seqz", + "description": "Sequenza-utils bam2seqz process BAM and Wiggle files to produce a seqz file", + "keywords": ["sequenzautils", "copy number", "bam2seqz"], + "tools": [ + { + "sequenzautils": { + "description": "Sequenza-utils provides 3 main command line programs to transform common NGS file format - such as FASTA, BAM - to input files for the Sequenza R package. The program - bam2seqz - process a paired set of BAM/pileup files (tumour and matching normal), and GC-content genome-wide information, to extract the common positions with A and B alleles frequencies.", + "homepage": "https://sequenza-utils.readthedocs.io/en/latest/index.html", + "documentation": "https://sequenza-utils.readthedocs.io/en/latest/index.html", + "doi": "10.1093/annonc/mdu479", + "licence": ["GPL-3.0-or-later"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "normalbam": { + "type": "file", + "description": "BAM file from the reference/normal sample", + "pattern": "*.{bam}", + "ontologies": [] + } + }, + { + "tumourbam": { + "type": "file", + "description": "BAM file from the tumour sample", + "pattern": "*.{bam}", + "ontologies": [] + } + } + ], + { + "fasta": { + "type": "file", + "description": "Reference FASTA file", + "pattern": "*.{fasta}", + "ontologies": [] + } + }, + { + "wigfile": { + "type": "file", + "description": "GC content wiggle file", + "pattern": "*.{wig.gz}", + "ontologies": [] + } + } + ], + "output": { + "seqz": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.gz": { + "type": "file", + "description": "Seqz file", + "pattern": "*.{seqz.gz}", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@kaurravneet4123"], + "maintainers": ["@kaurravneet4123"] + } }, { - "name": "seqinspector", - "version": "1.0.1" + "name": "sequenzautils_gcwiggle", + "path": "modules/nf-core/sequenzautils/gcwiggle/meta.yml", + "type": "module", + "meta": { + "name": "sequenzautils_gcwiggle", + "description": "Sequenza-utils gc_wiggle computes the GC percentage across the sequences, and returns a file in the UCSC wiggle format, given a fasta file and a window size.", + "keywords": ["sequenzautils", "copy number", "gc_wiggle"], + "tools": [ + { + "sequenzautils": { + "description": "Sequenza-utils provides 3 main command line programs to transform common NGS file format - such as FASTA, BAM - to input files for the Sequenza R package. The program -gc_wiggle- takes fasta file as an input, computes GC percentage across the sequences and returns a file in the UCSC wiggle format.", + "homepage": "https://sequenza-utils.readthedocs.io/en/latest/index.html", + "documentation": "https://sequenza-utils.readthedocs.io/en/latest/index.html", + "doi": "10.1093/annonc/mdu479", + "licence": ["GPL-3.0-or-later"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA file", + "pattern": "*.{fasta}", + "ontologies": [] + } + } + ] + ], + "output": { + "wig": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.wig.gz": { + "type": "file", + "description": "GC Wiggle track file", + "pattern": "*.{wig.gz}", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@kaurravneet4123"], + "maintainers": ["@kaurravneet4123"] + } }, { - "name": "variantcatalogue", - "version": "dev" - } - ] - }, - { - "name": "picard_collectinsertsizemetrics", - "path": "modules/nf-core/picard/collectinsertsizemetrics/meta.yml", - "type": "module", - "meta": { - "name": "picard_collectinsertsizemetrics", - "description": "Collect metrics about the insert size distribution of a paired-end library.", - "keywords": [ - "metrics", - "alignment", - "insert", - "statistics", - "bam" - ], - "tools": [ - { - "picard": { - "description": "Java tools for working with NGS data in the BAM format", - "homepage": "https://broadinstitute.github.io/picard/", - "documentation": "https://broadinstitute.github.io/picard/", - "tool_dev_url": "https://github.com/broadinstitute/picard", - "licence": [ - "MIT" - ], - "identifier": "biotools:picard_tools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } - } - ] - ], - "output": { - "metrics": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.txt": { - "type": "file", - "description": "Values used by Picard to generate the insert size histograms", - "pattern": "*.txt", - "ontologies": [] - } - } - ] - ], - "histogram": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.pdf": { - "type": "file", - "description": "Insert size histogram in PDF format", - "pattern": "*.pdf", - "ontologies": [] - } - } - ] - ], - "versions_picard": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "picard": { - "type": "string", - "description": "The tool name" - } - }, - { - "picard CollectInsertSizeMetrics --version 2>&1 | sed -n 's/.*Version://p'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "picard": { - "type": "string", - "description": "The tool name" - } - }, - { - "picard CollectInsertSizeMetrics --version 2>&1 | sed -n 's/.*Version://p'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@FerriolCalvet" - ], - "maintainers": [ - "@FerriolCalvet" - ] - }, - "pipelines": [ - { - "name": "rnafusion", - "version": "4.1.2" - } - ] - }, - { - "name": "picard_collectmultiplemetrics", - "path": "modules/nf-core/picard/collectmultiplemetrics/meta.yml", - "type": "module", - "meta": { - "name": "picard_collectmultiplemetrics", - "description": "Collect multiple metrics from a BAM file", - "keywords": [ - "alignment", - "metrics", - "statistics", - "insert", - "quality", - "bam" - ], - "tools": [ - { - "picard": { - "description": "A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS)\ndata and formats such as SAM/BAM/CRAM and VCF.\n", - "homepage": "https://broadinstitute.github.io/picard/", - "documentation": "https://broadinstitute.github.io/picard/", - "licence": [ - "MIT" - ], - "identifier": "biotools:picard_tools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "SAM/BAM/CRAM file", - "pattern": "*.{sam,bam,cram}", - "ontologies": [] - } - }, - { - "bai": { - "type": "file", - "description": "Optional SAM/BAM/CRAM file index", - "pattern": "*.{sai,bai,crai}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome']\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Genome fasta file", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome']\n" - } + "name": "seqwish_induce", + "path": "modules/nf-core/seqwish/induce/meta.yml", + "type": "module", + "meta": { + "name": "seqwish_induce", + "description": "Induce a variation graph in GFA format from alignments in PAF format", + "keywords": ["induce", "paf", "gfa", "graph", "variation graph"], + "tools": [ + { + "seqwish": { + "description": "seqwish implements a lossless conversion from pairwise alignments between\nsequences to a variation graph encoding the sequences and their alignments.\n", + "homepage": "https://github.com/ekg/seqwish", + "documentation": "https://github.com/ekg/seqwish", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "paf": { + "type": "list", + "description": "comma-separated PAF file(s) of alignments, single entry allowed", + "pattern": "[*.{paf,paf.gz},*.{paf,paf.gz},...]" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA file used to generate alignments", + "pattern": "*.{fa,fa.gz,fasta,fasta.gz}", + "ontologies": [] + } + } + ] + ], + "output": { + "gfa": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.gfa": { + "type": "file", + "description": "Variation graph in GFA 1.0 format", + "pattern": "*.{gfa}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3975" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@heuermh"], + "maintainers": ["@heuermh"] }, - { - "fai": { - "type": "file", - "description": "Index of FASTA file. Only needed when fasta is supplied.", - "pattern": "*.fai", - "ontologies": [] - } - } - ] - ], - "output": { - "metrics": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_metrics": { - "type": "file", - "description": "Alignment metrics files generated by picard", - "pattern": "*_{metrics}", - "ontologies": [] - } - } - ] - ], - "pdf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.pdf": { - "type": "file", - "description": "PDF plots of metrics", - "pattern": "*.{pdf}", - "ontologies": [] - } - } - ] - ], - "versions_picard": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "picard": { - "type": "string", - "description": "The tool name" - } - }, - { - "picard CollectMultipleMetrics --version 2>&1 | sed -n 's/.*Version://p'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "picard": { - "type": "string", - "description": "The tool name" - } - }, - { - "picard CollectMultipleMetrics --version 2>&1 | sed -n 's/.*Version://p'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } + "pipelines": [ + { + "name": "pangenome", + "version": "1.1.3" + } ] - ] - }, - "authors": [ - "@drpatelh" - ], - "maintainers": [ - "@drpatelh" - ] - }, - "pipelines": [ - { - "name": "atacseq", - "version": "2.1.2" - }, - { - "name": "callingcards", - "version": "1.0.0" - }, - { - "name": "chipseq", - "version": "2.1.0" - }, - { - "name": "raredisease", - "version": "3.0.0" }, { - "name": "seqinspector", - "version": "1.0.1" + "name": "seroba_run", + "path": "modules/nf-core/seroba/run/meta.yml", + "type": "module", + "meta": { + "name": "seroba_run", + "description": "Determine Streptococcus pneumoniae serotype from Illumina paired-end reads", + "keywords": ["fastq", "serotype", "Streptococcus pneumoniae"], + "tools": [ + { + "seroba": { + "description": "SeroBA is a k-mer based pipeline to identify the Serotype from Illumina NGS reads for given references.", + "homepage": "https://sanger-pathogens.github.io/seroba/", + "documentation": "https://sanger-pathogens.github.io/seroba/", + "tool_dev_url": "https://github.com/sanger-pathogens/seroba", + "doi": "10.1099/mgen.0.000186", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "Input Illunina paired-end FASTQ files", + "pattern": "*.{fq.gz,fastq.gz}", + "ontologies": [] + } + } + ] + ], + "output": { + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/${prefix}.tsv": { + "type": "file", + "description": "The predicted serotype in tab-delimited format", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "txt": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/detailed_serogroup_info.txt": { + "type": "file", + "description": "A detailed description of the predicted serotype", + "pattern": "*.txt", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@rpetit3"], + "maintainers": ["@rpetit3"] + } }, { - "name": "ssds", - "version": "dev" + "name": "severus", + "path": "modules/nf-core/severus/meta.yml", + "type": "module", + "meta": { + "name": "severus", + "description": "Severus is a somatic structural variation (SV) caller for long reads (both PacBio and ONT)", + "keywords": ["structural", "variation", "somatic", "germline", "long-read"], + "tools": [ + { + "severus": { + "description": "A tool for somatic structural variant calling using long reads", + "homepage": "https://github.com/KolmogorovLab/Severus", + "documentation": "https://github.com/KolmogorovLab/Severus", + "tool_dev_url": "https://github.com/KolmogorovLab/Severus", + "doi": "10.1101/2024.03.22.24304756", + "licence": ["BSD-3-clause"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "target_input": { + "type": "file", + "description": "path to one or multiple target BAM/CRAM files (e.g. tumor, must be indexed)", + "pattern": "*.{bam,cram}", + "ontologies": [] + } + }, + { + "target_index": { + "type": "file", + "description": "path to one or multiple target BAM/CRAM index files", + "pattern": "*.{bai,crai,csi}", + "ontologies": [] + } + }, + { + "control_input": { + "type": "file", + "description": "path to the control BAM/CRAM file (e.g. normal, must be indexed)", + "pattern": "*.{bam,cram}", + "ontologies": [] + } + }, + { + "control_index": { + "type": "file", + "description": "path to the control BAM/CRAM file index", + "pattern": "*.{bai,crai,csi}", + "ontologies": [] + } + }, + { + "vcf": { + "type": "file", + "description": "path to vcf file used for phasing (if using haplotype specific SV calling", + "pattern": "*.{vcf,vcf.gz}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing tandem repeat regions information\ne.g. `[ id:'hg38']`\n" + } + }, + { + "bed": { + "type": "file", + "description": "path to bed file for tandem repeat regions (must be ordered)", + "pattern": "*.bed", + "ontologies": [] + } + } + ] + ], + "output": { + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\n" + } + }, + { + "${prefix}/severus.log": { + "type": "file", + "description": "log file\n", + "pattern": "${prefix}/severus.log", + "ontologies": [] + } + } + ] + ], + "read_qual": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\n" + } + }, + { + "${prefix}/read_qual.txt": { + "type": "file", + "description": "txt file containing read quality information\n", + "pattern": "${prefix}/read_qual.txt", + "ontologies": [] + } + } + ] + ], + "breakpoints_double": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\n" + } + }, + { + "${prefix}/breakpoints_double.csv": { + "type": "file", + "description": "Detailed info about the detected breakpoints for all samples in text format, intended for an advanced user.\n", + "pattern": "${prefix}/breakpoints_double.csv", + "ontologies": [] + } + } + ] + ], + "read_alignments": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\n" + } + }, + { + "${prefix}/read_alignments": { + "type": "file", + "description": "A directory containing read alignments in BAM format for all samples, intended for an advanced user.\n", + "pattern": "${prefix}/read_alignments", + "ontologies": [] + } + } + ] + ], + "read_ids": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\n" + } + }, + { + "${prefix}/read_ids.csv": { + "type": "file", + "description": "Contains supporting read IDs for each SV\n", + "pattern": "${prefix}/read_ids.csv", + "ontologies": [] + } + } + ] + ], + "collapsed_dup": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\n" + } + }, + { + "${prefix}/severus_collaped_dup.bed": { + "type": "file", + "description": "BED file containing collapsed duplications\n", + "pattern": "${prefix}/severus_collaped_dup", + "ontologies": [] + } + } + ] + ], + "loh": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\n" + } + }, + { + "${prefix}/severus_LOH.bed": { + "type": "file", + "description": "BED file containing loss of heterozygosity information\n", + "pattern": "${prefix}/severus_LOH.bed", + "ontologies": [] + } + } + ] + ], + "all_vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\n" + } + }, + { + "${prefix}/all_SVs/severus_all.vcf": { + "type": "map", + "description": "VCF file containing somatic and germline structural variants\n", + "pattern": "${prefix}/all_SVs/severus_all.vcf", + "ontologies": [] + } + } + ] + ], + "all_breakpoints_clusters_list": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\n" + } + }, + { + "${prefix}/all_SVs/breakpoints_clusters_list.tsv": { + "type": "file", + "description": "a TSV containing a list of all breakpoint clusters\n", + "pattern": "${prefix}/all_SVs/breakpoints_clusters_list.tsv", + "ontologies": [] + } + } + ] + ], + "all_breakpoints_clusters": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\n" + } + }, + { + "${prefix}/all_SVs/breakpoints_clusters.tsv": { + "type": "file", + "description": "TSV file listing meta information in breakpoint clusters\n", + "pattern": "${prefix}/all_SVs/breakpoints_clusters.tsv", + "ontologies": [] + } + } + ] + ], + "all_plots": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\n" + } + }, + { + "${prefix}/all_SVs/plots/severus*.html": { + "type": "file", + "description": "HTML files containing plots for all SVs\n", + "pattern": "${prefix}/all_SVs/plots/severus*.html", + "ontologies": [] + } + } + ] + ], + "somatic_vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\n" + } + }, + { + "${prefix}/somatic_SVs/severus_somatic.vcf": { + "type": "file", + "description": "VCF file containing somatic structural variants (SV)\n", + "pattern": "${prefix}/somatic_SVs/severus_all.vcf", + "ontologies": [] + } + } + ] + ], + "somatic_breakpoints_clusters_list": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\n" + } + }, + { + "${prefix}/somatic_SVs/breakpoints_clusters_list.tsv": { + "type": "file", + "description": "TSV file containing full list of somatic breakpoint clusters\n", + "pattern": "${prefix}/somatic_SVs/breakpoints_clusters_list.tsv", + "ontologies": [] + } + } + ] + ], + "somatic_breakpoints_clusters": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\n" + } + }, + { + "${prefix}/somatic_SVs/breakpoints_clusters.tsv": { + "type": "file", + "description": "TSV file containing meta information of somatic breakpoint clusters\n", + "pattern": "${prefix}/somatic_SVs/breakpoints_clusters.tsv", + "ontologies": [] + } + } + ] + ], + "somatic_plots": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\n" + } + }, + { + "${prefix}/somatic_SVs/plots/severus*.html": { + "type": "file", + "description": "HTML files containing plots for somatic SVs\n", + "pattern": "${prefix}/somatic_SVs/plots/severus*.html", + "ontologies": [] + } + } + ] + ], + "versions_severus": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "severus": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "severus --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "severus": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "severus --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@fellen31"], + "maintainers": ["@fellen31"] + }, + "pipelines": [ + { + "name": "pacsomatic", + "version": "dev" + } + ] }, { - "name": "viralmetagenome", - "version": "1.1.1" + "name": "sexdeterrmine", + "path": "modules/nf-core/sexdeterrmine/meta.yml", + "type": "module", + "meta": { + "name": "sexdeterrmine", + "description": "Calculate the relative coverage on the Gonosomes vs Autosomes from the output of samtools depth, with error bars.", + "keywords": ["sex determination", "genetic sex", "relative coverage", "ancient dna"], + "tools": [ + { + 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"description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.json": { + "type": "file", + "description": "JSON formatted table of relative coverages on the X and Y, with associated error bars.", + "pattern": "*.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "TSV table of relative coverages on the X and Y, with associated error bars.", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@TCLamnidis"], + "maintainers": ["@TCLamnidis"] + } }, { - "name": "viralrecon", - "version": "3.0.0" - } - ] - }, - { - "name": "picard_collectrnaseqmetrics", - "path": "modules/nf-core/picard/collectrnaseqmetrics/meta.yml", - "type": "module", - "meta": { - "name": "picard_collectrnaseqmetrics", - "description": "Collect metrics from a RNAseq BAM file", - "keywords": [ - "rna", - "bam", - "metrics", - "alignment", - "statistics", - "quality" - ], - "tools": [ - { - "picard": { - "description": "A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS)\ndata and formats such as SAM/BAM/CRAM and VCF.\n", - "homepage": "https://broadinstitute.github.io/picard/", - "documentation": "https://broadinstitute.github.io/picard/", - "tool_dev_url": "https://github.com/broadinstitute/picard", - "licence": [ - "MIT" - ], - "identifier": "biotools:picard_tools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false, strandedness:true ]\n" - } + "name": "sgdemux", + "path": "modules/nf-core/sgdemux/meta.yml", + "type": "module", + "meta": { + "name": "sgdemux", + "description": "Demultiplex bgzip'd fastq files", + "keywords": ["demultiplex", "fastq", "bgzip"], + "tools": [ + { + "sgdemux": { + "description": "Tool for demultiplexing sequencing data generated on Singular Genomics' sequencing instruments.", + "homepage": "https://github.com/Singular-Genomics/singular-demux", + "documentation": "https://github.com/Singular-Genomics/singular-demux#sgdemux", + "licence": ["For Singular G4™ Sequencing Platform only"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "sample_sheet": { + "type": "file", + "description": "sample_sheet file (either a Singular Genomics sample sheet, or a two column csv with Sample_Barcode and Sample_ID)", + "pattern": "*.{csv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + }, + { + "fastqs_dir": { + "type": "directory", + "description": "Input directory containing bgzipped (not gzip) FASTQ files" + } + } + ] + ], + "output": { + "sample_fastq": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/*_R*.fastq.gz": { + "type": "file", + "description": "Demultiplexed per-sample FASTQ files", + "pattern": "${prefix}/*_R*.fastq.gz", + "ontologies": [] + } + } + ] + ], + "metrics": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/metrics.tsv": { + "type": "file", + "description": "Demultiplexing summary stats; control_reads_omitted failing_reads_omitted, total_templates\n", + 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containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/per_sample_metrics.tsv": { + "type": "file", + "description": "Summary metrics for each sample", + "pattern": "${prefix}/per_sample_metrics.tsv", + "ontologies": [] + } + } + ] + ], + "sample_barcode_hop_metrics": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/sample_barcode_hop_metrics.tsv": { + "type": "file", + "description": "File output for dual-indexed runs with barcodes which are unexpected combinations of\nexpected barcodes e.g. expected barcodes = AA-TT/GG-CC and observed barcodes = AA-CC/GG-TT\n", + "pattern": "${prefix}/sample_barcode_hop_metrics/tsv", + "ontologies": [] + } + } + ] + ], + "versions_sgdemux": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "sgdemux": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "sgdemux --version | cut -d \" \" -f2": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "sgdemux": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "sgdemux --version | cut -d \" \" -f2": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@nh13", "@sam-white04"], + "maintainers": ["@nh13", "@sam-white04"] }, - { - "bam": { - "type": "file", - "description": "BAM/SAM file", - "pattern": "*.{bam,sam}", - "ontologies": [] - } - } - ], - { - "ref_flat": { - "type": "file", - "description": "Genome ref_flat file", - "ontologies": [] - } - }, - { - "fasta": { - "type": "file", - "description": "Genome fasta file", - "ontologies": [] - } - }, - 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"description": "The tool name" - } - }, - { - "picard CollectRnaSeqMetrics --version 2>&1 | sed -n 's/.*Version://p'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "picard": { - "type": "string", - "description": "The tool name" - } - }, - { - "picard CollectRnaSeqMetrics --version 2>&1 | sed -n 's/.*Version://p'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } + "pipelines": [ + { + "name": "demultiplex", + "version": "1.7.1" + } ] - ] - }, - "authors": [ - "@anoronh4" - ], - "maintainers": [ - "@anoronh4" - ] - }, - "pipelines": [ - { - "name": "rnafusion", - "version": "4.1.2" - } - ] - }, - { - "name": "picard_collectvariantcallingmetrics", - "path": "modules/nf-core/picard/collectvariantcallingmetrics/meta.yml", - "type": "module", - "meta": { - "name": "picard_collectvariantcallingmetrics", - "description": "Collects per-sample and aggregate (spanning all samples) metrics from the provided VCF file", - "keywords": [ - "vcf", - "metrics", - "variant calling", - "statistics" - ], - "tools": [ - { - "picard": { - "description": "A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.", - "homepage": "https://broadinstitute.github.io/picard/", - "documentation": "https://broadinstitute.github.io/picard/", - "tool_dev_url": "https://github.com/broadinstitute/picard", - "licence": [ - "MIT" - ], - "identifier": "biotools:picard_tools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "vcf": { - "type": "file", - "description": "Input VCF file for analysis", - "pattern": "*.{vcf,vcf.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - } - ] - } - }, - { - "index": { - "type": "file", - "description": "Index file for the input VCF file", - "pattern": "*.{idx,tbi}", - "ontologies": [] - } - }, - { - "intervals_file": { - "type": "file", - "description": "Optional BED file specifying target intervals", - "pattern": "*.{bed,bed.gz,intervals_list}", - "ontologies": [] - } - }, - { - "fasta": { - "type": "file", - "description": "Reference sequence file", - "pattern": "*.{fasta,fa,fasta.gz,fa.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - }, - { - "dict": { - "type": "file", - "description": "Reference sequence dictionary file", - "pattern": "*.{dict}", - "ontologies": [] - } - }, - { - "dbsnp": { - "type": "file", - "description": "Reference dbSNP file in dbSNP or VCF format", - "pattern": "*.{vcf,vcf.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - } - ] - } + }, + { + "name": "shapeit5_ligate", + "path": "modules/nf-core/shapeit5/ligate/meta.yml", + "type": "module", + "meta": { + "name": "shapeit5_ligate", + "description": "Ligate multiple phased BCF/VCF files into a single whole chromosome file.\nTypically run to ligate multiple chunks of phased common variants.\n", + "keywords": ["ligate", "haplotype", "shapeit"], + "tools": [ + { + "shapeit5": { + "description": "Fast and accurate method for estimation of haplotypes (phasing)", + "homepage": "https://odelaneau.github.io/shapeit5/", + "documentation": "https://odelaneau.github.io/shapeit5/docs/documentation", + "tool_dev_url": "https://github.com/odelaneau/shapeit5", + "doi": "10.1101/2022.10.19.512867", + "licence": ["MIT"], + "identifier": "biotools:shapeit5" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input_list": { + "type": "file", + "description": "VCF/BCF files containing genotype probabilities (GP field).\nThe files should be ordered by genomic position.\n", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", + "ontologies": [] + } + }, + { + "input_list_index": { + "type": "file", + "description": "VCF/BCF files index.", + "pattern": "*.csi", + "ontologies": [] + } + } + ], + { + "suffix_": { + "type": "string", + "description": "Output format", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" + } + } + ], + "output": { + "merged_variants": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{vcf,bcf,vcf.gz,bcf.gz}": { + "type": "file", + "description": "Output VCF/BCF file for the merged regions.\nPhased information (HS field) is updated accordingly for the full region.\n", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", + "ontologies": [] + } + } + ] + ], + "versions_shapeit5": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "shapeit5": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "SHAPEIT5_ligate | sed \"5!d;s/^.*Version *: //; s/ .*$//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "shapeit5": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "SHAPEIT5_ligate | sed \"5!d;s/^.*Version *: //; s/ .*$//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@louislenezet"], + "maintainers": ["@louislenezet"] }, - { - "dbsnp_index": { - "type": "file", - "description": "Reference dbSNP file in dbSNP or VCF format", - "pattern": "*.{idx,tbi}", - "ontologies": [] - } - } - ] - ], - 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CollectVariantCallingMetrics --version 2>&1 | sed -n 's/.*Version://p'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "picard": { - "type": "string", - "description": "The tool name" - } - }, - { - "picard CollectVariantCallingMetrics --version 2>&1 | sed -n 's/.*Version://p'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } + "pipelines": [ + { + "name": "phaseimpute", + "version": "1.1.0" + } ] - ] - }, - "authors": [ - "@georgiakes" - ], - "maintainers": [ - "@georgiakes" - ] - } - }, - { - "name": "picard_collectwgsmetrics", - "path": "modules/nf-core/picard/collectwgsmetrics/meta.yml", - "type": "module", - "meta": { - "name": "picard_collectwgsmetrics", - "description": "Collect metrics about coverage 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- "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Genome fasta file", - "pattern": "*.{fa,fasta,fna}", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } + }, + { + "name": "shapeit5_phasecommon", + "path": "modules/nf-core/shapeit5/phasecommon/meta.yml", + "type": "module", + "meta": { + "name": "shapeit5_phasecommon", + "description": "Tool to phase common sites, typically SNP array data, or the first step of WES/WGS data.", + "keywords": ["phasing", "haplotype", "shapeit"], + "tools": [ + { + "shapeit5": { + "description": "Fast and accurate method for estimation of haplotypes (phasing)", + "homepage": "https://odelaneau.github.io/shapeit5/", + "documentation": "https://odelaneau.github.io/shapeit5/docs/documentation", + "tool_dev_url": "https://github.com/odelaneau/shapeit5", + "doi": "10.1101/2022.10.19.512867 ", + "licence": ["MIT"], + "identifier": "biotools:shapeit5" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "Target dataset in VCF/BCF format defined at all variable positions.\nThe file could possibly be without GT field (for efficiency reasons a file containing only the positions is recommended).\n", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", + "ontologies": [] + } + }, + { + "input_index": { + "type": "file", + "description": "Index file of the input VCF/BCF file containing genotype likelihoods.", + "pattern": "*.{vcf.gz.csi,bcf.gz.csi}", + "ontologies": [] + } + }, + { + "pedigree": { + "type": "file", + "description": "Pedigree information in the following format: offspring father mother.\n", + "pattern": "*.{txt, tsv}", + "ontologies": [] + } + }, + { + "region": { + "type": "string", + "description": "Target region, usually a full chromosome (e.g. chr20:1000000-2000000 or chr20).\nFor chrX, please treat PAR and non-PAR regions as different choromosome in order to avoid mixing ploidy.\n", + "pattern": "chrXX:leftBufferPosition-rightBufferPosition" + } + }, + { + "reference": { + "type": "file", + "description": "Reference panel of haplotypes in VCF/BCF format.", + "pattern": "*.{vcf.gz,bcf.gz}", + "ontologies": [] + } + }, + { + "reference_index": { + "type": "file", + "description": "Index file of the Reference panel file.", + "pattern": "*.{vcf.gz.csi,bcf.gz.csi}", + "ontologies": [] + } + }, + { + "scaffold": { + "type": "file", + "description": "Scaffold of haplotypes in VCF/BCF format.", + "pattern": "*.{vcf.gz,bcf.gz}", + "ontologies": [] + } + }, + { + "scaffold_index": { + "type": "file", + "description": "Index file of the scaffold file.", + "pattern": "*.{vcf.gz.csi,bcf.gz.csi}", + "ontologies": [] + } + }, + { + "map": { + "type": "file", + "description": "File containing the genetic map in Glimpse format.", + "pattern": "*.gmap", + "ontologies": [] + } + } + ] + ], + "output": { + "phased_variant": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{bcf,graph,bh}": { + "type": "file", + "description": "Phased variant dataset in BCF, GRAPH or XCF binary format.", + "pattern": "*.{bcf,graph,bh}", + "ontologies": [] + } + } + ] + ], + "versions_shapeit5": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "shapeit5": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "SHAPEIT5_phase_common | sed \"5!d;s/^.*Version *: //; s/ .*$//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "shapeit5": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "SHAPEIT5_phase_common | sed \"5!d;s/^.*Version *: //; s/ .*$//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@LouisLeNezet"], + "maintainers": ["@LouisLeNezet"] }, - { - "fai": { - "type": "file", - "description": "Genome fasta file index", - "pattern": "*.{fai}", - "ontologies": [] - } - } - ], - { - "intervallist": { - "type": "file", - "description": "Picard Interval List. Defines which contigs to include. Can be generated from a BED file with GATK BedToIntervalList.", - "ontologies": [] - } - } - ], - "output": { - "metrics": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_metrics": { - "type": "file", - "description": "Alignment metrics files generated by picard", - "pattern": "*_{metrics}", - "ontologies": [] - } - } - ] - ], - "versions_picard": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "picard": { - "type": "string", - "description": "The tool name" - } - }, - { - "picard CollectWgsMetrics --version 2>&1 | sed -n 's/.*Version://p'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "picard": { - "type": "string", - "description": "The tool name" - } - }, - { - "picard CollectWgsMetrics --version 2>&1 | sed -n 's/.*Version://p'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } + "pipelines": [ + { + "name": "phaseimpute", + "version": "1.1.0" + } ] - ] }, - "authors": [ - "@drpatelh", - "@flowuenne", - "@lassefolkersen", - "@ramprasadn" - ], - "maintainers": [ - "@drpatelh", - "@flowuenne", - "@lassefolkersen", - "@ramprasadn" - ] - }, - "pipelines": [ { - "name": "raredisease", - "version": "3.0.0" + "name": "shapeit5_phaserare", + "path": "modules/nf-core/shapeit5/phaserare/meta.yml", + "type": "module", + "meta": { + "name": "shapeit5_phaserare", + "description": "Tool to phase rare variants onto a scaffold of common variants (output of phase_common / ligate).\nRequire feature AVX2.\n", + "keywords": ["phasing", "rare variants", "haplotype", "shapeit"], + "tools": [ + { + "shapeit5": { + "description": "Fast and accurate method for estimation of haplotypes (phasing)", + "homepage": "https://odelaneau.github.io/shapeit5/", + "documentation": "https://odelaneau.github.io/shapeit5/docs/documentation", + "tool_dev_url": "https://github.com/odelaneau/shapeit5", + "doi": "10.1101/2022.10.19.512867 ", + "licence": ["MIT"], + "identifier": "biotools:shapeit5" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "Genotypes to be phased in plain VCF/BCF format.\n", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", + "ontologies": [] + } + }, + { + "input_index": { + "type": "file", + "description": "Index file of the input_plain VCF/BCF file containing genotype likelihoods.", + "pattern": "*.{vcf.gz.csi,bcf.gz.csi}", + "ontologies": [] + } + }, + { + "pedigree": { + "type": "file", + "description": "Pedigree information in the following format: offspring father mother.\n", + "pattern": "*.{txt, tsv}", + "ontologies": [] + } + }, + { + "input_region": { + "type": "string", + "description": "Region to be considered in --input-plain (e.g. chr20:1000000-2000000 or chr20).\nFor chrX, please treat PAR and non-PAR regions as different choromosome in order to avoid mixing ploidy.\n", + "pattern": "chrXX:leftBufferPosition-rightBufferPosition" + } + }, + { + "scaffold": { + "type": "file", + "description": "Scaffold of haplotypes in VCF/BCF format.", + "pattern": "*.{vcf.gz,bcf.gz}", + "ontologies": [] + } + }, + { + "scaffold_index": { + "type": "file", + "description": "Index file of the scaffold file.", + "pattern": "*.{vcf.gz.csi,bcf.gz.csi}", + "ontologies": [] + } + }, + { + "scaffold_region": { + "type": "string", + "description": "Region to be considered in --scaffold (e.g. chr20:1000000-2000000 or chr20).\n", + "pattern": "chrXX:leftBufferPosition-rightBufferPosition" + } + }, + { + "map": { + "type": "file", + "description": "File containing the genetic map in Glimpse format.", + "pattern": "*.gmap", + "ontologies": [] + } + } + ], + { + "output_suffix": { + "type": "string", + "description": "Module output format", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" + } + } + ], + "output": { + "phased_variant": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{vcf,bcf,vcf.gz,bcf.gz}": { + "type": "file", + "description": "Phased variants in VCF/BCF format.", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", + "ontologies": [] + } + } + ] + ], + "versions_shapeit5": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "shapeit5": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "SHAPEIT5_phase_rare | sed \"5!d;s/^.*Version *: //; s/ .*$//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "shapeit5": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "SHAPEIT5_phase_rare | sed \"5!d;s/^.*Version *: //; s/ .*$//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@LouisLeNezet"], + "maintainers": ["@LouisLeNezet"], + "requirement": "AVX2" + } }, { - "name": "rnafusion", - "version": "4.1.2" + "name": "shapeit5_switch", + "path": "modules/nf-core/shapeit5/switch/meta.yml", + "type": "module", + "meta": { + "name": "shapeit5_switch", + "description": "Program to compute switch error rate and genotyping error rate given simulated or trio data.", + "keywords": ["error", "phasing", "genotype", "switch"], + "tools": [ + { + "shapeit5": { + "description": "Fast and accurate method for estimation of haplotypes (phasing)", + "homepage": "https://odelaneau.github.io/shapeit5/", + "documentation": "https://odelaneau.github.io/shapeit5/docs/documentation", + "tool_dev_url": "https://github.com/odelaneau/shapeit5", + "doi": "10.1101/2022.10.19.512867 ", + "licence": ["MIT"], + "identifier": "biotools:shapeit5" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "estimate": { + "type": "file", + "description": "Imputed data.", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", + "ontologies": [] + } + }, + { + "estimate_index": { + "type": "file", + "description": "Index file of the freq VCF/BCF file.", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", + "ontologies": [] + } + }, + { + "region": { + "type": "string", + "description": "Target region used for imputation, including left and right buffers (e.g. chr20:1000000-2000000).", + "pattern": "chrXX:leftBufferPosition-rightBufferPosition" + } + }, + { + "pedigree": { + "type": "file", + "description": "Pedigree information in the following format: offspring father mother.\n", + "pattern": "*.{txt, tsv}", + "ontologies": [] + } + }, + { + "truth": { + "type": "file", + "description": "Validation dataset called at the same positions as the imputed file.", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", + "ontologies": [] + } + }, + { + "truth_index": { + "type": "file", + "description": "Index file of the truth VCF/BCF file.", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", + "ontologies": [] + } + }, + { + "freq": { + "type": "file", + "description": "File containing allele frequencies at each site.", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", + "ontologies": [] + } + }, + { + "freq_index": { + "type": "file", + "description": "Index file of the freq VCF/BCF file.", + "pattern": "*.{vcf.gz.csi,bcf.gz.csi}", + "ontologies": [] + } + } + ] + ], + "output": { + "errors": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt.gz": { + "type": "file", + "description": "Estimates errors from the phased file.", + "pattern": "*.txt.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "versions_shapeit5": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "shapeit5": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "SHAPEIT5_switch | sed \"5!d;s/^.*Version *: //; s/ .*$//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "shapeit5": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "SHAPEIT5_switch | sed \"5!d;s/^.*Version *: //; s/ .*$//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@LouisLeNezet"], + "maintainers": ["@LouisLeNezet"] + } }, { - "name": "variantcatalogue", - "version": "dev" - } - ] - }, - { - "name": "picard_createsequencedictionary", - "path": "modules/nf-core/picard/createsequencedictionary/meta.yml", - "type": "module", - "meta": { - "name": "picard_createsequencedictionary", - "description": "Creates a sequence dictionary for a reference sequence.", - "keywords": [ - "sequence", - "dictionary", - "picard" - ], - "tools": [ - { - "picard": { - "description": "Creates a sequence dictionary file (with \".dict\" extension) from a reference sequence provided in FASTA format, which is required by many processing and analysis tools. The output file contains a header but no SAMRecords, and the header contains only sequence records.\n", - "homepage": "https://broadinstitute.github.io/picard/", - "documentation": "https://gatk.broadinstitute.org/hc/en-us/articles/360036712531-CreateSequenceDictionary-Picard-", - "tool_dev_url": "https://github.com/broadinstitute/picard", - "licence": [ - "MIT" - ], - "identifier": "biotools:picard_tools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference fasta file", - "pattern": "*.fasta", - "ontologies": [] - } + "name": "shasta", + "path": "modules/nf-core/shasta/meta.yml", + "type": "module", + "meta": { + "name": "shasta", + "description": "The goal of the Shasta long read assembler is to rapidly produce accurate assembled sequence using DNA reads generated by Oxford Nanopore flow cells as input. Please note Assembler is design to focus on speed, so assembly may be considered somewhat non-deterministic as final assembly may vary across executions. See https://github.com/chanzuckerberg/shasta/issues/296.", + "keywords": ["nanopore", "de-novo", "assembly", "longread"], + "tools": [ + { + "shasta": { + "description": "Rapidly produce accurate assembled sequence using as input DNA reads generated by Oxford Nanopore flow cells.", + "homepage": "https://chanzuckerberg.github.io/shasta/index.html", + "documentation": "https://chanzuckerberg.github.io/shasta/index.html", + "tool_dev_url": "https://github.com/chanzuckerberg/shasta", + "doi": "10.1038/s41587-020-0503-6", + "licence": ["MIT"], + "identifier": "biotools:shasta" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "Input file in FASTQ format.", + "pattern": "*.{fastq,fastq.gz,fq,fq.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ], + { + "model": { + "type": "string", + "description": "Shasta assembly configuration model name\n(e.g. 'Nanopore-Oct2021', 'Nanopore-Dec2019')\n" + } + } + ], + "output": { + "assembly": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_Assembly.fasta.gz": { + "type": "file", + "description": "Assembled FASTA file", + "pattern": "${prefix}_Assembly.fasta.gz", + "ontologies": [] + } + } + ] + ], + "gfa": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_Assembly.gfa.gz": { + "type": "file", + "description": "Repeat graph", + "pattern": "${prefix}_Assembly.gfa.gz", + "ontologies": [] + } + } + ] + ], + "results": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "ShastaRun/": { + "type": "directory", + "description": "Resulting assembly directory", + "pattern": "ShastaRun" + } + } + ] + ], + "versions_shasta": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "shasta": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "shasta --version | sed -n '1s/.* //p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "shasta": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "shasta --version | sed -n '1s/.* //p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@fmalmeida"], + "maintainers": ["@fmalmeida"] } - ] - ], - "output": { - "reference_dict": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.dict": { - "type": "file", - "description": "picard dictionary file", - "pattern": "*.{dict}", - "ontologies": [] - } - } - ] - ], - "versions_picard": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "picard": { - "type": "string", - "description": "The tool name" - } - }, - { - "picard CreateSequenceDictionary --version 2>&1 | sed -n 's/.*Version://p'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "picard": { - "type": "string", - "description": "The tool name" - } - }, - { - "picard CreateSequenceDictionary --version 2>&1 | sed -n 's/.*Version://p'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] }, - "authors": [ - "@sateeshperi", - "@mjcipriano", - "@hseabolt" - ], - "maintainers": [ - "@sateeshperi", - "@mjcipriano", - "@hseabolt" - ] - }, - "pipelines": [ { - "name": "methylseq", - "version": "4.2.0" + "name": "shasum", + "path": "modules/nf-core/shasum/meta.yml", + "type": "module", + "meta": { + "name": "shasum", + "description": "Print SHA256 (256-bit) checksums.", + "keywords": ["checksum", "sha256", "256 bit"], + "tools": [ + { + "md5sum": { + "description": "Create an SHA256 (256-bit) checksum.", + "homepage": "https://www.gnu.org", + "documentation": "https://linux.die.net/man/1/shasum", + "licence": ["GPLv3+"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "file": { + "type": "file", + "description": "Any file", + "pattern": "*.*", + "ontologies": [] + } + } + ] + ], + "output": { + "checksum": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.sha256": { + "type": "file", + "description": "File containing checksum", + "pattern": "*.sha256", + "ontologies": [] + } + } + ] + ], + "versions_sha256sum": [ + [ + { + "${task.process}": { + "type": "string", + "description": "Process name" + } + }, + { + "sha256sum": { + "type": "string", + "description": "Tool name" + } + }, + { + "sha256sum --version 2>&1 | head -n 1 | sed 's/.* //'": { + "type": "eval", + "description": "Software version" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "Process name" + } + }, + { + "sha256sum": { + "type": "string", + "description": "Tool name" + } + }, + { + "sha256sum --version 2>&1 | head -n 1 | sed 's/.* //'": { + "type": "eval", + "description": "Software version" + } + } + ] + ] + }, + "authors": ["@matthdsm"], + "maintainers": ["@matthdsm"] + } }, { - "name": "pathogensurveillance", - "version": "1.1.0" + "name": "shigapass", + "path": "modules/nf-core/shigapass/meta.yml", + "type": "module", + "meta": { + "name": "shigapass", + "description": "ShigaPass is an in silico tool used to predict Shigella serotypes and to differentiate between Shigella, EIEC (Enteroinvasive E. coli), and non Shigella/EIEC using assembled whole genomes.", + "keywords": ["bacteria", "shigella", "stec"], + "tools": [ + { + "shigapass": { + "description": "ShigaPass is an in silico tool used to predict Shigella serotypes", + "homepage": "https://github.com/imanyass/ShigaPass", + "documentation": "https://github.com/imanyass/ShigaPass", + "tool_dev_url": "https://github.com/imanyass/ShigaPass", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA, GenBank or EMBL formatted file. Note that the standard input for ShigaPass is a file of file paths - here for paralellisation a fasta file is required.", + "pattern": "*.{fa,fasta,fna,fa.gz,fasta.gz,fna.gz}", + "ontologies": [] + } + } + ] + ], + "output": { + "report": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.tsv": { + "type": "file", + "description": "Tab-delimited report of results", + "pattern": "${prefix}.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "flex_tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_ShigaPass_Flex_summary.tsv": { + "type": "file", + "description": "Tab-delimited report of results", + "pattern": "*_ShigaPass_Flex_summary.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_shigapass": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "shigapass": { + "type": "string", + "description": "The tool name" + } + }, + { + "ShigaPass.sh -v 2>&1 | sed 's/^.*ShigaPass version //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "shigapass": { + "type": "string", + "description": "The tool name" + } + }, + { + "ShigaPass.sh -v 2>&1 | sed 's/^.*ShigaPass version //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@maxlcummins"], + "maintainers": ["@maxlcummins"] + } }, { - "name": "seqinspector", - "version": "1.0.1" + "name": "shigatyper", + "path": "modules/nf-core/shigatyper/meta.yml", + "type": "module", + "meta": { + "name": "shigatyper", + "description": "Determine Shigella serotype from Illumina or Oxford Nanopore reads", + "keywords": ["fastq", "shigella", "serotype"], + "tools": [ + { + "shigatyper": { + "description": "Typing tool for Shigella spp. from WGS Illumina sequencing", + "homepage": "https://github.com/CFSAN-Biostatistics/shigatyper", + "documentation": "https://github.com/CFSAN-Biostatistics/shigatyper", + "tool_dev_url": "https://github.com/CFSAN-Biostatistics/shigatyper", + "doi": "10.1128/AEM.00165-19", + "licence": ["Public Domain"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false, is_ont:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "Illumina or Nanopore FASTQ file", + "pattern": "*.fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "output": { + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.tsv": { + "type": "file", + "description": "A TSV formatted file with ShigaTyper results", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "hits": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}-hits.tsv": { + "type": "file", + "description": "A TSV formatted file with individual gene hits", + "pattern": "*-hits.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@rpetit3"], + "maintainers": ["@rpetit3"] + } }, { - "name": "variantbenchmarking", - "version": "1.5.0" - } - ] - }, - { - "name": "picard_crosscheckfingerprints", - "path": "modules/nf-core/picard/crosscheckfingerprints/meta.yml", - "type": "module", - "meta": { - "name": "picard_crosscheckfingerprints", - "description": "Checks that all data in the set of input files appear to come from the same individual", - "keywords": [ - "alignment", - "metrics", - "statistics", - "fingerprint", - "bam" - ], - "tools": [ - { - "picard": { - "description": "A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS)\ndata and formats such as SAM/BAM/CRAM and VCF.\n", - "homepage": "https://broadinstitute.github.io/picard/", - "documentation": "https://broadinstitute.github.io/picard/", - "tool_dev_url": "https://github.com/broadinstitute/picard/", - "licence": [ - "MIT" - ], - "identifier": "biotools:picard_tools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input1": { - "type": "file", - "description": "List containing 1 or more bam/vcf files or a file containing filepaths", - "pattern": "*.{bam,vcf,vcf.gz,txt,fofn}", - "ontologies": [] - } - }, - { - "input1_index": { - "type": "file", - "description": "List containing 1 or more bam/vcf files indexes", - "pattern": "*.{bai,csi,crai,tbi}", - "ontologies": [] - } - }, - { - "input2": { - "type": "file", - "description": "Optional list containing 1 or more bam/vcf files or a file containing filepaths", - "pattern": "*.{bam,vcf,vcf.gz,txt,fofn}", - "ontologies": [] - } - }, - { - "input2_index": { - "type": "file", - "description": "List containing 1 or more bam/vcf files indexes", - "pattern": "*.{bai,csi,crai,tbi}", - "ontologies": [] - } - }, - { - "haplotype_map": { - "type": "file", - "description": "Haplotype map file", - "pattern": "*.{txt,vcf,vcf.gz}", - "ontologies": [] - } + "name": "shigeifinder", + "path": "modules/nf-core/shigeifinder/meta.yml", + "type": "module", + "meta": { + "name": "shigeifinder", + "description": "Determine Shigella serotype from assemblies or Illumina paired-end reads", + "keywords": ["fastq", "fasta", "shigella", "serotype"], + "tools": [ + { + "shigeifinder": { + "description": "Cluster informed Shigella and EIEC serotyping tool from Illumina reads and assemblies", + "homepage": "https://mgtdb.unsw.edu.au/ShigEiFinder/", + "documentation": "https://github.com/LanLab/ShigEiFinder", + "tool_dev_url": "https://github.com/LanLab/ShigEiFinder", + "doi": "10.1099/mgen.0.000704", + "licence": ["GPL v3"], + "identifier": "biotools:shigeifinder" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "seqs": { + "type": "file", + "description": "Assembly or paired-end Illumina reads", + "pattern": "*.{fasta,fasta.gz,fastq.gz}", + "ontologies": [] + } + } + ] + ], + "output": { + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "A TSV formatted file with ShigEiFinder results", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@rpetit3"], + "maintainers": ["@rpetit3"] } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } + }, + { + "name": "shinyngs_app", + "path": "modules/nf-core/shinyngs/app/meta.yml", + "type": "module", + "meta": { + "name": "shinyngs_app", + "description": "build and deploy Shiny apps for interactively mining differential abundance data", + "keywords": ["differential", "expression", "rna-seq", "deseq2"], + "tools": [ + { + "shinyngs": { + "description": "Provides Shiny applications for various array and NGS applications. Currently very RNA-seq centric, with plans for expansion.", + "homepage": "https://github.com/pinin4fjords/shinyngs", + "documentation": "https://rawgit.com/pinin4fjords/shinyngs/master/vignettes/shinyngs.html", + "tool_dev_url": "https://github.com/pinin4fjords/shinyngs", + "licence": ["AGPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information on experiment, at a minimum an id.\ne.g. [ id:'test' ]\n" + } + }, + { + "sample": { + "type": "file", + "description": "CSV-format sample sheet with sample metadata\n", + "ontologies": [] + } + }, + { + "feature_meta": { + "type": "file", + "description": "TSV-format feature (e.g. gene) metadata\n", + "ontologies": [] + } + }, + { + "assay_files": { + "type": "file", + "description": "List of TSV-format matrix files representing different measures for the same samples (e.g. raw and normalised).\n", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing information on experiment, at a minimum an id. To match meta.\ne.g. [ id:'test' ]\n" + } + }, + { + "contrasts": { + "type": "file", + "description": "CSV-format file with four columns identifying the sample sheet variable, reference level, treatment level, and optionally a comma-separated list of covariates used as blocking factors.\n", + "ontologies": [] + } + }, + { + "differential_results": { + "type": "file", + "description": "List of TSV-format differential analysis outputs, one per row of the contrasts file\n", + "ontologies": [] + } + } + ], + { + "contrast_stats_assay": { + "type": "file", + "description": "contrast statistics", + "ontologies": [] + } + } + ], + "output": { + "app": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information on experiment.\ne.g. [ id:'test' ]\n" + } + }, + { + "*/data.rds": { + "type": "file", + "description": "The mini R script required build an application from data.rds.\n", + "pattern": "app/app.R", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3999" + } + ] + } + }, + { + "*/app.R": { + "type": "file", + "description": "The mini R script required build an application from data.rds.\n", + "pattern": "app/app.R", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3999" + } + ] + } + } + ] + ], + "versions_shinyngs": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "shinyngs": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "Rscript -e \"library(shinyngs); cat(as.character(packageVersion('shinyngs')))\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "shinyngs": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "Rscript -e \"library(shinyngs); cat(as.character(packageVersion('shinyngs')))\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@pinin4fjords"], + "maintainers": ["@pinin4fjords"] }, - { - "fasta": { - "type": "file", - "description": "Reference genome file", - "pattern": "*.{fasta,fa,fasta.gz,fa.gz}", - "ontologies": [] - } - } - ] - ], - "output": { - "crosscheck_metrics": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.crosscheck_metrics.txt": { - "type": "file", - "description": "Metrics created by crosscheckfingerprints", - "pattern": "*.{crosscheck_metrics.txt}", - "ontologies": [] - } - } - ] - ], - "versions_picard": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "picard": { - "type": "string", - "description": "The tool name" - } - }, - { - "picard CrosscheckFingerprints --version 2>&1 | sed -n 's/.*Version://p'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "picard": { - "type": "string", - "description": "The tool name" - } - }, - { - "picard CrosscheckFingerprints --version 2>&1 | sed -n 's/.*Version://p'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } + "pipelines": [ + { + "name": "differentialabundance", + "version": "1.5.0" + } ] - ] - }, - "authors": [ - "@matthdsm" - ], - "maintainers": [ - "@matthdsm" - ] - } - }, - { - "name": "picard_extractfingerprint", - "path": "modules/nf-core/picard/extractfingerprint/meta.yml", - "type": "module", - "meta": { - "name": "picard_extractfingerprint", - "description": "Computes/Extracts the fingerprint genotype likelihoods from the supplied file. It is given as a list of PLs at the fingerprinting sites.", - "keywords": [ - "picard", - "extract", - "fingerprint", - "bam" - ], - "tools": [ - { - "picard": { - "description": "A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS)\ndata and formats such as SAM/BAM/CRAM and VCF.\n", - "homepage": "https://broadinstitute.github.io/picard/", - "documentation": "https://broadinstitute.github.io/picard/", - "tool_dev_url": "https://github.com/broadinstitute/picard/", - "licence": [ - "MIT" - ], - "identifier": "biotools:picard_tools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "file", - "description": "Input SAM/BAM/CRAM file\n", - "ontologies": [] - } - }, - { - "bam": { - "type": "file", - "description": "BAM file", - "pattern": "*.{bam}", - "ontologies": [] - } - }, - { - "bai": { - "type": "file", - "description": "BAM index file", - "pattern": "*.{bai}", - "ontologies": [] - } - } - ], - { - "haplotype_map": { - "type": "file", - "description": "A file of haplotype information. The file lists a set of SNPs, optionally arranged in high-LD blocks, to be used for fingerprinting.\nSee https://software.broadinstitute.org/gatk/documentation/article?id=9526 for details.\n", - "pattern": "*.{txt,vcf,vcf.gz}", - "ontologies": [] - } - }, - { - "fasta": { - "type": "file", - "description": "Reference sequence file", - "pattern": "*.{fasta,fna,fa}", - "ontologies": [] - } - }, - { - "fasta_fai": { - "type": "file", - "description": "Reference sequence index file", - "pattern": "*.{fai}", - "ontologies": [] - } - }, - { - "sequence_dictionary": { - "type": "file", - "description": "Reference sequence dictionary file", - "ontologies": [] - } - } - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.vcf.gz": { - "type": "file", - "description": "VCF file", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.vcf.gz.tbi": { - "type": "file", - "description": "Tabix index file", - "pattern": "*.vcf.gz.tbi", - "ontologies": [] - } - } - ] - ], - "versions_picard": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "picard": { - "type": "string", - "description": "The tool name" - } - }, - { - "picard ExtractFingerprint --version 2>&1 | sed -n 's/.*Version://p'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "picard": { - "type": "string", - "description": "The tool name" - } - }, - { - "picard ExtractFingerprint --version 2>&1 | sed -n 's/.*Version://p'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@adamrtalbot", - "@mauro-saporita" - ], - "maintainers": [ - "@adamrtalbot", - "@mauro-saporita" - ] - } - }, - { - "name": "picard_fastqtosam", - "path": "modules/nf-core/picard/fastqtosam/meta.yml", - "type": "module", - "meta": { - "name": "picard_fastqtosam", - "description": "Converts a FASTQ file to an unaligned BAM or SAM file.", - "keywords": [ - "fastq", - "unaligned", - "bam" - ], - "tools": [ - { - "picard": { - "description": "A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS)\ndata and formats such as SAM/BAM/CRAM and VCF.\n", - "homepage": "https://broadinstitute.github.io/picard/", - "documentation": "https://gatk.broadinstitute.org/hc/en-us/articles/360036510672-FastqToSam-Picard-", - "tool_dev_url": "https://github.com/broadinstitute/picard", - "licence": [ - "MIT" - ], - "identifier": "biotools:picard_tools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", - "ontologies": [] - } - } - ] - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "Unaligned bam file", - "pattern": "*.{bam}", - "ontologies": [] - } - } - ] - ], - "versions_picard": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "picard": { - "type": "string", - "description": "The tool name" - } - }, - { - "picard FastqToSam --version 2>&1 | sed -n 's/.*Version://p'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "picard": { - "type": "string", - "description": "The tool name" - } - }, - { - "picard FastqToSam --version 2>&1 | sed -n 's/.*Version://p'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@matthdsm" - ], - "maintainers": [ - "@matthdsm" - ] - } - }, - { - "name": "picard_filtersamreads", - "path": "modules/nf-core/picard/filtersamreads/meta.yml", - "type": "module", - "meta": { - "name": "picard_filtersamreads", - "description": "Filters SAM/BAM files to include/exclude either aligned/unaligned reads or based on a read list", - "keywords": [ - "bam", - "filter", - "picard", - "sam" - ], - "tools": [ - { - "picard": { - "description": "A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS)\ndata and formats such as SAM/BAM/CRAM and VCF.\n", - "homepage": "https://broadinstitute.github.io/picard/", - "documentation": "https://broadinstitute.github.io/picard/", - "tool_dev_url": "https://github.com/broadinstitute/picard", - "licence": [ - "MIT" - ], - "identifier": "biotools:picard_tools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "List of BAM files. If filtering without read list must be sorted by queryname with picard sortsam", - "pattern": "*.{bam}", - "ontologies": [] - } + }, + { + "name": "shinyngs_staticdifferential", + "path": "modules/nf-core/shinyngs/staticdifferential/meta.yml", + "type": "module", + "meta": { + "name": "shinyngs_staticdifferential", + "description": "Make plots for interpretation of differential abundance statistics", + "keywords": ["rnaseq", "plot", "differential", "shinyngs"], + "tools": [ + { + "shinyngs": { + "description": "Provides Shiny applications for various array and NGS applications. Currently very RNA-seq centric, with plans for expansion.", + "homepage": "https://github.com/pinin4fjords/shinyngs", + "documentation": "https://rawgit.com/pinin4fjords/shinyngs/master/vignettes/shinyngs.html", + "tool_dev_url": "https://github.com/pinin4fjords/shinyngs", + "licence": ["AGPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing contrast information, to be passed as reference\nand target levels, like '--reference_level $meta.reference\n--treatment_level $meta.target'\ne.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ]\n" + } + }, + { + "differential_result": { + "type": "file", + "description": "statistic differential results", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing information on experiment represented by max,\nfeatures and samples, at a minimum an id.\ne.g. [ id:'test' ]\n" + } + }, + { + "sample": { + "type": "file", + "description": "CSV or TSV-format sample sheet with sample metadata\n", + "ontologies": [] + } + }, + { + "feature_meta": { + "type": "file", + "description": "CSV or TSV-format feature (e.g. gene) metadata\n", + "ontologies": [] + } + }, + { + "assay_file": { + "type": "file", + "description": "CSV or TSV matrix file to use alongside differential statistics in\ninterpretation. Usually a normalised form.\n", + "ontologies": [] + } + } + ] + ], + "output": { + "volcanos_png": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing contrast information\ne.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ]\n" + } + }, + { + "*/png/volcano.png": { + "type": "file", + "description": "Meta-keyed tuple containing a PNG output for a volcano plot built from\nthe differential result table.\n", + "ontologies": [] + } + } + ] + ], + "volcanos_html": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing contrast information\ne.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ]\n" + } + }, + { + "*/html/volcano.html": { + "type": "file", + "description": "Meta-keyed tuple containing an HTML output for a volcano plot built\nfrom the differential result table.\n", + "ontologies": [] + } + } + ] + ], + "versions_shinyngs": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "shinyngs": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "Rscript -e \"library(shinyngs); cat(as.character(packageVersion('shinyngs')))\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "shinyngs": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "Rscript -e \"library(shinyngs); cat(as.character(packageVersion('shinyngs')))\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@pinin4fjords"], + "maintainers": ["@pinin4fjords"] }, - { - "readlist": { - "type": "file", - "description": "Optional text file containing reads IDs to include or exclude", - "ontologies": [] - } - } - ], - { - "filter": { - "type": "string", - "description": "Picard filter type", - "pattern": "includeAligned|excludeAligned|includeReadList|excludeReadList" - } - } - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "Filtered BAM file", - "pattern": "*.{bam}", - "ontologies": [] - } - } - ] - ], - "versions_picard": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "picard": { - "type": "string", - "description": "The tool name" - } - }, - { - "picard FilterSamReads --version 2>&1 | sed -n 's/.*Version://p'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "picard": { - "type": "string", - "description": "The tool name" - } - }, - { - "picard FilterSamReads --version 2>&1 | sed -n 's/.*Version://p'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } + "pipelines": [ + { + "name": "differentialabundance", + "version": "1.5.0" + } ] - ] - }, - "authors": [ - "@jfy133" - ], - "maintainers": [ - "@jfy133" - ] - }, - "pipelines": [ - { - "name": "rnadnavar", - "version": "dev" - } - ] - }, - { - "name": "picard_fixmateinformation", - "path": "modules/nf-core/picard/fixmateinformation/meta.yml", - "type": "module", - "meta": { - "name": "picard_fixmateinformation", - "description": "Verify mate-pair information between mates and fix if needed", - "keywords": [ - "mate-pair", - "picard", - "bam", - "sam" - ], - "tools": [ - { - "picard": { - "description": "A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS)\ndata and formats such as SAM/BAM/CRAM and VCF.\n", - "homepage": "https://broadinstitute.github.io/picard/", - "documentation": "https://gatk.broadinstitute.org/hc/en-us/articles/360036713471-FixMateInformation-Picard-", - "tool_dev_url": "https://github.com/broadinstitute/picard", - "licence": [ - "MIT" - ], - "identifier": "biotools:picard_tools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + }, + { + "name": "shinyngs_staticexploratory", + "path": "modules/nf-core/shinyngs/staticexploratory/meta.yml", + "type": "module", + "meta": { + "name": "shinyngs_staticexploratory", + "description": "Make exploratory plots for analysis of matrix data, including PCA, Boxplots and density plots", + "keywords": ["exploratory", "plot", "boxplot", "density", "PCA"], + "tools": [ + { + "shinyngs": { + "description": "Provides Shiny applications for various array and NGS applications. Currently very RNA-seq centric, with plans for expansion.", + "homepage": "https://github.com/pinin4fjords/shinyngs", + "documentation": "https://rawgit.com/pinin4fjords/shinyngs/master/vignettes/shinyngs.html", + "tool_dev_url": "https://github.com/pinin4fjords/shinyngs", + "licence": ["AGPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information on variables for use in plots,\nprobably experimental information, but at a minimum an id.\ne.g. [ id:'treatment' ]\n" + } + }, + { + "sample": { + "type": "file", + "description": "CSV-format sample sheet with sample metadata\n", + "ontologies": [] + } + }, + { + "feature_meta": { + "type": "file", + "description": "TSV-format feature (e.g. gene) metadata\n", + "ontologies": [] + } + }, + { + "assay_files": { + "type": "file", + "description": "List of TSV-format matrix files representing different measures for the same samples (e.g. raw and normalised).\n", + "ontologies": [] + } + }, + { + "variable": { + "type": "string", + "description": "Variable to use for the contrast variable in the plots.\n" + } + } + ] + ], + "output": { + "boxplots_png": [ + [ + { + "meta": { + "type": "file", + "description": "Meta-keyed tuple containing PNG output for box plots covering input\nmatrices.\n", + "ontologies": [] + } + }, + { + "*/png/boxplot.png": { + "type": "file", + "description": "Meta-keyed tuple containing PNG output for box plots covering input\nmatrices.\n", + "ontologies": [] + } + } + ] + ], + "boxplots_html": [ + [ + { + "meta": { + "type": "file", + "description": "Meta-keyed tuple containing PNG output for box plots covering input\nmatrices.\n", + "ontologies": [] + } + }, + { + "*/html/boxplot.html": { + "type": "file", + "description": "Meta-keyed tuple containing HTML output for box plots covering input\nmatrices.\n", + "ontologies": [] + } + } + ] + ], + "densities_png": [ + [ + { + "meta": { + "type": "file", + "description": "Meta-keyed tuple containing PNG output for box plots covering input\nmatrices.\n", + "ontologies": [] + } + }, + { + "*/png/density.png": { + "type": "file", + "description": "Meta-keyed tuple containing PNG output for density plots\ncovering input matrices.\n", + "ontologies": [] + } + } + ] + ], + "densities_html": [ + [ + { + "meta": { + "type": "file", + "description": "Meta-keyed tuple containing PNG output for box plots covering input\nmatrices.\n", + "ontologies": [] + } + }, + { + "*/html/density.html": { + "type": "file", + "description": "Meta-keyed tuple containing HTML output for density plots\ncovering input matrices.\n", + "ontologies": [] + } + } + ] + ], + "pca2d_png": [ + [ + { + "meta": { + "type": "file", + "description": "Meta-keyed tuple containing PNG output for box plots covering input\nmatrices.\n", + "ontologies": [] + } + }, + { + "*/png/pca2d.png": { + "type": "file", + "description": "Meta-keyed tuple containing a PNG output for 2D PCA plots covering\nspecified input matrix (by default the last one in the input list.\n", + "ontologies": [] + } + } + ] + ], + "pca2d_html": [ + [ + { + "meta": { + "type": "file", + "description": "Meta-keyed tuple containing PNG output for box plots covering input\nmatrices.\n", + "ontologies": [] + } + }, + { + "*/html/pca2d.html": { + "type": "file", + "description": "Meta-keyed tuple containing an HTML output for 2D PCA plots covering\nspecified input matrix (by default the last one in the input list.\n", + "ontologies": [] + } + } + ] + ], + "pca3d_png": [ + [ + { + "meta": { + "type": "file", + "description": "Meta-keyed tuple containing PNG output for box plots covering input\nmatrices.\n", + "ontologies": [] + } + }, + { + "*/png/pca3d.png": { + "type": "file", + "description": "Meta-keyed tuple containing a PNG output for 3D PCA plots covering\nspecified input matrix (by default the last one in the input list.\n", + "ontologies": [] + } + } + ] + ], + "pca3d_html": [ + [ + { + "meta": { + "type": "file", + "description": "Meta-keyed tuple containing PNG output for box plots covering input\nmatrices.\n", + "ontologies": [] + } + }, + { + "*/html/pca3d.html": { + "type": "file", + "description": "Meta-keyed tuple containing an HTML output for 3D PCA plots covering\nspecified input matrix (by default the last one in the input list.\n", + "ontologies": [] + } + } + ] + ], + "mad_png": [ + [ + { + "meta": { + "type": "file", + "description": "Meta-keyed tuple containing PNG output for box plots covering input\nmatrices.\n", + "ontologies": [] + } + }, + { + "*/png/mad_correlation.png": { + "type": "file", + "description": "Meta-keyed tuple containing a PNG output for MAD correlation plots\ncovering specified input matrix (by default the last one in the input\nlist.\n", + "ontologies": [] + } + } + ] + ], + "mad_html": [ + [ + { + "meta": { + "type": "file", + "description": "Meta-keyed tuple containing PNG output for box plots covering input\nmatrices.\n", + "ontologies": [] + } + }, + { + "*/html/mad_correlation.html": { + "type": "file", + "description": "HTML output for MAD correlation plots", + "pattern": "*{.html}", + "ontologies": [] + } + } + ] + ], + "dendro": [ + [ + { + "meta": { + "type": "file", + "description": "Meta-keyed tuple containing PNG output for box plots covering input\nmatrices.\n", + "ontologies": [] + } + }, + { + "*/png/sample_dendrogram.png": { + "type": "file", + "description": "Meta-keyed tuple containing a PNG, for a sample clustering\ndendrogramcovering specified input matrix (by default the last one in\nthe input list.\n", + "ontologies": [] + } + } + ] + ], + "versions_shinyngs": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "shinyngs": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "Rscript -e \"library(shinyngs); cat(as.character(packageVersion('shinyngs')))\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "shinyngs": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "Rscript -e \"library(shinyngs); cat(as.character(packageVersion('shinyngs')))\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@pinin4fjords"], + "maintainers": ["@pinin4fjords"] }, - { - "bam": { - "type": "file", - "description": "BAM file", - "pattern": "*.{bam}", - "ontologies": [] - } - } - ] - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "mate-pair verified BAM file", - "pattern": "*.{bam}", - "ontologies": [] - } - } - ] - ], - 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"maintainers": [ - "@sateeshperi", - "@mjcipriano", - "@hseabolt" - ] - } - }, - { - "name": "picard_liftovervcf", - "path": "modules/nf-core/picard/liftovervcf/meta.yml", - "type": "module", - "meta": { - "name": "picard_liftovervcf", - "description": "Lifts over a VCF file from one reference build to another.", - "keywords": [ - "vcf", - "picard", - "liftovervcf" - ], - "tools": [ - { - "picard": { - "description": "Move annotations from one assembly to another", - "homepage": "https://gatk.broadinstitute.org/hc/en-us/articles/360037060932-LiftoverVcf-Picard", - "documentation": "https://gatk.broadinstitute.org/hc/en-us/articles/360037060932-LiftoverVcf-Picard", - "tool_dev_url": "https://github.com/broadinstitute/picard", - "licence": [ - "MIT" - ], - "identifier": "biotools:picard_tools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]" - } - }, - { - "input_vcf": { - 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of feature and sample annotations with matrices and contrasts", + "keywords": ["expression", "features", "observations", "validation"], + "tools": [ + { + "shinyngs": { + "description": "Provides Shiny applications for various array and NGS applications. Currently very RNA-seq centric, with plans for expansion.", + "homepage": "https://github.com/pinin4fjords/shinyngs", + "documentation": "https://rawgit.com/pinin4fjords/shinyngs/master/vignettes/shinyngs.html", + "tool_dev_url": "https://github.com/pinin4fjords/shinyngs", + "licence": ["AGPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information on experiment, at a minimum an id.\ne.g. [ id:'test' ]\n" + } + }, + { + "sample": { + "type": "file", + "description": "CSV-format sample sheet with sample metadata\n", + "ontologies": [] + } + }, + { + "assay_files": { + "type": "file", + "description": "List of TSV-format matrix files representing different measures for the same samples (e.g. raw and normalised).\n", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing information on features.\ne.g. [ id:'test' ]\n" + } + }, + { + "feature_meta": { + "type": "file", + "description": "TSV-format feature (e.g. gene) metadata\n", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing information on contrasts.\ne.g. [ id:'test' ]\n" + } + }, + { + "contrasts": { + "type": "file", + "description": "CSV-format file with four columns identifying the sample sheet variable, reference level, treatment level, and optionally a comma-separated list of covariates used as blocking factors.\n", + "ontologies": [] + } + } + ] + ], + "output": { + "sample_meta": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information on experiment.\ne.g. [ id:'test' ]\n" + } + }, + { + "*/*.sample_metadata.tsv": { + "type": "file", + "description": "File containing validated sample metadata", + "pattern": "/*.sample_metadata.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "feature_meta": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information on experiment.\ne.g. [ id:'test' ]\n" + } + }, + { + "*/*.feature_metadata.tsv": { + "type": "file", + "description": "File containing validated feature metadata", + "pattern": "/*.feature_metadata.tsv", + "optional": true, + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "assays": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information on experiment.\ne.g. [ id:'test' ]\n" + } + }, + { + "*/*.assay.tsv": { + "type": "file", + "description": "Files containing validated matrices", + "pattern": "/*.assay.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "contrasts": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information on experiment.\ne.g. [ id:'test' ]\n" + } + }, + { + "*/*.contrasts_file.tsv": { + "type": "file", + "description": "Files containing validated matrices", + "pattern": "/*.contrasts_file.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_shinyngs": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "shinyngs": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "Rscript -e \"library(shinyngs); cat(as.character(packageVersion('shinyngs')))\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "shinyngs": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "Rscript -e \"library(shinyngs); cat(as.character(packageVersion('shinyngs')))\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@pinin4fjords"], + "maintainers": ["@pinin4fjords"] }, - { - "chain": { - "type": "file", - "description": "The liftover chain file", - "ontologies": [] - } - } - ] - ], - "output": { - "vcf_lifted": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]" - } - }, - { - "*.lifted.vcf.gz": { - "type": "file", - "description": "VCF file containing successfully lifted variants", - "pattern": "*.{lifted.vcf.gz}", - "ontologies": [] - } - } - ] - ], - "vcf_unlifted": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]" - } - }, - { - "*.unlifted.vcf.gz": { - "type": "file", - "description": "VCF file containing unsuccessfully lifted variants", - "pattern": "*.{unlifted.vcf.gz}", - "ontologies": [] - } - } - ] - ], - "versions_picard": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "picard": { - "type": "string", - "description": "The tool name" - } - }, - { - "picard LiftoverVcf --version 2>&1 | sed -n 's/.*Version://p'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "picard": { - "type": "string", - "description": "The tool name" - } - }, - { - "picard LiftoverVcf --version 2>&1 | sed -n 's/.*Version://p'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } + "pipelines": [ + { + "name": "differentialabundance", + "version": "1.5.0" + } ] - ] }, - "authors": [ - "@lucpen", - "@ramprasadn" - ], - "maintainers": [ - "@lucpen", - "@ramprasadn" - ] - }, - "pipelines": [ { - "name": "raredisease", - "version": "3.0.0" + "name": "shovill", + "path": "modules/nf-core/shovill/meta.yml", + "type": "module", + "meta": { + "name": "shovill", + "description": "Assemble bacterial isolate genomes from Illumina paired-end reads", + "keywords": ["bacterial", "assembly", "illumina"], + "tools": [ + { + "shovill": { + "description": "Microbial assembly pipeline for Illumina paired-end reads", + "homepage": "https://github.com/tseemann/shovill", + "documentation": "https://github.com/tseemann/shovill/blob/master/README.md", + "licence": ["GPL v2"], + "identifier": "biotools:shovill" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input paired-end FastQ files", + "ontologies": [] + } + } + ] + ], + "output": { + "contigs": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "contigs.fa": { + "type": "file", + "description": "The final assembly produced by Shovill", + "pattern": "contigs.fa", + "ontologies": [] + } + } + ] + ], + "corrections": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "shovill.corrections": { + "type": "file", + "description": "List of post-assembly corrections made by Shovill", + "pattern": "shovill.corrections", + "ontologies": [] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "shovill.log": { + "type": "file", + "description": "Full log file for bug reporting", + "pattern": "shovill.log", + "ontologies": [] + } + } + ] + ], + "raw_contigs": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "{skesa,spades,megahit,velvet}.fasta": { + "type": "file", + "description": "Raw assembly produced by the assembler (SKESA, SPAdes, MEGAHIT, or Velvet)", + "pattern": "{skesa,spades,megahit,velvet}.fasta", + "ontologies": [] + } + } + ] + ], + "gfa": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "contigs.{fastg,gfa,LastGraph}": { + "type": "file", + "description": "Assembly graph produced by MEGAHIT, SPAdes, or Velvet", + "pattern": "contigs.{fastg,gfa,LastGraph}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3975" + } + ] + } + } + ] + ], + "versions_shovill": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "shovill": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "shovill --version 2>&1 | sed \"s/^.*shovill //\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "shovill": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "shovill --version 2>&1 | sed \"s/^.*shovill //\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@rpetit3", "@eit-maxlcummins"], + "maintainers": ["@rpetit3"] + } }, { - "name": "variantbenchmarking", - "version": "1.5.0" - } - ] - }, - { - "name": "picard_markduplicates", - "path": "modules/nf-core/picard/markduplicates/meta.yml", - "type": "module", - "meta": { - "name": "picard_markduplicates", - "description": "Locate and tag duplicate reads in a BAM file", - "keywords": [ - "markduplicates", - "pcr", - "duplicates", - "bam", - "sam", - "cram" - ], - "tools": [ - { - "picard": { - "description": "A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS)\ndata and formats such as SAM/BAM/CRAM and VCF.\n", - "homepage": "https://broadinstitute.github.io/picard/", - "documentation": "https://broadinstitute.github.io/picard/", - "licence": [ - "MIT" - ], - "identifier": "biotools:picard_tools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "Sequence reads file, can be SAM/BAM/CRAM format", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } + "name": "sickle", + "path": "modules/nf-core/sickle/meta.yml", + "type": "module", + "meta": { + "name": "sickle", + "description": "A windowed adaptive trimming tool for FASTQ files using quality", + "keywords": ["fastq", "sliding window", "trimming"], + "tools": [ + { + "sickle": { + "description": "a tool that determines clipping of reads on 3' end and 5'end based on base quality ", + "homepage": "https://github.com/najoshi/sickle", + "tool_dev_url": "https://github.com/najoshi/sickle", + "licence": ["MIT License"], + "identifier": "biotools:sickle" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively. File of forward reads must be supplied first and reverse reads as the second e.g. [\"read.1.fastq.gz\",\"read.2.fastq.gz\"]", + "pattern": "*.{fq,fastq,fq.gz,fastq.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + }, + { + "qual_type": { + "type": "string", + "description": "sickle needs a base quality values, which could be either illumina, solexa or sanger", + "pattern": "illumina or solexa or sanger" + } + } + ] + ], + "output": { + "single_trimmed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false, qual:'Illumina' ]\n" + } + }, + { + "*.se.trimmed.fastq.gz": { + "type": "file", + "description": "Single end trimmed reads", + "pattern": "*.se.trimmed.fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "paired_trimmed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false, qual:'Illumina' ]\n" + } + }, + { + "*.pe{1,2}.trimmed.fastq.gz": { + "type": "file", + "description": "Paired end trimmed reads", + "pattern": "*.pe{1,2}.trimmed.fastq.gz", + "ontologies": [] + } + } + ] + ], + "singleton_trimmed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false, qual:'Illumina' ]\n" + } + }, + { + "*.singleton.trimmed.fastq.gz": { + "type": "file", + "description": "Singleton trimmed reads", + "pattern": "*.singleton.trimmed.fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false, qual:'Illumina' ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "log file", + "pattern": "*.log", + "ontologies": [] + } + } + ] + ], + "versions_sickle": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "sickle": { + "type": "string", + "description": "The tool name" + } + }, + { + "sickle --version 2>&1 | head -1 | sed \"s/sickle version //\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "sickle": { + "type": "string", + "description": "The tool name" + } + }, + { + "sickle --version 2>&1 | head -1 | sed \"s/sickle version //\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@BioInf2305"], + "maintainers": ["@BioInf2305"] } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome fasta file, required for CRAM input", - "pattern": "*.{fasta,fa}", - "ontologies": [] - } + }, + { + "name": "sigprofiler", + "path": "modules/nf-core/sigprofiler/meta.yml", + "type": "module", + "meta": { + "name": "sigprofiler", + "description": "mutational signature deconvolution of cancer cells", + "keywords": ["mutational signatures", "SBSs, DBSs, IDs", "cancer genomics"], + "tools": [ + { + "sigprofilermatrixgenerator": { + "description": "Sigprofilermatrixgenerator is a Python-based tool. It creates mutational matrices for all types of somatic mutations (SBS, DBS, and IDs)", + "documentation": "https://osf.io/s93d5/wiki/home/", + "tool_dev_url": "https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/tree/master/SigProfilerMatrixGenerator", + "doi": "10.1186/s12864-019-6041-2", + "licence": ["BSD-2-clause"], + "identifier": "biotools:sigprofilermatrixgenerator" + } + }, + { + "sigprofilerextractor": { + "description": "SigProfilerExtractor is a Python-based tool. It allows de novo extraction of mutational signatures from data generated in a matrix format, identification of the number of operative mutational signatures, and their activities in each sample.", + "documentation": "https://osf.io/t6j7u/wiki/home/", + "tool_dev_url": "https://github.com/AlexandrovLab/SigProfilerExtractor", + "doi": "10.1016/j.xgen.2022.100179 ", + "licence": ["BSD-2-clause"], + "identifier": "biotools:sigprofilerextractor" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "tsv_list": { + "type": "file", + "description": "joint tsv file with validated mutations by CNAqc", + "pattern": "*.{tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + { + "genome": { + "type": "string", + "description": "Reference genome name to use with SigProfiler (e.g. \"GRCh37\", \"GRCh38\")", + "ontologies": [] + } + }, + { + "genome_installed_path": { + "type": "file", + "description": "path to installed reference genome (optional)", + "ontologies": [] + } + } + ], + "output": { + "results_sigprofiler": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'test' ]" + } + }, + { + "results/*": { + "type": "directory", + "description": "folder with saved output results", + "pattern": "results/*", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@kdavydzenka"] }, - { - "fai": { - "type": "file", - "description": "Reference genome fasta index", - "pattern": "*.{fai}", - "ontologies": [] - } - } - ] - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "BAM file with duplicate reads marked/removed", - "pattern": "*.{bam}", - "ontologies": [] - } - } - ] - ], - "bai": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bai": { - "type": "file", - "description": "An optional BAM index file. If desired, --CREATE_INDEX must be passed as a flag", - "pattern": "*.{bai}", - "ontologies": [] - } - } - ] - ], - "cram": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.cram": { - "type": "file", - "description": "Output CRAM file", - "pattern": "*.{cram}", - "ontologies": [] - } - } - ] - ], - "metrics": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.metrics.txt": { - "type": "file", - "description": "Duplicate metrics file generated by picard", - "pattern": "*.{metrics.txt}", - "ontologies": [] - } - } - ] - ], - "versions_picard": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "picard": { - "type": "string", - "description": "The tool name" - } - }, - { - "picard MarkDuplicates --version 2>&1 | sed -n 's/.*Version://p'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "picard": { - "type": "string", - "description": "The tool name" - } - }, - { - "picard MarkDuplicates --version 2>&1 | sed -n 's/.*Version://p'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } + "pipelines": [ + { + "name": "tumourevo", + "version": "dev" + } ] - ] }, - "authors": [ - "@drpatelh", - "@projectoriented", - "@ramprasadn" - ], - "maintainers": [ - "@drpatelh", - "@projectoriented", - "@ramprasadn" - ] - }, - "pipelines": [ { - "name": "atacseq", - "version": "2.1.2" + "name": "simpleaf_index", + "path": "modules/nf-core/simpleaf/index/meta.yml", + "type": "module", + "meta": { + "name": "simpleaf_index", + "description": "Indexing of transcriptome for gene expression quantification using SimpleAF", + "keywords": ["indexing", "transcriptome", "gene expression", "SimpleAF"], + "tools": [ + { + "simpleaf": { + "description": "SimpleAF is a tool for quantification of gene expression from RNA-seq data\n", + "homepage": "https://github.com/COMBINE-lab/simpleaf", + "licence": ["BSD-3-Clause"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information on genome_fasta and genome_gtf\n" + } + }, + { + "genome_fasta": { + "type": "file", + "description": "FASTA file containing the genome sequence. It must be provided together with the corresponding genome_gtf file.\nWhen another input set is provided, it must be empty (provided as []).\n", + "ontologies": [] + } + }, + { + "genome_gtf": { + "type": "file", + "description": "GTF file containing gene annotations. It must be provided together with its corresponding genome_fasta file.\nWhen another input set rather than genome_fasta + genome_gtf is provided, it must be empty (provided as []).\n", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing information on transcript_fasta\n" + } + }, + { + "transcript_fasta": { + "type": "file", + "description": "FASTA file containing the transcript sequences to build index directly on.\nWhen another input set is provided, it must be empty (provided as []).\n", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing information on probe_csv.\n" + } + }, + { + "probe_csv": { + "type": "file", + "description": "CSV file containing the reference probe sequences to build index directly on.\nWhen another input set is provided, it must be empty (provided as []).\n", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing information on feature_csv.\n" + } + }, + { + "feature_csv": { + "type": "file", + "description": "CSV file containing the reference feature barcodes to build index directly on.\nWhen another input set is provided, it must be empty (provided as []).\n", + "ontologies": [] + } + } + ] + ], + "output": { + "index": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information on the index generated by simpleaf\n" + } + }, + { + "${prefix}/index": { + "type": "map", + "description": "Groovy Map containing information on the index generated by simpleaf\n" + } + } + ] + ], + "ref": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information on the index generated by simpleaf\n" + } + }, + { + "${prefix}/ref": { + "type": "map", + "description": "Groovy Map containing information on the transcriptomic reference constructed by simpleaf.\n" + } + } + ] + ], + "t2g": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information on the index generated by simpleaf\n" + } + }, + { + "${prefix}/ref/{t2g,t2g_3col}.tsv": { + "type": "file", + "description": "Path to the tsv file containing the transcript-to-gene mapping information generated by simpleaf. This is used as --t2g-map when invoking simpleaf quant.\n", + "ontologies": [] + } + } + ] + ], + "versions_alevin_fry": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "alevin-fry": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "alevin-fry --version | sed 's/alevin-fry //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_piscem": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "piscem": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "piscem --version | sed 's/piscem //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_simpleaf": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "simpleaf": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "ALEVIN_FRY_HOME=. simpleaf --version | sed 's/simpleaf //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "alevin-fry": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "alevin-fry --version | sed 's/alevin-fry //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "piscem": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "piscem --version | sed 's/piscem //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "simpleaf": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "ALEVIN_FRY_HOME=. simpleaf --version | sed 's/simpleaf //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@fmalmeida", "@maxulysse", "@Khajidu", "@apeltzer", "@pinin4fjords", "@dongzehe"], + "maintainers": ["@fmalmeida", "@maxulysse", "@Khajidu", "@apeltzer", "@pinin4fjords", "@dongzehe"] + }, + "pipelines": [ + { + "name": "scrnaseq", + "version": "4.1.0" + } + ] }, { - "name": "chipseq", - "version": "2.1.0" + "name": "simpleaf_quant", + "path": "modules/nf-core/simpleaf/quant/meta.yml", + "type": "module", + "meta": { + "name": "simpleaf_quant", + "description": "simpleaf is a program to simplify and customize the running and configuration of single-cell processing with alevin-fry.", + "keywords": ["quantification", "gene expression", "SimpleAF"], + "tools": [ + { + "simpleaf": { + "description": "SimpleAF is a program to simplify and customize the running and configuration of single-cell processing with alevin-fry.\n", + "homepage": "https://github.com/COMBINE-lab/simpleaf", + "licence": ["BSD-3-Clause"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "chemistry": { + "type": "string", + "description": "Chemistry used for library preparation. It can be a string describing the specific chemistry or the geometry of the barcode, UMI, and mappable read. For example, \"10xv2\" and \"10xv3\" will apply the appropriate settings for 10x Chromium v2 and v3 protocols, respectively. Alternatively, you can provide a general geometry string if your chemistry is not pre-registered. For example, instead of \"10xv2\", you could use \"1{b[16]u[10]x:}2{r:}\", or instead of \"10xv3\", you could use \"1{b[16]u[12]x:}2{r:}\". Details at https://hackmd.io/@PI7Og0l1ReeBZu_pjQGUQQ/rJMgmvr13\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files for paired-end data.\nReads should be grouped by pairs.\nFor example, [ [R1_1.fastq.gz, R2_1.fastq.gz], [R1_2.fastq.gz, R2_2.fastq.gz] ]\n", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing index information\ne.g. [ tool:'piscem' ]\n" + } + }, + { + "index": { + "type": "directory", + "description": "Folder containing the index files. For a *salmon* index that is not generated by simpleaf to be taken, '--no-piscem' MUST be specified in ext.args." + } + }, + { + "txp2gene": { + "type": "file", + "description": "File mapping transcripts to genes. It can be either a two-column TSV file for a standard transcriptomic index containing the transcript-to-gene ID mapping information, or a three-column TSV file for an augmented transcriptomic index with the third column representing the splicing status of each transcript.\n", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing txp2gene information\ne.g. [ mode:'usa' ]\n" + } + }, + { + "cell_filter": { + "type": "string", + "enum": ["knee", "forced-cells", "explicit-pl", "expect-cells", "unfiltered-pl"], + "description": "Cell filtering mode. Possible values are 'usa' and 'whitelist'. 'usa' will use the default cell filtering mode, while 'whitelist' will use the whitelist file provided in the 'whitelist' input.\n" + } + }, + { + "number_cb": { + "type": "integer", + "description": "Number of cell barcodes to use for cell filtering. Set as empty ('[]') unless 'cell_filter' is set to 'forced-cells' or 'expect-cells'.\n" + } + }, + { + "cb_list": { + "type": "file", + "description": "File containing a list of cell barcodes to use for cell filtering. Set as empty ('[]') unless 'cell_filter' is set to 'unfiltered-pl' or 'explicit-pl'.\n", + "ontologies": [] + } + } + ], + { + "resolution": { + "type": "string", + "description": "UMI resolution (https://alevin-fry.readthedocs.io/en/latest/quant.html). Possible values are 'cr-like', 'cr-like-em', 'parsimony', 'parsimony-em', 'parsimony-gene', and 'parsimony-gene-em'.\n" + } + }, + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing existing mapping results.\ne.g. [ tool:'piscem' ]\n" + } + }, + { + "map_dir": { + "type": "directory", + "description": "Folder containing the existing mapping results. It must be generated by simpleaf or alevin-fry, and contain the mapping file named map.rad." + } + } + ] + ], + "output": { + "map": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "simpleaf/af_map" + } + }, + { + "${prefix}/af_map": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + } + ] + ], + "quant": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "simpleaf/af_map" + } + }, + { + "${prefix}/af_quant": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + } + ] + ], + "versions_alevin_fry": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "alevin-fry": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "alevin-fry --version | sed 's/alevin-fry //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_piscem": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "piscem": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "piscem --version | sed 's/piscem //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_simpleaf": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "simpleaf": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "ALEVIN_FRY_HOME=. simpleaf --version | sed 's/simpleaf //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "alevin-fry": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "alevin-fry --version | sed 's/alevin-fry //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "piscem": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "piscem --version | sed 's/piscem //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "simpleaf": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "ALEVIN_FRY_HOME=. simpleaf --version | sed 's/simpleaf //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@fmalmeida", "@maxulysse", "@Khajidu", "@apeltzer", "@pinin4fjords", "@dongzehe"], + "maintainers": ["@fmalmeida", "@maxulysse", "@Khajidu", "@apeltzer", "@pinin4fjords", "@dongzehe"] + }, + "pipelines": [ + { + "name": "scrnaseq", + "version": "4.1.0" + } + ] }, { - "name": "circdna", - "version": "1.1.0" + "name": "singlem_dbdownload", + "path": "modules/nf-core/singlem/dbdownload/meta.yml", + "type": "module", + "meta": { + "name": "singlem_dbdownload", + "description": "Download the SingleM metapackage database used for metagenome profiling", + "keywords": ["metagenomics", "database", "download", "profiling", "singlem", "metapackage"], + "tools": [ + { + "singlem": { + "description": "SingleM is a tool for profiling shotgun metagenomes. It determines the relative\nabundance of bacterial and archaeal taxa in a sample and can also profile dsDNA\nphages. It has particular strength in dealing with novel lineages and is suitable\nfor tasks such as assessing eukaryotic contamination, finding bias in genome\nrecovery, and lineage-targeted MAG recovery.\n", + "homepage": "https://wwood.github.io/singlem", + "documentation": "https://wwood.github.io/singlem", + "tool_dev_url": "https://github.com/wwood/singlem", + "doi": "10.1038/s41587-024-02492-w", + "licence": ["GPL-3.0-or-later"], + "identifier": "biotools:singlem" + } + } + ], + "output": { + "singlem_database": [ + { + "*.smpkg.zb": { + "type": "file", + "description": "SingleM metapackage database file used for taxonomic profiling", + "pattern": "*.smpkg.zb", + "ontologies": [ + { + "edam": "http://edamontology.org/data_0955" + } + ] + } + } + ], + "versions_singlem": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "singlem": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "singlem --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "singlem": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "singlem --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@TheGreatJack"], + "maintainers": ["@TheGreatJack"] + } }, { - "name": "cutandrun", - "version": "3.2.2" + "name": "sistr", + "path": "modules/nf-core/sistr/meta.yml", + "type": "module", + "meta": { + "name": "sistr", + "description": "Serovar prediction of salmonella assemblies", + "keywords": ["bacteria", "fasta", "salmonella"], + "tools": [ + { + "sistr": { + "description": "Salmonella In Silico Typing Resource (SISTR) commandline tool for serovar prediction", + "homepage": "https://github.com/phac-nml/sistr_cmd", + "documentation": "https://github.com/phac-nml/sistr_cmd", + "tool_dev_url": "https://github.com/phac-nml/sistr_cmd", + "doi": "10.1371/journal.pone.0147101", + "licence": ["Apache-2.0"], + "identifier": "biotools:SISTR" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Nucleotide or protein sequences in FASTA format", + "pattern": "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}", + "ontologies": [] + } + } + ] + ], + "output": { + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tab": { + "type": "file", + "description": "SISTR serovar prediction", + "pattern": "*.{tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "allele_fasta": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*-allele.fasta": { + "type": "file", + "description": "FASTA file destination of novel cgMLST alleles", + "pattern": "*.{fasta}", + "ontologies": [] + } + } + ] + ], + "allele_json": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*-allele.json": { + "type": "file", + "description": "Allele sequences and info to JSON", + "pattern": "*.{json}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "cgmlst_csv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*-cgmlst.csv": { + "type": "file", + "description": "CSV file destination for cgMLST allelic profiles", + "pattern": "*.{csv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "versions_sistr": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "sistr": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "sistr --version 2>&1 | sed \"s/^.*sistr_cmd //; s/ .*\\$//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "sistr": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "sistr --version 2>&1 | sed \"s/^.*sistr_cmd //; s/ .*\\$//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@rpetit3"], + "maintainers": ["@rpetit3"] + } }, { - "name": "methylseq", - "version": "4.2.0" + "name": "ska_distance", + "path": "modules/nf-core/ska/distance/meta.yml", + "type": "module", + "meta": { + "name": "ska_distance", + "description": "Calculate pairwise distances and basic clustering from SKA sketches", + "keywords": ["genomics", "metagenomics", "kmer", "split_kmers", "distance", "clustering"], + "tools": [ + { + "ska": { + "description": "SKA (Split Kmer Analysis)", + "homepage": "https://github.com/simonrharris/SKA", + "documentation": "https://github.com/simonrharris/SKA/wiki", + "tool_dev_url": "https://github.com/simonrharris/SKA", + "doi": "10.1101/453142", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "sketch_files": { + "type": "file", + "description": "SKA sketch files", + "pattern": "*.skf", + "ontologies": [] + } + }, + { + "sketch_list": { + "type": "file", + "description": "List of SKA sketch files", + "pattern": "*.txt", + "ontologies": [] + } + } + ] + ], + "output": { + "distances": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*distances.tsv": { + "type": "file", + "description": "Pairwise distance table", + "pattern": "*distance.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "cluster_list": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*clusters.tsv": { + "type": "file", + "description": "List of samples and their clusters", + "pattern": "*clusters.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "cluster_files": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*cluster*.txt": { + "type": "file", + "description": "Cluster files", + "pattern": "*cluster*.txt", + "ontologies": [] + } + } + ] + ], + "dot": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.dot": { + "type": "file", + "description": "DOT file for visualization", + "pattern": "*.dot", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@itrujnara"], + "maintainers": ["@itrujnara"] + } }, { - "name": "pathogensurveillance", - "version": "1.1.0" + "name": "ska_fasta", + "path": "modules/nf-core/ska/fasta/meta.yml", + "type": "module", + "meta": { + "name": "ska_fasta", + "description": "Create genome sketch using split k-mers", + "keywords": ["genomics", "metagenomics", "kmer", "split_kmers", "sketch"], + "tools": [ + { + "ska": { + "description": "SKA (Split Kmer Analysis)", + "homepage": "https://github.com/simonrharris/SKA", + "documentation": "https://github.com/simonrharris/SKA/wiki", + "tool_dev_url": "https://github.com/simonrharris/SKA", + "doi": "10.1101/453142", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "fastas": { + "type": "file", + "description": "FASTA files with contigs/reads", + "pattern": "*.fa(sta)", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + }, + { + "fasta_list": { + "type": "file", + "description": "List of FASTA files with contigs/reads", + "pattern": "*.txt", + "ontologies": [] + } + } + ] + ], + "output": { + "skf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "*.skf": { + "type": "file", + "description": "File containing genome sketch", + "pattern": "*.skf", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@itrujnara"], + "maintainers": ["@itrujnara"] + } }, { - "name": "raredisease", - "version": "3.0.0" + "name": "skani_dist", + "path": "modules/nf-core/skani/dist/meta.yml", + "type": "module", + "meta": { + "name": "skani_dist", + "description": "Simple ANI calculation between reference and query genomes.", + "keywords": ["skani", "metagenomics", "genome", "alignment", "sketch", "distance", "dist"], + "tools": [ + { + "skani": { + "description": "skani is a fast and robust tool for calculating ANI between metagenome assembled genomes and 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+ "name": "smncopynumbercaller", + "description": "tool to call the copy number of full-length SMN1, full-length SMN2, as well as SMN2Δ7–8 (SMN2 with a deletion of Exon7-8) from a whole-genome sequencing (WGS) BAM file.", + "keywords": ["copy number", "BAM", "CRAM", "SMN1", "SMN2"], + "tools": [ + { + "smncopynumbercaller": { + "description": "call copy number of SMN1, SMN2, SMN2Δ7–8 from a bam file", + "homepage": "https://github.com/Illumina/SMNCopyNumberCaller", + "documentation": "https://github.com/Illumina/SMNCopyNumberCaller", + "tool_dev_url": "https://github.com/Illumina/SMNCopyNumberCaller", + "doi": "10.1038/s41436-020-0754-0", + "licence": ["Apache License Version 2.0"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM file", + "pattern": "*.{bam,cram}", + "ontologies": [] + } + }, + { + "bai": { + "type": "file", + "description": "BAM/CRAM index file", + "pattern": "*.{bai,crai}", + "ontologies": [] + } + } + ] + ], + "output": { + "smncopynumber": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "out/*.tsv": { + "type": "file", + "description": "File containing the output of SMNCopyNumberCaller", + "pattern": "*.{tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "run_metrics": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "out/*.json": { + "type": "file", + "description": "File containing run parameters of SMNCopyNumberCaller", + "pattern": "*.{json}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "versions_smncopynumbercaller": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "smncopynumbercaller": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "1.1.2": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "smncopynumbercaller": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "1.1.2": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@peterpru"], + "maintainers": ["@peterpru"] }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } - } - ] - ], - "output": { - "metrics": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.txt": { - "type": "file", - "description": "Values used by Picard to generate chart.", - "pattern": "*.txt", - "ontologies": [] - } - } - ] - ], - "pdf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.pdf": { - "type": "file", - "description": "Chart in PDF format", - "pattern": "*.pdf", - "ontologies": [] - } - } - ] - ], - "versions_picard": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "picard": { - "type": "string", - "description": "The tool name" - } - }, - { - "picard MeanQualityByCycle --version 2>&1 | sed -n 's/.*Version://p'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": 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"input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "gfa": { + "type": "file", + "description": "Variation graph in GFA 1.0 format", + "pattern": "*.{gfa}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3975" + } + ] + } + } + ] + ], + "output": { + "gfa": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*smoothxg.gfa": { + "type": "file", + "description": "Linearized and simplified graph in GFA 1.0 format", + "pattern": "*.smoothxg.{gfa}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3975" + } + ] + } + } + ] + ], + "maf": [ + { + "*.maf": { + "type": "file", + "description": "write the multiple sequence alignments (MSAs) in MAF format in this file (optional)", + "pattern": "*.{maf}", + "ontologies": [] + } + } + ], + "versions_smoothxg": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "smoothxg": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "smoothxg --version 2>&1 | sed 's/^v//; s/-.*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "smoothxg": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "smoothxg --version 2>&1 | sed 's/^v//; s/-.*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@heuermh, @subwaystation"], + "maintainers": ["@heuermh, @subwaystation"] }, - { - "bams": { - "type": "list", - "description": "List of input BAM files to be merged", - "pattern": "*.{bam}" - } - } - ] - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "Merged BAM file", - "pattern": "*.{bam}", - "ontologies": [] - } - } - ] - ], - "versions_picard": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "picard": { - "type": "string", - "description": "The tool name" - } - }, - { - "picard MergeSamFiles --version 2>&1 | sed -n 's/.*Version://p'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "picard": { - "type": "string", - "description": "The tool name" - } - }, - { - "picard MergeSamFiles --version 2>&1 | sed -n 's/.*Version://p'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } + "pipelines": [ + { + "name": "pangenome", + "version": "1.1.3" + } ] - ] }, - "authors": [ - "@drpatelh" - ], - "maintainers": [ - "@drpatelh" - ] - }, - "pipelines": [ { - "name": "atacseq", - "version": "2.1.2" + "name": "smoove_call", + "path": "modules/nf-core/smoove/call/meta.yml", + "type": "module", + "meta": { + "name": "smoove_call", + "description": "smoove simplifies and speeds calling and genotyping SVs for short reads. It also improves specificity by removing many spurious alignment signals that are indicative of low-level noise and often contribute to spurious calls. Developed by Brent Pedersen.", + "keywords": ["structural variants", "SV", "vcf", "wgs"], + "tools": [ + { + "smoove": { + "description": "structural variant calling and genotyping with existing tools, but, smoothly", + "homepage": "https://github.com/brentp/smoove", + "documentation": "https://brentp.github.io/post/smoove/", + "tool_dev_url": "https://github.com/brentp/smoove", + "licence": ["Apache-2.0"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM file", + "pattern": "*.{bam,cram}", + "ontologies": [] + } + }, + { + "index": { + "type": "file", + "description": "Index of BAM/CRAM file", + "pattern": "*.{bai,crai}", + "ontologies": [] + } + }, + { + "exclude_beds": { + "type": "file", + "description": "A BED file containing the regions to exclude from the SV calling", + "pattern": "*.bed", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The reference fasta file", + "pattern": "*.{fasta,fna,fa}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Index of reference fasta file", + "pattern": "*.fai", + "ontologies": [] + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "Compressed VCF file", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "versions_smoove": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "smoove": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "smoove -v |& sed -n 's/smoove version: *//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "smoove": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "smoove -v |& sed -n 's/smoove version: *//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@scorreard", "@nvnieuwk"], + "maintainers": ["@scorreard", "@nvnieuwk"] + } }, { - "name": "chipseq", - "version": "2.1.0" - } - ] - }, - { - "name": "picard_positionbaseddownsamplesam", - "path": "modules/nf-core/picard/positionbaseddownsamplesam/meta.yml", - "type": "module", - "meta": { - "name": "picard_positionbaseddownsamplesam", - "description": "Samples a SAM/BAM/CRAM file using flowcell position information for the best approximation of having sequenced fewer reads", - "keywords": [ - "sample", - "bam", - "sam", - "cram" - ], - "tools": [ - { - "picard": { - "description": "A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS)\ndata and formats such as SAM/BAM/CRAM and VCF.\n", - "homepage": "https://broadinstitute.github.io/picard/", - "documentation": "https://broadinstitute.github.io/picard/", - "licence": [ - "MIT" - ], - "identifier": "biotools:picard_tools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } - }, - { - "fraction": { - "type": "float", - "description": "Fraction of reads to downsample to" - } - } - ] - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.ds*.bam": { - "type": "file", - "description": "A downsampled BAM file", - "pattern": "*.{bam}", - "ontologies": [] - } - } - ] - ], - "bai": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.ds*.bai": { - "type": "file", - "description": "An optional BAM index file. If desired, --CREATE_INDEX must be passed as a flag", - "pattern": "*.{bai}", - "ontologies": [] - } - } - ] - ], - "num_reads": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "ACTUAL_NUM_READS": { - "type": "integer", - "description": "The actual number of downsampled reads" - } - } - ] - ], - "versions_picard": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "picard": { - "type": "string", - "description": "The tool name" - } - }, - { - "picard PositionBasedDownsampleSam --version 2>&1 | sed -n 's/.*Version://p'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "picard": { - "type": "string", - "description": "The tool name" - } - }, - { - "picard PositionBasedDownsampleSam --version 2>&1 | sed -n 's/.*Version://p'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@bwlang" - ] - } - }, - { - "name": "picard_renamesampleinvcf", - "path": "modules/nf-core/picard/renamesampleinvcf/meta.yml", - "type": "module", - "meta": { - "name": "picard_renamesampleinvcf", - "description": "changes name of sample in the vcf file", - "keywords": [ - "picard", - "picard/renamesampleinvcf", - "vcf" - ], - "tools": [ - { - "picard": { - "description": "A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS)\ndata and formats such as SAM/BAM/CRAM and VCF.\n", - "homepage": "https://broadinstitute.github.io/picard/", - "documentation": "https://broadinstitute.github.io/picard/", - "tool_dev_url": "https://github.com/broadinstitute/picard", - "licence": [ - "MIT" - ], - "identifier": "biotools:picard_tools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF file", - "pattern": "*.{vcf,vcf.gz}", - "ontologies": [] - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.vcf.gz": { - "type": "file", - "description": "VCF file", - "pattern": "*.{vcf,vcf.gz}", - "ontologies": [] - } - } - ] - ], - "versions_picard": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "picard": { - "type": "string", - "description": "The tool name" - } - }, - { - "picard RenameSampleInVcf --version 2>&1 | sed -n 's/.*Version://p'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "picard": { - "type": "string", - "description": "The tool name" - } - }, - { - "picard RenameSampleInVcf --version 2>&1 | sed -n 's/.*Version://p'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@Lucpen" - ], - "maintainers": [ - "@Lucpen" - ] - }, - "pipelines": [ - { - "name": "raredisease", - "version": "3.0.0" - } - ] - }, - { - "name": "picard_scatterintervalsbyns", - "path": "modules/nf-core/picard/scatterintervalsbyns/meta.yml", - "type": "module", - "meta": { - "name": "picard_scatterintervalsbyns", - "description": "Writes an interval list created by splitting a reference at Ns.A Program for breaking up a reference into intervals of alternating regions of N and ACGT bases", - "keywords": [ - "interval_list", - "scatter", - "regions" - ], - "tools": [ - { - "picard": { - "description": "A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS)\ndata and formats such as SAM/BAM/CRAM and VCF.\n", - "homepage": "https://broadinstitute.github.io/picard/", - "documentation": "https://broadinstitute.github.io/picard/", - "tool_dev_url": "https://github.com/broadinstitute/picard", - "licence": [ - "MIT" - ], - "identifier": "biotools:picard_tools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing fasta information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Fasta file to derive the intervals from", - "pattern": "*.{fasta,fa,fna}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing fai information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fai": { - "type": "file", - "description": "Index of the fasta file", - "pattern": "*.fai", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing dictionary information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "dict": { - "type": "file", - "description": "Sequence dictionary of the fasta file", - "pattern": "*.dict", - "ontologies": [] - } - } - ] - ], - "output": { - "intervals": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.interval_list": { - "type": "file", - "description": "The scattered intervals", - "pattern": "*.interval_list", - "ontologies": [] - } - } - ] - ], - "versions_picard": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "picard": { - "type": "string", - "description": "The tool name" - } - }, - { - "picard ScatterIntervalsByNs --version 2>&1 | sed -n 's/.*Version://p'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "picard": { - "type": "string", - "description": "The tool name" - } - }, - { - "picard ScatterIntervalsByNs --version 2>&1 | sed -n 's/.*Version://p'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@nvnieuwk" - ], - "maintainers": [ - "@nvnieuwk" - ] - } - }, - { - "name": "picard_setnmmdanduqtags", - "path": "modules/nf-core/picard/setnmmdanduqtags/meta.yml", - "type": "module", - "meta": { - "name": "picard_setnmmdanduqtags", - "description": "This tool takes in a coordinate-sorted SAM or BAM and calculatesthe NM, MD, and UQ tags by comparing with the reference.", - "keywords": [ - "bam", - "uq", - "nm", - "md" - ], - "tools": [ - { - "picard": { - "description": "Java tools for working with NGS data in the BAM format", - "homepage": "https://broadinstitute.github.io/picard/", - "documentation": "https://broadinstitute.github.io/picard/", - "tool_dev_url": "https://github.com/broadinstitute/picard", - "licence": [ - "MIT" - ], - "identifier": "biotools:picard_tools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM/SAM file", - "pattern": "*.{bam,sam}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - }, - { - "edam": "http://edamontology.org/format_2573" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "reference": { - "type": "file", - "description": "Reference fasta file", - "pattern": "*.{fasta,fa}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "Sorted BAM file", - "pattern": "*.bam", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - } - ] - ], - "bai": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.bai": { - "type": "file", - "description": "BAM indexing file", - "pattern": "*.bai", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3327" - } - ] - } - } - ] - ], - "versions_picard": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "picard": { - "type": "string", - "description": "The tool name" - } - }, - { - "picard SetNmMdAndUqTags --version 2>&1 | sed -n 's/.*Version://p'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "picard": { - "type": "string", - "description": "The tool name" - } - }, - { - "picard SetNmMdAndUqTags --version 2>&1 | sed -n 's/.*Version://p'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@anoronh4" - ], - "maintainers": [ - "@anoronh4" - ] - } - }, - { - "name": "picard_sortsam", - "path": "modules/nf-core/picard/sortsam/meta.yml", - "type": "module", - "meta": { - "name": "picard_sortsam", - "description": "Sorts BAM/SAM files based on a variety of picard specific criteria", - "keywords": [ - "sort", - "bam", - "sam", - "picard" - ], - "tools": [ - { - "picard": { - "description": "A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS)\ndata and formats such as SAM/BAM/CRAM and VCF.\n", - "homepage": "https://broadinstitute.github.io/picard/", - "documentation": "https://broadinstitute.github.io/picard/", - "licence": [ - "MIT" - ], - "identifier": "biotools:picard_tools" + "name": "snakemake", + "path": "modules/nf-core/snakemake/meta.yml", + "type": "module", + "meta": { + "name": "snakemake", + "description": "The Snakemake workflow management system is a tool to create reproducible and scalable data analyses. This module runs a simple Snakemake pipeline based on input snakefile. Expect many limitations.\"", + "keywords": ["snakemake", "workflow", "workflow_mode"], + "tools": [ + { + "snakemake": { + "description": "A popular workflow management system aiming at full in-silico reproducibility.", + "homepage": "https://snakemake.readthedocs.io/en/stable/", + "documentation": "https://snakemake.readthedocs.io/en/stable/", + "tool_dev_url": "https://github.com/snakemake/snakemake", + "doi": "10.1093/bioinformatics/bty350", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "inputs": { + "type": "file", + "description": "Any input file required by Snakemake", + "pattern": "*", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Meta information for Snakefile\ne.g. [ id: 'snakefile' ]\n" + } + }, + { + "snakefile": { + "type": "file", + "description": "Snakefile to use with Snakemake. This is required for proper execution of Snakemake.\n", + "ontologies": [] + } + } + ] + ], + "output": { + "outputs": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "[!.snakemake|versions.yml]**": { + "type": "file", + "description": "Any file generated by Snakemake, excluding the inputs, hidden files and Snakemake log directory (.snakemake). This is set to optional because Snakemake can be used to run arbitrary commands, and we cannot know what files will be generated.\n", + "ontologies": [] + } + } + ] + ], + "snakemake_dir": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + ".snakemake": { + "type": "directory", + "description": "Hidden directory containing Snakemake execution logs and metadata", + "pattern": ".snakemake", + "ontologies": [] + } + } + ] + ], + "versions_snakemake": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "snakemake": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "snakemake --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "snakemake": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "snakemake --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@adamrtalbot"], + "maintainers": ["@adamrtalbot"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + }, + { + "name": "snapaligner_align", + "path": "modules/nf-core/snapaligner/align/meta.yml", + "type": "module", + "meta": { + "name": "snapaligner_align", + "description": "Performs fastq alignment to a fasta reference using SNAP", + "keywords": ["alignment", "map", "fastq", "bam", "sam"], + "tools": [ + { + "snapaligner": { + "description": "Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data", + "homepage": "http://snap.cs.berkeley.edu", + "documentation": "https://1drv.ms/b/s!AhuEg_0yZD86hcpblUt-muHKYsG8fA?e=R8ogug", + "tool_dev_url": "https://github.com/amplab/snap", + "doi": "10.1101/2021.11.23.469039", + "licence": ["Apache v2"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input fastq files of size 2 for paired fastq or 1 for bam or single fastq", + "pattern": "*.{fastq.gz,fq.gz,fastq,fq,bam}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "index": { + "type": "file", + "description": "List of SNAP genome index files", + "pattern": "{Genome,GenomeIndex,GenomeIndexHash,OverflowTable}", + "ontologies": [] + } + } + ] + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Aligned BAM file", + "pattern": "*.{bam}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + } + ] + ], + "bai": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bai": { + "type": "file", + "description": "Optional aligned BAM file index", + "pattern": "*.{bai}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + } + ] + ], + "versions_snapaligner": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "snap-aligner": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "snap-aligner 2>&1 | sed 's/^.*version //;s/.\\$//;q'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "snap-aligner": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "snap-aligner 2>&1 | sed 's/^.*version //;s/.\\$//;q'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@matthdsm"], + "maintainers": ["@matthdsm", "@delfiterradas", "@sofiromano"] }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,sam}", - "ontologies": [] - } - } - ], - { - "sort_order": { - "type": "string", - "description": "Picard sort order type", - "pattern": "unsorted|queryname|coordinate|duplicate|unknown" - } - } - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "Sorted BAM/CRAM/SAM file", - "pattern": "*.{bam}", - "ontologies": [] - } - } - ] - ], - "versions_picard": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "picard": { - "type": "string", - "description": "The tool name" - } - }, - { - "picard SortSam --version 2>&1 | sed -n 's/.*Version://p'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "picard": { - "type": "string", - "description": "The tool name" - } - }, - { - "picard SortSam --version 2>&1 | sed -n 's/.*Version://p'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } + "pipelines": [ + { + "name": "sammyseq", + "version": "dev" + } ] - ] }, - "authors": [ - "@jfy133" - ], - "maintainers": [ - "@jfy133" - ] - }, - "pipelines": [ { - "name": "pathogensurveillance", - "version": "1.1.0" + "name": "snapaligner_index", + "path": "modules/nf-core/snapaligner/index/meta.yml", + "type": "module", + "meta": { + "name": "snapaligner_index", + "description": "Create a SNAP index for reference genome", + "keywords": ["index", "fasta", "genome", "reference"], + "tools": [ + { + "snapaligner": { + "description": "Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data", + "homepage": "http://snap.cs.berkeley.edu", + "documentation": "https://1drv.ms/b/s!AhuEg_0yZD86hcpblUt-muHKYsG8fA?e=R8ogug", + "tool_dev_url": "https://github.com/amplab/snap", + "doi": "10.1101/2021.11.23.469039", + "licence": ["Apache v2"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input genome fasta file", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + }, + { + "altcontigfile": { + "type": "file", + "description": "Optional file with a list of alt contig names, one per line.", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + }, + { + "nonaltcontigfile": { + "type": "file", + "description": "Optional file that contains a list of contigs (one per line) that will not be marked ALT regardless of size.", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + }, + { + "altliftoverfile": { + "type": "file", + "description": "Optional file containing ALT-to-REF mappings (SAM format). e.g., hs38DH.fa.alt from bwa-kit.", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + ], + "output": { + "index": [ + [ + { + "meta": { + "type": "file", + "description": "SNAP genome index files", + "pattern": "{Genome,GenomeIndex,GenomeIndexHash,OverflowTable}", + "ontologies": [] + } + }, + { + "snap/*": { + "type": "file", + "description": "SNAP genome index files", + "pattern": "{Genome,GenomeIndex,GenomeIndexHash,OverflowTable}", + "ontologies": [] + } + } + ] + ], + "versions_snapaligner": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "snap-aligner": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "snap-aligner 2>&1 | sed 's/^.*version //;s/.\\$//;q'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "snap-aligner": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "snap-aligner 2>&1 | sed 's/^.*version //;s/.\\$//;q'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@matthdsm"], + "maintainers": ["@matthdsm"] + } }, { - "name": "ssds", - "version": "dev" - } - ] - }, - { - "name": "picard_sortvcf", - "path": "modules/nf-core/picard/sortvcf/meta.yml", - "type": "module", - "meta": { - "name": "picard_sortvcf", - "description": "Sorts vcf files", - "keywords": [ - "sort", - "vcf", - "sortvcf" - ], - "tools": [ - { - "picard": { - "description": "Java tools for working with NGS data in the BAM/CRAM/SAM and VCF format", - "homepage": "https://broadinstitute.github.io/picard/", - "documentation": "https://broadinstitute.github.io/picard/command-line-overview.html#SortVcf", - "licence": [ - "MIT" - ], - "identifier": "biotools:picard_tools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF file", - "pattern": "*.{vcf,vcf.gz}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome fasta file", - "pattern": "*.{fasta,fa}", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "dict": { - "type": "file", - "description": "Reference genome dictionary file", - "pattern": "*.{dict}", - "ontologies": [] - } + "name": "sniffles", + "path": "modules/nf-core/sniffles/meta.yml", + "type": "module", + "meta": { + "name": "sniffles", + "description": "structural-variant calling with sniffles", + "keywords": ["sniffles", "structural-variant calling", "long-read"], + "tools": [ + { + "sniffles": { + "description": "a fast structural variant caller for long-read sequencing", + "homepage": "https://github.com/fritzsedlazeck/Sniffles", + "documentation": "https://github.com/fritzsedlazeck/Sniffles#readme", + "tool_dev_url": "https://github.com/fritzsedlazeck/Sniffles", + "licence": ["MIT"], + "identifier": "biotools:sniffles" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "input": { + "type": "file", + "description": "A single .bam/.cram file - OR - one or more .snf files - OR - a single .tsv file containing a list of .snf files and optional sample ids as input", + "pattern": "*.{bam,cram,snf,tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, + { + "index": { + "type": "file", + "description": "Index of BAM/CAM file", + "pattern": "*.{bai,crai}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'fasta' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference database in FASTA format\n", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing tandem repeat information\ne.g. [ id:'hg38' ]\n" + } + }, + { + "tandem_file": { + "type": "file", + "description": "Tandem repeat file", + "pattern": "*.bed", + "ontologies": [] + } + } + ], + { + "vcf_output": { + "type": "file", + "description": "VCF output file", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + }, + { + "snf_output": { + "type": "file", + "description": "SNF output file", + "ontologies": [] + } + } + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "Compressed VCF file", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.vcf.gz.tbi": { + "type": "file", + "description": "Compressed VCF file index", + "pattern": "*.tbi", + "ontologies": [] + } + } + ] + ], + "snf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.snf": { + "type": "file", + "description": "SNF file", + "pattern": "*.snf", + "ontologies": [] + } + } + ] + ], + "versions_sniffles": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "sniffles": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "sniffles --version | sed 's/.* //g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "sniffles": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "sniffles --version | sed 's/.* //g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@christopher-hakkaart", "@yuukiiwa"], + "maintainers": ["@christopher-hakkaart", "@yuukiiwa", "@fellen31"] } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_sorted.vcf.gz": { - "type": "file", - "description": "Sorted VCF file", - "pattern": "*.{vcf}", - "ontologies": [] - } - } - ] - ], - "versions_picard": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "picard": { - "type": "string", - "description": "The tool name" - } - }, - { - "picard SortVcf --version 2>&1 | sed -n 's/.*Version://p'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "picard": { - "type": "string", - "description": "The tool name" - } - }, - { - "picard SortVcf --version 2>&1 | sed -n 's/.*Version://p'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@ramprasadn" - ], - "maintainers": [ - "@ramprasadn" - ] - }, - "pipelines": [ - { - "name": "raredisease", - "version": "3.0.0" - } - ] - }, - { - "name": "picard_splitsambynumberofreads", - "path": "modules/nf-core/picard/splitsambynumberofreads/meta.yml", - "type": "module", - "meta": { - "name": "picard_splitsambynumberofreads", - "description": "Splits a SAM/BAM/CRAM file to multiple files. This tool splits the input query-grouped SAM/BAM/CRAM file into multiple files while maintaining the sort order. This can be used to split a large unmapped input in order to parallelize alignment.", - "keywords": [ - "split", - "parallel", - "bam", - "subset", - "downsample", - "sam", - "cram" - ], - "tools": [ - { - "picard": { - "description": "Splits a SAM or BAM file to multiple BAMs by number of reads.", - "homepage": "https://gatk.broadinstitute.org/hc/en-us/articles/360037064232-SplitSamByNumberOfReads-Picard", - "documentation": "https://gatk.broadinstitute.org/hc/en-us/articles/360037064232-SplitSamByNumberOfReads-Picard", - "tool_dev_url": "https://github.com/broadinstitute/picard", - "licence": [ - "MIT" - ], - "identifier": "biotools:picard_tools" + }, + { + "name": "snippy_core", + "path": "modules/nf-core/snippy/core/meta.yml", + "type": "module", + "meta": { + "name": "snippy_core", + "description": "Core-SNP alignment from Snippy outputs", + "keywords": ["core", "alignment", "bacteria", "snippy"], + "tools": [ + { + "snippy": { + "description": "Rapid bacterial SNP calling and core genome alignments", + "homepage": "https://github.com/tseemann/snippy", + "documentation": "https://github.com/tseemann/snippy", + "tool_dev_url": "https://github.com/tseemann/snippy", + "licence": ["GPL v2"], + "identifier": "biotools:snippy" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "Annotated variants in VCF format", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + }, + { + "aligned_fa": { + "type": "file", + "description": "A version of the reference but with - at position with depth=0 and N for 0 < depth < --mincov (does not have variants)", + "pattern": "*.aligned.fa.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ], + { + "reference": { + "type": "file", + "description": "Reference genome in GenBank (preferred) or FASTA format", + "pattern": "*.{gbk,gbk.gz,gbff,gbff.gz,fa,fa.gz}", + "ontologies": [] + } + } + ], + "output": { + "aln": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.aln": { + "type": "file", + "description": "A core SNP alignment in FASTA format", + "pattern": "*.aln", + "ontologies": [] + } + } + ] + ], + "full_aln": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.full.aln": { + "type": "file", + "description": "A whole genome SNP alignment (includes invariant sites)", + "pattern": "*.full.aln", + "ontologies": [] + } + } + ] + ], + "tab": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.tab": { + "type": "file", + "description": "Tab-separated columnar list of core SNP sites with alleles but NO annotations", + "pattern": "*.tab", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.vcf": { + "type": "file", + "description": "Multi-sample VCF file with genotype GT tags for all discovered alleles", + "pattern": "*.vcf", + "ontologies": [] + } + } + ] + ], + "txt": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.txt": { + "type": "file", + "description": "Tab-separated columnar list of alignment/core-size statistics", + "pattern": "*.txt", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@rpetit3", "@delfiterradas", "@sofiromano"], + "maintainers": ["@rpetit3"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/SAM/CRAM file", - "pattern": "*.{bam,sam,cram}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - }, - { - "edam": "http://edamontology.org/format_2573" - }, - { - "edam": "http://edamontology.org/format_3462" - } - ] - } + }, + { + "name": "snippy_run", + "path": "modules/nf-core/snippy/run/meta.yml", + "type": "module", + "meta": { + "name": "snippy_run", + "description": "Rapid haploid variant calling", + "keywords": ["variant", "fastq", "bacteria"], + "tools": [ + { + "snippy": { + "description": "Rapid bacterial SNP calling and core genome alignments", + "homepage": "https://github.com/tseemann/snippy", + "documentation": "https://github.com/tseemann/snippy", + "tool_dev_url": "https://github.com/tseemann/snippy", + "licence": ["GPL v2"], + "identifier": "biotools:snippy" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", + "pattern": "*.{fq,fastq,fq.gz,fastq.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ], + { + "reference": { + "type": "file", + "description": "Reference genome in FASTA format", + "pattern": "*.{fasta,fna,fa}", + "ontologies": [] + } + } + ], + "output": { + "tab": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/${prefix}.tab": { + "type": "file", + "description": "A simple tab-separated summary of all the variants", + "pattern": "*.tab", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "csv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/${prefix}.csv": { + "type": "file", + "description": "A comma-separated version of the .tab file", + "pattern": "*.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "html": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/${prefix}.html": { + "type": "file", + "description": "A HTML version of the .tab file", + "pattern": "*.html", + "ontologies": [] + } + } + ] + ], + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/${prefix}.vcf": { + "type": "file", + "description": "The final annotated variants in VCF format", + "pattern": "*.vcf", + "ontologies": [] + } + } + ] + ], + "bed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/${prefix}.bed": { + "type": "file", + "description": "The variants in BED format", + "pattern": "*.bed", + "ontologies": [] + } + } + ] + ], + "gff": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/${prefix}.gff": { + "type": "file", + "description": "The variants in GFF3 format", + "pattern": "*.gff", + "ontologies": [] + } + } + ] + ], + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/${prefix}.bam": { + "type": "file", + "description": "The alignments in BAM format. Includes unmapped, multimapping reads. Excludes duplicates.", + "pattern": "*.bam", + "ontologies": [] + } + } + ] + ], + "bai": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/${prefix}.bam.bai": { + "type": "file", + "description": "Index for the .bam file", + "pattern": "*.bam.bai", + "ontologies": [] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/${prefix}.log": { + "type": "file", + "description": "A log file with the commands run and their outputs", + "pattern": "*.log", + "ontologies": [] + } + } + ] + ], + "aligned_fa": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/${prefix}.aligned.fa": { + "type": "file", + "description": "A version of the reference but with - at position with depth=0 and N for 0 < depth < --mincov (does not have variants)", + "pattern": "*.aligned.fa", + "ontologies": [] + } + } + ] + ], + "consensus_fa": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/${prefix}.consensus.fa": { + "type": "file", + "description": "A version of the reference genome with all variants instantiated", + "pattern": "*.consensus.fa", + "ontologies": [] + } + } + ] + ], + "consensus_subs_fa": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/${prefix}.consensus.subs.fa": { + "type": "file", + "description": "A version of the reference genome with only substitution variants instantiated", + "pattern": "*.consensus.subs.fa", + "ontologies": [] + } + } + ] + ], + "raw_vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/${prefix}.raw.vcf": { + "type": "file", + "description": "The unfiltered variant calls from Freebayes", + "pattern": "*.raw.vcf", + "ontologies": [] + } + } + ] + ], + "filt_vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/${prefix}.filt.vcf": { + "type": "file", + "description": "The filtered variant calls from Freebayes", + "pattern": "*.filt.vcf", + "ontologies": [] + } + } + ] + ], + "vcf_gz": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/${prefix}.vcf.gz": { + "type": "file", + "description": "Compressed .vcf file via BGZIP", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "vcf_csi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/${prefix}.vcf.gz.csi": { + "type": "file", + "description": "Index for the .vcf.gz via bcftools index", + "pattern": "*.vcf.gz.csi", + "ontologies": [] + } + } + ] + ], + "txt": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/${prefix}.txt": { + "type": "file", + "description": "Tab-separated columnar list of statistics", + "pattern": "*.txt", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@rpetit3", "@delfiterradas"], + "maintainers": ["@rpetit3"] } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference fasta (optional - only required for CRAM input)", - "pattern": "*.{fasta,fa}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } + }, + { + "name": "snpdists", + "path": "modules/nf-core/snpdists/meta.yml", + "type": "module", + "meta": { + "name": "snpdists", + "description": "Pairwise SNP distance matrix from a FASTA sequence alignment", + "keywords": ["snp", "dist", "distance", "matrix"], + "tools": [ + { + "snpdists": { + "description": "Convert a FASTA alignment to SNP distance matrix", + "homepage": "https://github.com/tseemann/snp-dists", + "documentation": "https://github.com/tseemann/snp-dists", + "tool_dev_url": "https://github.com/tseemann/snp-dists", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "alignment": { + "type": "file", + "description": "The input FASTA sequence alignment file", + "pattern": "*.{fasta,fasta.gz}", + "ontologies": [] + } + } + ] + ], + "output": { + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "The output TSV file containing SNP distance matrix", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_snpdists": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "snpdists": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "snp-dists -v 2>&1 | sed \"s/snp-dists //;\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "snpdists": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "snp-dists -v 2>&1 | sed \"s/snp-dists //;\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@abhi18av"], + "maintainers": ["@abhi18av"] }, - { - "fai": { - "type": "file", - "description": "FAI file (optional - only required for CRAM input)", - "pattern": "*.{fai}" - } - } - ], - { - "split_to_N_reads": { - "type": "integer", - "description": "Split to have approximately N reads per output file, e.g. `4000000`.\nThe actual number of reads per output file will vary by no more than the number of output files * (the maximum number of reads with the same queryname - 1).\nIncompatible with `split_to_N_files`\n" - } - }, - { - "split_to_N_files": { - "type": "integer", - "description": "Split to N files, e.g. `3`.\n`Incompatible with split_to_N_files`\n" - } - }, - { - "arguments_file": { - "type": "file", - "description": "optional Picard arguments file", - "pattern": "*.{txt,list,args,arguments}" - } - } - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "picardsplit/*.{bam,sam,cram}": { - "type": "file", - "description": "Split BAM files", - "pattern": "*.{bam,sam,cram}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - } - ] - ], - "versions_picard": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "picard": { - "type": "string", - "description": "The tool name" - } - }, - { - "picard SplitSamByNumberOfReads --version 2>&1 | sed -n 's/.*Version://p'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "picard": { - "type": "string", - "description": "The tool name" - } - }, - { - "picard SplitSamByNumberOfReads --version 2>&1 | sed -n 's/.*Version://p'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } + "pipelines": [ + { + "name": "tbanalyzer", + "version": "dev" + } ] - ] - }, - "authors": [ - "@Y-Pei" - ], - "maintainers": [ - "@Y-Pei" - ] - } - }, - { - "name": "picrust2_pipeline", - "path": "modules/nf-core/picrust2/pipeline/meta.yml", - "type": "module", - "meta": { - "name": "picrust2_pipeline", - "description": "Predict metagenome functional content from marker gene sequences and OTU/ASV abundance data", - "keywords": [ - "metagenomics", - "functional prediction", - "16S", - "microbiome" - ], - "tools": [ - { - "picrust2": { - "description": "PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States", - "homepage": "https://github.com/picrust/picrust2/wiki", - "documentation": "https://github.com/picrust/picrust2/wiki", - "tool_dev_url": "https://github.com/picrust/picrust2", - "doi": "10.1038/s41587-020-0548-6", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:picrust2" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "sequences": { - "type": "file", - "description": "FASTA file containing study sequences (e.g., 16S rRNA sequences)", - "pattern": "*.{fasta,fa,fna}", - "ontologies": [] - } + }, + { + "name": "snpeff_download", + "path": "modules/nf-core/snpeff/download/meta.yml", + "type": "module", + 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"modules/nf-core/snpeff/snpeff/meta.yml", + "type": "module", + "meta": { + "name": "snpeff_snpeff", + "description": "Genetic variant annotation and functional effect prediction toolbox", + "keywords": ["annotation", "effect prediction", "snpeff", "variant", "vcf"], + "tools": [ + { + "snpeff": { + "description": "SnpEff is a variant annotation and effect prediction tool.\nIt annotates and predicts the effects of genetic variants on genes and proteins (such as amino acid changes).\n", + "homepage": "https://pcingola.github.io/SnpEff/", + "documentation": "https://pcingola.github.io/SnpEff/se_introduction/", + "licence": ["MIT"], + "identifier": "biotools:snpeff" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "vcf to annotate\n", + "ontologies": [] + } + } + ], + { + "db": { + "type": "string", + "description": 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variants affecting each transcript and gene", + "pattern": "*.genes.txt", + "ontologies": [] + } + } + ] + ], + "versions_snpeff": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "snpeff": { + "type": "string", + "description": "The tool name" + } + }, + { + "snpEff -version 2>&1 | cut -f 2 -d '\t'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "multiqc_files": [ + [ + { + "meta": { + "type": "file", + "description": "annotated vcf\n", + "pattern": "*.ann.vcf", + "ontologies": [] + } + }, + { + "${task.process}": { + "type": "string", + "description": "The process" + } + }, + { + "snpeff": { + "type": "string", + "description": "The tool name" + } + }, + { + "*.csv": { + "type": "file", + "description": "snpEff report csv file", + "pattern": "*.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" 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Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF file to annotate", + "pattern": "*.{vcf,vcf.gz}", + "ontologies": [] + } + }, + { + "vcf_tbi": { + "type": "file", + "description": "Tabix index for input VCF (optional)", + "pattern": "*.tbi", + "ontologies": [] + } + } + ], + [ + { + "db_vcf": { + "type": "file", + "description": "VCF database file(s) for annotation.\nCan provide multiple databases for multi-database annotation.\n", + "pattern": "*.{vcf,vcf.gz}", + "ontologies": [] + } + }, + { + "db_vcf_tbi": { + "type": "file", + "description": "Tabix index for database VCF file(s)", + "pattern": "*.tbi", + "ontologies": [] + } + }, + { + "db_vardb": { + "type": "directory", + "description": "Pre-built .snpsift.vardb directory (used instead of db_vcf if provided)", + "pattern": "*.snpsift.vardb" + } + }, + { + "db_fields": { + "type": "list", + "description": "INFO field names to annotate with.\nCan be a list or a single string.\n" + } + }, + { + "db_prefixes": { + "type": "string", + "description": "Prefix to add to annotated field names" + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "Annotated VCF file", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "*.vcf.gz.tbi": { + "type": "file", + "description": "Tabix index for annotated VCF", + "pattern": "*.vcf.gz.tbi", + "ontologies": [] + } + } + ] + ], + "versions_snpsift": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "snpsift": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "SnpSift -version 2>&1 | grep -oE '[0-9]+\\.[0-9]+[a-z]?'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "snpsift": { + "type": "string", + "description": "The tool name" + } + }, + { + "SnpSift -version 2>&1 | grep -oE '[0-9]+\\.[0-9]+[a-z]?'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@friederike-hanssen"], + "maintainers": ["@friederike-hanssen"] + }, + "pipelines": [ + { + "name": "sarek", + "version": "3.8.1" + } + ] }, { - "name": "magmap", - "version": "1.0.0" + "name": "snpsift_annmemcreate", + "path": "modules/nf-core/snpsift/annmemcreate/meta.yml", + "type": "module", + "meta": { + "name": "snpsift_annmemcreate", + "description": "Create memory-optimized SnpSift vardb databases from VCF files for use with SnpSift annMem annotation.\nConverts VCF files (e.g. ClinVar, dbSNP, Cosmic) into indexed dataframes for fast lookup.\n", + "keywords": ["vcf", "annotation", "snpsift", "variant", "database"], + "tools": [ + { + "snpsift": { + "description": "Genetic variant annotations and functional effect prediction toolbox", + "homepage": "https://pcingola.github.io/SnpEff/snpsift/annotate_mem/", + "documentation": "https://pcingola.github.io/SnpEff/snpsift/annotate_mem/", + "tool_dev_url": "https://github.com/pcingola/SnpSift", + "doi": "10.3389/fgene.2012.00035", + "licence": ["MIT"], + "identifier": "biotools:snpsift" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "db_vcf": { + "type": "file", + "description": "VCF file to build the database from", + "pattern": "*.{vcf,vcf.gz}", + "ontologies": [] + } + }, + { + "db_vcf_tbi": { + 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"name": "multiplesequencealign", - "version": "1.1.1" + "name": "somalier_relate", + "path": "modules/nf-core/somalier/relate/meta.yml", + "type": "module", + "meta": { + "name": "somalier_relate", + "description": "Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs", + "keywords": [ + "relatedness", + "QC", + "bam", + "cram", + "vcf", + "gvcf", + "ancestry", + "identity", + "kinship", + "informative sites", + "family" + ], + "tools": [ + { + "somalier": { + "description": "Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs", + "homepage": "https://github.com/brentp/somalier", + "documentation": "https://github.com/brentp/somalier/blob/master/README.md", + "tool_dev_url": "https://github.com/brentp/somalier", + "doi": "10.1186/s13073-020-00761-2", + "licence": ["MIT"], + "identifier": "biotools:somalier" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "extract": { + "type": "file", + "description": "extract file(s) from Somalier extract", + "pattern": "*.somalier", + "ontologies": [] + } + }, + { + "ped": { + "type": "file", + "description": "optional path to a ped or fam file indicating the expected relationships among samples", + "pattern": "*.{ped,fam}", + "ontologies": [] + } + } + ], + { + "sample_groups": { + "type": "file", + "description": "optional path to expected groups of samples such as tumor normal pairs specified as comma-separated groups per line", + "pattern": "*.{txt,csv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ], + "output": { + "html": [ + [ + { + "meta": { + "type": "file", + "description": "html file", + "pattern": "*.html", + "ontologies": [] + } + }, + { + "*.html": { + "type": "file", + "description": "html file", + "pattern": "*.html", + "ontologies": [] + } + } + ] + ], + "pairs_tsv": [ + [ + { + "meta": { + "type": "file", + "description": "html file", + "pattern": "*.html", + "ontologies": [] + } + }, + { + "*.pairs.tsv": { + "type": "file", + "description": "tsv file with output stats for pairs of samples", + "pattern": "*.pairs.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "samples_tsv": [ + [ + { + "meta": { + "type": "file", + "description": "html file", + "pattern": "*.html", + "ontologies": [] + } + }, + { + "*.samples.tsv": { + "type": "file", + "description": "tsv file with sample-level information", + "pattern": "*.samples.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_somalier": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "somalier": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "somalier 2>&1 | sed -n 's/.*version: \\([0-9.]*\\).*/\\1/p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "somalier": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "somalier 2>&1 | sed -n 's/.*version: \\([0-9.]*\\).*/\\1/p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@ashotmarg", "@nvnieuwk"], + "maintainers": ["@ashotmarg", "@nvnieuwk"] + } }, { - "name": "scnanoseq", - "version": "1.2.2" - } - ] - }, - { - "name": "pilon", - "path": "modules/nf-core/pilon/meta.yml", - "type": "module", - "meta": { - "name": "pilon", - "description": "Automatically improve draft assemblies and find variation among strains, including large event detection", - "keywords": [ - "polishing", - "assembly", - "variant calling" - ], - "tools": [ - { - "pilon": { - "description": "Pilon is an automated genome assembly improvement and variant detection tool.", - "homepage": "https://github.com/broadinstitute/pilon/wiki", - "documentation": "https://github.com/broadinstitute/pilon/wiki/Requirements-&-Usage", - "tool_dev_url": "https://github.com/broadinstitute/pilon", - "doi": "10.1371/journal.pone.0112963", - "licence": [ - "GPL-2.0-or-later" - ], - "identifier": "biotools:pilon" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information for the fasta\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA of the input genome", - "pattern": "*.{fasta}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information for the bam file\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file of reads aligned to the input genome", - "pattern": "*.{bam}", - "ontologies": [] - } - }, - { - "bai": { - "type": "file", - "description": "BAI file (BAM index) of BAM reads aligned to the input genome", - "pattern": "*.{bai}", - "ontologies": [] - } - } - ], - { - "pilon_mode": { - "type": "string", - "description": "Indicates the type of bam file used (frags for paired-end sequencing of DNA fragments, such as Illumina paired-end reads of fragment size <1000bp, jumps for paired sequencing data of larger insert size, such as Illumina mate pair libraries, typically of insert size >1000bp, unpaired for unpaired sequencing reads, bam will automatically classify the BAM as one of the three types above (version 1.17 and higher).", - "enum": [ - "frags", - "jumps", - "unpaired", - "bam" - ] - } - } - ], - "output": { - "improved_assembly": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.fasta": { - "type": "file", - "description": "fasta file, improved assembly", - "pattern": "*.{fasta}", - "ontologies": [] - } - } - ] - ], - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.vcf": { - "type": "file", - "description": "Pilon variant output", - "pattern": "*.{vcf}", - "ontologies": [] - } - } - ] - ], - "change_record": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.change": { - "type": "file", - "description": "file containing a space-delimited record of every change made in the assembly as instructed by the --fix option", - "pattern": "*.{change}", - "ontologies": [] - } - } - ] - ], - "tracks_bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bed": { - "type": "file", - "description": "files that may be viewed in genome browsers such as IGV, GenomeView, and other applications that support these formats", - "pattern": "*.{bed}", - "ontologies": [] - } - } - ] - ], - "tracks_wig": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.wig": { - "type": "file", - "description": "files that may be viewed in genome browsers such as IGV, GenomeView, and other applications that support these formats", - "pattern": "*.{wig}", - "ontologies": [] - } - } - ] - ], - "versions_pilon": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pilon": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pilon --version | sed 's/^.*version //; s/ .*\\$//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pilon": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pilon --version | sed 's/^.*version //; s/ .*\\$//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@scorreard" - ], - "maintainers": [ - "@scorreard" - ] - }, - "pipelines": [ - { - "name": "genomeassembler", - "version": "1.1.0" - } - ] - }, - { - "name": "pindel_pindel", - "path": "modules/nf-core/pindel/pindel/meta.yml", - "type": "module", - "meta": { - "name": "pindel_pindel", - "description": "Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data", - "keywords": [ - "deletions", - "insertions", - "tandem duplications" - ], - "tools": [ - { - "pindel": { - "description": "Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data", - "homepage": "https://gmt.genome.wustl.edu/packages/pindel/", - "documentation": "https://gmt.genome.wustl.edu/packages/pindel/user-manual.html", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:pindel" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information, insert_size is either determined using Picard/CollectInsertSizeMetrics\nor a sensible default - setting ext.args2 to either in modules.conf\ne.g. [ id:'test', single_end:false, insert_size:500 ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file", - "pattern": "*.bam", - "ontologies": [] - } - }, - { - "bai": { - "type": "file", - "description": "BAM index file", - "pattern": "*.bai", - "ontologies": [] - } - } - ], - { - "fasta": { - "type": "file", - "description": "Input reference genome fasta file", - "ontologies": [] - } - }, - { - "fai": { - "type": "file", - "description": "Input reference genome fasta index file", - "ontologies": [] - } - }, - { - "bed": { - "type": "file", - "description": "BED file containing regions of interest", - "ontologies": [] - } - } - ], - "output": { - "bp": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_BP": { - "type": "file", - "description": "File containing breakpoints", - "pattern": "*_{BP}", - "ontologies": [] - } - } - ] - ], - "cem": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_CloseEndMapped": { - "type": "file", - "description": "File containing close end reads", - "pattern": "*_{CloseEndMapped}", - "ontologies": [] - } - } - ] - ], - "del": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_D": { - "type": "file", - "description": "File containing deletions", - "pattern": "*_{D}", - "ontologies": [] - } - } - ] - ], - "dd": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_DD": { - "type": "file", - "description": "File containing dispersed duplications", - "pattern": "*_{DD}", - "ontologies": [] - } - } - ] - ], - "int_final": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_INT_final": { - "type": "file", - "description": "int file", - "pattern": "*_INT_final", - "ontologies": [] - } - } - ] - ], - "inv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_INV": { - "type": "file", - "description": "File containing inversions", - "pattern": "*_{INV}", - "ontologies": [] - } - } - ] - ], - "li": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_LI": { - "type": "file", - "description": "File containing long insertions", - "pattern": "*_{LI}", - "ontologies": [] - } - } - ] - ], - "rp": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_RP": { - "type": "file", - "description": "File containing read-pair evidence", - "pattern": "*_{RP}", - "ontologies": [] - } - } - ] - ], - "si": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_SI": { - "type": "file", - "description": "File containing short insertions", - "pattern": "*_{SI}", - "ontologies": [] - } - } - ] - ], - "td": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_TD": { - "type": "file", - "description": "File containing tandem duplications", - "pattern": "*_{TD}", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@marrip" - ], - "maintainers": [ - "@marrip" - ] - } - }, - { - "name": "pints_caller", - "path": "modules/nf-core/pints/caller/meta.yml", - "type": "module", - "meta": { - "name": "pints_caller", - "description": "Main caller script for peak calling", - "keywords": [ - "peak-calling", - "CoPRO", - "GRO-cap", - "PRO-cap", - "CAGE", - "NETCAGE", - "RAMPAGE", - "csRNA-seq", - "STRIPE-seq", - "PRO-seq", - "GRO-seq" - ], - "tools": [ - { - "pints": { - "description": "Peak Identifier for Nascent Transcripts Starts (PINTS)", - "homepage": "https://pints.yulab.org/", - "documentation": "https://github.com/hyulab/PINTS/blob/main/README.md", - "tool_dev_url": "https://github.com/hyulab/PINTS", - "doi": "10.1038/s41587-022-01211-7", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:pyPINTS" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bams": { - "type": "file", - "description": "One or more BAM files", - "pattern": "*.{bam}", - "ontologies": [] - } - }, - { - "bais": { - "type": "file", - "description": "Corresponding BAM file indexes", - "pattern": "*.bam.bai", - "ontologies": [] - } - } - ], - { - "assay_type": { - "type": "string", - "description": "Assay type" - } - } - ], - "output": { - "divergent_TREs": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_divergent_peaks.bed": { - "type": "file", - "description": "Divergent TREs", - "pattern": "*_divergent_peaks.bed", - "optional": true, - "ontologies": [] - } - } - ] - ], - "bidirectional_TREs": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_bidirectional_peaks.bed": { - "type": "file", - "description": "Divergent TREs and convergent TREs", - "pattern": "*_bidirectional_peaks.bed", - "optional": true, - "ontologies": [] - } - } - ] - ], - "unidirectional_TREs": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_unidirectional_peaks.bed": { - "type": "file", - "description": "Unidirectional TREs, maybe lncRNAs transcribed from enhancers (e-lncRNAs)", - "pattern": "*_unidirectional_peaks.bed", - "optional": true, - "ontologies": [] - } - } - ] - ], - "peakcalling_log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "peakcalling_*.log": { - "type": "file", - "description": "Peakcalling log for debugging purposes", - "pattern": "peakcalling_*.log", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@edmundmiller" - ], - "maintainers": [ - "@edmundmiller" - ] - }, - "pipelines": [ - { - "name": "nascent", - "version": "2.3.0" - } - ] - }, - { - "name": "pirate", - "path": "modules/nf-core/pirate/meta.yml", - "type": "module", - "meta": { - "name": "pirate", - "description": "Pangenome toolbox for bacterial genomes", - "keywords": [ - "gff", - "pan-genome", - "alignment" - ], - "tools": [ - { - "pirate": { - "description": "Pangenome analysis and threshold evaluation toolbox", - "homepage": "https://github.com/SionBayliss/PIRATE", - "documentation": "https://github.com/SionBayliss/PIRATE/wiki", - "tool_dev_url": "https://github.com/SionBayliss/PIRATE", - "doi": "10.1093/gigascience/giz119", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:PIRATE" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "gff": { - "type": "file", - "description": "A set of GFF3 formatted files", - "pattern": "*.{gff}", - "ontologies": [] - } - } - ] - ], - "output": { - "results": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}_results/*": { - "type": "directory", - "description": "Directory containing PIRATE result files", - "pattern": "*/*" - } - } - ] - ], - "aln": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}_results/core_alignment.fasta": { - "type": "file", - "description": "Core-genome alignment produced by PIRATE (Optional)", - "pattern": "*.{fasta}", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@rpetit3", - "@zachary-foster" - ], - "maintainers": [ - "@rpetit3" - ] - }, - "pipelines": [ - { - "name": "pathogensurveillance", - "version": "1.1.0" - } - ] - }, - { - "name": "plasmidfinder", - "path": "modules/nf-core/plasmidfinder/meta.yml", - "type": "module", - "meta": { - "name": "plasmidfinder", - "description": "Identify plasmids in bacterial sequences and assemblies", - "keywords": [ - "fasta", - "fastq", - "plasmid" - ], - "tools": [ - { - "plasmidfinder": { - "description": "PlasmidFinder allows identification of plasmids in total or partial sequenced isolates of bacteria.", - "homepage": "https://cge.cbs.dtu.dk/services/PlasmidFinder/", - "documentation": "https://bitbucket.org/genomicepidemiology/plasmidfinder", - "tool_dev_url": "https://bitbucket.org/genomicepidemiology/plasmidfinder", - "doi": "10.1128/AAC.02412-14", - "licence": [ - "Apache-2.0" - ], - "identifier": "biotools:PlasmidFinder" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input FASTA or FASTQ formatted genome sequences", - "pattern": "*.{fastq.gz,fq.gz,fastq.gz,fna.gz,fa.gz}", - "ontologies": [] - } - } - ] - ], - "output": { - "json": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.json": { - "type": "file", - "description": "The results from analysis in JSON format", - "pattern": "*.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "txt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.txt": { - "type": "file", - "description": "The summary of results from analysis", - "pattern": "*.txt", - "ontologies": [] - } - } - ] - ], - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "The results from analysis in TSV format", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "genome_seq": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*-hit_in_genome_seq.fsa": { - "type": "file", - "description": "FASTA of sequences in the input with a hit", - "pattern": "*-hit_in_genome_seq.fsa", - "ontologies": [] - } - } - ] - ], - "plasmid_seq": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*-plasmid_seqs.fsa": { - "type": "file", - "description": "FASTA of plasmid sequences with a hit against the input", - "pattern": "*-plasmid_seqs.fsa", - "ontologies": [] - } - } - ] - ], - "versions_plasmidfinder": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "plasmidfinder": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "2.1.6": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "plasmidfinder": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "2.1.6": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@eit-maxlcummins", - "@rpetit3" - ], - "maintainers": [ - "@rpetit3" - ] - } - }, - { - "name": "plasmidid", - "path": "modules/nf-core/plasmidid/meta.yml", - "type": "module", - "meta": { - "name": "plasmidid", - "description": "assembles bacterial plasmids", - "keywords": [ - "assembly", - "plasmid", - "bacterial" - ], - "tools": [ - { - "plasmidid": { - "description": "Pipeline for plasmid identification and reconstruction", - "homepage": "https://github.com/BU-ISCIII/plasmidID/wiki", - "documentation": "https://github.com/BU-ISCIII/plasmidID#readme", - "tool_dev_url": "https://github.com/BU-ISCIII/plasmidID", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:plasmidid" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + "name": "sortmerna", + "path": "modules/nf-core/sortmerna/meta.yml", + "type": "module", + "meta": { + "name": "sortmerna", + "description": "Local sequence alignment tool for filtering, mapping and clustering.", + "keywords": ["filtering", "mapping", "clustering", "rRNA", "ribosomal RNA"], + "tools": [ + { + "SortMeRNA": { + "description": "The core algorithm is based on approximate seeds and allows for sensitive analysis of NGS reads. The main application of SortMeRNA is filtering rRNA from metatranscriptomic data. SortMeRNA takes as input files of reads (fasta, fastq, fasta.gz, fastq.gz) and one or multiple rRNA database file(s), and sorts apart aligned and rejected reads into two files. Additional applications include clustering and taxonomy assignation available through QIIME v1.9.1. SortMeRNA works with Illumina, Ion Torrent and PacBio data, and can produce SAM and BLAST-like alignments.", + "homepage": "https://hpc.nih.gov/apps/sortmeRNA.html", + "documentation": "https://github.com/biocore/sortmerna/wiki/", + "licence": ["GPL-3.0-or-later"], + "identifier": "biotools:sortmerna" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "fastas": { + "type": "file", + "description": "Path to reference file(s)\n", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing index information\ne.g. [ id:'test' ]\n" + } + }, + { + "index": { + "type": "directory", + "description": "Path to index directory of a previous sortmerna run\n" + } + } + ] + ], + "output": { + "reads": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ], or reference information from an\nindexing-only run\n" + } + }, + { + "*non_rRNA.fastq.gz": { + "type": "file", + "description": "The filtered fastq reads", + "pattern": "*fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ], or reference information from an\nindexing-only run\n" + } + }, + { + "*.log": { + "type": "file", + "description": "SortMeRNA log file", + "pattern": "*sortmerna.log", + "ontologies": [] + } + } + ] + ], + "index": [ + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "idx": { + "type": "directory", + "description": "Path to index directory generated by sortmern\n" + } + } + ] + ], + "versions_sortmerna": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "sortmerna": { + "type": "string", + "description": "The tool name" + } + }, + { + "sortmerna --version 2>&1 | grep -oE \"[0-9]+\\.[0-9]+\\.[0-9]+\" | head -1": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "sortmerna": { + "type": "string", + "description": "The tool name" + } + }, + { + "sortmerna --version 2>&1 | grep -oE \"[0-9]+\\.[0-9]+\\.[0-9]+\" | head -1": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@drpatelh", "@mashehu"], + "maintainers": ["@drpatelh", "@mashehu"] }, - 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{ - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/images/": { - "type": "directory", - "description": "Directory containing the images produced by plasmidid", - "pattern": "images" - } - } - ] - ], - "logs": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/logs/": { - "type": "directory", - "description": "Directory containing the logs produced by plasmidid", - "pattern": "logs" - } - } - ] - ], - "data": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/data/": { - "type": "directory", - "description": "Directory containing the data produced by plasmidid", - "pattern": "data" - } - } - ] - ], - "database": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/database/": { - "type": "directory", - "description": "Directory containing the database produced by plasmidid", - "pattern": "database" - } - } - ] - ], - "fasta_files": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/fasta_files/": { - "type": "directory", - "description": "Directory containing the fasta files produced by plasmidid", - "pattern": "fasta_files" - } - } - ] - ], - "kmer": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/kmer/": { - "type": "directory", - "description": "Directory containing the kmer files produced by plasmidid", - "pattern": "database" - } - } + "pipelines": [ + { + "name": "denovotranscript", + "version": "1.2.1" + }, + { + "name": "lncpipe", + "version": "dev" + }, + { + "name": "references", + "version": "0.1" + }, + { + "name": "riboseq", + "version": "1.2.0" + }, + { + "name": "rnaseq", + "version": "3.26.0" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@joseespinosa", - "@drpatelh" - ], - "maintainers": [ - "@joseespinosa", - "@drpatelh" - ] - }, - "pipelines": [ - { - "name": "viralrecon", - "version": "3.0.0" - } - ] - }, - { - "name": "plastid_make_wiggle", - "path": "modules/nf-core/plastid/make_wiggle/meta.yml", - "type": "module", - "meta": { - "name": "plastid_make_wiggle", - "description": "Create wiggle or bedGraph files from alignment files after applying a read mapping rule (e.g. to map ribosome-protected footprints at their P-sites), for visualization in a genome browser", - "keywords": [ - "genomics", - "riboseq", - "psite", - "wiggle", - "bedgraph" - ], - "tools": [ - { - "plastid": { - "description": "Nucleotide-resolution analysis of next-generation sequencing and genomics data", - "homepage": "https://github.com/joshuagryphon/plastid", - "documentation": "https://plastid.readthedocs.io/en/latest/", - "tool_dev_url": "https://github.com/joshuagryphon/plastid", - "doi": "10.1186/s12864-016-3278-x", - "licence": [ - "BSD-3-clause" - ], - "identifier": "biotools:plastid" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "Genome BAM file", - "pattern": "*.bam", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - }, - { - "bam_index": { - "type": "file", - "description": "Genome BAM index file", - "pattern": "*.bai", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3327" - } - ] - } - }, - { - "p_offsets": { - "type": "file", - "description": "Selected p-site offset for each read length (output from plastid_psite).\nRequired when mapping_rule is 'fiveprime_variable', otherwise pass empty list [].\n", - "pattern": "*_p_offsets.txt", - "ontologies": [] - } - } - ], - { - "mapping_rule": { - "type": "string", - "description": "Read mapping rule. Use 'fiveprime_variable' with p_offsets file to map reads to P-sites.\n", - "enum": [ - "fiveprime", - "threeprime", - "center", - "fiveprime_variable" - ] + }, + { + "name": "souporcell", + "path": "modules/nf-core/souporcell/meta.yml", + "type": "module", + "meta": { + "name": "souporcell", + "description": "souporcell is a method for clustering mixed-genotype scRNAseq experiments by individual.", + "keywords": ["clustering", "mixed-genotype", "genomics"], + "tools": [ + { + "souporcell": { + "description": "Clustering scRNAseq by genotypes.", + "homepage": "https://github.com/wheaton5/souporcell", + "documentation": "https://demultiplexing-doublet-detecting-docs.readthedocs.io/en/latest/Souporcell.html", + "tool_dev_url": "https://github.com/wheaton5/souporcell", + "doi": "10.1101/699637v1", + "licence": ["MIT"], + "identifier": "biotools:souporcell" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "bam": { + "type": "file", + "description": "A BAM file from cellranger containing single-cell RNA-seq alignments.", + "pattern": "*.bam", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + }, + { + "barcodes": { + "type": "file", + "description": "A barcode or whitelist TSV file from cellranger identifying individual cell barcodes.", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, + { + "clusters": { + "type": "integer", + "description": "Number of clusters." + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "A reference fasta file.", + "pattern": "*.fasta", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ] + ], + "output": { + "clusters": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*/clusters.tsv": { + "type": "file", + "description": "TSV file listing cell barcodes with singlet/doublet status, assigned cluster, and per-cluster log-loss metrics", + "pattern": "clusters.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*/cluster_genotypes.vcf": { + "type": "file", + "description": "A `vcf` with genotypes for each cluster for each variant in the input `vcf` from freebayes.", + "pattern": "cluster_genotypes.vcf", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + } + ] + } + } + ] + ], + "ambient_rna": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*/ambient_rna.txt": { + "type": "file", + "description": "Contains the ambient RNA percentage detected", + "pattern": "ambient_rna.txt", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@seohyonkim", "@LuisHeinzlmeier"], + "maintainers": ["@seohyonkim", "@LuisHeinzlmeier"] } - } - ], - "output": { - "tracks": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.{wig,bedgraph}": { - "type": "file", - "description": "wig/bedgraph tracks for forward and reverse strands", - "pattern": "*.{wig,bedgraph}", - "ontologies": [ + }, + { + "name": "soupx", + "path": "modules/nf-core/soupx/meta.yml", + "type": "module", + "meta": { + "name": "soupx", + "description": "Estimation and removal of cell free mRNA contamination in droplet based single cell RNA-seq data.\n\nThe filtered counts are preprocessed with Seurat (LogNormalize, PCA, kNN graph, clustering) to\nprovide cluster assignments to SoupX, which then estimates per-cluster contamination and adjusts\ncounts. The adjusted counts are written to the output H5AD as an `ambient` layer.\n", + "keywords": ["single-cell", "transcriptomics", "ambient"], + "tools": [ + { + "soupx": { + "description": "Estimation and removal of cell free mRNA contamination in droplet based single cell RNA-seq data", + "documentation": "https://rawcdn.githack.com/constantAmateur/SoupX/204b602418df12e9fdb4b68775a8b486c6504fe4/inst/doc/pbmcTutorial.html", + "tool_dev_url": "https://github.com/constantAmateur/SoupX", + "doi": "10.1093/gigascience/giaa151", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "h5ad_filtered": { + "type": "file", + "description": "filtered H5AD file (after CellRanger filtering)", + "pattern": "*.h5ad", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3590" + } + ] + } + }, + { + "h5ad_raw": { + "type": "file", + "description": "raw H5AD file (before CellRanger filtering)", + "pattern": "*.h5ad", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3590" + } + ] + } + } + ], { - "edam": "http://edamontology.org/format_3005" + "npcs": { + "type": "integer", + "description": "Number of principal components for Seurat PCA (also controls FindNeighbors dims = 1:npcs).\n" + } }, { - "edam": "http://edamontology.org/format_3583" + "cluster_algorithm": { + "type": "integer", + "description": "Seurat FindClusters algorithm identifier passed to `FindClusters(algorithm = ...)`.\nValid values:\n - 1: louvain\n - 2: louvain_multilevel\n - 3: slm\n - 4: leiden\n" + } } - ] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@suhrig" - ], - "maintainers": [ - "@suhrig" - ] - } - }, - { - "name": "plastid_metagene_generate", - "path": "modules/nf-core/plastid/metagene_generate/meta.yml", - "type": "module", - "meta": { - "name": "plastid_metagene_generate", - "description": "Compute a metagene profile of read alignments, counts, or quantitative data over one or more regions of interest, optionally applying a mapping rule", - "keywords": [ - "genomics", - "riboseq", - "psite" - ], - "tools": [ - { - "plastid": { - "description": "Nucleotide-resolution analysis of next-generation sequencing and genomics data", - "homepage": "https://github.com/joshuagryphon/plastid", - "documentation": "https://plastid.readthedocs.io/en/latest/", - "tool_dev_url": "https://github.com/joshuagryphon/plastid", - "doi": "10.1186/s12864-016-3278-x", - "licence": [ - "BSD-3-clause" - ], - "identifier": "biotools:plastid" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Map containing reference information for the reference genome annotation file\ne.g. `[ id:'Ensembl human v.111' ]`\n" - } - }, - { - "annotation": { - "type": "file", - "description": "annotation file of reference genome (BED, bigBed, GTF, GFF3)", - "pattern": "*.{bed,bigbed,gtf,gff3}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3003" - }, - { - "edam": "http://edamontology.org/format_3004" - }, - { - "edam": "http://edamontology.org/format_2306" - }, - { - "edam": "http://edamontology.org/format_1975" - } - ] - } - } - ] - ], - "output": { - "rois_txt": [ - [ - { - "meta": { - "type": "map", - "description": "Map containing reference information for the reference genome annotation file\ne.g. `[ id:'Ensembl human v.111' ]`\n" - } - }, - { - "*_rois.txt": { - "type": "file", - "description": "Tab-delimited text file describing the maximal spanning window for each gene", - "pattern": "*_rois.txt", - "ontologies": [] - } - } - ] - ], - "rois_bed": [ - [ - { - "meta": { - "type": "map", - "description": "Map containing reference information for the reference genome annotation file\ne.g. `[ id:'Ensembl human v.111' ]`\n" - } - }, - { - "*_rois.bed": { - "type": "file", - "description": "Maximal spanning windows in BED format for visualization in a genome\nbrowser. The thickly-rendered portion of a window indicates its landmark.\n", - "pattern": "*_rois.bed", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3003" - } - ] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@suhrig" - ], - "maintainers": [ - "@suhrig" - ] - } - }, - { - "name": "plastid_psite", - "path": "modules/nf-core/plastid/psite/meta.yml", - "type": "module", - "meta": { - "name": "plastid_psite", - "description": "Estimate position of ribosomal P-site within ribosome profiling read alignments as a function of read length", - "keywords": [ - "genomics", - "riboseq", - "psite" - ], - "tools": [ - { - "plastid": { - "description": "Nucleotide-resolution analysis of next-generation sequencing and genomics data", - "homepage": "https://github.com/joshuagryphon/plastid", - "documentation": "https://plastid.readthedocs.io/en/latest/", - "tool_dev_url": "https://github.com/joshuagryphon/plastid", - "doi": "10.1186/s12864-016-3278-x", - "licence": [ - "BSD-3-clause" - ], - "identifier": "biotools:plastid" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "Genome BAM file", - "pattern": "*.bam", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - }, - { - "bam_index": { - "type": "file", - "description": "Genome BAM index file", - "pattern": "*.bai", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3327" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Map containing reference information for the reference genome GTF file\ne.g. `[ id:'Ensembl human v.111' ]`\n" - } - }, - { - "rois_txt": { - "type": "file", - "description": "Tab-delimited text file describing the maximal spanning\nwindow for each gene (output from plastid_metagene_generate)\n", - "pattern": "*.txt", - "ontologies": [] - } - } - ] - ], - "output": { - "metagene_profiles": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*_metagene_profiles.txt": { - "type": "file", - "description": "Matrix containing metagene profile for each read length", - "pattern": "*_metagene_profiles.txt", - "ontologies": [] - } - } - ] - ], - "p_offsets_png": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*_p_offsets.png": { - "type": "file", - "description": "Graphical illustration of metagene profiles", - "pattern": "*_p_offsets.png", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3603" - } - ] - } - } - ] - ], - "p_offsets": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*_p_offsets.txt": { - "type": "file", - "description": "Selected p-site offset for each read length", - "pattern": "*_p_offsets.txt", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@suhrig" - ], - "maintainers": [ - "@suhrig" - ] - } - }, - { - "name": "platypus", - "path": "modules/nf-core/platypus/meta.yml", - "type": "module", - "meta": { - "name": "platypus", - "description": "Platypus is a tool that efficiently and accurately calling genetic variants from next-generation DNA sequencing data", - "keywords": [ - "variant", - "call", - "dna", - "genetic" - ], - "tools": [ - { - "platypus": { - "description": "Platypus is a tool designed for efficient and accurate variant-detection in high-throughput sequencing data.", - "homepage": "https://www.well.ox.ac.uk/research/research-groups/lunter-group/lunter-group/platypus-a-haplotype-based-variant-caller-for-next-generation-sequence-data", - "documentation": "https://www.well.ox.ac.uk/research/research-groups/lunter-group/lunter-group/platypus-documentation", - "tool_dev_url": "https://github.com/andyrimmer/Platypus", - "doi": "10.1038/ng.3036", - "licence": [ - "BSD-3-clause" - ], - "identifier": "biotools:platypus" + ], + "output": { + "h5ad": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.h5ad": { + "type": "file", + "description": "H5AD anndata object with ambient RNA removed", + "pattern": "*.h5ad", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3590" + } + ] + } + } + ] + ], + "versions_soupx": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "topics": { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@LeonHafner"], + "maintainers": ["@LeonHafner", "@nictru"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "tumor_file": { - "type": "file", - "description": "Tumor or metastatic sample, BAM or CRAM file", - "pattern": "*.{bam,cram}", - "ontologies": [] - } - }, - { - "tumor_file_bai": { - "type": "file", - "description": "Index of BAM file", - "pattern": "*.{bai,crai}", - "ontologies": [] - } - }, - { - "control_file": { - "type": "file", - "description": "Control (or blood) of matching tumor/metastatic sample, BAM or CRAM file", - "pattern": "*.{bam,cram}", - "ontologies": [] - } + }, + { + "name": "sourcepredict", + "path": "modules/nf-core/sourcepredict/meta.yml", + "type": "module", + "meta": { + "name": "sourcepredict", + "description": "Classifies and predicts the origin of metagenomic samples", + "keywords": ["source tracking", "metagenomics", "machine learning"], + "tools": [ + { + "sourcepredict": { + "description": "Classification and prediction of the origin of metagenomic samples.", + "homepage": "https://github.com/maxibor/sourcepredict", + "documentation": "https://sourcepredict.readthedocs.io/en/latest/index.html", + "tool_dev_url": "https://github.com/maxibor/sourcepredict", + "doi": "10.21105/joss.01540", + "licence": ["GPL v3-or-later"], + "identifier": "biotools:sourcepredict" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "kraken_parse": { + "type": "file", + "description": "Sink TAXID count table in csv format", + "pattern": "*.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ], + { + "sources": { + "type": "file", + "description": "Sources TAXID count table in csv format. Default can be downloaded from https://raw.githubusercontent.com/maxibor/sourcepredict/master/data/modern_gut_microbiomes_sources.csv", + "pattern": "*.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + }, + { + "labels": { + "type": "file", + "description": "Labels for the sources table in csv format. Default can be downloaded from https://raw.githubusercontent.com/maxibor/sourcepredict/master/data/modern_gut_microbiomes_labels.csv", + "pattern": "*.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + }, + { + "taxa_sqlite": { + "type": "file", + "description": "taxa.sqlite file downloaded with ete3 toolkit", + "pattern": "taxa.sqlite", + "ontologies": [] + } + }, + { + "taxa_sqlite_traverse_pkl": { + "type": "file", + "description": "taxa.sqlite.traverse.pkl file downloaded with ete3 toolkit", + "pattern": "taxa.sqlite.traverse.pkl", + "ontologies": [] + } + } + ], + "output": { + "report": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.sourcepredict.csv": { + "type": "file", + "description": "Table containing the predicted proportion of each source in each sample", + "pattern": "*.sourcepredict.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "versions_sourcepredict": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "sourcepredict": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python -c \"import sourcepredict; print(sourcepredict.__version__)\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_python": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "python": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python -V | sed \"s/Python //g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_sklearn": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "sklearn": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python -c \"import sklearn; print(sklearn.__version__)\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "sourcepredict": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python -c \"import sourcepredict; print(sourcepredict.__version__)\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "python": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python -V | sed \"s/Python //g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "sklearn": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python -c \"import sklearn; print(sklearn.__version__)\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@MeriamOs"], + "maintainers": ["@MeriamOs"] }, - { - "control_file_bai": { - "type": "file", - "description": "Index of BAMfile", - "pattern": "*.{bai,crai}", - "ontologies": [] - } - } - ], - { - "fasta": { - "type": "file", - "description": "The reference fasta file", - "pattern": "*.fa", - "ontologies": [] - } - }, - { - "fai": { - "type": "file", - "description": "Index of reference fasta file", - "pattern": "*.fai", - "ontologies": [] - } - }, - { - "skipregions_file": { - "type": "file", - "description": "File with regions to skip, region as comma-separated list of chr:start-end, or just list of chr, or nothing", - "pattern": "*.bed|*.txt|*.tab", - "ontologies": [ + "pipelines": [ { - "edam": "http://edamontology.org/format_3475" + "name": "coproid", + "version": "2.0.1" } - ] - } - } - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "*.vcf.gz": { - "type": "file", - "description": "Output VCF file", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "*.vcf.gz.tbi": { - "type": "file", - "description": "Index of VCF file", - "pattern": "*.vcf.gz.tbi", - "ontologies": [] - } - } ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "*.log": { - "type": "file", - "description": "Log file", - "pattern": "*.log", - "ontologies": [] - } - } - ] - ], - "version": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software version", - "pattern": "*.{version.txt}", - "ontologies": [] - } - } - ] - }, - "authors": [ - "@kubranarci" - ], - "maintainers": [ - "@kubranarci" - ] - } - }, - { - "name": "plink2_extract", - "path": "modules/nf-core/plink2/extract/meta.yml", - "type": "module", - "meta": { - "name": "plink2_extract", - "description": "Subset plink pfiles with a text file of variant identifiers", - "keywords": [ - "plink2", - "extract", - "identifiers" - ], - "tools": [ - { - "plink2": { - "description": "Whole genome association analysis toolset, designed to perform a range\nof basic, large-scale analyses in a computationally efficient manner\n", - "homepage": "http://www.cog-genomics.org/plink/2.0/", - "documentation": "http://www.cog-genomics.org/plink/2.0/general_usage", - "doi": "10.1186/s13742-015-0047-8", - "licence": [ - "GPL v3" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "pgen": { - "type": "file", - "description": "PLINK 2 binary genotype table", - "pattern": "*.{pgen}", - "ontologies": [] - } - }, - { - "psam": { - "type": "file", - "description": "PLINK 2 sample information file", - "pattern": "*.{psam}", - "ontologies": [] - } - }, - { - "pvar": { - "type": "file", - "description": "PLINK 2 variant information file", - "pattern": "*.{pvar}", - "ontologies": [] - } + }, + { + "name": "sourmash_compare", + "path": "modules/nf-core/sourmash/compare/meta.yml", + "type": "module", + "meta": { + "name": "sourmash_compare", + "description": "Compare many FracMinHash signatures generated by sourmash sketch.", + "keywords": [ + "compare", + "FracMinHash sketch", + "containment", + "sourmash", + "metagenomics", + "genomics", + "kmer" + ], + "tools": [ + { + "sourmash": { + "description": "Compute and compare FracMinHash signatures for DNA and protein data sets.", + "homepage": "https://sourmash.readthedocs.io/", + "documentation": "https://sourmash.readthedocs.io/", + "tool_dev_url": "https://github.com/sourmash-bio/sourmash", + "doi": "10.21105/joss.00027", + "licence": ["BSD-3-clause"], + "identifier": "biotools:sourmash" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "signatures": { + "type": "file", + "description": "Files containing signatures (hash sketches) of samples", + "pattern": "*.{sig}", + "ontologies": [] + } + } + ], + { + "file_list": { + "type": "file", + "description": "An optional file specifying a list of file paths that should be appended to the input signatures.\n", + "ontologies": [] + } + }, + { + "save_numpy_matrix": { + "type": "boolean", + "description": "If true, output will contain a (dis)similarity matrix numpy binary format.\nAt least one of save_numpy_matrix or save_csv is required.\n" + } + }, + { + "save_csv": { + "type": "boolean", + "description": "If true, output will contain a (dis)similarity matrix in CSV format\nAt least one of save_numpy_matrix or save_csv is required.\n" + } + } + ], + "output": { + "matrix": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*comp.npy": { + "type": "file", + "description": "An optional (dis)similarity matrix numpy binary format", + "pattern": "*.comp", + "ontologies": [] + } + } + ] + ], + "labels": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*comp.npy.labels.txt": { + "type": "file", + "description": "A text file that specifies the labels in the output numpy_matrix", + "pattern": "*.comp.labels.txt", + "ontologies": [] + } + } + ] + ], + "csv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*comp.csv": { + "type": "file", + "description": "An optional (dis)similarity matrix in CSV format", + "pattern": "*.comp.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "versions_sourmash": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "sourmash": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "sourmash --version 2>&1 | sed 's/^sourmash //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "sourmash": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "sourmash --version 2>&1 | sed 's/^sourmash //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@taylorreiter"], + "maintainers": ["@taylorreiter"] }, - { - "variants": { - "type": "file", - "description": "A text file containing variant identifiers to keep (one per line)", - "pattern": "*.{keep}", - "ontologies": [] - } - } - ] - ], - "output": { - "extract_pgen": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.pgen": { - "type": "file", - "description": "PLINK 2 binary genotype table, containing extracted variants", - "pattern": "*.{pgen}", - "ontologies": [] - } - } - ] - ], - "extract_psam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.psam": { - "type": "file", - "description": "PLINK 2 sample information file associated with the extracted data", - "pattern": "*.{psam}", - "ontologies": [] - } - } - ] - ], - "extract_pvar": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.pvar.zst": { - "type": "file", - "description": "PLINK 2 variant information file, containing extracted variants", - "pattern": "*.{pvar.zst}", - "ontologies": [] - } - } + "pipelines": [ + { + "name": "pathogensurveillance", + "version": "1.1.0" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@nebfield" - ], - "maintainers": [ - "@nebfield" - ] - } - }, - { - "name": "plink2_filter", - "path": "modules/nf-core/plink2/filter/meta.yml", - "type": "module", - "meta": { - "name": "plink2_filter", - "description": "Filters plink bfiles or pfiles with filters such as maf or var", - "keywords": [ - "plink2", - "filter", - "samples", - "variants", - "missingness", - "qualty" - ], - "tools": [ - { - "plink2": { - "description": "Whole genome association analysis toolset, designed to perform a range\nof basic, large-scale analyses in a computationally efficient manner\n", - "homepage": "http://www.cog-genomics.org/plink/2.0/", - "documentation": "http://www.cog-genomics.org/plink/2.0/general_usage", - "doi": "10.1186/s13742-015-0047-8", - "licence": [ - "GPL v3" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "plink_genotype_file": { - "type": "file", - "description": "PLINK binary genotype table file or PLINK 2 binary genotype table file", - "pattern": "*.{bed,pgen}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3003" - } - ] - } - }, - { - "plink_variant_file": { - "type": "file", - "description": "PLINK extended MAP file or PLINK 2 variant information file", - "pattern": "*.{bim,pvar}", - "ontologies": [] - } + }, + { + "name": "sourmash_gather", + "path": "modules/nf-core/sourmash/gather/meta.yml", + "type": "module", + "meta": { + "name": "sourmash_gather", + "description": "Search a metagenome sourmash signature against one or many reference databases and return the minimum set of genomes that contain the k-mers in the metagenome.", + "keywords": [ + "FracMinHash sketch", + "signature", + "kmer", + "containment", + "sourmash", + "genomics", + "metagenomics", + "taxonomic classification", + "taxonomic profiling" + ], + "tools": [ + { + "sourmash": { + "description": "Compute and compare FracMinHash signatures for DNA data sets.", + "homepage": "https://sourmash.readthedocs.io/", + "documentation": "https://sourmash.readthedocs.io/", + "tool_dev_url": "https://github.com/sourmash-bio/sourmash", + "doi": "10.21105/joss.00027", + "licence": ["BSD-3-clause"], + "identifier": "biotools:sourmash" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "signature": { + "type": "file", + "description": "File containing signatures (hash sketches) of a sample", + "pattern": "*.{sig}", + "ontologies": [] + } + } + ], + { + "database": { + "type": "file", + "description": "database", + "ontologies": [] + } + }, + { + "save_unassigned": { + "type": "boolean", + "description": "If true, output will contain a file that is a sourmash signature containing the unassigned hashes from the query\n" + } + }, + { + "save_matches_sig": { + "type": "boolean", + "description": "If true, output will contain a file that is a sourmash signature composed of the FracMinHash sketches that were matched in the database and that matched the query\n" + } + }, + { + "save_prefetch": { + "type": "boolean", + "description": "If true, output will contain a file with all prefetch-matched signatures from the database\n" + } + }, + { + "save_prefetch_csv": { + "type": "boolean", + "description": "If true, output will contain a csv file with the names of all prefetch-matched signatures\n" + } + } + ], + "output": { + "result": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.csv.gz": { + "type": "file", + "description": "Table with signatures classified as belonging to any of the genomes\nin the sourmash database(s).\n", + "pattern": "*{csv.gz}", + "ontologies": [] + } + } + ] + ], + "unassigned": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_unassigned.sig.zip": { + "type": "file", + "description": "A FracMinHash sketch containing hashes (k-mers) that did not match to any of the genomes\nin the sourmash database(s).\n", + "pattern": "*{sig.zip}", + "ontologies": [] + } + } + ] + ], + "matches": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_matches.sig.zip": { + "type": "file", + "description": "A signature containing FracMinHash sketches of genomes\nin the sourmash database.\n", + "pattern": "*{sig.zip}", + "ontologies": [] + } + } + ] + ], + "prefetch": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_prefetch.sig.zip": { + "type": "file", + "description": "All prefetch-matched signatures from the database.\n", + "pattern": "*{sig.zip}", + "ontologies": [] + } + } + ] + ], + "prefetchcsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_prefetch.csv.gz": { + "type": "file", + "description": "The names of all prefetch-matched signatures from the database in CSV format.\n", + "pattern": "*{csv.gz}", + "ontologies": [] + } + } + ] + ], + "versions_sourmash": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "sourmash": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "sourmash --version 2>&1 | sed 's/^sourmash //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "sourmash": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "sourmash --version 2>&1 | sed 's/^sourmash //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@vmikk", "@taylorreiter"], + "maintainers": ["@vmikk", "@taylorreiter"] }, - { - "plink_sample_file": { - "type": "file", - "description": "PLINK sample information file or PLINK 2 sample information file", - "pattern": "*.{fam,psam}", - "ontologies": [] - } - } - ] - ], - "output": { - "bim": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bim": { - "type": "file", - "description": "PLINK extended map file", - "pattern": "*.bim", - "ontologies": [] - } - } - ] - ], - "bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bed": { - "type": "file", - "description": "PLINK binary allelic genotype table", - "pattern": "*.bed", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3003" - } - ] - } - } - ] - ], - "fam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.fam": { - "type": "file", - "description": "PLINK sample information file", - "pattern": "*.fam", - "ontologies": [] - } - } - ] - ], - "pgen": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.pgen": { - "type": "file", - "description": "PLINK 2 binary genotype table", - "pattern": "*.pgen", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3003" - } - ] - } - } - ] - ], - "psam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.psam": { - "type": "file", - "description": "PLINK 2 sample information file", - "pattern": "*.psam", - "ontologies": [] - } - } - ] - ], - "pvar": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.pvar": { - "type": "file", - "description": "PLINK 2 variant information file", - "pattern": "*.pvar", - "ontologies": [] - } - } + "pipelines": [ + { + "name": "magmap", + "version": "1.0.0" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@jodennehy" - ], - "maintainers": [ - "@jodennehy" - ] - } - }, - { - "name": "plink2_het", - "path": "modules/nf-core/plink2/het/meta.yml", - "type": "module", - "meta": { - "name": "plink2_het", - "description": "Calculate Inbreeding data with plink2", - "keywords": [ - "plink2", - "inbreeding", - "heterozygous genotypes", - "homozygous genotypes", - "f coefficient", - "population genomics" - ], - "tools": [ - { - "plink2": { - "description": "Whole genome association analysis toolset, designed to perform a range\nof basic, large-scale analyses in a computationally efficient manner\n", - "homepage": "http://www.cog-genomics.org/plink/2.0/", - "documentation": "http://www.cog-genomics.org/plink/2.0/general_usage", - "doi": "10.1186/s13742-015-0047-8", - "licence": [ - "GPL v3" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "plink_genotype_file": { - "type": "file", - "description": "PLINK binary genotype table file or PLINK 2 binary genotype table file", - "pattern": "*.{bed,pgen}", - "ontologies": [] - } - }, - { - "plink_variant_file": { - "type": "file", - "description": "PLINK extended MAP file or PLINK 2 variant information file", - "pattern": "*.{bim,pvar}", - "ontologies": [] - } + }, + { + "name": "sourmash_index", + "path": "modules/nf-core/sourmash/index/meta.yml", + "type": "module", + "meta": { + "name": "sourmash_index", + "description": "Create a database of sourmash signatures (a group of FracMinHash sketches) to be used as references.", + "keywords": ["signatures", "sourmash", "genomics", "metagenomics", "mapping", "kmer"], + "tools": [ + { + "sourmash": { + "description": "Compute and compare FracMinHash signatures for DNA data sets.", + "homepage": "https://sourmash.readthedocs.io/", + "documentation": "https://sourmash.readthedocs.io/", + "tool_dev_url": "https://github.com/sourmash-bio/sourmash", + "doi": "10.21105/joss.00027", + "licence": ["BSD-3-clause"], + "identifier": "biotools:sourmash" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "signatures": { + "type": "file", + "description": "Files containing signature (hash sketches) of reference genomes", + "pattern": "*.{sig}", + "ontologies": [] + } + } + ], + { + "ksize": { + "type": "integer", + "description": "ksize value" + } + } + ], + "output": { + "signature_index": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.sbt.zip": { + "type": "file", + "description": "Database of signatures", + "pattern": "*.{sbt.zip}", + "ontologies": [] + } + } + ] + ], + "versions_sourmash": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "sourmash": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "sourmash --version 2>&1 | sed 's/^sourmash //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "sourmash": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "sourmash --version 2>&1 | sed 's/^sourmash //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@emnilsson"], + "maintainers": ["@emnilsson"] }, - { - "plink_sample_file": { - "type": "file", - "description": "PLINK sample information file or PLINK 2 sample information file", - "pattern": "*.{fam,psam}", - "ontologies": [] - } - } - ] - ], - "output": { - "het": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.het": { - "type": "file", - "description": "observed and expected homozygous/heterozygous genotype counts for each sample and method-of-moments F coefficient estimates", - "pattern": "*.het", - "ontologies": [] - } - } + "pipelines": [ + { + "name": "createtaxdb", + "version": "3.0.0" + }, + { + "name": "magmap", + "version": "1.0.0" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@RuthEberhardt" - ], - "maintainers": [ - "@RuthEberhardt" - ] - } - }, - { - "name": "plink2_hwe", - "path": "modules/nf-core/plink2/hwe/meta.yml", - "type": "module", - "meta": { - "name": "plink2_hwe", - "description": "Filters plink bfiles or pfiles with maf filters", - "keywords": [ - "plink2", - "filter", - "samples", - "variants", - "hwe", - "qualty" - ], - "tools": [ - { - "plink2": { - "description": "Whole genome association analysis toolset, designed to perform a range\nof basic, large-scale analyses in a computationally efficient manner\n", - "homepage": "http://www.cog-genomics.org/plink/2.0/", - "documentation": "http://www.cog-genomics.org/plink/2.0/general_usage", - "doi": "10.1186/s13742-015-0047-8", - "licence": [ - "GPL v3" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "plink_genotype_file": { - "type": "file", - "description": "PLINK binary genotype table file or PLINK 2 binary genotype table file", - "pattern": "*.{bed,pgen}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3003" - } - ] - } - }, - { - "plink_variant_file": { - "type": "file", - "description": "PLINK extended MAP file or PLINK 2 variant information file", - "pattern": "*.{bim,pvar}" - } + }, + { + "name": "sourmash_sketch", + "path": "modules/nf-core/sourmash/sketch/meta.yml", + "type": "module", + "meta": { + "name": "sourmash_sketch", + "description": "Create a signature (a group of FracMinHash sketches) of a sequence using sourmash", + "keywords": [ + "hash sketch", + "sourmash", + "genomics", + "metagenomics", + "taxonomic classification", + "taxonomic profiling", + "kmer" + ], + "tools": [ + { + "sourmash": { + "description": "Compute and compare FracMinHash signatures for DNA and protein data sets.", + "homepage": "https://sourmash.readthedocs.io/", + "documentation": "https://sourmash.readthedocs.io/", + "tool_dev_url": "https://github.com/sourmash-bio/sourmash", + "doi": "10.21105/joss.00027", + "licence": ["BSD-3-clause"], + "identifier": "biotools:sourmash" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "library": { + "type": "file", + "description": "One or more FASTA or FASTQ file(s) containing (genomic, transcriptomic, or proteomic) sequence data", + "pattern": "*.{fna,fa,fasta,fastq,fq,faa}.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ] + ], + "output": { + "signatures": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.sig": { + "type": "file", + "description": "FracMinHash signature of the given sequence", + "pattern": "*.{sig}", + "ontologies": [] + } + } + ] + ], + "versions_sourmash": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "sourmash": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "sourmash --version 2>&1 | sed 's/^sourmash //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "sourmash": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "sourmash --version 2>&1 | sed 's/^sourmash //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@Midnighter"], + "maintainers": ["@Midnighter"] }, - { - "plink_sample_file": { - "type": "file", - "description": "PLINK sample information file or PLINK 2 sample information file", - "pattern": "*.{fam,psam}" - } - } - ], - [ - { - "hwe": { - "type": "float", - "description": "Threshold to use for maf filtering" - } - } - ] - ], - "output": [ - { - "bed": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bed": { - "type": "file", - "description": "PLINK binary allelic genotype table", - "pattern": "*.bed", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3003" - } - ] - } - } - ] - }, - { - "bim": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bim": { - "type": "file", - "description": "PLINK extended map file", - "pattern": "*.bim", - "ontologies": [] - } - } - ] - }, - { - "fam": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.fam": { - "type": "file", - "description": "PLINK sample information file", - "pattern": "*.fam", - "ontologies": [] - } - } - ] - }, - { - "pgen": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.pgen": { - "type": "file", - "description": "PLINK 2 binary genotype table", - "pattern": "*.pgen", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3003" - } - ] - } - } - ] - }, - { - "pvar": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.pvar": { - "type": "file", - "description": "PLINK 2 variant information file", - "pattern": "*.pvar", - "ontologies": [] - } - } - ] - }, - { - "psam": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.psam": { - "type": "file", - "description": "PLINK 2 sample information file", - "pattern": "*.psam", - "ontologies": [] - } - } - ] - }, - { - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [] - } - } + "pipelines": [ + { + "name": "createtaxdb", + "version": "3.0.0" + }, + { + "name": "magmap", + "version": "1.0.0" + }, + { + "name": "pathogensurveillance", + "version": "1.1.0" + } ] - } - ], - "authors": [ - "@jodennehy" - ], - "maintainers": [ - "@jodennehy" - ] - } - }, - { - "name": "plink2_indeppairwise", - "path": "modules/nf-core/plink2/indeppairwise/meta.yml", - "type": "module", - "meta": { - "name": "plink2_indeppairwise", - "description": "Produce pruned set of variants in approximatelinkage equilibrium", - "keywords": [ - "plink2", - "linkage equilibrium", - "pruning" - ], - "tools": [ - { - "plink2": { - "description": "Whole genome association analysis toolset, designed to perform a range\nof basic, large-scale analyses in a computationally efficient manner\n", - "homepage": "http://www.cog-genomics.org/plink/2.0/", - "documentation": "http://www.cog-genomics.org/plink/2.0/general_usage", - "doi": "10.1186/s13742-015-0047-8", - "licence": [ - "GPL v3" - ], - "identifier": "" + }, + { + "name": "sourmash_taxannotate", + "path": "modules/nf-core/sourmash/taxannotate/meta.yml", + "type": "module", + "meta": { + "name": "sourmash_taxannotate", + "description": "Annotate list of metagenome members (based on sourmash signature matches) with taxonomic information.", + "keywords": [ + "fracminhash sketch", + "signature", + "kmer", + "containment", + "sourmash", + "genomics", + "metagenomics", + "taxonomic classification", + "taxonomic profiling" + ], + "tools": [ + { + "sourmash": { + "description": "Compute and compare FracMinHash signatures for DNA data sets.", + "homepage": "https://sourmash.readthedocs.io/", + "documentation": "https://sourmash.readthedocs.io/", + "tool_dev_url": "https://github.com/sourmash-bio/sourmash", + "doi": "10.21105/joss.00027", + "licence": ["BSD-3-clause"], + "identifier": "biotools:sourmash" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "gather_results": { + "type": "file", + "description": "Mandatory table with signatures classified as belonging to any of the genomes\nin the sourmash database(s), result of `sourmash gather` command.\n", + "ontologies": [] + } + } + ], + { + "taxonomy": { + "type": "file", + "description": "One or more databases with lineages (in CSV format, Mandatory)", + "ontologies": [] + } + } + ], + "output": { + "result": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.with-lineages.csv.gz": { + "type": "file", + "description": "Table with signatures classified as belonging to any of the genomes\nin the sourmash database(s) with an additional 'lineage' column\ncontaining the taxonomic information for each database match.\n", + "pattern": "*{csv.gz}", + "ontologies": [] + } + } + ] + ], + "versions_sourmash": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "sourmash": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "sourmash --version 2>&1 | sed 's/^sourmash //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "sourmash": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "sourmash --version 2>&1 | sed 's/^sourmash //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@vmikk", "@taylorreiter"], + "maintainers": ["@vmikk", "@taylorreiter"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "plink_genotype_file": { - "type": "file", - "description": "PLINK binary genotype table file or PLINK 2 binary genotype table file", - "pattern": "*.{bed,pgen}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3003" - } - ] - } - }, - { - "plink_variant_file": { - "type": "file", - "description": "PLINK extended MAP file or PLINK 2 variant information file", - "pattern": "*.{bim,pvar}", - "ontologies": [] - } + }, + { + "name": "spaceranger_count", + "path": "modules/nf-core/spaceranger/count/meta.yml", + "type": "module", + "meta": { + "name": "spaceranger_count", + "description": "Module to use the 10x Space Ranger pipeline to process 10x spatial transcriptomics data", + "keywords": ["align", "count", "spatial", "spaceranger", "imaging"], + "tools": [ + { + "spaceranger": { + "description": "Visium Spatial Gene Expression is a next-generation molecular profiling solution for classifying tissue\nbased on total mRNA. Space Ranger is a set of analysis pipelines that process Visium Spatial Gene Expression\ndata with brightfield and fluorescence microscope images. Space Ranger allows users to map the whole\ntranscriptome in formalin fixed paraffin embedded (FFPE) and fresh frozen tissues to discover novel\ninsights into normal development, disease pathology, and clinical translational research. Space Ranger provides\npipelines for end to end analysis of Visium Spatial Gene Expression experiments.\n", + "homepage": "https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger", + "documentation": "https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger", + "tool_dev_url": "https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger", + "licence": ["10x Genomics EULA"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', slide:'10L13-020', area: 'B1']\n\n`id`, `slide` and `area` are mandatory information!\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", + "pattern": "${Sample_Name}_S1_L00${Lane_Number}_${I1,I2,R1,R2}_001.fastq.gz", + "ontologies": [] + } + }, + { + "image": { + "type": "file", + "description": "Brightfield tissue H&E image in JPEG or TIFF format.", + "pattern": "*.{tif,tiff,jpg,jpeg}", + "ontologies": [] + } + }, + { + "slide": { + "type": "string", + "description": "Visium slide ID used for the sample." + } + }, + { + "area": { + "type": "string", + "description": "Visium slide capture area used for the sample." + } + }, + { + "cytaimage": { + "type": "file", + "description": "CytAssist instrument captured eosin stained Brightfield tissue image with fiducial\nframe in TIFF format. The size of this image is set at 3k in both dimensions and this image should\nnot be modified any way before passing it as input to either Space Ranger or Loupe Browser.\n", + "pattern": "*.{tif,tiff}", + "ontologies": [] + } + }, + { + "darkimage": { + "type": "file", + "description": "Optional for dark background fluorescence microscope image input. Multi-channel, dark-background fluorescence\nimage as either a single, multi-layer TIFF file or as multiple TIFF or JPEG files.\n", + "pattern": "*.{tif,tiff,jpg,jpeg}", + "ontologies": [] + } + }, + { + "colorizedimage": { + "type": "file", + "description": "Required for color composite fluorescence microscope image input.\nA color composite of one or more fluorescence image channels saved as a single-page,\nsingle-file color TIFF or JPEG.\n", + "pattern": "*.{tif,tiff,jpg,jpeg}", + "ontologies": [] + } + }, + { + "alignment": { + "type": "file", + "description": "OPTIONAL - Path to manual image alignment.", + "pattern": "*.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + }, + { + "slidefile": { + "type": "file", + "description": "OPTIONAL - Path to slide specifications.", + "pattern": "*.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ], + { + "reference": { + "type": "directory", + "description": "Folder containing all the reference indices needed by Space Ranger" + } + }, + { + "probeset": { + "type": "file", + "description": "OPTIONAL - Probe set specification.", + "pattern": "*.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ], + "output": { + "outs": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "outs/**": { + "type": "file", + "description": "Files containing the outputs of Space Ranger, see official 10X Genomics documentation for a complete list", + "pattern": "outs/*", + "ontologies": [] + } + } + ] + ], + "versions_spaceranger": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "spaceranger": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "spaceranger -V | sed \"s/spaceranger spaceranger-//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "spaceranger": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "spaceranger -V | sed \"s/spaceranger spaceranger-//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@grst"], + "maintainers": ["@grst", "@fasterius"] }, - { - "plink_sample_file": { - "type": "file", - "description": "PLINK sample information file or PLINK 2 sample information file", - "pattern": "*.{fam,psam}", - "ontologies": [] - } - } - ], - { - "win": { - "type": "integer", - "description": "Window size in variant count or kilobase (if the 'kb' modifier is present) units, a variant count to shift the window at the end of each step, and a variance inflation factor (VIF) threshold.", - "pattern": "*.{}" - } - }, - { - "step": { - "type": "integer", - "description": "Variant count to shift the window at the end of each step.", - "pattern": "*.{}" - } - }, - { - "r2": { - "type": "float", - "description": "R squared threshold", - "pattern": "*.{}" - } - } - ], - "output": { - "prune_in": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.prune.in": { - "type": "file", - "description": "Variants in linkage equilibrium", - "pattern": "*.prune.in", - "ontologies": [] - } - } - ] - ], - "prune_out": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.prune.out": { - "type": "file", - "description": "Excluded variants", - "pattern": "*.prune.out", - "ontologies": [] - } - } + "pipelines": [ + { + "name": "sopa", + "version": "dev" + }, + { + "name": "spatialvi", + "version": "dev" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } + }, + { + "name": "spaceranger_mkgtf", + "path": "modules/nf-core/spaceranger/mkgtf/meta.yml", + "type": "module", + "meta": { + "name": "spaceranger_mkgtf", + "description": "Module to build a filtered GTF needed by the 10x Genomics Space Ranger tool. Uses the spaceranger mkgtf command.", + "keywords": ["reference", "mkref", "index", "spaceranger"], + "tools": [ + { + "spaceranger": { + "description": "Visium Spatial Gene Expression is a next-generation molecular profiling solution for classifying tissue\nbased on total mRNA. Space Ranger is a set of analysis pipelines that process Visium Spatial Gene Expression\ndata with brightfield and fluorescence microscope images. Space Ranger allows users to map the whole\ntranscriptome in formalin fixed paraffin embedded (FFPE) and fresh frozen tissues to discover novel\ninsights into normal development, disease pathology, and clinical translational research. Space Ranger provides\npipelines for end to end analysis of Visium Spatial Gene Expression experiments.\n", + "homepage": "https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger", + "documentation": "https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger", + "tool_dev_url": "https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger", + "licence": ["10x Genomics EULA"], + "identifier": "" + } + } + ], + "input": [ + { + "gtf": { + "type": "file", + "description": "The reference GTF transcriptome file", + "pattern": "*.gtf", + "ontologies": [] + } + } + ], + "output": { + "gtf": [ + { + "*.gtf": { + "type": "directory", + "description": "The filtered GTF transcriptome file", + "pattern": "*.filtered.gtf" + } + } + ], + "versions_spaceranger": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "spaceranger": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "spaceranger -V | sed \"s/spaceranger spaceranger-//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "spaceranger": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "spaceranger -V | sed \"s/spaceranger spaceranger-//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@grst"], + "maintainers": ["@grst", "@fasterius"] } - ] - }, - "authors": [ - "@tdkaliki" - ], - "maintainers": [ - "@tdkaliki" - ] - } - }, - { - "name": "plink2_pca", - "path": "modules/nf-core/plink2/pca/meta.yml", - "type": "module", - "meta": { - "name": "plink2_pca", - "description": "Perform PCA analysis using PLINK", - "keywords": [ - "plink2", - "pca", - "plink2_pca" - ], - "tools": [ - { - "plink2": { - "description": "Whole genome association analysis toolset, designed to perform a range\nof basic, large-scale analyses in a computationally efficient manner\n", - "homepage": "http://www.cog-genomics.org/plink/2.0/", - "documentation": "http://www.cog-genomics.org/plink/2.0/general_usage", - "doi": "10.1186/s13742-015-0047-8", - "licence": [ - "GPL v3" - ], - "identifier": "" + }, + { + "name": "spaceranger_mkref", + "path": "modules/nf-core/spaceranger/mkref/meta.yml", + "type": "module", + "meta": { + "name": "spaceranger_mkref", + "description": "Module to build the reference needed by the 10x Genomics Space Ranger tool. Uses the spaceranger mkref command.", + "keywords": ["reference", "mkref", "index", "spaceranger"], + "tools": [ + { + "spaceranger": { + "description": "Visium Spatial Gene Expression is a next-generation molecular profiling solution for classifying tissue\nbased on total mRNA. Space Ranger is a set of analysis pipelines that process Visium Spatial Gene Expression\ndata with brightfield and fluorescence microscope images. Space Ranger allows users to map the whole\ntranscriptome in formalin fixed paraffin embedded (FFPE) and fresh frozen tissues to discover novel\ninsights into normal development, disease pathology, and clinical translational research. Space Ranger provides\npipelines for end to end analysis of Visium Spatial Gene Expression experiments.\n", + "homepage": "https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger", + "documentation": "https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger", + "tool_dev_url": "https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger", + "licence": ["10x Genomics EULA"], + "identifier": "" + } + } + ], + "input": [ + { + "fasta": { + "type": "file", + "description": "Reference genome FASTA file", + "pattern": "*.{fasta,fa}", + "ontologies": [] + } + }, + { + "gtf": { + "type": "file", + "description": "Reference transcriptome GTF file", + "pattern": "*.gtf", + "ontologies": [] + } + }, + { + "reference_name": { + "type": "string", + "description": "The name to give the new reference folder", + "pattern": "str" + } + } + ], + "output": { + "reference": [ + { + "${reference_name}": { + "type": "directory", + "description": "Folder containing all the reference indices needed by Space Ranger" + } + } + ], + "versions_spaceranger": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "spaceranger": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "spaceranger -V | sed \"s/spaceranger spaceranger-//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "spaceranger": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "spaceranger -V | sed \"s/spaceranger spaceranger-//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@grst"], + "maintainers": ["@grst", "@fasterius"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "npcs": { - "type": "integer", - "description": "Number of PCs to compute" - } - }, - { - "use_approx": { - "type": "boolean", - "description": "If true, use the approximate method" - } - }, - { - "pgen": { - "type": "file", - "description": "PLINK 2 binary genotype table", - "pattern": "*.{pgen}", - "ontologies": [] - } - }, - { - "psam": { - "type": "file", - "description": "PLINK 2 sample information file", - "pattern": "*.{psam}", - "ontologies": [] - } + }, + { + "name": "spades", + "path": "modules/nf-core/spades/meta.yml", + "type": "module", + "meta": { + "name": "spades", + "description": "Assembles a small genome (bacterial, fungal, viral)", + "keywords": ["genome", "assembly", "genome assembler", "small genome", "de novo assembler"], + "tools": [ + { + "spades": { + "description": "SPAdes (St. Petersburg genome assembler) is intended for both standard isolates and single-cell MDA bacteria assemblies.", + "homepage": "http://cab.spbu.ru/files/release3.15.0/manual.html", + "documentation": "http://cab.spbu.ru/files/release3.15.0/manual.html", + "tool_dev_url": "https://github.com/ablab/spades", + "doi": "10.1089/cmb.2012.0021", + "licence": ["GPL v2"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "illumina": { + "type": "file", + "description": "List of input FastQ (Illumina or PacBio CCS reads) files\nof size 1 and 2 for single-end and paired-end data,\nrespectively. This input data type is required.\n", + "ontologies": [] + } + }, + { + "pacbio": { + "type": "file", + "description": "List of input PacBio CLR FastQ files of size 1.\n", + "ontologies": [] + } + }, + { + "nanopore": { + "type": "file", + "description": "List of input FastQ files of size 1, originating from Oxford Nanopore technology.\n", + "ontologies": [] + } + } + ], + { + "yml": { + "type": "file", + "description": "Path to yml file containing read information.\nThe raw FASTQ files listed in this YAML file MUST be supplied to the respective illumina/pacbio/nanopore input channel(s) _in addition_ to this YML.\nFile entries in this yml must contain only the file name and no paths.\n", + "pattern": "*.{yml,yaml}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + }, + { + "hmm": { + "type": "file", + "description": "File or directory with amino acid HMMs for Spades HMM-guided mode.", + "ontologies": [] + } + } + ], + "output": { + "scaffolds": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*.fa.gz" + } + }, + { + "*.scaffolds.fa.gz": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*.fa.gz" + } + } + ] + ], + "contigs": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*.fa.gz" + } + }, + { + "*.contigs.fa.gz": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*.fa.gz" + } + } + ] + ], + "transcripts": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*.fa.gz" + } + }, + { + "*.transcripts.fa.gz": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*.fa.gz" + } + } + ] + ], + "gene_clusters": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*.fa.gz" + } + }, + { + "*.gene_clusters.fa.gz": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*.fa.gz" + } + } + ] + ], + "gfa": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*.fa.gz" + } + }, + { + "*.assembly.gfa.gz": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*.gfa.gz" + } + } + ] + ], + "warnings": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*.fa.gz" + } + }, + { + "*.warnings.log": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*.fa.gz" + } + }, + { + "*.spades.log": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*.spades.log" + } + } + ] + ], + "versions_spades": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "spades": { + "type": "string", + "description": "The tool name" + } + }, + { + "spades.py --version 2>&1 | sed -n 's/^.*SPAdes genome assembler v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "spades": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "spades.py --version 2>&1 | sed -n 's/^.*SPAdes genome assembler v//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@JoseEspinosa", "@drpatelh", "@d4straub"], + "maintainers": ["@JoseEspinosa", "@drpatelh", "@d4straub"] }, - { - "pvar": { - "type": "file", - "description": "PLINK 2 variant information file", - "pattern": "*.{pvar}", - "ontologies": [] - } - } - ] - ], - "output": { - "evecfile": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\n", - "pattern": "*.eigenvec" - } - }, - { - "*.eigenvec": { - "type": "map", - "description": "Groovy Map containing sample information\n", - "pattern": "*.eigenvec" - } - } - ] - ], - "evfile": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\n", - "pattern": "*.eigenvec" - } - }, - { - "*.eigenval": { - "type": "map", - "description": "Groovy Map containing sample information\n", - "pattern": "*.eigenval" - } - } - ] - ], - "logfile": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\n", - "pattern": "*.eigenvec" - } - }, - { - "*.log": { - "type": "map", - "description": "Groovy Map containing sample information\n", - "pattern": "*.log" - } - } + "pipelines": [ + { + "name": "denovotranscript", + "version": "1.2.1" + }, + { + "name": "mag", + "version": "5.4.2" + }, + { + "name": "metatdenovo", + "version": "1.3.0" + }, + { + "name": "pathogensurveillance", + "version": "1.1.0" + }, + { + "name": "viralmetagenome", + "version": "1.1.1" + }, + { + "name": "viralrecon", + "version": "3.0.0" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing the version of the program\n", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@bruno-ariano" - ], - "maintainers": [ - "@bruno-ariano" - ] - } - }, - { - "name": "plink2_remove", - "path": "modules/nf-core/plink2/remove/meta.yml", - "type": "module", - "meta": { - "name": "plink2_remove", - "description": "Remove samples from a plink2 dataset", - "keywords": [ - "plink2", - "remove samples", - "population genomics" - ], - "tools": [ - { - "plink2": { - "description": "Whole genome association analysis toolset, designed to perform a range\nof basic, large-scale analyses in a computationally efficient manner\n", - "homepage": "http://www.cog-genomics.org/plink/2.0/", - "documentation": "http://www.cog-genomics.org/plink/2.0/general_usage", - "doi": "10.1186/s13742-015-0047-8", - "licence": [ - "GPL v3" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "plink_genotype_file": { - "type": "file", - "description": "PLINK binary genotype table file or PLINK 2 binary genotype table file", - "pattern": "*.{bed,pgen}", - "ontologies": [] - } - }, - { - "plink_variant_file": { - "type": "file", - "description": "PLINK extended MAP file or PLINK 2 variant information file", - "pattern": "*.{bim,pvar}", - "ontologies": [] - } + }, + { + "name": "sparsesignatures", + "path": "modules/nf-core/sparsesignatures/meta.yml", + "type": "module", + "meta": { + "name": "sparse_signatures", + "description": "mutational signature deconvolution of cancer cells", + "keywords": ["mutational signatures", "SBS", "bs genome reference"], + "tools": [ + { + "sparsesignatures": { + "description": "SparseSignatures is an R-based computational framework which performs de novo extraction, inference, interpretation, or deconvolution of mutational counts of a large number of 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- ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "vcf": { - "type": "file", - "description": "A vcf or vcf.gz file with genetic variants", - "pattern": "*.{vcf,vcf.gz}", - "ontologies": [] - } - }, - { - "dosage_field": { - "type": "string", - "description": "The FORMAT field that contains the dosage information. Set to DS to when a dosage field is not present." - } - }, - { - "bgen_reffirst": { - "type": "boolean", - "description": "Set true to write BGEN file with ref-first flag. With this option the first allele in the BGEN correspond to the REF allele." - } + }, + { + "name": "sratools_fasterqdump", + "path": "modules/nf-core/sratools/fasterqdump/meta.yml", + "type": "module", + "meta": { + "name": "sratools_fasterqdump", + "description": "Extract sequencing reads in FASTQ format from a given NCBI Sequence Read Archive (SRA).", + "keywords": ["sequencing", "FASTQ", "dump"], + "tools": [ + { + "sratools": { + "description": "SRA Toolkit and SDK from NCBI", + "homepage": "https://github.com/ncbi/sra-tools", + "documentation": "https://github.com/ncbi/sra-tools/wiki", + "tool_dev_url": "https://github.com/ncbi/sra-tools", + "licence": ["Public Domain"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]\n" + } + }, + { + "sra": { + "type": "directory", + "description": "Directory containing ETL data for the given SRA.", + "pattern": "*/*.sra" + } + } + ], + { + "ncbi_settings": { + "type": "file", + "description": "An NCBI user settings file.\n", + "pattern": "*.mkfg", + "ontologies": [] + } + }, + { + "certificate": { + "type": "file", + "description": "Path to a JWT cart file used to access protected dbGAP data on SRA using the sra-toolkit\n", + "pattern": "*.cart", + "ontologies": [] + } + } + ], + "output": { + "reads": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fastq.gz": { + "type": "file", + "description": "Extracted FASTQ file or files if the sequencing reads are paired-end.", + "pattern": "*.fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "versions_sratools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "sratools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "prefetch --version 2>&1 | grep -Eo '[0-9.]+'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_pigz": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "pigz": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pigz --version 2>&1 | sed 's/pigz //g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "sratools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "prefetch --version 2>&1 | grep -Eo '[0-9.]+'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "pigz": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pigz --version 2>&1 | sed 's/pigz //g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@Midnighter"], + "maintainers": ["@Midnighter", "@gallvp"] }, - { - "sample_name_mode": { - "type": "string", - "description": "Option to use to set IID/FID in the BGEN file. Allowed values are double-id, const-fid , or id-delim ." - } - } - ] - ], - "output": { - "bgen_file": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.bgen": { - "type": "file", - "description": "BGEN file version 1.2", - "pattern": "*.bgen", - "ontologies": [] - } - } - ] - ], - "sample_file": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.sample": { - "type": "file", - "description": "Sample file defining samples in the BGEN", - "pattern": "*.sample", - "ontologies": [] - } - } - ] - ], - "log_file": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.log": { - "type": "file", - "description": "Log file generated by plink2 with information on the process applied", - "pattern": "*.log", - "ontologies": [] - } - } + "pipelines": [ + { + "name": "fetchngs", + "version": "1.12.0" + }, + { + "name": "pathogensurveillance", + "version": "1.1.0" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@edg1983" - ], - "maintainers": [ - "@edg1983" - ] - } - }, - { - "name": "plink_bcf", - "path": "modules/nf-core/plink/bcf/meta.yml", - "type": "module", - "meta": { - "name": "plink_bcf", - "description": "Analyses binary variant call format (BCF) files using plink", - "keywords": [ - "plink", - "bcf", - "bed", - "bim", - "fam" - ], - "tools": [ - { - "plink": { - "description": "Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.", - "homepage": "https://www.cog-genomics.org/plink", - "documentation": "https://www.cog-genomics.org/plink/1.9/data#", - "tool_dev_url": "https://www.cog-genomics.org/plink/1.9/dev", - "licence": [ - "GPL" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + }, + { + "name": "sratools_prefetch", + "path": "modules/nf-core/sratools/prefetch/meta.yml", + "type": "module", + "meta": { + "name": "sratools_prefetch", + "description": "Download sequencing data from the NCBI Sequence Read Archive (SRA).", + "keywords": ["sequencing", "fastq", "prefetch"], + "tools": [ + { + "sratools": { + "description": "SRA Toolkit and SDK from NCBI", + "homepage": "https://github.com/ncbi/sra-tools", + "documentation": "https://github.com/ncbi/sra-tools/wiki", + "tool_dev_url": "https://github.com/ncbi/sra-tools", + "licence": ["Public Domain"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]\n" + } + }, + { + "id": { + "type": "string", + "description": "A string denoting an SRA id.\n" + } + } + ], + { + "ncbi_settings": { + "type": "file", + "description": "An NCBI user settings file.\n", + "pattern": "*.mkfg", + "ontologies": [] + } + }, + { + "certificate": { + "type": "file", + "description": "Path to a JWT cart file used to access protected dbGAP data on SRA using the sra-toolkit\n", + "pattern": "*.cart", + "ontologies": [] + } + } + ], + "output": { + "sra": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${id}": { + "type": "directory", + "description": "Directory containing SRA data files", + "pattern": "*/*.sra", + "ontologies": [] + } + } + ] + ], + "versions_sratools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "sratools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "prefetch --version 2>&1 | grep -Eo '[0-9.]+'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_curl": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "curl": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "curl --version | sed '1!d;s/^curl //; s/ .*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "sratools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "prefetch --version 2>&1 | grep -Eo '[0-9.]+'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "curl": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "curl --version | sed '1!d;s/^curl //; s/ .*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@Midnighter"], + "maintainers": ["@Midnighter", "@gallvp"] }, - { - "bcf": { - "type": "file", - "description": "Binary variant call format file (bcf)", - "pattern": "*.{bcf}", - "ontologies": [] - } - } - ] - ], - "output": { - "bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bed": { - "type": "file", - "description": "PLINK binary biallelic genotype table", - "pattern": "*.{bed}", - "ontologies": [] - } - } - ] - ], - "bim": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bim": { - "type": "file", - "description": "PLINK extended MAP file", - "pattern": "*.{bim}", - "ontologies": [] - } - } - ] - ], - "fam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.fam": { - "type": "file", - "description": "PLINK sample information file", - "pattern": "*.{fam}", - "ontologies": [] - } - } - ] - ], - "versions_plink": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "plink": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "plink --version 2>&1 | sed 's/^PLINK v//;s/ .*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@atrigila" - ], - "maintainers": [ - "@atrigila" - ], - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "plink": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "plink --version 2>&1 | sed 's/^PLINK v//;s/ .*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "fetchngs", + "version": "1.12.0" + } ] - ] - } - } - }, - { - "name": "plink_epistasis", - "path": "modules/nf-core/plink/epistasis/meta.yml", - "type": "module", - "meta": { - "name": "plink_epistasis", - "description": "Epistasis in PLINK, analyzing how the effects of one gene depend on the presence of others.", - "keywords": [ - "interactions", - "variants", - "regression" - ], - "tools": [ - { - "plink": { - "description": "Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.", - "homepage": "https://www.cog-genomics.org/plink", - "documentation": "https://www.cog-genomics.org/plink/1.9/data#recode", - "tool_dev_url": "https://www.cog-genomics.org/plink/1.9/dev", - "licence": [ - "GPL" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\nmeta is associated to the PLINK native file input\n" - } - }, - { - "bed": { - "type": "file", - "description": "PLINK binary biallelic genotype table file", - "pattern": "*.{bed}", - "ontologies": [] - } - }, - { - "bim": { - "type": "file", - "description": "PLINK extended MAP file", - "pattern": "*.{bim}", - "ontologies": [] - } - }, - { - "fam": { - "type": "file", - "description": "PLINK sample information file", - "pattern": "*.{fam}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information,\ne.g. [ id:'test', single_end:false ]\nmeta2 is associated to VCF file input\n" - } - }, - { - "vcf": { - "type": "file", - "description": "Variant calling file (vcf)", - "pattern": "*.{vcf}", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information,\ne.g. [ id:'test', single_end:false ]\nmeta3 is associated to BCF file input\n" - } - }, - { - "bcf": { - "type": "file", - "description": "PLINK variant information + sample ID + genotype call binary file", - "pattern": "*.{bcf}", - "ontologies": [] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing sample information,\ne.g. [ id:'test', single_end:false ]\nmeta4 is associated to phenotype file input\n" - } - }, - { - "phe": { - "type": "file", - "description": "PLINK file containing phenotype information. This phenotype information can be read from the third column with the --pheno option or from a specific column with the --pheno-name option.", - "pattern": "*.{phe}", - "ontologies": [] - } + }, + { + "name": "srst2_srst2", + "path": "modules/nf-core/srst2/srst2/meta.yml", + "type": "module", + "meta": { + "name": "srst2_srst2", + "description": "Short Read Sequence Typing for Bacterial Pathogens is a program designed to take Illumina sequence data,\na MLST database and/or a database of gene sequences (e.g. resistance genes, virulence genes, etc)\nand report the presence of STs and/or reference genes.\n", + "keywords": ["mlst", "typing", "illumina"], + "tools": [ + { + "srst2": { + "description": "Short Read Sequence Typing for Bacterial Pathogens", + "homepage": "http://katholt.github.io/srst2/", + "documentation": "https://github.com/katholt/srst2/blob/master/README.md", + "tool_dev_url": "https://github.com/katholt/srst2", + "doi": "10.1186/s13073-014-0090-6", + "licence": ["BSD"], + "identifier": "biotools:srst2" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\nid: should be the identification number or sample name\nsingle_end: should be true for single end data and false for paired in data\ndb: should be either 'gene' to use the --gene_db option or \"mlst\" to use the --mlst_db option\ne.g. [ id:'sample', single_end:false , db:'gene']\n" + } + }, + { + "fastq_s": { + "type": "file", + "description": "input FastQ files", + "pattern": "*.{fq,fastq,fq.gz,fastq.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + }, + { + "db": { + "type": "file", + "description": "Database in FASTA format", + "pattern": "*.fasta", + "ontologies": [] + } + } + ], + { + "db_type": { + "type": "string", + "description": "Type of database to use, either 'gene' or 'mlst'" + } + } + ], + "output": { + "gene_results": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample', single_end:false ]\n" + } + }, + { + "*_genes_*_results.txt": { + "type": "file", + "description": "SRST2 gene results", + "pattern": "*_genes_*_results.txt", + "ontologies": [] + } + } + ] + ], + "fullgene_results": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample', single_end:false ]\n" + } + }, + { + "*_fullgenes_*_results.txt": { + "type": "file", + "description": "SRST2 full gene results", + "pattern": "*_fullgenes_*_results.txt", + "ontologies": [] + } + } + ] + ], + "mlst_results": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample', single_end:false ]\n" + } + }, + { + "*_mlst_*_results.txt": { + "type": "file", + "description": "SRST2 MLST results", + "pattern": "*_mlst_*_results.txt", + "ontologies": [] + } + } + ] + ], + "pileup": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample', single_end:false ]\n" + } + }, + { + "*.pileup": { + "type": "file", + "description": "SAMtools pileup file", + "pattern": "*.pileup", + "ontologies": [] + } + } + ] + ], + "sorted_bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample', single_end:false ]\n" + } + }, + { + "*.sorted.bam": { + "type": "file", + "description": "Sorted BAM file", + "pattern": "*.sorted.bam", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@jvhagey"], + "maintainers": ["@jvhagey"] } - ] - ], - "output": { - "epi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.epi.cc": { - "type": "file", - "description": "PLINK epistasis file", - "pattern": "*.{epi.cc}", - "ontologies": [] - } - } - ] - ], - "episummary": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.epi.cc.summary": { - "type": "file", - "description": "PLINK epistasis summary file", - "pattern": "*.{epi.cc.summary}", - "ontologies": [] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.log": { - "type": "file", - "description": "PLINK epistasis log file", - "pattern": "*.{log}", - "ontologies": [] - } - } - ] - ], - "nosex": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.nosex": { - "type": "file", - "description": "Ambiguous sex ID file", - "pattern": "*.{nosex}", - "ontologies": [] - } - } - ] - ], - "versions_plink": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "plink": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "plink --version 2>&1 | sed 's/^PLINK v//;s/ .*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@davidebag" - ], - "maintainers": [ - "@davidebag" - ], - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "plink": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "plink --version 2>&1 | sed 's/^PLINK v//;s/ .*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - } - } - }, - { - "name": "plink_exclude", - "path": "modules/nf-core/plink/exclude/meta.yml", - "type": "module", - "meta": { - "name": "plink_exclude", - "description": "Exclude variant identifiers from plink bfiles", - "keywords": [ - "exclude", - "plink", - "variant identifiers" - ], - "tools": [ - { - "plink": { - "description": "Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.", - "homepage": "https://www.cog-genomics.org/plink", - "licence": [ - "GPL" - ], - "identifier": "" + }, + { + "name": "ssuissero", + "path": "modules/nf-core/ssuissero/meta.yml", + "type": "module", + "meta": { + "name": "ssuissero", + "description": "Serotype prediction of Streptococcus suis assemblies", + "keywords": ["bacteria", "fasta", "streptococcus"], + "tools": [ + { + "ssuissero": { + "description": "Rapid Streptococcus suis serotyping pipeline for Nanopore Data", + "homepage": "https://github.com/jimmyliu1326/SsuisSero", + 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"keywords": [ - "interactions", - "variants", - "regression" - ], - "tools": [ - { - "plink": { - "description": "Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.", - "homepage": "https://www.cog-genomics.org/plink", - "documentation": "https://www.cog-genomics.org/plink/1.9/data#recode", - "tool_dev_url": "https://www.cog-genomics.org/plink/1.9/dev", - "licence": [ - "GPL" - ], - "identifier": "" + }, + { + "name": "stainwarpy_register", + "path": "modules/nf-core/stainwarpy/register/meta.yml", + "type": "module", + "meta": { + "name": "stainwarpy_register", + "description": "Register H&E stained and Multiplexed tissue images using feature-based image registration", + "keywords": ["image registration", "histology", "hne", "multiplexed"], + "tools": [ + { + "stainwarpy": { + "description": "Register H&E stained and Multiplexed tissue images using feature-based image registration", + "homepage": "https://github.com/tckumarasekara/stainwarpy", + "documentation": "https://github.com/tckumarasekara/stainwarpy", + "tool_dev_url": "https://github.com/tckumarasekara/stainwarpy", + "licence": ["MIT License", "Apache-2.0"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "hne_img": { + "type": "file", + "description": "H&E stained image file", + "pattern": "*.{ome.tif,ome.tiff,tif,tiff}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3727" + }, + { + "edam": "http://edamontology.org/format_3591" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "multiplx_img": { + "type": "file", + "description": "Multiplexed image file", + "pattern": "*.{ome.tif,ome.tiff,tif,tiff}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3727" + }, + { + "edam": "http://edamontology.org/format_3591" + } + ] + } + } + ], + { + "fixed_img": { + "type": "string", + "description": "Which image to use as fixed image for registration. 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} - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\nmeta is associated to the PLINK native file input\n" - } - }, - { - "bed": { - "type": "file", - "description": "PLINK binary biallelic genotype table file", - "pattern": "*.{bed}", - "ontologies": [] - } - }, - { - "bim": { - "type": "file", - "description": "PLINK extended MAP file", - "pattern": "*.{bim}", - "ontologies": [] - } - }, - { - "fam": { - "type": "file", - "description": "PLINK sample information file", - "pattern": "*.{fam}", - "ontologies": [] - } + }, + { + "name": "stainwarpy_transformsegmask", + "path": "modules/nf-core/stainwarpy/transformsegmask/meta.yml", + "type": "module", + "meta": { + "name": "stainwarpy_transformsegmask", + "description": "Transform segmentation mask of multiplexed or H&E stained tissue images using stainwarpy", + "keywords": ["image registration", "histology", "hne", "multiplexed", "segmentation mask"], + "tools": [ + { + "stainwarpy": { + "description": "Register H&E stained and Multiplexed tissue images using feature-based image registration", + "homepage": "https://github.com/tckumarasekara/stainwarpy", + "documentation": "https://github.com/tckumarasekara/stainwarpy", + "tool_dev_url": "https://github.com/tckumarasekara/stainwarpy", + "licence": ["MIT License", "Apache-2.0"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "hne_img": { + "type": "file", + "description": "H&E stained image file", + "pattern": "*.{ome.tif,ome.tiff,tif,tiff}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3727" + }, + { + "edam": "http://edamontology.org/format_3591" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "multiplx_img": { + "type": "file", + "description": "Multiplexed image file", + "pattern": "*.{ome.tif,ome.tiff,tif,tiff}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3727" + }, + { + "edam": "http://edamontology.org/format_3591" + } + ] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "seg_mask": { + "type": "file", + "description": "Segmentation mask file", + "pattern": "*.{ome.tif,ome.tiff,tif,tiff,npy}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3727" + }, + { + "edam": "http://edamontology.org/format_3591" + } + ] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "tform_map": { + "type": "file", + "description": "Transformation map file", + "pattern": "*.npy", + "ontologies": [] + } + } + ], + { + "fixed_img": { + "type": "string", + "description": "Which image to use as fixed image for registration. Options - 'hne' or 'multiplexed'", + "ontologies": [] + } + }, + { + "final_sz": { + "type": "string", + "description": "In which pixel size to output the registered image and segmentation mask. Options - 'hne' or 'multiplexed'", + "ontologies": [] + } + } + ], + "output": { + "transformed_seg_mask": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_transformed_segmentation_mask.ome.tif": { + "type": "file", + "description": "Transformed segmentation mask in OME-TIFF format", + "pattern": "*_transformed_segmentation_mask.ome.tif", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3727" + } + ] + } + } + ] + ], + "versions_stainwarpy": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "stainwarpy": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "stainwarpy --version | sed 's/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "stainwarpy": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "stainwarpy --version | sed 's/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@tckumarasekara"], + "maintainers": ["@tckumarasekara"] } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information,\ne.g. [ id:'test', single_end:false ]\nmeta2 is associated to VCF file input\n" - } - }, - { - "vcf": { - "type": "file", - "description": "Variant calling file (vcf)", - "pattern": "*.{vcf}", - "ontologies": [] - } + }, + { + "name": "staphopiasccmec", + "path": "modules/nf-core/staphopiasccmec/meta.yml", + "type": "module", + "meta": { + "name": "staphopiasccmec", + "description": "Predicts Staphylococcus aureus SCCmec type based on primers.", + "keywords": ["amr", "fasta", "sccmec"], + "tools": [ + { + "staphopiasccmec": { + "description": "Predicts Staphylococcus aureus SCCmec type based on primers.", + "homepage": "https://staphopia.emory.edu", + "documentation": "https://github.com/staphopia/staphopia-sccmec", + "tool_dev_url": "https://github.com/staphopia/staphopia-sccmec", + "doi": "10.7717/peerj.5261", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA assembly file", + "pattern": "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}", + "ontologies": [] + } + } + ] + ], + "output": { + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "Tab-delimited results", + "pattern": "*.{tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_staphopiasccmec": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "staphopiasccmec": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "staphopia-sccmec --version 2>&1 | sed \"s/^.*staphopia-sccmec //\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "staphopiasccmec": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "staphopia-sccmec --version 2>&1 | sed \"s/^.*staphopia-sccmec //\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@rpetit3"], + "maintainers": ["@rpetit3"] } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information,\ne.g. [ id:'test', single_end:false ]\nmeta3 is associated to BCF file input\n" - } - }, - { - "bcf": { - "type": "file", - "description": "PLINK variant information + sample ID + genotype call binary file", - "pattern": "*.{bcf}", - "ontologies": [] - } + }, + { + "name": "staphscan", + "path": "modules/nf-core/staphscan/meta.yml", + "type": "module", + "meta": { + "name": "staphscan", + "description": "staphscan is a tool to screen genome assemblies of Staphylococcus aureus", + "keywords": ["screen", "assembly", "Staphylococcus", "aureus"], + "tools": [ + { + "staphscan": { + "description": "a genomic surveillance framework for Staphylococcus aureus", + "homepage": "https://github.com/riccabolla/StaphSCAN", + "documentation": "https://staphscan.readthedocs.io/en/latest/", + "tool_dev_url": "https://github.com/riccabolla/StaphSCAN", + "doi": "10.5281/zenodo.18458858", + "licence": ["MIT"], + "identifier": "biotools:staphscan" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fastas": { + "type": "list", + "description": "Staphylococcus aureus genome assemblies to be screened", + "pattern": "*.fasta" + } + } + ] + ], + "output": { + "tsv": [ + [ + { + "meta": { + "type": "string", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "Result file generated after screening", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_staphscan": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "staphscan": { + "type": "string", + "description": "The tool name" + } + }, + { + "staphscan --version | sed 's/staphscan //;'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "staphscan": { + "type": "string", + "description": "The tool name" + } + }, + { + "staphscan --version | sed 's/staphscan //;'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@riccabolla"], + "maintainers": ["@riccabolla"] } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing sample information,\ne.g. [ id:'test', single_end:false ]\nmeta4 is associated to phenotype file input\n" - } + }, + { + "name": "star_align", + "path": "modules/nf-core/star/align/meta.yml", + "type": "module", + "meta": { + "name": "star_align", + "description": "Align reads to a reference genome using STAR", + "keywords": ["align", "fasta", "genome", "reference"], + "tools": [ + { + "star": { + "description": "STAR is a software package for mapping DNA sequences against\na large reference genome, such as the human genome.\n", + "homepage": "https://github.com/alexdobin/STAR", + "manual": "https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf", + "doi": "10.1093/bioinformatics/bts635", + "licence": ["MIT"], + "identifier": "biotools:star" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "index": { + "type": "directory", + "description": "STAR genome index", + "pattern": "star" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "gtf": { + "type": "file", + "description": "Annotation GTF file", + "pattern": "*.{gtf}", + "ontologies": [] + } + } + ], + { + "star_ignore_sjdbgtf": { + "type": "boolean", + "description": "Ignore annotation GTF file" + } + } + ], + "output": { + "log_final": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*Log.final.out": { + "type": "file", + "description": "STAR final log file", + "pattern": "*Log.final.out", + "ontologies": [] + } + } + ] + ], + "log_out": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*Log.out": { + "type": "file", + "description": "STAR lot out file", + "pattern": "*Log.out", + "ontologies": [] + } + } + ] + ], + "log_progress": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*Log.progress.out": { + "type": "file", + "description": "STAR log progress file", + "pattern": "*Log.progress.out", + "ontologies": [] + } + } + ] + ], + "versions_star": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "star": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "STAR --version | sed \"s/STAR_//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_samtools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "samtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "samtools --version | sed -n '1s/samtools //p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_gawk": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "gawk": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "gawk --version | sed -n '1s/GNU Awk \\([0-9.]*\\).*/\\1/p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*d.out.bam": { + "type": "file", + "description": "Output BAM file containing read alignments", + "pattern": "*.{bam}", + "ontologies": [] + } + } + ] + ], + "bam_sorted": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.sortedByCoord.out.bam": { + 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"Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*Aligned.unsort.out.bam": { + "type": "file", + "description": "Unsorted BAM file of read alignments (optional)", + "pattern": "*Aligned.unsort.out.bam", + "ontologies": [] + } + } + ] + ], + "fastq": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*fastq.gz": { + "type": "file", + "description": "Unmapped FastQ files (optional)", + "pattern": "*fastq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "tab": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tab": { + "type": "file", + "description": "STAR output tab file(s) (optional)", + "pattern": "*.tab", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + 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Produced with the option --allow-no-sex", - "pattern": "*.{nosex}", - "ontologies": [] - } - } - ] - ], - "versions_plink": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "plink": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "plink --version 2>&1 | sed 's/^PLINK v//;s/ .*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@LorenzoS96" - ], - "maintainers": [ - "@LorenzoS96" - ], - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "plink": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "plink --version 2>&1 | sed 's/^PLINK v//;s/ .*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "rnavar", + "version": "1.2.3" + } ] - ] - } - }, - "pipelines": [ + }, { - "name": "gwas", - "version": "dev" - } - ] - }, - { - "name": "plink_hwe", - "path": "modules/nf-core/plink/hwe/meta.yml", - "type": "module", - "meta": { - "name": "plink_hwe", - "description": "Generate Hardy-Weinberg statistics for provided input", - "keywords": [ - "hardy-weinberg", - "hwe statistics", - "hwe equilibrium" - ], - "tools": [ - { - "plink": { - "description": "Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.", - "homepage": "https://www.cog-genomics.org/plink", - "documentation": "https://www.cog-genomics.org/plink/1.9/data#recode", - "tool_dev_url": "https://www.cog-genomics.org/plink/1.9/dev", - "licence": [ - "GPL" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\nmeta is associated to PLINK native files input\n" - } - }, - { - "bed": { - "type": "file", - "description": "PLINK binary biallelic genotype table file", - "pattern": "*.{bed}", - "ontologies": [] - } - }, - { - "bim": { - "type": "file", - "description": "PLINK extended MAP file", - "pattern": "*.{bim}", - "ontologies": [] - } - }, - { - "fam": { - "type": "file", - "description": "PLINK sample information file", - "pattern": "*.{fam}", - "ontologies": [] - } + "name": "star_starsolo", + "path": "modules/nf-core/star/starsolo/meta.yml", + "type": "module", + "meta": { + "name": "starsolo", + "description": "Create a counts matrix for single-cell data using STARSolo, handling cell barcodes and UMI information.", + "keywords": ["align", "count", "genome", "reference"], + "tools": [ + { + "starsolo": { + "description": "Mapping, demultiplexing and quantification for single cell RNA-seq.", + "homepage": "https://github.com/alexdobin/STAR/", + "documentation": "https://github.com/alexdobin/STAR/blob/master/docs/STARsolo.md", + "doi": "10.1101/2021.05.05.442755", + "licence": ["MIT"], + "identifier": "biotools:star" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information.\nHere, you should add all the specific barcode/umi\ninformation for each sample.\ne.g. `[ id:'test_starsolo', umi_len:'12', cb_start:1 ]`\n" + } + }, + { + "solotype": { + "type": "string", + "description": "Type of single-cell library.\nIt can be CB_UMI_Simple for most common ones such as 10xv2 and 10xv3,\nCB_UMI_Complex for method such as inDrop and SmartSeq for SMART-Seq.\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", + "ontologies": [] + } + } + ], + { + "opt_whitelist": { + "type": "file", + "description": "Optional whitelist file", + "ontologies": [] + } + }, + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing the STAR index information." + } + }, + { + "index": { + "type": "directory", + "description": "STAR genome index", + "pattern": "star" + } + } + ] + ], + "output": { + "counts": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information.\nHere, you should add all the specific barcode/umi\ninformation for each sample.\ne.g. `[ id:'test_starsolo', umi_len:'12', cb_start:1 ]`\n" + } + }, + { + "*.Solo.out": { + "type": "file", + "description": "STARSolo counts matrix", + "pattern": "*.Solo.out", + "ontologies": [] + } + } + ] + ], + "log_final": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information.\nHere, you should add all the specific barcode/umi\ninformation for each sample.\ne.g. `[ id:'test_starsolo', umi_len:'12', cb_start:1 ]`\n" + } + }, + { + "*Log.final.out": { + "type": "file", + "description": "STAR final log file", + "pattern": "*Log.final.out", + "ontologies": [] + } + } + ] + ], + "log_out": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information.\nHere, you should add all the specific barcode/umi\ninformation for each sample.\ne.g. `[ id:'test_starsolo', umi_len:'12', cb_start:1 ]`\n" + } + }, + { + "*Log.out": { + "type": "file", + "description": "STAR lot out file", + "pattern": "*Log.out", + "ontologies": [] + } + } + ] + ], + "log_progress": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information.\nHere, you should add all the specific barcode/umi\ninformation for each sample.\ne.g. `[ id:'test_starsolo', umi_len:'12', cb_start:1 ]`\n" + } + }, + { + "*Log.progress.out": { + "type": "file", + "description": "STAR log progress file", + "pattern": "*Log.progress.out", + "ontologies": [] + } + } + ] + ], + "summary": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information.\nHere, you should add all the specific barcode/umi\ninformation for each sample.\ne.g. `[ id:'test_starsolo', umi_len:'12', cb_start:1 ]`\n" + } + }, + { + "*/Gene/Summary.csv": { + "type": "file", + "description": "STARSolo metrics summary CSV file.", + "pattern": "*/Gene/Summary.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": [ + "@kevinmenden", + "@ggabernet", + "@grst", + "@fmalmeida", + "@rhreynolds", + "@apeltzer", + "@vivian-chen16", + "@maxulysse", + "@joaodemeirelles" + ], + "maintainers": [ + "@kevinmenden", + "@ggabernet", + "@grst", + "@fmalmeida", + "@rhreynolds", + "@apeltzer", + "@vivian-chen16", + "@maxulysse", + "@joaodemeirelles" + ] } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\nmeta2 is associated to VCF files input\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF format input file", - "pattern": "*.{vcf} | *{vcf.gz}", - "ontologies": [] - } + }, + { + "name": "staramr_search", + "path": "modules/nf-core/staramr/search/meta.yml", + "type": "module", + "meta": { + "name": "staramr_search", + "description": "Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.", + "keywords": ["amr", "plasmid", "mlst", "genomics"], + "tools": [ + { + "staramr": { + "description": "Scan genome contigs against the ResFinder and PointFinder databases. In order to use the PointFinder databases, you will have to add --pointfinder-organism ORGANISM to the ext.args options.\n", + "homepage": "https://github.com/phac-nml/staramr", + "documentation": "https://github.com/phac-nml/staramr", + "tool_dev_url": "https://github.com/phac-nml/staramr", + "doi": "10.3390/microorganisms10020292", + "licence": ["Apache Software License"], + "identifier": "biotools:staramr" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "genome_fasta": { + "type": "file", + "description": "Assembled/complete genome(s) in FASTA format to search for AMR/MLST/Plasmids.\n", + "pattern": "*.{fasta,fna,fsa,fa,fasta.gz,fna.gz,fsa.gz,fa.gz}", + "ontologies": [] + } + } + ] + ], + "output": { + "results_xlsx": [ + [ + { + "meta": { + "type": "file", + "description": "Excel spreadsheet containing summary of StarAMR results.", + "pattern": "*_results/results.xlsx", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3977" + } + ] + } + }, + { + "*_results/results.xlsx": { + "type": "file", + "description": "Excel spreadsheet containing summary of StarAMR results.", + "pattern": "*_results/results.xlsx", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3977" + } + ] + } + } + ] + ], + "summary_tsv": [ + [ + { + "meta": { + "type": "file", + "description": "Excel spreadsheet containing summary of StarAMR results.", + "pattern": "*_results/results.xlsx", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3977" + } + ] + } + }, + { + "*_results/summary.tsv": { + "type": "file", + "description": "A summary of all detected AMR genes/mutations/plasmids/sequence type in each genome, one genome per line.\nA series of descriptive statistics is also provided for each genome,\nas well as feedback for whether or not the genome passes several quality metrics and if not,\nfeedback on why the genome fails.\n", + "pattern": "*_results/summary.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "detailed_summary_tsv": [ + [ + { + "meta": { + "type": "file", + "description": "Excel spreadsheet containing summary of StarAMR results.", + "pattern": "*_results/results.xlsx", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3977" + } + ] + } + }, + { + "*_results/detailed_summary.tsv": { + "type": "file", + "description": "A summary of all detected AMR genes/mutations/plasmids/sequence type in each genome, one genome per line.\nA series of descriptive statistics is also provided for each genome,\nas well as feedback for whether or not the genome passes several quality metrics and if not,\nfeedback on why the genome fails.\n", + "pattern": "*_results/detailed_summary.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "resfinder_tsv": [ + [ + { + "meta": { + "type": "file", + "description": "Excel spreadsheet containing summary of StarAMR results.", + "pattern": "*_results/results.xlsx", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3977" + } + ] + } + }, + { + "*_results/resfinder.tsv": { + "type": "file", + "description": "A tabular file of each AMR gene and additional BLAST information from the ResFinder database, one gene per line.", + "pattern": "*_results/resfinder.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "plasmidfinder_tsv": [ + [ + { + "meta": { + "type": "file", + "description": "Excel spreadsheet containing summary of StarAMR results.", + "pattern": "*_results/results.xlsx", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3977" + } + ] + } + }, + { + "*_results/plasmidfinder.tsv": { + "type": "file", + "description": "A tabular file of each AMR plasmid type and additional BLAST information from the PlasmidFinder database, one plasmid type per line.", + "pattern": "*_results/plasmidfinder.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "mlst_tsv": [ + [ + { + "meta": { + "type": "file", + "description": "Excel spreadsheet containing summary of StarAMR results.", + "pattern": "*_results/results.xlsx", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3977" + } + ] + } + }, + { + "*_results/mlst.tsv": { + "type": "file", + "description": "A tabular file of each multi-locus sequence type (MLST) and it's corresponding locus/alleles, one genome per line.", + "pattern": "*_results/mlst.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "settings_txt": [ + [ + { + "meta": { + "type": "file", + "description": "Excel spreadsheet containing summary of StarAMR results.", + "pattern": "*_results/results.xlsx", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3977" + } + ] + } + }, + { + "*_results/settings.txt": { + "type": "file", + "description": "The command-line, database versions, and other settings used to run staramr.", + "pattern": "*_results/settings.txt", + "ontologies": [] + } + } + ] + ], + "pointfinder_tsv": [ + [ + { + "meta": { + "type": "file", + "description": "Excel spreadsheet containing summary of StarAMR results.", + "pattern": "*_results/results.xlsx", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3977" + } + ] + } + }, + { + "*_results/pointfinder.tsv": { + "type": "file", + "description": "An optional tabular file of each AMR point mutation and additional BLAST information from the PointFinder database, one gene per line.", + "pattern": "*_results/pointfinder.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@apetkau"], + "maintainers": ["@apetkau"] } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\nmeta is associated to BCF files input\n" - } + }, + { + "name": "stardist", + "path": "modules/nf-core/stardist/meta.yml", + "type": "module", + "meta": { + "name": "stardist", + "description": "Cell and nuclear segmentation with star-convex shapes", + "keywords": ["stardist", "segmentation", "image", "gpu", "spatial-transcriptomics"], + "tools": [ + { + "stardist": { + "description": "Stardist is an cell segmentation tool developed in Python by Martin Weigert and Uwe Schmidt", + "homepage": "https://stardist.net/", + "documentation": "https://stardist.net/faq/", + "tool_dev_url": "https://github.com/stardist/stardist", + "doi": "10.1109/ISBIC56247.2022.9854534", + "licence": ["BSD 3-Clause"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "image": { + "type": "file", + "description": "Single channel nuclear image", + "pattern": "*.{tiff,tif}", + "ontologies": [] + } + } + ], + [ + { + "model_name": { + "type": "string", + "description": "Name of a pretrained StarDist model (e.g. '2D_versatile_fluo',\n'2D_versatile_he'). Used when model_path is not provided.\nPass '' (empty string) if providing a custom model path or\npassing -m via ext.args.\n" + } + }, + { + "model_path": { + "type": "file", + "description": "Optional path to a custom StarDist model directory. When provided,\ntakes precedence over model_name. Pass [] (empty list) to use a\npretrained model name instead.\n", + "pattern": "*", + "ontologies": [] + } + } + ] + ], + "output": { + "mask": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.stardist.tif": { + "type": "file", + "description": "labelled mask output from stardist in tif format.", + "pattern": "*.{tiff,tif}", + "ontologies": [] + } + } + ] + ], + "versions_stardist": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "stardist": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pip show stardist | sed -n 's/^Version: //p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_python": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "python": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python --version | sed 's/Python //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_tensorflow": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "tensorflow": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pip show tensorflow | sed -n 's/^Version: //p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_tifffile": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "tifffile": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pip show tifffile | sed -n 's/^Version: //p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "stardist": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pip show stardist | sed -n 's/^Version: //p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "python": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python --version | sed 's/Python //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "tensorflow": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pip show tensorflow | sed -n 's/^Version: //p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "tifffile": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pip show tifffile | sed -n 's/^Version: //p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@migueLib", "@dongzehe"], + "maintainers": ["@migueLib"], + "notes": "GPU support: The container (built via Seqera Containers) includes TensorFlow 2.20.0\nwith CUDA support and falls back to CPU automatically when no GPU is available.\nUse the `process_gpu` label to request GPU resources from your executor.\nWhen running with conda/mamba, GPU support depends on having a CUDA-enabled\nTensorFlow installation in your environment.\n\nModel selection via the model input channel [model_name, model_path]:\n - Pretrained model: [ '2D_versatile_fluo', [] ]\n - Custom model directory: [ '', file(\"/path/to/model\") ]\n - Via ext.args only: [ '', [] ] (then set ext.args = '-m ...')\n\nAdditional stardist CLI arguments can be passed via `task.ext.args`:\n ext.args = '--n_tiles 4,4 --prob_thresh 0.5 --nms_thresh 0.3'\n\nModel weights are not bundled in the container. StarDist downloads pretrained\nmodels on first use to ~/.keras/models/.\n" }, - { - "bcf": { - "type": "file", - "description": "BCF format input file", - "pattern": "*.{bcf}", - "ontologies": [] - } - } - ] - ], - "output": { - "hwe": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.hwe": { - "type": "file", - "description": "Summary file containing observed vs expected heterozygous frequencies and the\np-value of the hardy-weinberg statistics\n", - "ontologies": [] - } - } - ] - ], - "versions_plink": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "plink": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "plink --version 2>&1 | sed 's/^PLINK v//;s/ .*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@lescai" - ], - "maintainers": [ - "@lescai" - ], - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "plink": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "plink --version 2>&1 | sed 's/^PLINK v//;s/ .*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "molkart", + "version": "1.2.0" + }, + { + "name": "spatialxe", + "version": "dev" + } ] - ] - } - } - }, - { - "name": "plink_indep", - "path": "modules/nf-core/plink/indep/meta.yml", - "type": "module", - "meta": { - "name": "plink_indep", - "description": "Produce a pruned subset of markers that are in approximate linkage equilibrium with each other.", - "keywords": [ - "plink", - "indep", - "variant pruning", - "bim", - "fam" - ], - "tools": [ - { - "plink": { - "description": "Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.", - "homepage": "https://www.cog-genomics.org/plink", - "documentation": "https://www.cog-genomics.org/plink/1.9/data#", - "tool_dev_url": "https://www.cog-genomics.org/plink/1.9/dev", - "licence": [ - "GPL" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bed": { - "type": "file", - "description": "PLINK binary biallelic genotype table file", - "pattern": "*.{bed}", - "ontologies": [] - } - }, - { - "bim": { - "type": "file", - "description": "PLINK extended MAP file", - "pattern": "*.{bim}", - "ontologies": [] - } + }, + { + "name": "stare", + "path": "modules/nf-core/stare/meta.yml", + "type": "module", + "meta": { + "name": "stare", + "description": "Framework that scores enhancer–gene interactions using the Activity-By-Contact model and derives transcription factor affinities on gene level", + "keywords": ["enhancer", "tf_affinity", "abc_model", "genomics", "gene_regulation"], + "tools": [ + { + "stare": { + "description": "Score enhancer–gene interactions with ABC and compute TF-gene affinity matrices", + "homepage": "https://github.com/SchulzLab/STARE", + "documentation": "https://stare.readthedocs.io/en/latest/Main.html", + "tool_dev_url": "https://github.com/SchulzLab/STARE", + "doi": "10.1093/bioinformatics/btad062", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "bed_file": { + "type": "file", + "description": "BED file with non-overlapping candidate regions; optional—if omitted runs in promoter-mode around TSS", + "pattern": "*.bed", + "optional": true, + "ontologies": [ + { + "ucsc": "https://genome.ucsc.edu/FAQ/FAQformat#format1" + } + ] + } + }, + { + "contact_folder": { + "type": "directory", + "description": "Directory of gzipped chromatin contact files per chromosome; if not provided use distance-based estimate", + "optional": true + } + }, + { + "existing_abc": { + "type": "file", + "description": "Precomputed ABC‐scoring file (must contain Ensembl ID, PeakID, intergenicScore columns) to reuse interactions", + "pattern": "*.txt.gz", + "optional": true, + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "annotation": { + "type": "file", + "description": "Gene annotation file in GTF format (e.g. Gencode); full annotation recommended for ABC scoring", + "pattern": "*.gtf", + "ontologies": [ + { + "bioontology": "http://edamontology.org/format_2306" + } + ] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "genome": { + "type": "file", + "description": "Genome FASTA file in RefSeq format", + "pattern": "*.{fa,fasta}", + "ontologies": [ + { + "bioontology": "http://edamontology.org/format_1929" + } + ] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "psem": { + "type": "file", + "description": "Position Specific Energy Matrix or Count Matrix in transfac format; converted automatically to PSEM using sequence background from bed_file", + "pattern": "*.transfac", + "ontologies": [] + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "exclude_bed": { + "type": "file", + "description": "BED file with regions to exclude; overlapping regions are discarded", + "pattern": "*.bed", + "optional": true, + "ontologies": [ + { + "ucsc": "https://genome.ucsc.edu/FAQ/FAQformat#format1" + } + ] + } + } + ], + [ + { + "meta6": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "genes": { + "type": "file", + "description": "File listing gene IDs or symbols to restrict output; optional", + "pattern": "*.{txt,tsv}", + "optional": true, + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "output": { + "affinities": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n", + "pattern": "${prefix}/Gene_TF_matrices/${prefix}_TF_Gene_Affinities.txt" + } + }, + { + "${meta.id}/Gene_TF_matrices/${meta.id}_TF_Gene_Affinities.txt": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n", + "pattern": "${prefix}/Gene_TF_matrices/${prefix}_TF_Gene_Affinities.txt" + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@LeonHafner"], + "maintainers": ["@LeonHafner"] }, - { - "fam": { - "type": "file", - "description": "PLINK sample information file", - "pattern": "*.{fam}", - "ontologies": [] - } - } - ], - { - "window_size": { - "type": "string", - "description": "Window size in variant count or kilobase (if the 'kb' modifier is present) units, a variant count to shift the window at the end of each step, and a variance inflation factor (VIF) threshold." - } - }, - { - "variant_count": { - "type": "string", - "description": "Variant count to shift the window at the end of each step." - } - }, - { - "variance_inflation_factor": { - "type": "string", - "description": "Variance inflation factor (VIF) threshold. At each step, all variants in the current window with VIF exceeding the threshold are removed." - } - } - ], - "output": { - "prunein": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.prune.in": { - "type": "file", - "description": "File with IDs of pruned subset of markers that are in approximate linkage equilibrium with each other", - "pattern": "*.{prune.in}", - "ontologies": [] - } - } - ] - ], - "pruneout": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.prune.out": { - "type": "file", - "description": "File with IDs of excluded variants", - "pattern": "*.{prune.out}", - "ontologies": [] - } - } - ] - ], - "versions_plink": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "plink": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "plink --version 2>&1 | sed 's/^PLINK v//;s/ .*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@atrigila" - ], - "maintainers": [ - "@atrigila" - ], - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "plink": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "plink --version 2>&1 | sed 's/^PLINK v//;s/ .*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "tfactivity", + "version": "dev" + } ] - ] - } - } - }, - { - "name": "plink_indeppairwise", - "path": "modules/nf-core/plink/indeppairwise/meta.yml", - "type": "module", - "meta": { - "name": "plink_indeppairwise", - "description": "Produce a pruned subset of markers that are in approximate linkage equilibrium with each other. Pairs of variants in the current window with squared correlation greater than the threshold are noted and variants are greedily pruned from the window until no such pairs remain.", - "keywords": [ - "plink", - "indep pairwise", - "variant pruning", - "bim", - "fam" - ], - "tools": [ - { - "plink": { - "description": "Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.", - "homepage": "https://www.cog-genomics.org/plink", - "documentation": "https://www.cog-genomics.org/plink/1.9/data", - "tool_dev_url": "https://www.cog-genomics.org/plink/1.9/dev", - "licence": [ - "GPL" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bed": { - "type": "file", - "description": "PLINK binary biallelic genotype table file", - "pattern": "*.{bed}", - "ontologies": [] - } - }, - { - "bim": { - "type": "file", - "description": "PLINK extended MAP file", - "pattern": "*.{bim}", - "ontologies": [] - } + }, + { + "name": "starfusion_build", + "path": "modules/nf-core/starfusion/build/meta.yml", + "type": "module", + "meta": { + "name": "starfusion_build", + "description": "Download STAR-fusion genome resource required to run STAR-Fusion caller", + "keywords": ["download", "starfusion", "build"], + "tools": [ + { + "star-fusion": { + "description": "Fusion calling algorithm for RNAseq data", + "homepage": "https://github.com/STAR-Fusion/", + "documentation": "https://github.com/STAR-Fusion/STAR-Fusion/wiki/installing-star-fusion", + "tool_dev_url": "https://github.com/STAR-Fusion/STAR-Fusion", + "doi": "10.1186/s13059-019-1842-9", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Metadata map", + "required": true + } + }, + { + "fasta": { + "type": "file", + "description": "Input FASTA file", + "pattern": "*.{fa,fasta}", + "required": true, + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Second metadata map", + "required": true + } + }, + { + "gtf": { + "type": "file", + "description": "Input GTF (Gene Transfer Format) file", + "pattern": "*.gtf", + "required": true, + "ontologies": [ + { + "edam": "http://edamontology.org/format_2306" + } + ] + } + } + ], + { + "fusion_annot_lib": { + "type": "file", + "description": "Fusion annotation library file containing known fusion genes", + "required": true, + "ontologies": [ + { + "edam": "http://edamontology.org/topic_0203" + } + ] + } + }, + { + "dfam_species": { + "type": "string", + "description": "Dfam species name" + } + } + ], + "output": { + "reference": [ + [ + { + "meta": { + "type": "map", + "description": "Metadata map" + } + }, + { + "${prefix}_genome_lib_build_dir": { + "type": "directory", + "description": "Genome library build directory", + "pattern": "*_genome_lib_build_dir" + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@praveenraj2018", "@martings", "@alanmmobbs93", "@delfiterradas", "@sofiromano"], + "maintainers": ["@praveenraj2018"] }, - { - "fam": { - "type": "file", - "description": "PLINK sample information file", - "pattern": "*.{fam}", - "ontologies": [] - } - } - ], - { - "window_size": { - "type": "string", - "description": "Window size in variant count or kilobase (if the 'kb' modifier is present) units, a variant count to shift the window at the end of each step, and a variance inflation factor (VIF) threshold." - } - }, - { - "variant_count": { - "type": "string", - "description": "Variant count to shift the window at the end of each step." - } - }, - { - "r2_threshold": { - "type": "string", - "description": "Pairwise r2 threshold. At each step, pairs of variants in the current window with squared correlation greater than the threshold are noted, and variants are greedily pruned from the window until no such pairs remain" - } - } - ], - "output": { - "prunein": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.prune.in": { - "type": "file", - "description": "File with IDs of pruned subset of markers that are in approximate linkage equilibrium with each other", - "pattern": "*.{prune.in}", - "ontologies": [] - } - } - ] - ], - "pruneout": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.prune.out": { - "type": "file", - "description": "File with IDs of excluded variants", - "pattern": "*.{prune.out}", - "ontologies": [] - } - } - ] - ], - "versions_plink": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "plink": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "plink --version 2>&1 | sed 's/^PLINK v//;s/ .*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@atrigila" - ], - "maintainers": [ - "@atrigila" - ], - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "plink": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "plink --version 2>&1 | sed 's/^PLINK v//;s/ .*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "rnafusion", + "version": "4.1.2" + } ] - ] - } - } - }, - { - "name": "plink_ld", - "path": "modules/nf-core/plink/ld/meta.yml", - "type": "module", - "meta": { - "name": "plink_ld", - "description": "LD analysis in PLINK examines genetic variant associations within populations", - "keywords": [ - "genetics", - "associations", - "variants" - ], - "tools": [ - { - "plink": { - "description": "Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.", - "homepage": "https://www.cog-genomics.org/plink", - "documentation": "https://www.cog-genomics.org/plink/1.9/data#recode", - "tool_dev_url": "https://www.cog-genomics.org/plink/1.9/dev", - "licence": [ - "GPL" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\nmeta is associated to PLINK native files input\n" - } - }, - { - "bed": { - "type": "file", - "description": "PLINK binary biallelic genotype table file", - "pattern": "*.{bed}", - "ontologies": [] - } - }, - { - "bim": { - "type": "file", - "description": "PLINK extended MAP file", - "pattern": "*.{bim}", - "ontologies": [] - } - }, - { - "fam": { - "type": "file", - "description": "PLINK sample information file", - "pattern": "*.{fam}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\nmeta2 is associated to VCF files input\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF format input file", - "pattern": "*.{vcf} | *{vcf.gz}", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\nmeta is associated to BCF files input\n" - } - }, - { - "bcf": { - "type": "file", - "description": "BCF format input file", - "pattern": "*.{bcf}", - "ontologies": [] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\nmeta is associated to randomly selected snp files input\n" - } + }, + { + "name": "starfusion_detect", + "path": "modules/nf-core/starfusion/detect/meta.yml", + "type": "module", + "meta": { + "name": "starfusion_detect", + "description": "Fast and Accurate Fusion Transcript Detection from RNA-Seq", + "keywords": ["Fusion", "starfusion", "RNA-Seq", "detect"], + "tools": [ + { + "star-fusion": { + "description": "Fast and Accurate Fusion Transcript Detection from RNA-Seq", + "homepage": "https://github.com/STAR-Fusion/STAR-Fusion", + "documentation": "https://github.com/STAR-Fusion/STAR-Fusion/wiki", + "tool_dev_url": "https://github.com/STAR-Fusion/STAR-Fusion/releases", + "doi": "10.1101/120295v1", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "Input fastq files", + "pattern": "*.{fq,fastq,fq.gz,fastq.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + }, + { + "junction": { + "type": "file", + "description": "Chimeric junction output from STAR aligner", + "pattern": "*.{out.junction}", + "ontologies": [] + } + } + ], + { + "reference": { + "type": "directory", + "description": "STAR-fusion reference genome lib folder", + "pattern": "*genome_lib_build_dir" + } + } + ], + "output": { + "fusions": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fusion_predictions.tsv": { + "type": "file", + "description": "Fusion events from STAR-fusion", + "pattern": "*.{fusion_predictions.tsv}" + } + } + ] + ], + "abridged": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.abridged.tsv": { + "type": "file", + "description": "Abridged version of fusion events from STAR-fusion", + "pattern": "*.{fusion.abridged.tsv}" + } + } + ] + ], + "coding_effect": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.coding_effect.tsv": { + "type": "file", + "description": "Fusion events with their coding effect from STAR-fusion", + "pattern": "*.{coding_effect.tsv}" + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@praveenraj2018"] }, - { - "snpfile": { - "type": "file", - "description": "randomly selected snp identifiers, used to calculate linkage disequilibrium", - "pattern": "*.{txt}", - "ontologies": [] - } - } - ] - ], - "output": { - "ld": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.ld": { - "type": "file", - "description": "The output of a linkage disequilibrium analysis in PLINK typically includes a table showing variant pairs and their associated LD values, often expressed as R².\n", - "ontologies": [] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.log": { - "type": "file", - "description": "Log file of the ld process\n", - "ontologies": [] - } - } - ] - ], - "nosex": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.nosex": { - "type": "file", - "description": "Ambiguous sex ID file\n", - "ontologies": [] - } - } - ] - ], - "versions_plink": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "plink": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "plink --version 2>&1 | sed 's/^PLINK v//;s/ .*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@davidebag" - ], - "maintainers": [ - "@davidebag" - ], - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "plink": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "plink --version 2>&1 | sed 's/^PLINK v//;s/ .*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "rnafusion", + "version": "4.1.2" + } ] - ] - } - } - }, - { - "name": "plink_recode", - "path": "modules/nf-core/plink/recode/meta.yml", - "type": "module", - "meta": { - "name": "plink_recode", - "description": "Recodes plink bfiles into a new text fileset applying different modifiers", - "keywords": [ - "recode", - "bfiles", - "plink", - "whole genome association" - ], - "tools": [ - { - "plink": { - "description": "Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.", - "homepage": "https://www.cog-genomics.org/plink", - "documentation": "https://www.cog-genomics.org/plink/1.9/data#recode", - "tool_dev_url": "https://www.cog-genomics.org/plink/1.9/dev", - "licence": [ - "GPL" - ], - "identifier": "" + }, + { + "name": "stecfinder", + "path": "modules/nf-core/stecfinder/meta.yml", + "type": "module", + "meta": { + "name": "stecfinder", + "description": "Serotype STEC samples from paired-end reads or assemblies", + "keywords": ["serotype", "Escherichia coli", "fastq", "fasta"], + "tools": [ + { + "stecfinder": { + "description": "Cluster informed Shigatoxin producing E. coli (STEC) serotyping tool from Illumina reads and assemblies", + "homepage": "https://github.com/LanLab/STECFinder", + "documentation": "https://github.com/LanLab/STECFinder", + "tool_dev_url": "https://github.com/LanLab/STECFinder", + "doi": "10.3389/fcimb.2021.772574", + "licence": ["GPL v3"], + "identifier": "biotools:stecfinder" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "seqs": { + "type": "file", + "description": "Illumina paired-end reads or an assembly", + "pattern": "*.{fastq.gz,fasta.gz,fna.gz}", + "ontologies": [] + } + } + ] + ], + "output": { + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "A tab-delimited report of results", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@rpetit3"], + "maintainers": ["@rpetit3"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bed": { - "type": "file", - "description": "PLINK binary biallelic genotype table file", - "pattern": "*.{bed}", - "ontologies": [] - } - }, - { - "bim": { - "type": "file", - "description": "PLINK extended MAP file", - "pattern": "*.{bim}", - "ontologies": [] - } + }, + { + "name": "stitch", + "path": "modules/nf-core/stitch/meta.yml", + "type": "module", + "meta": { + "name": "stitch", + "description": "STITCH is an R program for reference panel free, read aware, low coverage sequencing genotype imputation. STITCH runs on a set of samples with sequencing reads in BAM format, as well as a list of positions to genotype, and outputs imputed genotypes in VCF format.", + "keywords": ["imputation", "genomics", "vcf", "bgen", "cram", "bam", "sam"], + "tools": [ + { + "stitch": { + "description": "STITCH - Sequencing To Imputation Through Constructing Haplotypes", + "homepage": "https://github.com/rwdavies/stitch", + "documentation": "https://github.com/rwdavies/stitch", + "tool_dev_url": "https://github.com/rwdavies/stitch", + "doi": "10.1038/ng.3594", + "licence": ["GPL v3"], + "identifier": "biotools:stitch-snijderlab" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information about the set of samples\ne.g. `[ id:'test' ]`\n" + } + }, + { + "collected_crams": { + "type": "file", + "description": "List of sorted BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}", + "ontologies": [] + } + }, + { + "collected_crais": { + "type": "file", + "description": "List of BAM/CRAM/SAM index files", + "pattern": "*.{bai,crai,sai}", + "ontologies": [] + } + }, + { + "cramlist": { + "type": "file", + "description": "Text file with the path to the cram files to use in imputation, one per line. Since the cram files are staged to the working directory for the process, this file should just contain the file names without any pre-pending path.\n", + "pattern": "*.txt", + "ontologies": [] + } + }, + { + "samplename": { + "type": "file", + "description": "(Optional) File with list of samples names in the same order as in bamlist to impute. One file per line.", + "pattern": "*.{txt}", + "ontologies": [] + } + }, + { + "posfile": { + "type": "file", + "description": "Tab-separated file describing the variable positions to be used for imputation. Refer to the documentation for the `--posfile` argument of STITCH for more information.\n", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, + { + "input": { + "type": "directory", + "description": "Folder of pre-generated input RData objects used when STITCH is called with the `--regenerateInput FALSE` flag. It is generated by running STITCH with the `--generateInputOnly TRUE` flag.\n", + "pattern": "input" + } + }, + { + "genetic_map": { + "type": "file", + "description": "(Optional) File with genetic map information, a file with 3 white-space delimited entries giving position (1-based), genetic rate map in cM/Mbp, and genetic map in cM. If no file included, rate is based on physical distance and expected rate (expRate).", + "pattern": "*.{txt,map}{,gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + }, + { + "rdata": { + "type": "directory", + "description": "Folder of pre-generated input RData objects used when STITCH is called with the `--regenerateInput FALSE` flag. It is generated by running STITCH with the `--generateInputOnly TRUE` flag.\n", + "pattern": "RData" + } + }, + { + "chromosome_name": { + "type": "string", + "description": "Name of the chromosome to impute. Should match a chromosome name in the reference genome." + } + }, + { + "start": { + "type": "integer", + "description": "Start position of the region to impute." + } + }, + { + "end": { + "type": "integer", + "description": "End position of the region to impute." + } + }, + { + "buffer": { + "type": "integer", + "description": "Buffer, in base pairs, around the region to impute." + } + }, + { + "K": { + "type": "integer", + "description": "Number of ancestral haplotypes to use for imputation. Refer to the documentation for the `--K` argument of STITCH for more information." + } + }, + { + "nGen": { + "type": "integer", + "description": "Number of generations since founding of the population to use for imputation. Refer to the documentation for the `--nGen` argument of STITCH for more information." + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing information about the reference genome used\ne.g. `[ id:'test' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA reference genome file", + "pattern": "*.{fa,fasta}", + "ontologies": [] + } + }, + { + "fasta_fai": { + "type": "file", + "description": "FASTA index file", + "pattern": "*.{fai}", + "ontologies": [] + } + } + ], + { + "seed": { + "type": "integer", + "description": "Seed for random number generation" + } + } + ], + "output": { + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "input": { + "type": "directory", + "description": "Folder of pre-generated input RData objects used when STITCH is called with the `--regenerateInput FALSE` flag. It is generated by running STITCH with the `--generateInputOnly TRUE` flag.\n", + "pattern": "input" + } + } + ] + ], + "rdata": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "RData": { + "type": "directory", + "description": "Folder of RData objects generated during the imputation process.\n", + "pattern": "RData" + } + } + ] + ], + "plots": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "plots": { + "type": "directory", + "description": "Folder of plots generated during the imputation process.\n", + "pattern": "plots" + } + } + ] + ], + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "Imputed genotype calls for the positions in `posfile`, in vcf format. This is the default output.\n", + "pattern": ".vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "bgen": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "*.bgen": { + "type": "file", + "description": "Imputed genotype calls for the positions in `posfile`, in vcf format. This is the produced if `--output_format bgen` is specified.\n", + "pattern": ".bgen", + "ontologies": [] + } + } + ] + ], + "versions_r_quilt": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "r-quilt": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "Rscript -e \"cat(as.character(packageVersion('STITCH')))\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_r_base": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "r-base": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "R --version | sed \"1!d; s/.*version //; s/ .*//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_rsync": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "rsync": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "rsync --version | sed '1!d;s/^rsync version //; s/ .*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "r-quilt": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "Rscript -e \"cat(as.character(packageVersion('STITCH')))\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "r-base": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "R --version | sed \"1!d; s/.*version //; s/ .*//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "rsync": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "rsync --version | sed '1!d;s/^rsync version //; s/ .*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@saulpierotti"], + "maintainers": ["@saulpierotti"] }, - { - "fam": { - "type": "file", - "description": "PLINK sample information file", - "pattern": "*.{fam}", - "ontologies": [] - } - } - ] - ], - "output": { - "ped": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.ped": { - "type": "file", - "description": "PLINK/MERLIN/Haploview text pedigree + genotype table file. Produced by the default \"--recode\" or by \"--recode 12\".", - "pattern": "*.{ped}", - "ontologies": [] - } - } - ] - ], - "map": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.map": { - "type": "file", - "description": "PLINK text fileset variant information file. Produced by the default \"--recode\" or by \"--recode 12\".", - "pattern": "*.{map}", - "ontologies": [] - } - } + "pipelines": [ + { + "name": "phaseimpute", + "version": "1.1.0" + } ] - ], - "txt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.txt": { - "type": "file", - "description": "Text file. Produced by \"--recode 23\". Can only be used in a file with only one sample.", - "pattern": "*.{txt}", - "ontologies": [] - } - } + }, + { + "name": "stranger", + "path": "modules/nf-core/stranger/meta.yml", + "type": "module", + "meta": { + "name": "stranger", + "description": "Annotates output files from ExpansionHunter with the pathologic implications of the repeat sizes.", + "keywords": ["STR", "repeat_expansions", "annotate", "vcf"], + "tools": [ + { + "stranger": { + "description": "Annotate VCF files with str variants", + "homepage": "https://github.com/moonso/stranger", + "documentation": "https://github.com/moonso/stranger", + "tool_dev_url": "https://github.com/moonso/stranger", + "doi": "10.5281/zenodo.4548873", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF with repeat expansions", + "pattern": "*.{vcf.gz,vcf}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "variant_catalog": { + "type": "file", + "description": "json file with repeat expansion sites to genotype", + "pattern": "*.{json}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Annotated VCF file", + "pattern": "*.{vcf.gz}" + } + }, + { + "*.vcf.gz": { + "type": "map", + "description": "Annotated VCF file", + "pattern": "*.{vcf.gz}" + } + } + ] + ], + "tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Annotated VCF file", + "pattern": "*.{vcf.gz}" + } + }, + { + "*.vcf.gz.tbi": { + "type": "map", + "description": "Index of the annotated VCF file", + "pattern": "*.{vcf.gz.tbi}" + } + } + ] + ], + "versions_stranger": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "stranger": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "stranger --version | sed 's/stranger, version //g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_tabix": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "tabix": { + "type": "string", + "description": "The tool name" + } + }, + { + "tabix -h 2>&1 | grep -oP 'Version:\\s*\\K[^\\s]+'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "stranger": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "stranger --version | sed 's/stranger, version //g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "tabix": { + "type": "string", + "description": "The tool name" + } + }, + { + "tabix -h 2>&1 | grep -oP 'Version:\\s*\\K[^\\s]+'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@ljmesi"], + "maintainers": ["@ljmesi"] + }, + "pipelines": [ + { + "name": "raredisease", + "version": "3.0.0" + } ] - ], - "raw": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.raw": { - "type": "file", - "description": "Additive + dominant component file. Produced by \"--recode AD\" or \"--recode A\".", - "pattern": "*.{raw}", - "ontologies": [] - } - } - ] - ], - "traw": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.traw": { - "type": "file", - "description": "Variant-major additive component file. Produced by \"--recode A-transpose\".", - "pattern": "*.{traw}", - "ontologies": [] - } - } - ] - ], - "beagledat": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.beagle.dat": { - "type": "file", - "description": "BEAGLE file", - "pattern": "*.{beagle.dat}", - "ontologies": [] - } - } - ] - ], - "chrdat": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.chr-*.dat": { - "type": "file", - "description": "chr file", - "pattern": "*.{chr-*.dat}", - "ontologies": [] - } - } - ] - ], - "chrmap": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - ".*chr-*.map": { - "type": "file", - "description": "chr map file", - "pattern": "*.{chr-*.map}", - "ontologies": [] - } - } - ] - ], - "geno": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.recode.geno.txt": { - "type": "file", - "description": "BIMBAM genotype file. Produced by \"--recode bimbam\".", - "pattern": "*.{recode.geno.txt}", - "ontologies": [] - } - } - ] - ], - "pheno": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.recode.pheno.txt": { - "type": "file", - "description": "BIMBAM phenotype file. Produced by \"--recode bimbam\".", - "pattern": "*.{recode.pheno.txt}", - "ontologies": [] - } - } - ] - ], - "pos": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.recode.pos.txt": { - "type": "file", - "description": "BIMBAM variant position file. Produced by \"--recode bimbam\".", - "pattern": "*.{recode.pos.txt}", - "ontologies": [] - } - } - ] - ], - "phase": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.recode.phase.inp": { - "type": "file", - "description": "fastPHASE format. Produced by \"--recode fastphase\".", - "pattern": "*.{recode.phase.inp}", - "ontologies": [] - } - } - ] - ], - "info": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.info": { - "type": "file", - "description": "Haploview map file. Produced by \"--recode HV\".", - "pattern": "*.{info}", - "ontologies": [] - } - } - ] - ], - "lgen": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.lgen": { - "type": "file", - "description": "PLINK long-format genotype file. Produced by \"--recode lgen\".", - "pattern": "*.{lgen}", - "ontologies": [] - } - } - ] - ], - "list": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.list": { - "type": "file", - "description": "Genotype list file. Produced by \"--recode list\".", - "pattern": "*.{list}", - "ontologies": [] - } - } - ] - ], - "gen": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.gen": { - "type": "file", - "description": "Oxford genotype file format. Produced by \"--recode oxford\".", - "pattern": "*.{gen}", - "ontologies": [] - } - } - ] - ], - "gengz": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.gen.gz": { - "type": "file", - "description": "Compressed Oxford genotype file format", - "pattern": "*.{gen.gz}", - "ontologies": [] - } - } - ] - ], - "sample": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.sample": { - "type": "file", - "description": "Oxford sample information file. Produced by \"--recode oxford\".", - "pattern": "*.{sample}", - "ontologies": [] - } - } - ] - ], - "rlist": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.rlist": { - "type": "file", - "description": "Rare genotype list file. Produced by \"--recode rlist\".", - "pattern": "*.{rlist}", - "ontologies": [] - } - } - ] - ], - "strctin": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.strct_in": { - "type": "file", - "description": "Structure-format file. Produced by \"--recode structure\".", - "pattern": "*.{strct_in}", - "ontologies": [] - } - } - ] - ], - "tped": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tped": { - "type": "file", - "description": "Transposed text PED file. Produced by \"--recode transpose\".", - "pattern": "*.{tped}", - "ontologies": [] - } - } - ] - ], - "tfam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tfam": { - "type": "file", - "description": "Transposed text FAM file. Produced by \"--recode transpose\".", - "pattern": "*.{tfam}", - "ontologies": [] - } - } - ] - ], - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.vcf": { - "type": "file", - "description": "Variant calling file (VCF). Produced by \"--recode vcf\".", - "pattern": "*.{vcf}", - "ontologies": [] - } - } - ] - ], - "vcfgz": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.vcf.gz": { - "type": "file", - "description": "Compressed variant calling file (VCF). Produced by \"--recode vcf bgz\".", - "pattern": "*.{vcf.gz}", - "ontologies": [] - } - } - ] - ], - "versions_plink": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "plink": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "plink --version 2>&1 | sed 's/^PLINK v//;s/ .*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@atrigila" - ], - "maintainers": [ - "@atrigila" - ], - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "plink": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "plink --version 2>&1 | sed 's/^PLINK v//;s/ .*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - } - } - }, - { - "name": "plink_vcf", - "path": "modules/nf-core/plink/vcf/meta.yml", - "type": "module", - "meta": { - "name": "plink_vcf", - "description": "Analyses variant calling files using plink", - "keywords": [ - "plink", - "vcf", - "variant", - "call" - ], - "tools": [ - { - "plink": { - "description": "Whole genome association analysis toolset, designed to perform a range\nof basic, large-scale analyses in a computationally efficient manner\n", - "homepage": "https://www.cog-genomics.org/plink", - "tool_dev_url": "https://www.cog-genomics.org/plink/1.9/dev", - "licence": [ - "GPL" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "Variant calling file (vcf)", - "pattern": "*.{vcf}", - "ontologies": [] - } - } - ] - ], - "output": { - "bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bed": { - "type": "file", - "description": "PLINK binary biallelic genotype table", - "pattern": "*.{bed}", - "ontologies": [] - } - } - ] - ], - "bim": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bim": { - "type": "file", - "description": "PLINK extended MAP file", - "pattern": "*.{bim}", - "ontologies": [] - } - } - ] - ], - "fam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.fam": { - "type": "file", - "description": "PLINK sample information file", - "pattern": "*.{fam}", - "ontologies": [] - } - } - ] - ], - "versions_plink": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "plink": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "plink --version 2>&1 | sed 's/^PLINK v//;s/ .*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@Mxrcon", - "@abhi18av" - ], - "maintainers": [ - "@Mxrcon", - "@abhi18av" - ], - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "plink": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "plink --version 2>&1 | sed 's/^PLINK v//;s/ .*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - } - }, - "pipelines": [ + }, { - "name": "gwas", - "version": "dev" - } - ] - }, - { - "name": "plotsr", - "path": "modules/nf-core/plotsr/meta.yml", - "type": "module", - "meta": { - "name": "plotsr", - "description": "Plotsr generates high-quality visualisation of synteny and structural rearrangements between multiple genomes.", - "keywords": [ - "genomics", - "synteny", - "rearrangements", - "chromosome" - ], - "tools": [ - { - "plotsr": { - "description": "Visualiser for structural annotations between multiple genomes", - "homepage": "https://github.com/schneebergerlab/plotsr", - "documentation": "https://github.com/schneebergerlab/plotsr", - "tool_dev_url": "https://github.com/schneebergerlab/plotsr", - "doi": "10.1093/bioinformatics/btac196", - "licence": [ - "MIT" - ], - "identifier": "biotools:plotsr" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "syri": { - "type": "file", - "description": "Structural annotation mappings (syri.out) identified by SyRI", - "pattern": "*syri.out", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "fastas": { - "type": "list", - "description": "Fasta files in the sequence specified by the `genomes` file", - "pattern": "*.{fasta,fa,fsa,faa}" - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "genomes": { - "type": "string", - "description": "A genomes.txt file including the header: #file\tname\ttags\nand Fasta file names, title for the plot and plotsr configuration tags. As example is:\n#file name tags\ngenome.fasta test lw:1.5\ngenome2.fasta reference lw:1.5\n", - "pattern": "*.txt" - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "bedpe": { - "type": "file", - "description": "Structural annotation mappings in BEDPE format", - "pattern": "*.bedpe", - "ontologies": [] - } - } - ], - [ - { - "meta5": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "markers": { - "type": "file", - "description": "File containing path to markers", - "pattern": "*.bed", - "ontologies": [] - } - } - ], - [ - { - "meta6": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "tracks": { - "type": "file", - "description": "File listing paths and details for all tracks to be plotted", - "pattern": "*.txt", - "ontologies": [] - } - } - ], - [ - { - "meta7": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "chrord": { - "type": "file", - "description": "File containing reference (first genome) chromosome IDs in the order in which they are to be plotted.\nFile requires one chromosome ID per line. Not compatible with --chr\n", - "pattern": "*.txt", - "ontologies": [] - } - } - ], - [ - { - "meta8": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "chrname": { - "type": "file", - "description": "File containing reference (first genome) chromosome names to be used in the plot.\nFile needs to be a TSV with the chromosome ID in first column and chromosome name in the second.\n", - "pattern": "*.txt", - "ontologies": [] - } - } - ] - ], - "output": { - "png": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.png": { - "type": "file", - "description": "Synteny plot", - "pattern": "*.png", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@GallVp" - ], - "maintainers": [ - "@GallVp" - ] - } - }, - { - "name": "pmdtools_filter", - "path": "modules/nf-core/pmdtools/filter/meta.yml", - "type": "module", - "meta": { - "name": "pmdtools_filter", - "description": "pmdtools command to filter ancient DNA molecules from others", - "keywords": [ - "pmdtools", - "aDNA", - "filter", - "damage" - ], - "tools": [ - { - "pmdtools": { - "description": "Compute postmortem damage patterns and decontaminate ancient genomes", - "homepage": "https://github.com/pontussk/PMDtools", - "documentation": "https://github.com/pontussk/PMDtools", - "tool_dev_url": "https://github.com/pontussk/PMDtools", - "doi": "10.1073/pnas.1318934111", - "licence": [ - "GPL v3" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file", - "pattern": "*.bam", - "ontologies": [] - } - }, - { - "bai": { - "type": "file", - "description": "BAM index file", - "pattern": "*.bai", - "ontologies": [] - } - } - ], - { - "threshold": { - "type": "float", - "description": "Post-mortem damage score threshold" - } - }, - { - "reference": { - "type": "file", - "description": "FASTA file", - "pattern": "*.{fa,fasta}", - "ontologies": [] - } - } - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "Filtered BAM file", - "pattern": "*.bam", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@alexandregilardet" - ], - "maintainers": [ - "@alexandregilardet" - ] - } - }, - { - "name": "pneumocat", - "path": "modules/nf-core/pneumocat/meta.yml", - "type": "module", - "meta": { - "name": "pneumocat", - "description": "Determine Streptococcus pneumoniae serotype from Illumina paired-end reads", - "keywords": [ - "fastq", - "serotype", - "Streptococcus pneumoniae" - ], - "tools": [ - { - "pneumocat": { - "description": "PneumoCaT (Pneumococcal Capsular Typing) uses a two-step step approach to assign capsular type to S.pneumoniae genomic data (Illumina)", - "homepage": "https://github.com/ukhsa-collaboration/PneumoCaT", - "documentation": "https://github.com/ukhsa-collaboration/PneumoCaT", - "tool_dev_url": "https://github.com/ukhsa-collaboration/PneumoCaT", - "doi": "10.7717/peerj.2477", - "licence": [ - "GPL v3" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "Input Illunina paired-end FASTQ files", - "pattern": "*.{fq.gz,fastq.gz}", - "ontologies": [] - } - } - ] - ], - "output": { - "xml": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*.xml": { - "type": "file", - "description": "The predicted serotype in XML format", - "pattern": "*.xml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2332" - } - ] - } - } - ] - ], - "txt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*.txt": { - "type": "file", - "description": "A detailed description of the predicted serotype", - "pattern": "*.txt", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@rpetit3" - ], - "maintainers": [ - "@rpetit3" - ] - } - }, - { - "name": "polypolish_polish", - "path": "modules/nf-core/polypolish/polish/meta.yml", - "type": "module", - "meta": { - "name": "polypolish_polish", - "description": "Polishing genome assemblies with short reads.", - "keywords": [ - "assembly polishing", - "genome polishing", - "ont" - ], - "tools": [ - { - "polypolish": { - "description": "Polishing genome assemblies with short reads.", - "homepage": "https://github.com/rrwick/Polypolish", - "documentation": "https://github.com/rrwick/Polypolish/wiki", - "tool_dev_url": "https://github.com/rrwick/Polypolish", - "doi": "10.1099/mgen.0.001254", - "licence": [ - "GPL3" - ], - "identifier": "biotools:polypolish" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA file with draft assembly of ONT data", - "pattern": "*.{fasta,fna,fa,fas}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "sam": { - "type": "file", - "description": "List of SAM files of short reads mapped against the FASTA input file", - "pattern": "*.sam", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2573" - } - ] - } - } - ], - { - "save_debug": { - "type": "boolean", - "description": "Turn debug output on", - "pattern": "true|false" - } - } - ], - "output": { - "fasta": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.fasta": { - "type": "file", - "description": "FASTA file with polished draft assembly", - "pattern": "*.{fasta,fna,fa,fas}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ], - "debug": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.txt": { - "type": "file", - "description": "File with debug base information", - "pattern": "*.txt", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@ktrappe" - ], - "maintainers": [ - "@ktrappe" - ] - } - }, - { - "name": "poolsnp", - "path": "modules/nf-core/poolsnp/meta.yml", - "type": "module", - "meta": { - "name": "poolsnp", - "description": "PoolSNP is a heuristic SNP caller, which uses an MPILEUP file and a reference genome in FASTA format as inputs.", - "keywords": [ - "poolseq", - "mpileup", - "variant-calling" - ], - "tools": [ - { - "poolsnp": { - "description": "PoolSNP is a heuristic SNP caller, which uses an MPILEUP file and a reference genome in FASTA format as inputs.", - "homepage": "https://github.com/capoony/PoolSNP", - "documentation": "https://github.com/capoony/PoolSNP/blob/master/README.md", - "licence": [ - "Apache-2.0" - ], - "args_id": "$args", - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information.\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "mpileup": { - "type": "file", - "description": "MPILEUP file. This file contains the base calls and alignment information\nfor each position in the reference genome.\nIt is used as input for variant calling and other downstream analyses.\n", - "pattern": "*.mpileup", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information.\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "reference": { - "type": "file", - "description": "Reference genome in FASTA format.\nMay NOT contain any special characters such as \"/|,:\"\n", - "pattern": "*.{fasta,fa}", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information.\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "max_cov": { - "type": "float", - "description": "Maximum coverage is calculated for every library and chromosomal arm\nas the percentile of a coverage distribution,\ne.g. max-cov=0.98 will only consider positions within the 98% coverage percentile\nfor a given sample and chromosomal arm.\nNote: Provide `max_cov` or `max_cov_file` but not both.\nRead more: https://github.com/capoony/PoolSNP\n" - } - }, - { - "max_cov_file": { - "type": "file", - "description": "File containing the maximum coverage thresholds for all chromosomal arms and libraries.\nThis file needs to be tab-delimited with two columns:\n1. Chromosomal name\n2. Comma-separated list of coverage thresholds for each sample in the mpileup file.\ne.g. `2L 100,100,100,200,200` would mean a threshold of 100 for the first three samples\nand 200 for the last two samples on chromosomal arm 2L.\nNote: Provide `max_cov` or `max_cov_file` but not both.\nRead more: https://github.com/capoony/PoolSNP\n", - "ontologies": [] - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.vcf.gz": { - "type": "file", - "description": "Gzipped VCF file containing allele counts and frequencies for every position and library", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "max_cov": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*cov-*.txt": { - "type": "file", - "description": "File containing the maximum coverage thresholds for all chromosomal arms and libraries", - "pattern": "*cov-*.txt", - "ontologies": [] - } - } - ] - ], - "bad_sites": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*BS.txt.gz": { - "type": "file", - "description": "File containing a list of sites (variable and invariable) that did not pass the SNP calling criteria", - "pattern": "*BS.txt.gz", - "optional": true, - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@abhilesh" - ], - "maintainers": [ - "@abhilesh" - ] - } - }, - { - "name": "popscle_demuxlet", - "path": "modules/nf-core/popscle/demuxlet/meta.yml", - "type": "module", - "meta": { - "name": "popscle_demuxlet", - "description": "Software to deconvolute sample identity and identify multiplets when multiple samples are pooled by barcoded single cell sequencing and external genotyping data for each sample is available.", - "keywords": [ - "popscle", - "demultiplexing", - "genotype-based deconvoltion", - "single cell" - ], - "tools": [ - { - "popscle": { - "description": "A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and auxiliary tools", - "homepage": "https://github.com/statgen/popscle", - "documentation": "https://github.com/statgen/popscle", - "tool_dev_url": "https://github.com/statgen/popscle", - "doi": "10.1038/nbt.4042", - "licence": [ - "Apache-2.0" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } - }, - { - "plp_prefix": { - "type": "string", - "description": "Prefix of pileup files (CEL,VAR and PLP) produced by popscle/dsc_pileup." - } - }, - { - "bam": { - "type": "file", - "description": "Input SAM/BAM/CRAM file without running popscle/dsc_pileup, must be sorted by coordinates and indexed.", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } - }, - { - "donor_genotype": { - "type": "file", - "description": "Input VCF/BCF file, containing the individual genotypes (GT), posterior probability (GP), or genotype likelihood (PL) to assign each barcode to a specific sample (or a pair of samples) in the VCF file.", - "pattern": "*.{vcf,bcf}", - "ontologies": [] - } - } - ] - ], - "output": { - "demuxlet_result": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } - }, - { - "*.best": { - "type": "file", - "description": "Result of demuxlet containing the best guess of the sample identity, with detailed statistics to reach to the best guess.", - "pattern": "*.best", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@mari-ga", - "@maxozo", - "@wxicu", - "@Zethson" - ], - "maintainers": [ - "@mari-ga", - "@maxozo", - "@wxicu", - "@Zethson" - ] - } - }, - { - "name": "popscle_dscpileup", - "path": "modules/nf-core/popscle/dscpileup/meta.yml", - "type": "module", - "meta": { - "name": "popscle_dscpileup", - "description": "Software to pileup reads and corresponding base quality for each overlapping SNPs and each barcode.", - "keywords": [ - "popscle", - "demultiplexing", - "genotype-based deconvoltion", - "single cell", - "pile up" - ], - "tools": [ - { - "popscle": { - "description": "A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and auxiliary tools", - "homepage": "https://github.com/statgen/popscle", - "documentation": "https://github.com/statgen/popscle", - "tool_dev_url": "https://github.com/statgen/popscle", - "doi": "10.1038/nbt.4042", - "licence": [ - "Apache-2.0" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "Input SAM/BAM/CRAM file produced by the standard 10x sequencing platform, or any other barcoded single cell RNA-seq.", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } - }, - { - "vcf": { - "type": "file", - "description": "Input VCF/BCF file files containing (AC) and (AN) from referenced population (e.g. 1000g).", - "pattern": "*.{vcf,bcf}", - "ontologies": [] - } - } - ] - ], - "output": { - "cel": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } - }, - { - "*.cel.gz": { - "type": "file", - "description": "Contains the relation between numerated barcode ID and barcode and the number of SNP and number of UMI for each barcoded droplet.", - "pattern": "*.cel.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "plp": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } - }, - { - "*.plp.gz": { - "type": "file", - "description": "Contains the overlapping SNP and the corresponding read and base quality for each barcode ID.", - "pattern": "*.plp.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "var": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } - }, - { - "*.var.gz": { - "type": "file", - "description": "Contains the position, reference allele and allele frequency for each SNP.", - "pattern": "*.var.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "umi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } - }, - { - "*.umi.gz": { - "type": "file", - "description": "Contains the position covered by each umi.", - "pattern": "*.umi.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@mari-ga", - "@maxozo", - "@wxicu", - "@Zethson" - ], - "maintainers": [ - "@mari-ga", - "@maxozo", - "@wxicu", - "@Zethson" - ] - } - }, - { - "name": "popscle_freemuxlet", - "path": "modules/nf-core/popscle/freemuxlet/meta.yml", - "type": "module", - "meta": { - "name": "popscle_freemuxlet", - "description": "Software to deconvolute sample identity and identify multiplets when multiple samples are pooled by barcoded single cell sequencing and external genotyping data for each sample is not available.", - "keywords": [ - "popscle", - "demultiplexing", - "genotype-based deconvoltion", - "single cell" - ], - "tools": [ - { - "popscle": { - "description": "A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and auxiliary tools", - "homepage": "https://github.com/statgen/popscle", - "documentation": "https://github.com/statgen/popscle", - "tool_dev_url": "https://github.com/statgen/popscle", - "doi": "10.1038/nbt.4042", - "licence": [ - "Apache-2.0" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } - }, - { - "plp": { - "type": "directory", - "description": "Directory contains pileup files (CEL,VAR and PLP) produced by popscle/dsc_pileup." - } - }, - { - "n_sample": { - "type": "integer", - "description": "Number of samples multiplexed together." - } - } - ] - ], - "output": { - "result": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.clust1.samples.gz": { - "type": "file", - "description": "Output file contains the best guess of the sample identity, with detailed statistics to reach to the best guess.", - "pattern": "*.clust1.samples.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.clust1.vcf.gz": { - "type": "file", - "description": "Output vcf file for each sample inferred and clustered from freemuxlet.", - "pattern": "*.clust1.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "lmix": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.lmix": { - "type": "file", - "description": "Output file contains basic statistics for each barcode.", - "pattern": "*.lmix", - "ontologies": [] - } - } - ] - ], - "singlet_result": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.clust0.samples.gz": { - "type": "file", - "description": "Optional output file contains the best sample identity assuming all droplets are singlets when writing auxiliary output files is turned on.", - "pattern": "*.clust0.samples.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "singlet_vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.clust0.vcf.gz": { - "type": "file", - "description": "Optional output vcf file for each sample inferred and clustered from freemuxlet assuming all droplets are singlets when writing auxiliary output files is turned on.", - "pattern": "*.clust0.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@wxicu" - ], - "maintainers": [ - "@wxicu" - ] - } - }, - { - "name": "porechop_abi", - "path": "modules/nf-core/porechop/abi/meta.yml", - "type": "module", - "meta": { - "name": "porechop_abi", - "description": "Extension of Porechop whose purpose is to process adapter sequences in ONT reads.", - "keywords": [ - "porechop_abi", - "adapter", - "nanopore" - ], - "tools": [ - { - "porechop_abi": { - "description": "Extension of Porechop whose purpose is to process adapter sequences in ONT reads.", - "homepage": "https://github.com/bonsai-team/Porechop_ABI", - "documentation": "https://github.com/bonsai-team/Porechop_ABI", - "tool_dev_url": "https://github.com/bonsai-team/Porechop_ABI", - "doi": "10.1101/2022.07.07.499093", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "fastq/fastq.gz file", - "pattern": "*.{fastq,fastq.gz,fq,fq.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ], - { - "custom_adapters": { - "type": "file", - "description": "Text file containing custom adapters", - "ontologies": [] - } - } - ], - "output": { - "reads": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - 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"description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } - } - ] - ], - "output": { - "lc_extrap": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.lc_extrap.txt": { - "type": "file", - "description": "File containing output of Preseq lcextrap", - "pattern": "*.{lc_extrap.txt}", - "ontologies": [] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.log": { - "type": "file", - "description": "Log file containing stderr produced by Preseq", - "pattern": "*.{log}", - "ontologies": [] - } - } - ] - ], - "versions_preseq": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "preseq": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "preseq 2>&1 | sed -n 's/.*Version: \\(.*\\)/\\1/p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "preseq": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "preseq 2>&1 | sed -n 's/.*Version: \\(.*\\)/\\1/p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "circrna", + "version": "dev" + }, + { + "name": "lncpipe", + "version": "dev" + }, + { + "name": "rnafusion", + "version": "4.1.2" + }, + { + "name": "rnaseq", + "version": "3.26.0" + } ] - ] }, - "authors": [ - "@drpatelh", - "@edmundmiller" - ], - "maintainers": [ - "@drpatelh", - "@edmundmiller" - ] - }, - "pipelines": [ { - "name": "atacseq", - "version": "2.1.2" + "name": "strobealign", + "path": "modules/nf-core/strobealign/meta.yml", + "type": "module", + "meta": { + "name": "strobealign", + "description": "Align short reads using dynamic seed size with strobemers", + "keywords": ["strobealign", "strobemers", "alignment", "map", "fastq", "bam", "sam"], + "tools": [ + { + "strobealign": { + "description": "Align short reads using dynamic seed size with strobemers", + "homepage": "https://github.com/ksahlin/strobealign", + "documentation": "https://github.com/ksahlin/strobealign?tab=readme-ov-file#usage", + "tool_dev_url": "https://github.com/ksahlin/strobealign", + "doi": "10.1186/s13059-022-02831-7", + "licence": ["MIT"], + "identifier": "biotools:strobealign" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", + "ontologies": [ + { + "edam": "http://edamontology.org/data_2044" + }, + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference genome in FASTA format", + "pattern": "*.{fasta,fa}", + "ontologies": [ + { + "edam": "http://edamontology.org/data_2044" + }, + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "index": { + "type": "file", + "description": "Strobealign genome index file", + "pattern": "*.sti", + "ontologies": [ + { + "edam": "http://edamontology.org/data_3210" + } + ] + } + } + ], + { + "sort_bam": { + "type": "boolean", + "description": "use samtools sort (true) or samtools view (false)", + "pattern": "true or false" + } + } + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.bam": { + "type": "file", + "description": "Output BAM file containing read alignments", + "pattern": "*.{bam}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + } + ] + ], + "cram": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.cram": { + "type": "file", + "description": "Output CRAM file containing read alignments", + "pattern": "*.{cram}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3462" + } + ] + } + } + ] + ], + "csi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.csi": { + "type": "file", + "description": "Optional index file for BAM file", + "pattern": "*.{csi}", + "ontologies": [] + } + } + ] + ], + "crai": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.crai": { + "type": "file", + "description": "Optional index file for CRAM file", + "pattern": "*.{crai}", + "ontologies": [] + } + } + ] + ], + "paf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.paf.gz": { + "type": "file", + "description": "Output PAF file containing read alignments", + "pattern": "*.{paf.gz}", + "ontologies": [] + } + } + ] + ], + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.tsv.gz": { + "type": "file", + "description": "Output TSV file containing read alignments", + "pattern": "*.{tsv.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "sti": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.sti": { + "type": "file", + "description": "Optional strobealign index file for fasta reference", + "pattern": "*.{sti}", + "ontologies": [] + } + } + ] + ], + "versions_strobealign": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "strobealign": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "strobealign --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_samtools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "samtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "samtools version | sed '1!d;s/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_pigz": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "pigz": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pigz --version 2>&1 | sed 's/pigz //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "strobealign": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "strobealign --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "samtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "samtools version | sed '1!d;s/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "pigz": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pigz --version 2>&1 | sed 's/pigz //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@matthdsm"], + "maintainers": ["@matthdsm", "@nvnieuwk"] + }, + "pipelines": [ + { + "name": "sammyseq", + "version": "dev" + } + ] }, { - "name": "chipseq", - "version": "2.1.0" + "name": "strvctvre_strvctvre", + "path": "modules/nf-core/strvctvre/strvctvre/meta.yml", + "type": "module", + "meta": { + "name": "strvctvre_strvctvre", + "description": "a structural variant classifier for exonic deletions and duplications", + "keywords": ["structural variants", "sv", "deletions", "duplications", "annotations"], + "tools": [ + { + "strvctvre": { + "description": "StrVCTVRE, a structural variant classifier for exonic deletions and duplications", + "homepage": "https://github.com/andrewSharo/StrVCTVRE/tree/master", + "documentation": "https://github.com/andrewSharo/StrVCTVRE/tree/master", + "tool_dev_url": "https://github.com/andrewSharo/StrVCTVRE/tree/master", + "licence": ["MIT"], + "identifier": "biotools:strvctvre" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" + } + }, + { + "sv_file": { + "type": "file", + "description": "Structural variants file in VCF or BED format", + "pattern": "*.{vcf,bed}", + "ontologies": [] + } + }, + { + "sv_file_index": { + "type": "file", + "description": "Index file for the structural variants file VCF file", + "pattern": "*.tbi", + "ontologies": [] + } + }, + { + "assembly": { + "type": "string", + "description": "Genome assembly version, has to be one of 'GRCh38' or 'GRCh37'", + "enum": ["GRCh38", "GRCh37"] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" + } + }, + { + "phylop": { + "type": "file", + "description": "PhyloP bigWig file (fetched from https://hgdownload.cse.ucsc.edu/goldenpath/hg38/phyloP100way/)", + "pattern": "*.bw", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" + } + }, + { + "data_directory": { + "type": "directory", + "description": "Directory containing the StrVCTVRE data files (fetched from https://github.com/andrewSharo/StrVCTVRE/tree/master/data)" + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" + } + }, + { + "*.vcf": { + "type": "file", + "description": "Structural variants file in VCF format", + "pattern": "*.vcf", + "ontologies": [] + } + } + ] + ], + "bed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" + } + }, + { + "*.bed": { + "type": "file", + "description": "Structural variants file in BED format", + "pattern": "*.bed", + "ontologies": [] + } + } + ] + ], + "versions_strvctvre": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "strvctvre": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "StrVCTVRE.py --help |& sed -n 's/StrVCTVRE: version *//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "strvctvre": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "StrVCTVRE.py --help |& sed -n 's/StrVCTVRE: version *//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@nvnieuwk"], + "maintainers": ["@nvnieuwk"] + } }, { - "name": "cutandrun", - "version": "3.2.2" + "name": "subread_featurecounts", + "path": "modules/nf-core/subread/featurecounts/meta.yml", + "type": "module", + "meta": { + "name": "subread_featurecounts", + "description": "Count reads that map to genomic features", + "keywords": ["counts", "fasta", "genome", "reference"], + "tools": [ + { + "featurecounts": { + "description": "featureCounts is a highly efficient general-purpose read summarization program that counts mapped reads for genomic features such as genes, exons, promoter, gene bodies, genomic bins and chromosomal locations. It can be used to count both RNA-seq and genomic DNA-seq reads.", + "homepage": "http://bioinf.wehi.edu.au/featureCounts/", + "documentation": "http://bioinf.wehi.edu.au/subread-package/SubreadUsersGuide.pdf", + "doi": "10.1093/bioinformatics/btt656", + "licence": ["GPL v3"], + "identifier": "biotools:subread" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bams": { + "type": "file", + "description": "BAM files containing mapped reads", + "pattern": "*.bam", + "ontologies": [] + } + }, + { + "annotation": { + "type": "file", + "description": "Genomic features annotation in GTF or SAF", + "pattern": "*.{gtf,saf}", + "ontologies": [] + } + } + ] + ], + "output": { + "counts": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*featureCounts.tsv": { + "type": "file", + "description": "Counts of reads mapping to features", + "pattern": "*featureCounts.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "summary": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*featureCounts.tsv.summary": { + "type": "file", + "description": "Summary log file", + "pattern": "*.featureCounts.tsv.summary", + "ontologies": [] + } + } + ] + ], + "versions_subread": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "subread": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "featureCounts -v 2>&1 | sed 's/featureCounts v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "subread": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "featureCounts -v 2>&1 | sed 's/featureCounts v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@ntoda03"], + "maintainers": ["@ntoda03"] + }, + "pipelines": [ + { + "name": "atacseq", + "version": "2.1.2" + }, + { + "name": "callingcards", + "version": "1.0.0" + }, + { + "name": "chipseq", + "version": "2.1.0" + }, + { + "name": "lncpipe", + "version": "dev" + }, + { + "name": "magmap", + "version": "1.0.0" + }, + { + "name": "metatdenovo", + "version": "1.3.0" + }, + { + "name": "nascent", + "version": "2.3.0" + }, + { + "name": "panoramaseq", + "version": "dev" + }, + { + "name": "rnaseq", + "version": "3.26.0" + }, + { + "name": "rnasplice", + "version": "1.0.4" + } + ] }, { - "name": "genomicrelatedness", - "version": "dev" + "name": "summarizedexperiment_summarizedexperiment", + "path": "modules/nf-core/summarizedexperiment/summarizedexperiment/meta.yml", + "type": "module", + "meta": { + "name": "summarizedexperiment_summarizedexperiment", + "description": "SummarizedExperiment container\n", + "keywords": ["gene", "transcript", "sample", "matrix", "assay"], + "tools": [ + { + "summarizedexperiment": { + "description": "The SummarizedExperiment container contains one or more assays, each represented by a matrix-like object of numeric or other mode. The rows typically represent genomic ranges of interest and the columns represent samples.", + "homepage": "https://bioconductor.org/packages/release/bioc/html/SummarizedExperiment.html", + "documentation": "https://bioconductor.org/packages/release/bioc/vignettes/SummarizedExperiment/inst/doc/SummarizedExperiment.html", + "tool_dev_url": "https://github.com/Bioconductor/SummarizedExperiment", + "doi": "10.18129/B9.bioc.SummarizedExperiment", + "licence": ["Artistic-2.0"], + "identifier": "biotools:summarizedexperiment" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information related to the experiment as a whole\ne.g. `[ id:'SRP123456' ]`\n" + } + }, + { + "matrix_files": { + "type": "directory", + "description": "One or more paths to CSV or TSV matrix files. All files must have the\nsame rows and columns.\n", + "pattern": "*.{csv,tsv}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information related to the species\nreference from which matrix rows are derived e.g. `[ id:'yeast' ]`\n" + } + }, + { + "rowdata": { + "type": "file", + "description": "Metadata on matrix features. One column must contain all matrix row\nIDs.\n", + "pattern": "*.{csv,tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + }, + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing information related to the experiment as a whole,\nas represented by the matrix columns and the sample sheet e.g.\n`[id:'SRP123456' ]`\n" + } + }, + { + "coldata": { + "type": "file", + "description": "Metadata on matrix columns. One column must contain all matrix column\nIDs.\n", + "pattern": "*.{csv,tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + }, + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "output": { + "rds": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information related to the experiment as a whole\ne.g. `[ id:'SRP123456' ]`\n" + } + }, + { + "*.rds": { + "type": "file", + "description": "Serialised SummarizedExperiment object", + "pattern": "*.SummarizedExperiment.rds", + "ontologies": [] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information related to the experiment as a whole\ne.g. `[ id:'SRP123456' ]`\n" + } + }, + { + "*.R_sessionInfo.log": { + "type": "file", + "description": "dump of R SessionInfo", + "pattern": "*.log", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "YAML file containing versions of tools used in the module", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "topics": { + "versions": [ + { + "versions.yml": { + "type": "string", + "description": "The name of the process" + } + } + ] + }, + "authors": ["@pinin4fjords"], + "maintainers": ["@pinin4fjords"] + }, + "pipelines": [ + { + "name": "riboseq", + "version": "1.2.0" + }, + { + "name": "rnaseq", + "version": "3.26.0" + } + ] }, { - "name": "methylseq", - "version": "4.2.0" + "name": "survivor_bedpetovcf", + "path": "modules/nf-core/survivor/bedpetovcf/meta.yml", + "type": "module", + "meta": { + "name": "survivor_bedpetovcf", + "description": "Converts a bedpe file to a VCF file (beta version)", + "keywords": ["bedpe", "conversion", "vcf", "structural variants"], + "tools": [ + { + "survivor": { + "description": "Toolset for SV simulation, comparison and filtering", + "homepage": "https://github.com/fritzsedlazeck/SURVIVOR/wiki", + "documentation": "https://github.com/fritzsedlazeck/SURVIVOR/wiki", + "tool_dev_url": "https://github.com/fritzsedlazeck/SURVIVOR", + "doi": "10.1038/NCOMMS14061", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bedpe": { + "type": "file", + "description": "BEDPE file", + "ontologies": [] + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf": { + "type": "file", + "description": "Output VCF file", + "pattern": "*.{vcf}", + "ontologies": [] + } + } + ] + ], + "versions_survivor": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "survivor": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "SURVIVOR 2>&1 | grep 'Version' | sed 's/Version: //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "survivor": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "SURVIVOR 2>&1 | grep 'Version' | sed 's/Version: //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@kubranarci"], + "maintainers": ["@kubranarci"] + } }, { - "name": "nascent", - "version": "2.3.0" + "name": "survivor_filter", + "path": "modules/nf-core/survivor/filter/meta.yml", + "type": "module", + "meta": { + "name": "survivor_filter", + "description": "Filter a vcf file based on size and/or regions to ignore", + "keywords": ["survivor", "filter", "vcf", "structural variants"], + "tools": [ + { + "survivor": { + "description": "Toolset for SV simulation, comparison and filtering", + "homepage": "https://github.com/fritzsedlazeck/SURVIVOR/wiki", + "documentation": "https://github.com/fritzsedlazeck/SURVIVOR/wiki", + "tool_dev_url": "https://github.com/fritzsedlazeck/SURVIVOR", + "doi": "10.1038/NCOMMS14061", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf_file": { + "type": "file", + "description": "VCF file to filter", + "ontologies": [] + } + }, + { + "bed": { + "type": "file", + "description": "BED file with regions to ignore (NA to disable)", + "ontologies": [] + } + } + ], + { + "minsv": { + "type": "integer", + "description": "Min SV size (-1 to disable)" + } + }, + { + "maxsv": { + "type": "integer", + "description": "Max SV size (-1 to disable)" + } + }, + { + "minallelefreq": { + "type": "float", + "description": "Min allele frequency (0-1)" + } + }, + { + "minnumreads": { + "type": "integer", + "description": "Min number of reads support [RE flag (-1 to disable)]" + } + } + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf": { + "type": "file", + "description": "Filtered VCF file", + "pattern": "*.{vcf}", + "ontologies": [] + } + } + ] + ], + "versions_survivor": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "survivor": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "SURVIVOR 2>&1 | grep 'Version' | sed 's/Version: //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "survivor": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "SURVIVOR 2>&1 | grep 'Version' | sed 's/Version: //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@LlaneroHiboreo"], + "maintainers": ["@LlaneroHiboreo"] + }, + "pipelines": [ + { + "name": "variantbenchmarking", + "version": "1.5.0" + } + ] }, { - "name": "rnaseq", - "version": "3.26.0" - } - ] - }, - { - "name": "president", - "path": "modules/nf-core/president/meta.yml", - "type": "module", - "meta": { - "name": "president", - "description": "Calculate pairwise nucleotide identity with respect to a reference sequence", - "keywords": [ - "fasta", - "genome", - "qc", - "nucleotides" - ], - "tools": [ - { - "president": { - "description": "Calculate pairwise nucleotide identity with respect to a reference sequence", - "homepage": "https://github.com/rki-mf1/president", - "documentation": "https://github.com/rki-mf1/president", - "tool_dev_url": "https://github.com/rki-mf1/president", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing information, e.g. [ id:'test', single_end:false ]" - } - }, - { - "fasta": { - "type": "file", - "description": "One fasta file or a list of multiple fasta files to perform president on. Has to be uncompressed!", - "pattern": "*.{fasta,fas,fa,fna,ffn,faa,mpfa,frn}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing information about the reference genome" - } + "name": "survivor_merge", + "path": "modules/nf-core/survivor/merge/meta.yml", + "type": "module", + "meta": { + "name": "survivor_merge", + "description": "Compare or merge VCF files to generate a consensus or multi sample VCF files.", + "keywords": ["survivor", "merge", "vcf", "structural variants"], + "tools": [ + { + "survivor": { + "description": "Toolset for SV simulation, comparison and filtering", + "homepage": "https://github.com/fritzsedlazeck/SURVIVOR/wiki", + "documentation": "https://github.com/fritzsedlazeck/SURVIVOR/wiki", + "tool_dev_url": "https://github.com/fritzsedlazeck/SURVIVOR", + "doi": "10.1038/NCOMMS14061", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcfs": { + "type": "list", + "description": "The VCF files to be merged\nGzipped VCF files are not supported: https://github.com/fritzsedlazeck/SURVIVOR/issues/158\n", + "pattern": "*.vcf" + } + } + ], + { + "max_distance_breakpoints": { + "type": "integer", + "description": "Max distance between breakpoints (0-1 percent of length, 1- number of bp)" + } + }, + { + "min_supporting_callers": { + "type": "integer", + "description": "Minimum number of supporting caller" + } + }, + { + "account_for_type": { + "type": "integer", + "description": "Take the type into account (1==yes, else no)" + } + }, + { + "account_for_sv_strands": { + "type": "integer", + "description": "Take the strands of SVs into account (1==yes, else no)" + } + }, + { + "estimate_distanced_by_sv_size": { + "type": "integer", + "description": "Estimate distance based on the size of SV (1==yes, else no)" + } + }, + { + "min_sv_size": { + "type": "integer", + "description": "Minimum size of SVs to be taken into account" + } + } + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf": { + "type": "file", + "description": "The merged VCF file", + "pattern": "*.vcf", + "ontologies": [] + } + } + ] + ], + "versions_survivor": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "survivor": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "SURVIVOR 2>&1 | grep 'Version' | sed 's/Version: //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "survivor": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "SURVIVOR 2>&1 | grep 'Version' | sed 's/Version: //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@nvnieuwk"], + "maintainers": ["@nvnieuwk"] }, - { - "reference": { - "type": "file", - "description": "Fasta of a reference genome. Has to be uncompressed!", - "pattern": "*.{fasta,fas,fa,fna,ffn,faa,mpfa,frn}", - "ontologies": [] - } - } - ], - { - "compress": { - "type": "boolean", - "description": "Set to \"true\" if fasta output should be compressed" - } - } - ], - "output": { - "valid_fasta": [ - [ - { - "meta": { - "type": "file", - "description": "Fasta file containing sequences which passed the qc (\"valid.fasta\"). If true is set on the \"compress\" input value, the file is gz-compressed.", - "pattern": "*.{fasta.gz, fasta}", - "ontologies": [] - } - }, - { - "${prefix}_valid.fasta*": { - "type": "file", - "description": "Fasta file containing sequences which passed the qc (\"valid.fasta\"). If true is set on the \"compress\" input value, the file is gz-compressed.", - "pattern": "*.{fasta.gz, fasta}", - "ontologies": [] - } - } - ] - ], - "invalid_fasta": [ - [ - { - "meta": { - "type": "file", - "description": "Fasta file containing sequences which passed the qc (\"valid.fasta\"). If true is set on the \"compress\" input value, the file is gz-compressed.", - "pattern": "*.{fasta.gz, fasta}", - "ontologies": [] - } - }, - { - "${prefix}_invalid.fasta*": { - "type": "file", - "description": "Fasta file containing sequences which didn't pass the qc (\"invalid.fasta\"). If true is set on the \"compress\" input value, the files are gz-compressed.", - "pattern": "*_invalid.{fasta.gz, fasta}", - "ontologies": [] - } - } + "pipelines": [ + { + "name": "variantbenchmarking", + "version": "1.5.0" + } ] - ], - "report": [ - [ - { - "meta": { - "type": "file", - "description": "Fasta file containing sequences which passed the qc (\"valid.fasta\"). If true is set on the \"compress\" input value, the file is gz-compressed.", - "pattern": "*.{fasta.gz, fasta}", - "ontologies": [] - } - }, - { - "*.tsv": { - "type": "file", - "description": "Report with some information for every sample, like statistic values. See docs for details", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "file", - "description": "Fasta file containing sequences which passed the qc (\"valid.fasta\"). If true is set on the \"compress\" input value, the file is gz-compressed.", - "pattern": "*.{fasta.gz, fasta}", - "ontologies": [] - } - }, - { - "*.log": { - "type": "file", - "description": "Log file of president", - "pattern": "*.log", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@paulwolk" - ], - "maintainers": [ - "@paulwolk", - "@gallvp" - ] - } - }, - { - "name": "presto_filterseq", - "path": "modules/nf-core/presto/filterseq/meta.yml", - "type": "module", - "meta": { - "name": "presto_filterseq", - "description": "Filter reads by quality score.", - "keywords": [ - "immcantation", - "airrseq", - "genomics", - "immunoinformatics" - ], - "tools": [ - { - "presto": { - "description": "A bioinformatics toolkit for processing high-throughput lymphocyte receptor sequencing data.", - "homepage": "https://immcantation.readthedocs.io", - "documentation": "https://presto.readthedocs.io", - "tool_dev_url": "https://bitbucket.org/kleinstein/presto", - "doi": "10.1093/bioinformatics/btu138", - "licence": [ - "AGPL v3" - ], - "identifier": "biotools:presto-measure" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "reads": { - "type": "file", - "description": "fastq file", - "pattern": "*.{fastq}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "output": { - "reads": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*_quality-pass.fastq": { - "type": "file", - "description": "filtered fastq file", - "pattern": "*.{fastq}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "logs": [ - { - "*_command_log.txt": { - "type": "file", - "description": "command logs", - "pattern": "*.txt", - "ontologies": [] - } - } - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ], - "log_tab": [ - { - "*.tab": { - "type": "file", - "description": "parsed log table", - "pattern": "*.tab", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - }, - "authors": [ - "@ggabernet" - ] - } - }, - { - "name": "pretextmap", - "path": "modules/nf-core/pretextmap/meta.yml", - "type": "module", - "meta": { - "name": "pretextmap", - "description": "converts sam/bam/cram/pairs into genome contact map", - "keywords": [ - "contact", - "bam", - "map" - ], - "tools": [ - { - "pretextmap": { - "description": "Paired REad TEXTure Mapper. Converts SAM formatted read pairs into genome contact maps.", - "homepage": "https://github.com/wtsi-hpag/PretextMap", - "documentation": "https://github.com/wtsi-hpag/PretextMap/blob/master/README.md", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM/SAM file or pairs formatted reads file", - "pattern": "*.{bam,cram,sam,pairs.gz}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference sequence file", - "pattern": "*.{fasta,fna,fa}", - "ontologies": [] - } - }, - { - "fai": { - "type": "file", - "description": "Reference sequence index file", - "pattern": "*.{fai}", - "ontologies": [] - } - } - ] - ], - "output": { - "pretext": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.pretext": { - "type": "file", - "description": "pretext map", - "pattern": "*.pretext", - "ontologies": [] - } - } - ] - ], - "versions_pretextmap": [ - [ - { - "${task.process}": { - "type": "string", - "description": "Name of the process" - } - }, - { - "PretextMap": { - "type": "string", - "description": "Name of the tool" - } - }, - { - "PretextMap | sed \"/Version/!d; s/.*Version //\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_samtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "Name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "Name of the tool" - } - }, - { - "samtools --version | sed \"1!d; s/samtools //\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "Name of the process" - } - }, - { - "PretextMap": { - "type": "string", - "description": "Name of the tool" - } - }, - { - "PretextMap | sed \"/Version/!d; s/.*Version //\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "Name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "Name of the tool" - } - }, - { - "samtools --version | sed \"1!d; s/samtools //\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@marrip", - "@getrudeln" - ], - "maintainers": [ - "@marrip", - "@getrudeln" - ] - } - }, - { - "name": "pretextsnapshot", - "path": "modules/nf-core/pretextsnapshot/meta.yml", - "type": "module", - "meta": { - "name": "pretextsnapshot", - "description": "A module to generate images from Pretext contact maps.", - "keywords": [ - "pretext", - "image", - "hic", - "png", - "jpg", - "bmp", - "contact maps" - ], - "tools": [ - { - "pretextsnapshot": { - "description": "Commandline image generator for Pretext Hi-C genome contact maps.", - "homepage": "https://github.com/wtsi-hpag/PretextSnapshot", - "tool_dev_url": "https://github.com/wtsi-hpag/PretextSnapshot", - "licence": [ - "https://github.com/wtsi-hpag/PretextSnapshot/blob/master/LICENSE" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "pretext_map": { - "type": "file", - "description": "pretext hic map", - "pattern": "*.pretext", - "ontologies": [] - } - }, - { - "order_file": { - "type": "file", - "description": "Custom ordering of scaffolds in pretext snapshot output.\nThis is a single column file of scaffold names\n" - } - } - ] - ], - "output": { - "image": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.{jpeg,png,bmp}": { - "type": "file", - "description": "image of a hic contact map", - "pattern": "*.{jpeg,png,bmp}", - "ontologies": [] - } - } - ] - ], - "versions_pretextsnapshot": [ - [ - { - "${task.process}": { - "type": "string", - "description": "Name of the process" - } - }, - { - "PretextSnapshot": { - "type": "string", - "description": "Name of the tool" - } - }, - { - "PretextSnapshot --version | sed 's/^.*PretextSnapshot Version //g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "PretextSnapshot": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "PretextSnapshot --version | sed 's/^.*PretextSnapshot Version //g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@epaule" - ], - "maintainers": [ - "@epaule", - "@DLBPointon" - ] - } - }, - { - "name": "pridepy_downloadfile", - "path": "modules/nf-core/pridepy/downloadfile/meta.yml", - "type": "module", - "meta": { - "name": "pridepy_downloadfile", - "description": "Download a single file from the PRIDE Archive by name using pridepy.", - "keywords": [ - "pride", - "download", - "proteomics", - "mass spectrometry" - ], - "tools": [ - { - "pridepy": { - "description": "Python client library and command-line tool to access PRIDE Archive data\nprogrammatically, including downloading files from public proteomics datasets.\n", - "homepage": "https://github.com/PRIDE-Archive/pridepy", - "documentation": "https://github.com/PRIDE-Archive/pridepy", - "tool_dev_url": "https://github.com/PRIDE-Archive/pridepy", - "licence": [ - "Apache-2.0" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "file_name": { - "type": "string", - "description": "Name of the file to download from the PRIDE Archive dataset" - } - }, - { - "pride_accession": { - "type": "string", - "description": "PRIDE Archive project accession (e.g. PXD000001) identifying the dataset" - } - } - ] - ], - "output": { - "file": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${file_name}": { - "type": "file", - "description": "The file downloaded from the PRIDE Archive", - "pattern": "*" - } - } - ] - ], - "versions_pridepy": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pridepy": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python -c \"from importlib.metadata import version; print(version('pridepy'))\"": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pridepy": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python -c \"from importlib.metadata import version; print(version('pridepy'))\"": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@jonasscheid" - ], - "maintainers": [ - "@jonasscheid" - ] - } - }, - { - "name": "pridepy_fetchsdrf", - "path": "modules/nf-core/pridepy/fetchsdrf/meta.yml", - "type": "module", - "meta": { - "name": "pridepy_fetchsdrf", - "description": "Fetch an SDRF file from the PRIDE Archive for a given project accession.", - "keywords": [ - "pride", - "sdrf", - "proteomics", - "download", - "metadata" - ], - "tools": [ - { - "pridepy": { - "description": "Python client library to access PRIDE Archive data programmatically,\nincluding downloading files and metadata for public proteomics datasets.\n", - "homepage": "https://github.com/PRIDE-Archive/pridepy", - "documentation": "https://github.com/PRIDE-Archive/pridepy", - "tool_dev_url": "https://github.com/PRIDE-Archive/pridepy", - "licence": [ - "Apache-2.0" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'PXD004684' ]`\n" - } - }, - { - "pride_id": { - "type": "string", - "description": "PRIDE Archive project accession (e.g. PXD004684)" - } - } - ] - ], - "output": { - "sdrf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'PXD004684' ]`\n" - } - }, - { - "${prefix}.sdrf.tsv": { - "type": "file", - "description": "SDRF (Sample and Data Relationship Format) file describing the experimental design of the PRIDE project", - "pattern": "*.sdrf.tsv" - } - } - ] - ], - "versions_pridepy": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "pridepy": { - "type": "string", - "description": "The tool name" - } - }, - { - "python -c \"from importlib.metadata import version; print(version('pridepy'))\"": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "pridepy": { - "type": "string", - "description": "The tool name" - } - }, - { - "python -c \"from importlib.metadata import version; print(version('pridepy'))\"": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@jonasscheid" - ], - "maintainers": [ - "@jonasscheid" - ] - }, - "pipelines": [ - { - "name": "mhcquant", - "version": "3.2.0" - } - ] - }, - { - "name": "primerprospector_analyzeprimers", - "path": "modules/nf-core/primerprospector/analyzeprimers/meta.yml", - "type": "module", - "meta": { - "name": "primerprospector_analyzeprimers", - "description": "Score PCR primers for binding to target sequences", - "keywords": [ - "primer design", - "pcr", - "fasta", - "sequence analysis", - "primer scoring" - ], - "tools": [ - { - "primerprospector": { - "description": "Primer Prospector is a pipeline of programs to design and analyze PCR primers.", - "homepage": "https://pprospector.sourceforge.net/", - "documentation": "https://pprospector.sourceforge.net/scripts/analyze_primers.html", - "tool_dev_url": "https://sourceforge.net/p/pprospector/code/", - "doi": "10.1093/bioinformatics/btr087", - "licence": [ - "GPL" - ], - "args_id": "$args", - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information. Mandatory.\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Target FASTA file or files to score primers against. Mandatory.", - "pattern": "*.{fasta,fa,fna}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - }, - { - "primers": { - "type": "file", - "description": "Tab-delimited primers file containing primer names and sequences. Optional\nwhen primer name and sequence are supplied with task.ext.args.\n", - "pattern": "*.{txt,tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "output": { - "hits": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*_hits.txt": { - "type": "file", - "description": "Primer hit detail files, including mismatches, gaps, positions, and weighted scores. One file is produced per primer.", - "pattern": "*_hits.txt", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "plots": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.ps": { - "type": "file", - "description": "PostScript summary plots of primer mismatch and weighted score information. One file is produced per primer.", - "pattern": "*.ps", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2330" - } - ] - } - } - ] - ], - "versions_primerprospector": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "primerprospector": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "analyze_primers.py --version 2>&1 | grep -Eo '[0-9]+(\\.[0-9]+)+' | tail -n 1": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "primerprospector": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "analyze_primers.py --version 2>&1 | grep -Eo '[0-9]+(\\.[0-9]+)+' | tail -n 1": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@vagkaratzas" - ], - "maintainers": [ - "@vagkaratzas" - ] - } - }, - { - "name": "prinseqplusplus", - "path": "modules/nf-core/prinseqplusplus/meta.yml", - "type": "module", - "meta": { - "name": "prinseqplusplus", - "description": "PRINSEQ++ is a C++ implementation of the prinseq-lite.pl program. It can be used to filter, reformat or trim genomic and metagenomic sequence data", - "keywords": [ - "fastq", - "fasta", - "filter", - "trim" - ], - "tools": [ - { - "prinseqplusplus": { - "description": "PRINSEQ++ - Multi-threaded C++ sequence cleaning", - "homepage": "https://github.com/Adrian-Cantu/PRINSEQ-plus-plus", - "documentation": "https://github.com/Adrian-Cantu/PRINSEQ-plus-plus", - "tool_dev_url": "https://github.com/Adrian-Cantu/PRINSEQ-plus-plus", - "doi": "10.7287/peerj.preprints.27553v1", - "licence": [ - "GPL v2" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end\ndata, respectively.\n", - "ontologies": [] - } - } - ] - ], - "output": { - "good_reads": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_good_out*.fastq.gz": { - "type": "file", - "description": "Reads passing filter(s) in gzipped FASTQ format", - "pattern": "*_good_out_{R1,R2}.fastq.gz", - "ontologies": [] - } - } - ] - ], - "single_reads": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_single_out*.fastq.gz": { - "type": "file", - "description": "Single reads without the pair passing filter(s) in gzipped FASTQ format\n", - "pattern": "*_single_out_{R1,R2}.fastq.gz", - "ontologies": [] - } - } - ] - ], - "bad_reads": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_bad_out*.fastq.gz": { - "type": "file", - "description": "Reads without not passing filter(s) in gzipped FASTQ format\n", - "pattern": "*_bad_out_{R1,R2}.fastq.gz", - "ontologies": [] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.log": { - "type": "file", - "description": "Verbose level 2 STDOUT information in a log file\n", - "pattern": "*.log", - "ontologies": [] - } - } - ] - ], - "versions_prinseqplusplus": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "prinseqplusplus": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "prinseq++ --version | cut -f 2 -d ' '": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "prinseqplusplus": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "prinseq++ --version | cut -f 2 -d ' '": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] }, - "authors": [ - "@jfy133" - ], - "maintainers": [ - "@jfy133" - ] - }, - "pipelines": [ { - "name": "taxprofiler", - "version": "2.0.0" - }, - { - "name": "viralmetagenome", - "version": "1.1.1" - } - ] - }, - { - "name": "prodigal", - "path": "modules/nf-core/prodigal/meta.yml", - "type": "module", - "meta": { - "name": "prodigal", - "description": "Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program", - "keywords": [ - "prokaryotes", - "gene finding", - "microbial" - ], - "tools": [ - { - "prodigal": { - "description": "Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program", - "homepage": "https://github.com/hyattpd/Prodigal", - "documentation": "https://github.com/hyattpd/prodigal/wiki", - "tool_dev_url": "https://github.com/hyattpd/Prodigal", - "doi": "10.1186/1471-2105-11-119", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:prodigal" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "genome": { - "type": "file", - "description": "fasta/fasta.gz file", - "ontologies": [] - } - } - ], - { - "output_format": { - "type": "string", - "description": "Output format (\"gbk\"/\"gff\"/\"sqn\"/\"sco\")" - } - } - ], - "output": { - "gene_annotations": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.${output_format}.gz": { - "type": "file", - "description": "gene annotations in output_format given as input", - "pattern": "*.{output_format}", - "ontologies": [] - } - } - ] - ], - "nucleotide_fasta": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.fna.gz": { - "type": "file", - "description": "nucleotide sequences file", - "pattern": "*.{fna}", - "ontologies": [] - } - } - ] - ], - "amino_acid_fasta": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.faa.gz": { - "type": "file", - "description": "protein translations file", - "pattern": "*.{faa}", - "ontologies": [] - } - } - ] - ], - "all_gene_annotations": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}_all.txt.gz": { - "type": "file", - "description": "complete starts file", - "pattern": "*.{_all.txt}", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@grst" - ], - "maintainers": [ - "@grst" - ] - }, - "pipelines": [ - { - "name": "funcscan", - "version": "3.0.0" - }, - { - "name": "mag", - "version": "5.4.2" - }, - { - "name": "metapep", - "version": "1.0.0" - }, - { - "name": "metatdenovo", - "version": "1.3.0" - } - ] - }, - { - "name": "prokka", - "path": "modules/nf-core/prokka/meta.yml", - "type": "module", - "meta": { - "name": "prokka", - "description": "Whole genome annotation of small genomes (bacterial, archeal, viral)", - "keywords": [ - "annotation", - "fasta", - "prokka" - ], - "tools": [ - { - "prokka": { - "description": "Rapid annotation of prokaryotic genomes", - "homepage": "https://github.com/tseemann/prokka", - "doi": "10.1093/bioinformatics/btu153", - "licence": [ - "GPL v2" - ], - "identifier": "biotools:prokka" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA file to be annotated. Has to contain at least a non-empty string dummy value.\n", - "ontologies": [] - } - } - ], - { - "proteins": { - "type": "file", - "description": "FASTA file of trusted proteins to first annotate from (optional)", - "ontologies": [] - } - }, - { - "prodigal_tf": { - "type": "file", - "description": "Training file to use for Prodigal (optional)", - "ontologies": [] + "name": "survivor_simsv", + "path": "modules/nf-core/survivor/simsv/meta.yml", + "type": "module", + "meta": { + "name": "survivor_simsv", + "description": "Simulate an SV VCF file based on a reference genome", + "keywords": ["structural variants", "simulation", "sv", "vcf"], + "tools": [ + { + "survivor": { + "description": "Toolset for SV simulation, comparison and filtering", + "homepage": "https://github.com/fritzsedlazeck/SURVIVOR/wiki", + "documentation": "https://github.com/fritzsedlazeck/SURVIVOR/wiki", + "tool_dev_url": "https://github.com/fritzsedlazeck/SURVIVOR", + "doi": "10.1038/NCOMMS14061", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing fasta information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The reference genome", + "pattern": "*.{fasta,fna,fa}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing fasta index information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "fai": { + "type": "file", + "description": "The index of the reference genome", + "pattern": "*.fai", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing parameters information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "parameters": { + "type": "file", + "description": "A text file containing the parameters to be used for the simulation. Gets automatically generated using defaults when this is not supplied", + "pattern": "*.txt", + "ontologies": [] + } + } + ], + { + "snp_mutation_frequency": { + "type": "float", + "description": "The SNP mutation frequency in the output VCF (0-1)" + } + }, + { + "sim_reads": { + "type": "integer", + "description": "Whether or not to simulate reads (1==yes, else no)" + } + } + ], + "output": { + "parameters": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "The created parameters file", + "pattern": "*.txt", + "ontologies": [] + } + } + ] + ], + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.vcf": { + "type": "file", + "description": "A VCF containing the simulated variants", + "pattern": "*.vcf", + "ontologies": [] + } + } + ] + ], + "bed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "A BED file of the simulated structural variants", + "pattern": "*.bed", + "ontologies": [] + } + } + ] + ], + "fasta": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.fasta": { + "type": "file", + "description": "A Fasta file file containing the variants from the output VCF", + "pattern": "*.fasta", + "ontologies": [] + } + } + ] + ], + "insertions": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.insertions.fa": { + "type": "file", + "description": "A Fasta file file containing insertion sequences", + "pattern": "*.insertions.fa", + "ontologies": [] + } + } + ] + ], + "versions_survivor": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "survivor": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "SURVIVOR 2>&1 | grep 'Version' | sed 's/Version: //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "survivor": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "SURVIVOR 2>&1 | grep 'Version' | sed 's/Version: //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@nvnieuwk"], + "maintainers": ["@nvnieuwk"] } - } - ], - "output": { - "gff": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/*.gff": { - "type": "file", - "description": "annotation in GFF3 format, containing both sequences and annotations", - "pattern": "*.{gff}", - "ontologies": [] - } - } - ] - ], - "gbk": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/*.gbk": { - "type": "file", - "description": "annotation in GenBank format, containing both sequences and annotations", - "pattern": "*.{gbk}", - "ontologies": [] - } - } - ] - ], - "fna": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/*.fna": { - "type": "file", - "description": "nucleotide FASTA file of the input contig sequences", - "pattern": "*.{fna}", - "ontologies": [] - } - } - ] - ], - "faa": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/*.faa": { - "type": "file", - "description": "protein FASTA file of the translated CDS sequences", - "pattern": "*.{faa}", - "ontologies": [] - } - } - ] - ], - "ffn": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/*.ffn": { - "type": "file", - "description": "nucleotide FASTA file of all the prediction transcripts (CDS, rRNA, tRNA, tmRNA, misc_RNA)", - "pattern": "*.{ffn}", - "ontologies": [] - } - } - ] - ], - "sqn": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/*.sqn": { - "type": "file", - "description": "an ASN1 format \"Sequin\" file for submission to Genbank", - "pattern": "*.{sqn}", - "ontologies": [] - } - } - ] - ], - "fsa": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/*.fsa": { - "type": "file", - "description": "nucleotide FASTA file of the input contig sequences, used by \"tbl2asn\" to create the .sqn file", - "pattern": "*.{fsa}", - "ontologies": [] - } - } - ] - ], - "tbl": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/*.tbl": { - "type": "file", - "description": "feature Table file, used by \"tbl2asn\" to create the .sqn file", - "pattern": "*.{tbl}", - "ontologies": [] - } - } - ] - ], - "err": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/*.err": { - "type": "file", - "description": "unacceptable annotations - the NCBI discrepancy report.", - "pattern": "*.{err}", - "ontologies": [] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/*.log": { - "type": "file", - "description": "contains all the output that Prokka produced during its run", - "pattern": "*.{log}", - "ontologies": [] - } - } - ] - ], - "txt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/*.txt": { - "type": "file", - "description": "statistics relating to the annotated features found", - "pattern": "*.{txt}", - "ontologies": [] - } - } - ] - ], - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/*.tsv": { - "type": "file", - "description": "tab-separated file of all features (locus_tag,ftype,len_bp,gene,EC_number,COG,product)", - "pattern": "*.{tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_prokka": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "prokka": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "prokka --version 2>&1 | sed 's/^.*prokka //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "prokka": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "prokka --version 2>&1 | sed 's/^.*prokka //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@rpetit3" - ], - "maintainers": [ - "@rpetit3" - ] - }, - "pipelines": [ - { - "name": "bacass", - "version": "2.6.0" }, { - "name": "funcscan", - "version": "3.0.0" - }, - { - "name": "mag", - "version": "5.4.2" - }, - { - "name": "magmap", - "version": "1.0.0" - }, - { - "name": "metatdenovo", - "version": "1.3.0" - }, - { - "name": "viralmetagenome", - "version": "1.1.1" - } - ] - }, - { - "name": "proovframe_fix", - "path": "modules/nf-core/proovframe/fix/meta.yml", - "type": "module", - "meta": { - "name": "proovframe_fix", - "description": "frame-shift correction for long read (meta)genomics - fix frameshifts in reads", - "keywords": [ - "frame-shift correction", - "long-read sequencing", - "sequence analysis" - ], - "tools": [ - { - "proovframe": { - "description": "frame-shift correction for long read (meta)genomics", - "homepage": "https://github.com/thackl/proovframe", - "documentation": "https://github.com/thackl/proovframe", - "tool_dev_url": "https://github.com/thackl/proovframe", - "doi": "10.1101/2021.08.23.457338", - "licence": [ - "MIT" - ], - "identifier": "biotools:proovframe" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "fa": { - "type": "file", - "description": "A FASTA file containing a database of guide protein sequences", - "pattern": "*.{faa,fasta,fa}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "tsv": { - "type": "file", - "description": "Output TSV file from proovframe/map with the frameshift-aware protein to read alignments from proovframe/map", - "pattern": "*.{tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "output": { - "out_fa": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.fa": { - "type": "file", - "description": "Result FASTA with fixed frameshift reads", - "pattern": "*.{fa}", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@mcarbajo", - "@vagkaratzas" - ], - "maintainers": [ - "@vagkaratzas", - "@Ge94" - ] - } - }, - { - "name": "proovframe_map", - "path": "modules/nf-core/proovframe/map/meta.yml", - "type": "module", - "meta": { - "name": "proovframe_map", - "description": "frame-shift correction for long read (meta)genomics - maps proteins to reads", - "keywords": [ - "frame-shift correction", - "long-read sequencing", - "sequence analysis" - ], - "tools": [ - { - "proovframe": { - "description": "frame-shift correction for long read (meta)genomics", - "homepage": "https://github.com/thackl/proovframe", - "documentation": "https://github.com/thackl/proovframe", - "tool_dev_url": "https://github.com/thackl/proovframe", - "doi": "10.1101/2021.08.23.457338", - "licence": [ - "MIT" - ], - "identifier": "biotools:proovframe" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "A FASTA fna file containing raw read nucleotide sequences", - "pattern": "*.{fasta,fa}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "faa": { - "type": "file", - "description": "A proteome fasta file to create a database of guide protein sequences from", - "pattern": "*.{faa,fasta,fa}", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "db": { - "type": "file", - "description": "A previously generated diamond database of guide protein sequences", - "pattern": "*.{dmnd}", - "ontologies": [] - } - } - ] - ], - "output": { - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "Output TSV file with the frameshift-aware protein to read alignments", - "pattern": "*.{tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@manuelcarbajo", - "@MGS-sails", - "@vagkaratzas" - ], - "maintainers": [ - "@vagkaratzas", - "@Ge94" - ] - } - }, - { - "name": "propr_grea", - "path": "modules/nf-core/propr/grea/meta.yml", - "type": "module", - "meta": { - "name": "propr_grea", - "description": "Perform Gene Ratio Enrichment Analysis", - "keywords": [ - "propr", - "grea", - "logratio", - "differential expression", - "functional enrichment", - "functional analysis" - ], - "tools": [ - { - "grea": { - "description": "Gene Ratio Enrichment Analysis", - "homepage": "https://github.com/tpq/propr", - "documentation": "https://rdrr.io/cran/propr/man/propr.html", - "tool_dev_url": "https://github.com/tpq/propr", - "doi": "10.2202/1544-6115.1175", - "licence": [ - "GPL-2" - ], - "identifier": "biotools:propr" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing data information.\nThis can be used at the workflow level to pass optional parameters to the module.\n[id: 'test', ...]\n" - } - }, - { - "adjacency": { - "type": "file", - "description": "Adjacency matrix representing the graph connections (ie. 1 for edges, 0 otherwise).\nThis can be the adjacency matrix output from gene ratio approaches like propr/propd.\n", - "pattern": "*.{csv,tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - }, - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing data information.\nThis can be used at the workflow level to pass optional parameters to the module.\n[id: 'test', ...]\n" - } - }, - { - "gmt": { - "type": "file", - "description": "A tab delimited file format that describes gene sets. The first column is the\nconcept id (eg. GO term, pathway, etc), the second column is the concept description, and the\nrest are nodes (eg. genes) that is associated to the given concept.\n", - "pattern": "*.{gmt}", - "ontologies": [] - } - } - ] - ], - "output": { - "results": [ - [ - { - "meta": { - "type": "file", - "description": "Groovy Map containing sample information.\nThis can be used at the workflow level to pass optional parameters to the module.\n[id: 'test', ...]\n", - "ontologies": [] - } - }, - { - "*.grea.tsv": { - "type": "file", - "description": "Output file containing the information about the tested concepts (ie. gene sets)\nand enrichment statistics.\n", - "pattern": "*.grea.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ], - "session_info": [ - { - "*.R_sessionInfo.log": { - "type": "file", - "description": "dump of R SessionInfo", - "pattern": "*.R_sessionInfo.log", - "ontologies": [] - } - } - ] - }, - "authors": [ - "@caraiz2001", - "@suzannejin" - ], - "maintainers": [ - "@caraiz2001", - "@suzannejin" - ] - } - }, - { - "name": "propr_logratio", - "path": "modules/nf-core/propr/logratio/meta.yml", - "type": "module", - "meta": { - "name": "propr_logratio", - "description": "Transform the data matrix using centered logratio transformation (CLR) or additive logratio transformation (ALR)", - "keywords": [ - "alr", - "clr", - "logratio", - "boxcox", - "transformation", - "propr" - ], - "tools": [ - { - "propr": { - "description": "Logratio methods for omics data", - "homepage": "https://github.com/tpq/propr", - "documentation": "https://rdrr.io/cran/propr/man/propr.html", - "tool_dev_url": "https://github.com/tpq/propr", - "doi": "10.1038/s41598-017-16520-0", - "licence": [ - "GPL-2" - ], - "identifier": "biotools:propr" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing additional information.\nmeta.id can be used to name the output files.\n[id: 'test', ...]\n" - } - }, - { - "count": { - "type": "file", - "description": "Count matrix, where rows = variables or genes, columns = samples or cells.\nThis matrix should not contain zeros. Otherwise, they will be first replaced by the minimum value.\nYou may want to handle the zeros with a different method beforehand.\n", - "pattern": "*.{csv,tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - }, - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "output": { - "logratio": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing additional information.\nmeta.id can be used to name the output files.\n[id: 'test', ...]\n" - } - }, - { - "*.logratio.tsv": { - "type": "file", - "description": "ALR/CLR transformed data matrix. With rows = variables or genes, columns = samples or cells.", - "pattern": "*.logratio.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "session_info": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing additional information.\nmeta.id can be used to name the output files.\n[id: 'test', ...]\n" - } - }, - { - "*.R_sessionInfo.log": { - "type": "file", - "description": "dump of R SessionInfo", - "pattern": "*.R_sessionInfo.log", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@suzannejin", - "@oprana22" - ], - "maintainers": [ - "@suzannejin", - "@oprana22" - ] - } - }, - { - "name": "propr_propd", - "path": "modules/nf-core/propr/propd/meta.yml", - "type": "module", - "meta": { - "name": "propr_propd", - "description": "Perform differential proportionality analysis", - "keywords": [ - "differential", - "proportionality", - "logratio", - "expression", - "propr", - "propd" - ], - "tools": [ - { - "propr": { - "description": "Logratio methods for omics data", - "homepage": "https://github.com/tpq/propr", - "documentation": "https://rdrr.io/cran/propr/man/propr.html", - "tool_dev_url": "https://github.com/tpq/propr", - "doi": "10.1038/s41598-017-16520-0", - "licence": [ - "GPL-2" - ], - "identifier": "biotools:propr" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing contrast information. This can be used at the\nworkflow level to pass optional parameters to the module, e.g.\n[ id:'contrast1', blocking:'patient' ] passed in as ext.args like:\n'--blocking_variable $meta.blocking'.\n" - } - }, - { - "contrast_variable": { - "type": "string", - "description": "The column in the sample sheet that should be used to define groups for\ncomparison\n" - } - }, - { - "reference": { - "type": "string", - "description": "The value within the contrast_variable column of the sample sheet that\nshould be used to derive the reference samples\n" - } - }, - { - "target": { - "type": "string", - "description": "The value within the contrast_variable column of the sample sheet that\nshould be used to derive the target samples\n" - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy map containing study-wide metadata related to the sample sheet\nand matrix\n" - } - }, - { - "samplesheet": { - "type": "file", - "description": "CSV or TSV format sample sheet with sample metadata\n", - "ontologies": [] - } - }, - { - "counts": { - "type": "file", - "description": "Raw TSV or CSV format expression matrix as output from the nf-core\nRNA-seq workflow\n", - "ontologies": [] - } - } - ] - ], - "output": { - "results_genewise": [ - [ - { - "meta": { - "type": "file", - "description": "TSV-format table of genes associated with differential expression\ninformation as compiled from the propd results\n", - "pattern": "*.propd.genewise.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - }, - { - "*.propd.genewise.tsv": { - "type": "file", - "description": "TSV-format table of genes associated with differential expression\ninformation as compiled from the propd results\n", - "pattern": "*.propd.genewise.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "genewise_plot": [ - [ - { - "meta": { - "type": "file", - "description": "TSV-format table of genes associated with differential expression\ninformation as compiled from the propd results\n", - "pattern": "*.propd.genewise.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - }, - { - "*.propd.genewise.png": { - "type": "file", - "description": "PNG-format plot of accumulated between group variance vs median log\nfold change. Genes with high between group variance and high log fold\nchange are likely to be differentially expressed.\n", - "pattern": "*.propd.genewise.png", - "ontologies": [] - } - } - ] - ], - "rdata": [ - [ - { - "meta": { - "type": "file", - "description": "TSV-format table of genes associated with differential expression\ninformation as compiled from the propd results\n", - "pattern": "*.propd.genewise.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - }, - { - "*.propd.rds": { - "type": "file", - "description": "(Optional) R data containing propd object\n", - "pattern": "*.propd.rds", - "ontologies": [] - } - } - ] - ], - "results_pairwise": [ - [ - { - "meta": { - "type": "file", - "description": "TSV-format table of genes associated with differential expression\ninformation as compiled from the propd results\n", - "pattern": "*.propd.genewise.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" + "name": "survivor_stats", + "path": "modules/nf-core/survivor/stats/meta.yml", + "type": "module", + "meta": { + "name": "survivor_stats", + "description": "Report multiple stats over a VCF file", + "keywords": ["survivor", "statistics", "vcf", "structural variants"], + "tools": [ + { + "survivor": { + "description": "Toolset for SV simulation, comparison and filtering", + "homepage": "https://github.com/fritzsedlazeck/SURVIVOR/wiki", + "documentation": "https://github.com/fritzsedlazeck/SURVIVOR/wiki", + "tool_dev_url": "https://github.com/fritzsedlazeck/SURVIVOR", + "doi": "10.1038/NCOMMS14061", + "licence": ["MIT"], + "identifier": "" + } } - ] - } - }, - { - "*.propd.pairwise.tsv": { - "type": "file", - "description": "(Optional) TSV-format table of the native propd pairwise results. This\ntable contains the differential proportionality values associated to\neach pair of genes.\n", - "pattern": "*.propd.pairwise.tsv", - "ontologies": [ + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF file to filter", + "pattern": "*.{vcf}", + "ontologies": [] + } + } + ], { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "results_pairwise_filtered": [ - [ - { - "meta": { - "type": "file", - "description": "TSV-format table of genes associated with differential expression\ninformation as compiled from the propd results\n", - "pattern": "*.propd.genewise.tsv", - "ontologies": [ + "minsv": { + "type": "integer", + "description": "Min SV size (-1 to disable)" + } + }, { - "edam": "http://edamontology.org/format_3475" - } - ] - } - }, - { - "*.propd.pairwise_filtered.tsv": { - "type": "file", - "description": "(Optional) TSV-format table of the filtered propd pairwise results. This\ntable contains the pairs of genes with significant differential\nproportionality values.\n", - "pattern": "*.propd.pairwise_filtered.tsv", - "ontologies": [ + "maxsv": { + "type": "integer", + "description": "Max SV size (-1 to disable)" + } + }, { - "edam": "http://edamontology.org/format_3475" + "minnumreads": { + "type": "integer", + "description": "Min number of reads support [RE flag (-1 to disable)]" + } } - ] + ], + "output": { + "stats": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.stats": { + "type": "file", + "description": "File containing statistics given input VCF file", + "pattern": "*.{stats}", + "ontologies": [] + } + } + ] + ], + "versions_survivor": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "survivor": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "SURVIVOR 2>&1 | grep 'Version' | sed 's/Version: //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "survivor": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "SURVIVOR 2>&1 | grep 'Version' | sed 's/Version: //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@kubranarci"], + "maintainers": ["@kubranarci"] + }, + "pipelines": [ + { + "name": "variantbenchmarking", + "version": "1.5.0" } - } ] - ], - "adjacency": [ - [ - { - "meta": { - "type": "file", - "description": "TSV-format table of genes associated with differential expression\ninformation as compiled from the propd results\n", - "pattern": "*.propd.genewise.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" + }, + { + "name": "sushie", + "path": "modules/nf-core/sushie/meta.yml", + "type": "module", + "meta": { + "name": "sushie", + "description": "Software to perform multi-ancestry SNP fine-mapping on molecular data", + "keywords": ["gwas", "fine mapping", "ancestry"], + "tools": [ + { + "sushie": { + "description": "Software to perform multi-ancestry SNP fine-mapping on molecular data", + "homepage": "https://github.com/mancusolab/sushie/", + "documentation": "https://mancusolab.github.io/sushie/", + "tool_dev_url": "https://github.com/mancusolab/sushie/", + "doi": "10.1038/s41588-025-02262-7", + "licence": ["MIT"], + "identifier": "biotools:sushie" + } } - ] - } - }, - { - "*.propd.adjacency.csv": { - "type": "file", - "description": "(Optional) CSV-format table of the adjacency matrix defining a graph, with\nedges (1) associated to pairs of genes that are significantly differentially\nproportional.\n", - "pattern": "*.propd.adjacency.csv", - "ontologies": [ + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "study_locus_files": { + "type": "file", + "description": "Study locus file(s)", + "pattern": "*.gwas", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + { + "ld_files": { + "type": "file", + "description": "LD file(s)", + "pattern": "*.ld", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, { - "edam": "http://edamontology.org/format_3752" + "sample_sizes": { + "type": "string", + "description": "Sample size(s)" + } + } + ], + "output": { + "corr": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.sushie.corr.tsv.gz": { + "type": "file", + "description": "Effect size correlation", + "pattern": "*.sushie.corr.tsv.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "cs": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.sushie.cs.tsv.gz": { + "type": "file", + "description": "Credible set", + "pattern": "*.sushie.cs.tsv.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "weights": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.sushie.weights.tsv.gz": { + "type": "file", + "description": "Prediction weights", + "pattern": "*.sushie.weights.tsv.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "versions_sushie": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "sushie": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "0.19": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.log": { + "type": "file", + "description": "Log file", + "pattern": "*.log", + "ontologies": [] + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "sushie": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "0.19": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@camlloyd"], + "maintainers": ["@camlloyd"] + } + }, + { + "name": "svaba", + "path": "modules/nf-core/svaba/meta.yml", + "type": "module", + "meta": { + "name": "svaba", + "description": "SvABA is an efficient and accurate method for detecting SVs from short-read sequencing data using genome-wide local assembly with low memory and computing requirements", + "keywords": ["sv", "structural variants", "detecting svs", "short-read sequencing"], + "tools": [ + { + "svaba": { + "description": "Structural variation and indel detection by local assembly", + "homepage": "https://github.com/walaj/svaba", + "documentation": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5880247/", + "tool_dev_url": "https://github.com/walaj/svaba", + "doi": "10.1101/gr.221028.117", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\nid: should be the identification number or sample name. If there is normal file meta should be common\ne.g. [ id:'test' ]\n" + } + }, + { + "tumorbam": { + "type": "file", + "description": "Tumor or metastatic sample, BAM, SAM or CRAM file", + "pattern": "*.{bam,cram,sam}", + "ontologies": [] + } + }, + { + "tumorbai": { + "type": "file", + "description": "Index of the tumor or metastatic sample", + "pattern": "*.{bai,crai,sai}", + "ontologies": [] + } + }, + { + "normalbam": { + "type": "file", + "description": "Control (or normal) of matching tumor/metastatic sample, BAM, SAM or CRAM file", + "pattern": "*.{bam,cram,sam}", + "ontologies": [] + } + }, + { + "normalbai": { + "type": "file", + "description": "Index", + "pattern": "*.{bai,crai,sai}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing FASTA information\nid: should be the identification number for alignment file and should be the same used to create BWA index files\ne.g. [ id:'fasta' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA file", + "pattern": "*.{fasta|fa}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing FASTA information\nid: should be the identification number for alignment file and should be the same used to create BWA index files\ne.g. [ id:'fasta' ]\n" + } + }, + { + "fasta_fai": { + "type": "file", + "description": "Index of FASTA file", + "pattern": "*.{fai}", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing BWA information\nid: should be the identification number same as fasta file\ne.g. [ id:'bwa' ]\n" + } + }, + { + "bwa_index": { + "type": "file", + "description": "BWA genome index files. Note that this tool requires the bwa index files to be of the format `prefix.suffix.amb`, where `prefix.suffix` is the full name of the fasta file, not just the prefix.", + "pattern": "Directory containing BWA index *.{amb,ann,bwt,pac,sa}", + "ontologies": [] + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing dbSNP information\nid: should be the identification number for dbSNP files\ne.g. [ id:'test' ]\n" + } + }, + { + "dbsnp": { + "type": "file", + "description": "VCF file including dbSNP variants", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ], + [ + { + "meta6": { + "type": "map", + "description": "Groovy Map containing dbSNP information\nid: should be the identification number for dbSNP files\ne.g. [ id:'test' ]\n" + } + }, + { + "dbsnp_tbi": { + "type": "file", + "description": "Index of VCF file including dbSNP variants", + "pattern": "*.vcf.gz.tbi", + "ontologies": [] + } + } + ], + [ + { + "meta7": { + "type": "map", + "description": "Groovy Map containing regions information\nid: should be the identification number for regions\ne.g. [ id:'test' ]\n" + } + }, + { + "regions": { + "type": "file", + "description": "Targeted intervals. Accepts BED file or Samtools-style string", + "pattern": "*.bed|*.txt|*.tab", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "output": { + "sv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.svaba.sv.vcf.gz": { + "type": "file", + "description": "Filtered SVs for tumor only cases", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "indel": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.svaba.indel.vcf.gz": { + "type": "file", + "description": "Filtered Indels for tumor only cases", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "germ_indel": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.svaba.germline.indel.vcf.gz": { + "type": "file", + "description": "Germline filtered Indels for tumor/normal paired samples", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "germ_sv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.svaba.germline.sv.vcf.gz": { + "type": "file", + "description": "Germline filtered SVs for tumor/normal paired samples", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "som_indel": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.svaba.somatic.indel.vcf.gz": { + "type": "file", + "description": "Somatic filtered Indels for tumor/normal paired samples", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "som_sv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.svaba.somatic.sv.vcf.gz": { + "type": "file", + "description": "Somatic filtered SVs for tumor/normal paired samples", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "unfiltered_sv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.svaba.unfiltered.sv.vcf.gz": { + "type": "file", + "description": "Unfiltered SVs for tumor only cases", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "unfiltered_indel": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.svaba.unfiltered.indel.vcf.gz": { + "type": "file", + "description": "Unfiltered Indels for tumor only cases", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "unfiltered_germ_indel": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.svaba.unfiltered.germline.indel.vcf.gz": { + "type": "file", + "description": "Unfiltered germline Indels for tumor/normal paired samples", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "unfiltered_germ_sv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.svaba.unfiltered.germline.sv.vcf.gz": { + "type": "file", + "description": "Unfiltered germline SVs for tumor/normal paired samples", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "unfiltered_som_indel": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.svaba.unfiltered.somatic.indel.vcf.gz": { + "type": "file", + "description": "Unfiltered somatic Indels for tumor/normal paired samples", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "unfiltered_som_sv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.svaba.unfiltered.somatic.sv.vcf.gz": { + "type": "file", + "description": "Unfiltered somatic SVs for tumor/normal paired samples", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "discordants": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.discordants.txt.gz": { + "type": "file", + "description": "Information on all clusters of discordant reads identified with 2+ reads", + "pattern": "*.txt.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "raw_calls": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.bps.txt.gz": { + "type": "file", + "description": "Raw, unfiltered variants", + "pattern": "*.txt.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "Log file", + "pattern": "*.txt.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "versions_svaba": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "svaba": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "svaba --version 2>&1 | grep -oE '[0-9]+\\.[0-9]+\\.[0-9]+' | head -n 1": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "svaba": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "svaba --version 2>&1 | grep -oE '[0-9]+\\.[0-9]+\\.[0-9]+' | head -n 1": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@kubranarci"], + "maintainers": ["@kubranarci"] + } + }, + { + "name": "svanalyzer_svbenchmark", + "path": "modules/nf-core/svanalyzer/svbenchmark/meta.yml", + "type": "module", + "meta": { + "name": "svanalyzer_svbenchmark", + "description": "SVbenchmark compares a set of “test” structural variants in VCF format to a known truth set (also in VCF format) and outputs estimates of sensitivity and specificity.", + "keywords": ["structural variant", "sv", "benchmarking"], + "tools": [ + { + "svanalyzer": { + "description": "SVanalyzer: tools for the analysis of structural variation in genomes", + "homepage": "https://svanalyzer.readthedocs.io/en/latest/index.html", + "documentation": "https://svanalyzer.readthedocs.io/en/latest/index.html", + "tool_dev_url": "https://github.com/nhansen/SVanalyzer", + "licence": ["CC0"], + "identifier": "" + } } - ] + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing test sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "test": { + "type": "file", + "description": "A VCF-formatted file of structural variants to test (required)", + "pattern": "*.{vcf,vcf.gz}", + "ontologies": [] + } + }, + { + "test_tbi": { + "type": "file", + "description": "A VCF-formatted file index of structural variants to test only for zipped files", + "pattern": "*.{vcf.gz.tbi}", + "ontologies": [] + } + }, + { + "truth": { + "type": "file", + "description": "A VCF-formatted file of variants to compare against (required)", + "pattern": "*.{vcf,vcf.gz}", + "ontologies": [] + } + }, + { + "truth_tbi": { + "type": "file", + "description": "A VCF-formatted file of variants to compare against only for zipped files", + "pattern": "*.{vcf.gz.tbi}", + "ontologies": [] + } + }, + { + "bed": { + "type": "file", + "description": "BED File of regions from which to include variants. Used to filter both test and truth variants.", + "pattern": "*.{bed}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference genome information for fasta\ne.g. `[ id:'test2' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The reference FASTA file for the supplied VCF file or files (required)", + "pattern": "*.{fa,fasta,fa.gz,fasta.gz}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference genome information for fai\ne.g. `[ id:'test3' ]`\n" + } + }, + { + "fai": { + "type": "file", + "description": "The reference FASTA index file", + "pattern": "*.{fai}", + "ontologies": [] + } + } + ] + ], + "output": { + "fns": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information inherited from test vcf\ne.g. `[ id:'test']`\n" + } + }, + { + "*.falsenegatives.vcf.gz": { + "type": "file", + "description": "VCF file with False Negatives", + "pattern": "*.{vcf.gz}", + "ontologies": [] + } + } + ] + ], + "fps": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information inherited from test vcf\ne.g. `[ id:'test']`\n" + } + }, + { + "*.falsepositives.vcf.gz": { + "type": "file", + "description": "VCF file with False Positives", + "pattern": "*.{vcf.gz}", + "ontologies": [] + } + } + ] + ], + "distances": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information inherited from test vcf\ne.g. `[ id:'test']`\n" + } + }, + { + "*.distances": { + "type": "file", + "description": "TSV file with genomic distances and size differences between structural variants compared", + "pattern": "*.{distances}", + "ontologies": [] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information inherited from test vcf\ne.g. `[ id:'test']`\n" + } + }, + { + "*.log": { + "type": "file", + "description": "LOG file of the run", + "pattern": "*.{log}", + "ontologies": [] + } + } + ] + ], + "report": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information inherited from test vcf\ne.g. `[ id:'test']`\n" + } + }, + { + "*.report": { + "type": "file", + "description": "Text file reporting RECALL, PRECISION and F1.", + "pattern": "*.{report}", + "ontologies": [] + } + } + ] + ], + "versions_svanalyzer": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "svanalyzer": { + "type": "string", + "description": "The tool name" + } + }, + { + "0.36": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "svanalyzer": { + "type": "string", + "description": "The tool name" + } + }, + { + "0.36": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@kubranarci"] + }, + "pipelines": [ + { + "name": "variantbenchmarking", + "version": "1.5.0" } - } ] - ], - "fdr": [ - [ - { - "meta": { - "type": "file", - "description": "TSV-format table of genes associated with differential expression\ninformation as compiled from the propd results\n", - "pattern": "*.propd.genewise.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" + }, + { + "name": "svdb_build", + "path": "modules/nf-core/svdb/build/meta.yml", + "type": "module", + "meta": { + "name": "svdb_build", + "description": "Build a structural variant database", + "keywords": ["structural variants", "build", "svdb"], + "tools": [ + { + "svdb": { + "description": "structural variant database software", + "homepage": "https://github.com/J35P312/SVDB", + "documentation": "https://github.com/J35P312/SVDB/blob/master/README.md", + "licence": ["MIT"], + "identifier": "" + } } - ] - } - }, - { - "*.propd.fdr.tsv": { - "type": "file", - "description": "(Optional) TSV-format table of FDR values. When permutation tests is performed,\nthis table is generated with the FDR values calculated by the permutation tests.\nThis is a more conservative test than the default BH method, but more\ncomputationally expensive.\n", - "pattern": "*.propd.fdr.tsv", - "ontologies": [ + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "Input VCF file(s) or folder", + "pattern": "*", + "ontologies": [] + } + } + ], { - "edam": "http://edamontology.org/format_3475" + "input_type": { + "type": "string", + "description": "input type" + } } - ] - } - } - ] - ], - "session_info": [ - { - "*.R_sessionInfo.log": { - "type": "file", - "description": "dump of R SessionInfo", - "pattern": "*.R_sessionInfo.log", - "ontologies": [] - } - } - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "topics": { - "versions": [ - { - "versions.yml": { - "type": "string", - "description": "The name of the process" - } - } - ] - }, - "authors": [ - "@suzannejin", - "@caraiz2001" - ], - "maintainers": [ - "@suzannejin" - ] - } - }, - { - "name": "propr_propr", - "path": "modules/nf-core/propr/propr/meta.yml", - "type": "module", - "meta": { - "name": "propr_propr", - "description": "Perform logratio-based correlation analysis -> get proportionality & basis shrinkage partial correlation coefficients.\nOne can also compute standard correlation coefficients, if required.\n", - "keywords": [ - "coexpression", - "correlation", - "proportionality", - "logratio", - "propr", - "corpcor" - ], - "tools": [ - { - "propr": { - "description": "Logratio methods for omics data", - "homepage": "https://github.com/tpq/propr", - "documentation": "https://rdrr.io/cran/propr/man/propr.html", - "tool_dev_url": "https://github.com/tpq/propr", - "doi": "10.1038/s41598-017-16520-0", - "licence": [ - "GPL-2" - ], - "identifier": "biotools:propr" - } - }, - { - "corpcor": { - "description": "Efficient Estimation of Covariance and (Partial) Correlation", - "homepage": "https://cran.r-project.org/web/packages/corpcor/index.html", - "documentation": "https://cran.r-project.org/web/packages/corpcor/corpcor.pdf", - "doi": "10.2202/1544-6115.1175", - "licence": [ - "GPL >=3" - ], - "identifier": "biotools:propr" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information.\nThis can be used at the workflow level to pass optional parameters to the module.\n[id: 'test', ...]\n" - } - }, - { - "count": { - "type": "file", - "description": "Count matrix, where rows = variables or genes, columns = samples or cells.\nThis matrix should not contain zeros. Otherwise, they will be replaced by the minimum number.\nIt is recommended to handle the zeros beforehand with the method of preference.\n", - "pattern": "*.{csv,tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - }, - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "output": { - "propr": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information.\nThis can be used at the workflow level to pass optional parameters to the module.\n[id: 'test', ...]\n" - } - }, - { - "*.propr.rds": { - "type": "file", - "description": "R propr object", - "pattern": "*.propr.rds", - "ontologies": [] - } - } - ] - ], - "matrix": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information.\nThis can be used at the workflow level to pass optional parameters to the module.\n[id: 'test', ...]\n" - } - }, - { - "*.propr.tsv": { - "type": "file", - "description": "Coefficient matrix", - "pattern": "*.propr.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "fdr": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information.\nThis can be used at the workflow level to pass optional parameters to the module.\n[id: 'test', ...]\n" - } - }, - { - "*.fdr.tsv": { - "type": "file", - "description": "(optional) propr fdr table", - "pattern": "*.fdr.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "adj": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information.\nThis can be used at the workflow level to pass optional parameters to the module.\n[id: 'test', ...]\n" - } - }, - { - "*.adj.csv": { - "type": "file", - "description": "(optional) propr adjacency table", - "pattern": "*.adj.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "warnings": [ - { - "*.warnings.log": { - "type": "file", - "description": "Warnings", - "pattern": "*.warnings.log", - "ontologies": [] - } - } - ], - "session_info": [ - { - "*.R_sessionInfo.log": { - "type": "file", - "description": "dump of R SessionInfo", - "pattern": "*.R_sessionInfo.log", - "ontologies": [] - } - } - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@suzannejin" - ] - } - }, - { - "name": "proseg_proseg", - "path": "modules/nf-core/proseg/proseg/meta.yml", - "type": "module", - "meta": { - "name": "proseg", - "description": "Proseg (probabilistic segmentation) is a cell segmentation method for in situ spatial transcriptomics.", - "keywords": [ - "segmentation", - "spatial", - "transcriptomics" - ], - "tools": [ - { - "proseg": { - "description": "Proseg (probabilistic segmentation) is a cell segmentation method for in situ spatial transcriptomics.", - "homepage": "https://github.com/dcjones/proseg", - "documentation": "https://github.com/dcjones/proseg", - "tool_dev_url": "https://github.com/dcjones/proseg", - "doi": "10.1038/s41592-025-02697-0", - "licence": [ - "GPLv3" - ] - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "transcripts": { - "type": "file", - "description": "Transcript ids, genes, revised positions, assignment probability, etc.", - "pattern": "*transcript-metadata.{csv.gz,csv,parquet}" - } - } - ], - { - "mode": { - "type": "string", - "description": "Proseg preset mode", - "enum": [ - "xenium", - "merfish", - "cosmx" - ] - } - }, - [ - { - "transcript_metadata_fmt": { - "type": "string", - "description": "Format of the transcript metadata file", - "enum": [ - "csv", - "csv.gz", - "parquet" - ] - } - }, - { - "cell_metadata_fmt": { - "type": "file", - "description": "Format of the cell metadata file", - "enum": [ - "csv", - "csv.gz", - "parquet" - ] - } - }, - { - "expected_counts_fmt": { - "type": "file", - "description": "Format of the expected counts file", - "enum": [ - "csv", - "csv.gz", - "parquet" - ] - } + ], + "output": { + "db": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.db": { + "type": "file", + "description": "SVDB database", + "ontologies": [] + } + } + ] + ], + "versions_svdb": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "svdb": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "svdb | sed -nE 's/.*SVDB-([0-9.]+).*/\\1/p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "svdb": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "svdb | sed -nE 's/.*SVDB-([0-9.]+).*/\\1/p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@fellen31"] } - ] - ], - "output": { - "transcript_metadata": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*transcript-metadata.{csv,csv.gz,parquet}": { - "type": "file", - "description": "Transcript ids, genes, revised positions, assignment probability, etc.", - "pattern": "*transcript-metadata.{csv.gz,csv,parquet}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - }, - { - "edam": "http://edamontology.org/format_3989" + }, + { + "name": "svdb_merge", + "path": "modules/nf-core/svdb/merge/meta.yml", + "type": "module", + "meta": { + "name": "svdb_merge", + "description": "The merge module merges structural variants within one or more vcf files.", + "keywords": ["structural variants", "vcf", "merge"], + "tools": [ + { + "svdb": { + "description": "structural variant database software", + "homepage": "https://github.com/J35P312/SVDB", + "documentation": "https://github.com/J35P312/SVDB/blob/master/README.md", + "licence": ["MIT"], + "identifier": "" + } } - ] - } - } - ] - ], - "union_cell_polygons": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*cell-polygons-union.geojson.gz": { - "type": "file", - "description": "Union cell polygons", - "pattern": "*cell-polygons-union.geojson.gz" - } - } - ] - ], - "cell_polygons": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*cell-polygons.geojson.gz": { - "type": "file", - "description": "Cell polygons file", - "pattern": "*cell-polygons.geojson.gz" - } - } - ] - ], - "cell_metadata": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*cell-metadata.{csv,csv.gz,parquet}": { - "type": "file", - "description": "Cell metadata file", - "pattern": "*cell-metadata.{csv.gz,csv,parquet}", - "ontologies": [ + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "vcfs": { + "type": "list", + "description": "One or more VCF files. The order and number of files should correspond to\nthe order and number of tags in the `priority` input channel.\n", + "pattern": "*.{vcf,vcf.gz}" + } + } + ], { - "edam": "http://edamontology.org/format_3752" + "input_priority": { + "type": "list", + "description": "Prioritize the input VCF files according to this list,\ne.g ['tiddit','cnvnator']. The order and number of tags should correspond to\nthe order and number of VCFs in the `vcfs` input channel.\n" + } }, { - "edam": "http://edamontology.org/format_3989" + "sort_inputs": { + "type": "boolean", + "description": "Should the input files be sorted by name. The priority tag will be sorted\ntogether with it's corresponding VCF file.\n" + } } - ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{vcf,vcf.gz,bcf,bcf.gz}": { + "type": "file", + "description": "VCF output file", + "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}", + "ontologies": [] + } + } + ] + ], + "tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tbi": { + "type": "file", + "description": "Alternative VCF file index", + "pattern": "*.tbi", + "ontologies": [] + } + } + ] + ], + "csi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.csi": { + "type": "file", + "description": "Default VCF file index", + "pattern": "*.csi", + "ontologies": [] + } + } + ] + ], + "versions_svdb": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "svdb": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "svdb | sed -nE 's/.*SVDB-([0-9.]+).*/\\1/p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_bcftools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bcftools": { + "type": "string", + "description": "The tool name" + } + }, + { + "bcftools --version | sed '1!d; s/^.*bcftools //'": { + "type": "eval", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "svdb": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "svdb | sed -nE 's/.*SVDB-([0-9.]+).*/\\1/p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "bcftools": { + "type": "string", + "description": "The tool name" + } + }, + { + "bcftools --version | sed '1!d; s/^.*bcftools //'": { + "type": "eval", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@ramprasadn"], + "maintainers": ["@ramprasadn", "@fellen31"] + }, + "pipelines": [ + { + "name": "raredisease", + "version": "3.0.0" + }, + { + "name": "sarek", + "version": "3.8.1" } - } - ] - ], - "cell_polygons_layers": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*cell-polygons-layers.geojson.gz": { - "type": "file", - "description": "Cell polygon layers file", - "pattern": "*cell-polygons-layers.geojson.gz" - } - } ] - ], - "expected_counts": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*expected-counts.{csv,csv.gz,parquet}": { - "type": "file", - "description": "Expected transcript counts file", - "pattern": "*expected-counts.{csv.gz,csv,parquet}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - }, - { - "edam": "http://edamontology.org/format_3989" + }, + { + "name": "svdb_query", + "path": "modules/nf-core/svdb/query/meta.yml", + "type": "module", + "meta": { + "name": "svdb_query", + "description": "Query a structural variant database, using a vcf file as query", + "keywords": ["structural variants", "query", "svdb"], + "tools": [ + { + "svdb": { + "description": "structural variant database software", + "homepage": "https://github.com/J35P312/SVDB", + "documentation": "https://github.com/J35P312/SVDB/blob/master/README.md", + "licence": ["MIT"], + "identifier": "" + } } - ] - } - } - ] - ], - "maxpost_counts": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*maxpost-counts.{csv,csv.gz,parquet}": { - "type": "file", - "description": "point estimate of counts per cell", - "pattern": "*maxpost-counts.{csv.gz,csv,parquet}", - "optional": true, - "ontologies": [ + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "query vcf file", + "pattern": "*.{vcf,vcf.gz}", + "ontologies": [] + } + } + ], { - "edam": "http://edamontology.org/format_3752" + "in_occs": { + "type": "list", + "description": "A list of allele count tags" + } }, { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "output_rates": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*output-rates.{csv,csv.gz,parquet}": { - "type": "file", - "description": "Estimated poisson expression rates for each cell", - "pattern": "*output-rates.{csv.gz,csv,parquet}", - "optional": true, - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" + "in_frqs": { + "type": "list", + "description": "A list of allele frequency tags" + } }, { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "cell_hulls": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*cell-hulls.{csv,csv.gz,parquet}": { - "type": "file", - "description": "Cell convex hulls", - "pattern": "*cell-hulls.{csv.gz,csv,parquet}", - "optional": true, - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" + "out_occs": { + "type": "list", + "description": "A list of allele count tags" + } }, { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "gene_metadata": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*gene-metadata.{csv,csv.gz,parquet}": { - "type": "file", - "description": "gene metadata", - "pattern": "*gene-metadata.{csv.gz,csv,parquet}", - "optional": true, - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" + "out_frqs": { + "type": "list", + "description": "A list of allele frequency tags" + } }, { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "metagene_rates": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*metagene-rates.{csv,csv.gz,parquet}": { - "type": "file", - "description": "metagene rates", - "pattern": "*metagene-rates.{csv.gz,csv,parquet}", - "optional": true, - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" + "vcf_dbs": { + "type": "file", + "description": "path to a database vcf, or a comma separated list of vcfs", + "pattern": "*.{vcf,vcf.gz}", + "ontologies": [] + } }, { - "edam": "http://edamontology.org/format_3989" + "bedpe_dbs": { + "type": "file", + "description": "path to a SV database of the following format chrA-posA-chrB-posB-type-count-frequency, or a comma separated list of files", + "pattern": "*.{bedpe}", + "ontologies": [] + } } - ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*_query.vcf": { + "type": "file", + "description": "Annotated output VCF file", + "pattern": "*_query.vcf", + "ontologies": [] + } + } + ] + ], + "versions_svdb": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "svdb": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "svdb | sed -nE 's/.*SVDB-([0-9.]+).*/\\1/p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "svdb": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "svdb | sed -nE 's/.*SVDB-([0-9.]+).*/\\1/p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@ramprasadn"] + }, + "pipelines": [ + { + "name": "raredisease", + "version": "3.0.0" } - } ] - ], - "metagene_loadings": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*metagene-loadings.{csv,csv.gz,parquet}": { - "type": "file", - "description": "metagene loadings", - "pattern": "*metagene-loadings.{csv.gz,csv,parquet}", - "optional": true, - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - }, - { - "edam": "http://edamontology.org/format_3989" + }, + { + "name": "svdss_index", + "path": "modules/nf-core/svdss/index/meta.yml", + "type": "module", + "meta": { + "name": "svdss_index", + "description": "Index a reference genome FASTA file using SVDSS (via ropebwt3), producing either an FMD or FMR index for use with SVDSS smooth and search subcommands", + "keywords": ["structural variants", "sv calling", "indexing", "reference genome", "fm-index"], + "tools": [ + { + "svdss": { + "description": "SVDSS is a tool for structural variant discovery from short-read sequencing data.\nIt implements an FM-index-based approach to efficiently detect SVs against a reference genome.\n", + "homepage": "https://github.com/Parsoa/SVDSS", + "documentation": "https://github.com/Parsoa/SVDSS", + "tool_dev_url": "https://github.com/Parsoa/SVDSS", + "doi": "10.1038/s41592-022-01674-1", + "licence": ["MIT"], + "identifier": "" + } } - ] - } - } - ] - ], - "cell_voxels": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*cell-voxels.{csv,csv.gz,parquet}": { - "type": "file", - "description": "table of each voxel in each cell", - "pattern": "*cell-voxels.{csv.gz,csv,parquet}", - "optional": true, - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - }, + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference genome in FASTA format", + "pattern": "*.{fasta,fa,fna}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], { - "edam": "http://edamontology.org/format_3989" + "output_format": { + "type": "string", + "description": "Output index format. Use 'fmd' for the fermi-delta format (adds -d flag)\nor 'fmr' for the ropebwt format (adds -b flag).\n", + "pattern": "fmd|fmr" + } } - ] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@derrik-gratz" - ], - "maintainers": [ - "@derrik-gratz" - ] - } - }, - { - "name": "proseg_proseg_to_baysor", - "path": "modules/nf-core/proseg/proseg_to_baysor/meta.yml", - "type": "module", - "meta": { - "name": "proseg_to_baysor", - "description": "Convert proseg outputs to baysor format for import to Xenium explorer", - "keywords": [ - "segmentation", - "spatial", - "transcriptomics" - ], - "tools": [ - { - "proseg": { - "description": "Proseg (probabilistic segmentation) is a cell segmentation method for in situ spatial transcriptomics.", - "homepage": "https://github.com/dcjones/proseg", - "documentation": "https://github.com/dcjones/proseg", - "tool_dev_url": "https://github.com/dcjones/proseg", - "doi": "10.1038/s41592-025-02697-0", - "licence": [ - "GPLv3" - ] + ], + "output": { + "index": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}.${output_format}": { + "type": "file", + "description": "FM-index file produced by SVDSS index, used as input for SVDSS smooth and search", + "pattern": "*.{fmd,fmr}", + "ontologies": [] + } + } + ] + ], + "versions_svdss": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "svdss": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "SVDSS --version 2>&1 | sed 's/SVDSS, v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "svdss": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "SVDSS --version 2>&1 | sed 's/SVDSS, v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@vagkaratzas"], + "maintainers": ["@vagkaratzas"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "transcript_metadata": { - "type": "file", - "description": "Transcript ids, genes, revised positions, assignment probability, etc.", - "pattern": "*transcript-metadata.csv.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - }, - { - "edam": "http://edamontology.org/format_3989" - } - ] - } + }, + { + "name": "svim_alignment", + "path": "modules/nf-core/svim/alignment/meta.yml", + "type": "module", + "meta": { + "name": "svim_alignment", + "description": "Structural variant detection from long-read sequencing alignments using SVIM.", + "keywords": ["structural variants", "long reads", "nanopore", "pacbio", "genomics", "variant calling"], + "tools": [ + { + "svim": { + "description": "SVIM is a structural variant caller for long-read sequencing data that detects deletions, insertions, duplications, inversions and translocations from read alignments.", + "homepage": "https://github.com/eldariont/svim", + "documentation": "https://github.com/eldariont/svim/wiki", + "tool_dev_url": "https://github.com/eldariont/svim", + "doi": "10.1093/bioinformatics/btz041", + "licence": ["GPL-3.0"], + "identifier": "biotools:svim" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "Coordinate-sorted BAM/CRAM/SAM alignment file generated from long-read mapping", + "pattern": "*.{bam,cram,sam}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + }, + { + "edam": "http://edamontology.org/format_2573" + }, + { + "edam": "http://edamontology.org/format_3462" + } + ] + } + }, + { + "bai": { + "type": "file", + "description": "BAM index file", + "pattern": "*.bai", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3327" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference genome in FASTA format", + "pattern": "*.{fa,fasta,fna}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.vcf": { + "type": "file", + "description": "Structural variant calls in VCF format generated by SVIM", + "pattern": "*.vcf", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + } + ] + } + } + ] + ], + "versions_svim": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "svim": { + "type": "string", + "description": "The tool name" + } + }, + { + "svim --version | sed \"s/^.*svim //; s/ .*//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "svim": { + "type": "string", + "description": "The tool name" + } + }, + { + "svim --version | sed \"s/^.*svim //; s/ .*//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@nourmahfel"], + "maintainers": ["@nourmahfel"] } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "cell_polygons": { - "type": "file", - "description": "Path to the cell polygons file.", - "pattern": "*cell-polygons.geojson.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - }, - { - "edam": "http://edamontology.org/format_3989" - } - ] - } + }, + { + "name": "svtk_baftest", + "path": "modules/nf-core/svtk/baftest/meta.yml", + "type": "module", + "meta": { + "name": "svtk_baftest", + "description": "Performs tests on BAF files", + "keywords": ["svtk", "svtk/baftest", "baftest", "baf", "bed", "structural variants"], + "tools": [ + { + "svtk": { + "description": "Utilities for consolidating, filtering, resolving, and annotating structural variants.", + "homepage": "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk", + "documentation": "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk", + "tool_dev_url": "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bed": { + "type": "file", + "description": "A BED file created with `svtk vcf2bed`", + "pattern": "*.bed", + "ontologies": [] + } + }, + { + "baf": { + "type": "file", + "description": "A BAF file created with `gatk PrintSVEvidence`", + "pattern": "*.baf.txt.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + }, + { + "baf_index": { + "type": "file", + "description": "The index of the BAF file", + "pattern": "*.baf.txt.gz.tbi", + "ontologies": [] + } + }, + { + "batch": { + "type": "file", + "description": "A text file containing information about the sample(s)", + "pattern": "*.txt", + "ontologies": [] + } + } + ] + ], + "output": { + "metrics": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.metrics": { + "type": "file", + "description": "The results file from the BAF test", + "pattern": "*.metrics", + "ontologies": [] + } + } + ] + ], + "versions_svtk": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "svtk": { + "type": "string", + "description": "The tool name" + } + }, + { + "0.0.20190615": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "svtk": { + "type": "string", + "description": "The tool name" + } + }, + { + "0.0.20190615": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@nvnieuwk"], + "maintainers": ["@nvnieuwk"] } - ] - ], - "output": { - "baysor_cell_polygons": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*baysor-cell-polygons.geojson": { - "type": "file", - "description": "Path to the cell polygons file.", - "pattern": "*baysor-cell-polygons.geojson", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "baysor_transcript_metadata": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*baysor-transcript-metadata.csv": { - "type": "file", - "description": "Transcript ids, genes, revised positions, assignment probability, etc.", - "pattern": "*baysor-transcript-metadata.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } + }, + { + "name": "svtk_countsvtypes", + "path": "modules/nf-core/svtk/countsvtypes/meta.yml", + "type": "module", + "meta": { + "name": "svtk_countsvtypes", + "description": "Count the instances of each SVTYPE observed in each sample in a VCF.", + "keywords": ["svtk", "countsvtypes", "vcf", "structural variants"], + "tools": [ + { + "svtk": { + "description": "Utilities for consolidating, filtering, resolving, and annotating structural variants.", + "homepage": "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk", + "documentation": "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk", + "tool_dev_url": "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk", + "doi": "10.1038/s41586-020-2287-8", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "The VCF file containing structural variants", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "output": { + "counts": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "A tab-delimited file containing the counts of the SV types", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_svtk": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "svtk": { + "type": "string", + "description": "The tool name" + } + }, + { + "0.0.20190615": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "svtk": { + "type": "string", + "description": "The tool name" + } + }, + { + "0.0.20190615": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@nvnieuwk"], + "maintainers": ["@nvnieuwk"] } - 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} - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } + }, + { + "name": "svtk_standardize", + "path": "modules/nf-core/svtk/standardize/meta.yml", + "type": "module", + "meta": { + "name": "svtk_standardize", + "description": "Convert SV calls to a standardized format.", + "keywords": ["svtk", "structural variants", "SV", "vcf", "standardization"], + "tools": [ + { + "svtk": { + "description": "Utilities for consolidating, filtering, resolving, and annotating structural variants.", + "homepage": "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk", + "documentation": "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk", + "tool_dev_url": "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information. Caller can be one of the tools: delly, manta, melt, wham\ne.g. [ id:'test', caller:\"delly\" ]\n" + } + }, + { + "input": { + "type": "file", + "description": "A gzipped VCF file to be standardized", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test2' ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Optional fasta index file that specifies the contigs to be used in the VCF header (defaults to all contigs of GRCh37)", + "pattern": "*.fai", + "ontologies": [] + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', caller:\"delly\" ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "A gzipped version of the standardized VCF file", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "versions_svtk": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "svtk": { + "type": "string", + "description": "The tool name" + } + }, + { + "0.0.20190615": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "svtk": { + "type": "string", + "description": "The tool name" + } + }, + { + "0.0.20190615": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@nvnieuwk"], + "maintainers": ["@nvnieuwk"] }, - { - "fasta_files": { - "type": "file", - "description": "Input fasta files (proteomes or transcriptomes), at least 2 are needed", - "pattern": "*.{fa,fasta,faa,fna,fn}", - "ontologies": [] - } - } - ] - ], - "output": { - "orthologgroups": [ - [ - { - "meta": { - "type": "file", - "description": "Orthology table", - "pattern": "*.proteinortho.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - }, - { - "${prefix}.proteinortho.tsv": { - "type": "file", - "description": "Orthology table", - "pattern": "*.proteinortho.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "orthologgraph": [ - [ - { - "meta": { - "type": "file", - "description": "Orthology table", - "pattern": "*.proteinortho.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - }, - { - "${prefix}.proteinortho-graph": { - "type": "file", - "description": "Orthology graph", - "pattern": "*.proteinortho-graph", - "ontologies": [] - } - } - ] - ], - "blastgraph": [ - [ - { - "meta": { - "type": "file", - "description": "Orthology table", - "pattern": "*.proteinortho.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - }, - { - "${prefix}.blast-graph": { - "type": "file", - "description": "BLAST graph", - "pattern": "*.blast-graph", - "ontologies": [] - } - } + "pipelines": [ + { + "name": "variantbenchmarking", + "version": "1.5.0" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@pmjklemm" - ], - "maintainers": [ - "@pmjklemm" - ] - } - }, - { - "name": "proteus_readproteingroups", - "path": "modules/nf-core/proteus/readproteingroups/meta.yml", - "type": "module", - "meta": { - "name": "proteus_readproteingroups", - "description": "reads a maxQuant proteinGroups file with Proteus", - "keywords": [ - "proteomics", - "proteus", - "readproteingroups" - ], - "tools": [ - { - "proteus": { - "description": "R package for analysing proteomics data", - "homepage": "https://github.com/bartongroup/Proteus", - "documentation": "https://rdrr.io/github/bartongroup/Proteus/", - "tool_dev_url": "https://github.com/bartongroup/Proteus", - "doi": "10.1101/416511", - "licence": [ - "GPL v2" - ], - "identifier": "biotools:proteus-engineering" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ]\n" - } - }, - { - "samplesheet": { - "type": "file", - "description": "CSV or TSV format sample sheet with sample metadata; 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dendrogram of the normalized samples hierarchically clustered by their intensities\n", - "ontologies": [] - } - }, - { - "*raw_proteingroups.rds": { - "type": "file", - "description": "RDS file of a proteinGroups object from Proteus, contains raw protein intensities and additional info\n", - "ontologies": [] - } - } - ] - ], - "norm_rdata": [ - [ - { - "meta": { - "type": "file", - "description": "PNG file; dendrogram of the normalized samples hierarchically clustered by their intensities\n", - "ontologies": [] - } - }, - { - "*normalized_proteingroups.rds": { - "type": "file", - "description": "RDS file of a proteinGroups object from Proteus, contains normalized protein intensities and additional info\n", - "ontologies": [] - } - } - ] - ], - "raw_tab": [ - [ - { - "meta": { - "type": "file", - "description": "PNG file; dendrogram of the normalized samples hierarchically clustered by their intensities\n", - "ontologies": [] - } - }, - { - "*raw_proteingroups_tab.tsv": { - "type": "file", - "description": "TSV-format intensities table from Proteus, contains raw protein intensities\n", - "ontologies": [] - } - } - ] - ], - "norm_tab": [ - [ - { - "meta": { - "type": "file", - "description": "PNG file; dendrogram of the normalized samples hierarchically clustered by their intensities\n", - "ontologies": [] - } - }, - { - "*normalized_proteingroups_tab.tsv": { - "type": "file", - "description": "TSV-format intensities table from Proteus, contains normalized protein intensities\n", - "ontologies": [] - } - } - ] - ], - "session_info": [ - [ - { - "meta": { - "type": "file", - "description": "PNG file; dendrogram of the normalized samples hierarchically clustered by their intensities\n", - "ontologies": [] - } - }, - { - "*R_sessionInfo.log": { - "type": "file", - "description": "LOG file of the R sessionInfo from the module run\n", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "topics": { - "versions": [ - { - "versions.yml": { - "type": "string", - "description": "The name of the process" - } - } - ] - }, - "authors": [ - "@WackerO" - ], - "maintainers": [ - "@WackerO" - ] - }, - "pipelines": [ - { - "name": "differentialabundance", - "version": "1.5.0" - } - ] - }, - { - "name": "pureclip", - "path": "modules/nf-core/pureclip/meta.yml", - "type": "module", - "meta": { - "name": "pureclip", - "description": "PureCLIP is a tool to detect protein-RNA interaction footprints from single-nucleotide CLIP-seq data, such as iCLIP and eCLIP.", - "keywords": [ - "iCLIP", - "eCLIP", - "CLIP" - ], - "tools": [ - { - "pureclip": { - "description": "PureCLIP is a tool to detect protein-RNA interaction footprints from single-nucleotide CLIP-seq data, such as iCLIP and eCLIP.", - "homepage": "https://github.com/skrakau/PureCLIP", - "documentation": "https://pureclip.readthedocs.io/en/latest/GettingStarted/index.html", - "tool_dev_url": "https://github.com/skrakau/PureCLIP", - "doi": "10.1186/s13059-017-1364-2", - "licence": [ - "GPL v3" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "ipbam": { - "type": "file", - "description": "Sorted BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } - }, - { - "controlbam": { - "type": "file", - "description": "Sorted BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "ipbai": { - "type": "file", - "description": "BAM index", - "pattern": "*.{bai}", - "ontologies": [] - } - }, - { - "controlbai": { - "type": "file", - "description": "BAM index", - "pattern": "*.{bai}", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "genome_fasta": { - "type": "file", - "description": "FASTA file of reference genome", - "pattern": "*.{fa,fasta,fa.gz,fasta.gz}", - "ontologies": [] - } - } - ], - { - "input_control": { - "type": "boolean", - "description": "Whether to run PureCLIP with an input control" - } - } - ], - "output": { - "crosslinks": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "${crosslinks_output_name}": { - "type": "file", - "description": "Bed file of crosslinks", - "pattern": "*.{bed}", - "ontologies": [] - } - } - ] - ], - "peaks": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "${peaks_output_name}": { - "type": "file", - "description": "Bed file of peaks", - "pattern": "*.{bed}", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@charlotteanne", - "@marcjones" - ], - "maintainers": [ - "@charlotteanne", - "@marcjones" - ] - } - }, - { - "name": "purecn_coverage", - "path": "modules/nf-core/purecn/coverage/meta.yml", - "type": "module", - "meta": { - "name": "purecn_coverage", - "description": "Calculate intervals coverage for each sample. N.B. the tool can not handle staging files with symlinks, stageInMode should be set to 'link'.", - "keywords": [ - "copy number alteration calling", - "intervals coverage", - "hybrid capture sequencing", - "targeted sequencing", - "DNA sequencing" - ], - "tools": [ - { - "purecn": { - "description": "Copy number calling and SNV classification using targeted short read sequencing", - "homepage": "https://bioconductor.org/packages/release/bioc/html/PureCN.html", - "documentation": "https://bioconductor.org/packages/release/bioc/html/PureCN.html", - "tool_dev_url": "https://github.com/lima1/PureCN", - "doi": "10.1186/s13029-016-0060-z", - "license": [ - "Artistic-2.0" - ], - "args_id": "$args", - "identifier": "biotools:purecn" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } - }, - { - "bai": { - "type": "file", - "description": "BAM index file", - "pattern": "*.{bai}", - "ontologies": [] - } - } - ], - { - "intervals": { - "type": "file", - "description": "Annotated targets optimized for copy number calling", - "pattern": "*.txt", - "ontologies": [] - } - } - ], - "output": { - "txt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.txt.gz": { - "type": "file", - "description": "Intervals coverage file", - "pattern": "*.txt.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "png": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.png": { - "type": "file", - "description": "GC-normalized intervals coverage plot.\nGenerated only when GC-normalization is enabled.\n", - "pattern": "*.png", - "ontologies": [] - } - } - ] - ], - "loess_qc_txt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_loess_qc.txt": { - "type": "file", - "description": "GC-normalized intervals coverage metrics.\nGenerated only when GC-normalization is enabled.\n", - "pattern": "*_loess_qc.txt", - "ontologies": [] - } - } - ] - ], - "loess_txt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_loess.txt.gz": { - "type": "file", - "description": "GC-normalized intervals coverage file.\nGenerated only when GC-normalization is enabled.\n", - "pattern": "*_loess.txt.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@aldosr", - "@lbeltrame" - ], - "maintainers": [ - "@aldosr", - "@lbeltrame" - ] - } - }, - { - "name": "purecn_intervalfile", - "path": "modules/nf-core/purecn/intervalfile/meta.yml", - "type": "module", - "meta": { - "name": "purecn_intervalfile", - "description": "Generate on and off-target intervals for PureCN from a list of targets", - "keywords": [ - "copy number alteration calling", - "genomic intervals", - "hybrid capture sequencing", - "targeted sequencing", - "DNA sequencing" - ], - "tools": [ - { - "purecn": { - "description": "Copy number calling and SNV classification using targeted short read sequencing", - "homepage": "https://bioconductor.org/packages/release/bioc/html/PureCN.html", - "documentation": "https://bioconductor.org/packages/release/bioc/html/PureCN.html", - "tool_dev_url": "https://github.com/lima1/PureCN", - "doi": "10.1186/s13029-016-0060-z.", - "licence": [ - "Artistic-2.0" - ], - "identifier": "biotools:purecn" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "target_bed": { - "type": "file", - "description": "BED file of target intervals", - "pattern": "*.bed", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'fasta' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA reference sequence of the genome being used", - "pattern": "*.fasta", - "ontologies": [] - } - } - ], - { - "genome": { - "type": "string", - "description": "Genome used for the BED file (e.g., \"hg38\", \"mm10\"...)" - } - } - ], - "output": { - "txt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.txt": { - "type": "file", - "pattern": "*.txt", - "description": "Annotated targets optimized for copy number calling\n", - "ontologies": [] - } - } - ] - ], - "bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bed": { - "type": "file", - "pattern": "*.bed", - "description": "Modified and optimized targets exported as a BED file.\nGenerate the file using the --export command-line switch\nIntervalFile.R.\n", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@aldosr", - "@lbeltrame" - ], - "maintainers": [ - "@aldosr", - "@lbeltrame" - ] - } - }, - { - "name": "purecn_normaldb", - "path": "modules/nf-core/purecn/normaldb/meta.yml", - "type": "module", - "meta": { - "name": "purecn_normaldb", - "description": "Build a normal database for coverage normalization from all the (GC-normalized) normal coverage files. N.B. as reported in https://www.bioconductor.org/packages/devel/bioc/vignettes/PureCN/inst/doc/Quick.html, it is advised to provide a normal panel (VCF format) to precompute mapping bias for faster runtimes.", - "keywords": [ - "copy number alteration calling", - "normal database", - "panel of normals", - "hybrid capture sequencing", - "targeted sequencing", - "DNA sequencing" - ], - "tools": [ - { - "purecn": { - "description": "Copy number calling and SNV classification using targeted short read sequencing", - "homepage": "https://bioconductor.org/packages/release/bioc/html/PureCN.html", - "documentation": "https://bioconductor.org/packages/release/bioc/html/PureCN.html", - "tool_dev_url": "https://github.com/lima1/PureCN", - "doi": "10.1186/s13029-016-0060-z", - "licence": [ - "Artistic-2.0" - ], - "args_id": "$args", - "identifier": "biotools:purecn" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "coverage_files": { - "type": "file", - "description": "Coverage files from normal samples", - "pattern": "*.txt.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - }, - { - "normal_vcf": { - "type": "file", - "description": "Normal panel in VCF format, used to precompute mapping bias\nfor faster runtimes. Optional.\n", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - }, - { - "normal_vcf_tbi": { - "type": "file", - "description": "Normal panel in VCF format", - "pattern": "*.vcf.gz.tbi", - "ontologies": [] - } - } - ], - { - "genome": { - "type": "string", - "description": "Genome build" - } - }, - { - "assay": { - "type": "string", - "description": "Assay name" - } - } - ], - "output": { - "rds": [ - [ - { - "meta": { - "type": "file", - "description": "File containing the generated panel of normals", - "pattern": "normalDB*.rds", - "ontologies": [] - } - }, - { - "normalDB*.rds": { - "type": "file", - "description": "File containing the generated panel of normals", - "pattern": "normalDB*.rds", - "ontologies": [] - } - } - ] - ], - "png": [ - [ - { - "meta": { - "type": "file", - "description": "File containing the generated panel of normals", - "pattern": "normalDB*.rds", - "ontologies": [] - } - }, - { - "interval_weights*.png": { - "type": "file", - "description": "Plot of interval weights calculated from the panel of normals", - "pattern": "interval_weights*.png", - "ontologies": [] - } - } - ] - ], - "bias_rds": [ - [ - { - "meta": { - "type": "file", - "description": "File containing the generated panel of normals", - "pattern": "normalDB*.rds", - "ontologies": [] - } - }, - { - "mapping_bias*.rds": { - "type": "file", - "description": "Calculated mapping bias from the normal files", - "pattern": "mapping_bias*.rds", - "ontologies": [] - } - } - ] - ], - "bias_bed": [ - [ - { - "meta": { - "type": "file", - "description": "File containing the generated panel of normals", - "pattern": "normalDB*.rds", - "ontologies": [] - } - }, - { - "mapping_bias_hq_sites*.bed": { - "type": "file", - "description": "Calculated mapping bias sites from the normal files", - "pattern": "mapping_bias_hq_sites*.bed", - "ontologies": [] - } - } - ] - ], - "low_cov_bed": [ - [ - { - "meta": { - "type": "file", - "description": "File containing the generated panel of normals", - "pattern": "normalDB*.rds", - "ontologies": [] - } - }, - { - "low_coverage_targets*.bed": { - "type": "file", - "description": "BED with possibly low coverage targets identified, only\ngenerated if there are low coverage targets\n", - "pattern": "low_coverage_targets*.bed", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@aldosr", - "@lbeltrame" - ], - "maintainers": [ - "@aldosr", - "@lbeltrame" - ] - } - }, - { - "name": "purecn_run", - "path": "modules/nf-core/purecn/run/meta.yml", - "type": "module", - "meta": { - "name": "purecn_run", - "description": "Run PureCN workflow to normalize, segment and determine purity and ploidy", - "keywords": [ - "copy number alteration calling", - "hybrid capture sequencing", - "targeted sequencing", - "DNA sequencing" - ], - "tools": [ - { - "purecn": { - "description": "Copy number calling and SNV classification using targeted short read sequencing", - "homepage": "https://bioconductor.org/packages/release/bioc/html/PureCN.html", - "documentation": "https://bioconductor.org/packages/release/bioc/html/PureCN.html", - "tool_dev_url": "https://github.com/lima1/PureCN", - "doi": "10.1186/s13029-016-0060-z", - "license": [ - "Artistic-2.0" - ], - "args_id": "$args", - "identifier": "biotools:purecn" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "intervals": { - "type": "file", - "description": "BED file of target intervals, generated from IntervalFile.R\n", - "pattern": "{*.bed,*.txt}", - "ontologies": [] - } - }, - { - "coverage": { - "type": "file", - "description": "Coverage file generated from Coverage.R", - "pattern": "*.txt", - "ontologies": [] - } - }, - { - "vcf": { - "type": "file", - "description": "VCF containing variant calls", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ], - { - "normal_db": { - "type": "file", - "description": "Normal panel database", - "ontologies": [] - } - }, - { - "mapping_bias": { - "type": "file", - "description": "Mapping bias file generated with normal panel", - "ontologies": [] - } - }, - { - "genome": { - "type": "string", - "description": "Genome build" - } - } - ], - "output": { - "pdf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.pdf": { - "type": "file", - "description": "PDF file containing copy number plots\n", - "pattern": "*.pdf", - "ontologies": [] - } - } - ] - ], - "local_optima_pdf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*_local_optima.pdf": { - "type": "file", - "description": "PDF file containing local optima plots\n", - "pattern": "*_local_optima.pdf", - "ontologies": [] - } - } - ] - ], - "seg": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*_dnacopy.seg": { - "type": "file", - "description": "Tab-delimited file containing segmentation results\n", - "pattern": "*_dnacopy.seg", - "ontologies": [] - } - } - ] - ], - "csv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "${prefix}.csv": { - "type": "file", - "description": "Tab-delimited file containing sample purity, ploidy\nand flags information\n", - "pattern": "${prefix}.csv", - "ontologies": [] - } - } - ] - ], - "genes_csv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*_genes.csv": { - "type": "file", - "description": "CSV file containing gene copy number calls. Optional\n", - "pattern": "*_genes.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "amplification_pvalues_csv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*_amplification_pvalues.csv": { - "type": "file", - "description": "CSV file containing amplification p-values. Optional\n", - "pattern": "*_amplification_pvalues.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "vcf_gz": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.vcf.gz": { - "type": "file", - "description": "GZipped VCF file containing SNV calls. Optional\n", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "variants_csv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*_variants.csv": { - "type": "file", - "description": "CSV file containing SNV calls. Optional\n", - "pattern": "*_variants.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "loh_csv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*_loh.csv": { - "type": "file", - "description": "CSV file containing LOH calls. Optional\n", - "pattern": "*_loh.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "chr_pdf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*_chromosomes.pdf": { - "type": "file", - "description": "PDF file containing chromosome plots. Optional\n", - "pattern": "*_chromosomes.pdf", - "ontologies": [] - } - } - ] - ], - "segmentation_pdf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*_segmentation.pdf": { - "type": "file", - "description": "PDF file containing segmentation plots. 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} - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "basecov": { - "type": "file", - "description": "A file containing a histogram of base coverage. Obtained from PURGEDUPS_PBCSTAT", - "pattern": "*.PB.base.cov", - "ontologies": [] - } - }, - { - "cutoff": { - "type": "file", - "description": "A file containing duplication cutoff points. Obtained from PURGEDUPS_CALCUTS", - "pattern": "*.cutoffs", - "ontologies": [] - } + }, + { + "name": "svync", + "path": "modules/nf-core/svync/meta.yml", + "type": "module", + "meta": { + "name": "svync", + "description": "A tool to standardize VCF files from structural variant callers", + "keywords": ["structural variants", "vcf", "standardization", "standardize", "sv"], + "tools": [ + { + "svync": { + "description": "A tool to standardize VCF files from structural variant callers", + "homepage": "https://github.com/nvnieuwk/svync", + "documentation": "https://github.com/nvnieuwk/svync", + "tool_dev_url": "https://github.com/nvnieuwk/svync", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "vcf": { + "type": "file", + "description": "The input VCF file containing structural variants", + "pattern": "*.{vcf,vcf.gz}", + "ontologies": [] + } + }, + { + "tbi": { + "type": "file", + "description": "The index of the input VCF file containing structural variants", + "pattern": "*.tbi", + "ontologies": [] + } + }, + { + "config": { + "type": "file", + "description": "The config stating how the standardization should happen", + "pattern": "*.{yml,yaml}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "The standardized VCF file", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.tbi": { + "type": "file", + "description": "The index of the standardized VCF file", + "pattern": "*.tbi", + "ontologies": [] + } + } + ] + ], + "versions_svync": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "svync": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "svync --version | sed 's/svync version //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "svync": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "svync --version | sed 's/svync version //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@nvnieuwk"], + "maintainers": ["@nvnieuwk"] }, - { - "paf": { - "type": "file", - "description": "A file of assembly alignments to itself", - "pattern": "*.paf(.gz)?", - "ontologies": [] - } - } - ] - ], - "output": { - "bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + "pipelines": [ + { + "name": "variantbenchmarking", + "version": "1.5.0" } - }, - { - "*.dups.bed.gz": { - "type": "file", - "description": "A bed file of sequences purged of false duplications", - "pattern": "*.bed.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3003" - }, + ] + }, + { + "name": "sylph_profile", + "path": "modules/nf-core/sylph/profile/meta.yml", + "type": "module", + "meta": { + "name": "sylph_profile", + "description": "Sylph profile command for taxonoming profiling", + "keywords": ["profile", "metagenomics", "sylph", "classification"], + "tools": [ + { + "sylph": { + "description": "Sylph quickly enables querying of genomes against even low-coverage shotgun metagenomes to find nearest neighbour ANI.", + "homepage": "https://github.com/bluenote-1577/sylph", + "documentation": "https://github.com/bluenote-1577/sylph", + "tool_dev_url": "https://github.com/bluenote-1577/sylph", + "doi": "10.1038/s41587-024-02412-y", + "licence": ["MIT"], + "identifier": "biotools:sylph" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ/FASTA files of size 1 and 2 for single-end and paired-end data,\nrespectively. They are automatically sketched to .sylsp/.syldb\n", + "pattern": "*.{fasta,fastq,fna,fa,fq,fas,fasta.gz,fastq.gz,fna,fa.gz,fq,fas.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + }, + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ], { - "edam": "http://edamontology.org/format_3989" + "database": { + "type": "file", + "description": "Pre-sketched *.syldb/*.sylsp files. Raw single-end fastq/fasta are allowed and will be automatically sketched to .sylsp/.syldb.", + "pattern": "*.{syldb,sylsp}" + } } - ] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.purge_dups.log": { - "type": "file", - "description": "A log of the tool output", - "pattern": "*.log", - "ontologies": [] - } - } - ] - ], - "versions_purgedups": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "purge_dups": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "1.2.6": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "purge_dups": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "1.2.6": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@mahesh-panchal" - ], - "maintainers": [ - "@mahesh-panchal" - ] - } - }, - { - "name": "purgedups_splitfa", - "path": "modules/nf-core/purgedups/splitfa/meta.yml", - "type": "module", - "meta": { - "name": "purgedups_splitfa", - "description": "Split fasta file by 'N's to aid in self alignment for duplicate purging", - "keywords": [ - "split", - "assembly", - "duplicate", - "purging" - ], - "tools": [ - { - "purgedups": { - "description": "Purge_dups is a package used to purge haplotigs and overlaps in an assembly based on read depth", - "homepage": "https://github.com/dfguan/purge_dups", - "documentation": "https://github.com/dfguan/purge_dups", - "tool_dev_url": "https://github.com/dfguan/purge_dups", - "doi": "10.1093/bioinformatics/btaa025", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "assembly": { - "type": "file", - "description": "Draft assembly file", - "pattern": "*.fasta", - "ontologies": [] - } - } - ] - ], - "output": { - "split_fasta": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.split.fasta.gz": { - "type": "file", - "description": "Fasta split by N's", - "pattern": "*.fasta.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "versions_purgedups": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "purge_dups": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "1.2.6": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "purge_dups": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "1.2.6": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@mahesh-panchal" - ], - "maintainers": [ - "@mahesh-panchal" - ] - } - }, - { - "name": "pychopper", - "path": "modules/nf-core/pychopper/meta.yml", - "type": "module", - "meta": { - "name": "pychopper", - "description": "Identify, orient and trim nanopore cDNA reads", - "keywords": [ - "sort", - "trimming", - "nanopore" - ], - "tools": [ - { - "pychopper": { - "description": "A tool to identify, orient and rescue full length cDNA reads from nanopore data.", - "homepage": "https://github.com/epi2me-labs/pychopper", - "documentation": "https://github.com/epi2me-labs/pychopper", - "tool_dev_url": "https://github.com/epi2me-labs/pychopper", - "licence": [ - "Oxford Nanopore Technologies PLC. Public License Version 1.0" - ], - "identifier": "" - } - }, - { - "gzip": { - "description": "Gzip reduces the size of the named files using Lempel-Ziv coding (LZ77).", - "documentation": "https://linux.die.net/man/1/gzip", - "args_id": "$args3", - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } + ], + "output": { + "profile_out": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.tsv": { + "type": "file", + "description": "Output file of species-level taxonomic profiling with abundances and ANIs.", + "pattern": "*tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_sylph": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "sylph": { + "type": "string", + "description": "The tool name" + } + }, + { + "sylph -V | sed \"s/sylph //g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "sylph": { + "type": "string", + "description": "The tool name" + } + }, + { + "sylph -V | sed \"s/sylph //g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@jiahang1234", "@sofstam"], + "maintainers": ["@sofstam"] }, - { - "fastq": { - "type": "file", - "description": "FastQ with reads from long read sequencing e.g. nanopore", - "pattern": "*.{fastq.gz}", - "ontologies": [] - } - } - ] - ], - "output": { - "fastq": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", - "pattern": "*.{fastq.gz}" - } - }, - { - "*.out.fastq.gz": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", - "pattern": "*.{fastq.gz}" - } - } + "pipelines": [ + { + "name": "rnaseq", + "version": "3.26.0" + }, + { + "name": "taxprofiler", + "version": "2.0.0" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@chriswyatt1" - ], - "maintainers": [ - "@chriswyatt1" - ] - }, - "pipelines": [ - { - "name": "evexplorer", - "version": "dev" - } - ] - }, - { - "name": "pyclonevi", - "path": "modules/nf-core/pyclonevi/meta.yml", - "type": "module", - "meta": { - "name": "pyclonevi", - "description": "PyClone-VI is a software for inferring the clonal population structure of cancers by using variant allele frequencies and copy number data of single or multiple samples.", - "keywords": [ - "clonal population", - "WGS", - "subclonal deconvolution", - "copy number alterations", - "somatic mutations" - ], - "tools": [ - { - "pyclonevi": { - "description": "PyClone-VI, a computationally efficient Bayesian statistical method for inferring the clonal population structure of cancers.", - "homepage": "https://github.com/Roth-Lab/pyclone-vi", - "documentation": "https://github.com/Roth-Lab/pyclone-vi", - "tool_dev_url": "https://github.com/Roth-Lab/pyclone-vi", - "doi": "10.1186/s12859-020-03919-2", - "licence": [ - "GPL v3-or-later" - ], - "identifier": "" + }, + { + "name": "sylph_sketch", + "path": "modules/nf-core/sylph/sketch/meta.yml", + "type": "module", + "meta": { + "name": "sylph_sketch", + "description": "Sketching/indexing sequencing reads", + "keywords": ["sketch", "metagenomics", "sylph", "indexing"], + "tools": [ + { + "sylph": { + "description": "Sylph quickly enables querying of genomes against even low-coverage shotgun metagenomes to find nearest neighbour ANI.", + "homepage": "https://github.com/bluenote-1577/sylph", + "documentation": "https://github.com/bluenote-1577/sylph", + "tool_dev_url": "https://github.com/bluenote-1577/sylph", + "doi": "10.1038/s41587-024-02412-y", + "licence": ["MIT"], + "identifier": "biotools:sylph" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "reads": { + "type": "file", + "description": "Input FASTQ files", + "pattern": "*.{fq,fastq,fq.gz,fastq.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ], + { + "reference": { + "type": "file", + "description": "Reference genome file in FASTA format", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + "output": { + "sketch_fastq_genome": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "my_sketches/*.sylsp": { + "type": "map", + "description": "Output sylph sketch files of input reads for profiling\n", + "pattern": "my_sketches/*.sylsp" + } + }, + { + "database.syldb": { + "type": "map", + "description": "Output sylph database files for profiling against database\n", + "pattern": "*.syldb" + } + } + ] + ], + "versions_sylph": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "sylph": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "sylph -V | sed \"s/sylph //g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "sylph": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "sylph -V | sed \"s/sylph //g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@jiahang1234", "@sofstam"], + "maintainers": ["@sofstam"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "rds_join": { - "type": "file", - "description": "RDS file containing the mCNAqc object with joint mutations and copy number segments", - "pattern": "*.rds", - "ontologies": [] - } + }, + { + "name": "sylph_sketchgenomes", + "path": "modules/nf-core/sylph/sketchgenomes/meta.yml", + "type": "module", + "meta": { + "name": "sylph_sketchgenomes", + "description": "Sylph profile command for taxonoming profiling of genomes", + "keywords": ["profile", "metagenomics", "sylph", "classification", "genomes", "sketch"], + "tools": [ + { + "sylph": { + "description": "Sylph quickly enables querying of genomes against even low-coverage shotgun metagenomes to find nearest neighbour ANI.", + "homepage": "https://github.com/bluenote-1577/sylph", + "documentation": "https://github.com/bluenote-1577/sylph", + "tool_dev_url": "https://github.com/bluenote-1577/sylph", + "doi": "10.1038/s41587-024-02412-y", + "licence": ["MIT"], + "identifier": "biotools:sylph" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "List of reference genome FASTA files to convert to sylph database file", + "pattern": "*.{fasta,fas,fa,fna}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ] + ], + "output": { + "syldb": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.syldb": { + "type": "file", + "description": "Sylph database sketch file for profiling", + "pattern": "*.syldb" + } + } + ] + ], + "versions_sylph": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "sylph": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "sylph -V | sed \"s/sylph //g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "sylph": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "sylph -V | sed \"s/sylph //g\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@jfy133"], + "maintainers": ["@jfy133"] }, - { - "tumour_samples": { - "type": "list", - "description": "List of tumour sample identifiers for a specific patient" - } - } - ] - ], - "output": { - "ctree_input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample inforSanRafCocoGnd-2024.5\nmation\n" - } - }, - { - "*_cluster_table.csv": { - "type": "file", - "description": "Files containing information about identified clusters", - "pattern": "*_cluster_table.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "pyclone_input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample inforSanRafCocoGnd-2024.5\nmation\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "Files containing the input table for pyclone-vi", - "pattern": "*tsv", - "ontologies": [] - } - } - ] - ], - "pyclone_all_fits": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample inforSanRafCocoGnd-2024.5\nmation\n" - 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The database file(s) used to create this file with sylph must be the same as those of the taxonomy input channel of this module.", + "pattern": "*.{tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + { + "taxonomy": { + "type": "file", + "description": "A list of sylph-tax identifiers (e.g. GTDB_r220 or IMGVR_4.1). Multiple taxonomy metadata files can be input. Custom taxonomy files are also possible.", + "ontologies": [] + } + } + ], + "output": { + "taxprof_output": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.sylphmpa": { + "type": "file", + "description": "A tab-separated file containing a metagenomic taxonomic profile generated by sylph-tax, including columns for lineage and taxid\n", + "pattern": "*{.sylphmpa}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_sylphtax": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "sylph-tax": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "sylph-tax --version 2>&1 | tail -1": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "sylph-tax": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "sylph-tax --version 2>&1 | tail -1": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@sofstam"], + "maintainers": ["@sofstam"] }, - { - "bai": { - "type": "file", - "description": "BAM/CRAM/SAM index file", - "pattern": "*.{bai,crai,sai}", - "ontologies": [] - } - } - ] - ], - "output": { - "csv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}_pydamage_results.csv": { - "type": "file", - "description": "PyDamage results as csv files", - "pattern": "*.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } + "pipelines": [ + { + "name": "rnaseq", + "version": "3.26.0" + }, + { + "name": "taxprofiler", + "version": "2.0.0" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } + }, + { + "name": "syri", + "path": "modules/nf-core/syri/meta.yml", + "type": "module", + "meta": { + "name": "syri", + "description": "Syri compares alignments between two chromosome-level assemblies and identifies synteny and structural rearrangements.", + "keywords": ["genomics", "synteny", "rearrangements", "chromosome"], + "tools": [ + { + "syri": { + "description": "Synteny and rearrangement identifier between whole-genome assemblies", + "homepage": "https://github.com/schneebergerlab/syri", + "documentation": "https://github.com/schneebergerlab/syri", + "tool_dev_url": "https://github.com/schneebergerlab/syri", + "doi": "10.1186/s13059-019-1911-0", + "licence": ["MIT License"], + "identifier": "biotools:SyRI" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "infile": { + "type": "file", + "description": "File containing alignment coordinates", + "pattern": "*.{table, sam, bam, paf}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "query_fasta": { + "type": "file", + "description": "Query genome for the alignments", + "pattern": "*.{fasta}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "reference_fasta": { + "type": "file", + "description": "Reference genome for the alignments", + "pattern": "*.{fasta}", + "ontologies": [] + } + } + ], + { + "file_type": { + "type": "string", + "description": "Input file type which is one of T: Table, S: SAM, B: BAM, P: PAF\n" + } + } + ], + "output": { + "syri": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*syri.out": { + "type": "file", + "description": "Syri output file", + "pattern": "*syri.{out}", + "ontologies": [] + } + } + ] + ], + "error": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.error.log": { + "type": "file", + "description": "Error log if syri fails. This error log enables the pipeline to detect if syri has failed due to one of its\nknown limitations and pass the information to the user in a user-friendly manner such as a HTML report\n", + "pattern": "*.error.{log}", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@GallVp"], + "maintainers": ["@GallVp"] } - ] }, - "authors": [ - "@maxibor" - ], - "maintainers": [ - "@maxibor" - ] - }, - "pipelines": [ { - "name": "coproid", - "version": "2.0.1" + "name": "t1k_build", + "path": "modules/nf-core/t1k/build/meta.yml", + "type": "module", + "meta": { + "name": "t1k_build", + "description": "A module to create a reference database and coordinate files for T1K.", + "keywords": ["polymorphic", "genes", "HLA", "Kir"], + "tools": [ + { + "t1k": { + "description": "T1K is a versatile methods to genotype highly polymorphic genes (e.g. KIR, HLA) with RNA-seq, WGS or WES data.", + "homepage": "https://github.com/mourisl/T1K/blob/v1.0.9/README.md", + "documentation": "https://github.com/mourisl/T1K/blob/v1.0.9/README.md", + "tool_dev_url": "https://github.com/mourisl/T1K", + "doi": "10.1101/gr.277585.122", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "ena": { + "type": "file", + "description": "EMBL-ENA dat file.", + "pattern": "*.dat" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA file containing gene sequences.", + "pattern": "*.fa", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + }, + { + "annotation": { + "type": "file", + "description": "Gene annotation in GTF format.", + "pattern": "*.gtf", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2532" + } + ] + } + } + ] + ], + "output": { + "rna_sequences": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_rna_seq.fa": { + "type": "file", + "description": "RNA gene sequences file output.", + "pattern": "*_rna_seq.fa", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ] + ], + "dna_sequences": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_dna_seq.fa": { + "type": "file", + "description": "DNA gene sequences file output.", + "pattern": "*_dna_seq.fa", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ] + ], + "rna_coordinates": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_rna_coord.fa": { + "type": "file", + "description": "A fasta file with the coordinates of the gene alleles in the header as created form the t1k/build", + "pattern": "*_rna_coord.fa", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ] + ], + "dna_coordinates": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_dna_coord.fa": { + "type": "file", + "description": "A fasta file with the coordinates of the gene alleles in the header as created form the t1k/build", + "pattern": "*_dna_coord.fa", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ] + ], + "database": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.dat": { + "type": "file", + "description": "EMBL-ENA dat file.", + "pattern": "*.dat" + } + } + ] + ], + "versions_t1k": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "t1k": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "run-t1k 2>&1 | head -n 1 | cut -d '-' -f 1 | cut -d v -f 2": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "t1k": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "run-t1k 2>&1 | head -n 1 | cut -d '-' -f 1 | cut -d v -f 2": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@georgiakes"], + "maintainers": ["@georgiakes"] + } }, { - "name": "mag", - "version": "5.4.2" - } - ] - }, - { - "name": "pydamage_filter", - "path": "modules/nf-core/pydamage/filter/meta.yml", - "type": "module", - "meta": { - "name": "pydamage_filter", - "description": "Damage parameter estimation for ancient DNA", - "keywords": [ - "ancient DNA", - "aDNA", - "de novo assembly", - "filtering", - "damage", - "deamination", - "miscoding lesions", - "C to T", - "palaeogenomics", - "archaeogenomics", - "palaeogenetics", - "archaeogenetics" - ], - "tools": [ - { - "pydamage": { - "description": "Damage parameter estimation for ancient DNA", - "homepage": "https://github.com/maxibor/pydamage", - "documentation": "https://pydamage.readthedocs.io/", - "tool_dev_url": "https://github.com/maxibor/pydamage", - "licence": [ - "GPL v3" - ], - "identifier": "" + "name": "t1k_run", + "path": "modules/nf-core/t1k/run/meta.yml", + "type": "module", + "meta": { + "name": "t1k_run", + "description": "write your description here", + "keywords": ["polymorphic", "genes", "HLA", "Kir"], + "tools": [ + { + "t1k": { + "description": "T1K is a versatile methods to genotype highly polymorphic genes (e.g. KIR, HLA) with RNA-seq, WGS or WES data.", + "homepage": "https://github.com/mourisl/T1K/blob/v1.0.8/README.md", + "documentation": "https://github.com/mourisl/T1K/blob/v1.0.8/README.md", + "tool_dev_url": "https://github.com/mourisl/T1K", + "doi": "10.1101/gr.277585.122", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample id and single_end label for fastq input files.\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM or FASTQ file(s).", + "pattern": "*.{bam,fastq}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + }, + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + }, + { + "fasta": { + "type": "file", + "description": "Reference fasta file.", + "pattern": "*.{fa,fasta}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + }, + { + "cordinates": { + "type": "file", + "description": "A fasta file with the coordinates of the gene alleles in the header as created form the t1k/build", + "pattern": "*.fa", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + }, + { + "barcodes": { + "type": "file", + "description": "A file with a list of barcodes.", + "pattern": "*.txt", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + }, + { + "barcodewhitelist": { + "type": "file", + "description": "A file with a whitelist of barcodes.", + "pattern": "*.txt", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + } + ] + ], + "output": { + "genotype_tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_genotype.tsv": { + "type": "file", + "description": "Genotyping file where the allele for each gene has its own line.", + "pattern": "*_genotype.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "allele_tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_allele.tsv": { + "type": "file", + "description": "File with the representative alleles and their quality scores.", + "pattern": "*_allele.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "allele_vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_allele.vcf": { + "type": "file", + "description": "A vcf file with the novel SNPs.", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + } + ] + } + } + ] + ], + "candidate_reads": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_candidate*.fq": { + "type": "file", + "description": "Fastq file containing candidate reads extracted from raw data for genotyping.", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ] + ], + "aligned_reads_single": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_aligned.fa": { + "type": "file", + "description": "Aligned reads in fasta format from single-end input.", + "pattern": "*_aligned.fa", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ] + ], + "aligned_reads_paired": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_aligned_{1,2}.fa": { + "type": "file", + "description": "Aligned reads in fasta format from paired-end input.", + "pattern": "*_aligned_{1,2}.fa", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ] + ], + "barcode_tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_barcode_expr.tsv": { + "type": "file", + "description": "Data matrix where rows are the barcodes and columns are the allele abundances.", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "barcode_candidate": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_candidate_bc.fa": { + "type": "file", + "description": "Barcodes form candidate reads.", + "pattern": "*_candidate_bc.fa", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ] + ], + "barcode_aligned": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_aligned_bc.fa": { + "type": "file", + "description": "Barcodes form aligned reads.", + "pattern": "*_aligned_bc.fa", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ] + ], + "versions_t1k": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "t1k": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "run-t1k 2>&1 | head -n 1 | cut -d '-' -f 1 | cut -d v -f 2": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "t1k": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "run-t1k 2>&1 | head -n 1 | cut -d '-' -f 1 | cut -d v -f 2": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@georgiakes"], + "maintainers": ["@georgiakes"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + }, + { + "name": "tabix_bgzip", + "path": "modules/nf-core/tabix/bgzip/meta.yml", + "type": "module", + "meta": { + "name": "tabix_bgzip", + "description": "DEPRECATED. Use HTSLIB/BGZIPTABIX instead. Compresses/decompresses files", + "keywords": ["compress", "decompress", "bgzip", "tabix"], + "tools": [ + { + "bgzip": { + "description": "Bgzip compresses or decompresses files in a similar manner to, and compatible with, gzip.\n", + "homepage": "https://www.htslib.org/doc/tabix.html", + "documentation": "http://www.htslib.org/doc/bgzip.html", + "doi": "10.1093/bioinformatics/btp352", + "licence": ["MIT"], + "identifier": "biotools:tabix" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "file to compress or to decompress", + "ontologies": [] + } + } + ] + ], + "output": { + "output": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "output.gz": { + "type": "file", + "description": "Output compressed/decompressed file", + "pattern": "*.", + "ontologies": [] + } + } + ] + ], + "gzi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.gzi": { + "type": "file", + "description": "Optional gzip index file for compressed inputs", + "pattern": "*.gzi", + "ontologies": [] + } + } + ] + ], + "versions_tabix": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "tabix": { + "type": "string", + "description": "The tool name" + } + }, + { + "tabix -h 2>&1 | grep -oP 'Version:\\s*\\K[^\\s]+'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "tabix": { + "type": "string", + "description": "The tool name" + } + }, + { + "tabix -h 2>&1 | grep -oP 'Version:\\s*\\K[^\\s]+'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@joseespinosa", "@drpatelh", "@maxulysse", "@nvnieuwk"], + "maintainers": ["@joseespinosa", "@drpatelh", "@maxulysse", "@nvnieuwk"] }, - { - "csv": { - "type": "file", - "description": "csv file from pydamage analyze", - "pattern": "*.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "output": { - "csv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}_pydamage_filtered_results.csv": { - "type": "file", - "description": "PyDamage filtered results as csv file", - "pattern": "*.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } + "pipelines": [ + { + "name": "funcscan", + "version": "3.0.0" + }, + { + "name": "nanoseq", + "version": "3.1.0" + }, + { + "name": "pacvar", + "version": "1.0.1" + }, + { + "name": "pangenome", + "version": "1.1.3" + }, + { + "name": "pathogensurveillance", + "version": "1.1.0" + }, + { + "name": "phaseimpute", + "version": "1.1.0" + }, + { + "name": "raredisease", + "version": "3.0.0" + }, + { + "name": "rnadnavar", + "version": "dev" + }, + { + "name": "tbanalyzer", + "version": "dev" + }, + { + "name": "variantbenchmarking", + "version": "1.5.0" + }, + { + "name": "viralrecon", + "version": "3.0.0" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@maxibor" - ], - "maintainers": [ - "@maxibor" - ] - }, - "pipelines": [ - { - "name": "mag", - "version": "5.4.2" - } - ] - }, - { - "name": "pygenprop_build", - "path": "modules/nf-core/pygenprop/build/meta.yml", - "type": "module", - "meta": { - "name": "pygenprop_build", - "description": "Generate a Micromeda file containing pathway annotations for one or more genomes.\nSupporting InterProScan and protein sequence information can also be optionally incorporated.\n", - "keywords": [ - "genome properties", - "functional annotation", - "interproscan", - "pathway analysis", - "micromeda" - ], - "tools": [ - { - "pygenprop": { - "description": "A python library for programmatic usage of EBI InterPro Genome Properties.", - "homepage": "https://github.com/Micromeda/pygenprop", - "documentation": "https://pygenprop.readthedocs.io/en/latest/", - "tool_dev_url": "https://github.com/Micromeda/pygenprop", - "licence": [ - "Apache-2.0" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } + }, + { + "name": "tabix_bgziptabix", + "path": "modules/nf-core/tabix/bgziptabix/meta.yml", + "type": "module", + "meta": { + "name": "tabix_bgziptabix", + "description": "DEPRECATED. Use HTSLIB/BGZIPTABIX instead. bgzip a sorted tab-delimited genome file and then create tabix index", + "keywords": ["bgzip", "compress", "index", "tabix", "vcf"], + "tools": [ + { + "tabix": { + "description": "Generic indexer for TAB-delimited genome position files.", + "homepage": "https://www.htslib.org/doc/tabix.html", + "documentation": "https://www.htslib.org/doc/tabix.1.html", + "doi": "10.1093/bioinformatics/btq671", + "licence": ["MIT"], + "identifier": "biotools:tabix" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "Sorted tab-delimited genome file", + "ontologies": [] + } + } + ] + ], + "output": { + "gz_index": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.gz": { + "type": "file", + "description": "bgzipped tab-delimited genome file", + "pattern": "*.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + }, + { + "*.{tbi,csi}": { + "type": "file", + "description": "Tabix index file (either tbi or csi)", + "pattern": "*.{tbi,csi}", + "ontologies": [] + } + } + ] + ], + "versions_tabix": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "tabix": { + "type": "string", + "description": "The tool name" + } + }, + { + "tabix -h 2>&1 | grep -oP 'Version:\\s*\\K[^\\s]+'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_bgzip": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bgzip": { + "type": "string", + "description": "The tool name" + } + }, + { + "bgzip --version | sed '1!d;s/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "tabix": { + "type": "string", + "description": "The tool name" + } + }, + { + "tabix -h 2>&1 | grep -oP 'Version:\\s*\\K[^\\s]+'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "bgzip": { + "type": "string", + "description": "The tool name" + } + }, + { + "bgzip --version | sed '1!d;s/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@maxulysse", "@DLBPointon"], + "maintainers": ["@maxulysse", "@DLBPointon"] }, - { - "ips": { - "type": "file", - "description": "InterProScan TSV output file", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - { - "gp_txt": { - "type": "file", - "description": "Genome Properties flatfile (e.g. genomeProperties.txt)\nThis file can be found on the original archived repository link below:\nhttps://raw.githubusercontent.com/ebi-pf-team/genome-properties/refs/heads/master/flatfiles/genomeProperties.txt\n", - "pattern": "*.txt", - "ontologies": [ + "pipelines": [ + { + "name": "cutandrun", + "version": "3.2.2" + }, + { + "name": "methylong", + "version": "2.0.0" + }, + { + "name": "nanoseq", + "version": "3.1.0" + }, + { + "name": "pacsomatic", + "version": "dev" + }, + { + "name": "raredisease", + "version": "3.0.0" + }, + { + "name": "rnadnavar", + "version": "dev" + }, { - "edam": "http://edamontology.org/format_2330" + "name": "rnavar", + "version": "1.2.3" + }, + { + "name": "sarek", + "version": "3.8.1" + }, + { + "name": "variantbenchmarking", + "version": "1.5.0" + }, + { + "name": "variantprioritization", + "version": "1.0.0" } - ] - } - } - ], - "output": { - "meda": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.micro": { - "type": "file", - "description": "Micromeda SQLite database containing Genome Properties assignments\n", - "pattern": "*.micro", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3621" - } - ] - } - } - ] - ], - "versions_pygenprop": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pygenprop": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "\"1.1\"": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } ] - ], - "versions_python": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "python": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python -V | sed \"s/Python //g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pygenprop": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "\"1.1\"": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "python": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python -V | sed \"s/Python //g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@vagkaratzas" - ], - "maintainers": [ - "@vagkaratzas" - ] - } - }, - { - "name": "pygenprop_info", - "path": "modules/nf-core/pygenprop/info/meta.yml", - "type": "module", - "meta": { - "name": "pygenprop_info", - "description": "Display a summary of the contents of a Micromeda file, including the number of samples,\ngenome property assignments, step assignments, InterProScan matches, and protein sequences.\n", - "keywords": [ - "genome properties", - "functional annotation", - "interproscan", - "pathway analysis", - "micromeda", - "summary" - ], - "tools": [ - { - "pygenprop": { - "description": "A python library for programmatic usage of EBI InterPro Genome Properties.", - "homepage": "https://github.com/Micromeda/pygenprop", - "documentation": "https://pygenprop.readthedocs.io/en/latest/", - "tool_dev_url": "https://github.com/Micromeda/pygenprop", - "licence": [ - "Apache-2.0" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } + }, + { + "name": "tabix_tabix", + "path": "modules/nf-core/tabix/tabix/meta.yml", + "type": "module", + "meta": { + "name": "tabix_tabix", + "description": "DEPRECATED. Use HTSLIB/BGZIPTABIX instead. Create a tabix index from a sorted\nbgzip TAB-delimited genome file, or extract regions from a bgzipped VCF file\nusing an optional regions file.\n", + "keywords": ["index", "tabix", "vcf", "extract", "regions"], + "tools": [ + { + "tabix": { + "description": "Generic indexer for TAB-delimited genome position files.", + "homepage": "https://www.htslib.org/doc/tabix.html", + "documentation": "https://www.htslib.org/doc/tabix.1.html", + "doi": "10.1093/bioinformatics/btq671", + "licence": ["MIT"], + "identifier": "biotools:tabix" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "tab": { + "type": "file", + "description": "TAB-delimited genome position file compressed with bgzip", + "pattern": "*.{bed.gz,gff.gz,sam.gz,vcf.gz}", + "ontologies": [] + } + }, + { + "tai": { + "type": "file", + "description": "Tabix index for the input file. Required when extracting regions.\nPass [] when creating an index instead.\n", + "pattern": "*.{tbi,csi}", + "ontologies": [] + } + }, + { + "regions": { + "type": "file", + "description": "Optional file of regions to extract (BED or chr:start-end format).\nPass [] to create an index instead of extracting regions.\n", + "pattern": "*.{bed,txt,tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "output": { + "index": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{tbi,csi}": { + "type": "file", + "description": "Tabix index file (tbi or csi). Emitted when no regions file is provided.", + "pattern": "*.{tbi,csi}", + "ontologies": [] + } + } + ] + ], + "extracted": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "output.*gz": { + "type": "file", + "description": "Bgzipped file of extracted regions, preserving the input file extension. Emitted when a regions file is provided.", + "pattern": "*.*gz", + "ontologies": [] + } + } + ] + ], + "versions_tabix": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "tabix": { + "type": "string", + "description": "The tool name" + } + }, + { + "tabix -h 2>&1 | grep -oP 'Version:\\s*\\K[^\\s]+'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "tabix": { + "type": "string", + "description": "The tool name" + } + }, + { + "tabix -h 2>&1 | grep -oP 'Version:\\s*\\K[^\\s]+'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@joseespinosa", "@drpatelh", "@maxulysse"], + "maintainers": ["@joseespinosa", "@drpatelh", "@maxulysse"] }, - { - "meda": { - "type": "file", - "description": "Micromeda SQLite database containing Genome Properties assignments\n(output of pygenprop build)\n", - "pattern": "*.micro", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3621" - } - ] - } - } - ] - ], - "output": { - "info": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.info": { - "type": "file", - "description": "Plain-text summary report of the Micromeda file contents, including counts of\nsamples, genome property assignments, step assignments, InterProScan matches,\nand protein sequences\n", - "pattern": "*.info", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2330" - } - ] - } - } - ] - ], - "versions_pygenprop": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pygenprop": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "\"1.1\"": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_python": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "python": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python -V | sed \"s/Python //g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pygenprop": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "\"1.1\"": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "python": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python -V | sed \"s/Python //g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "drop", + "version": "1.0.0" + }, + { + "name": "nanoseq", + "version": "3.1.0" + }, + { + "name": "pathogensurveillance", + "version": "1.1.0" + }, + { + "name": "phaseimpute", + "version": "1.1.0" + }, + { + "name": "radseq", + "version": "dev" + }, + { + "name": "raredisease", + "version": "3.0.0" + }, + { + "name": "references", + "version": "0.1" + }, + { + "name": "rnadnavar", + "version": "dev" + }, + { + "name": "rnavar", + "version": "1.2.3" + }, + { + "name": "sarek", + "version": "3.8.1" + }, + { + "name": "variantbenchmarking", + "version": "1.5.0" + }, + { + "name": "variantcatalogue", + "version": "dev" + }, + { + "name": "variantprioritization", + "version": "1.0.0" + }, + { + "name": "viralmetagenome", + "version": "1.1.1" + }, + { + "name": "viralrecon", + "version": "3.0.0" + } ] - ] - }, - "authors": [ - "@vagkaratzas" - ], - "maintainers": [ - "@vagkaratzas" - ] - } - }, - { - "name": "pypgx_computecontrolstatistics", - "path": "modules/nf-core/pypgx/computecontrolstatistics/meta.yml", - "type": "module", - "meta": { - "name": "pypgx_computecontrolstatistics", - "description": "Compute summary statistics for control gene from BAM files.", - "keywords": [ - "pypgx", - "pharmacogenetics", - "controlstatistics" - ], - "tools": [ - { - "pypgx": { - "description": "A Python package for pharmacogenomics research", - "homepage": "https://pypgx.readthedocs.io/en/latest/", - "documentation": "https://pypgx.readthedocs.io/en/latest/", - "tool_dev_url": "https://github.com/sbslee/pypgx", - "doi": "10.1371/journal.pone.0272129", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM file", - "pattern": "*.{bam}", - "ontologies": [] - } - }, - { - "bai": { - "type": "file", - "description": "BAM index file", - "pattern": "*.{bai}", - "ontologies": [] - } - } - ], - { - "control_gene": { - "type": "string", - "description": "Gene to use as control gene", - "pattern": "{VDR,EGFR,RYR1}" - } - } - ], - "output": { - "control_stats": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n", - "pattern": "*.{zip}" - } - }, - { - "*.zip": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n", - "pattern": "*.{zip}" - } - } - ] - ], - "versions_pypgx": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pypgx": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pypgx -v 2>&1 | grep -oE \"[0-9]+\\.[0-9]+\\.[0-9]+\" | head -1": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pypgx": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pypgx -v 2>&1 | grep -oE \"[0-9]+\\.[0-9]+\\.[0-9]+\" | head -1": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@jorisvansteenbrugge" - ], - "maintainers": [ - "@jorisvansteenbrugge" - ] - } - }, - { - "name": "pypgx_createinputvcf", - "path": "modules/nf-core/pypgx/createinputvcf/meta.yml", - "type": "module", - "meta": { - "name": "pypgx_createinputvcf", - "description": "Call SNVs/indels from BAM files for all target genes.", - "keywords": [ - "pypgx", - "Pharmacogenetics", - "variants" - ], - "tools": [ - { - "pypgx": { - "description": "A Python package for pharmacogenomics research", - "homepage": "https://pypgx.readthedocs.io/en/latest/", - "documentation": "https://pypgx.readthedocs.io/en/latest/", - "tool_dev_url": "https://github.com/sbslee/pypgx", - "doi": "10.1371/journal.pone.0272129", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [id: 'test']\n" - } - }, - { - "bam": { - "type": "file", - "description": "Input BAM file", - "pattern": "*.{bam}", - "ontologies": [] - } - }, - { - "bai": { - "type": "file", - "description": "Input BAM index file", - "pattern": "*.{bam.bai}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [id: 'test']\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome file", - "pattern": "*.{fasta,fa,fna,fasta.gz,fa.gz,fna.gz}", - "ontologies": [] - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [id: 'test']\n" - } - }, - { - "*.vcf.gz": { - "type": "file", - "description": "VCF file containing called SNVs/indels", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [id: 'test']\n" - } - }, - { - "*.vcf.gz.tbi": { - "type": "file", - "description": "File containing the VCF tabix index", - "pattern": "*.vcf.gz.tbi", - "ontologies": [] - } - } - ] - ], - "versions_pypgx": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pypgx": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pypgx -v 2>&1 | grep -oE \"[0-9]+\\.[0-9]+\\.[0-9]+\" | head -1": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pypgx": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pypgx -v 2>&1 | grep -oE \"[0-9]+\\.[0-9]+\\.[0-9]+\" | head -1": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@jorisvansteenbrugge" - ], - "maintainers": [ - "@jorisvansteenbrugge" - ] - } - }, - { - "name": "pypgx_preparedepthofcoverage", - "path": "modules/nf-core/pypgx/preparedepthofcoverage/meta.yml", - "type": "module", - "meta": { - "name": "pypgx_preparedepthofcoverage", - "description": "Prepare a depth of coverage file for all target genes with SV from BAM files.", - "keywords": [ - "Pharmacogenetics", - "pypgx", - "SV" - ], - "tools": [ - { - "pypgx": { - "description": "A Python package for pharmacogenomics research", - "homepage": "https://pypgx.readthedocs.io/en/latest/", - "documentation": "https://pypgx.readthedocs.io/en/latest/", - "tool_dev_url": "https://github.com/sbslee/pypgx", - "doi": "10.1371/journal.pone.0272129", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "Input BAM file", - "pattern": "*.{bam}", - "ontologies": [] - } - }, - { - "bai": { - "type": "file", - "description": "Input BAM index file", - "pattern": "*.{bam.bai}", - "ontologies": [] - } - } - ] - ], - "output": { - "coverage": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n", - "pattern": "*.{zip}" - } - }, - { - "*.zip": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n", - "pattern": "*.{zip}" - } - } - ] - ], - "versions_pypgx": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pypgx": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pypgx -v 2>&1 | grep -oE \"[0-9]+\\.[0-9]+\\.[0-9]+\" | head -1": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pypgx": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pypgx -v 2>&1 | grep -oE \"[0-9]+\\.[0-9]+\\.[0-9]+\" | head -1": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@jorisvansteenbrugge" - ], - "maintainers": [ - "@jorisvansteenbrugge" - ] - } - }, - { - "name": "pypgx_runngspipeline", - "path": "modules/nf-core/pypgx/runngspipeline/meta.yml", - "type": "module", - "meta": { - "name": "pypgx_runngspipeline", - "description": "PyPGx pharmacogenomics genotyping pipeline for NGS data.", - "keywords": [ - "pypgx", - "pharmacogenetics", - "genotyping" - ], - "tools": [ - { - "pypgx": { - "description": "A Python package for pharmacogenomics research", - "homepage": "https://pypgx.readthedocs.io/en/latest/", - "documentation": "https://pypgx.readthedocs.io/en/latest/", - "tool_dev_url": "https://github.com/sbslee/pypgx", - "doi": "10.1371/journal.pone.0272129", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`.\n" - } - }, - { - "vcf": { - "type": "file", - "description": "BGZIP compressed VCF file with SNVs/indels. Output of pypgx/createinputvcf.", - "pattern": "*.{vcf.gz}", - "ontologies": [] - } - }, - { - "tbi": { - "type": "file", - "description": "VCF tabix index.", - "pattern": "*.{vcf.gz.tbi}", - "ontologies": [] - } - }, - { - "coverage": { - "type": "file", - "description": "ZIP compressed file with depth of coverage information. Output of pypgx/preparedepthofcoverage. Coverage information is only required when running the module on a pharmacogene with known structural variants.", - "pattern": "*.{zip}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3987" - } - ] - } - }, - { - "control_stats": { - "type": "file", - "description": "ZIP compressed file with control statistics. Output of pypgx/computecontrolstatistics. Control statistics are only required when running the module on a pharmacogene with known structural variants.", - "ontologies": [] - } - }, - { - "pgx_gene": { - "type": "string", - "description": "Pharmacogene to genotype/phenotype. A list of supported genes is available in the pypgx documentation \"https://pypgx.readthedocs.io/en/latest/genes.html\"" - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`.\n" - } - }, - { - "resource_bundle": { - "type": "directory", - "description": "Path to the pypgx resource bundle (https://github.com/sbslee/pypgx-bundle)." - } - } - ] - ], - "output": { - "results": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*pypgx_output/results.zip": { - "type": "file", - "description": "Main output file of the pipeline in ZIP format, containing a table with star-alleles per sample and CNV calls where applicable.", - "ontologies": [] - } - } - ] - ], - "cnv_calls": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*pypgx_output/cnv-calls.zip": { - "type": "file", - "description": "Optional output file in ZIP format, containing CNV calls per sample.", - "ontologies": [] - } - } - ] - ], - "consolidated_variants": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*pypgx_output/consolidated-variants.zip": { - "type": "file", - "description": "Output file in ZIP format, containing a consolidated (and phased) VCF file.", - "ontologies": [] - } - } - ] - ], - "versions_pypgx": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pypgx": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pypgx -v 2>&1 | grep -oE \"[0-9]+\\.[0-9]+\\.[0-9]+\" | head -1": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pypgx": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pypgx -v 2>&1 | grep -oE \"[0-9]+\\.[0-9]+\\.[0-9]+\" | head -1": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@jorisvansteenbrugge" - ], - "maintainers": [ - "@jorisvansteenbrugge" - ] - } - }, - { - "name": "pypolca_run", - "path": "modules/nf-core/pypolca/run/meta.yml", - "type": "module", - "meta": { - "name": "pypolca_run", - "description": "Short read polisher for long read assemblies", - "keywords": [ - "polish", - "python", - "genomics" - ], - "tools": [ - { - "pypolca": { - "description": "Standalone Python re-implementation of the POLCA polisher from MaSuRCA", - "homepage": "https://github.com/gbouras13/pypolca", - "documentation": "https://github.com/gbouras13/pypolca?tab=readme-ov-file#usage", - "doi": "10.1099/mgen.0.001254", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of short reads for assembly polishing. Length 1 for single-end and 2 for paired-end", - "pattern": "*.{fastq,fq}.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "contigs": { - "type": "file", - "description": "Genome assembly from long reads", - "pattern": "*.{fa,fasta,fna}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ], - "output": { - "polished": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}/*_corrected.fasta": { - "type": "file", - "description": "Polished assembly", - "pattern": "*.{fasta}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ], - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}/*.vcf": { - "type": "file", - "description": "variant calls", - "pattern": "*.vcf", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - } - ] - } - } - ] - ], - "report": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}/*.report": { - "type": "file", - "description": "Pypolca report", - "pattern": "*.report", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2330" - } - ] - } - } - ] - ], - "versions_pypolca": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pypolca": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pypolca --version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pypolca": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pypolca --version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@dwells-eit" - ], - "maintainers": [ - "@dwells-eit" - ] - } - }, - { - "name": "pyrodigal", - "path": "modules/nf-core/pyrodigal/meta.yml", - "type": "module", - "meta": { - "name": "pyrodigal", - "description": "Pyrodigal is a Python module that provides bindings to Prodigal, a fast, reliable protein-coding gene prediction for prokaryotic genomes.", - "keywords": [ - "sort", - "annotation", - "prediction", - "prokaryote" - ], - "tools": [ - { - "pyrodigal": { - "description": "Pyrodigal is a Python module that provides bindings to Prodigal (ORF finder for microbial sequences) using Cython.", - "homepage": "https://pyrodigal.readthedocs.org/", - "documentation": "https://pyrodigal.readthedocs.org/", - "tool_dev_url": "https://github.com/althonos/pyrodigal/", - "doi": "10.21105/joss.04296", - "licence": [ - "GPL v3" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA file", - "pattern": "*.{fasta.gz,fa.gz,fna.gz}", - "ontologies": [] - } - } - ], - { - "output_format": { - "type": "string", - "description": "Output format", - "pattern": "{gbk,gff}" - } - } - ], - "output": { - "annotations": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.${output_format}.gz": { - "type": "file", - "description": "Gene annotations. The file format is specified via input channel \"output_format\".", - "pattern": "*.{gbk,gff}.gz", - "ontologies": [] - } - } - ] - ], - "fna": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.fna.gz": { - "type": "file", - "description": "nucleotide sequences file", - "pattern": "*.{fna.gz}", - "ontologies": [] - } - } - ] - ], - "faa": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.faa.gz": { - "type": "file", - "description": "protein translations file", - "pattern": "*.{faa.gz}", - "ontologies": [] - } - } - ] - ], - "score": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.score.gz": { - "type": "file", - "description": "all potential genes (with scores)", - "pattern": "*.{score.gz}", - "ontologies": [] - } - } - ] - ], - "versions_pyrodigal": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pyrodigal": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pyrodigal --version |& sed 's/pyrodigal v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pyrodigal": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pyrodigal --version |& sed 's/pyrodigal v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@louperelo" - ], - "maintainers": [ - "@louperelo" - ] - }, - "pipelines": [ - { - "name": "funcscan", - "version": "3.0.0" - } - ] - }, - { - "name": "qcat", - "path": "modules/nf-core/qcat/meta.yml", - "type": "module", - "meta": { - "name": "qcat", - "description": "Demultiplexer for Nanopore samples", - "keywords": [ - "demultiplex", - "nanopore", - "sample" - ], - "tools": [ - { - "qcat": { - "description": "A demultiplexer for Nanopore samples\n", - "homepage": "https://github.com/nanoporetech/qcat", - "documentation": "https://github.com/nanoporetech/qcat#qcat", - "licence": [ - "MPL-2.0" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "Non-demultiplexed fastq files\n", - "ontologies": [] - } - } - ], - { - "barcode_kit": { - "type": "string", - "description": "Barcode kit used for demultiplexing" + }, + { + "name": "tagbam", + "path": "modules/nf-core/tagbam/meta.yml", + "type": "module", + "meta": { + "name": "tagbam", + "description": "A tool for tagging BAM files.", + "keywords": ["long-read", "bam", "genomics"], + "tools": [ + { + "tagbam": { + "description": "A tool for tagging BAM files.", + "homepage": "https://github.com/fellen31/tagbam", + "documentation": "https://github.com/fellen31/tagbam", + "tool_dev_url": "https://github.com/fellen31/tagbam", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:true ]`\n" + } + }, + { + "bam": { + "type": "file", + "description": "(u)BAM file", + "pattern": "*.{bam}", + "ontologies": [] + } + } + ] + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Tagged bam file", + "pattern": "*.{bam}", + "ontologies": [] + } + } + ] + ], + "versions_tagbam": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "tagbam": { + "type": "string", + "description": "The tool name" + } + }, + { + "tagbam --version | sed 's/tagbam //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "tagbam": { + "type": "string", + "description": "The tool name" + } + }, + { + "tagbam --version | sed 's/tagbam //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@fellen31"], + "maintainers": ["@fellen31"] } - } - ], - "output": { - "reads": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fastq/*.fastq.gz": { - "type": "file", - "description": "Demultiplexed fastq samples", - "pattern": "*.fastq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } + }, + { + "name": "tailfindr", + "path": "modules/nf-core/tailfindr/meta.yml", + "type": "module", + "meta": { + "name": "tailfindr", + "description": "Estimating poly(A)-tail lengths from basecalled fast5 files produced by Nanopore sequencing of RNA and DNA", + "keywords": ["polya tail", "fast5", "nanopore"], + "tools": [ + { + "tailfindr": { + "description": "An R package for estimating poly(A)-tail lengths in Oxford Nanopore RNA and DNA reads.", + "homepage": "https://github.com/adnaniazi/tailfindr", + "documentation": "https://github.com/adnaniazi/tailfindr/blob/master/README.md", + "tool_dev_url": "https://github.com/adnaniazi/tailfindr", + "doi": "10.1261/rna.071332.119", + "licence": ["AGPL v3"], + "identifier": "biotools:tailfindr" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "fast5": { + "type": "file", + "description": "fast5 file", + "pattern": "*.fast5", + "ontologies": [] + } + } + ] + ], + "output": { + "csv_gz": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.csv.gz": { + "type": "file", + "description": "Compressed csv file", + "pattern": "*.csv.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "versions_tailfindr": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "tailfindr": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "Rscript -e \"cat(paste(packageVersion('tailfindr'), collapse='.'))\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_ont_fast5_api": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "ont-fast5-api": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python -c \"import ont_fast5_api; print(ont_fast5_api.__version__)\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "tailfindr": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "Rscript -e \"cat(paste(packageVersion('tailfindr'), collapse='.'))\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "ont-fast5-api": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python -c \"import ont_fast5_api; print(ont_fast5_api.__version__)\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@lucacozzuto"], + "maintainers": ["@lucacozzuto"] } - ] - }, - "authors": [ - "@yuukiiwa", - "@drpatelh" - ], - "maintainers": [ - "@yuukiiwa", - "@drpatelh" - ] - } - }, - { - "name": "qcatch", - "path": "modules/nf-core/qcatch/meta.yml", - "type": "module", - "meta": { - "name": "qcatch", - "description": "Cell-filtering and QC reporting tool for alevin-fry quantification results", - "keywords": [ - "single-cell", - "quality control", - "alevin-fry", - "cell filtering", - "QC report" - ], - "tools": [ - { - "qcatch": { - "description": "QCatch is a quality control and cell filtering tool designed for single-cell RNA-seq data processed by alevin-fry.\nIt generates comprehensive QC reports and filtered count matrices.\n", - "homepage": "https://github.com/COMBINE-lab/QCatch", - "licence": [ - "BSD-3-Clause" - ], - "identifier": "" + }, + { + "name": "tar", + "path": "modules/nf-core/tar/meta.yml", + "type": "module", + "meta": { + "name": "tar", + "description": "Compress directories into tarballs with various compression options", + "keywords": ["untar", "tar", "tarball", "compression", "archive", "gzip", "targz"], + "tools": [ + { + "tar": { + "description": "GNU Tar provides the ability to create tar archives, as well as various other kinds of manipulation.", + "homepage": "https://www.gnu.org/software/tar/", + "documentation": "https://www.gnu.org/software/tar/manual/", + "licence": ["GPLv3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "input": { + "type": "directory", + "description": "A file or directory to be archived", + "pattern": "*/", + "ontologies": [ + { + "edam": "http://edamontology.org/data_1049" + } + ] + } + } + ], + { + "compress_type": { + "type": "string", + "description": "A string defining which type of (optional) compression to apply to the archive.\nProvide an empty string in quotes for no compression\n", + "pattern": ".bz2|.xz|.lz|.lzma|.lzo|.zst|.gz" + } + } + ], + "output": { + "archive": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n", + "pattern": "*.tar{.bz2,.xz,.lz,.lzma,.lzo,.zst,.gz,}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_25722" + }, + { + "edam": "http://edamontology.org/format_2573" + }, + { + "edam": "http://edamontology.org/format_3462" + } + ] + } + }, + { + "*.tar${compress_type}": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n", + "pattern": "*.tar{.bz2,.xz,.lz,.lzma,.lzo,.zst,.gz,}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_25722" + }, + { + "edam": "http://edamontology.org/format_2573" + }, + { + "edam": "http://edamontology.org/format_3462" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@jfy133"], + "maintainers": ["@jfy133"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "chemistry": { - "type": "string", - "description": "Chemistry type for the single-cell experiment, which determines the partition range for the empty_drops step.\nSupported values: '10X_3p_v2', '10X_3p_v3', '10X_3p_v4', '10X_5p_v3', '10X_3p_LT', '10X_HT'.\nIf using a standard 10X chemistry and quantification was performed with simpleaf (v0.19.5 or later),\nQCatch will try to infer the correct chemistry from the metadata.\n" - } + }, + { + "name": "taxonkit_lineage", + "path": "modules/nf-core/taxonkit/lineage/meta.yml", + "type": "module", + "meta": { + "name": "taxonkit_lineage", + "description": "Convert taxonids to taxon lineages", + "keywords": ["taxonomy", "taxids", "taxon name", "conversion"], + "tools": [ + { + "taxonkit": { + "description": "A Cross-platform and Efficient NCBI Taxonomy Toolkit", + "homepage": "https://bioinf.shenwei.me/taxonkit/", + "documentation": "https://bioinf.shenwei.me/taxonkit/usage/#name2taxid", + "tool_dev_url": "https://github.com/shenwei356/taxonkit", + "doi": "10.1016/j.jgg.2021.03.006", + "licence": ["MIT"], + "identifier": "biotools:taxonkit" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "taxid": { + "type": "string", + "description": "Taxon id to look up (provide either this or taxidfile, not both)" + } + }, + { + "taxidfile": { + "type": "file", + "description": "File with taxon ids to look up, each on their own line (provide either this or name, not both; the file can contain other information, see the tool's docs)", + "ontologies": [] + } + } + ], + { + "taxdb": { + "type": "file", + "description": "Taxonomy database unpacked from ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz", + "ontologies": [] + } + } + ], + "output": { + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "TSV file with added taxon lineages", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@erikrikarddaniel"], + "maintainers": ["@erikrikarddaniel"] }, - { - "quant_dir": { - "type": "directory", - "description": "Directory containing alevin-fry quantification results (af_quant output from simpleaf quant).\nMust contain the quantification matrix and associated metadata files.\n", - "ontologies": [] - } - } - ] - ], - "output": { - "report": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.html": { - "type": "file", - "description": "HTML QC report generated by QCatch containing visualizations and metrics\n", - "pattern": "*.html", - "ontologies": [] - } - } - ] - ], - "filtered_h5ad": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_filtered_quants.h5ad": { - "type": "file", - "description": "Filtered quantification matrix in h5ad format (AnnData)\n", - "pattern": "*_filtered_quants.h5ad", - "ontologies": [] - } - } - ] - ], - "metrics_summary": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_metrics_summary.csv": { - "type": "file", - "description": "CSV file containing summary metrics from QC analysis\n", - "pattern": "*_metrics_summary.csv", - "ontologies": [] - } - } + "pipelines": [ + { + "name": "metatdenovo", + "version": "1.3.0" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions\n", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@wzheng0520", - "@dongzehe" - ], - "maintainers": [ - "@wzheng0520", - "@dongzehe" - ] - } - }, - { - "name": "qsv_cat", - "path": "modules/nf-core/qsv/cat/meta.yml", - "type": "module", - "meta": { - "name": "qsv_cat", - "description": "Concatenate two or more CSV (or TSV) tables into a single table", - "keywords": [ - "concatenate", - "tsv", - "csv" - ], - "tools": [ - { - "csvtk": { - "description": "Blazing-fast Data-Wrangling toolkit", - "homepage": "https://qsv.dathere.com", - "documentation": "https://github.com/dathere/qsv", - "tool_dev_url": "https://github.com/dathere/qsv", - "licence": [ - "MIT", - "UNLICENSE" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "csv": { - "type": "file", - "description": "CSV/TSV formatted files", - "pattern": "*.{csv,tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - }, - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - { - "mode": { - "type": "string", - "description": "Concatenation mode (rows, columns or rowskey)", - "pattern": "^(rows|columns|rowskey)$" - } - }, - { - "out_format": { - "type": "string", - "description": "Output format (.csv for comma delimiter, .ssv for semicolon, and .tsv or .tab for tab)", - "pattern": "^(csv|ssv|tsv|tab)$" + }, + { + "name": "taxonkit_list", + "path": "modules/nf-core/taxonkit/list/meta.yml", + "type": "module", + "meta": { + "name": "taxonkit_list", + "description": "Generate taxonomic subtrees based on taxonids", + "keywords": ["taxonomy", "taxids", "lineage"], + "tools": [ + { + "taxonkit": { + "description": "A Cross-platform and Efficient NCBI Taxonomy Toolkit", + "homepage": "https://bioinf.shenwei.me/taxonkit/", + "documentation": "https://bioinf.shenwei.me/taxonkit/usage/#name2taxid", + "tool_dev_url": "https://github.com/shenwei356/taxonkit", + "doi": "10.1016/j.jgg.2021.03.006", + "licence": ["MIT"], + "identifier": "biotools:taxonkit" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "taxid": { + "type": "string", + "description": "Taxon id to look up (provide either this or taxidfile, not both)" + } + }, + { + "taxidfile": { + "type": "file", + "description": "File with taxon ids to look up, each on their own line (provide either this or name, not both)", + "ontologies": [] + } + } + ], + { + "taxdb": { + "type": "file", + "description": "Taxonomy database unpacked from ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz", + "ontologies": [] + } + } + ], + "output": { + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "TSV file with taxonomic subtrees", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@jcbioinformatics"], + "maintainers": ["@jcbioinformatics"] } - }, - { - "skip_input_format_check": { - "type": "boolean", - "description": "Skip input format check (by default QSV checks input format based on file extension)" + }, + { + "name": "taxonkit_name2taxid", + "path": "modules/nf-core/taxonkit/name2taxid/meta.yml", + "type": "module", + "meta": { + "name": "taxonkit_name2taxid", + "description": "Convert taxon names to TaxIds", + "keywords": ["taxonomy", "taxids", "taxon name", "conversion"], + "tools": [ + { + "taxonkit": { + "description": "A Cross-platform and Efficient NCBI Taxonomy Toolkit", + "homepage": "https://bioinf.shenwei.me/taxonkit/", + "documentation": "https://bioinf.shenwei.me/taxonkit/usage/#name2taxid", + "tool_dev_url": "https://github.com/shenwei356/taxonkit", + "doi": "10.1016/j.jgg.2021.03.006", + "licence": ["MIT"], + "identifier": "biotools:taxonkit" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "name": { + "type": "string", + "description": "Taxon name to look up (provide either this or names.txt, not both)" + } + }, + { + "names_txt": { + "type": "file", + "description": "File with taxon names to look up, each on their own line (provide either this or name, not both)", + "ontologies": [] + } + } + ], + { + "taxdb": { + "type": "file", + "description": "Taxonomy database unpacked from ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz", + "ontologies": [] + } + } + ], + "output": { + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "TSV file of Taxon names and their taxon ID", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@mahesh-panchal"], + "maintainers": ["@mahesh-panchal"] } - } - ], - "output": { - "csv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "${prefix}.${out_format}": { - "type": "file", - "description": "Concatenated CSV/TSV file", - "pattern": "*.{csv,tsv,tab,ssv}", - "ontologies": [ + }, + { + "name": "taxpasta_merge", + "path": "modules/nf-core/taxpasta/merge/meta.yml", + "type": "module", + "meta": { + "name": "taxpasta_merge", + "description": "Standardise and merge two or more taxonomic profiles into a single table", + "keywords": [ + "taxonomic profile", + "standardise", + "standardisation", + "metagenomics", + "taxonomic profiling", + "otu tables", + "taxon tables" + ], + "tools": [ + { + "taxpasta": { + "description": "TAXonomic Profile Aggregation and STAndardisation", + "homepage": "https://taxpasta.readthedocs.io/", + "documentation": "https://taxpasta.readthedocs.io/", + "tool_dev_url": "https://github.com/taxprofiler/taxpasta", + "licence": ["Apache-2.0"], + "identifier": "biotools:taxpasta" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "profiles": { + "type": "file", + "description": "A list of taxonomic profiler output files (typically in text format, mandatory)", + "pattern": "*.{tsv,csv,arrow,parquet,biom}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + }, + { + "edam": "http://edamontology.org/format_3752" + }, + { + "edam": "http://edamontology.org/format_3746" + } + ] + } + } + ], + { + "profiler": { + "type": "string", + "description": "Name of the profiler used to generate the profile (mandatory)", + "pattern": "bracken|centrifuge|diamond|ganon|kaiju|kmcp|kraken2|krakenuniq|megan6|metaphlan|motus" + } + }, + { + "format": { + "type": "string", + "description": "Type of output file to be generated", + "pattern": "tsv|csv|ods|xlsx|arrow|parquet|biom" + } + }, { - "edam": "http://edamontology.org/format_3752" + "taxonomy": { + "type": "directory", + "description": "Directory containing at a minimum nodes.dmp and names.dmp files (optional)", + "pattern": "*/" + } }, { - "edam": "http://edamontology.org/format_3475" + "samplesheet": { + "type": "file", + "description": "A samplesheet describing the sample name and a filepath to a taxonomic abundance profile that needs to be relative from the Nextflow work directory of the executed process. The profiles must be provided even if you give a samplesheet as argument (optional)", + "pattern": "*.{tsv,csv,ods,xlsx,arrow,parquet}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + }, + { + "edam": "http://edamontology.org/format_3752" + }, + { + "edam": "http://edamontology.org/format_3977" + } + ] + } } - ] - } - } - ] - ], - "versions_qsv": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "qsv": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "qsv --version | cut -d' ' -f2 | cut -d'-' -f1": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "qsv": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "qsv --version | cut -d' ' -f2 | cut -d'-' -f1": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@dialvarezs" - ], - "maintainers": [ - "@dialvarezs" - ] - }, - "pipelines": [ - { - "name": "mag", - "version": "5.4.2" - } - ] - }, - { - "name": "qualimap_bamqc", - "path": "modules/nf-core/qualimap/bamqc/meta.yml", - "type": "module", - "meta": { - "name": "qualimap_bamqc", - "description": "Evaluate alignment data", - "keywords": [ - "quality control", - "qc", - "bam" - ], - "tools": [ - { - "qualimap": { - "description": "Qualimap 2 is a platform-independent application written in\nJava and R that provides both a Graphical User Interface and\na command-line interface to facilitate the quality control of\nalignment sequencing data and its derivatives like feature counts.\n", - "homepage": "http://qualimap.bioinfo.cipf.es/", - "documentation": "http://qualimap.conesalab.org/doc_html/index.html", - "doi": "10.1093/bioinformatics/bts503", - "licence": [ - "GPL-2.0-only" - ], - "identifier": "biotools:qualimap" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + ], + "output": { + "merged_profiles": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{tsv,csv,arrow,parquet,biom}": { + "type": "file", + "description": "Output file with standardised multiple profiles in one go and have all profiles combined into a single table.", + "pattern": "*.{tsv,csv,ods,xlsx,arrow,parquet,biom}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + }, + { + "edam": "http://edamontology.org/format_3752" + }, + { + "edam": "http://edamontology.org/format_3977" + }, + { + "edam": "http://edamontology.org/format_3746" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@sofstam", "@jfy133"], + "maintainers": ["@sofstam", "@jfy133"] }, - { - "bam": { - "type": "file", - "description": "BAM file", - "pattern": "*.{bam}", - "ontologies": [] - } - } - ], - { - "gff": { - "type": "file", - "description": "Feature file with regions of interest", - "pattern": "*.{gff,gtf,bed}", - "ontologies": [] - } - } - ], - "output": { - "results": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}": { - "type": "directory", - "description": "Qualimap results dir", - "pattern": "*/*" - } - } - ] - ], - "versions_qualimap": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "qualimap": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "qualimap -h | sed -n 's/^QualiMap v.//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "qualimap": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "qualimap -h | sed -n 's/^QualiMap v.//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "taxprofiler", + "version": "2.0.0" + } ] - ] - }, - "authors": [ - "@phue" - ], - "maintainers": [ - "@phue" - ] - }, - "pipelines": [ - { - "name": "hgtseq", - "version": "1.1.0" }, { - "name": "methylseq", - "version": "4.2.0" - } - ] - }, - { - "name": "qualimap_bamqccram", - "path": "modules/nf-core/qualimap/bamqccram/meta.yml", - "type": "module", - "meta": { - "name": "qualimap_bamqccram", - "description": "Evaluate alignment data", - "keywords": [ - "quality control", - "qc", - "bam" - ], - "tools": [ - { - "qualimap": { - "description": "Qualimap 2 is a platform-independent application written in\nJava and R that provides both a Graphical User Interface and\na command-line interface to facilitate the quality control of\nalignment sequencing data and its derivatives like feature counts.\n", - "homepage": "http://qualimap.bioinfo.cipf.es/", - "documentation": "http://qualimap.conesalab.org/doc_html/index.html", - "doi": "10.1093/bioinformatics/bts503", - "licence": [ - "GPL-2.0-only" - ], - "identifier": "biotools:qualimap" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "cram": { - "type": "file", - "description": "Input cram file", - "pattern": "*.{cram}", - "ontologies": [] - } - }, - { - "crai": { - "type": "file", - "description": "Index file for cram file", - "pattern": "*.{crai}", - "ontologies": [] - } - } - ], - { - "gff": { - "type": "file", - "description": "Feature file with regions of interest", - "pattern": "*.{gff,gtf,bed}", - "ontologies": [] - } - }, - { - "fasta": { - "type": "file", - "description": "Reference file of cram file", - "pattern": "*.{fasta,fa,fna}", - "ontologies": [] - } - }, - { - "fasta_fai": { - "type": "file", - "description": "Index file for reference file", - "pattern": "*.{fai}", - "ontologies": [] - } - } - ], - "output": { - "results": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}": { - "type": "directory", - "description": "Qualimap results dir", - "pattern": "*/*" - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@FriederikeHanssen" - ], - "maintainers": [ - "@FriederikeHanssen" - ] - }, - "pipelines": [ - { - "name": "methylseq", - "version": "4.2.0" - } - ] - }, - { - "name": "qualimap_rnaseq", - "path": "modules/nf-core/qualimap/rnaseq/meta.yml", - "type": "module", - "meta": { - "name": "qualimap_rnaseq", - "description": "Evaluate alignment data", - "keywords": [ - "quality control", - "qc", - "rnaseq" - ], - "tools": [ - { - "qualimap": { - "description": "Qualimap 2 is a platform-independent application written in\nJava and R that provides both a Graphical User Interface and\na command-line interface to facilitate the quality control of\nalignment sequencing data and its derivatives like feature counts.\n", - "homepage": "http://qualimap.bioinfo.cipf.es/", - "documentation": "http://qualimap.conesalab.org/doc_html/index.html", - "doi": "10.1093/bioinformatics/bts503", - "licence": [ - "GPL-2.0-only" - ], - "identifier": "biotools:qualimap" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file", - "pattern": "*.{bam}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } + "name": "taxpasta_standardise", + "path": "modules/nf-core/taxpasta/standardise/meta.yml", + "type": "module", + "meta": { + "name": "taxpasta_standardise", + "description": "Standardise the output of a wide range of taxonomic profilers", + "keywords": [ + "taxonomic profile", + "standardise", + "standardisation", + "metagenomics", + "taxonomic profiling", + "otu tables", + "taxon tables" + ], + "tools": [ + { + "taxpasta": { + "description": "TAXonomic Profile Aggregation and STAndardisation", + "homepage": "https://taxpasta.readthedocs.io/", + "documentation": "https://taxpasta.readthedocs.io/", + "tool_dev_url": "https://github.com/taxprofiler/taxpasta", + "licence": ["Apache-2.0"], + "identifier": "biotools:taxpasta" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "profile": { + "type": "file", + "description": "profiler output file (mandatory)", + "pattern": "*", + "ontologies": [] + } + } + ], + { + "profiler": { + "type": "string", + "description": "Name of the profiler used to generate the profile (mandatory)", + "pattern": "bracken|centrifuge|diamond|ganon|kaiju|kmcp|kraken2|krakenuniq|megan6|metaphlan|motus" + } + }, + { + "format": { + "type": "string", + "description": "Type of output file to be generated", + "pattern": "tsv|csv|ods|xlsx|arrow|parquet|biom" + } + }, + { + "taxonomy": { + "type": "directory", + "description": "Directory containing at a minimum nodes.dmp and names.dmp files (optional)", + "pattern": "*/" + } + } + ], + "output": { + "standardised_profile": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{tsv,csv,arrow,parquet,biom}": { + "type": "file", + "description": "Standardised taxonomic profile", + "pattern": "*.{tsv,csv,arrow,parquet,biom}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + }, + { + "edam": "http://edamontology.org/format_3752" + }, + { + "edam": "http://edamontology.org/format_3746" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@Midnighter"], + "maintainers": ["@Midnighter"] }, - { - "gtf": { - "type": "file", - "description": "GTF file of the reference genome", - "pattern": "*.{gtf}", - "ontologies": [] - } - } - ] - ], - "output": { - "results": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}": { - "type": "directory", - "description": "Qualimap results dir", - "pattern": "*/*" - } - } - ] - ], - "versions_qualimap": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "qualimap": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "qualimap 2>&1 | sed -n 's/.*QualiMap v.\\(.*\\)/\\1/p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "qualimap": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "qualimap 2>&1 | sed -n 's/.*QualiMap v.\\(.*\\)/\\1/p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "taxprofiler", + "version": "2.0.0" + } ] - ] - }, - "authors": [ - "@FriederikeHanssen" - ], - "maintainers": [ - "@FriederikeHanssen" - ] - }, - "pipelines": [ - { - "name": "rnaseq", - "version": "3.26.0" - } - ] - }, - { - "name": "quantmsutils_diann2mztab", - "path": "modules/nf-core/quantmsutils/diann2mztab/meta.yml", - "type": "module", - "meta": { - "name": "quantmsutils_diann2mztab", - "description": "Convert DIA-NN results to mzTab, MSstats, and Triqler formats using quantms-utils", - "keywords": [ - "quantms-utils", - "diann", - "mztab", - "msstats", - "triqler", - "proteomics" - ], - "tools": [ - { - "quantms-utils": { - "description": "quantms-utils is a Python package for proteomics data processing", - "homepage": "https://github.com/bigbio/quantms-utils", - "documentation": "https://quantms-utils.readthedocs.io/", - "tool_dev_url": "https://github.com/bigbio/quantms-utils", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', name:'test', condition:'test' ]\n" - } - }, - { - "report": { - "type": "file", - "description": "DIA-NN main report file (tsv or parquet)", - "pattern": "*.{tsv,parquet}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - }, - { - "report_pg": { - "type": "file", - "description": "DIA-NN protein group matrix file", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - }, - { - "report_pr": { - "type": "file", - "description": "DIA-NN precursor matrix file", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - }, - { - "diann_version": { - "type": "string", - "description": "DIA-NN version\n" - } - }, - { - "exp_design": { - "type": "file", - "description": "Experimental design file describing sample conditions", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - }, - { - "ms_information": { - "type": "file", - "description": "MS statistics/information files in parquet format", - "pattern": "*.parquet", - "ontologies": [] - } + }, + { + "name": "tbprofiler_profile", + "path": "modules/nf-core/tbprofiler/profile/meta.yml", + "type": "module", + "meta": { + "name": "tbprofiler_profile", + "description": "A tool to detect resistance and lineages of M. tuberculosis genomes", + "keywords": ["Mycobacterium tuberculosis", "resistance", "serotype"], + "tools": [ + { + "tbprofiler": { + "description": "Profiling tool for Mycobacterium tuberculosis to detect drug resistance and lineage from WGS data", + "homepage": "https://github.com/jodyphelan/TBProfiler", + "documentation": "https://jodyphelan.gitbook.io/tb-profiler/", + "tool_dev_url": "https://github.com/jodyphelan/TBProfiler", + "doi": "10.1186/s13073-019-0650-x", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "FASTQ file", + "pattern": "*.{fastq.gz,fq.gz}", + "ontologies": [] + } + } + ] + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam/*.bam": { + "type": "file", + "description": "BAM file with alignment details", + "pattern": "*.bam", + "ontologies": [] + } + } + ] + ], + "csv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "results/*.csv": { + "type": "file", + "description": "Optional CSV formatted result file of resistance and strain type", + "pattern": "*.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "json": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "results/*.json": { + "type": "file", + "description": "JSON formatted result file of resistance and strain type", + "pattern": "*.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "txt": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "results/*.txt": { + "type": "file", + "description": "Optional text file of resistance and strain type", + "pattern": "*.txt", + "ontologies": [] + } + } + ] + ], + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf/*.vcf.gz": { + "type": "file", + "description": "VCF with variant info again reference genomes", + "pattern": "*.vcf", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@rpetit3"], + "maintainers": ["@rpetit3"] }, - { - "fasta": { - "type": "file", - "description": "FASTA database file used for the search", - "pattern": "*.{fasta,fa}", - "ontologies": [] - } - } - ] - ], - "output": { - "out_msstats": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', name:'test', condition:'test' ]\n" - } - }, - { - "*msstats_in.csv": { - "type": "file", - "description": "MSstats input file for statistical analysis", - "pattern": "*msstats_in.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "out_triqler": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', name:'test', condition:'test' ]\n" - } - }, - { - "*triqler_in.tsv": { - "type": "file", - "description": "Triqler input file for protein quantification with uncertainty", - "pattern": "*triqler_in.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "out_mztab": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', name:'test', condition:'test' ]\n" - } - }, - { - "*.mzTab": { - "type": "file", - "description": "mzTab output file (standard proteomics exchange format)", - "pattern": "*.mzTab", - "ontologies": [] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', name:'test', condition:'test' ]\n" - } - }, - { - "*.log": { - "type": "file", - "description": "Log file from conversion process", - "pattern": "*.log", - "ontologies": [] - } - } + "pipelines": [ + { + "name": "tbanalyzer", + "version": "dev" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@daichengxin", - "@wanghong", - "@pinin4fjords" - ], - "maintainers": [ - "@daichengxin", - "@pinin4fjords" - ] - } - }, - { - "name": "quantmsutils_dianncfg", - "path": "modules/nf-core/quantmsutils/dianncfg/meta.yml", - "type": "module", - "meta": { - "name": "quantmsutils_dianncfg", - "description": "Generate DIA-NN configuration arguments from enzyme and Unimod modification parameters.\nThis module uses quantms-utils to convert enzyme and modification specifications into DIA-NN-compatible command-line arguments.\nOnly supports Unimod modifications. For custom modifications, pass arguments directly to the DIANN module.\n", - "keywords": [ - "quantms-utils", - "diann", - "configuration", - "enzyme", - "modifications" - ], - "tools": [ - { - "quantms-utils": { - "description": "quantms-utils is a Python package with scripts and functions for quantitative proteomics data analysis.\nThe dianncfg command converts enzyme and modification parameters to DIA-NN-compatible format.\n", - "homepage": "https://github.com/bigbio/quantms-utils", - "documentation": "https://github.com/bigbio/quantms-utils", - "tool_dev_url": "https://github.com/bigbio/quantms-utils", - "licence": [ - "MIT" - ], - "identifier": "biotools:quantms-utils" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "enzyme": { - "type": "string", - "description": "Enzyme name for protein digestion (e.g., 'Trypsin', 'Trypsin/P')", - "pattern": ".*" - } - }, - { - "fixed_modifications": { - "type": "string", - "description": "Fixed modifications in Unimod format (e.g., 'Carbamidomethyl (C)')", - "pattern": ".*" - } + }, + { + "name": "tcoffee_align", + "path": "modules/nf-core/tcoffee/align/meta.yml", + "type": "module", + "meta": { + "name": "tcoffee_align", + "description": "Aligns sequences using T_COFFEE", + "keywords": ["alignment", "MSA", "genomics"], + "tools": [ + { + "tcoffee": { + "description": "A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures.", + "homepage": "http://www.tcoffee.org/Projects/tcoffee/", + "documentation": "https://tcoffee.readthedocs.io/en/latest/tcoffee_main_documentation.html", + "tool_dev_url": "https://github.com/cbcrg/tcoffee", + "doi": "10.1006/jmbi.2000.4042", + "licence": ["GPL v3"], + "identifier": "" + } + }, + { + "pigz": { + "description": "Parallel implementation of the gzip algorithm.", + "homepage": "https://zlib.net/pigz/", + "documentation": "https://zlib.net/pigz/pigz.pdf", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input sequences in FASTA format", + "pattern": "*.{fa,fasta}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1919" + }, + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing tree information\ne.g. `[ id:'test_tree']`\n" + } + }, + { + "tree": { + "type": "file", + "description": "Input guide tree in Newick format", + "pattern": "*.{dnd}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2006" + } + ] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing tree information\ne.g. `[ id:'test_infos']`\n" + } + }, + { + "template": { + "type": "file", + "description": "T_coffee template file that maps sequences to the accessory information files to be used.", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1476" + } + ] + } + }, + { + "accessory_information": { + "type": "file", + "description": "Accessory files to be used in the alignment. For example, it could be protein structures or secondary structures.", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1476" + }, + { + "edam": "http://edamontology.org/format_1477" + } + ] + } + } + ], + { + "compress": { + "type": "boolean", + "description": "Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded." + } + } + ], + "output": { + "alignment": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" + } + }, + { + "*.aln{.gz,}": { + "type": "file", + "description": "Alignment file in FASTA format. May be gzipped.", + "pattern": "*.aln{.gz,}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2554" + }, + { + "edam": "http://edamontology.org/format_1921" + }, + { + "edam": "http://edamontology.org/format_1984" + } + ] + } + } + ] + ], + "lib": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" + } + }, + { + "*.*lib": { + "type": "file", + "description": "optional output, the library generated from the MSA file.", + "pattern": "*.*lib", + "ontologies": [] + } + } + ] + ], + "versions_tcoffee": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "tcoffee": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "t_coffee -version | awk '{gsub(\"Version_\", \"\"); print \\$3}'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_pigz": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "pigz": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pigz --version 2>&1 | sed \"s/^.*pigz[[:space:]]*//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "tcoffee": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "t_coffee -version | awk '{gsub(\"Version_\", \"\"); print \\$3}'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "pigz": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pigz --version 2>&1 | sed \"s/^.*pigz[[:space:]]*//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@luisas", "@JoseEspinosa", "@alessiovignoli"], + "maintainers": ["@luisas", "@JoseEspinosa", "@lrauschning", "@alessiovignoli"] }, - { - "variable_modifications": { - "type": "string", - "description": "Variable modifications in Unimod format (e.g., 'Oxidation (M)')", - "pattern": ".*" - } - } - ] - ], - "output": { - "diann_cfg": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "diann_config.cfg": { - "type": "file", - "description": "DIA-NN configuration file containing command-line arguments", - "pattern": "diann_config.cfg" - } - } + "pipelines": [ + { + "name": "multiplesequencealign", + "version": "1.1.1" + } ] - ], - "log": [ - { - "*.log": { - "type": "file", - "description": "Log file from configuration generation", - "pattern": "*.log" - } - } - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@daichengxin", - "@pinin4fjords" - ], - "maintainers": [ - "@daichengxin", - "@pinin4fjords" - ] - } - }, - { - "name": "quantmsutils_mzmlstatistics", - "path": "modules/nf-core/quantmsutils/mzmlstatistics/meta.yml", - "type": "module", - "meta": { - "name": "quantmsutils_mzmlstatistics", - "description": "Generate statistics from mzML files using quantms-utils", - "keywords": [ - "quantms-utils", - "mzml", - "statistics", - "proteomics", - "mass spectrometry" - ], - "tools": [ - { - "quantms-utils": { - "description": "A Python package for quantitative mass spectrometry data analysis", - "homepage": "https://github.com/bigbio/quantms-utils", - "documentation": "https://quantms-utils.readthedocs.io/", - "tool_dev_url": "https://github.com/bigbio/quantms-utils", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', name:'test' ]\n" - } + }, + { + "name": "tcoffee_alncompare", + "path": "modules/nf-core/tcoffee/alncompare/meta.yml", + "type": "module", + "meta": { + "name": "tcoffee_alncompare", + "description": "Compares 2 alternative MSAs to evaluate them.", + "keywords": ["alignment", "MSA", "evaluation"], + "tools": [ + { + "tcoffee": { + "description": "A collection of tools for Multiple Alignments of DNA, RNA, Protein Sequence", + "homepage": "http://www.tcoffee.org/Projects/tcoffee/", + "documentation": "https://tcoffee.readthedocs.io/en/latest/tcoffee_main_documentation.html", + "tool_dev_url": "https://github.com/cbcrg/tcoffee", + "doi": "10.1006/jmbi.2000.4042", + "licence": ["GPL v3"], + "identifier": "" + } + }, + { + "pigz": { + "description": "Parallel implementation of the gzip algorithm.", + "homepage": "https://zlib.net/pigz/", + "documentation": "https://zlib.net/pigz/pigz.pdf", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', ... ]\n" + } + }, + { + "msa": { + "type": "file", + "description": "fasta file containing the alignment to be evaluated. Can be gzipped or uncompressed", + "pattern": "*.{aln,fa,fasta,fas}{.gz,}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1919" + }, + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + }, + { + "ref_msa": { + "type": "file", + "description": "fasta file containing the reference alignment used for the evaluation. Can be gzipped or uncompressed", + "pattern": "*.{aln,fa,fasta,fas}{.gz,}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + }, + { + "edam": "http://edamontology.org/format_2554" + }, + { + "edam": "http://edamontology.org/format_1921" + }, + { + "edam": "http://edamontology.org/format_1984" + } + ] + } + } + ] + ], + "output": { + "scores": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.scores": { + "type": "file", + "description": "a file containing the score of the alignment", + "pattern": "*.scores", + "ontologies": [] + } + } + ] + ], + "versions_tcoffee": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "tcoffee": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "t_coffee -version | awk '{gsub(\"Version_\", \"\"); print \\$3}'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_pigz": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "pigz": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pigz --version 2>&1 | sed \"s/^.*pigz[[:space:]]*//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "tcoffee": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "t_coffee -version | awk '{gsub(\"Version_\", \"\"); print \\$3}'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "pigz": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pigz --version 2>&1 | sed \"s/^.*pigz[[:space:]]*//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@l-mansouri", "@luisas"] }, - { - "ms_file": { - "type": "file", - "description": "Input mzML file", - "pattern": "*.{mzML,mzml}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3244" - } - ] - } - } - ] - ], - "output": { - "ms_statistics": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', name:'test' ]\n" - } - }, - { - "*_ms_info.parquet": { - "type": "file", - "description": "MS statistics in parquet format", - "pattern": "*_ms_info.parquet", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2330" - } - ] - } - } - ] - ], - "ms2_statistics": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', name:'test' ]\n" - } - }, - { - "*_ms2_info.parquet": { - "type": "file", - "description": "MS2 statistics in parquet format (optional)", - "pattern": "*_ms2_info.parquet", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2330" - } - ] - } - } - ] - ], - "feature_statistics": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', name:'test' ]\n" - } - }, - { - "*_feature_info.parquet": { - "type": "file", - "description": "Feature statistics in parquet format (optional)", - "pattern": "*_feature_info.parquet", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2330" - } - ] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', name:'test' ]\n" - } - }, - { - "*.log": { - "type": "file", - "description": "Log file", - "pattern": "*.log", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2330" - } - ] - } - } + "pipelines": [ + { + "name": "multiplesequencealign", + "version": "1.1.1" + } ] - ] - }, - "authors": [ - "@wanghong", - "@daichengxin", - "@pinin4fjords" - ], - "maintainers": [ - "@daichengxin", - "@pinin4fjords" - ] - } - }, - { - "name": "quartonotebook", - "path": "modules/nf-core/quartonotebook/meta.yml", - "type": "module", - "meta": { - "name": "quartonotebook", - "description": "Render a Quarto notebook, including parametrization.", - "keywords": [ - "quarto", - "notebook", - "reports", - "python", - "r" - ], - "tools": [ - { - "quartonotebook": { - "description": "An open-source scientific and technical publishing system.", - "homepage": "https://quarto.org/", - "documentation": "https://quarto.org/docs/reference/", - "tool_dev_url": "https://github.com/quarto-dev/quarto-cli", - "licence": [ - "MIT" - ], - "identifier": "" - } - }, - { - "papermill": { - "description": "Parameterize, execute, and analyze notebooks", - "homepage": "https://github.com/nteract/papermill", - "documentation": "http://papermill.readthedocs.io/en/latest/", - "tool_dev_url": "https://github.com/nteract/papermill", - "licence": [ - "BSD 3-clause" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`.\n" - } + }, + { + "name": "tcoffee_consensus", + "path": "modules/nf-core/tcoffee/consensus/meta.yml", + "type": "module", + "meta": { + "name": "tcoffee_consensus", + "description": "Computes a consensus alignment using T_COFFEE", + "keywords": ["alignment", "MSA", "genomics"], + "tools": [ + { + "tcoffee": { + "description": "A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures.", + "homepage": "http://www.tcoffee.org/Projects/tcoffee/", + "documentation": "https://tcoffee.readthedocs.io/en/latest/tcoffee_main_documentation.html", + "tool_dev_url": "https://github.com/cbcrg/tcoffee", + "doi": "10.1006/jmbi.2000.4042", + "licence": ["GPL v3"], + "identifier": "" + } + }, + { + "pigz": { + "description": "Parallel implementation of the gzip algorithm.", + "homepage": "https://zlib.net/pigz/", + "documentation": "https://zlib.net/pigz/pigz.pdf", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "aln": { + "type": "file", + "description": "List of multiple sequence alignments in FASTA format to be used to compute the consensus", + "pattern": "*.{fa,fasta}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing tree information\ne.g. `[ id:'test_tree']`\n" + } + }, + { + "tree": { + "type": "file", + "description": "Input guide tree in Newick format", + "pattern": "*.{dnd}", + "ontologies": [] + } + } + ], + { + "compress": { + "type": "boolean", + "description": "Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded." + } + } + ], + "output": { + "alignment": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n", + "pattern": "*.{fa,fasta,aln}" + } + }, + { + "*.{aln,aln.gz}": { + "type": "file", + "description": "Alignment file in FASTA format. May be gzipped.", + "pattern": "*.aln{.gz,}", + "ontologies": [] + } + } + ] + ], + "eval": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n", + "pattern": "*.{fa,fasta,aln}" + } + }, + { + "*.{score_html,sp_ascii}": { + "type": "file", + "description": "Consensus evaluation file.", + "pattern": "*.{score_html, score_ascii}", + "ontologies": [] + } + } + ] + ], + "versions_tcoffee": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "tcoffee": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "t_coffee -version | awk '{gsub(\"Version_\", \"\"); print \\$3}'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_pigz": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "pigz": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pigz --version 2>&1 | sed \"s/^.*pigz[[:space:]]*//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "tcoffee": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "t_coffee -version | awk '{gsub(\"Version_\", \"\"); print \\$3}'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "pigz": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pigz --version 2>&1 | sed \"s/^.*pigz[[:space:]]*//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@luisas"], + "maintainers": ["@luisas"] }, - { - "notebook": { - "type": "file", - "description": "The Quarto notebook to be rendered.", - "pattern": "*.{qmd}", - "ontologies": [] - } - } - ], - { - "parameters": { - "type": "map", - "description": "Groovy map with notebook parameters which will be passed to Quarto to\ngenerate parametrized reports.\n" - } - }, - { - "input_files": { - "type": "file", - "description": "One or multiple files serving as input data for the notebook.", - "pattern": "*", - "ontologies": [] - } - }, - { - "extensions": { - "type": "file", - "description": "A quarto `_extensions` directory with custom template(s) to be\navailable for rendering.\n", - "pattern": "*", - "ontologies": [] - } - } - ], - "output": { - "html": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`.\n" - } - }, - { - "*.html": { - "type": "file", - "description": "HTML report generated by Quarto.", - "pattern": "*.html", - "ontologies": [] - } - } - ] - ], - "notebook": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`.\n" - } - }, - { - "notebook": { - "type": "file", - "description": "The Quarto notebook that was rendered. Allows user to continue working on the notebook.", - "pattern": "*.{qmd}", - "ontologies": [] - } - } - ] - ], - "params_yaml": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`.\n" - } - }, - { - "params.yml": { - "type": "file", - "description": "Parameters used during report rendering.", - "pattern": "*", - "ontologies": [] - } - } - ] - ], - "artifacts": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`.\n" - } - }, - { - "${notebook_parameters.artifact_dir}/*": { - "type": "file", - "description": "Artifacts generated during report rendering.", - "pattern": "*", - "ontologies": [] - } - } - ] - ], - "extensions": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`.\n" - } - }, - { - "_extensions": { - "type": "file", - "description": "Quarto extensions used during report rendering.", - "pattern": "*", - "ontologies": [] - } - } - ] - ], - "versions_quarto": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "quarto": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "quarto -v": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_papermill": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "papermill": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "papermill --version | cut -f1 -d\" \"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "quarto": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "quarto -v": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "papermill": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "papermill --version | cut -f1 -d\" \"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "multiplesequencealign", + "version": "1.1.1" + } ] - ] }, - "authors": [ - "@fasterius" - ], - "maintainers": [ - "@fasterius" - ] - }, - "pipelines": [ { - "name": "coproid", - "version": "2.0.1" + "name": "tcoffee_extractfrompdb", + "path": "modules/nf-core/tcoffee/extractfrompdb/meta.yml", + "type": "module", + "meta": { + "name": "tcoffee_extractfrompdb", + "description": "Reformats the header of PDB files with t-coffee", + "keywords": ["reformatting", "pdb", "genomics"], + "tools": [ + { + "tcoffee": { + "description": "A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures.", + "homepage": "http://www.tcoffee.org/Projects/tcoffee/", + "documentation": "https://tcoffee.readthedocs.io/en/latest/tcoffee_main_documentation.html", + "tool_dev_url": "https://github.com/cbcrg/tcoffee", + "doi": "10.1006/jmbi.2000.4042", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "pdb": { + "type": "file", + "description": "Input pdb to be reformatted", + "ontologies": [] + } + } + ] + ], + "output": { + "formatted_pdb": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "${prefix}.pdb": { + "type": "file", + "description": "Formatted pdb file", + "pattern": "*", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@luisas"] + }, + "pipelines": [ + { + "name": "multiplesequencealign", + "version": "1.1.1" + } + ] }, { - "name": "scdownstream", - "version": "dev" + "name": "tcoffee_irmsd", + "path": "modules/nf-core/tcoffee/irmsd/meta.yml", + "type": "module", + "meta": { + "name": "tcoffee_irmsd", + "description": "Computes the irmsd score for a given alignment and the structures.", + "keywords": ["alignment", "MSA", "evaluation"], + "tools": [ + { + "tcoffee": { + "description": "A collection of tools for Multiple Alignments of DNA, RNA, Protein Sequence", + "homepage": "http://www.tcoffee.org/Projects/tcoffee/", + "documentation": "https://tcoffee.readthedocs.io/en/latest/tcoffee_main_documentation.html", + "tool_dev_url": "https://github.com/cbcrg/tcoffee", + "doi": "10.1006/jmbi.2000.4042", + "licence": ["GPL v3"], + "identifier": "" + } + }, + { + "pigz": { + "description": "Parallel implementation of the gzip algorithm.", + "homepage": "https://zlib.net/pigz/", + "documentation": "https://zlib.net/pigz/pigz.pdf", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', ... ]\n" + } + }, + { + "msa": { + "type": "file", + "description": "Multiple Sequence Alignment File\n", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + }, + { + "edam": "http://edamontology.org/format_2554" + }, + { + "edam": "http://edamontology.org/format_1921" + }, + { + "edam": "http://edamontology.org/format_1984" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "template": { + "type": "file", + "description": "Template file\n", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1476" + } + ] + } + }, + { + "structures": { + "type": "file", + "description": "Structure file\n", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1476" + } + ] + } + } + ] + ], + "output": { + "irmsd": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.irmsd": { + "type": "file", + "description": "File containing the irmsd of the alignment", + "ontologies": [] + } + } + ] + ], + "versions_tcoffee": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "tcoffee": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "t_coffee -version | awk '{gsub(\"Version_\", \"\"); print \\$3}'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_pigz": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "pigz": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pigz --version 2>&1 | sed \"s/^.*pigz[[:space:]]*//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "tcoffee": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "t_coffee -version | awk '{gsub(\"Version_\", \"\"); print \\$3}'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "pigz": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pigz --version 2>&1 | sed \"s/^.*pigz[[:space:]]*//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@luisas"] + }, + "pipelines": [ + { + "name": "multiplesequencealign", + "version": "1.1.1" + } + ] }, { - "name": "spatialvi", - "version": "dev" - } - ] - }, - { - "name": "quast", - "path": "modules/nf-core/quast/meta.yml", - "type": "module", - "meta": { - "name": "quast", - "description": "Quality Assessment Tool for Genome Assemblies", - "keywords": [ - "quast", - "assembly", - "quality", - "contig", - "scaffold" - ], - "tools": [ - { - "quast": { - "description": "QUAST calculates quality metrics for genome assemblies\n", - "homepage": "http://bioinf.spbau.ru/quast", - "doi": "10.1093/bioinformatics/btt086", - "licence": [ - "GPL-2.0-only" - ], - "identifier": "biotools:quast" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "consensus": { - "type": "file", - "description": "Fasta file containing the assembly of interest\n", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "The genome assembly to be evaluated. Has to contain at least a non-empty string dummy value.\n", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + "name": "tcoffee_regressive", + "path": "modules/nf-core/tcoffee/regressive/meta.yml", + "type": "module", + "meta": { + "name": "tcoffee_regressive", + "description": "Aligns sequences using the regressive algorithm as implemented in the T_COFFEE package", + "keywords": ["alignment", "MSA", "genomics"], + "tools": [ + { + "tcoffee": { + "description": "A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures.", + "homepage": "http://www.tcoffee.org/Projects/tcoffee/", + "documentation": "https://tcoffee.readthedocs.io/en/latest/tcoffee_main_documentation.html", + "tool_dev_url": "https://github.com/cbcrg/tcoffee", + "doi": "10.1038/s41587-019-0333-6", + "licence": ["GPL v3"], + "identifier": "" + } + }, + { + "pigz": { + "description": "Parallel implementation of the gzip algorithm.", + "homepage": "https://zlib.net/pigz/", + "documentation": "https://zlib.net/pigz/pigz.pdf", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input sequences in FASTA format", + "pattern": "*.{fa,fasta}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1919" + }, + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing tree information\ne.g. `[ id:'test_tree']`\n" + } + }, + { + "tree": { + "type": "file", + "description": "Input guide tree in Newick format", + "pattern": "*.{dnd}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2006" + } + ] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing tree information\ne.g. `[ id:'test_infos']`\n" + } + }, + { + "template": { + "type": "file", + "description": "T_coffee template file that maps sequences to the accessory information files to be used.", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1476" + } + ] + } + }, + { + "accessory_information": { + "type": "file", + "description": "Accessory files to be used in the alignment. For example, it could be protein structures or secondary structures.", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1476" + } + ] + } + } + ], + { + "compress": { + "type": "boolean", + "description": "Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded." + } + } + ], + "output": { + "alignment": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" + } + }, + { + "*.aln{.gz,}": { + "type": "file", + "description": "Alignment file in FASTA format. May be gzipped.", + "pattern": "*.aln{.gz,}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2554" + }, + { + "edam": "http://edamontology.org/format_1921" + }, + { + "edam": "http://edamontology.org/format_1984" + } + ] + } + } + ] + ], + "versions_tcoffee": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "tcoffee": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "t_coffee -version | awk '{gsub(\"Version_\", \"\"); print \\$3}'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_pigz": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "pigz": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pigz --version 2>&1 | sed \"s/^.*pigz[[:space:]]*//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "tcoffee": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "t_coffee -version | awk '{gsub(\"Version_\", \"\"); print \\$3}'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "pigz": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pigz --version 2>&1 | sed \"s/^.*pigz[[:space:]]*//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@luisas"], + "maintainers": ["@luisas"] }, - { - "gff": { - "type": "file", - "description": "The genome GFF file. Has to contain at least a non-empty string dummy value.", - "ontologies": [] - } - } - ] - ], - "output": { - "results": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}": { - "type": "directory", - "description": "Directory containing the results of the QUAST analysis\n" - } - } - ] - ], - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.tsv": { - "type": "file", - "description": "TSV file", - "pattern": "${prefix}.tsv", - "ontologies": [] - } - } - ] - ], - "transcriptome": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}_transcriptome.tsv": { - "type": "file", - "description": "Report containing all the alignments of transcriptome to the assembly, only when a reference fasta is provided\n", - "pattern": "${prefix}_transcriptome.tsv", - "ontologies": [] - } - } - ] - ], - "misassemblies": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}_misassemblies.tsv": { - "type": "file", - "description": "Report containing misassemblies, only when a reference fasta is provided\n", - "pattern": "${prefix}_misassemblies.tsv", - "ontologies": [] - } - } - ] - ], - "unaligned": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}_unaligned.tsv": { - "type": "file", - "description": "Report containing unaligned contigs, only when a reference fasta is provided\n", - "pattern": "${prefix}_unaligned.tsv", - "ontologies": [] - } - } - ] - ], - "versions_quast": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "quast": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "quast.py --version 2>&1 | grep \"QUAST\" | sed 's/^.*QUAST v//; s/ .*\\$//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "quast": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "quast.py --version 2>&1 | grep \"QUAST\" | sed 's/^.*QUAST v//; s/ .*\\$//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "multiplesequencealign", + "version": "1.1.1" + } ] - ] }, - "authors": [ - "@drpatelh", - "@kevinmenden" - ], - "maintainers": [ - "@drpatelh", - "@kevinmenden" - ] - }, - "pipelines": [ { - "name": "bacass", - "version": "2.6.0" + "name": "tcoffee_seqreformat", + "path": "modules/nf-core/tcoffee/seqreformat/meta.yml", + "type": "module", + "meta": { + "name": "tcoffee_seqreformat", + "description": "Reformats files with t-coffee", + "keywords": ["reformatting", "alignment", "genomics"], + "tools": [ + { + "tcoffee": { + "description": "A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures.", + "homepage": "http://www.tcoffee.org/Projects/tcoffee/", + "documentation": "https://tcoffee.readthedocs.io/en/latest/tcoffee_main_documentation.html", + "tool_dev_url": "https://github.com/cbcrg/tcoffee", + "doi": "10.1006/jmbi.2000.4042", + "licence": ["GPL v3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "infile": { + "type": "file", + "description": "Input file to be reformatted", + "ontologies": [] + } + } + ] + ], + "output": { + "formatted_file": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "${prefix}.txt": { + "type": "file", + "description": "Formatted file", + "pattern": "*", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@luisas", "@JoseEspinosa"] + }, + "pipelines": [ + { + "name": "multiplesequencealign", + "version": "1.1.1" + } + ] }, { - "name": "genomeqc", - "version": "dev" + "name": "tcoffee_tcs", + "path": "modules/nf-core/tcoffee/tcs/meta.yml", + "type": "module", + "meta": { + "name": "tcoffee_tcs", + "description": "Compute the TCS score for a MSA or for a MSA plus a library file. Outputs the tcs as it is and a csv with just the total TCS score.", + "keywords": ["alignment", "MSA", "evaluation"], + "tools": [ + { + "tcoffee": { + "description": "A collection of tools for Multiple Alignments of DNA, RNA, Protein Sequence", + "homepage": "http://www.tcoffee.org/Projects/tcoffee/", + "documentation": "https://tcoffee.readthedocs.io/en/latest/tcoffee_main_documentation.html", + "tool_dev_url": "https://github.com/cbcrg/tcoffee", + "doi": "10.1006/jmbi.2000.4042", + "licence": ["GPL v3"], + "identifier": "" + } + }, + { + "pigz": { + "description": "Parallel implementation of the gzip algorithm.", + "homepage": "https://zlib.net/pigz/", + "documentation": "https://zlib.net/pigz/pigz.pdf", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', ... ]\n" + } + }, + { + "msa": { + "type": "file", + "description": "fasta file containing the alignment to be evaluated. May be gzipped or uncompressed.", + "pattern": "*.{aln,fa,fasta,fas}{.gz,}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + }, + { + "edam": "http://edamontology.org/format_2554" + }, + { + "edam": "http://edamontology.org/format_1921" + }, + { + "edam": "http://edamontology.org/format_1984" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "lib": { + "type": "file", + "description": "lib file containing the alignment library of the given msa.", + "pattern": "*{.tc_lib,*_lib}", + "ontologies": [] + } + } + ] + ], + "output": { + "tcs": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.tcs": { + "type": "file", + "description": "The msa represented in tcs format, prepended with TCS scores", + "pattern": "*.tcs", + "ontologies": [] + } + } + ] + ], + "scores": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.scores": { + "type": "file", + "description": "a file containing the score of the alignment in csv format", + "pattern": "*.scores", + "ontologies": [] + } + } + ] + ], + "versions_tcoffee": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "tcoffee": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "t_coffee -version | awk '{gsub(\"Version_\", \"\"); print \\$3}'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_pigz": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "pigz": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pigz --version 2>&1 | sed \"s/^.*pigz[[:space:]]*//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "tcoffee": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "t_coffee -version | awk '{gsub(\"Version_\", \"\"); print \\$3}'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "pigz": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pigz --version 2>&1 | sed \"s/^.*pigz[[:space:]]*//\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@alessiovignoli"] + }, + "pipelines": [ + { + "name": "multiplesequencealign", + "version": "1.1.1" + } + ] }, { - "name": "pathogensurveillance", - "version": "1.1.0" + "name": "td2_longorfs", + "path": "modules/nf-core/td2/longorfs/meta.yml", + "type": "module", + "meta": { + "name": "td2_longorfs", + "description": "TD2 identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly", + "keywords": ["td2", "orfs", "longorfs", "transcripts"], + "tools": [ + { + "td2": { + "description": "TD2 identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly", + "homepage": "https://github.com/Markusjsommer/TD2", + "documentation": "https://github.com/Markusjsommer/TD2", + "tool_dev_url": "https://github.com/Markusjsommer/TD2", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Fasta file containing the target transcript sequences", + "pattern": "*.{fasta}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ] + ], + "output": { + "orfs": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}/longest_orfs.{cds,gff3,pep}": { + "type": "file", + "description": "Files containing the longest ORFs predicted from the input transcript sequences", + "pattern": "${prefix}/longest_orfs.{cds,gff3,pep}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + }, + { + "edam": "http://edamontology.org/format_1975" + }, + { + "edam": "http://edamontology.org/format_1960" + } + ] + } + } + ] + ], + "versions_td2": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "TD2.LongOrfs": { + "type": "string", + "description": "The tool name" + } + }, + { + "1.0.6": { + "type": "string", + "description": "The tool version" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "TD2.LongOrfs": { + "type": "string", + "description": "The tool name" + } + }, + { + "1.0.6": { + "type": "string", + "description": "The tool version" + } + } + ] + ] + }, + "authors": ["@khersameesh24"], + "maintainers": ["@khersameesh24"] + } }, { - "name": "viralmetagenome", - "version": "1.1.1" + "name": "td2_predict", + "path": "modules/nf-core/td2/predict/meta.yml", + "type": "module", + "meta": { + "name": "td2_predict", + "description": "TD2 identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly", + "keywords": ["predict", "orfs", "coding regions", "td2.predict"], + "tools": [ + { + "td2": { + "description": "TD2 identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly", + "homepage": "https://github.com/Markusjsommer/TD2", + "documentation": "https://github.com/Markusjsommer/TD2", + "tool_dev_url": "https://github.com/Markusjsommer/TD2", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Transcripts fasta file", + "pattern": "*.fasta", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + }, + { + "orfs_dir": { + "type": "file", + "description": "Directory containing the ORF prediction files generated by the `td2_longorfs` module", + "pattern": "orfs_dir/", + "ontologies": [] + } + } + ] + ], + "output": { + "predictions": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}/*.TD2.{bed,cds,gff3,pep}": { + "type": "file", + "description": "Files containing the TD2 ORF predictions for the input transcript sequences", + "pattern": "${prefix}/*.TD2.{bed,cds,gff3,pep}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3003" + }, + { + "edam": "http://edamontology.org/format_1929" + }, + { + "edam": "http://edamontology.org/format_1975" + } + ] + } + } + ] + ], + "versions_td2": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "TD2.Predict": { + "type": "string", + "description": "The tool name" + } + }, + { + "1.0.6": { + "type": "string", + "description": "The tool version" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "TD2.Predict": { + "type": "string", + "description": "The tool name" + } + }, + { + "1.0.6": { + "type": "string", + "description": "The tool version" + } + } + ] + ] + }, + "authors": ["@khersameesh24"], + "maintainers": ["@khersameesh24"] + } }, { - "name": "viralrecon", - "version": "3.0.0" - } - ] - }, - { - "name": "quilt_quilt", - "path": "modules/nf-core/quilt/quilt/meta.yml", - "type": "module", - "meta": { - "name": "quilt_quilt", - "description": "QUILT is an R and C++ program for rapid genotype imputation from low-coverage sequence using a large reference panel.", - "keywords": [ - "imputation", - "low-coverage", - "genotype", - "genomics", - "vcf" - ], - "tools": [ - { - "quilt": { - "description": "Read aware low coverage whole genome sequence imputation from a reference panel", - "homepage": "https://github.com/rwdavies/quilt", - "documentation": "https://github.com/rwdavies/quilt", - "tool_dev_url": "https://github.com/rwdavies/quilt", - "doi": "10.1038/s41588-021-00877-0", - "licence": [ - "GPL v3" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bams": { - "type": "file", - "description": "(Mandatory) BAM/CRAM files", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } - }, - { - "bais": { - "type": "file", - "description": "(Mandatory) BAM/CRAM index files", - "pattern": "*.{bai}", - "ontologies": [] - } - }, - { - "bamlist": { - "type": "file", - "description": "(Optional) File with list of BAM/CRAM files to impute. One file per line.", - "pattern": "*.{txt}", - "ontologies": [] - } - }, - { - "samplename": { - "type": "file", - "description": "(Optional) File with list of samples names in the same order as in bamlist to impute. One file per line.", - "pattern": "*.{txt}", - "ontologies": [] - } - }, - { - "reference_haplotype_file": { - "type": "file", - "description": "(Mandatory) Reference haplotype file in IMPUTE format (file with no header and no rownames, one row per SNP, one column per reference haplotype, space separated, values must be 0 or 1)", - "pattern": "*.{hap.gz}", - "ontologies": [] - } - }, - { - "reference_legend_file": { - "type": "file", - "description": "(Mandatory) Reference haplotype legend file in IMPUTE format (file with one row per SNP, and a header including position for the physical position in 1 based coordinates, a0 for the reference allele, and a1 for the alternate allele).", - "pattern": "*.{legend.gz}", - "ontologies": [] - } - }, - { - "posfile": { - "type": "file", - "description": "(Optional) File with positions of where to impute, lining up one-to-one with genfile. File is tab separated with no header, one row per SNP, with col 1 = chromosome, col 2 = physical position (sorted from smallest to largest), col 3 = reference base, col 4 = alternate base. Bases are capitalized.", - "pattern": "*.{txt}", - "ontologies": [] - } - }, - { - "phasefile": { - "type": "file", - "description": "(Optional) File with truth phasing results. Supersedes genfile if both options given. File has a header row with a name for each sample, matching what is found in the bam file. Each subject is then a tab separated column, with 0 = ref and 1 = alt, separated by a vertical bar |, e.g. 0|0 or 0|1. Note therefore this file has one more row than posfile which has no header.", - "pattern": "*.{txt}", - "ontologies": [] - } - }, - { - "genfile": { - "type": "file", - "description": "(Optional) Path to gen file with high coverage results. Empty for no genfile. If both genfile and phasefile are given, only phasefile is used, as genfile (unphased genotypes) is derivative to phasefile (phased genotypes). File has a header row with a name for each sample, matching what is found in the bam file. Each subject is then a tab seperated column, with 0 = hom ref, 1 = het, 2 = hom alt and NA indicating missing genotype, with rows corresponding to rows of the posfile. Note therefore this file has one more row than posfile which has no header [default \\\"\\\"]", - "pattern": "*.{txt}", - "ontologies": [] - } - }, - { - "chr": { - "type": "string", - "description": "(Mandatory) What chromosome to run. Should match BAM headers." - } - }, - { - "regions_start": { - "type": "integer", - "description": "(Mandatory) When running imputation, where to start from. The 1-based position x is kept if regionStart <= x <= regionEnd." - } - }, - { - "regions_end": { - "type": "integer", - "description": "(Mandatory) When running imputation, where to stop." - } - }, - { - "ngen": { - "type": "integer", - "description": "Number of generations since founding or mixing. Note that the algorithm is relatively robust to this. Use nGen = 4 * Ne / K if unsure." - } - }, - { - "buffer": { - "type": "integer", - "description": "Buffer of region to perform imputation over. So imputation is run form regionStart-buffer to regionEnd+buffer, and reported for regionStart to regionEnd, including the bases of regionStart and regionEnd." - } - }, - { - "genetic_map": { - "type": "file", - "description": "(Optional) File with genetic map information, a file with 3 white-space delimited entries giving position (1-based), genetic rate map in cM/Mbp, and genetic map in cM. If no file included, rate is based on physical distance and expected rate (expRate).", - "pattern": "*.{txt,map}{,gz}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "(Optional) File with reference genome.", - "pattern": "*.{fa,fasta}", - "ontologies": [] - } - }, - { - "fasta_fai": { - "type": "file", - "description": "(Optional) File with reference genome index.", - "pattern": "*.{fai}", - "ontologies": [] - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.vcf.gz": { - "type": "file", - "description": "VCF file with both SNP annotation information and per-sample genotype information.", - "pattern": "*.{vcf.gz}", - "ontologies": [] - } - } - ] - ], - "tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.vcf.gz.tbi": { - "type": "file", - "description": "TBI file of the VCF.", - "pattern": "*.{vcf.gz.tbi}", - "ontologies": [] - } - } - ] - ], - "rdata": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "RData": { - "type": "directory", - "description": "Folder of RData objects generated during the imputation process.\n", - "pattern": "RData" - } - } - ] - ], - "plots": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "plots": { - "type": "directory", - "description": "Folder of plots generated during the imputation process.\n", - "pattern": "plots" - } - } - ] - ], - "versions_r_quilt": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "r-quilt": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "Rscript -e \"cat(as.character(packageVersion('QUILT')))\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_r_base": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "r-base": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "R --version | sed \"1!d; s/.*version //; s/ .*//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "r-quilt": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "Rscript -e \"cat(as.character(packageVersion('QUILT')))\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "r-base": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "R --version | sed \"1!d; s/.*version //; s/ .*//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@atrigila" - ], - "maintainers": [ - "@atrigila" - ] - }, - "pipelines": [ - { - "name": "phaseimpute", - "version": "1.1.0" - } - ] - }, - { - "name": "quilt_quilt2", - "path": "modules/nf-core/quilt/quilt2/meta.yml", - "type": "module", - "meta": { - "name": "quilt_quilt2", - "description": "QUILT2 is an R and C++ program for fast genotype imputation from low-coverage sequence using a large phased reference panel in VCF/BCF format.", - "keywords": [ - "imputation", - "low-coverage", - "genotype", - "genomics", - "vcf" - ], - "tools": [ - { - "quilt": { - "description": "Fast read-aware genotype imputation from low-coverage sequence using a large phased reference panel", - "homepage": "https://github.com/rwdavies/QUILT", - "documentation": "https://github.com/rwdavies/QUILT", - "tool_dev_url": "https://github.com/rwdavies/QUILT", - "doi": "10.1038/s41467-025-67218-1", - "licence": [ - "GPL v3" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bams": { - "type": "file", - "description": "(Mandatory) BAM/CRAM files", - "pattern": "*.{bam,cram}", - "ontologies": [] - } - }, - { - "bais": { - "type": "file", - "description": "(Mandatory) BAM/CRAM index files", - "pattern": "*.{bai,crai}", - "ontologies": [] - } - }, - { - "bamlist": { - "type": "file", - "description": "(Optional) File with list of BAM/CRAM files to impute. One file per line.", - "pattern": "*.{txt}", - "ontologies": [] - } - }, - { - "samplename": { - "type": "file", - "description": "(Optional) File with list of samples names in the same order as in bamlist to impute. One file per line.", - "pattern": "*.{txt}", - "ontologies": [] - } - }, - { - "reference_vcf_file": { - "type": "file", - "description": "(Mandatory) Phased reference panel VCF/BCF file for imputation.", - "pattern": "*.{vcf,vcf.gz,bcf}", - "ontologies": [] - } - }, - { - "reference_vcf_index": { - "type": "file", - "description": "(Mandatory) Index for the reference panel VCF file.", - "pattern": "*.{tbi,csi}", - "ontologies": [] - } - }, - { - "posfile": { - "type": "file", - "description": "(Optional) File with positions of where to impute, lining up one-to-one with genfile. File is tab separated with no header, one row per SNP, with col 1 = chromosome, col 2 = physical position (sorted from smallest to largest), col 3 = reference base, col 4 = alternate base. Bases are capitalized.", - "pattern": "*.{txt}", - "ontologies": [] - } - }, - { - "phasefile": { - "type": "file", - "description": "(Optional) File with truth phasing results. Supersedes genfile if both options given. File has a header row with a name for each sample, matching what is found in the bam file. Each subject is then a tab separated column, with 0 = ref and 1 = alt, separated by a vertical bar |, e.g. 0|0 or 0|1. Note therefore this file has one more row than posfile which has no header.", - "pattern": "*.{txt}", - "ontologies": [] - } - }, - { - "genfile": { - "type": "file", - "description": "(Optional) Path to gen file with high coverage results. Empty for no genfile. If both genfile and phasefile are given, only phasefile is used, as genfile (unphased genotypes) is derivative to phasefile (phased genotypes). File has a header row with a name for each sample, matching what is found in the bam file. Each subject is then a tab seperated column, with 0 = hom ref, 1 = het, 2 = hom alt and NA indicating missing genotype, with rows corresponding to rows of the posfile. Note therefore this file has one more row than posfile which has no header [default \"\"]", - "pattern": "*.{txt}", - "ontologies": [] - } - }, - { - "chr": { - "type": "string", - "description": "(Mandatory) What chromosome to run. Should match BAM headers." - } - }, - { - "regions_start": { - "type": "integer", - "description": "(Mandatory) When running imputation, where to start from. The 1-based position x is kept if regionStart <= x <= regionEnd." - } - }, - { - "regions_end": { - "type": "integer", - "description": "(Mandatory) When running imputation, where to stop." - } - }, - { - "ngen": { - "type": "integer", - "description": "Number of generations since founding or mixing. Note that the algorithm is relatively robust to this. Use nGen = 4 * Ne / K if unsure." - } - }, - { - "buffer": { - "type": "integer", - "description": "Buffer of region to perform imputation over. So imputation is run form regionStart-buffer to regionEnd+buffer, and reported for regionStart to regionEnd, including the bases of regionStart and regionEnd." - } - }, - { - "genetic_map": { - "type": "file", - "description": "(Optional) File with genetic map information, a file with 3 white-space delimited entries giving position (1-based), genetic rate map in cM/Mbp, and genetic map in cM. If no file included, rate is based on physical distance and expected rate (expRate).", - "pattern": "*.{txt,map}{,gz}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "(Optional) File with reference genome.", - "pattern": "*.{fa,fasta}", - "ontologies": [] - } - }, - { - "fasta_fai": { - "type": "file", - "description": "(Optional) File with reference genome index.", - "pattern": "*.{fai}", - "ontologies": [] - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.vcf.gz": { - "type": "file", - "description": "VCF file with both SNP annotation information and per-sample genotype information.", - "pattern": "*.{vcf.gz}", - "ontologies": [] - } - } - ] - ], - "tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.vcf.gz.tbi": { - "type": "file", - "description": "TBI file of the VCF.", - "pattern": "*.{vcf.gz.tbi}", - "ontologies": [] - } - } - ] - ], - "rdata": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "RData": { - "type": "directory", - "description": "Folder of RData objects generated during the imputation process.\n", - "pattern": "RData" - } - } - ] - ], - "plots": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "plots": { - "type": "directory", - "description": "Folder of plots generated during the imputation process.\n", - "pattern": "plots" - } - } - ] - ], - "versions_r_quilt": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "r-quilt": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "Rscript -e \"cat(as.character(packageVersion('QUILT')))\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_r_base": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "r-base": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "R --version | sed \"1!d; s/.*version //; s/ .*//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "r-quilt": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "Rscript -e \"cat(as.character(packageVersion('QUILT')))\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "r-base": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "R --version | sed \"1!d; s/.*version //; s/ .*//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@atrigila" - ], - "maintainers": [ - "@atrigila" - ] - } - }, - { - "name": "racon", - "path": "modules/nf-core/racon/meta.yml", - "type": "module", - "meta": { - "name": "racon", - "description": "Consensus module for raw de novo DNA assembly of long uncorrected reads", - "keywords": [ - "assembly", - "pacbio", - "nanopore", - "polish" - ], - "tools": [ - { - "racon": { - "description": "Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads.", - "homepage": "https://github.com/lbcb-sci/racon", - "documentation": "https://github.com/lbcb-sci/racon", - "tool_dev_url": "https://github.com/lbcb-sci/racon", - "doi": "10.1101/gr.214270.116", - "licence": [ - "MIT" - ], - "identifier": "biotools:Racon" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files. Racon expects single end reads", - "pattern": "*.{fastq,fastq.gz,fq,fq.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - }, - { - "assembly": { - "type": "file", - "description": "Genome assembly to be improved", - "pattern": "*.{fasta,fa}", - "ontologies": [] - } - }, - { - "paf": { - "type": "file", - "description": "Alignment in PAF format", - "pattern": "*.paf", - "ontologies": [] - } + "name": "telescope_assign", + "path": "modules/nf-core/telescope/assign/meta.yml", + "type": "module", + "meta": { + "name": "telescope_assign", + "description": "The telescope assign program finds overlapping reads between an alignment (SAM/BAM) and an annotation (GTF) then reassigns reads using a statistical model.", + "keywords": ["EM", "single-locus", "transcriptomics"], + "tools": [ + { + "telescope": { + "description": "Single locus resolution of Transposable ELEment expression", + "homepage": "https://github.com/mlbendall/telescope", + "documentation": "https://github.com/mlbendall/telescope", + "tool_dev_url": "https://github.com/mlbendall/telescope", + "doi": "10.1371/journal.pcbi.1006453", + "licence": ["MIT"], + "identifier": "biotools:Telescope-expression" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "bam": { + "type": "file", + "description": "Sorted BAM/CRAM/SAM file, File must be collated so that all alignments for a read pair appear sequentially in the file", + "pattern": "*.{bam,sam}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + }, + { + "edam": "http://edamontology.org/format_3462" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[id:'sample1' ]`\n" + } + }, + { + "gtf": { + "type": "file", + "description": "Annotation file which includes TE loci.", + "pattern": "*.{gtf}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2306" + } + ] + } + } + ] + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*{updated,other}.bam": { + "type": "file", + "description": "The updated SAM file contains those fragments that has at least 1 initial alignment to a transposable element.", + "pattern": "*{updated,other}.bam", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + } + ] + ], + "sam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*{updated,other}.sam": { + "type": "file", + "description": "The updated SAM file contains those fragments that has at least 1 initial alignment to a transposable element.", + "pattern": "*{updated,other}.bam", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3462" + } + ] + } + } + ] + ], + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "Statistical report associated with the run", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.log": { + "type": "file", + "description": "Log file for telescope run output.", + "pattern": "*.log" + } + } + ] + ], + "versions_telescope": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "telescope": { + "type": "string", + "description": "The tool name" + } + }, + { + "telescope --version | sed '1!d;s/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "telescope": { + "type": "string", + "description": "The tool name" + } + }, + { + "telescope --version | sed '1!d;s/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@hanalysis"], + "maintainers": ["@hanalysis"] } - ] - ], - "output": { - "improved_assembly": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_assembly_consensus.fasta.gz": { - "type": "file", - "description": "Improved genome assembly", - "pattern": "*_assembly_consensus.fasta.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "versions_racon": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "racon": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "racon --version 2>&1 | sed \"s/^.*v//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "racon": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "racon --version 2>&1 | sed \"s/^.*v//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] }, - "authors": [ - "@avantonder" - ], - "maintainers": [ - "@avantonder" - ] - }, - "pipelines": [ { - "name": "bacass", - "version": "2.6.0" + "name": "telogator2", + "path": "modules/nf-core/telogator2/meta.yml", + "type": "module", + "meta": { + "name": "telogator2", + "description": "Allele-specific telomere length estimation and TVR characterization from long reads", + "keywords": ["bam", "cram", "genomics", "telomere", "long-read", "pacbio", "nanopore"], + "tools": [ + { + "telogator2": { + "description": "A method for measuring allele-specific TL and characterizing telomere variant repeat (TVR) sequences from long reads", + "homepage": "https://github.com/zstephens/telogator2", + "documentation": "https://github.com/zstephens/telogator2", + "tool_dev_url": "https://github.com/zstephens/telogator2", + "doi": "10.1186/s12859-024-05807-5", + "licence": ["MIT"], + "args_id": "$args", + "identifier": "biotools:telogator2" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "BAM or CRAM file of long reads (PacBio or ONT)", + "pattern": "*.{bam,cram}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + }, + { + "reads_index": { + "type": "file", + "description": "Index file for the input BAM/CRAM", + "pattern": "*.{bai,crai}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Optional reference genome FASTA file", + "pattern": "*.{fa,fasta,fa.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + }, + { + "fai": { + "type": "file", + "description": "Optional FASTA index file", + "pattern": "*.fai", + "ontologies": [] + } + } + ] + ], + "output": { + "tlens": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "${prefix}/tlens_by_allele.tsv": { + "type": "file", + "description": "TSV file with telomere length estimates per allele", + "pattern": "*/tlens_by_allele.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "plots": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "${prefix}/*.png": { + "type": "file", + "description": "PNG plots including allele visualizations and violin plots", + "pattern": "*/*.png", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3603" + } + ] + } + } + ] + ], + "cmd": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "${prefix}/qc/cmd.txt": { + "type": "file", + "description": "Text file recording the telogator2 command that was run", + "pattern": "*/qc/cmd.txt", + "ontologies": [] + } + } + ] + ], + "stats": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "${prefix}/qc/stats.txt": { + "type": "file", + "description": "Text file with QC statistics including read counts and telomere read filtering", + "pattern": "*/qc/stats.txt", + "ontologies": [] + } + } + ] + ], + "qc_readlens": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "${prefix}/qc/qc_readlens.png": { + "type": "file", + "description": "PNG plot of read length distribution", + "pattern": "*/qc/qc_readlens.png", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3603" + } + ] + } + } + ] + ], + "readlens": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "${prefix}/qc/readlens.npz": { + "type": "file", + "description": "Numpy compressed array of read length data", + "pattern": "*/qc/readlens.npz", + "ontologies": [] + } + } + ] + ], + "rng": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "${prefix}/qc/rng.txt": { + "type": "file", + "description": "Text file recording the random seed used", + "pattern": "*/qc/rng.txt", + "ontologies": [] + } + } + ] + ], + "versions_telogator2": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "telogator2": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "telogator2 --version | sed 's/telogator2 //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "telogator2": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "telogator2 --version | sed 's/telogator2 //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@pinin4fjords"], + "maintainers": ["@pinin4fjords"] + } }, { - "name": "crisprseq", - "version": "2.3.0" - } - ] - }, - { - "name": "ragtag_patch", - "path": "modules/nf-core/ragtag/patch/meta.yml", - "type": "module", - "meta": { - "name": "ragtag_patch", - "description": "Homology-based assembly patching: Make continuous joins and fill gaps in 'target.fa' using sequences from 'query.fa'", - "keywords": [ - "assembly", - "consensus", - "ragtag", - "patch" - ], - "tools": [ - { - "ragtag": { - "description": "Fast reference-guided genome assembly scaffolding", - "homepage": "https://github.com/malonge/RagTag/wiki", - "documentation": "https://github.com/malonge/RagTag/wiki", - "tool_dev_url": "https://github.com/malonge/RagTag", - "doi": "10.1186/s13059-022-02823-7", - "licence": [ - "MIT" - ], - "identifier": "biotools:ragtag" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "target": { - "type": "file", - "description": "Target assembly", - "pattern": "*.{fasta,fasta.gz}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "query": { - "type": "file", - "description": "Query assembly", - "pattern": "*.{fasta,fasta.gz}", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "exclude": { - "type": "file", - "description": "list of target sequences to ignore", - "pattern": "*.txt", - "ontologies": [] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "skip": { - "type": "file", - "description": "list of query sequences to ignore", - "pattern": "*.txt", - "ontologies": [] - } - } - ] - ], - "output": { - "patch_fasta": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.patch.fasta": { - "type": "file", - "description": "FASTA file containing the patched assembly", - "pattern": "*.patch.fasta", - "ontologies": [] - } - } - ] - ], - "patch_agp": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.patch.agp": { - "type": "file", - "description": "AGP file defining how ragtag.patch.fasta is built", - "pattern": "*.patch.agp", - "ontologies": [] - } - } - ] - ], - "patch_components_fasta": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.comps.fasta": { - "type": "file", - "description": "The split target assembly and the renamed query assembly combined into one FASTA file. This file contains all components in ragtag.patch.agp", - "pattern": "*.comps.fasta", - "ontologies": [] - } - } - ] - ], - "assembly_alignments": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.ragtag.patch.asm.*": { - "type": "file", - "description": "Assembly alignment files", - "pattern": "*.ragtag.patch.asm.*", - "ontologies": [] - } - } - ] - ], - "target_splits_agp": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.ctg.agp": { - "type": "file", - "description": "An AGP file defining how the target assembly was split at gaps", - "pattern": "*.ctg.agp", - "ontologies": [] - } - } - ] - ], - "target_splits_fasta": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.ctg.fasta": { - "type": "file", - "description": "FASTA file containing the target assembly split at gaps", - "pattern": "*.ctg.fasta", - "ontologies": [] - } - } - ] - ], - "qry_rename_agp": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.rename.agp": { - "type": "file", - "description": "An AGP file defining the new names for query sequences", - "pattern": "*.rename.agp", - "ontologies": [] - } - } - ] - ], - "qry_rename_fasta": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.rename.fasta": { - "type": "file", - "description": "A FASTA file with the original query sequence, but with new names", - "pattern": "*.rename.fasta", - "ontologies": [] - } - } - ] - ], - "stderr": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.patch.err": { - "type": "file", - "description": "Standard error logging for all external RagTag commands", - "pattern": "*.patch.err", - "ontologies": [] - } - } - ] - ], - "versions_ragtag": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "ragtag": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "ragtag.py -v | sed 's/v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "ragtag": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "ragtag.py -v | sed 's/v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@nschan" - ], - "maintainers": [ - "@nschan" - ] - }, - "pipelines": [ - { - "name": "genomeassembler", - "version": "1.1.0" - } - ] - }, - { - "name": "ragtag_scaffold", - "path": "modules/nf-core/ragtag/scaffold/meta.yml", - "type": "module", - "meta": { - "name": "ragtag_scaffold", - "description": "Scaffolding is the process of ordering and orienting draft assembly (query)\nsequences into longer sequences. Gaps (stretches of \"N\" characters) are placed\nbetween adjacent query sequences to indicate the presence of unknown sequence.\nRagTag uses whole-genome alignments to a reference assembly to scaffold query sequences.\nRagTag does not alter input query sequence in any way and only orders and orients sequences, joining them with gaps.\n", - "keywords": [ - "scaffolding", - "ragtag", - "assembly", - "genome" - ], - "tools": [ - { - "ragtag": { - "description": "Fast reference-guided genome assembly scaffolding", - "homepage": "https://github.com/malonge/RagTag/wiki", - "documentation": "https://github.com/malonge/RagTag/wiki", - "tool_dev_url": "https://github.com/malonge/RagTag", - "doi": "10.1186/s13059-022-02823-7", - "licence": [ - "MIT" - ], - "identifier": "biotools:ragtag" + "name": "telomerehunter", + "path": "modules/nf-core/telomerehunter/meta.yml", + "type": "module", + "meta": { + "name": "telomerehunter", + "description": "In silico estimation of telomere content and composition from cancer genomes", + "keywords": ["bam", "genomics", "telomere", "telomerehunter", "cancer"], + "tools": [ + { + "telomerehunter": { + "description": "In silico estimation of telomere content and composition from cancer genomes", + "homepage": "https://github.com/linasieverling/TelomereHunter", + "documentation": "https://github.com/linasieverling/TelomereHunter", + "tool_dev_url": "https://github.com/linasieverling/TelomereHunter", + "doi": "10.1186/s12859-019-2851-0", + "licence": ["GPL v3"], + "args_id": "$args", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "tumor_bam": { + "type": "file", + "description": "Indexed BAM/CRAM file of the tumor sample. CRAM files are automatically converted to BAM (telomerehunter uses pysam in BAM-only mode).", + "pattern": "*.{bam,cram}", + "ontologies": [] + } + }, + { + "tumor_bai": { + "type": "file", + "description": "BAM/CRAM index file for the tumor sample", + "pattern": "*.{bai,crai}", + "ontologies": [] + } + }, + { + "control_bam": { + "type": "file", + "description": "Optional indexed BAM/CRAM file of the control sample", + "pattern": "*.{bam,cram}", + "ontologies": [] + } + }, + { + "control_bai": { + "type": "file", + "description": "Optional BAM/CRAM index file for the control sample", + "pattern": "*.{bai,crai}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference FASTA file (required when input is CRAM)", + "pattern": "*.{fa,fasta,fna}", + "ontologies": [] + } + }, + { + "fai": { + "type": "file", + "description": "Reference FASTA index", + "pattern": "*.fai", + "ontologies": [] + } + }, + { + "cytoband": { + "type": "file", + "description": "Optional cytoband file for the reference genome.\nWhen not provided ([]), telomerehunter uses its bundled hg19 cytoband.\nMust be supplied for hg38 data to avoid an IndexError caused by\nchromosomes that are longer in hg38 than hg19.\n", + "pattern": "*.txt", + "ontologies": [] + } + } + ] + ], + "output": { + "summary": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "${prefix}/${prefix}_summary.tsv": { + "type": "file", + "description": "Combined summary TSV with telomere content estimates", + "pattern": "*_summary.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "tumor": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "${prefix}/tumor_TelomerCnt_${prefix}/": { + "type": "directory", + "description": "Directory with tumor telomere analysis results", + "ontologies": [] + } + } + ] + ], + "control": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "${prefix}/control_TelomerCnt_${prefix}/": { + "type": "directory", + "description": "Directory with control telomere analysis results", + "ontologies": [] + } + } + ] + ], + "versions_telomerehunter": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "telomerehunter": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pip show telomerehunter | sed -n 's/^Version: //p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_samtools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "samtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "samtools --version |& sed '1!d; s/^.*samtools //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "telomerehunter": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pip show telomerehunter | sed -n 's/^Version: //p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "samtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "samtools --version |& sed '1!d; s/^.*samtools //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@pinin4fjords"], + "maintainers": ["@pinin4fjords"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "assembly": { - "type": "file", - "description": "Assembly to be scaffolded", - "pattern": "*.{fasta,fasta.gz,fa,fa.gz}", - "ontologies": [] - } + }, + { + "name": "telseq", + "path": "modules/nf-core/telseq/meta.yml", + "type": "module", + "meta": { + "name": "telseq", + "description": "Telseq: a software for calculating telomere length", + "keywords": ["bam", "cram", "genomics", "samtools", "telomere", "telseq"], + "tools": [ + { + "telseq": { + "description": "A software for calculating telomere length", + "homepage": "https://github.com/zd1/telseq", + "documentation": "https://github.com/zd1/telseq", + "tool_dev_url": "https://github.com/zd1/telseq", + "doi": "10.1093/nar/gku181", + "licence": ["GPL v3"], + "args_id": "$args", + "identifier": "" + } + }, + { + "samtools": { + "description": "Tools for dealing with SAM, BAM and CRAM files", + "homepage": "http://www.htslib.org/", + "documentation": "http://www.htslib.org/doc/samtools.html", + "tool_dev_url": "https://github.com/samtools/samtools", + "doi": "10.1093/bioinformatics/btp352", + "licence": ["MIT"], + "identifier": "biotools:samtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}", + "ontologies": [] + } + }, + { + "bai": { + "type": "file", + "description": "bam index file", + "pattern": "*.{bai,crai}", + "ontologies": [] + } + }, + { + "bed": { + "type": "file", + "description": "Optional exome regions in BED format. These regions will be excluded", + "pattern": "*.bed", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference genome file", + "pattern": "*.{fa,fasta}", + "ontologies": [] + } + }, + { + "fai": { + "type": "file", + "description": "Fasta index file", + "pattern": "*.fai", + "ontologies": [] + } + } + ] + ], + "output": { + "output": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.telseq.tsv": { + "type": "file", + "description": "Telseq output", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_telseq": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "telseq": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "echo 0.0.2": { + "type": "eval", + "description": "The expression to obtain the version of telseq" + } + } + ] + ], + "versions_samtools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "samtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "samtools --version | sed -n '1s/samtools //p'": { + "type": "eval", + "description": "The expression to obtain the version of samtools" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "telseq": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "echo 0.0.2": { + "type": "eval", + "description": "The expression to obtain the version of telseq" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "samtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "samtools --version | sed -n '1s/samtools //p'": { + "type": "eval", + "description": "The expression to obtain the version of samtools" + } + } + ] + ] + }, + "authors": ["@lindenb"], + "maintainers": ["@lindenb"] } - 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}, - { - "name": "rastair_mbias", - "path": "modules/nf-core/rastair/mbias/meta.yml", - "type": "module", - "meta": { - "name": "rastair_mbias", - "description": "Assess C->T conversion as a readout for methylation on a per-read-position basis.", - "keywords": [ - "methylation", - "rastair", - "C->T conversion", - "bisulphite", - "bisulfite", - "bam", - "mCtoT", - "mbias", - "methylation bias" - ], - "tools": [ - { - "rastair": { - "description": "A tool for rapid genome-wide assessment of positive C->T conversion as a readout for methylation.\n", - "homepage": "https://bitbucket.org/bsblabludwig/rastair/src/master/", - "documentation": "https://bitbucket.org/bsblabludwig/rastair/src/master/README.md", - "licence": [ - "GPL-3.0" - ] - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM file", - "pattern": "*.{bam,cram}" - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bai": { - "type": "file", - "description": "BAM/CRAM index file", - "pattern": "*.{bai,crai}" - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input genome fasta file", - "pattern": "*.{fasta,fa}" - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + }, + { + "name": "tiddit_cov", + "path": "modules/nf-core/tiddit/cov/meta.yml", + "type": "module", + "meta": { + "name": "tiddit_cov", + "description": "Computes the coverage of different regions from the bam file.", + "keywords": ["coverage", "bam", "statistics", "chromosomal rearrangements"], + "tools": [ + { + "tiddit": { + "description": "TIDDIT - structural variant calling.", + "homepage": "https://github.com/SciLifeLab/TIDDIT", + "documentation": "https://github.com/SciLifeLab/TIDDIT/blob/master/README.md", + "doi": "10.12688/f1000research.11168.1", + "licence": ["GPL v3"], + "identifier": "biotools:tiddit" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM file", + "pattern": "*.{bam,cram}", + "ontologies": [] + } + }, + { + "index": { + "type": "file", + "description": "Index of BAM/CRAM file", + "pattern": "*.{bai,crai,csi}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3327" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference genome file. Only needed when passing in CRAM instead of BAM.\nIf not using CRAM, please pass an empty file instead.\n", + "pattern": "*.fasta", + "ontologies": [] + } + } + ] + ], + "output": { + "cov": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.bed": { + "type": "file", + "description": "The coverage of different regions in bed format. Optional.", + "pattern": "*.bed", + "ontologies": [] + } + } + ] + ], + "wig": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.wig": { + "type": "file", + "description": "The coverage of different regions in WIG format. Optional.", + "pattern": "*.wig", + "ontologies": [] + } + } + ] + ], + "versions_tiddit": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "tiddit": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "tiddit | sed -n 's/^usage: tiddit-//; s/ .*//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "tiddit": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "tiddit | sed -n 's/^usage: tiddit-//; s/ .*//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@projectoriented", "@ramprasadn"], + "maintainers": ["@projectoriented", "@ramprasadn"] }, - { - "fai": { - "type": "file", - "description": "FASTA index file", - "pattern": "*.fai" - } - } - ] - ], - "output": { - "txt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.rastair_mbias.txt": { - "type": "file", - "description": "Text file from Rastair mbias containing per-read-position C->T conversion metrics.", - "pattern": "*.rastair_mbias.txt" - } - } + "pipelines": [ + { + "name": "raredisease", + "version": "3.0.0" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@eduard-casas" - ], - "maintainers": [ - "@eduard-casas" - ] - }, - "pipelines": [ - { - "name": "methylseq", - "version": "4.2.0" - } - ] - }, - { - "name": "rastair_mbias_parser", - "path": "modules/nf-core/rastair/mbias_parser/meta.yml", - "type": "module", - "meta": { - "name": "rastair_mbias_parser", - "description": "Parses Rastair mbias output to assess the ideal cutoff for read trimming and reports the values.", - "keywords": [ - "methylation", - "rastair", - "C->T conversion", - "bisulphite", - "bisulfite", - "bam", - "mCtoT", - "mbias", - "methylation bias", - "parser", - "cutoff" - ], - "tools": [ - { - "rastair": { - "description": "A tool for rapid genome-wide assessment of C->T conversion as a readout for methylation. The module uses R scripts bundled with Rastair.\n", - "homepage": "https://bitbucket.org/bsblabludwig/rastair/src/master/", - "documentation": "https://bitbucket.org/bsblabludwig/rastair/src/master/README.md", - "licence": [ - "GPL-3.0" - ] - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + }, + { + "name": "tiddit_sv", + "path": "modules/nf-core/tiddit/sv/meta.yml", + "type": "module", + "meta": { + "name": "tiddit_sv", + "description": "Identify chromosomal rearrangements.", + "keywords": ["structural", "variants", "vcf"], + "tools": [ + { + "sv": { + "description": "Search for structural variants.", + "homepage": "https://github.com/SciLifeLab/TIDDIT", + "documentation": "https://github.com/SciLifeLab/TIDDIT/blob/master/README.md", + "doi": "10.12688/f1000research.11168.1", + "licence": ["GPL-3.0-or-later"], + "identifier": "biotools:tiddit" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM file", + "pattern": "*.{bam,cram}", + "ontologies": [] + } + }, + { + "input_index": { + "type": "file", + "description": "BAM/CRAM index file", + "pattern": "*.{bai,crai}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test_fasta']`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input FASTA file", + "pattern": "*.{fasta,fa}", + "ontologies": [] + } + }, + { + "fai": { + "type": "file", + "description": "Input FASTA index file", + "pattern": "*.{fai}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information from bwa index\ne.g. `[ id:'test_bwa-index' ]`\n" + } + }, + { + "bwa_index": { + "type": "file", + "description": "BWA genome index files", + "pattern": "Directory containing BWA index *.{amb,ann,bwt,pac,sa}", + "ontologies": [] + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.vcf": { + "type": "file", + "description": "vcf", + "pattern": "*.{vcf}", + "ontologies": [] + } + } + ] + ], + "ploidy": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.ploidies.tab": { + "type": "file", + "description": "tab", + "pattern": "*.{ploidies.tab}", + "ontologies": [] + } + } + ] + ], + "versions_tiddit": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "tiddit": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "tiddit | sed -n 's/^usage: tiddit-//; s/ .*//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "tiddit": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "tiddit | sed -n 's/^usage: tiddit-//; s/ .*//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@maxulysse"], + "maintainers": ["@maxulysse"] }, - { - "rastair_mbias_txt": { - "type": "file", - "description": "Text file from `rastair mbias`", - "pattern": "*.rastair_mbias.txt" - } - } - ] - ], - "output": { - "mbias_processed_pdf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.rastair_mbias_processed.pdf": { - "type": "file", - "description": "PDF plot of the methylation bias across reads.", - "pattern": "*.rastair_mbias_processed.pdf" - } - } - ] - ], - "mbias_processed_csv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.rastair_mbias_processed.csv": { - "type": "file", - "description": "CSV file containing the recommended trimming values for OT and OB reads.", - "pattern": "*.rastair_mbias_processed.csv" - } - } - ] - ], - "mbias_processed_str": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "trim_OT": { - "type": "string", - "description": "Recommended trimming value for Original Top (OT) reads." - } - }, - { - "trim_OB": { - "type": "string", - "description": "Recommended trimming value for Original Bottom (OB) reads." - } - } + "pipelines": [ + { + "name": "raredisease", + "version": "3.0.0" + }, + { + "name": "sarek", + "version": "3.8.1" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@eduard-casas" - ], - "maintainers": [ - "@eduard-casas" - ] - } - }, - { - "name": "rastair_mbiasparser", - "path": "modules/nf-core/rastair/mbiasparser/meta.yml", - "type": "module", - "meta": { - "name": "rastair_mbiasparser", - "description": "Parses Rastair mbias output to assess the ideal cutoff for read trimming and reports the values.", - "keywords": [ - "methylation", - "rastair", - "C->T conversion", - "bisulphite", - "bisulfite", - "bam", - "mCtoT", - "mbias", - "methylation bias", - "mbiasparser", - "cutoff" - ], - "tools": [ - { - "rastair": { - "description": "A tool for rapid genome-wide assessment of C->T conversion as a readout for methylation. The module uses R scripts bundled with Rastair.\n", - "homepage": "https://bitbucket.org/bsblabludwig/rastair/src/master/", - "documentation": "https://bitbucket.org/bsblabludwig/rastair/src/master/README.md", - "licence": [ - "GPL-3.0" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + }, + { + "name": "tidk_explore", + "path": "modules/nf-core/tidk/explore/meta.yml", + "type": "module", + "meta": { + "name": "tidk_explore", + "description": "`tidk explore` attempts to find the simple telomeric repeat unit in the genome provided.\nIt will report this repeat in its canonical form (e.g. TTAGG -> AACCT).\n", + "keywords": ["genomics", "telomere", "search"], + "tools": [ + { + "tidk": { + "description": "tidk is a toolkit to identify and visualise telomeric repeats in genomes", + "homepage": "https://github.com/tolkit/telomeric-identifier", + "documentation": "https://github.com/tolkit/telomeric-identifier", + "tool_dev_url": "https://github.com/tolkit/telomeric-identifier", + "doi": "10.5281/zenodo.10091385", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The input fasta file", + "pattern": "*.{fsa,fa,fasta}", + "ontologies": [] + } + } + ] + ], + "output": { + "explore_tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.tidk.explore.tsv": { + "type": "file", + "description": "Telomeres and their frequencies in TSV format", + "pattern": "*.tidk.explore.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "top_sequence": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.top.sequence.txt": { + "type": "file", + "description": "The most frequent telomere sequence if one or more\nsequences are identified by the toolkit\n", + "pattern": "*.top.sequence.txt", + "ontologies": [] + } + } + ] + ], + "versions_tidk": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "tidk": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "tidk --version | sed 's/tidk //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "tidk": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "tidk --version | sed 's/tidk //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@GallVp"], + "maintainers": ["@GallVp"] }, - { - "rastair_mbias_txt": { - "type": "file", - "description": "Text file from `rastair mbias`", - "pattern": "*.rastair_mbias.txt", - "ontologies": [] - } - } - ] - ], - "output": { - "mbias_processed_pdf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.rastair_mbias_processed.pdf": { - "type": "file", - "description": "PDF plot of the methylation bias across reads.", - "pattern": "*.rastair_mbias_processed.pdf", - "ontologies": [] - } - } - ] - ], - "mbias_processed_csv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.rastair_mbias_processed.csv": { - "type": "file", - "description": "CSV file containing the recommended trimming values for OT and OB reads.", - "pattern": "*.rastair_mbias_processed.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "mbias_processed_str": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "TRIM_OT": { - "type": "string", - "description": "Recommended trimming value for Original Top (OT) reads." - } - }, - { - "TRIM_OB": { - "type": "string", - "description": "Recommended trimming value for Original Bottom (OB) reads." - } - } + "pipelines": [ + { + "name": "genomeqc", + "version": "dev" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@eduard-casas" - ], - "maintainers": [ - "@eduard-casas" - ] - }, - "pipelines": [ - { - "name": "methylseq", - "version": "4.2.0" - } - ] - }, - { - "name": "rastair_methylkit", - "path": "modules/nf-core/rastair/methylkit/meta.yml", - "type": "module", - "meta": { - "name": "rastair_methylkit", - "description": "Parses rastair call output and converts it into a MethylKit-compatible format.", - "keywords": [ - "methylation", - "rastair", - "C->T conversion", - "bisulphite", - "bisulfite", - "mCtoT", - "methylkit", - "convert", - "parser" - ], - "tools": [ - { - "rastair": { - "description": "A tool for rapid genome-wide assessment of C->T conversion as a readout for methylation. The module uses a script bundled with Rastair to convert formats.\n", - "homepage": "https://bitbucket.org/bsblabludwig/rastair/src/master/", - "documentation": "https://bitbucket.org/bsblabludwig/rastair/src/master/README.md", - "licence": [ - "GPL-3.0" - ] - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + }, + { + "name": "tidk_plot", + "path": "modules/nf-core/tidk/plot/meta.yml", + "type": "module", + "meta": { + "name": "tidk_plot", + "description": "Plots telomeric repeat frequency against sliding window location\nusing data produced by `tidk/search`\n", + "keywords": ["genomics", "telomere", "search", "plot"], + "tools": [ + { + "tidk": { + "description": "tidk is a toolkit to identify and visualise telomeric repeats in genomes", + "homepage": "https://github.com/tolkit/telomeric-identifier", + "documentation": "https://github.com/tolkit/telomeric-identifier", + "tool_dev_url": "https://github.com/tolkit/telomeric-identifier", + "doi": "10.5281/zenodo.10091385", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "tsv": { + "type": "file", + "description": "Search results in TSV format from `tidk search`", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "output": { + "svg": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.svg": { + "type": "file", + "description": "Telomere search plot", + "pattern": "*.svg", + "ontologies": [] + } + } + ] + ], + "versions_tidk": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "tidk": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "tidk --version | sed 's/tidk //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "tidk": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "tidk --version | sed 's/tidk //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@GallVp"], + "maintainers": ["@GallVp"] }, - 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{ - "genome_size": { - "type": "string", - "description": "Genome size of the species" - } - } - ], - { - "depth_cutoff": { - "type": "integer", - "description": "Depth of coverage cutoff" - } - } - ], - "output": { - "reads": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.fastq.gz": { - "type": "file", - "description": "Reads with subsampled coverage", - "pattern": "*.fastq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "versions_rasusa": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "rasusa": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "rasusa --version 2>&1 | sed -e \"s/rasusa //g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - 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The approach uses evolutionary theory applied to read counts data from whole-genome sequencing assays.", + "keywords": ["genomics", "tumour contamination", "normal", "purity"], + "tools": [ + { + "tinc": { + "description": "TINC is a package that implements algorithms to determine the contamination of a bulk sequencing sample in the context of cancer studies (matched tumour/ normal). The contamination estimated by TINC can be either due to normal cells sampled in the tumour biopsy or to tumour cells in the normal biopsy. The former case is traditionally called purity, or cellularity, and a number of tools exist to estimate it. The latter case is less common, and that is the main reason TINC has been developed. For this reason, the package takes name TINC, Tumour-in-Normal contamination. TINC is part of the evoverse, a package that gathers multiple R packages to implement Cancer Evolution analyses.", + "homepage": "https://caravagnalab.github.io/TINC/", + "documentation": "https://caravagnalab.github.io/TINC/", + "tool_dev_url": "https://github.com/caravagnalab/TINC/", + "doi": "10.1038/s41467-023-44158-2", + "licence": ["GPL v3"], + "identifier": "biotools:r-tinc" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', tumour_sample:'tumour_sample1_name', normal_sample:'normal_sample_name' ]`\n" + } + }, + { + "cna_rds": { + "type": "file", + "description": "RDS file with copy number segments and purity", + "ontologies": [] + } + }, + { + "vcf_rds": { + "type": "file", + "description": "RDS file with vcf calls from tumour and normal sample", + "ontologies": [] + } + } + ] + ], + "output": { + "rds": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', tumour_sample:'tumour_sample1_name', normal_sample:'normal_sample_name' ]`\n" + } + }, + { + "*_fit.rds": { + "type": "file", + "description": "RDS file with the fit results", + "pattern": "*.{rds}", + "ontologies": [] + } + } + ] + ], + "plot_rds": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', tumour_sample:'tumour_sample1_name', normal_sample:'normal_sample_name' ]`\n" + } + }, + { + "*_plot.rds": { + "type": "file", + "description": "RDS file with the plot of the results", + "pattern": "*.{rds}", + "ontologies": [] + } + } + ] + ], + "plot_pdf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', tumour_sample:'tumour_sample1_name', normal_sample:'normal_sample_name' ]`\n" + } + }, + { + "*.pdf": { + "type": "file", + "description": "PDF file with the plot of the results", + "pattern": "*.{pdf}", + "ontologies": [] + } + } + ] + ], + "tinc_csv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', tumour_sample:'tumour_sample1_name', normal_sample:'normal_sample_name' ]`\n" + } + }, + { + "*_qc.csv": { + "type": "file", + "description": "CSV file with the output of TINC qc flag", + "pattern": "*.{csv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@valerianilucrezia"], + "maintainers": ["@valerianilucrezia"] }, - 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Required if `eff_genome_size` is not provided.\n", + "pattern": "*.bed", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3003" + } + ] + } + }, + { + "eff_genome_size": { + "type": "string", + "description": "Effective genome size (in bases). Required if `bed` is not provided.\n" + } + }, + { + "var_config": { + "type": "file", + "description": "YAML file defining variant annotation parsing rules. See [example here](modules/nf-core/tmb/pytmb/tests/snpeff.yml).\n", + "pattern": "*.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + }, + { + "db_config": { + "type": "file", + "description": "YAML file defining the database configuration for variant annotations. See [example here](modules/nf-core/tmb/pytmb/tests/haplotc.yml).\n", + "pattern": "*.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + ], + "output": { + "tmb_log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.log": { + "type": "file", + "description": "Log file containing TMB calculation details\n" + } + } + ] + ], + "export_vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_export.vcf.gz": { + "type": "file", + "description": "Export VCF file containing TMB annotations\n", + "pattern": "*_export.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + } + ] + } + } + ] + ], + "debug_vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_debug.vcf.gz": { + "type": "file", + "description": "Debug VCF file containing detailed TMB calculation information\n", + "pattern": "*_debug.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + } + ] + } + } + ] + ], + "versions_tmb": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "tmb": { + "type": "string", + "description": "The name of the tool" + } + }, + { + " pyTMB.py --version | awk '{print \\$2}' | tr -d '()' ": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "tmb": { + "type": "string", + "description": "The name of the tool" + } + }, + { + " pyTMB.py --version | awk '{print \\$2}' | tr -d '()' ": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@georgiakes"], + "maintainers": ["@georgiakes"] } - ] - ], - "output": { - "fasta": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', suffix:'bacteria' ]\n" - } - }, - { - "*.fasta.gz": { - "type": "file", - "description": "Assembled FASTA file", - "pattern": "*.fasta.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "gfa": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', suffix:'bacteria' ]\n" - } - }, - { - "*.gfa.gz": { - "type": "file", - "description": "Repeat graph", - "pattern": "*.gfa.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "versions_raven": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "raven": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "raven --version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "raven": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "raven --version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@fmalmeida" - ], - "maintainers": [ - "@fmalmeida" - ] - }, - "pipelines": [ - { - "name": "bacass", - "version": "2.6.0" - } - ] - }, - { - "name": "raw2ometiff", - "path": "modules/nf-core/raw2ometiff/meta.yml", - "type": "module", - "meta": { - "name": "raw2ometiff", - "description": "write your description here", - "keywords": [ - "ome", - "tiff", - "imaging" - ], - "tools": [ - { - "raw2ometiff": { - "description": "Java application to convert a directory of tiles to an OME-TIFF pyramid.", - "homepage": "https://github.com/glencoesoftware/raw2ometiff", - "documentation": "https://github.com/glencoesoftware/raw2ometiff", - "tool_dev_url": "https://github.com/glencoesoftware/raw2ometiff", - "licence": [ - "GPL-2.0" - ], - "identifier": "biotools:raw2ometiff" + }, + { + "name": "topas_gencons", + "path": "modules/nf-core/topas/gencons/meta.yml", + "type": "module", + "meta": { + "name": "topas_gencons", + "description": "Create fasta consensus with TOPAS toolkit with options to penalize substitutions for typical DNA damage present in ancient DNA", + "keywords": ["consensus", "fasta", "ancient DNA"], + "tools": [ + { + "topas": { + "description": "This toolkit allows the efficient manipulation of sequence data in various ways. It is organized into modules: The FASTA processing modules, the FASTQ processing modules, the GFF processing modules and the VCF processing modules.", + "homepage": "https://github.com/subwaystation/TOPAS", + "documentation": "https://github.com/subwaystation/TOPAS/wiki/Overview-Modules", + "tool_dev_url": "https://github.com/subwaystation/TOPAS", + "doi": "10.1038/s41598-017-17723-1", + "licence": ["CC-BY"], + "identifier": "biotools:TOPAS" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "Gzipped compressed vcf file generated with GATK UnifiedGenotyper containing the called snps", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf_indels": { + "type": "file", + "description": "Optional gzipped compressed vcf file generated with GATK UnifiedGenotyper containing the called indels", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reference": { + "type": "file", + "description": "Fasta file of reference genome", + "pattern": "*.fasta", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Optional index for the fasta file of reference genome", + "pattern": "*.fai", + "ontologies": [] + } + } + ], + { + "vcf_output": { + "type": "boolean", + "description": "Boolean value to indicate if a compressed vcf file with the consensus calls included as SNPs should be produced" + } + } + ], + "output": { + "fasta": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fasta.gz": { + "type": "file", + "description": "Gzipped consensus fasta file with bases under threshold replaced with Ns", + "pattern": "*.fasta.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "Gzipped vcf file with updated calls for the SNPs used in the consensus generation and for bases under threshold replaced with Ns", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "ccf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.ccf": { + "type": "file", + "description": "Statistics file containing information about the consensus calls in the fasta file", + "pattern": "*.ccf", + "ontologies": [] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "Log file", + "pattern": "*.log", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@aidaanva"], + "maintainers": ["@aidaanva"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } + }, + { + "name": "toulligqc", + "path": "modules/nf-core/toulligqc/meta.yml", + "type": "module", + "meta": { + "name": "toulligqc", + "description": "A post sequencing QC tool for Oxford Nanopore sequencers", + "keywords": ["nanopore sequencing", "quality control", "genomics"], + "tools": [ + { + "toulligqc": { + "description": "A post sequencing QC tool for Oxford Nanopore sequencers", + "homepage": "https://github.com/GenomiqueENS/toulligQC", + "documentation": "https://github.com/GenomiqueENS/toulligQC", + "tool_dev_url": "https://github.com/GenomiqueENS/toulligQC", + "licence": ["CECILL-2.1"], + "identifier": "biotools:ToulligQC" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "ontfile": { + "type": "file", + "description": "Input ONT file", + "pattern": "*.{fastq,fastq.gz,fq,fq.gz,txt,txt.gz,bam}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ] + ], + "output": { + "report_data": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*/*.data": { + "type": "file", + "description": "Report data emitted from toulligqc", + "pattern": "*.data", + "ontologies": [] + } + } + ] + ], + "report_html": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*/*.html": { + "type": "file", + "description": "Report data in html format", + "pattern": "*.html", + "ontologies": [] + } + } + ] + ], + "plots_html": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*/images/*.html": { + "type": "file", + "description": "Plots emitted in html format", + "pattern": "*.html", + "ontologies": [] + } + } + ] + ], + "plotly_js": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*/images/plotly.min.js": { + "type": "file", + "description": "Plots emitted from toulligqc", + "pattern": "plotly.min.js", + "ontologies": [] + } + } + ] + ], + "versions_toulligqc": [ + [ + { + "${task.process}": { + "type": "string", + "description": "Name of the process" + } + }, + { + "toulligqc": { + "type": "string", + "description": "Name of the tool" + } + }, + { + "toulligqc --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "Name of the process" + } + }, + { + "toulligqc": { + "type": "string", + "description": "Name of the tool" + } + }, + { + "toulligqc --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@Salome-Brunon"], + "maintainers": ["@Salome-Brunon"] }, - { - "zarr_dir": { - "type": "directory", - "description": "Tile directory must contain a full pyramid in a Zarr container.", - "pattern": "*.{zarr}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3915" - } - ] - } - } - ] - ], - "output": { - "ometiff": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } - }, - { - "*.ome.tiff": { - "type": "file", - "description": "OME-TIFF pyramid", - "pattern": "*.ome.tiff", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3727" - } - ] - } - } - ] - ], - "versions_raw2ometiff": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "raw2ometiff": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "raw2ometiff --version |& sed -n \"1s/Version = //p\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_bioformats": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bioformats": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "raw2ometiff --version |& sed -n \"2s/Bio-Formats version = //p\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "raw2ometiff": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "raw2ometiff --version |& sed -n \"1s/Version = //p\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bioformats": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "raw2ometiff --version |& sed -n \"2s/Bio-Formats version = //p\"": { - 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"GPL v2-or-later" - ], - "identifier": "" + }, + { + "name": "traitar_pfamget", + "path": "modules/nf-core/traitar/pfamget/meta.yml", + "type": "module", + "meta": { + "name": "traitar_pfamget", + "description": "Download PFAM database for traitar phenotype prediction", + "keywords": ["pfam", "database", "phenotype", "traitar"], + "tools": [ + { + "traitar": { + "description": "Microbial trait prediction from genome sequences", + "homepage": "https://github.com/hzi-bifo/traitar3", + "documentation": "https://github.com/hzi-bifo/traitar3", + "tool_dev_url": "https://github.com/hzi-bifo/traitar3", + "licence": ["GPL v3"], + "identifier": "biotools:traitar" + } + } + ], + "output": { + "pfam_db": [ + { + "pfam_data": { + "type": "directory", + "description": "PFAM database directory containing HMM profiles", + "pattern": "pfam_data" + } + } + ], + "versions_traitar": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "traitar": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "traitar --version 2>&1 | tail -1": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "traitar": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "traitar --version 2>&1 | tail -1": { + "type": "eval", + "description": "Version extraction command" + } + } + ] + ] + }, + "authors": ["@brovolia"], + "maintainers": ["@brovolia"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information (e.g. [ id:'sample1' ])" - } - }, - { - "alignment": { - "type": "file", - "description": "A FASTA format multiple sequence alignment file", - "pattern": "*.{fasta,fas,fa,mfa}", - "ontologies": [] - } - }, - { - "model": { - "type": "string", - "description": "The substitution model to use for the phylogenetic inference" - } + }, + { + "name": "traitar_run", + "path": "modules/nf-core/traitar/run/meta.yml", + "type": "module", + "meta": { + "name": "traitar", + "description": "Traitar3 - predict microbial phenotypes from genomic sequences using protein families", + "keywords": ["phenotype", "prediction", "microbial", "traits", "genomics", "protein families"], + "tools": [ + { + "traitar": { + "description": "Traitar3 - the microbial trait analyzer (for Python3)", + "homepage": "https://github.com/nick-youngblut/traitar3", + "documentation": "https://github.com/nick-youngblut/traitar3", + "tool_dev_url": "https://github.com/nick-youngblut/traitar3", + "doi": "10.1128/mSystems.00101-16", + "licence": ["GPL-3.0"], + "identifier": "biotools:traitar" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input sequences in FASTA format (nucleotides, genes, or annotation summary), can be gzipped", + "pattern": "*.{fa,fasta,faa,fna,fa.gz,fasta.gz,faa.gz,fna.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + { + "input_type": { + "type": "string", + "description": "Input type specifying the format of input sequences (from_nucleotides, from_genes, or from_annotation_summary)" + } + }, + { + "pfam_db": { + "type": "directory", + "description": "PFAM database directory created by traitar/pfamget module or downloaded from https://ftp.ebi.ac.uk/pub/databases/Pfam/\n", + "pattern": "pfam_data" + } + } + ], + "output": { + "predictions_combined": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*/phenotype_prediction/predictions_majority-vote_combined.txt": { + "type": "file", + "description": "Combined phenotype predictions using majority voting", + "ontologies": [] + } + } + ] + ], + "predictions_single_votes": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*/phenotype_prediction/predictions_single-votes_combined.txt": { + "type": "file", + "description": "Single vote phenotype predictions", + "ontologies": [] + } + } + ] + ], + "predictions_flat": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*/phenotype_prediction/predictions_flat_*.txt": { + "type": "file", + "description": "Flattened phenotype predictions", + "ontologies": [] + } + } + ] + ], + "predictions_raw": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*/predictions_*.txt": { + "type": "file", + "description": "Raw phenotype predictions", + "ontologies": [] + } + } + ] + ], + "pfam_annotation": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*/annotation/pfam/": { + "type": "directory", + "description": "Pfam annotation directory" + } + } + ] + ], + "gene_prediction": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*/gene_prediction/": { + "type": "directory", + "description": "Gene prediction directory" + } + } + ] + ], + "versions_traitar": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "traitar": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "traitar --version 2>&1 | tail -1": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "traitar": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "traitar --version 2>&1 | tail -1": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@brovolia"], + "maintainers": ["@brovolia"] } - ] - ], - "output": { - "phylogeny": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information", - "pattern": "*.{raxml.bestTree}" - } - }, - { - "*.raxml.bestTree": { - "type": "file", - "description": "A phylogeny in Newick format", - "pattern": "*.{raxml.bestTree}", - "ontologies": [] - } - } - ] - ], - "phylogeny_bootstrapped": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information", - "pattern": "*.{raxml.bestTree}" - } - }, - { - "*.raxml.bootstraps": { - "type": "file", - "description": "A phylogeny in Newick format with bootstrap values", - "pattern": "*.{raxml.bootstraps}", - "optional": true, - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } + }, + { + "name": "transdecoder_longorf", + "path": "modules/nf-core/transdecoder/longorf/meta.yml", + "type": "module", + "meta": { + "name": "transdecoder_longorf", + "description": "TransDecoder identifies candidate coding regions within transcript sequences. it is used to build gff file.", + "keywords": ["eucaryotes", "gff", "transcript", "coding"], + "tools": [ + { + "transdecoder": { + "description": "TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.", + "homepage": "https://github.com/TransDecoder", + "documentation": "https://github.com/TransDecoder/TransDecoder/wiki", + "tool_dev_url": "https://github.com/TransDecoder/TransDecoder", + "licence": ["Broad Institute"], + "identifier": "biotools:TransDecoder" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "fasta file", + "pattern": "*.{fasta}", + "ontologies": [] + } + } + ] + ], + "output": { + "pep": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${output_dir_name}/*.pep": { + "type": "file", + "description": "all ORFs meeting the minimum length criteria, regardless of coding potential. file", + "pattern": "*.{pep}", + "ontologies": [] + } + } + ] + ], + "gff3": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${output_dir_name}/*.gff3": { + "type": "file", + "description": "positions of all ORFs as found in the target transcripts. file", + "pattern": "*.{gff3}", + "ontologies": [] + } + } + ] + ], + "cds": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${output_dir_name}/*.cds": { + "type": "file", + "description": "the nucleotide coding sequence for all detected ORFs. file", + "pattern": "*{cds}", + "ontologies": [] + } + } + ] + ], + "dat": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${output_dir_name}/*.dat": { + "type": "file", + "description": "nucleotide frequencies", + "pattern": "*{dat}", + "ontologies": [] + } + } + ] + ], + "folder": [ + { + "${output_dir_name}": { + "type": "directory", + "description": "contains all the files from the run" + } + } + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@Danilo2771"], + "maintainers": ["@Danilo2771"] } - ] - }, - "authors": [ - "@avantonder", - "@aunderwo" - ], - "maintainers": [ - "@avantonder", - "@aunderwo" - ] - } - }, - { - "name": "rbt_vcfsplit", - "path": "modules/nf-core/rbt/vcfsplit/meta.yml", - "type": "module", - "meta": { - "name": "rbt_vcfsplit", - "description": "A tool for splitting VCF/BCF files into N equal chunks, including BND support", - "keywords": [ - "genomics", - "splitting", - "VCF", - "BCF", - "variants" - ], - "tools": [ - { - "rust-bio-tools": { - "description": "A growing collection of fast and secure command line utilities for dealing with NGS data implemented on top of Rust-Bio.", - "homepage": "https://github.com/rust-bio/rust-bio-tools", - "documentation": "https://github.com/rust-bio/rust-bio-tools", - "tool_dev_url": "https://github.com/rust-bio/rust-bio-tools", - "doi": "no DOI available", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF file with variants to be split", - "pattern": "*.{vcf,bcf,vcf.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - }, - { - "edam": "http://edamontology.org/format_3020" - } - ] - } - } - ], - { - "numchunks": { - "type": "integer", - "description": "Number of chunks to split the VCF file into. The default is 15." - } - } - ], - "output": { - "bcfchunks": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.bcf": { - "type": "file", - "description": "Chunks of the input VCF file, split into `numchunks` equal parts.", - "pattern": "*.bcf", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3020" - } - ] - } - } - ] - ], - "versions_rbt": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "rbt": { - "type": "string", - "description": "The tool name" - } - }, - { - "rbt --version | grep -oE '[0-9]+(\\.[0-9]+)+' | head -n 1": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "rbt": { - "type": "string", - "description": "The tool name" - } - }, - { - "rbt --version | grep -oE '[0-9]+(\\.[0-9]+)+' | head -n 1": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@famosab" - ], - "maintainers": [ - "@famosab" - ] - }, - "pipelines": [ - { - "name": "sarek", - "version": "3.8.1" - } - ] - }, - { - "name": "regenie_step1", - "path": "modules/nf-core/regenie/step1/meta.yml", - "type": "module", - "meta": { - "name": "regenie_step1", - "description": "Run REGENIE step 1 to fit whole-genome regression models and emit LOCO predictions", - "keywords": [ - "regenie", - "gwas", - "association", - "burden test", - "genomics" - ], - "tools": [ - { - "regenie": { - "description": "Regenie is a C++ program for whole genome regression modelling of large genome-wide association studies (GWAS).", - "homepage": "https://rgcgithub.github.io/regenie/", - "documentation": "https://rgcgithub.github.io/regenie/options/", - "tool_dev_url": "https://github.com/rgcgithub/regenie", - "doi": "10.1038/s41588-021-00870-7", - "licence": [ - "MIT" - ], - "identifier": "biotools:regenie" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing genotype information\nKeep only the genotype analysis identifier in this map\nREGENIE consumes the staged basename of `plink_genotype_file` as the `--bed` or `--pgen` prefix, so the `.bed/.bim/.fam` or `.pgen/.pvar/.psam` files must share one basename\ne.g. `[ id:'cohort' ]`\n" - } - }, - { - "plink_genotype_file": { - "type": "file", - "description": "PLINK primary genotype file in BED or PGEN format", - "pattern": "*.{bed,pgen}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3003" - } - ] - } - }, - { - "plink_variant_file": { - "type": "file", - "description": "PLINK variant metadata file in BIM or PVAR format", - "pattern": "*.{bim,pvar,zst}", - "ontologies": [] - } - }, - { - "plink_sample_file": { - "type": "file", - "description": "PLINK sample metadata file in FAM or PSAM format", - "pattern": "*.{fam,psam}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing genotype/sample information associated with the phenotype file input\nKeep only the shared genotype/sample identifier in this map\ne.g. `[ id:'plink_simulated' ]`\n" - } - }, - { - "pheno": { - "type": "file", - "description": "Phenotype file passed to `--phenoFile`", - "pattern": "*.{phe,pheno,txt,tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } + }, + { + "name": "transdecoder_predict", + "path": "modules/nf-core/transdecoder/predict/meta.yml", + "type": "module", + "meta": { + "name": "transdecoder_predict", + "description": "TransDecoder identifies candidate coding regions within transcript sequences. It is used to build gff file. You can use this module after transdecoder_longorf", + "keywords": ["eukaryotes", "gff", "cds", "transcroder"], + "tools": [ + { + "transdecoder": { + "description": "TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.", + "homepage": "https://github.com/TransDecoder", + "documentation": "https://github.com/TransDecoder/TransDecoder/wiki", + "tool_dev_url": "https://github.com/TransDecoder/TransDecoder", + "licence": ["Broad Institute"], + "identifier": "biotools:TransDecoder" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "fasta file", + "pattern": "*.{fasta}", + "ontologies": [] + } + } + ], + { + "fold": { + "type": "directory", + "description": "Output from the module transdecoder_longorf", + "pattern": "*" + } + } + ], + "output": { + "pep": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.transdecoder.pep": { + "type": "file", + "description": "All ORFs meeting the minimum length criteria, regardless of coding potential", + "pattern": "*.{pep}", + "ontologies": [] + } + } + ] + ], + "gff3": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.transdecoder.gff3": { + "type": "file", + "description": "Positions of all ORFs as found in the target transcripts", + "pattern": "*.{gff3}", + "ontologies": [] + } + } + ] + ], + "cds": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.transdecoder.cds": { + "type": "file", + "description": "the nucleotide coding sequence for all detected ORFs", + "pattern": "*{cds}", + "ontologies": [] + } + } + ] + ], + "bed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.transdecoder.bed": { + "type": "file", + "description": "bed file", + "pattern": "*{bed}", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@Danilo2771"], + "maintainers": ["@Danilo2771"] } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing genotype/sample information associated with the covariate input\ne.g. `[ id:'plink_simulated' ]`\n" - } + }, + { + "name": "trgt_genotype", + "path": "modules/nf-core/trgt/genotype/meta.yml", + "type": "module", + "meta": { + "name": "trgt_genotype", + "description": "Tandem repeat genotyping from PacBio HiFi data", + "keywords": ["repeat expansion", "pacbio", "genomics"], + "tools": [ + { + "trgt": { + "description": "Tandem repeat genotyping and visualization from PacBio HiFi data", + "homepage": "https://github.com/PacificBiosciences/trgt", + "documentation": "https://github.com/PacificBiosciences/trgt/blob/main/docs/tutorial.md", + "tool_dev_url": "https://github.com/PacificBiosciences/trgt", + "doi": "10.1038/s41587-023-02057-3", + "licence": [ + "Pacific Biosciences Software License (https://github.com/PacificBiosciences/trgt/blob/main/LICENSE.md)" + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "bam": { + "type": "file", + "description": "Sorted BAM file", + "pattern": "*.bam", + "ontologies": [] + } + }, + { + "bai": { + "type": "file", + "description": "Index of the BAM file", + "pattern": "*.bam", + "ontologies": [] + } + }, + { + "karyotype": { + "type": "string", + "description": "Karyotype of the sample. Either XX or XY. Defaults to XX if not given", + "enum": ["XX", "XY"] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy map containing reference information\ne.g. `[ id: 'genome' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA reference file", + "pattern": "*.{fasta,fa,fna}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy map containing reference information\ne.g. `[ id: 'genome' ]`\n" + } + }, + { + "fai": { + "type": "file", + "description": "Index for FASTA file", + "pattern": "*.fai", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy map containing repeat information\ne.g. `[ id: 'repeats' ]`\n" + } + }, + { + "repeats": { + "type": "file", + "description": "BED file with repeat coordinates", + "pattern": "*.bed", + "ontologies": [] + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "VCF file with repeat genotypes", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.spanning.bam": { + "type": "file", + "description": "BAM file with pieces of reads aligning to repeats", + "pattern": "*.spanning.bam", + "ontologies": [] + } + } + ] + ], + "versions_trgt": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "trgt": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "trgt --version | sed 's/.* //g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "trgt": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "trgt --version | sed 's/.* //g'": { + "type": "eval", + "description": "The expression to obtain the version" + } + } + ] + ] + }, + "authors": ["@Schmytzi", "@fellen31"], + "maintainers": ["@Schmytzi"] }, - { - "covar": { - "type": "file", - "optional": true, - "description": "Optional covariate file passed to `--covarFile`; provide `[]` when absent", - "pattern": "*.{covar,cov,txt,tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - { - "bsize": { - "type": "integer", - "description": "Optional block size passed to `--bsize`; pass `[]` to use the module default of `1000`" - } - } - ], - "output": { - "predictions": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing genotype/sample information\ne.g. `[ id:'plink_simulated' ]`\n" - } - }, - { - "*_pred.list": { - "type": "file", - "description": "REGENIE prediction list file", - "pattern": "*_pred.list", - "ontologies": [] - } - } - ] - ], - "loco": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing genotype/sample information\ne.g. `[ id:'plink_simulated' ]`\n" - } - }, - { - "*.loco.gz": { - "type": "file", - "description": "REGENIE LOCO prediction files", - "pattern": "*.loco.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3987" - } - ] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing genotype information\ne.g. `[ id:'plink_simulated' ]`\n" - } - }, - { - "*.log": { - "type": "file", - "description": "REGENIE step 1 log file", - "pattern": "*.log", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2330" - } - ] - } - } - ] - ], - "versions_regenie": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "regenie": { - "type": "string", - "description": "The tool name" - } - }, - { - "regenie --version 2>&1 | sed -n \"1{s/^v//;s/\\.gz$//;p}\"": { - "type": "eval", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "regenie": { - "type": "string", - "description": "The tool name" - } - }, - { - "regenie --version 2>&1 | sed -n \"1{s/^v//;s/\\.gz$//;p}\"": { - "type": "eval", - "description": "The command used to generate the version of the tool" - } - } + "pipelines": [ + { + "name": "pacvar", + "version": "1.0.1" + } ] - ] - }, - "authors": [ - "@lyh970817" - ], - "maintainers": [ - "@lyh970817" - ], - "containers": { - "conda": { - "linux_amd64": { - "lock_file": "modules/nf-core/regenie/step1/.conda-lock/linux_amd64-bd-5d361f9fcb2f85cf_1.txt" - } - }, - "docker": { - "linux_amd64": { - "build_id": "bd-5d361f9fcb2f85cf_1", - "name": "community.wave.seqera.io/library/regenie:4.1.2--5d361f9fcb2f85cf", - "scanId": "sc-cc9eb5ed5eb381dd_2" - } - }, - "singularity": { - "linux_amd64": { - "build_id": "bd-7c121fb4ecd57890_1", - "name": "oras://community.wave.seqera.io/library/regenie:4.1.2--7c121fb4ecd57890", - "https": "https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/7a/7a05bf71ea09adc5ebf9f0c656c9b326c0f16ba8e4966914972e58313469a466/data" - } - } - } - } - }, - { - "name": "regtools_junctionsextract", - "path": "modules/nf-core/regtools/junctionsextract/meta.yml", - "type": "module", - "meta": { - "name": "regtools_junctionsextract", - "description": "Extract exon-exon junctions from an RNAseq BAM file. 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} - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM file", - "pattern": "*.{bam}", - "ontologies": [] - } + }, + { + "name": "trgt_plot", + "path": "modules/nf-core/trgt/plot/meta.yml", + "type": "module", + "meta": { + "name": "trgt_plot", + "description": "Visualize tandem repeats genotyped by TRGT", + "keywords": ["trgt", "repeat expansion", "plotting", "pacbio", "genomics"], + "tools": [ + { + "trgt": { + "description": "Tandem repeat genotyping and visualization from PacBio HiFi data", + "homepage": "https://github.com/PacificBiosciences/trgt", + "documentation": "https://github.com/PacificBiosciences/trgt/blob/main/docs/tutorial.md", + "tool_dev_url": "https://github.com/PacificBiosciences/trgt", + "doi": "10.1038/s41587-023-02057-3", + "licence": [ + "Pacific Biosciences Software License (https://github.com/PacificBiosciences/trgt/blob/main/LICENSE.md)" + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "bam": { + "type": "file", + "description": "Sorted reads spanning tandem repeat from TRGT output", + "pattern": "*.bam", + "ontologies": [] + } + }, + { + "bai": { + "type": "file", + "description": "Index for reads", + "pattern": "*.bai", + "ontologies": [] + } + }, + { + "vcf": { + "type": "file", + "description": "Sorted tandem repeat genotypes called by TRGT", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + }, + { + "tbi": { + "type": "file", + "description": "Index for genotypes", + "pattern": "*.{tbi,csi}", + "ontologies": [] + } + }, + { + "repeat_id": { + "type": "string", + "description": "ID of tandem repeat to plot" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy map containing reference information\ne.g. `[ id: 'genome' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA reference file", + "pattern": "*.{fasta,fa,fna}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy map containing reference information\ne.g. `[ id: 'genome' ]`\n" + } + }, + { + "fai": { + "type": "file", + "description": "Index for FASTA file", + "pattern": "*.fai", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy map containing repeat information\ne.g. `[ id: 'repeats' ]`\n" + } + }, + { + "repeats": { + "type": "file", + "description": "BED file with repeat coordinates and structure", + "pattern": "*.bed", + "ontologies": [] + } + } + ] + ], + "output": { + "plot": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.{png,pdf,svg}": { + "type": "file", + "description": "Plot of region and reads spanning tandem repeat", + "pattern": "*.{png,pdf,svg}", + "ontologies": [] + } + } + ] + ], + "versions_trgt": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "trgt": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "trgt --version | sed 's/.* //g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "trgt": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "trgt --version | sed 's/.* //g'": { + "type": "eval", + "description": "The expression to obtain the version" + } + } + ] + ] + }, + "authors": ["@Schmytzi"], + "maintainers": ["@Schmytzi"] }, - 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Default is set to \"trimal\".", + "pattern": "*" + } + } + ], + "output": { + "trimal": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "${prefix}.${out_extension}": { + "type": "file", + "description": "Trimmed multiple sequence alignment file", + "pattern": "*.*", + "ontologies": [ + { + "edam": "http://edamontology.org/data_1916" + }, + { + "edam": "http://edamontology.org/format_1982" + }, + { + "edam": "http://edamontology.org/format_1997" + }, + { + "edam": "http://edamontology.org/format_1998" + }, + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ] + ], + "summary": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "${prefix}.html": { + "type": "file", + "description": "HTML summary file, needs -htmlout to be set in ext.args along with a trimming method", + "pattern": "*.html", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2331" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@IceGreb"], + "maintainers": ["@IceGreb"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } + }, + { + "name": "trimgalore", + "path": "modules/nf-core/trimgalore/meta.yml", + "type": "module", + "meta": { + "name": "trimgalore", + "description": "A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files,\nwith extra functionality for RRBS data\n", + "keywords": ["trimming", "adapters", "sequencing", "fastq"], + "tools": [ + { + "trimgalore": { + "description": "A wrapper tool around Cutadapt and FastQC to consistently apply quality\nand adapter trimming to FastQ files, with some extra functionality for\nMspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.\n", + "homepage": "https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/", + "documentation": "https://github.com/FelixKrueger/TrimGalore/blob/master/Docs/Trim_Galore_User_Guide.md", + "licence": ["GPL-3.0-or-later"], + "identifier": "biotools:trim_galore" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ] + ], + "output": { + "reads": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*{3prime,5prime,trimmed,val}{,_1,_2}.fq.gz": { + "type": "file", + "description": "The trimmed/modified fastq reads", + "pattern": "*{3prime,5prime,trimmed,val}{,_1,_2}.fq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*report.txt": { + "type": "file", + "description": "trimgalore log file", + "pattern": "*report.txt", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + } + ] + ], + "unpaired": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*unpaired{,_1,_2}.fq.gz": { + "type": "file", + "description": "unpaired reads when --retain_unpaired flag is used", + "pattern": "*unpaired*.fq.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "html": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.html": { + "type": "file", + "description": "FastQC HTML report after trimming when the --fastqc flag is used", + "pattern": "*_fastqc.html", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2331" + } + ] + } + } + ] + ], + "zip": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.zip": { + "type": "file", + "description": "FastQC report output zip after trimming when the --fastqc flag is used", + "pattern": "*_fastqc.zip", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3987" + } + ] + } + } + ] + ], + "versions_trimgalore": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "trimgalore": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "trim_galore --version | grep -Eo \"[0-9]+(\\.[0-9]+)+\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "trimgalore": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "trim_galore --version | grep -Eo \"[0-9]+(\\.[0-9]+)+\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@drpatelh", "@ewels", "@FelixKrueger"], + "maintainers": ["@drpatelh", "@ewels", "@FelixKrueger", "@vagkaratzas"] }, - { - "fasta": { - "type": "file", - "description": "Genome assembly", - "pattern": "*.{fasta,fa,fas,fsa,faa,fna}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - { - "lib": { - "type": "file", - "description": "Custom library (e.g. from another species)", - "pattern": "*.{fasta,fa,fas,fsa,faa,fna}", - "ontologies": [ + "pipelines": [ + { + "name": "atacseq", + "version": "2.1.2" + }, + { + "name": "chipseq", + "version": "2.1.0" + }, + { + "name": "circdna", + "version": "1.1.0" + }, + { + "name": "circrna", + "version": "dev" + }, + { + "name": "dartseq", + "version": "dev" + }, { - "edam": "http://edamontology.org/format_1929" + "name": "genomeassembler", + "version": "1.1.0" + }, + { + "name": "hgtseq", + "version": "1.1.0" + }, + { + "name": "lncpipe", + "version": "dev" + }, + { + "name": "magmap", + "version": "1.0.0" + }, + { + "name": "metatdenovo", + "version": "1.3.0" + }, + { + "name": "methylseq", + "version": "4.2.0" + }, + { + "name": "riboseq", + "version": "1.2.0" + }, + { + "name": "rnaseq", + "version": "3.26.0" + }, + { + "name": "rnasplice", + "version": "1.0.4" + }, + { + "name": "sammyseq", + "version": "dev" + }, + { + "name": "ssds", + "version": "dev" } - ] - } - } - ], - "output": { - "masked": [ - [ - { - "meta": { - "type": "file", - "description": "Masked fasta", - "pattern": "*.{masked}", - "ontologies": [] - } - }, - { - "${prefix}.masked": { - "type": "file", - "description": "Masked fasta", - "pattern": "*.{masked}", - "ontologies": [] - } - } - ] - ], - "out": [ - [ - { - "meta": { - "type": "file", - "description": "Masked fasta", - "pattern": "*.{masked}", - "ontologies": [] - } - }, - { - "${prefix}.out": { - "type": "file", - "description": "Out file", - "pattern": "*.{out}", - "ontologies": [] - } - } - ] - ], - "tbl": [ - [ - { - "meta": { - "type": "file", - "description": "Masked fasta", - "pattern": "*.{masked}", - "ontologies": [] - } - }, - { - "${prefix}.tbl": { - "type": "file", - "description": "tbl file", - "pattern": "*.{tbl}", - "ontologies": [] - } - } - ] - ], - "gff": [ - [ - { - "meta": { - "type": "file", - "description": "Masked fasta", - "pattern": "*.{masked}", - "ontologies": [] - } - }, - { - "${prefix}.gff": { - "type": "file", - "description": "GFF file", - "pattern": "*.{gff}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2305" - } - ] - } - } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@kherronism", - "@gallvp" - ], - "maintainers": [ - "@kherronism", - "@gallvp" - ] - } - }, - { - "name": "repeatmasker_rmouttogff3", - "path": "modules/nf-core/repeatmasker/rmouttogff3/meta.yml", - "type": "module", - "meta": { - "name": "repeatmasker_rmouttogff3", - "description": "A utility script to assist to convert old RepeatMasker *.out files to version 3 gff files.", - "keywords": [ - "sort", - "repeatmasker", - "genomics" - ], - "tools": [ - { - "repeatmasker": { - "description": "RepeatMasker is a program that screens DNA sequences for interspersed\nrepeats and low complexity DNA sequences\n", - 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{ - "out": { - "type": "file", - "description": "RepeatMasker out file", - "pattern": "*.{out}", - "ontologies": [] - } - } - ] - ], - "output": { - "gff3": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.gff3": { - "type": "file", - "description": "Sorted BAM/CRAM/SAM file", - "pattern": "*.{gff3}", - "ontologies": [] - } - } + "pipelines": [ + { + "name": "callingcards", + "version": "1.0.0" + }, + { + "name": "mag", + "version": "5.4.2" + }, + { + "name": "sammyseq", + "version": "dev" + }, + { + "name": "variantcatalogue", + "version": "dev" + }, + { + "name": "viralintegration", + "version": "0.1.1" + }, + { + "name": "viralmetagenome", + "version": "1.1.1" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@GallVp" - ], - "maintainers": [ - "@GallVp" - ] - } - }, - { - "name": "repeatmodeler_builddatabase", - "path": "modules/nf-core/repeatmodeler/builddatabase/meta.yml", - "type": "module", - "meta": { - "name": "repeatmodeler_builddatabase", - "description": "Create a database for RepeatModeler", - "keywords": [ - "genomics", - "fasta", - "repeat" - ], - "tools": [ - { - "repeatmodeler": { - "description": "RepeatModeler is a de-novo repeat family identification and modeling package.", - "homepage": "https://github.com/Dfam-consortium/RepeatModeler", - "documentation": "https://github.com/Dfam-consortium/RepeatModeler", - "tool_dev_url": "https://github.com/Dfam-consortium/RepeatModeler", - "licence": [ - "Open Software License v2.1" - ], - "identifier": "biotools:repeatmodeler" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } + }, + { + "name": "trinity", + "path": "modules/nf-core/trinity/meta.yml", + "type": "module", + "meta": { + "name": "trinity", + "description": "Assembles a de novo transcriptome from RNAseq reads", + "keywords": ["assembly", "de novo assembler", "fasta", "fastq"], + "tools": [ + { + "trinity": { + "description": "Trinity assembles transcript sequences from Illumina RNA-Seq data.", + "homepage": "https://github.com/trinityrnaseq/trinityrnaseq/wiki", + "documentation": "https://github.com/trinityrnaseq/trinityrnaseq/wiki", + "tool_dev_url": "https://github.com/trinityrnaseq/trinityrnaseq/", + "doi": "10.1038/nbt.1883", + "licence": ["BSD-3-clause"], + "identifier": "biotools:trinity" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input fasta/fastq reads to be assembled into a transcriptome.\n", + "pattern": "*.{fa,fasta,fq,fastq}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ] + ], + "output": { + "transcript_fasta": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fa.gz": { + "type": "file", + "description": "de novo assembled transcripts fasta file compressed", + "pattern": "*.fa.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "Log from trinity", + "pattern": "*.log", + "ontologies": [] + } + } + ] + ], + "versions_trinity": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "trinity": { + "type": "string", + "description": "The tool name" + } + }, + { + "Trinity --version | grep 'Trinity version' | sed 's/.*Trinity-v//'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "trinity": { + "type": "string", + "description": "The tool name" + } + }, + { + "Trinity --version | grep 'Trinity version' | sed 's/.*Trinity-v//'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@timslittle", "@gallvp"], + "maintainers": ["@timslittle", "@gallvp"] }, - { - "fasta": { - "type": "file", - "description": "Fasta file", - "pattern": "*.{fasta,fsa,fa}", - "ontologies": [] - } - } - ] - ], - "output": { - "db": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}.*": { - "type": "file", - "description": "Database files for repeatmodeler", - "pattern": "`${prefix}.*`", - "ontologies": [] - } - } + "pipelines": [ + { + "name": "circrna", + "version": "dev" + }, + { + "name": "denovotranscript", + "version": "1.2.1" + }, + { + "name": "viralmetagenome", + "version": "1.1.1" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@GallVp" - ], - "maintainers": [ - "@GallVp" - ] - } - }, - { - "name": "repeatmodeler_repeatmodeler", - "path": "modules/nf-core/repeatmodeler/repeatmodeler/meta.yml", - 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"*.fp.vcf.gz.tbi", + "ontologies": [] + } + } + ] + ], + "tp_base_vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "*.tp-base.vcf.gz": { + "type": "file", + "description": "VCF file with base true positives", + "pattern": "*.tp-base.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "tp_base_tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "*.tp-base.vcf.gz.tbi": { + "type": "file", + "description": "VCF index file with base true positives", + "pattern": "*.tp-base.vcf.gz.tbi", + "ontologies": [] + } + } + ] + ], + "tp_comp_vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "*.tp-comp.vcf.gz": { + "type": "file", + "description": "VCF file with compared true positives", + "pattern": "*.tp-comp.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "tp_comp_tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "*.tp-comp.vcf.gz.tbi": { + "type": "file", + "description": "VCF index file with compared true positives", + "pattern": "*.tp-comp.vcf.gz.tbi", + "ontologies": [] + } + } + ] + ], + "summary": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "*.summary.json": { + "type": "file", + "description": "Summary JSON file with results from the benchmark", + "pattern": "*.summary.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "*.log.txt": { + "type": "file", + "description": "Log file from Truvari run", + "pattern": "*.log.txt", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1964" + } + ] + } + } + ] + ], + "versions_truvari": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "truvari": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "truvari version | sed 's/Truvari v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "truvari": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "truvari version | sed 's/Truvari v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@nvnieuwk"], + "maintainers": ["@nvnieuwk"] }, - { - "reads": { - "type": "file", - "description": "Single-end or paired-end nucleotide sequences in FASTQ or FASTA format", - "pattern": "*.{fastq,fastq.gz,fq,fq.gz,fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ], - { - "card": { - "type": "directory", - "description": "Directory containing the CARD database. This is expected to be the unarchived but otherwise unaltered download folder (see RGI documentation for download instructions).", - "pattern": "*/" - } - }, - { - "wildcard": { - "type": "directory", - "description": "Directory containing the WildCARD database (optional). This is expected to be the unarchived but otherwise unaltered download folder (see RGI documentation for download instructions).", - "pattern": "*/" - } - } - ], - "output": { - "json": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.json": { - "type": "file", - "description": "JSON formatted file with RGI results", - "pattern": "*.{json}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.txt": { - "type": "file", - "description": "Tab-delimited file with RGI results", - "pattern": "*.{txt}", - "ontologies": [] - } - } - ] - ], - "tmp": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "temp/": { - "type": "directory", - "description": "Directory containing various intermediate files", - "pattern": "temp/" - } - } - ] - ], - "versions_rgi": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "rgi": { - "type": "string", - "description": "The tool name" - } - }, - { - "rgi main --version": { - "type": "string", - "description": "The version string returned by the command" - } - } - ] - ], - "versions_db": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "rgi-database": { - "type": "string", - "description": "The tool name" - } - }, - { - "echo \\$DB_VERSION": { - "type": "string", - "description": "The CARD database version string" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "rgi": { - "type": "string", - "description": "The tool name" - } - }, - { - "rgi main --version": { - "type": "string", - "description": "Command used to collect the version" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "rgi-database": { - "type": "string", - "description": "The tool name" - } - }, - { - "echo \\$DB_VERSION": { - "type": "string", - "description": "Command used to collect the version" - } - } + "pipelines": [ + { + "name": "variantbenchmarking", + "version": "1.5.0" + } ] - ] - }, - "authors": [ - "@vinisalazar" - ], - "maintainers": [ - "@nickp60", - "@vinisalazar" - ] - }, - "pipelines": [ - { - "name": "funcprofiler", - "version": "dev" - } - ] - }, - { - "name": "rgi_cardannotation", - "path": "modules/nf-core/rgi/cardannotation/meta.yml", - "type": "module", - "meta": { - "name": "rgi_cardannotation", - "description": "Preprocess the CARD database for RGI to predict antibiotic resistance from protein or nucleotide data", - "keywords": [ - "bacteria", - "fasta", - "antibiotic resistance" - ], - "tools": [ - { - "rgi": { - "description": "This module preprocesses the downloaded Comprehensive Antibiotic Resistance Database (CARD) which can then be used as input for RGI.", - "homepage": "https://card.mcmaster.ca", - "documentation": "https://github.com/arpcard/rgi", - "tool_dev_url": "https://github.com/arpcard/rgi", - "doi": "10.1093/nar/gkz935", - "licence": [ - "https://card.mcmaster.ca/about" - ], - "identifier": "" - } - } - ], - "input": [ - { - "card": { - "type": "directory", - "description": "Directory containing the CARD database", - "pattern": "*/" - } - } - ], - "output": { - "db": [ - { - "card_database_processed": { - "type": "directory", - "description": "Directory containing the processed CARD database files", - "pattern": "*/" - } + }, + { + "name": "truvari_consistency", + "path": "modules/nf-core/truvari/consistency/meta.yml", + "type": "module", + "meta": { + "name": "truvari_consistency", + "description": "Over multiple vcfs, calculate their intersection/consistency.", + "keywords": ["structural variants", "sv", "vcf", "intersection", "comparison"], + "tools": [ + { + "truvari": { + "description": "Structural variant comparison tool for VCFs", + "homepage": "https://github.com/ACEnglish/truvari", + "documentation": "https://github.com/acenglish/truvari/wiki", + "tool_dev_url": "https://github.com/ACEnglish/truvari", + "doi": "10.1186/s13059-022-02840-6", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "vcfs": { + "type": "file", + "description": "two or more VCF files to compare", + "pattern": "*.{vcf,gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "output": { + "consistency": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.{txt,json}": { + "type": "file", + "description": "Output report in txt or json format", + "pattern": "*.{txt,json}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "versions_truvari": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "truvari": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "truvari version | sed 's/Truvari v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "truvari": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "truvari version | sed 's/Truvari v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@kubranarci"], + "maintainers": ["@kubranarci"] } - ], - "tool_version": [ - { - "RGI_VERSION": { - "type": "string", - "description": "The version of the tool in string format (useful for downstream tools such as hAMRronization)" - } + }, + { + "name": "truvari_segment", + "path": "modules/nf-core/truvari/segment/meta.yml", + "type": "module", + "meta": { + "name": "truvari_segment", + "description": "Normalization of SVs into disjointed genomic regions", + "keywords": ["structural variants", "sv", "vcf", "benchmark", "normalization"], + "tools": [ + { + "truvari": { + "description": "Structural variant comparison tool for VCFs", + "homepage": "https://github.com/ACEnglish/truvari", + "documentation": "https://github.com/acenglish/truvari/wiki", + "tool_dev_url": "https://github.com/ACEnglish/truvari", + "doi": "10.1186/s13059-022-02840-6", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "vcf": { + "type": "file", + "description": "Input VCF file", + "pattern": "*.{vcf,gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.vcf": { + "type": "file", + "description": "Segmented VCF file", + "pattern": "*.{vcf}", + "ontologies": [] + } + } + ] + ], + "versions_truvari": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "truvari": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "truvari version | sed 's/Truvari v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "truvari": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "truvari version | sed 's/Truvari v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@kubranarci"], + "maintainers": ["@kubranarci"] } - ], - "db_version": [ - { - "DB_VERSION": { - "type": "string", - "description": "The version of the used database in string format (useful for downstream tools such as hAMRronization)" - } + }, + { + "name": "trycycler_cluster", + "path": "modules/nf-core/trycycler/cluster/meta.yml", + "type": "module", + "meta": { + "name": "trycycler_cluster", + "description": "Cluster contigs from multiple assemblies by similarity", + "keywords": ["cluster", "alignment", "fastq", "fasta", "genomics"], + "tools": [ + { + "trycycler": { + "description": "Trycycler is a tool for generating consensus long-read assemblies for bacterial genomes", + "homepage": "https://github.com/rrwick/Trycycler", + "documentation": "https://github.com/rrwick/Trycycler/wiki", + "doi": "10.1186/s13059-021-02483-z", + "licence": ["GPL v3"], + "identifier": "biotools:trycycler" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "contigs": { + "type": "file", + "description": "Contigs file", + "ontologies": [] + } + }, + { + "reads": { + "type": "file", + "description": "Long-read FASTQ file, optionally gzip compressed", + "ontologies": [] + } + } + ] + ], + "output": { + "cluster_dir": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*": { + "type": "directory", + "description": "Output directory containing clustering results" + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@watsonar"], + "maintainers": ["@watsonar"] } - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } + }, + { + "name": "trycycler_subsample", + "path": "modules/nf-core/trycycler/subsample/meta.yml", + "type": "module", + "meta": { + "name": "trycycler_subsample", + "description": "Subsample a long-read sequencing fastq file for multiple assemblies", + "keywords": ["subsample", "fastq", "genomics"], + "tools": [ + { + "trycycler": { + "description": "Trycycler is a tool for generating consensus long-read assemblies for bacterial genomes", + "homepage": "https://github.com/rrwick/Trycycler", + "documentation": "https://github.com/rrwick/Trycycler/wiki", + "doi": "10.1186/s13059-021-02483-z", + "licence": ["GPL v3"], + "identifier": "biotools:trycycler" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "reads": { + "type": "file", + "description": "Long-read FASTQ file, optionally gzip compressed", + "ontologies": [] + } + } + ] + ], + "output": { + "subreads": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*/*.fastq.gz": { + "type": "file", + "description": "Subsampled read sets", + "pattern": "*.{fastq.gz}", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@watsonar"], + "maintainers": ["@watsonar"] } - ] - }, - "authors": [ - "@rpetit3", - "@jfy133", - "@jasmezz" - ], - "maintainers": [ - "@rpetit3", - "@jfy133", - "@jasmezz" - ] - }, - "pipelines": [ - { - "name": "funcscan", - "version": "3.0.0" - } - ] - }, - { - "name": "rgi_main", - "path": "modules/nf-core/rgi/main/meta.yml", - "type": "module", - "meta": { - "name": "rgi_main", - "description": "Predict antibiotic resistance from protein or nucleotide data", - "keywords": [ - "bacteria", - "fasta", - "antibiotic resistance" - ], - "tools": [ - { - "rgi": { - "description": "This tool provides a preliminary annotation of your DNA sequence(s) based upon the data available in The Comprehensive Antibiotic Resistance Database (CARD). Hits to genes tagged with Antibiotic Resistance ontology terms will be highlighted. As CARD expands to include more pathogens, genomes, plasmids, and ontology terms this tool will grow increasingly powerful in providing first-pass detection of antibiotic resistance associated genes. See license at CARD website", - "homepage": "https://card.mcmaster.ca", - "documentation": "https://github.com/arpcard/rgi", - "tool_dev_url": "https://github.com/arpcard/rgi", - "doi": "10.1093/nar/gkz935", - "licence": [ - "https://card.mcmaster.ca/about" - ], - "identifier": "" + }, + { + "name": "tsebra", + "path": "modules/nf-core/tsebra/meta.yml", + "type": "module", + "meta": { + "name": "tsebra", + "description": "Transcript Selector for BRAKER TSEBRA combines gene predictions by selecting transcripts based on their extrisic evidence support", + "keywords": ["genomics", "transcript", "selector", "gene", "prediction", "evidence"], + "tools": [ + { + "tsebra": { + "description": "TSEBRA is a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons", + "homepage": "https://github.com/Gaius-Augustus/TSEBRA", + "documentation": "https://github.com/Gaius-Augustus/TSEBRA", + "tool_dev_url": "https://github.com/Gaius-Augustus/TSEBRA", + "doi": "10.1186/s12859-021-04482-0", + "licence": ["Artistic-2.0"], + "identifier": "biotools:tsebra" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "gtfs": { + "type": "list", + "description": "List of gene prediction files in gtf", + "pattern": "*.gtf" + } + } + ], + { + "hints_files": { + "type": "list", + "description": "List of files containing extrinsic evidence in gff", + "pattern": "*.gff" + } + }, + { + "keep_gtfs": { + "type": "list", + "description": "List of gene prediction files in gtf. These gene sets are used the same way as other inputs, but TSEBRA ensures that all\ntranscripts from these gene sets are included in the output\n", + "pattern": "*.gtf" + } + }, + { + "config": { + "type": "file", + "description": "Configuration file that sets the parameter for TSEBRA", + "pattern": "*.cfg", + "ontologies": [ + { + "edam": "http://edamontology.org/format_4005" + } + ] + } + } + ], + "output": { + "tsebra_gtf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.gtf": { + "type": "file", + "description": "Output file for the combined gene predictions in gtf", + "pattern": "*.gtf", + "ontologies": [] + } + } + ] + ], + "tsebra_scores": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "Transcript scores as a table", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@GallVp"], + "maintainers": ["@GallVp"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + }, + { + "name": "tximeta_tximport", + "path": "modules/nf-core/tximeta/tximport/meta.yml", + "type": "module", + "meta": { + "name": "tximeta_tximport", + "description": "Import transcript-level abundances and estimated counts for gene-level\nanalysis packages\n", + "keywords": ["gene", "kallisto", "pseudoalignment", "rsem", "salmon", "transcript"], + "tools": [ + { + "tximeta": { + "description": "Transcript Quantification Import with Automatic Metadata", + "homepage": "https://bioconductor.org/packages/release/bioc/html/tximeta.html", + "documentation": "https://bioconductor.org/packages/release/bioc/vignettes/tximeta/inst/doc/tximeta.html", + "tool_dev_url": "https://github.com/thelovelab/tximeta", + "doi": "10.1371/journal.pcbi.1007664", + "licence": ["GPL-2"], + "identifier": "biotools:tximeta" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information related to the experiment as a whole\ne.g. `[ id:'SRP123456' ]`\n" + } + }, + { + "quants/*": { + "type": "file", + "description": "Quantification files\n" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information related to the species\nreference e.g. `[ id:'yeast' ]`\n" + } + }, + { + "tx2gene": { + "type": "file", + "description": "A transcript to gene mapping table such as those generated by custom/tx2gene", + "pattern": "*.{csv,tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + }, + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + { + "quant_type": { + "type": "string", + "description": "Quantification type, `kallisto`, `salmon`, or `rsem`" + } + } + ], + "output": { + "tpm_gene": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information related to the experiment as a whole\ne.g. `[ id:'SRP123456' ]`\n" + } + }, + { + "*gene_tpm.tsv": { + "type": "file", + "description": "Abundance (TPM) values derived from tximport output after\nsummarizeToGene(), without a 'countsFromAbundance' specification\n", + "pattern": "*gene_tpm.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "counts_gene": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information related to the experiment as a whole\ne.g. `[ id:'SRP123456' ]`\n" + } + }, + { + "*gene_counts.tsv": { + "type": "file", + "description": "Count values derived from tximport output after\nsummarizeToGene(), without a 'countsFromAbundance' specification\n", + "pattern": "*gene_counts.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "counts_gene_length_scaled": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information related to the experiment as a whole\ne.g. `[ id:'SRP123456' ]`\n" + } + }, + { + "*gene_counts_length_scaled.tsv": { + "type": "file", + "description": "Count values derived from tximport output after summarizeToGene(), with\na 'countsFromAbundance' specification of 'lengthScaledTPM'\n", + "pattern": "*gene_counts_length_scaled.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "counts_gene_scaled": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information related to the experiment as a whole\ne.g. `[ id:'SRP123456' ]`\n" + } + }, + { + "*gene_counts_scaled.tsv": { + "type": "file", + "description": "Count values derived from tximport output after summarizeToGene(), with\na 'countsFromAbundance' specification of 'scaledTPM'\n", + "pattern": "*gene_counts_scaled.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "lengths_gene": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information related to the experiment as a whole\ne.g. `[ id:'SRP123456' ]`\n" + } + }, + { + "*gene_lengths.tsv": { + "type": "file", + "description": "Length values derived from tximport output after summarizeToGene(),\nwithout a 'countsFromAbundance' specification\n", + "pattern": "*gene_lengths.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "tpm_transcript": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information related to the experiment as a whole\ne.g. `[ id:'SRP123456' ]`\n" + } + }, + { + "*transcript_tpm.tsv": { + "type": "file", + "description": "Abundance (TPM) values derived from tximport output without\nsummarizeToGene(), without a 'countsFromAbundance' specification\n", + "pattern": "*transcript_tpm.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "counts_transcript": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information related to the experiment as a whole\ne.g. `[ id:'SRP123456' ]`\n" + } + }, + { + "*transcript_counts.tsv": { + "type": "file", + "description": "Count values derived from tximport output without\nsummarizeToGene(), without a 'countsFromAbundance' specification\n", + "pattern": "*transcript_counts.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "lengths_transcript": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information related to the experiment as a whole\ne.g. `[ id:'SRP123456' ]`\n" + } + }, + { + "*transcript_lengths.tsv": { + "type": "file", + "description": "Length values derived from tximport output without summarizeToGene(),\nwithout a 'countsFromAbundance' specification\n", + "pattern": "*transcript_lengths.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "tx2gene_augmented": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information related to the experiment as a whole\ne.g. `[ id:'SRP123456' ]`\n" + } + }, + { + "*tx2gene_augmented.tsv": { + "type": "file", + "description": "tx2gene mapping table actually used by tximport, equal to the input\ntx2gene with self-mappings appended for any transcripts present in\nthe quantification output but missing from the input. Use this file\n(not the input tx2gene) to reproduce the published gene-level\noutputs from the per-sample quantification files.\n", + "pattern": "*tx2gene_augmented.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "YAML file containing versions of tools used in the module", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "topics": { + "versions": [ + { + "versions.yml": { + "type": "string", + "description": "The name of the process" + } + } + ] + }, + "authors": ["@pinin4fjords"], + "maintainers": ["@pinin4fjords"] }, - { - "fasta": { - "type": "file", - "description": "Nucleotide or protein sequences in FASTA format", - "pattern": "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}", - "ontologies": [] - } - } - ], - { - "card": { - "type": "directory", - "description": "Directory containing the CARD database. This is expected to be the unarchived but otherwise unaltered download folder (see RGI documentation for download instructions).", - "pattern": "*/" - } - }, - { - "wildcard": { - "type": "directory", - "description": "Directory containing the WildCARD database (optional). This is expected to be the unarchived but otherwise unaltered download folder (see RGI documentation for download instructions).", - "pattern": "*/" - } - } - ], - "output": { - "json": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.json": { - "type": "file", - "description": "JSON formatted file with RGI results", - "pattern": "*.{json}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.txt": { - "type": "file", - "description": "Tab-delimited file with RGI results", - "pattern": "*.{txt}", - "ontologies": [] - } - } - ] - ], - "tmp": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "temp/": { - "type": "directory", - "description": "Directory containing various intermediate files", - "pattern": "temp/" - } - } + "pipelines": [ + { + "name": "circrna", + "version": "dev" + }, + { + "name": "riboseq", + "version": "1.2.0" + }, + { + "name": "rnaseq", + "version": "3.26.0" + } ] - ], - "tool_version": [ - { - "RGI_VERSION": { - "type": "string", - "description": "The version of the tool in string format (useful for downstream tools such as hAMRronization)" - } - } - ], - "db_version": [ - { - "DB_VERSION": { - "type": "string", - "description": "The version of the used database in string format (useful for downstream tools such as hAMRronization)" - } - } - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@rpetit3", - "@jfy133", - "@jasmezz" - ], - "maintainers": [ - "@rpetit3", - "@jfy133", - "@jasmezz" - ] - }, - "pipelines": [ - { - "name": "funcscan", - "version": "3.0.0" - } - ] - }, - { - "name": "rhocall_annotate", - "path": "modules/nf-core/rhocall/annotate/meta.yml", - "type": "module", - "meta": { - "name": "rhocall_annotate", - "description": "Markup VCF file using rho-calls.", - "keywords": [ - "roh", - "rhocall", - "runs_of_homozygosity" - ], - "tools": [ - { - "rhocall": { - "description": "Call regions of homozygosity and make tentative UPD calls.", - "homepage": "https://github.com/dnil/rhocall", - "documentation": "https://github.com/dnil/rhocall", - "tool_dev_url": "https://github.com/dnil", - "licence": [ - "GPL v3" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "vcf file", - "pattern": "*.{vcf,vcf.gz}", - "ontologies": [] - } - }, - { - "tbi": { - "type": "file", - "description": "vcf index file", - "pattern": "*.{tbi}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + }, + { + "name": "ucsc_bedclip", + "path": "modules/nf-core/ucsc/bedclip/meta.yml", + "type": "module", + "meta": { + "name": "ucsc_bedclip", + "description": "Remove lines from bed file that refer to off-chromosome locations.", + "keywords": ["bed", "genomics", "ucsc"], + "tools": [ + { + "ucsc": { + "description": "Remove lines from bed file that refer to off-chromosome locations.", + "homepage": "http://hgdownload.cse.ucsc.edu/admin/exe/", + "licence": ["varies; see http://genome.ucsc.edu/license"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bedgraph": { + "type": "file", + "description": "bedGraph file", + "pattern": "*.{bedgraph}", + "ontologies": [] + } + } + ], + { + "sizes": { + "type": "file", + "description": "Chromosome sizes file", + "ontologies": [] + } + } + ], + "output": { + "bedgraph": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bedGraph": { + "type": "file", + "description": "bedGraph file", + "pattern": "*.{bedgraph}", + "ontologies": [] + } + } + ] + ], + "versions_ucsc": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "ucsc": { + "type": "string", + "description": "The tool name" + } + }, + { + "482": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "ucsc": { + "type": "string", + "description": "The tool name" + } + }, + { + "482": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@drpatelh"], + "maintainers": ["@drpatelh"] }, - { - "roh": { - "type": "file", - "description": "Bcftools roh style TSV file with CHR,POS,AZ,QUAL", - "pattern": "*.{roh}", - "ontologies": [] - } - } - ], - { - "bed": { - "type": "file", - "description": "BED file with AZ windows.", - "pattern": "*.{bed}", - "ontologies": [] - } - } - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_rhocall.vcf": { - "type": "file", - "description": "vcf file", - "pattern": "*.{vcf,vcf.gz}", - "ontologies": [] - } - } - ] - ], - "versions_rhocall": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "rhocall": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "rhocall --version | sed 's/rhocall, version //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "rhocall": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "rhocall --version | sed 's/rhocall, version //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "cutandrun", + "version": "3.2.2" + }, + { + "name": "hicar", + "version": "1.0.0" + }, + { + "name": "rnaseq", + "version": "3.26.0" + }, + { + "name": "rnasplice", + "version": "1.0.4" + } ] - ] - }, - "authors": [ - "@ramprasadn" - ], - "maintainers": [ - "@ramprasadn" - ] - }, - "pipelines": [ - { - "name": "raredisease", - "version": "3.0.0" - } - ] - }, - { - "name": "rhocall_viz", - "path": "modules/nf-core/rhocall/viz/meta.yml", - "type": "module", - "meta": { - "name": "rhocall_viz", - "description": "Call regions of homozygosity and make tentative UPD calls", - "keywords": [ - "roh", - "bcftools", - "runs_of_homozygosity" - ], - "tools": [ - { - "rhocall": { - "description": "Call regions of homozygosity and make tentative UPD calls.", - "homepage": "https://github.com/dnil/rhocall", - "documentation": "https://github.com/dnil/rhocall", - "tool_dev_url": "https://github.com/dnil", - "licence": [ - "GPL v3" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF file", - "pattern": "*.{vcf}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } + }, + { + "name": "ucsc_bedgraphtobigwig", + "path": "modules/nf-core/ucsc/bedgraphtobigwig/meta.yml", + "type": "module", + "meta": { + "name": "ucsc_bedgraphtobigwig", + "description": "Convert a bedGraph file to bigWig format.", + "keywords": ["bedgraph", "bigwig", "ucsc", "bedgraphtobigwig", "converter"], + "tools": [ + { + "ucsc": { + "description": "Convert a bedGraph file to bigWig format.", + "homepage": "http://hgdownload.cse.ucsc.edu/admin/exe/", + "documentation": "https://genome.ucsc.edu/goldenPath/help/bigWig.html", + "licence": ["varies; see http://genome.ucsc.edu/license"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bedgraph": { + "type": "file", + "description": "bedGraph file", + "pattern": "*.{bedGraph}", + "ontologies": [] + } + } + ], + { + "sizes": { + "type": "file", + "description": "chromosome sizes file", + "pattern": "*.{sizes}", + "ontologies": [] + } + } + ], + "output": { + "bigwig": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bigWig": { + "type": "file", + "description": "bigWig file", + "pattern": "*.{bigWig}", + "ontologies": [] + } + } + ] + ], + "versions_ucsc": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "ucsc": { + "type": "string", + "description": "The tool name" + } + }, + { + "482": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "ucsc": { + "type": "string", + "description": "The tool name" + } + }, + { + "482": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@drpatelh"], + "maintainers": ["@drpatelh"] }, - { - "roh": { - "type": "file", - "description": "Input RHO file produced from rhocall", - "pattern": "*.{roh}", - "ontologies": [] - } - } - ] - ], - "output": { - "bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "${prefix}/${prefix}.bed": { - "type": "file", - "description": "Bed file containing roh calls", - "pattern": "*.{bed}", - "ontologies": [] - } - } - ] - ], - "wig": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "${prefix}/${prefix}.wig": { - "type": "file", - "description": "Wig file containing roh calls", - "pattern": "*.{wig}", - "ontologies": [] - } - } - ] - ], - "versions_rhocall": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "rhocall": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "rhocall --version | sed 's/rhocall, version //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "rhocall": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "rhocall --version | sed 's/rhocall, version //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@ramprasadn" - ], - "maintainers": [ - "@ramprasadn" - ] - }, - "pipelines": [ - { - "name": "raredisease", - "version": "3.0.0" - } - ] - }, - { - "name": "ribocode_gtfupdate", - "path": "modules/nf-core/ribocode/gtfupdate/meta.yml", - "type": "module", - "meta": { - "name": "ribocode_gtfupdate", - "description": "Update GTF annotation file for RiboCode compatibility", - "keywords": [ - "ribo-seq", - "ribosome profiling", - "gtf", - "annotation" - ], - "tools": [ - { - "ribocode": { - "description": "A package for detecting the actively translated ORFs using ribosome-profiling data", - "homepage": "https://github.com/xryanglab/RiboCode", - "documentation": "https://github.com/xryanglab/RiboCode", - "tool_dev_url": "https://github.com/xryanglab/RiboCode", - "doi": "10.1093/nar/gky179", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "gtf": { - "type": "file", - "description": "GTF annotation file to update (uncompressed)", - "pattern": "*.{gtf}", - "ontologies": [] - } - } - ] - ], - "output": { - "gtf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*.gtf": { - "type": "file", - "description": "Updated GTF annotation file", - "pattern": "*_updated.gtf" - } - } - ] - ], - "versions_ribocode": [ - [ - { - "${task.process}": { - "type": "string", - "description": "Name of the process" - } - }, - { - "ribocode": { - "type": "string", - "description": "Name of the tool" - } - }, - { - "RiboCode --version 2>&1": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "Name of the process" - } - }, - { - "ribocode": { - "type": "string", - "description": "Name of the tool" - } - }, - { - "RiboCode --version 2>&1": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@JackCurragh" - ] - } - }, - { - "name": "ribocode_metaplots", - "path": "modules/nf-core/ribocode/metaplots/meta.yml", - "type": "module", - "meta": { - "name": "ribocode_metaplots", - "description": "Set up RiboCode ORF calling with metaplots", - "keywords": [ - "ribo-seq", - "ribosome profiling", - "orf calling" - ], - "tools": [ - { - "ribocode": { - "description": "A package for detecting the actively translated ORFs using ribosome-profiling data", - "homepage": "https://github.com/xryanglab/RiboCode", - "documentation": "https://github.com/xryanglab/RiboCode", - "tool_dev_url": "https://github.com/xryanglab/RiboCode", - "doi": "10.1093/nar/gky179", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing annotation information\ne.g. `[ id:'genome' ]`\n" - } - }, - { - "annotation": { - "type": "directory", - "description": "Directory containing annotation files from ribocode/prepare", - "pattern": "annotation" - } - } - ] - ], - "output": { - "config": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*config.txt": { - "type": "file", - "description": "RiboCode configuration file containing P-site offsets", - "pattern": "*_config.txt", - "ontologies": [] - } - } - ] - ], - "pdf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*.pdf": { - "type": "file", - "description": "PDF file containing P-site metaplots for quality control", - "pattern": "*_report.pdf", - "ontologies": [] - } - } - ] - ], - "versions_ribocode": [ - [ - { - "${task.process}": { - "type": "string", - "description": "Name of the process" - } - }, - { - "ribocode": { - "type": "string", - "description": "Name of the tool" - } - }, - { - "RiboCode --version 2>&1": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "Name of the process" - } - }, - { - "ribocode": { - "type": "string", - "description": "Name of the tool" - } - }, - { - "RiboCode --version 2>&1": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@JackCurragh" - ] - } - }, - { - "name": "ribocode_prepare", - "path": "modules/nf-core/ribocode/prepare/meta.yml", - "type": "module", - "meta": { - "name": "ribocode_prepare", - "description": "Prepare the annotation files for RiboCode ORF calling", - "keywords": [ - "ribo-seq", - "ribosome profiling", - "orf calling" - ], - "tools": [ - { - "ribocode": { - "description": "A package for detecting the actively translated ORFs using ribosome-profiling data", - "homepage": "https://github.com/xryanglab/RiboCode", - "documentation": "https://github.com/xryanglab/RiboCode", - "tool_dev_url": "https://github.com/xryanglab/RiboCode", - "doi": "10.1093/nar/gky179", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome FASTA file (uncompressed)", - "pattern": "*.{fasta,fa,fna}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. `[ id:'genome' ]`\n" - } - }, - { - "gtf": { - "type": "file", - "description": "Reference genome GTF annotation file (uncompressed, updated with ribocode/gtfupdate)", - "pattern": "*.{gtf}", - "ontologies": [] - } - } - ] - ], - "output": { - "annotation": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "annotation": { - "type": "directory", - "description": "Directory containing RiboCode annotation files (transcripts_cds.txt, transcripts_sequence.fa, transcripts.pickle)", - "pattern": "annotation/" - } - } - ] - ], - "versions_ribocode": [ - [ - { - "${task.process}": { - "type": "string", - "description": "Name of the process" - } - }, - { - "ribocode": { - "type": "string", - "description": "Name of the tool" - } - }, - { - "RiboCode --version 2>&1": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "Name of the process" - } - }, - { - "ribocode": { - "type": "string", - "description": "Name of the tool" - } - }, - { - "RiboCode --version 2>&1": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@JackCurragh" - ] - } - }, - { - "name": "ribocode_ribocode", - "path": "modules/nf-core/ribocode/ribocode/meta.yml", - "type": "module", - "meta": { - "name": "ribocode_ribocode", - "description": "Call ORFs with RiboCode from Ribo-Seq data", - "keywords": [ - "ribo-seq", - "ribosome profiling", - "orf calling" - ], - "tools": [ - { - "ribocode": { - "description": "A package for detecting the actively translated ORFs using ribosome-profiling data", - "homepage": "https://github.com/xryanglab/RiboCode", - "documentation": "https://github.com/xryanglab/RiboCode", - "tool_dev_url": "https://github.com/xryanglab/RiboCode", - "doi": "10.1093/nar/gky179", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing annotation information\ne.g. [ id:'genome' ]\n" - } - }, - { - "annotation": { - "type": "directory", - "description": "Directory containing RiboCode annotation files from ribocode/prepare", - "pattern": "annotation" - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing config information\ne.g. [ id:'config' ]\n" - } - }, - { - "config": { - "type": "file", - "description": "RiboCode configuration file containing P-site offsets from ribocode/metaplots", - "pattern": "*_config.txt", - "ontologies": [] - } - } - ] - ], - "output": { - "orf_txt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.txt": { - "type": "file", - "description": "Text file containing all detected ORFs with detailed information", - "pattern": "*.txt", - "ontologies": [] - } - } - ] - ], - "orf_txt_collapsed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}_collapsed.txt": { - "type": "file", - "description": "Text file containing collapsed ORFs (merged isoforms)", - "pattern": "*_collapsed.txt", - "ontologies": [] - } - } - ] - ], - "orf_pdf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_ORFs_category.pdf": { - "type": "file", - "description": "PDF file with ORF category distribution plots", - "pattern": "*_ORFs_category.pdf", - "ontologies": [] - } - } - ] - ], - "psites_hd5": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_psites.hd5": { - "type": "file", - "description": "HDF5 file containing P-site positions", - "pattern": "*_psites.hd5", - "ontologies": [] - } - } - ] - ], - "versions_ribocode": [ - [ - { - "${task.process}": { - "type": "string", - "description": "Name of the process" - } - }, - { - "ribocode": { - "type": "string", - "description": "Name of the tool" - } - }, - { - "RiboCode --version 2>&1": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "Name of the process" - } - }, - { - "ribocode": { - "type": "string", - "description": "Name of the tool" - } - }, - { - "RiboCode --version 2>&1": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@JackCurragh" - ] - } - }, - { - "name": "ribodetector", - "path": "modules/nf-core/ribodetector/meta.yml", - "type": "module", - "meta": { - "name": "ribodetector", - "description": "Accurate and rapid RiboRNA sequences Detector based on deep learning", - "keywords": [ - "RNA", - "RNAseq", - "rRNA", - "ribosomal RNA", - "rRNA depletion", - "rRNA removal", - "rRNA filtering", - "deep learning", - "Riboseq", - "genomics" - ], - "tools": [ - { - "ribodetector": { - "description": "Accurate and rapid RiboRNA sequences detector based on deep learning. RiboDetector uses a deep learning approach to identify rRNA sequences in ribosome profiling (Ribo-seq) data. It can be used to filter out rRNA reads from Ribo-seq datasets, improving the quality of downstream analyses. As of version 0.3.1, Ribodetector doesn't support setting a random seed, so results may not be fully deterministic across runs.", - "homepage": "https://github.com/hzi-bifo/RiboDetector", - "documentation": "https://github.com/hzi-bifo/RiboDetector", - "tool_dev_url": "https://github.com/hzi-bifo/RiboDetector", - "doi": "10.1093/nar/gkac112", - "licence": [ - "GPL v3-or-later" - ], - "identifier": "biotools:ribodetector" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing riboseq sample information\ne.g. `[ id:'sample1', single_end:false ]\n" - } - }, - { - "fastq": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ], - { - "length": { - "type": "integer", - "description": "Sequencing read length (mean length). Note: the accuracy reduces for reads shorter than 40\n", - "pattern": "integer >= 1" - } - } - ], - "output": { - "fastq": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*.nonrna*.fastq.gz": { - "type": "file", - "description": "rRNA depleted FastQ files", - "pattern": "*.nonrna*.fastq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - }, - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*.log": { - "type": "file", - "description": "Log file from RiboDetector", - "pattern": "*.log", - "ontologies": [] - } - } - ] - ], - "versions_ribodetector": [ - [ - { - "${task.process}": { - "type": "string", - "description": "Name of the process" - } - }, - { - "ribodetector": { - "type": "string", - "description": "Name of the tool" - } - }, - { - "ribodetector --version | sed \"s/ribodetector //\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_cuda": [ - [ - { - "${task.process}": { - "type": "string", - "description": "Name of the process" - } - }, - { - "cuda": { - "type": "string", - "description": "Name of the runtime" - } - }, - { - "python -c \"import torch; print(torch.version.cuda or 'no CUDA available')\"": { - "type": "eval", - "description": "CUDA version bundled with the task's pytorch build, or `no CUDA available` on the non-GPU path" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "Name of the process" - } - }, - { - "ribodetector": { - "type": "string", - "description": "Name of the tool" - } - }, - { - "ribodetector --version | sed \"s/ribodetector //\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "Name of the process" - } - }, - { - "cuda": { - "type": "string", - "description": "Name of the runtime" - } - }, - { - "python -c \"import torch; print(torch.version.cuda or 'no CUDA available')\"": { - "type": "eval", - "description": "CUDA version bundled with the task's pytorch build, or `no CUDA available` on the non-GPU path" - } - } - ] - ] - }, - "authors": [ - "@maxibor" - ], - "maintainers": [ - "@maxibor" - ] - }, - "pipelines": [ - { - "name": "rnaseq", - "version": "3.26.0" - } - ] - }, - { - "name": "ribotish_predict", - "path": "modules/nf-core/ribotish/predict/meta.yml", - "type": "module", - "meta": { - "name": "ribotish_predict", - "description": "Quality control of riboseq bam data", - "keywords": [ - "riboseq", - "predict", - "bam" - ], - "tools": [ - { - "ribotish": { - "description": "Ribo TIS Hunter (Ribo-TISH) identifies translation activities using ribosome profiling data.", - "homepage": "https://github.com/zhpn1024/ribotish", - "documentation": "https://github.com/zhpn1024/ribotish", - "tool_dev_url": "https://github.com/zhpn1024/ribotish", - "doi": "10.1038/s41467-017-01981-8", - "licence": [ - "GPL v3" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing riboseq sample information\ne.g. `[ id:'sample1', single_end:false ]\n" - } - }, - { - "bam_ribo": { - "type": "file", - "description": "Sorted riboseq BAM file(s)", - "pattern": "*.{bam}", - "ontologies": [] - } - }, - { - "bai_ribo": { - "type": "file", - "description": "Index for sorted riboseq bam file(s)", - "pattern": "*.{bai}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing TI-Seq sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "bam_ti": { - "type": "file", - "description": "Sorted TI-Seq BAM file(s)", - "pattern": "*.{bam}", - "ontologies": [] - } - }, - { - "bai_ti": { - "type": "file", - "description": "Index for sorted TI-Seq BAM file(s)", - "pattern": "*.{bai}", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. `[ id:'Ensembl human v.111' ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Fasta-format sequence file for reference sequences used in the bam file\n", - "pattern": "*.gtf", - "ontologies": [] - } - }, - { - "gtf": { - "type": "file", - "description": "GTF-format annotation file for reference sequences used in the bam file\n", - "pattern": "*.gtf", - "ontologies": [] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing information on candidate ORFs\n" - } - }, - { - "candidate_orfs": { - "type": "file", - "description": "3-column (transIDstarttstop) candidate ORFs file\n", - "pattern": "*.txt", - "ontologies": [] - } - } - ], - [ - { - "meta5": { - "type": "map", - "description": "Groovy Map containing information on riboseq P-site offset parameter\nfiles\n" - } - }, - { - "para_ribo": { - "type": "file", - "description": "Input P-site offset parameter files for riboseq bam files\n", - "pattern": "*.py", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3996" - } - ] - } - } - ], - [ - { - "meta6": { - "type": "map", - "description": "Groovy Map containing information on TI-seq P-site offset parameter\nfiles\n" - } - }, - { - "para_ti": { - "type": "file", - "description": "Input P-site offset parameter files for TI-seq bam files\n", - "pattern": "*.py", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3996" - } - ] - } - } - ], - [ - { - "meta7": { - "type": "map", - "description": "Groovy Map containing reference information for the secondary\nannotation file\n" - } - }, - { - "reference_gtf": { - "type": "file", - "description": "Optional secondary GTF annotation passed to ribotish as\n`-a ` (e.g. a MANE/RefSeq overlay applied on\ntop of the primary GTF). Pass `[]` to omit.\n", - "pattern": "*.gtf", - "ontologies": [] - } - } - ] - ], - "output": { - "predictions": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*_pred.txt": { - "type": "file", - "description": "txt file all possible ORF results that fit the thresholds\n", - "pattern": "*.{txt}", - "ontologies": [] - } - } - ] - ], - "all": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*_all.txt": { - "type": "file", - "description": "txt file similar to the predictions but do not use FDR (q-value) cutoff\n", - "pattern": "*.{txt}", - "ontologies": [] - } - } - ] - ], - "transprofile": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*_transprofile.py": { - "type": "file", - "description": "Output RPF P-site profile for each transcript. The profile data is in\npython dict format, recording non-zero read counts at different\npositions on transcript.\n", - "pattern": "*.{py}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3996" - } - ] - } - } - ] - ], - "versions_ribotish": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "ribotish": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "ribotish --version | sed 's/ribotish //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "ribotish": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "ribotish --version | sed 's/ribotish //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@pinin4fjords" - ], - "maintainers": [ - "@pinin4fjords" - ] - }, - "pipelines": [ - { - "name": "riboseq", - "version": "1.2.0" - } - ] - }, - { - "name": "ribotish_quality", - "path": "modules/nf-core/ribotish/quality/meta.yml", - "type": "module", - "meta": { - "name": "ribotish_quality", - "description": "Quality control of riboseq bam data", - "keywords": [ - "riboseq", - "quality", - "bam" - ], - "tools": [ - { - "ribotish": { - "description": "Ribo TIS Hunter (Ribo-TISH) identifies translation activities using ribosome profiling data.", - "homepage": "https://github.com/zhpn1024/ribotish", - "documentation": "https://github.com/zhpn1024/ribotish", - "tool_dev_url": "https://github.com/zhpn1024/ribotish", - "doi": "10.1038/s41467-017-01981-8", - "licence": [ - "GPL v3" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM/CRAM/SAM file", - "pattern": "*.{bam}", - "ontologies": [] - } - }, - { - "bai": { - "type": "file", - "description": "Index for sorted BAM/CRAM/SAM file", - "pattern": "*.{bai}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. `[ id:'Ensembl human v.111' ]`\n" - } - }, - { - "gtf": { - "type": "file", - "description": "GTF-format annotation file for reference sequences used in the bam file\n", - "pattern": "*.gtf", - "ontologies": [] - } - } - ] - ], - "output": { - "distribution": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.txt": { - "type": "file", - "description": "file containing distribution", - "pattern": "*.{txt}", - "ontologies": [] - } - } - ] - ], - "pdf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.pdf": { - "type": "file", - "description": "Pdf figure file is plot of all the distributions and illustration of\nquality and P-site offset\n", - "pattern": "*.{pdf}", - "ontologies": [] - } - } - ] - ], - "offset": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.para.py": { - "type": "file", - "description": "This file saves P-site offsets for different reads lengths in python\ncode dict format, and can be used in further analysis\n", - "pattern": "*.{para.py}", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@pinin4fjords" - ], - "maintainers": [ - "@pinin4fjords" - ] - }, - "pipelines": [ - { - "name": "riboseq", - "version": "1.2.0" - } - ] - }, - { - "name": "ribotricer_detectorfs", - "path": "modules/nf-core/ribotricer/detectorfs/meta.yml", - "type": "module", - "meta": { - "name": "ribotricer_detectorfs", - "description": "Accurate detection of short and long active ORFs using Ribo-seq data", - "keywords": [ - "riboseq", - "orf", - "genomics" - ], - "tools": [ - { - "ribotricer": { - "description": "Python package to detect translating ORF from Ribo-seq data", - "homepage": "https://github.com/smithlabcode/ribotricer", - "documentation": "https://github.com/smithlabcode/ribotricer", - "tool_dev_url": "https://github.com/smithlabcode/ribotricer", - "doi": "10.1093/bioinformatics/btz878", - "licence": [ - "GNU General Public v3 (GPL v3)" - ], - "identifier": "biotools:ribotricer" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Map containing riboseq sample information\ne.g. `[ id:'sample1', single_end:false, strandedness: 'single' ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM/SAM file", - 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] - } - } - ] - ], - "tp_tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tp.vcf.gz.tbi": { - "type": "file", - "description": "The index of the VCF file for the true positive variants", - "pattern": "*.tp.vcf.gz.tbi", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3616" - } - ] - } - } - ] - ], - "fn_vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.fn.vcf.gz": { - "type": "file", - "description": "A VCF file for the false negative variants", - "pattern": "*.fn.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - }, + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file containing reads to be deduplicated via UMIs.\n", + "pattern": "*.{bam}", + "ontologies": [] + } + }, + { + "bai": { + "type": "file", + "description": "BAM index files corresponding to the input BAM file.\n", + "pattern": "*.{bai}", + "ontologies": [] + } + } + ], { - "edam": "http://edamontology.org/format_3989" + "get_output_stats": { + "type": "boolean", + "description": "Whether or not to generate output stats.\n" + } } - ] + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.bam": { + "type": "file", + "description": "BAM file with deduplicated UMIs.", + "pattern": "*.{bam}", + "ontologies": [] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "File with logging information", + "pattern": "*.{log}", + "ontologies": [] + } + } + ] + ], + "tsv_edit_distance": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*edit_distance.tsv": { + "type": "file", + "description": "Reports the (binned) average edit distance between the UMIs at each position.", + "pattern": "*edit_distance.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "tsv_per_umi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*per_umi.tsv": { + "type": "file", + "description": "UMI-level summary statistics.", + "pattern": "*per_umi.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "tsv_umi_per_position": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*per_position.tsv": { + "type": "file", + "description": "Tabulates the counts for unique combinations of UMI and position.", + "pattern": "*per_position.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_umitools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "umitools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "umi_tools --version | sed 's/UMI-tools version: //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "umitools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "umi_tools --version | sed 's/UMI-tools version: //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@drpatelh", "@grst", "@klkeys"], + "maintainers": ["@drpatelh", "@grst", "@klkeys"] + }, + "pipelines": [ + { + "name": "alleleexpression", + "version": "dev" + }, + { + "name": "lncpipe", + "version": "dev" + }, + { + "name": "nascent", + "version": "2.3.0" + }, + { + "name": "radseq", + "version": "dev" + }, + { + "name": "riboseq", + "version": "1.2.0" + }, + { + "name": "rnaseq", + "version": "3.26.0" + }, + { + "name": "scnanoseq", + "version": "1.2.2" + }, + { + "name": "viralmetagenome", + "version": "1.1.1" } - } ] - ], - "fn_tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.fn.vcf.gz.tbi": { - "type": "file", - "description": "The index of the VCF file for the false negative variants", - "pattern": "*.fn.vcf.gz.tbi", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3616" - } - ] - } - } - ] - ], - "fp_vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.fp.vcf.gz": { - "type": "file", - "description": "A VCF file for the false positive variants", - "pattern": "*.fp.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - }, - { - "edam": "http://edamontology.org/format_3989" + }, + { + "name": "umitools_extract", + "path": "modules/nf-core/umitools/extract/meta.yml", + "type": "module", + "meta": { + "name": "umitools_extract", + "description": "Extracts UMI barcode from a read and add it to the read name, leaving any sample barcode in place", + "keywords": ["UMI", "barcode", "extract", "umitools"], + "tools": [ + { + "umi_tools": { + "description": "UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes\n", + "documentation": "https://umi-tools.readthedocs.io/en/latest/", + "license": "MIT", + "identifier": "" + } } - ] + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "list", + "description": "List of input FASTQ files whose UMIs will be extracted.\n" + } + } + ] + ], + "output": { + "reads": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fastq.gz": { + "type": "file", + "description": "Extracted FASTQ files. | For single-end reads, pattern is \\${prefix}.umi_extract.fastq.gz. | For paired-end reads, pattern is \\${prefix}.umi_extract_{1,2}.fastq.gz.\n", + "pattern": "*.{fastq.gz}", + "ontologies": [] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "Logfile for umi_tools", + "pattern": "*.{log}", + "ontologies": [] + } + } + ] + ], + "versions_umitools": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "umitools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "umi_tools --version | sed -n '/version:/s/.*: //p'": { + "type": "eval", + "description": "The expression to obtain the version of umitools" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "umitools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "umi_tools --version | sed -n '/version:/s/.*: //p'": { + "type": "eval", + "description": "The expression to obtain the version of umitools" + } + } + ] + ] + }, + "authors": ["@drpatelh", "@grst"], + "maintainers": ["@drpatelh", "@grst"] + }, + "pipelines": [ + { + "name": "atacseq", + "version": "2.1.2" + }, + { + "name": "callingcards", + "version": "1.0.0" + }, + { + "name": "chipseq", + "version": "2.1.0" + }, + { + "name": "lncpipe", + "version": "dev" + }, + { + "name": "panoramaseq", + "version": "dev" + }, + { + "name": "riboseq", + "version": "1.2.0" + }, + { + "name": "rnafusion", + "version": "4.1.2" + }, + { + "name": "rnaseq", + "version": "3.26.0" + }, + { + "name": "rnasplice", + "version": "1.0.4" + }, + { + "name": "rnavar", + "version": "1.2.3" + }, + { + "name": "smrnaseq", + "version": "2.4.1" + }, + { + "name": "viralmetagenome", + "version": "1.1.1" } - } ] - ], - "fp_tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.fp.vcf.gz.tbi": { - "type": "file", - "description": "The index of the VCF file for the false positive variants", - "pattern": "*.fp.vcf.gz.tbi", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3616" - } - ] - } - } - ] - ], - "baseline_vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tp-baseline.vcf.gz": { - "type": "file", - "description": "A VCF file for the true positive variants from the baseline", - "pattern": "*.tp-baseline.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - }, - { - "edam": "http://edamontology.org/format_3989" + }, + { + "name": "umitools_group", + "path": "modules/nf-core/umitools/group/meta.yml", + "type": "module", + "meta": { + "name": "umitools_group", + "description": "Group reads based on their UMI and mapping coordinates", + "keywords": ["umitools", "umi", "deduplication", "dedup", "clustering"], + "tools": [ + { + "umi_tools": { + "description": "UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes\n", + "documentation": "https://umi-tools.readthedocs.io/en/latest/", + "license": ["MIT"], + "identifier": "" + } } - ] - } - } - ] - ], - "baseline_tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tp-baseline.vcf.gz.tbi": { - "type": "file", - "description": "The index of the VCF file for the true positive variants from the baseline", - "pattern": "*.tp-baseline.vcf.gz.tbi", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3616" - } - ] - } - } - ] - ], - "weighted_roc": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.weighted_roc.tsv.gz": { - "type": "file", - "description": "TSV files containing weighted ROC data for all variants", - "pattern": "*.weighted_snp_roc.tsv.gz", - "ontologies": [ + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file containing reads to be deduplicated via UMIs.\n", + "pattern": "*.{bam}", + "ontologies": [] + } + }, + { + "bai": { + "type": "file", + "description": "BAM index files corresponding to the input BAM file.\n", + "pattern": "*.{bai}", + "ontologies": [] + } + } + ], { - "edam": "http://edamontology.org/format_3616" + "create_bam": { + "type": "boolean", + "description": "Whether or not to create a read group tagged BAM file.\n" + } }, { - "edam": "http://edamontology.org/format_3989" + "get_group_info": { + "type": "boolean", + "description": "Whether or not to generate the flatfile describing the read groups, see docs for complete info of all columns\n" + } } - ] - } - } - ] - ], - "summary": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.summary.txt": { - "type": "file", - "description": "A TXT file containing the summary of the evaluation", - "pattern": "*.summary.txt", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1964" - } - ] - } - } - ] - ], - "versions_rtgtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "rtgtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "rtg version | sed 's/Product: RTG Tools //; q'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "rtgtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "rtg version | sed 's/Product: RTG Tools //; q'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@kubranarci" - ], - "maintainers": [ - "@kubranarci" - ] - }, - "pipelines": [ - { - "name": "variantbenchmarking", - "version": "1.5.0" - } - ] - }, - { - "name": "rtgtools_cnveval", - "path": "modules/nf-core/rtgtools/cnveval/meta.yml", - "type": "module", - "meta": { - "name": "rtgtools_cnveval", - "description": "The cnveval tool of RTG tools. It is used to evaluate called CNV regions for agreement with a baseline CNV set.", - "keywords": [ - "benchmarking", - "vcf", - "rtg-tools", - "cnv-eval", - "copy-number-variants" - ], - "tools": [ - { - "rtgtools": { - "description": "RealTimeGenomics Tools -- Utilities for accurate VCF comparison and manipulation.", - "homepage": "https://www.realtimegenomics.com/products/rtg-tools", - "documentation": "https://cdn.jsdelivr.net/gh/RealTimeGenomics/rtg-tools@master/installer/resources/tools/RTGOperationsManual.pdf", - "tool_dev_url": "https://github.com/RealTimeGenomics/rtg-tools", - "licence": [ - "BSD-2-clause" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "query_vcf": { - "type": "file", - "description": "A VCF with called CNV variants to benchmark against the baseline. Records must contain INFO END and INFO SVTYPE (DUP or DEL).", - "pattern": "*.{vcf,vcf.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - } - ] - } - }, - { - "query_vcf_tbi": { - "type": "file", - "description": "The index of the VCF file with called variants", - "pattern": "*.{vcf.gz.tbi,vcf.tbi}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3616" - } - ] - } - }, - { - "truth_vcf": { - "type": "file", - "description": "A baseline VCF containing expected CNV calls. Records must contain INFO END and INFO SVTYPE (DUP or DEL).", - "pattern": "*.{vcf,vcf.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - } - ] - } - }, - { - "truth_vcf_tbi": { - "type": "file", - "description": "The index of the baseline VCF to compare against", - "pattern": "*.{vcf.gz.tbi,vcf.tbi}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3616" - } - ] - } - }, - { - "evaluation_regions_bed": { - "type": "file", - "description": "A BED file containing the regions of interest for evaluation (required). Regions are intersected with truth and calls VCFs to obtain CNV regions.", - "pattern": "*.bed", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3003" - } - ] - } + ], + "output": { + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "File with logging information", + "pattern": "*.{log}", + "ontologies": [] + } + } + ] + ], + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.bam": { + "type": "file", + "description": "a read group tagged BAM file.", + "pattern": "${prefix}.{bam}", + "ontologies": [] + } + } + ] + ], + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "Flatfile describing the read groups, see docs for complete info of all columns", + "pattern": "*.{tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@Joon-Klaps"], + "maintainers": ["@Joon-Klaps"] } - ] - ], - "output": { - "baseline_bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.baseline.bed.gz": { - "type": "file", - "description": "A BED file containing truth CNV regions with TP/FN status, SVTYPE, and the span of the original truth VCF record", - "pattern": "*.baseline.bed.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3003" - }, - { - "edam": "http://edamontology.org/format_3989" + }, + { + "name": "umitools_prepareforrsem", + "path": "modules/nf-core/umitools/prepareforrsem/meta.yml", + "type": "module", + "meta": { + "name": "umitools_prepareforrsem", + "description": "Make the output from umi_tools dedup or group compatible with RSEM", + "keywords": ["umitools", "rsem", "salmon", "dedup"], + "tools": [ + { + "umi_tools": { + "description": "UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes\n", + "documentation": "https://umi-tools.readthedocs.io/en/latest/", + "license": ["MIT"], + "identifier": "" + } } - 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If no backbone tree nor alignment is given, the sequence file will be randomly split into a backbone set and query set", + "pattern": "*.{fa,fna,faa,fasta}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1919" + }, + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + }, + { + "fasta_aligned": { + "type": "file", + "description": "Aligned sequence file. (optional)", + "pattern": "*.{fa,fna,faa,fasta,aln}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1919" + }, + { + "edam": "http://edamontology.org/format_1929" + }, + { + "edam": "http://edamontology.org/format_1984" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing tree information\ne.g. `[ id:'test_tree']`\n" + } + }, + { + "tree": { + "type": "file", + "description": "Input guide tree, in Newick format.", + "pattern": "*.{dnd}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2006" + } + ] + } + } + ], { - "edam": "http://edamontology.org/format_3989" + "compress": { + "type": "boolean", + "description": "Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression." + } } - ] - } - } - ] - ], - "index": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "*.vcf.gz.tbi": { - "type": "file", - "description": "Index of VCF file with SVTYPE BND variants", - "pattern": "*.vcf.gz.tbi", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3616" - } - ] - } - } - ] - ], - "versions_rtgtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "rtgtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "rtg version | sed 's/Product: RTG Tools //; q'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "rtgtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "rtg version | sed 's/Product: RTG Tools //; q'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@kubranarci" - ], - "maintainers": [ - "@kubranarci" - ] - }, - "pipelines": [ - { - "name": "variantbenchmarking", - "version": "1.5.0" - } - ] - }, - { - "name": "rtgtools_vcfeval", - "path": "modules/nf-core/rtgtools/vcfeval/meta.yml", - "type": "module", - "meta": { - "name": "rtgtools_vcfeval", - "description": "The VCFeval tool of RTG tools. 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May be gzipped or uncompressed, depending on if compress is set to true or false", + "pattern": "*.aln{.gz,}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2554" + }, + { + "edam": "http://edamontology.org/format_1921" + }, + { + "edam": "http://edamontology.org/format_1984" + } + ] + } + } + ] + ], + "versions_sepp": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "sepp": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "run_upp.py -v | grep \"run_upp\" | cut -f2 -d\" \"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "sepp": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "run_upp.py -v | grep \"run_upp\" | cut -f2 -d\" \"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@luisas"], + "maintainers": ["@luisas"] }, - { - "sdf": { - "type": "file", - "description": "The SDF (RTG Sequence Data File) folder of the reference genome", - "ontologies": [] - } - } - ] - ], - "output": { - "tp_vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tp.vcf.gz": { - "type": "file", - "description": "A VCF file for the true positive variants", - "pattern": "*.tp.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "tp_tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tp.vcf.gz.tbi": { - "type": "file", - "description": "The index of the VCF file for the true positive variants", - "pattern": "*.tp.vcf.gz.tbi", - "ontologies": [] - } - } - ] - ], - "fn_vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.fn.vcf.gz": { - "type": "file", - "description": "A VCF file for the false negative variants", - "pattern": "*.fn.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "fn_tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.fn.vcf.gz.tbi": { - "type": "file", - "description": "The index of the VCF file for the false negative variants", - "pattern": "*.fn.vcf.gz.tbi", - "ontologies": [] - } - } - ] - ], - "fp_vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.fp.vcf.gz": { - "type": "file", - "description": "A VCF file for the false positive variants", - "pattern": "*.fp.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "fp_tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.fp.vcf.gz.tbi": { - "type": "file", - "description": "The index of the VCF file for the false positive variants", - "pattern": "*.fp.vcf.gz.tbi", - "ontologies": [] - } - } - ] - ], - "baseline_vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tp-baseline.vcf.gz": { - "type": "file", - "description": "A VCF file for the true positive variants from the baseline", - "pattern": "*.tp-baseline.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "baseline_tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tp-baseline.vcf.gz.tbi": { - "type": "file", - "description": "The index of the VCF file for the true positive variants from the baseline", - "pattern": "*.tp-baseline.vcf.gz.tbi", - "ontologies": [] - } - } - ] - ], - "snp_roc": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.snp_roc.tsv.gz": { - "type": "file", - "description": "TSV files containing ROC data for the SNPs", - "pattern": "*.snp_roc.tsv.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "non_snp_roc": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.non_snp_roc.tsv.gz": { - "type": "file", - "description": "TSV files containing ROC data for all variants except SNPs", - "pattern": "*.non_snp_roc.tsv.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "weighted_roc": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.weighted_roc.tsv.gz": { - "type": "file", - "description": "TSV files containing weighted ROC data for all variants", - "pattern": "*.weighted_snp_roc.tsv.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "summary": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.summary.txt": { - "type": "file", - "description": "A TXT file containing the summary of the evaluation", - "pattern": "*.summary.txt", - "ontologies": [] - } - } - ] - ], - "phasing": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.phasing.txt": { - "type": "file", - "description": "A TXT file containing the data on the phasing", - "pattern": "*.phasing.txt", - "ontologies": [] - } - } - ] - ], - "versions_rtgtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "rtgtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "rtg version | sed 's/Product: RTG Tools //; q'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "rtgtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "rtg version | sed 's/Product: RTG Tools //; q'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "multiplesequencealign", + "version": "1.1.1" + } ] - ] }, - "authors": [ - "@nvnieuwk" - ], - "maintainers": [ - "@nvnieuwk" - ] - }, - "pipelines": [ { - "name": "raredisease", - "version": "3.0.0" + "name": "vamb_bin", + "path": "modules/nf-core/vamb/bin/meta.yml", + "type": "module", + "meta": { + "name": "vamb_bin", + "description": "Variational autoencoder for metagenomic binning", + "keywords": ["clustering", "binning", "metagenomics", "denovo assembly", "mag"], + "tools": [ + { + "vamb": { + "description": "Variational autoencoder for metagenomic binning.", + "homepage": "https://vamb.readthedocs.io/en/latest", + "documentation": "https://vamb.readthedocs.io/en/latest", + "tool_dev_url": "https://github.com/RasmussenLab/vamb", + "doi": "10.1038/s41587-020-00777-4", + "licence": ["MIT"], + "identifier": "biotools:vamb" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" + } + }, + { + "assembly": { + "type": "file", + "description": "FASTA file of contigs for binning", + "pattern": "*.{fa,fas,fasta,fna,fa.gz,fas.gz,fasta.gz,fna.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + }, + { + "abundance_tsv": { + "type": "file", + "description": "TSV describing abundance of contigs in the provided assembly with headers\ncontigname\\tsample1\\tsample2...\nctg00001\\t10.0\\t5.0\n\nNot compatible with bam input.\n", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, + { + "bams": { + "type": "file", + "description": "List of sorted bam files of reads mapped to the reference assembly. Not compatible with TSV input.\n", + "pattern": "*.bam", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + }, + { + "taxonomy": { + "type": "file", + "description": "TSV describing the taxonomic lineage of each contig, with headers\ncontigs\\tpredictions\nctg00001\\tBacteria;Pseudomonadati;Pseudomonadota;Gammaproteobacteria;Enterobacterales;Enterobacteriacea;Escherichia coli\n", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "output": { + "bins": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" + } + }, + { + "${prefix}/bins/*.fna.gz": { + "type": "file", + "description": "List of FASTA files of binned contigs", + "pattern": "*.fna.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ] + ], + "clusters_metadata": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" + } + }, + { + "${prefix}/vae*_clusters_metadata.tsv": { + "type": "file", + "description": "TSV describing the metadata of the output bin clusters\n", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "clusters_split": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" + } + }, + { + "${prefix}/vae*_clusters_split.tsv": { + "type": "file", + "description": "TSV defining the output bin clusters if binsplitting enabled\n", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "clusters_unsplit": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" + } + }, + { + "${prefix}/vae*_clusters_unsplit.tsv": { + "type": "file", + "description": "TSV defining the output bin clusters without binsplitting\n", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "taxometer_results": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" + } + }, + { + "${prefix}/results_taxometer.tsv": { + "type": "file", + "description": "TSV describing the refined taxonomic lineage of each contig, with headers\ncontigs\\tpredictions\\tscores\n", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "latent_encoding": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" + } + }, + { + "${prefix}/latent.npz": { + "type": "file", + "description": "Numpy array of the latent embedding of the contigs\n", + "pattern": "*.npz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_4003" + } + ] + } + } + ] + ], + "abundance": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" + } + }, + { + "${prefix}/abundance.npz": { + "type": "file", + "description": "Numpy array of the abundance of contigs\n", + "pattern": "*.npz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_4003" + } + ] + } + } + ] + ], + "composition": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" + } + }, + { + "${prefix}/composition.npz": { + "type": "file", + "description": "Numpy array of the kmer composition of the contigs\n", + "pattern": "*.npz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_4003" + } + ] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" + } + }, + { + "${prefix}/log.txt": { + "type": "file", + "description": "Vamb log file\n", + "pattern": "*.log", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3671" + } + ] + } + } + ] + ], + "versions_vamb": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "vamb": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "vamb --version | sed 's/Vamb //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "vamb": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "vamb --version | sed 's/Vamb //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@prototaxites"], + "maintainers": ["@prototaxites"] + } }, { - "name": "variantbenchmarking", - "version": "1.5.0" - } - ] - }, - { - "name": "rtn_tni", - "path": "modules/nf-core/rtn/tni/meta.yml", - "type": "module", - "meta": { - "name": "rtn_tni", - "description": "Uses the RTN R package for transcriptional regulatory network inference (TNI).", - "keywords": [ - "regulatory network", - "transcriptomics", - "transcription factors" - ], - "tools": [ - { - "rtn": { - "description": "RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons", - "homepage": "https://www.bioconductor.org/packages/release/bioc/html/RTN.html", - "documentation": "https://www.bioconductor.org/packages/release/bioc/vignettes/RTN/inst/doc/RTN.html", - "tool_dev_url": "https://www.bioconductor.org/packages/release/bioc/html/RTN.html", - "doi": "10.1038/ncomms3464", - "licence": [ - "Artistic-2.0" - ], - "identifier": "biotools:rtn" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "expression_matrix": { - "type": "file", - "description": "expression matrix in TSV format", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "output": { - "tni": [ - [ - { - "meta": { - "type": "file", - "description": "RDS R Object with the TNI object", - "pattern": "tni.rds", - "ontologies": [] - } - }, - { - "tni.rds": { - "type": "file", - "description": "RDS R Object with the TNI object", - "pattern": "tni.rds", - "ontologies": [] - } - } - ] - ], - "tni_perm": [ - [ - { - "meta": { - "type": "file", - "description": "RDS R Object with the TNI object", - "pattern": "tni.rds", - "ontologies": [] - } - }, - { - "tni_permutated.rds": { - "type": "file", - "description": "RDS R Object with the TNI object after permutation", - "pattern": "tni_permutated.rds", - "ontologies": [] - } - } - ] - ], - "tni_bootstrap": [ - [ - { - "meta": { - "type": "file", - "description": "RDS R Object with the TNI object", - "pattern": "tni.rds", - "ontologies": [] - } - }, - { - "tni_bootstrapped.rds": { - "type": "file", - "description": "RDS R Object with the TNI object after permutation and bootstrap", - "pattern": "tni_bootstrapped.rds", - "ontologies": [] - } - } - ] - ], - "tni_filtered": [ - [ - { - "meta": { - "type": "file", - "description": "RDS R Object with the TNI object", - "pattern": "tni.rds", - "ontologies": [] - } - }, - { - "tni_filtered.rds": { - "type": "file", - "description": "RDS R Object with the TNI object after permutation, bootstrap and filtering", - "pattern": "tni_filtered.rds", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "YAML file containing versions of tools used in the module", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "topics": { - "versions": [ - { - "versions.yml": { - "type": "string", - "description": "The name of the process" - } - } - ] - }, - "authors": [ - "@mribeirodantas" - ], - "maintainers": [ - "@mribeirodantas" - ] - } - }, - { - "name": "rundbcan_cazymeannotation", - "path": "modules/nf-core/rundbcan/cazymeannotation/meta.yml", - "type": "module", - "meta": { - "name": "rundbcan_cazymeannotation", - "description": "CAZyme annotation module for the dbcan pipeline. This module is used to annotate carbohydrate-active enzymes (CAZymes) from genomic data using the dbCAN annotation tool.", - "keywords": [ - "dbCAN", - "download", - "CAZyme", - "CAZyme gene Cluster", - "genomes" - ], - "tools": [ - { - "dbcan": { - "description": "Standalone version of dbCAN annotation tool for automated CAZyme annotation.", - "homepage": "https://bcb.unl.edu/dbCAN2/", - "documentation": "https://run-dbcan.readthedocs.io/en/latest/", - "tool_dev_url": "https://github.com/bcb-unl/run_dbcan", - "doi": "10.1093/nar/gkad328", - "licence": [ - "GPL v3-or-later" - ], - "identifier": "biotools:dbcan" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "input_raw_data": { - "type": "file", - "description": "FASTA file for protein sequences.", - "pattern": "*.{fasta,fa,faa}", - "ontologies": [ - { - "edam": "http://edamontology.org/data_2044" - }, - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - { - "dbcan_db": { - "type": "directory", - "description": "Path to the dbCAN database directory." - } - } - ], - "output": { - "cazyme_annotation": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } - }, - { - "${prefix}_overview.tsv": { - "type": "file", - "description": "TSV file containing the results of dbCAN CAZyme annotation.\n", - "ontologies": [] - } - } - ] - ], - "dbcanhmm_results": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } - }, - { - "${prefix}_dbCAN_hmm_results.tsv": { - "type": "file", - "description": "TSV file containing the detailed dbCAN HMM results for CAZyme annotation.\n", - "ontologies": [] - } - } - ] - ], - "dbcansub_results": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } - }, - { - "${prefix}_dbCANsub_hmm_results.tsv": { - "type": "file", - "description": "TSV file containing the detailed dbCAN subfamily results for CAZyme annotation.\n", - "ontologies": [] - } - } - ] - ], - "dbcandiamond_results": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } - }, - { - "${prefix}_diamond.out": { - "type": "file", - "description": "TSV file containing the detailed dbCAN diamond results for CAZyme annotation.\n", - "ontologies": [] - } - } - ] - ], - "versions_rundbcan": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "rundbcan": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "run_dbcan version | sed 's/dbCAN version: //g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "rundbcan": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "run_dbcan version | sed 's/dbCAN version: //g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@Xinpeng021001" - ], - "maintainers": [ - "@Xinpeng021001" - ] - } - }, - { - "name": "rundbcan_database", - "path": "modules/nf-core/rundbcan/database/meta.yml", - "type": "module", - "meta": { - "name": "rundbcan_database", - "description": "command from run_dbcan to prepare the database for dbCAN annotation.", - "keywords": [ - "dbCAN", - "download", - "CAZyme", - "CAZyme gene Cluster", - "genomes" - ], - "tools": [ - { - "run_dbcan": { - "description": "Standalone version of dbCAN annotation tool for automated CAZyme annotation.", - "homepage": "https://bcb.unl.edu/dbCAN2/", - "documentation": "https://run-dbcan.readthedocs.io/en/latest/", - "tool_dev_url": "https://github.com/bcb-unl/run_dbcan", - "doi": "10.1093/nar/gkad328", - "licence": [ - "GPL v3-or-later" - ], - "identifier": "biotools:dbcan" - } - } - ], - "input": [], - "output": { - "dbcan_db": [ - { - "dbcan_db": { - "type": "directory", - "description": "Download directory for dbCAN databases", - "pattern": "dbcan_db" - } - } - ], - "versions_rundbcan": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "rundbcan": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "run_dbcan version | sed 's/dbCAN version: //g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "rundbcan": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "run_dbcan version | sed 's/dbCAN version: //g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@Xinpeng021001" - ], - "maintainers": [ - "@Xinpeng021001" - ] - } - }, - { - "name": "rundbcan_easycgc", - "path": "modules/nf-core/rundbcan/easycgc/meta.yml", - "type": "module", - "meta": { - "name": "rundbcan_easycgc", - "description": "CGC annotation module for the dbcan pipeline. This module is used to annotate carbohydrate-active enzymes (CAZymes) from genomic data using the dbCAN annotation tool.", - "keywords": [ - "dbCAN", - "download", - "CAZyme", - "CAZyme gene Cluster", - "genomes" - ], - "tools": [ - { - "dbcan": { - "description": "Standalone version of dbCAN annotation tool for automated CAZyme annotation.", - "homepage": "https://bcb.unl.edu/dbCAN2/", - "documentation": "https://run-dbcan.readthedocs.io/en/latest/", - "tool_dev_url": "https://github.com/bcb-unl/run_dbcan", - "doi": "10.1093/nar/gkad328", - "licence": [ - "GPL v3-or-later" - ], - "identifier": "biotools:dbcan" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "input_raw_data": { - "type": "file", - "description": "FASTA file for protein sequences.", - "pattern": "*.{fasta,fa,faa}", - "ontologies": [ - { - "edam": "http://edamontology.org/data_2044" - }, - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "input_gff": { - "type": "file", - "description": "GFF file for protein sequences.", - "ontologies": [] - } - }, - { - "gff_type": { - "type": "string", - "description": "Type of GFF file. Options are `NCBI_prok`, `JGI`, `NCBI_euk`, and `prodigal`. This is used to parse the GFF file correctly.\n" - } - } - ], - { - "dbcan_db": { - "type": "directory", - "description": "Path to the dbCAN database directory." - } - } - ], - "output": { - "cazyme_annotation": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } - }, - { - "${prefix}_overview.tsv": { - "type": "file", - "description": "TSV file containing the results of dbCAN CAZyme annotation.\n", - "ontologies": [] - } - } - ] - ], - "dbcanhmm_results": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } - }, - { - "${prefix}_dbCAN_hmm_results.tsv": { - "type": "file", - "description": "TSV file containing the detailed dbCAN HMM results for CAZyme annotation.\n", - "ontologies": [] - } - } - ] - ], - "dbcansub_results": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } - }, - { - "${prefix}_dbCANsub_hmm_results.tsv": { - "type": "file", - "description": "TSV file containing the detailed dbCAN subfamily results for CAZyme annotation.\n", - "ontologies": [] - } - } - ] - ], - "dbcandiamond_results": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } - }, - { - "${prefix}_diamond.out": { - "type": "file", - "description": "TSV file containing the detailed dbCAN diamond results for CAZyme annotation.\n", - "ontologies": [] - } - } - ] - ], - "cgc_gff": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } - }, - { - "${prefix}_cgc.gff": { - "type": "file", - "description": "GFF file containing the CAZyme gene clusters (CGC) identified by dbCAN. This file is generated from the dbCAN annotation and contains the locations of CAZyme gene clusters in the genome.\n", - "ontologies": [] - } - } - ] - ], - "cgc_standard_out": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } - }, - { - "${prefix}_cgc_standard_out.tsv": { - "type": "file", - "description": "Standard output file from dbCAN for CAZyme gene clusters (CGC) in a tabular format. This file summarizes the CAZyme gene clusters identified in the genome.\n", - "ontologies": [] - } - } - ] - ], - "diamond_out_tc": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } - }, - { - "${prefix}_diamond.out.tc": { - "type": "file", - "description": "TSV file containing the diamond output for transporter annotation.\n", - "ontologies": [] - } - } - ] - ], - "tf_hmm_results": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } - }, - { - "${prefix}_TF_hmm_results.tsv": { - "type": "file", - "description": "TSV file containing the results of Transcription factor.\n", - "ontologies": [] - } - } - ] - ], - "stp_hmm_results": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } - }, - { - "${prefix}_STP_hmm_results.tsv": { - "type": "file", - "description": "TSV file containing the results of signaling transduction proteins (STP) annotation.\n", - "ontologies": [] - } - } - ] - ], - "versions_rundbcan": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "rundbcan": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "run_dbcan version | sed 's/dbCAN version: //g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "rundbcan": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "run_dbcan version | sed 's/dbCAN version: //g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@Xinpeng021001" - ], - "maintainers": [ - "@Xinpeng021001" - ] - } - }, - { - "name": "rundbcan_easysubstrate", - "path": "modules/nf-core/rundbcan/easysubstrate/meta.yml", - "type": "module", - "meta": { - "name": "rundbcan_easysubstrate", - "description": "Substrate annotation module for the dbcan pipeline. This module is used to annotate carbohydrate-active enzymes (CAZymes) from genomic data using the dbCAN annotation tool.", - "keywords": [ - "dbCAN", - "download", - "CAZyme", - "CAZyme gene Cluster", - "genomes" - ], - "tools": [ - { - "dbcan": { - "description": "Standalone version of dbCAN annotation tool for automated CAZyme annotation.", - "homepage": "https://bcb.unl.edu/dbCAN2/", - "documentation": "https://run-dbcan.readthedocs.io/en/latest/", - "tool_dev_url": "https://github.com/bcb-unl/run_dbcan", - "doi": "10.1093/nar/gkad328", - "licence": [ - "GPL v3-or-later" - ], - "identifier": "biotools:dbcan" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } - }, - { - "input_raw_data": { - "type": "file", - "description": "FASTA file for protein sequences.", - "pattern": "*.{fasta,fa,faa}", - "ontologies": [ - { - "edam": "http://edamontology.org/data_2044" - }, - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } - }, - { - "input_gff": { - "type": "file", - "description": "GFF file for protein sequences.", - "ontologies": [] - } - }, - { - "gff_type": { - "type": "string", - "description": "Type of GFF file. Options are `NCBI_prok`, `JGI`, `NCBI_euk`, and `prodigal`. This is used to parse the GFF file correctly.\n" - } - } - ], - { - "dbcan_db": { - "type": "directory", - "description": "Path to the dbCAN database directory." - } - } - ], - "output": { - "cazyme_annotation": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } - }, - { - "${prefix}_overview.tsv": { - "type": "file", - "description": "TSV file containing the results of dbCAN CAZyme annotation.\n", - "ontologies": [] - } - } - ] - ], - "dbcanhmm_results": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } - }, - { - "${prefix}_dbCAN_hmm_results.tsv": { - "type": "file", - "description": "TSV file containing the detailed dbCAN HMM results for CAZyme annotation.\n", - "ontologies": [] - } - } - ] - ], - "dbcansub_results": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } - }, - { - "${prefix}_dbCANsub_hmm_results.tsv": { - "type": "file", - "description": "TSV file containing the detailed dbCAN subfamily results for CAZyme annotation.\n", - "ontologies": [] - } - } - ] - ], - "dbcandiamond_results": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } - }, - { - "${prefix}_diamond.out": { - "type": "file", - "description": "TSV file containing the detailed dbCAN diamond results for CAZyme annotation.\n", - "ontologies": [] - } - } - ] - ], - "cgc_gff": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } - }, - { - "${prefix}_cgc.gff": { - "type": "file", - "description": "GFF file containing the CAZyme gene clusters (CGC) identified by dbCAN. This file is generated from the dbCAN annotation and contains the locations of CAZyme gene clusters in the genome.\n", - "ontologies": [] - } - } - ] - ], - "cgc_standard_out": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } - }, - { - "${prefix}_cgc_standard_out.tsv": { - "type": "file", - "description": "Standard output file from dbCAN for CAZyme gene clusters (CGC) in a tabular format. This file summarizes the CAZyme gene clusters identified in the genome.\n", - "ontologies": [] - } - } - ] - ], - "diamond_out_tc": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } - }, - { - "${prefix}_diamond.out.tc": { - "type": "file", - "description": "TSV file containing the diamond output for transporter annotation.\n", - "ontologies": [] - } - } - ] - ], - "tf_hmm_results": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } - }, - { - "${prefix}_TF_hmm_results.tsv": { - "type": "file", - "description": "TSV file containing the results of Transcription factor.\n", - "ontologies": [] - } - } - ] - ], - "stp_hmm_results": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } - }, - { - "${prefix}_STP_hmm_results.tsv": { - "type": "file", - "description": "TSV file containing the results of signaling transduction proteins (STP) annotation.\n", - "ontologies": [] - } - } - ] - ], - "total_cgc_info": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } - }, - { - "${prefix}_total_cgc_info.tsv": { - "type": "file", - "description": "TSV file summarizing the total additional genes in the genome.\n", - "ontologies": [] - } - } - ] - ], - "substrate_prediction": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } - }, - { - "${prefix}_substrate_prediction.tsv": { - "type": "file", - "description": "TSV file containing the substrate predictions based on the CGC annotations from dbCAN.\n", - "ontologies": [] - } - } - ] - ], - "synteny_pdf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } - }, - { - "${prefix}_synteny_pdf/": { - "type": "directory", - "description": "Directory containing the synteny plots in PDF format for the CAZyme gene clusters (CGC) identified by dbCAN. This directory will contain one or more PDF files showing the syntenic regions of the CGC in the genome.\n" - } - } - ] - ], - "versions_rundbcan": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "rundbcan": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "run_dbcan version | sed 's/dbCAN version: //g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "rundbcan": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "run_dbcan version | sed 's/dbCAN version: //g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@Xinpeng021001" - ], - "maintainers": [ - "@Xinpeng021001" - ] - } - }, - { - "name": "rustqc", - "path": "modules/nf-core/rustqc/meta.yml", - "type": "module", - "meta": { - "name": "rustqc", - "description": "All-in-one RNA-seq post-alignment QC replacing dupRadar, featureCounts biotype QC, RSeQC, Preseq, Qualimap, and SAMtools stats", - "keywords": [ - "rnaseq", - "quality control", - "qc", - "bam", - "dupradar", - "featurecounts", - "rseqc", - "preseq", - "qualimap", - "samtools" - ], - "tools": [ - { - "rustqc": { - "description": "RustQC is a high-performance, Rust-based tool that replaces multiple\npost-alignment RNA-seq QC tools in a single pass over the BAM file.\nIt produces output compatible with MultiQC for dupRadar, featureCounts\nbiotype QC, RSeQC (bam_stat, infer_experiment, read_distribution,\nread_duplication, junction_annotation, junction_saturation,\ninner_distance, TIN), Preseq, Qualimap, and SAMtools\n(flagstat, idxstats, stats).\n", - "homepage": "https://seqeralabs.github.io/RustQC/", - "documentation": "https://seqeralabs.github.io/RustQC/", - "tool_dev_url": "https://github.com/seqeralabs/rustqc", - "licence": [ - "GPL-3.0-or-later" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM file", - "pattern": "*.{bam}", - "ontologies": [] - } - }, - { - "bai": { - "type": "file", - "description": "BAM index file", - "pattern": "*.{bai}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "gtf": { - "type": "file", - "description": "GTF annotation file", - "pattern": "*.{gtf}", - "ontologies": [] - } - } - ] - ], - "output": { - "dupradar": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/dupradar/*": { - "type": "file", - "description": "dupRadar-compatible duplication rate plots and tables", - "pattern": "${prefix}/dupradar/*", - "ontologies": [] - } - } - ] - ], - "featurecounts": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/featurecounts/*": { - "type": "file", - "description": "featureCounts-compatible biotype quantification files", - "pattern": "${prefix}/featurecounts/*", - "ontologies": [] - } - } - ] - ], - "preseq": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/preseq/*": { - "type": "file", - "description": "Preseq-compatible library complexity extrapolation", - "pattern": "${prefix}/preseq/*", - "ontologies": [] - } - } - ] - ], - "samtools": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/samtools/*": { - "type": "file", - "description": "SAMtools flagstat, idxstats, and stats output", - "pattern": "${prefix}/samtools/*", - "ontologies": [] - } - } - ] - ], - "rseqc": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/rseqc/**": { - "type": "file", - "description": "RSeQC-compatible outputs (bam_stat, infer_experiment, read_distribution, read_duplication, junction_annotation, junction_saturation, inner_distance, TIN)", - "pattern": "${prefix}/rseqc/**", - "ontologies": [] - } - } - ] - ], - "qualimap": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/qualimap/**": { - "type": "file", - "description": "Qualimap RNA-seq QC report and raw data", - "pattern": "${prefix}/qualimap/**", - "ontologies": [] - } - } - ] - ], - "versions_rustqc": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "rustqc": { - "type": "string", - "description": "The tool name" - } - }, - { - "rustqc --version 2>&1 | sed -n '1s/rustqc //; 1s/ .*//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "rustqc": { - "type": "string", - "description": "The tool name" - } - }, - { - "rustqc --version 2>&1 | sed -n '1s/rustqc //; 1s/ .*//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@ewels", - "@pinin4fjords" - ], - "maintainers": [ - "@ewels", - "@pinin4fjords" - ], - "containers": { - "docker": { - "linux/amd64": { - "name": "community.wave.seqera.io/library/rustqc:0.2.1--00df1502b490e005", - "build_id": "bd-00df1502b490e005_1" - } - }, - "singularity": { - "linux/amd64": { - "name": "oras://community.wave.seqera.io/library/rustqc:0.2.1--3982097e14c103d4", - "build_id": "bd-3982097e14c103d4_1", - "https": "https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/2a/2a8a0514855c54307399fd0f664c2685e76c8cc07631e767c1e37c575b18d59f/data" + "name": "vardictjava", + "path": "modules/nf-core/vardictjava/meta.yml", + "type": "module", + "meta": { + "name": "vardictjava", + "description": "The Java port of the VarDict variant caller", + "keywords": ["variant calling", "vcf", "bam", "snv", "sv"], + "tools": [ + { + "vardictjava": { + "description": "Java port of the VarDict variant discovery program", + "homepage": "https://github.com/AstraZeneca-NGS/VarDictJava", + "documentation": "https://github.com/AstraZeneca-NGS/VarDictJava", + "tool_dev_url": "https://github.com/AstraZeneca-NGS/VarDictJava", + "doi": "10.1093/nar/gkw227 ", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bams": { + "type": "file", + "description": "One or two BAM files. Supply two BAM files to run Vardict in paired mode.", + "pattern": "*.bam", + "ontologies": [] + } + }, + { + "bais": { + "type": "file", + "description": "Index/indices of the BAM file(s)", + "pattern": "*.bai", + "ontologies": [] + } + }, + { + "bed": { + "type": "file", + "description": "BED with the regions of interest", + "pattern": "*.bed", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing fasta information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA of the reference genome", + "pattern": "*.{fa,fasta}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing fasta information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta_fai": { + "type": "file", + "description": "The index of the FASTA of the reference genome", + "pattern": "*.fai", + "ontologies": [] + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "VCF file output", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "versions_vardictjava": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "vardict-java": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "realpath \\$( command -v vardict-java ) | sed 's/.*java-//;s/-.*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_var2vcfvalid": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "var2vcf_valid.pl": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "var2vcf_valid.pl -h | sed '2!d;s/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_htslib": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "htslib": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "tabix -h 2>&1 | sed -n '2s/Version: *//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "vardict-java": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "realpath \\$( command -v vardict-java ) | sed 's/.*java-//;s/-.*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "var2vcf_valid.pl": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "var2vcf_valid.pl -h | sed '2!d;s/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "htslib": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "tabix -h 2>&1 | sed -n '2s/Version: *//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@nvnieuwk"], + "maintainers": ["@nvnieuwk"] } - } - } - }, - "pipelines": [ + }, { - "name": "rnaseq", - "version": "3.26.0" - } - ] - }, - { - "name": "s4pred_runmodel", - "path": "modules/nf-core/s4pred/runmodel/meta.yml", - "type": "module", - "meta": { - "name": "s4pred_runmodel", - "description": "Prediction of a protein's secondary structure from its amino acid sequence", - "keywords": [ - "protein", - "secondary structure", - "prediction" - ], - "tools": [ - { - "s4pred": { - "description": "Accurate prediction of a protein's secondary structure from its amino acid sequence", - "homepage": "https://github.com/psipred/s4pred", - "documentation": "https://github.com/psipred/s4pred", - "tool_dev_url": "https://github.com/psipred/s4pred", - "doi": "10.1093/bioinformatics/btab491", - "licence": [ - "GPL v3-or-later" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "fasta": { - 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] - }, - { - "name": "sageproteomics_sage", - "path": "modules/nf-core/sageproteomics/sage/meta.yml", - "type": "module", - "meta": { - "name": "sageproteomics_sage", - "description": "sage is a search software for proteomics data", - "keywords": [ - "proteomics", - "sage", - "mass spectrometry" - ], - "tools": [ - { - "sageproteomics": { - "description": "Proteomics searching so fast it feels like magic.", - "homepage": "https://lazear.github.io/sage/", - "documentation": "https://lazear.github.io/sage/", - "tool_dev_url": "https://github.com/lazear/sage", - "doi": "10.1021/acs.jproteome.3c00486", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } - }, - { - "*.mzML": { - "type": "file", - "description": "mzML files for proteomics search", - "pattern": "*.mzML", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3244" - } - ] - } + "name": "variancepartition_dream", + "path": "modules/nf-core/variancepartition/dream/meta.yml", + "type": "module", + "meta": { + "name": "variancepartition_dream", + "description": "Runs a differential expression analysis with dream() from variancePartition R package", + "keywords": ["rnaseq", "dream", "variancepartition"], + "tools": [ + { + "dream": { + "description": "Differential expression for repeated measures", + "homepage": "https://www.bioconductor.org/packages/release/bioc/html/variancePartition.html", + "documentation": "https://www.bioconductor.org/packages/release/bioc/manuals/variancePartition/man/variancePartition.pdf", + "tool_dev_url": "https://github.com/DiseaseNeuroGenomics/variancePartition", + "doi": "10.1093/bioinformatics/btaa687", + "licence": ["GPL >=2"], + "identifier": "biotools:dream_database" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing run and contrast information.\n" + } + }, + { + "contrast_variable": { + "type": "string", + "description": "The column in the sample sheet that should be used to define groups for\ncomparison\n" + } + }, + { + "reference": { + "type": "string", + "description": "The value within the contrast_variable column of the sample sheet that\nshould be used to derive the reference samples\n" + } + }, + { + "target": { + "type": "string", + "description": "The value within the contrast_variable column of the sample sheet that\nshould be used to derive the target samples\n" + } + }, + { + "formula": { + "type": "string", + "description": "(Optional) R formula string used for modeling, e.g. '~ treatment + (1 | sample_number)'." + } + }, + { + "comparison": { + "type": "string", + "description": "(Optional) Literal string passed to `limma::makeContrasts`, e.g. 'treatmenthND6 - treatmentmCherry'." + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy map containing study-wide metadata related to the sample sheet\nand matrix\n" + } + }, + { + "samplesheet": { + "type": "file", + "description": "Sample sheet file containing sample metadata.", + "ontologies": [] + } + }, + { + "counts": { + "type": "file", + "description": "TSV or CSV format expression matrix with genes as rows and samples as columns.\n", + "ontologies": [] + } + } + ] + ], + "output": { + "results": [ + [ + { + "meta": { + "type": "map", + "description": "groovy array with metadata information for the contrast generated\n" + } + }, + { + "*.dream.results.tsv": { + "type": "file", + "description": "TSV-format table of differential expression information as output by Dream\n", + "pattern": "*.dream.results.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "model": [ + [ + { + "meta": { + "type": "map", + "description": "groovy array with metadata information for the contrast generated\n" + } + }, + { + "*.dream.model.txt": { + "type": "file", + "description": "R model description text file.\n", + "pattern": "*.dream.model.txt", + "ontologies": [] + } + } + ] + ], + "normalised_counts": [ + [ + { + "meta": { + "type": "map", + "description": "groovy array with metadata information for the contrast generated\n" + } + }, + { + "*.normalised_counts.tsv": { + "type": "file", + "description": "normalised TSV format expression matrix with genes by row and samples by column", + "pattern": "*.normalised_counts.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "topics": { + "versions": [ + { + "versions.yml": { + "type": "string", + "description": "File containing software versions" + } + } + ] + }, + "authors": ["@alanmmobbs03", "@nschcolnicov", "@atrigila"], + "maintainers": ["@alanmmobbs03", "@nschcolnicov", "@atrigila"] } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing information about fasta_proteome\ne.g. `[ id:'sample1']`\n" - } - }, - { - "fasta_proteome": { - "type": "file", - "description": "proteome database in fasta format", - "pattern": "*.{fasta,fasta.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } + }, + { + "name": "variantbam", + "path": "modules/nf-core/variantbam/meta.yml", + "type": "module", + "meta": { + "name": "variantbam", + "description": "Filtering, downsampling and profiling alignments in BAM/CRAM formats", + "keywords": ["filter", "bam", "subsample", "downsample", "downsample bam", "subsample bam"], + "tools": [ + { + "variantbam": { + "description": "Filtering and profiling of next-generational sequencing data using region-specific rules", + "homepage": "https://github.com/walaj/VariantBam", + "documentation": "https://github.com/walaj/VariantBam#table-of-contents", + "tool_dev_url": "https://github.com/walaj/VariantBam", + "doi": "10.1093/bioinformatics/btw111", + "licence": ["Apache-2.0"], + "identifier": "biotools:variantbam" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM file", + "pattern": "*.{bam,cram}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + }, + { + "edam": "http://edamontology.org/format_3462" + } + ] + } + } + ] + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Filtered or downsampled BAM file", + "pattern": "*.{bam}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + } + ] + ], + "versions_variant": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "VariantBam": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "1.4.4a": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "VariantBam": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "1.4.4a": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@bjohnnyd"], + "maintainers": ["@bjohnnyd"] } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing information about base_config\ne.g. `[ id:'sample1']`\n" - } + }, + { + "name": "variantextractor", + "path": "modules/nf-core/variantextractor/meta.yml", + "type": "module", + "meta": { + "name": "variantextractor", + "description": "Deterministic and standard extractor of SNVs, indels and structural variants (SVs)\nfrom VCF files. Homogenizes multiallelic variants, MNPs and SVs (including imprecise\npaired breakends and single breakends) to facilitate downstream processing.\n", + "keywords": ["vcf", "variant", "structural variant", "normalization", "homogenization"], + "tools": [ + { + "variant-extractor": { + "description": "Deterministic and standard extractor of SNVs, indels and structural variants\nfrom VCF files built under the frame of EUCANCan.\n", + "homepage": "https://github.com/EUCANCan/variant-extractor", + "documentation": "https://eucancan.github.io/variant-extractor/", + "tool_dev_url": "https://github.com/EUCANCan/variant-extractor", + "doi": "10.1016/j.xgen.2024.100639", + "licence": ["MIT"], + "identifier": "biotools:variant_extractor" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information.\ne.g. [ id:'sample1' ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "Input VCF file containing variants to be extracted and homogenized.", + "pattern": "*.{vcf,vcf.gz}", + "ontologies": [] + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information.\ne.g. [ id:'sample1' ]\n" + } + }, + { + "*.vcf": { + "type": "file", + "description": "VCF file with variants extracted and homogenized (multiallelic split,\nMNPs decomposed, SV breakends deduplicated).\n", + "pattern": "*.vcf", + "ontologies": [] + } + } + ] + ], + "versions_variantextractor": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions.", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "topics": { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "YAML file containing versions of tools used in the module", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@sbreuch"], + "maintainers": ["@sbreuch"] }, - 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"type": "file", - "description": "Fasta file of the reference transcriptome", - "ontologies": [] - } - } - ], - "output": { - "index": [ - { - "salmon": { - "type": "directory", - "description": "Folder containing the star index files", - "pattern": "salmon" - } - } - ], - "versions_salmon": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "salmon": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "salmon --version | sed 's/salmon //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "salmon": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "salmon --version | sed 's/salmon //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "variantbenchmarking", + "version": "1.5.0" + } ] - ] }, - "authors": [ - "@kevinmenden", - "@drpatelh" - ], - "maintainers": [ - "@kevinmenden", - "@drpatelh" - ] - }, - "pipelines": [ { - "name": "denovotranscript", - "version": "1.2.1" + "name": "varlociraptor_callvariants", + "path": "modules/nf-core/varlociraptor/callvariants/meta.yml", + "type": "module", + "meta": { + "name": "varlociraptor_callvariants", + "description": "Call variants for a given scenario specified with the varlociraptor calling grammar, preprocessed by varlociraptor preprocessing", + "keywords": ["observations", "variants", "calling"], + "tools": [ + { + "varlociraptor": { + "description": "Flexible, uncertainty-aware variant calling with parameter free filtration via FDR control.", + "homepage": "https://varlociraptor.github.io/docs/estimating/", + "documentation": "https://varlociraptor.github.io/docs/calling/", + "tool_dev_url": "https://github.com/varlociraptor/varlociraptor", + "doi": "10.1186/s13059-020-01993-6", + "licence": ["GPL v3"], + "identifier": "biotools:varlociraptor" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcfs": { + "type": "file", + "description": "Sorted VCF/BCF file containing sample observations, Can also be a list of files", + "pattern": "*.{vcf,bcf,vcf.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + }, + { + "edam": "http://edamontology.org/format_3020" + } + ] + } + }, + { + "scenario": { + "type": "file", + "description": "Yaml file containing scenario information (optional)", + "pattern": "*.{yml,yaml}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + }, + { + "scenario_aliases": { + "type": "list", + "description": "List of aliases for the scenario (optional)" + } + } + ] + ], + "output": { + "bcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bcf": { + "type": "file", + "description": "BCF file containing sample observations", + "pattern": "*.bcf", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3020" + } + ] + } + } + ] + ], + "versions_varlociraptor": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "varlociraptor": { + "type": "string", + "description": "The tool name" + } + }, + { + "varlociraptor --version | sed 's/^varlociraptor //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "varlociraptor": { + "type": "string", + "description": "The tool name" + } + }, + { + "varlociraptor --version | sed 's/^varlociraptor //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@FriederikeHanssen"], + "maintainers": ["@FriederikeHanssen", "@famosab"] + }, + "pipelines": [ + { + "name": "sarek", + "version": "3.8.1" + } + ] }, { - "name": "lncpipe", - "version": "dev" + "name": "varlociraptor_estimatealignmentproperties", + "path": "modules/nf-core/varlociraptor/estimatealignmentproperties/meta.yml", + "type": "module", + "meta": { + "name": "varlociraptor_estimatealignmentproperties", + "description": "In order to judge about candidate indel and structural variants, Varlociraptor needs to know about certain properties of the underlying sequencing experiment in combination with the used read aligner.", + "keywords": ["estimation", "alignment", "variants"], + "tools": [ + { + "varlociraptor": { + "description": "Flexible, uncertainty-aware variant calling with parameter free filtration via FDR control.", + "homepage": "https://varlociraptor.github.io/docs/estimating/", + "documentation": "https://varlociraptor.github.io/docs/estimating/", + "tool_dev_url": "https://github.com/varlociraptor/varlociraptor", + "doi": "10.1186/s13059-020-01993-6", + "licence": ["GPL v3"], + "identifier": "biotools:varlociraptor" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "Sorted BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + }, + { + "bai": { + "type": "file", + "description": "Index of sorted BAM/CRAM/SAM file", + "pattern": "*.{bai,crai,sai}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3327" + } + ] + } + }, + { + "fasta": { + "type": "file", + "description": "Reference fasta file", + "pattern": "*.{fasta}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + }, + { + "fai": { + "type": "file", + "description": "Index for reference fasta file (must be with samtools index)", + "pattern": "*.{fai}", + "ontologies": [] + } + } + ] + ], + "output": { + "alignment_properties_json": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.alignment-properties.json": { + "type": "file", + "description": "File containing alignment properties", + "pattern": "*.alignment-properties.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "versions_varlociraptor": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "varlociraptor": { + "type": "string", + "description": "The tool name" + } + }, + { + "varlociraptor --version | sed 's/^varlociraptor //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "varlociraptor": { + "type": "string", + "description": "The tool name" + } + }, + { + "varlociraptor --version | sed 's/^varlociraptor //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@FriederikeHanssen"], + "maintainers": ["@FriederikeHanssen", "@famosab"] + }, + "pipelines": [ + { + "name": "sarek", + "version": "3.8.1" + } + ] }, { - "name": "references", - "version": "0.1" + "name": "varlociraptor_preprocess", + "path": "modules/nf-core/varlociraptor/preprocess/meta.yml", + "type": "module", + "meta": { + "name": "varlociraptor_preprocess", + "description": "Obtains per-sample observations for the actual calling process with varlociraptor calls", + "keywords": ["observations", "variants", "preprocessing"], + "tools": [ + { + "varlociraptor": { + "description": "Flexible, uncertainty-aware variant calling with parameter free\nfiltration via FDR control.\n", + "homepage": "https://varlociraptor.github.io/docs/estimating/", + "documentation": "https://varlociraptor.github.io/docs/calling/", + "tool_dev_url": "https://github.com/varlociraptor/varlociraptor", + "doi": "10.1186/s13059-020-01993-6", + "licence": ["GPL v3"], + "identifier": "biotools:varlociraptor" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "Sorted BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + }, + { + "bai": { + "type": "file", + "description": "Index of the BAM/CRAM/SAM file", + "pattern": "*.{bai,crai,sai}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3327" + } + ] + } + }, + { + "candidates": { + "type": "file", + "description": "Sorted BCF/VCF file", + "pattern": "*.{bcf,vcf,vcf.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + } + ] + } + }, + { + "alignment_json": { + "type": "file", + "description": "File containing alignment properties obtained with varlociraptor/estimatealignmentproperties", + "pattern": "*.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + }, + { + "fasta": { + "type": "file", + "description": "Reference fasta file", + "pattern": "*.{fasta}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + }, + { + "fai": { + "type": "file", + "description": "Index for reference fasta file (must be with samtools index)", + "pattern": "*.{fai}", + "ontologies": [] + } + } + ] + ], + "output": { + "bcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bcf": { + "type": "file", + "description": "BCF file containing sample observations", + "pattern": "*.bcf", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3020" + } + ] + } + } + ] + ], + "versions_varlociraptor": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "varlociraptor": { + "type": "string", + "description": "The tool name" + } + }, + { + "varlociraptor --version | sed 's/^varlociraptor //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "varlociraptor": { + "type": "string", + "description": "The tool name" + } + }, + { + "varlociraptor --version | sed 's/^varlociraptor //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@FriederikeHanssen"], + "maintainers": ["@FriederikeHanssen", "@famosab"] + }, + "pipelines": [ + { + "name": "sarek", + "version": "3.8.1" + } + ] }, { - "name": "riboseq", - "version": "1.2.0" + "name": "varscan_fpfilter", + "path": "modules/nf-core/varscan/fpfilter/meta.yml", + "type": "module", + "meta": { + "name": "varscan_fpfilter", + "description": "VarScan2 is a tool for variant detection in massively parallel sequencing data. It can detect SNPs, indels, and copy number variations in both somatic and germline samples. It is particularly useful for analyzing tumor/normal sample pairs. Subtool fpfilter is used to filter a set of SNPs/indels based on coverage, reads, p-value, etc.", + "keywords": ["variant calling", "germline", "somatic", "vcf", "variants", "genomics"], + "tools": [ + { + "varscan": { + "description": "variant detection in massively parallel sequencing data", + "homepage": "https://github.com/dkoboldt/varscan", + "documentation": "https://dkoboldt.github.io/varscan/", + "tool_dev_url": "https://github.com/dkoboldt/varscan", + "doi": "10.1101/gr.129684.111", + "licence": ["The Non-Profit Open Software License version 3.0 (NPOSL-3.0)"], + "identifier": "biotools:varscan" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF file", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + }, + { + "rc": { + "type": "file", + "description": "Read counts file from bam-readcount", + "pattern": "*.rc", + "ontologies": [] + } + } + ] + ], + "output": { + "pass_vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.pass.vcf.gz": { + "type": "file", + "description": "VCF file with PASS variants", + "pattern": "*.pass.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "fail_vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.fail.vcf.gz": { + "type": "file", + "description": "VCF file with FAIL variants", + "pattern": "*.fail.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@vmelichar"], + "maintainers": ["@vmelichar"] + } }, { - "name": "rnafusion", - "version": "4.1.2" + "name": "varscan_processsomatic", + "path": "modules/nf-core/varscan/processsomatic/meta.yml", + "type": "module", + "meta": { + "name": "varscan_processsomatic", + "description": "VarScan2 is a tool for variant detection in massively parallel sequencing data. It can detect SNPs, indels, and copy number variations in both somatic and germline samples. It is particularly useful for analyzing tumor/normal sample pairs. This subtool divides variants based on status (germline, somatic, loss of heterozygosity) and confidence level (high-confidence or not) and outputs them in separate VCF files.", + "keywords": ["variant calling", "germline", "somatic", "vcf", "variants", "genomics"], + "tools": [ + { + "varscan": { + "description": "variant detection in massively parallel sequencing data", + "homepage": "https://github.com/dkoboldt/varscan", + "documentation": "https://dkoboldt.github.io/varscan/", + "tool_dev_url": "https://github.com/dkoboldt/varscan", + "doi": "10.1101/gr.129684.111", + "licence": ["The Non-Profit Open Software License version 3.0 (NPOSL-3.0)"], + "identifier": "biotools:varscan" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF file", + "pattern": "*.{snvs,indels}.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "output": { + "germline_vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.Germline.vcf.gz": { + "type": "file", + "description": "VCF file with germline variants", + "pattern": "*.Germline.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "germline_hc_vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.Germline.hc.vcf.gz": { + "type": "file", + "description": "VCF file with high-confidence germline variants", + "pattern": "*.Germline.hc.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "somatic_vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.Somatic.vcf.gz": { + "type": "file", + "description": "VCF file with somatic variants", + "pattern": "*.Somatic.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "somatic_hc_vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.Somatic.hc.vcf.gz": { + "type": "file", + "description": "VCF file with high-confidence somatic variants", + "pattern": "*.Somatic.hc.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "loh_vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.LOH.vcf.gz": { + "type": "file", + "description": "VCF file with loss of heterozygosity variants", + "pattern": "*.LOH.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "loh_hc_vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.LOH.hc.vcf.gz": { + "type": "file", + "description": "VCF file with high-confidence loss of heterozygosity variants", + "pattern": "*.LOH.hc.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@vmelichar"], + "maintainers": ["@vmelichar"] + } }, { - "name": "rnaseq", - "version": "3.26.0" + "name": "varscan_somatic", + "path": "modules/nf-core/varscan/somatic/meta.yml", + "type": "module", + "meta": { + "name": "varscan_somatic", + "description": "VarScan2 is a tool for variant detection in massively parallel sequencing data. It can detect SNPs, indels, and copy number variations in both somatic and germline samples. It is particularly useful for analyzing tumor/normal sample pairs.", + "keywords": ["variant calling", "germline", "somatic", "vcf", "variants", "genomics"], + "tools": [ + { + "varscan": { + "description": "variant detection in massively parallel sequencing data", + "homepage": "https://github.com/dkoboldt/varscan", + "documentation": "https://dkoboldt.github.io/varscan/", + "tool_dev_url": "https://github.com/dkoboldt/varscan", + "doi": "10.1101/gr.129684.111", + "licence": ["The Non-Profit Open Software License version 3.0 (NPOSL-3.0)"], + "identifier": "biotools:varscan" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "normal_mpileup": { + "type": "file", + "description": "mpileup file from normal sample", + "pattern": "*.mpileup", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3015" + } + ] + } + }, + { + "tumour_mpileup": { + "type": "file", + "description": "mpileup file from tumour sample", + "pattern": "*.mpileup", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3015" + } + ] + } + } + ] + ], + "output": { + "vcf_snvs": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.snvs.vcf.gz": { + "type": "file", + "description": "VCF file with SNVs", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "vcf_indels": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.indels.vcf.gz": { + "type": "file", + "description": "VCF file with indels", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@vmelichar"], + "maintainers": ["@vmelichar"] + } }, { - "name": "rnasplice", - "version": "1.0.4" - } - ] - }, - { - "name": "salmon_quant", - "path": "modules/nf-core/salmon/quant/meta.yml", - "type": "module", - "meta": { - "name": "salmon_quant", - "description": "gene/transcript quantification with Salmon", - "keywords": [ - "index", - "fasta", - "genome", - "reference" - ], - "tools": [ - { - "salmon": { - "description": "Salmon is a tool for wicked-fast transcript quantification from RNA-seq data\n", - "homepage": "https://salmon.readthedocs.io/en/latest/salmon.html", - "manual": "https://salmon.readthedocs.io/en/latest/salmon.html", - "doi": "10.1038/nmeth.4197", - "licence": [ - "GPL-3.0-or-later" - ], - "identifier": "biotools:salmon" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + "name": "vcf2cytosure", + "path": "modules/nf-core/vcf2cytosure/meta.yml", + "type": "module", + "meta": { + "name": "vcf2cytosure", + "description": "Convert VCF with structural variations to CytoSure format", + "keywords": ["structural_variants", "array_cgh", "vcf", "cytosure"], + "tools": [ + { + "vcf2cytosure": { + "description": "Convert VCF with structural variations to CytoSure format", + "homepage": "https://github.com/NBISweden/vcf2cytosure", + "documentation": "https://github.com/NBISweden/vcf2cytosure", + "tool_dev_url": "https://github.com/NBISweden/vcf2cytosure", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "sv_vcf": { + "type": "file", + "description": "VCF file with structural variants", + "pattern": "*.{vcf,vcf.gz}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "coverage_bed": { + "type": "file", + "description": "Bed file with coverage data", + "pattern": "*.bed", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "cns": { + "type": "file", + "description": "CN file from CNVkit, not compatible with coverage_bed file", + "ontologies": [] + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "snv_vcf": { + "type": "file", + "description": "VCF file with SNVs to calculate probe coverage,\nnot compatible with coverage_bed\npattern: \"*.{vcf,vcf.gz}\"\n", + "ontologies": [] + } + } + ], + { + "blacklist_bed": { + "type": "file", + "description": "Bed file with regions to exclude", + "pattern": "*.bed", + "ontologies": [] + } + } + ], + "output": { + "cgh": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.cgh": { + "type": "file", + "description": "SV:s in CytoSure format", + "pattern": "*.cgh", + "ontologies": [] + } + } + ] + ], + "versions_vcf2cytosure": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "vcf2cytosure": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "vcf2cytosure --version 2>&1 | sed -n 's/.*cytosure //p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "vcf2cytosure": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "vcf2cytosure --version 2>&1 | sed -n 's/.*cytosure //p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@jemten"] }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files for single-end or paired-end data.\nMultiple single-end fastqs or pairs of paired-end fastqs are\nhandled.\n", - "ontologies": [] - } - } - ], - { - "index": { - "type": "directory", - "description": "Folder containing the star index files" - } - }, - { - "gtf": { - "type": "file", - "description": "GTF of the reference transcriptome", - "ontologies": [] - } - }, - { - "transcript_fasta": { - "type": "file", - "description": "Fasta file of the reference transcriptome", - "ontologies": [] - } - }, - { - "alignment_mode": { - "type": "boolean", - "description": "whether to run salmon in alignment mode" - } - }, - { - "lib_type": { - "type": "string", - "description": "Override library type inferred based on strandedness defined in meta object\n" - } - } - ], - "output": { - "results": [ - [ - { - "meta": { - "type": "directory", - "description": "Folder containing the quantification results for a specific sample", - "pattern": "${prefix}" - } - }, - { - "${prefix}": { - "type": "directory", - "description": "Folder containing the quantification results for a specific sample", - "pattern": "${prefix}" - } - } - ] - ], - "json_info": [ - [ - { - "meta": { - "type": "directory", - "description": "Folder containing the quantification results for a specific sample", - "pattern": "${prefix}" - } - }, - { - "*info.json": { - "type": "file", - "description": "File containing meta information from Salmon quant", - "pattern": "*info.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "lib_format_counts": [ - [ - { - "meta": { - "type": "directory", - "description": "Folder containing the quantification results for a specific sample", - "pattern": "${prefix}" - } - }, - { - "*lib_format_counts.json": { - "type": "file", - "description": "File containing the library format counts", - "pattern": "*lib_format_counts.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "versions_salmon": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "salmon": { - "type": "string", - "description": "The tool name" - } - }, - { - "salmon --version | sed -e \"s/salmon //g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "salmon": { - "type": "string", - "description": "The tool name" - } - }, - { - "salmon --version | sed -e \"s/salmon //g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "raredisease", + "version": "3.0.0" + } ] - ] - }, - "authors": [ - "@kevinmenden", - "@drpatelh" - ], - "maintainers": [ - "@kevinmenden", - "@drpatelh" - ] - }, - "pipelines": [ - { - "name": "denovotranscript", - "version": "1.2.1" }, { - "name": "lncpipe", - "version": "dev" + "name": "vcf2db", + "path": "modules/nf-core/vcf2db/meta.yml", + "type": "module", + "meta": { + "name": "vcf2db", + "description": "A tool to create a Gemini-compatible DB file from an annotated VCF", + "keywords": ["vcf2db", "vcf", "gemini"], + "tools": [ + { + "vcf2db": { + "description": "Create a gemini-compatible database from a VCF", + "homepage": "https://github.com/quinlan-lab/vcf2db", + "documentation": "https://github.com/quinlan-lab/vcf2db", + "tool_dev_url": "https://github.com/quinlan-lab/vcf2db", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF file", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + }, + { + "ped": { + "type": "file", + "description": "PED file", + "pattern": "*.ped", + "ontologies": [] + } + } + ] + ], + "output": { + "db": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.db": { + "type": "file", + "description": "Gemini-compatible database file", + "pattern": "*.db", + "ontologies": [] + } + } + ] + ], + "versions_vcf2db": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "vcf2db": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "2020.02.24": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_python_snappy": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "python-snappy": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "0.5.4": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_snappy": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "snappy": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "1.1.8": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_cyvcf2": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cyvcf2": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python -c 'import cyvcf2; print(cyvcf2.__version__)'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ], + "versions_python": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "python": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python --version 2>&1 | awk '{print \\$2}'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "vcf2db": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "2020.02.24": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "python-snappy": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "0.5.4": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "snappy": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "1.1.8": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "cyvcf2": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python -c 'import cyvcf2; print(cyvcf2.__version__)'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "python": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "python --version 2>&1 | awk '{print \\$2}'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@nvnieuwk"], + "maintainers": ["@nvnieuwk"] + } }, { - "name": "riboseq", - "version": "1.2.0" + "name": "vcf2maf", + "path": "modules/nf-core/vcf2maf/meta.yml", + "type": "module", + "meta": { + "name": "vcf2maf", + "description": "vcf2maf", + "keywords": ["vcf", "maf", "annotation"], + "tools": [ + { + "vcf2maf": { + "description": "\"Convert a VCF into a MAF where each variant is annotated to only one of all possible gene isoforms using vcf2maf. vcf2maf is designed to work with VEP, so it is recommended to have VEP and vcf2maf installed when running this module. Running VEP requires a VEP cache to be present. It is recommended to set the --species and --ncbi-build in ext.args (use the module config). If you wish to skip VEP, add `--inhibit-vep` to ext.args. It may also be necessary to set --tumor-id and --normal-id for correct parsing of the VCF.\"\n", + "homepage": "https://github.com/mskcc/vcf2maf", + "documentation": "https://github.com/mskcc/vcf2maf", + "tool_dev_url": "https://github.com/mskcc/vcf2maf", + "doi": "10.5281/zenodo.593251", + "licence": ["Apache-2.0"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "vcf to convert to MAF format. Must be uncompressed.\n", + "ontologies": [] + } + } + ], + { + "fasta": { + "type": "file", + "description": "Path to reference genome fasta file.\n", + "ontologies": [] + } + }, + { + "vep_cache": { + "type": "file", + "description": "Path to VEP cache dir. Required for correct running of VEP.\n", + "ontologies": [] + } + } + ], + "output": { + "maf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.maf": { + "type": "file", + "description": "MAF file produced from VCF", + "pattern": "*.maf", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@adamrtalbot"], + "maintainers": ["@adamrtalbot"] + }, + "pipelines": [ + { + "name": "tumourevo", + "version": "dev" + } + ] }, { - "name": "rnafusion", - "version": "4.1.2" + "name": "vcf2zarr_convert", + "path": "modules/nf-core/vcf2zarr/convert/meta.yml", + "type": "module", + "meta": { + "name": "vcf2zarr_convert", + "description": "Convert VCF data to the VCF Zarr specification reliably, in parallel or distributed over a cluster", + "deprecated": true, + "keywords": ["vcf", "zarr", "convert"], + "tools": [ + { + "vcf2zarr": { + "description": "Convert bioinformatics data to Zarr", + "homepage": "https://sgkit-dev.github.io/bio2zarr/vcf2zarr/overview.html", + "documentation": "https://sgkit-dev.github.io/bio2zarr/", + "tool_dev_url": "https://github.com/sgkit-dev/bio2zarr", + "doi": "10.1101/2024.06.11.598241", + "licence": ["Apache-2.0"], + "identifier": "biotools:bio2zarr" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "vcf": { + "type": "file", + "description": "Input VCF file", + "pattern": "*.{vcf,vcf.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + } + ] + } + } + ] + ], + "output": { + "vcz": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.vcz": { + "type": "directory", + "description": "Output VCF Zarr store", + "pattern": "*.{vcz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3915" + } + ] + } + } + ] + ], + "versions_vcf2zarr": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "vcf2zarr": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "vcf2zarr --version |& sed -n \"s/.* //p\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "vcf2zarr": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "vcf2zarr --version |& sed -n \"s/.* //p\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@camlloyd"], + "maintainers": ["@camlloyd"] + } }, { - "name": "rnaseq", - "version": "3.26.0" + "name": "vcf2zarr_explode", + "path": "modules/nf-core/vcf2zarr/explode/meta.yml", + "type": "module", + "meta": { + "name": "vcf2zarr_explode", + "description": "Convert VCF(s) to intermediate columnar format", + "deprecated": true, + "keywords": ["vcf", "icf", "convert"], + "tools": [ + { + "vcf2zarr": { + "description": "Convert bioinformatics data to Zarr", + "homepage": "https://sgkit-dev.github.io/bio2zarr/vcf2zarr/overview.html", + "documentation": "https://sgkit-dev.github.io/bio2zarr/", + "tool_dev_url": "https://github.com/sgkit-dev/bio2zarr", + "doi": "10.1101/2024.06.11.598241", + "licence": ["Apache-2.0"], + "identifier": "biotools:bio2zarr" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "vcf": { + "type": "file", + "description": "Input VCF file", + "pattern": "*.{vcf,vcf.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + } + ] + } + } + ] + ], + "output": { + "icf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.icf": { + "type": "directory", + "description": "Output intermediate columnar format (ICF)", + "pattern": "*.{icf}", + "ontologies": [] + } + } + ] + ], + "versions_vcf2zarr": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "vcf2zarr": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "vcf2zarr --version |& sed -n \"s/.* //p\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "vcf2zarr": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "vcf2zarr --version |& sed -n \"s/.* //p\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@camlloyd"], + "maintainers": ["@camlloyd"] + } }, { - "name": "rnasplice", - "version": "1.0.4" - } - ] - }, - { - "name": "salsa2", - "path": "modules/nf-core/salsa2/meta.yml", - "type": "module", - "meta": { - "name": "salsa2", - "description": "SALSA, A tool to scaffold long read assemblies with HiC", - "keywords": [ - "assembly", - "hi-c", - "scaffolding", - "long reads", - "salsa", - "salsa2" - ], - "tools": [ - { - "salsa2": { - "description": "Salsa is a tool to scaffold long read assemblies with Hi-C.", - "homepage": "https://github.com/marbl/SALSA", - "documentation": "https://github.com/marbl/SALSA", - "tool_dev_url": "https://github.com/marbl/SALSA", - "doi": "10.1186/s12864-017-3879-z", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Fasta file of assembly. Headers must not contain ':'", - "pattern": "*.{fa, fasta}", - "ontologies": [] - } - }, - { - "index": { - "type": "file", - "description": "Fasta index file of assembly containing the length of contigs.", - "pattern": "*.{fa.fai, fasta.fai}", - "ontologies": [] - } - } - ], - { - "bed": { - "type": "file", - "description": "BED file of alignments sorted by read names, e.g., from HiC-Pro", - "pattern": "*.{bed}", - "ontologies": [] - } - }, - { - "gfa": { - "type": "file", - "description": "GFA file of the assembly graph", - "ontologies": [] - } - }, - { - "dup": { - "type": "file", - "description": "File containing the duplicated contigs", - "ontologies": [] - } - }, - { - "filter_bed": { - "type": "file", - "description": "BED file of the filtered alignments", - "pattern": "*.{bed}", - "ontologies": [] - } - } - ], - "output": { - "fasta": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_scaffolds_FINAL.fasta": { - "type": "file", - "description": "Sequences for the scaffolds generated by the algorithm", - "pattern": "*_scaffolds_FINAL.fasta", - "ontologies": [] - } - } - ] - ], - "agp": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_scaffolds_FINAL.agp": { - "type": "file", - "description": "AGP style output for the scaffolds describing the assignment, orientation and ordering of contigs along the scaffolds", - "pattern": "*_scaffolds_FINAL.agp", - "ontologies": [] - } - } - ] - ], - "agp_original_coordinates": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*/*scaffolds_FINAL.original-coordinates.agp": { - "type": "file", - "description": "Secondary output AGP file with names and coordinates matching the original input assembly (optional)", - "pattern": "*scaffolds_FINAL.original-coordinates.agp", - "ontologies": [] - } - } - ] - ], - "versions_salsa2": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "salsa2": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "2.3": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "salsa2": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "2.3": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@scorreard" - ], - "maintainers": [ - "@scorreard" - ] - } - }, - { - "name": "saltshaker_call", - "path": "modules/nf-core/saltshaker/call/meta.yml", - "type": "module", - "meta": { - "name": "saltshaker_call", - "description": "mtDNA deletion and duplication calling downstream of mitosalt", - "keywords": [ - "saltshaker", - "mitosalt", - "mtDNA", - "structural-variant calling" - ], - "tools": [ - { - "saltshaker": { - "description": "A Python package for classifying and visualizing mitochondrial structural variants from MitoSAlt pipeline output.", - "homepage": "https://github.com/aksenia/saltshaker", - "documentation": "https://github.com/aksenia/saltshaker/tree/main/saltshaker/docs" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "breakpoint": { - "type": "file", - "description": "breakpoint file from mitosalt", - "pattern": "*.{breakpoint}", - "ontologies": [] - } - }, - { - "cluster": { - "type": "file", - "description": "cluster file from mitosalt", - "pattern": "*.{cluster}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'fasta' ]\n" - } - }, - { - "mtfasta": { - "type": "file", - "description": "Reference mitochondrial genome in FASTA format", - "pattern": "*.{fasta,fa}", - "ontologies": [] - } - } - ], - { - "flank": { - "type": "integer", - "description": "Basepairs flanking a deletion" - } - }, - { - "heteroplasmy_limit": { - "type": "float", - "description": "Minimum heteroplasmy level to report a deletion/duplication" - } - }, - { - "mito_length": { - "type": "integer", - "description": "Length of the mitochondrial genome" - } - }, - { - "heavy_strand_origin_start": { - "type": "integer", - "description": "Start position of the heavy strand origin of replication" - } - }, - { - "heavy_strand_origin_end": { - "type": "integer", - "description": "End position of the heavy strand origin of replication" - } - }, - { - "light_strand_origin_start": { - "type": "integer", - "description": "Start position of the light strand origin of replication" - } - }, - { - "light_strand_origin_end": { - "type": "integer", - "description": "End position of the light strand origin of replication" - } - } - ], - "output": { - "call": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*_call_metadata.tsv": { - "type": "file", - "description": "tsv with variant call metadata to be used in saltshaker_classify", - "pattern": "*_call_metadata.tsv", - "ontologies": [] - } - } - ] - ], - "versions_saltshaker": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "saltshaker": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "1.0.0": { - "type": "string", - "description": "Hardcoded version of saltshaker used in the module" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "saltshaker": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "1.0.0": { - "type": "string", - "description": "Hardcoded version of saltshaker used in the module" - } - } - ] - ] - }, - "authors": [ - "@ieduba" - ], - "maintainers": [ - "@ieduba" - ] - }, - "pipelines": [ - { - "name": "raredisease", - "version": "3.0.0" - } - ] - }, - { - "name": "saltshaker_classify", - "path": "modules/nf-core/saltshaker/classify/meta.yml", - "type": "module", - "meta": { - "name": "saltshaker_classify", - "description": "mtDNA deletion and duplication classification downstream of mitosalt", - "keywords": [ - "saltshaker", - "mitosalt", - "mtDNA", - "structural-variant calling" - ], - "tools": [ - { - "saltshaker": { - "description": "A Python package for classifying and visualizing mitochondrial structural variants from MitoSAlt pipeline output.", - "homepage": "https://github.com/aksenia/saltshaker", - "documentation": "https://github.com/aksenia/saltshaker/tree/main/saltshaker/docs" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "call": { - "type": "file", - "description": "call metadata file from saltshaker_call", - "pattern": "*_call_metadata.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/operation_3227" - }, - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - { - "mito_name": { - "type": "string", - "description": "Name of the mitochondrial chromosome" - } - } - ], - "output": { - "classify": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*_classify_metadata.tsv": { - "type": "file", - "description": "tsv with classified call metadata to be used in saltshaker_plot", - "pattern": "*_classify_metadata.tsv", - "ontologies": [ + "name": "vcfanno", + "path": "modules/nf-core/vcfanno/meta.yml", + "type": "module", + "meta": { + "name": "vcfanno", + "description": "quickly annotate your VCF with any number of INFO fields from any number of VCFs or BED files", + "keywords": ["vcf", "bed", "annotate", "variant", "lua", "toml"], + "tools": [ + { + "vcfanno": { + "description": "annotate a VCF with other VCFs/BEDs/tabixed files", + "documentation": "https://github.com/brentp/vcfanno#vcfanno", + "tool_dev_url": "https://github.com/brentp/vcfanno", + "doi": "10.1186/s13059-016-0973-5", + "license": ["MIT"], + "identifier": "biotools:vcfanno" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "query VCF file", + "pattern": "*.{vcf, vcf.gz}", + "ontologies": [] + } + }, + { + "tbi": { + "type": "file", + "description": "tabix index file for the query VCF", + "pattern": "*.tbi", + "ontologies": [] + } + }, + { + "specific_resources": { + "type": "map", + "description": "A list of sample specific reference files defined in toml config, must also include indices if bgzipped." + } + } + ], { - "edam": "http://edamontology.org/operation_3225" + "toml": { + "type": "file", + "description": "configuration file with reference file basenames", + "pattern": "*.toml", + "ontologies": [] + } }, { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "txt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*_classify.txt": { - "type": "file", - "description": "txt file with case classification", - "pattern": "*_classify.txt", - "ontologies": [ - { - "edam": "http://edamontology.org/operation_3225" + "lua": { + "type": "file", + "description": "Lua file for custom annotations", + "pattern": "*.lua", + "ontologies": [] + } }, { - "edam": "http://edamontology.org/format_2330" + "resources": { + "type": "map", + "description": "List of reference files defined in toml config, must also include indices if bgzipped." + } } - ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*.vcf.gz" + } + }, + { + "*.vcf.gz": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*.vcf.gz" + } + } + ] + ], + "tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*.vcf.gz" + } + }, + { + "*.vcf.gz.tbi": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*.vcf.gz.tbi" + } + } + ] + ], + "versions_vcfanno": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "vcfanno": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "vcfanno 2>&1 | sed -n 's/.*version \\([0-9.]\\+\\).*/\\1/p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "vcfanno": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "vcfanno 2>&1 | sed -n 's/.*version \\([0-9.]\\+\\).*/\\1/p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@projectoriented", "@matthdsm", "@nvnieuwk"], + "maintainers": ["@projectoriented", "@matthdsm", "@nvnieuwk"] + }, + "pipelines": [ + { + "name": "raredisease", + "version": "3.0.0" } - } ] - ], - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*saltshaker.vcf": { - "type": "file", - "description": "vcf file with classified calls", - "pattern": "*saltshaker.vcf", - "ontologies": [ - { - "edam": "http://edamontology.org/operation_3225" - }, + }, + { + "name": "vcfexpress", + "path": "modules/nf-core/vcfexpress/meta.yml", + "type": "module", + "meta": { + "name": "vcfexpress", + "description": "Filter a VCF/BCF and optionally print by template expression. If no template is given the output will be VCF/BCF", + "keywords": ["vcf", "bcf", "filter", "lua", "expressions", "genomics"], + "tools": [ + { + "vcfexpress": { + "description": "expressions on VCFs", + "homepage": "https://github.com/brentp/vcfexpress", + "documentation": "https://github.com/brentp/vcfexpress", + "tool_dev_url": "https://github.com/brentp/vcfexpress", + "doi": "10.5281/zenodo.14898003", + "licence": ["MIT"], + "identifier": "biotools:vcfexpress" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF file", + "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}" + } + } + ], { - "edam": "http://edamontology.org/format_3016" + "prelude": { + "type": "file", + "description": "File(s) containing lua(u) code to run once before any variants are processed. `header` is available here to access or modify the header", + "pattern": "*.lua" + } } - ] - } - } - ] - ], - "versions_saltshaker": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "saltshaker": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "1.0.1": { - "type": "string", - "description": "Hardcoded version of saltshaker used in the module" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "saltshaker": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "1.0.1": { - "type": "string", - "description": "Hardcoded version of saltshaker used in the module" - } - } - ] - ] - }, - "authors": [ - "@ieduba" - ], - "maintainers": [ - "@ieduba" - ] - }, - "pipelines": [ - { - "name": "raredisease", - "version": "3.0.0" - } - ] - }, - { - "name": "saltshaker_plot", - "path": "modules/nf-core/saltshaker/plot/meta.yml", - "type": "module", - "meta": { - "name": "saltshaker_plot", - "description": "mtDNA deletion and duplication plotting downstream of mitosalt", - "keywords": [ - "saltshaker", - "mitosalt", - "mtDNA", - "structural-variant calling" - ], - "tools": [ - { - "saltshaker": { - "description": "A Python package for classifying and visualizing mitochondrial structural variants from MitoSAlt pipeline output.", - "homepage": "https://github.com/aksenia/saltshaker", - "documentation": "https://github.com/aksenia/saltshaker/tree/main/saltshaker/docs" + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.{vcf,vcf.gz,bcf,bcf.gz}": { + "type": "file", + "description": "VCF file", + "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}" + } + } + ] + ], + "versions_vcfexpress": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "vcfexpress": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "vcfexpress --version | sed 's/vcfexpress //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "vcfexpress": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "vcfexpress --version | sed 's/vcfexpress //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@sofiademmou"], + "maintainers": ["@sofiademmou"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "classify": { - "type": "file", - "description": "classify metadata file from saltshaker_classify", - "pattern": "*_classify_metadata.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/operation_3225" - }, - { - "edam": "http://edamontology.org/format_3475" - } - ] - } + }, + { + "name": "vcflib_vcfbreakmulti", + "path": "modules/nf-core/vcflib/vcfbreakmulti/meta.yml", + "type": "module", + "meta": { + "name": "vcflib_vcfbreakmulti", + "description": "If multiple alleles are specified in a single record, break the record into several lines preserving allele-specific INFO fields", + "keywords": ["vcflib", "vcfbreakmulti", "allele-specific"], + "tools": [ + { + "vcflib": { + "description": "Command-line tools for manipulating VCF files", + "homepage": "https://github.com/vcflib/vcflib", + "documentation": "https://github.com/vcflib/vcflib#USAGE", + "doi": "10.1101/2021.05.21.445151", + "licence": ["MIT"], + "identifier": "biotools:vcflib" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "Compressed VCF file", + "pattern": "*.{.vcf.gz,vcf}", + "ontologies": [] + } + }, + { + "tbi": { + "type": "file", + "description": "Index of VCF file", + "pattern": "*.vcf.gz.tbi", + "ontologies": [] + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "Compressed VCF file", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "versions_vcflib": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "vcflib": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "1.0.14": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "vcflib": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "1.0.14": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@lucpen"], + "maintainers": ["@lucpen"] } - ] - ], - "output": { - "plot": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*saltshaker.png": { - "type": "file", - "description": "png file with saltshaker plot", - "pattern": "*saltshaker.png", - "ontologies": [ - { - "edam": "http://edamontology.org/operation_0337" - }, - { - "edam": "http://edamontology.org/format_3603" + }, + { + "name": "vcflib_vcffilter", + "path": "modules/nf-core/vcflib/vcffilter/meta.yml", + "type": "module", + "meta": { + "name": "vcflib_vcffilter", + "description": "Command line tools for parsing and manipulating VCF files.", + "keywords": ["filter", "variant", "vcf", "quality"], + "tools": [ + { + "vcflib": { + "description": "Command line tools for parsing and manipulating VCF files.", + "homepage": "https://github.com/vcflib/vcflib", + "documentation": "https://github.com/vcflib/vcflib", + "tool_dev_url": "https://github.com/vcflib/vcflib", + "doi": "10.1371/journal.pcbi.1009123", + "licence": ["MIT"], + "identifier": "biotools:vcflib" + } } - ] + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test_sample_1' ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF file", + "pattern": "*.{vcf,vcf.gz}", + "ontologies": [] + } + }, + { + "tbi": { + "type": "file", + "description": "Index file", + "pattern": "*.{tbi}", + "ontologies": [] + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "Filtered VCF file", + "pattern": "*.{vcf.gz}", + "ontologies": [] + } + } + ] + ], + "versions_vcflib": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "vcflib": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "1.0.14": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "vcflib": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "1.0.14": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@zachary-foster"], + "maintainers": ["@zachary-foster"] + }, + "pipelines": [ + { + "name": "pathogensurveillance", + "version": "1.1.0" + }, + { + "name": "sarek", + "version": "3.8.1" } - } - ] - ], - "versions_saltshaker": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "saltshaker": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "1.0.0": { - "type": "string", - "description": "Hardcoded version of saltshaker used in the module" - } - } ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "saltshaker": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "1.0.0": { - "type": "string", - "description": "Hardcoded version of saltshaker used in the module" - } - } - ] - ] - }, - "authors": [ - "@ieduba" - ], - "maintainers": [ - "@ieduba" - ] - }, - "pipelines": [ - { - "name": "raredisease", - "version": "3.0.0" - } - ] - }, - { - "name": "sam2lca_analyze", - "path": "modules/nf-core/sam2lca/analyze/meta.yml", - "type": "module", - "meta": { - "name": "sam2lca_analyze", - "description": "Calling lowest common ancestors from multi-mapped reads in SAM/BAM/CRAM files", - "keywords": [ - "LCA", - "alignment", - "bam", - "metagenomics", - "Ancestor", - "multimapper" - ], - "tools": [ - { - "sam2lca": { - "description": "Lowest Common Ancestor on SAM/BAM/CRAM alignment files", - "homepage": "https://github.com/maxibor/sam2lca", - "documentation": "https://sam2lca.readthedocs.io", - "doi": "10.21105/joss.04360", - "licence": [ - "GPL v3" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } + }, + { + "name": "vcflib_vcffixup", + "path": "modules/nf-core/vcflib/vcffixup/meta.yml", + "type": "module", + "meta": { + "name": "vcflib_vcffixup", + "description": "Generates a VCF stream where AC and NS have been generated for each record using sample genotypes.", + "keywords": ["vcf", "vcflib", "vcflib/vcffixup", "AC/NS/AF"], + "tools": [ + { + "vcflib": { + "description": "Command-line tools for manipulating VCF files", + "homepage": "https://github.com/vcflib/vcflib", + "documentation": "https://github.com/vcflib/vcflib#USAGE", + "doi": "10.1101/2021.05.21.445151", + "licence": ["MIT"], + "identifier": "biotools:vcflib" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "Compressed VCF file", + "pattern": "*.{.vcf.gz,vcf}", + "ontologies": [] + } + }, + { + "tbi": { + "type": "file", + "description": "Index of VCF file", + "pattern": "*.vcf.gz.tbi", + "ontologies": [] + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "Compressed VCF file", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "versions_vcflib": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "vcflib": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "1.0.14": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "vcflib": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "1.0.14": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@atrigila"], + "maintainers": ["@atrigila"] }, - { - "bai": { - "type": "file", - "description": "BAM/CRAM/SAM index", - "pattern": "*.{bai,.crai}", - "ontologies": [] - } - } - ], - { - "database": { - "type": "file", - "description": "Directory containing the sam2lca database", - "pattern": "*", - "ontologies": [] - } - } - ], - "output": { - "csv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.csv": { - "type": "file", - "description": "CSV file containing the sam2lca results", - "pattern": "*.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "json": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.json": { - "type": "file", - "description": "JSON file containing the sam2lca results", - "pattern": "*.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "Optional sorted BAM/CRAM/SAM file annotated with LCA taxonomic information", - "pattern": "*.bam", - "ontologies": [] - } - } + "pipelines": [ + { + "name": "phaseimpute", + "version": "1.1.0" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@maxibor" - ], - "maintainers": [ - "@maxibor" - ] - }, - "pipelines": [ - { - "name": "coproid", - "version": "2.0.1" - } - ] - }, - { - "name": "sambamba_depth", - "path": "modules/nf-core/sambamba/depth/meta.yml", - "type": "module", - "meta": { - "name": "sambamba_depth", - "description": "Outputs a coverage file from bam files", - "keywords": [ - "depth", - "coverage", - "sambamba" - ], - "tools": [ - { - "sambamba": { - "description": "Tools for working with SAM/BAM data", - "homepage": "https://lomereiter.github.io/sambamba/docs/sambamba-view.html", - "documentation": "https://lomereiter.github.io/sambamba/docs/sambamba-view.html", - "tool_dev_url": "https://github.com/biod/sambamba", - "doi": "10.1093/bioinformatics/btv098", - "licence": [ - "GPL v2" - ], - "identifier": "biotools:sambamba" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } + }, + { + "name": "vcflib_vcfuniq", + "path": "modules/nf-core/vcflib/vcfuniq/meta.yml", + "type": "module", + "meta": { + "name": "vcflib_vcfuniq", + "description": "List unique genotypes. Like GNU uniq, but for VCF records. Remove records which have the same position, ref, and alt as the previous record.", + "keywords": ["vcf", "uniq", "deduplicate"], + "tools": [ + { + "vcflib": { + "description": "Command-line tools for manipulating VCF files", + "homepage": "https://github.com/vcflib/vcflib", + "documentation": "https://github.com/vcflib/vcflib#USAGE", + "doi": "10.1101/2021.05.21.445151", + "licence": ["MIT"], + "identifier": "biotools:vcflib" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "Compressed VCF file", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + }, + { + "tbi": { + "type": "file", + "description": "Index of VCF file", + "pattern": "*.vcf.gz.tbi", + "ontologies": [] + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*.vcf.gz" + } + }, + { + "*.vcf.gz": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*.vcf.gz" + } + } + ] + ], + "versions_vcflib": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "vcflib": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "1.0.14": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "vcflib": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "1.0.14": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@drpatelh"], + "maintainers": ["@drpatelh"] }, - { - "bam": { - "type": "file", - "description": "BAM file", - "pattern": "*.{bam}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - }, - { - "bai": { - "type": "file", - "description": "BAI file", - "pattern": "*.{bai}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing regions information\n" - } - }, - { - "bed": { - "type": "file", - "description": "bed file", - "pattern": "*.{bed}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3003" - } - ] - } - } - ], - { - "mode": { - "type": "string", - "description": "Analysis mode can be region, window, base", - "pattern": "region|window|base" - } - } - ], - "output": { - "bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*.bed": { - "type": "file", - "description": "bed file", - "pattern": "*.bed", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3586" - } - ] - } - } - ] - ], - "versions_sambamba": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "sambamba": { - "type": "string", - "description": "The tool name" - } - }, - { - "sambamba --version 2>&1 | grep -oPm1 'sambamba \\\\K[0-9.]+'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "sambamba": { - "type": "string", - "description": "The tool name" - } - }, - { - "sambamba --version 2>&1 | grep -oPm1 'sambamba \\\\K[0-9.]+'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@peterpru" - ], - "maintainers": [ - "@peterpru" - ] - }, - "pipelines": [ - { - "name": "raredisease", - "version": "3.0.0" - } - ] - }, - { - "name": "sambamba_flagstat", - "path": "modules/nf-core/sambamba/flagstat/meta.yml", - "type": "module", - "meta": { - "name": "sambamba_flagstat", - "description": "Outputs some statistics drawn from read flags.", - "keywords": [ - "stats", - "flagstat", - "sambamba" - ], - "tools": [ - { - "sambamba": { - "description": "Tools for working with SAM/BAM data", - "homepage": "https://lomereiter.github.io/sambamba/docs/sambamba-view.html", - "documentation": "https://lomereiter.github.io/sambamba/docs/sambamba-view.html", - "tool_dev_url": "https://github.com/biod/sambamba", - "licence": [ - "GPL v2" - ], - "identifier": "biotools:sambamba" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file", - "pattern": "*.{bam}", - "ontologies": [] - } - } - ] - ], - "output": { - "stats": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.stats": { - "type": "file", - "description": "Stats file", - "pattern": "*.{stats}", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@kubranarci" - ], - "maintainers": [ - "@kubranarci" - ] - } - }, - { - "name": "sambamba_markdup", - "path": "modules/nf-core/sambamba/markdup/meta.yml", - "type": "module", - "meta": { - "name": "sambamba_markdup", - "description": "find and mark duplicate reads in BAM file", - "keywords": [ - "markduplicates", - "duplicates", - "bam" - ], - "tools": [ - { - "sambamba": { - "description": "process your BAM data faster!", - "homepage": "https://lomereiter.github.io/sambamba/docs/sambamba-view.html", - "documentation": "https://lomereiter.github.io/sambamba/docs/sambamba-view.html", - "tool_dev_url": "https://github.com/biod/sambamba", - "licence": [ - "GPL v2" - ], - "identifier": "biotools:sambamba" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } - } - ] - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "Sorted BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } - } - ] - ], - "bai": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bai": { - "type": "file", - "description": "An optional BAM index file.", - "pattern": "*.{bai}", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@BioInf2305" - ], - "maintainers": [ - "@BioInf2305" - ] - } - }, - { - "name": "samblaster", - "path": "modules/nf-core/samblaster/meta.yml", - "type": "module", - "meta": { - "name": "samblaster", - "description": "This module combines samtools and samblaster in order to use\nsamblaster capability to filter or tag SAM files, with the advantage\nof maintaining both input and output in BAM format.\nSamblaster input must contain a sequence header: for this reason it has been piped\nwith the \"samtools view -h\" command.\nAdditional desired arguments for samtools can be passed using:\noptions.args2 for the input bam file\noptions.args3 for the output bam file\n", - "keywords": [ - "sort", - "duplicate marking", - "bam" - ], - "tools": [ - { - "samblaster": { - "description": "samblaster is a fast and flexible program for marking duplicates in read-id grouped paired-end SAM files.\nIt can also optionally output discordant read pairs and/or split read mappings to separate SAM files,\nand/or unmapped/clipped reads to a separate FASTQ file.\nBy default, samblaster reads SAM input from stdin and writes SAM to stdout.\n", - "documentation": "https://github.com/GregoryFaust/samblaster", - "tool_dev_url": "https://github.com/GregoryFaust/samblaster", - "doi": "10.1093/bioinformatics/btu314", - "licence": [ - "MIT" - ], - "identifier": "biotools:samblaster" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file", - "pattern": "*.bam", - "ontologies": [] - } - } - ] - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "Tagged or filtered BAM file", - "pattern": "*.bam", - "ontologies": [] - } - } + "pipelines": [ + { + "name": "viralrecon", + "version": "3.0.0" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@lescai" - ], - "maintainers": [ - "@lescai", - "@gallvp" - ] - }, - "pipelines": [ - { - "name": "rnadnavar", - "version": "dev" - } - ] - }, - { - "name": "samclip", - "path": "modules/nf-core/samclip/meta.yml", - "type": "module", - "meta": { - "name": "samclip", - "description": "Filters SAM/BAM/CRAM files for soft and hard clipped alignments", - "keywords": [ - "soft-clipped reads", - "hard-clipped reads", - "clipping", - "genomics", - "sam", - "bam", - "cram" - ], - "tools": [ - { - "samclip": { - "description": "Filters SAM file for soft and hard clipped alignments", - "homepage": "https://github.com/tseemann/samclip", - "documentation": "https://github.com/tseemann/samclip", - "tool_dev_url": "https://github.com/tseemann/samclip", - "doi": "no DOI available", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:samclip" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file", - "pattern": "*.bam", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing fasta reference information\ne.g. `[ id:'ref' ]`\n" - } - }, - { - "reference": { - "type": "file", - "description": "reference FASTA file\n", - "pattern": "*.{fasta,fa,fasta.gz,fa.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - }, - { - "reference_index": { - "type": "file", - "description": "reference FASTA file index\n", - "pattern": "*.fai", - "ontologies": [] - } + }, + { + "name": "vcfpgloader_load", + "path": "modules/nf-core/vcfpgloader/load/meta.yml", + "type": "module", + "meta": { + "name": "vcfpgloader_load", + "description": "High-performance VCF to PostgreSQL loader using asyncpg for bulk variant ingestion", + "keywords": ["vcf", "postgresql", "database", "variants", "genomics", "clinical", "annotation"], + "tools": [ + { + "vcf-pg-loader": { + "description": "High-throughput async PostgreSQL VCF loader using cyvcf2 and asyncpg.\nSupports variant normalization, multi-allelic decomposition, and clinical-grade audit trails.\n", + "homepage": "https://github.com/Zacharyr41/vcf-pg-loader", + "documentation": "https://github.com/Zacharyr41/vcf-pg-loader#readme", + "tool_dev_url": "https://github.com/Zacharyr41/vcf-pg-loader", + "licence": ["MIT"], + "identifier": "", + "args_id": "$args" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample1', family:'FAM001', affected:true ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "Annotated VCF file containing variants to load", + "pattern": "*.{vcf,vcf.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + } + ] + } + }, + { + "tbi": { + "type": "file", + "description": "Tabix index for the VCF file", + "pattern": "*.tbi", + "ontologies": [] + } + }, + { + "db_host": { + "type": "string", + "description": "PostgreSQL server hostname or IP address" + } + }, + { + "db_port": { + "type": "integer", + "description": "PostgreSQL server port (default 5432)" + } + }, + { + "db_name": { + "type": "string", + "description": "Target database name" + } + }, + { + "db_user": { + "type": "string", + "description": "Database username for authentication" + } + }, + { + "db_schema": { + "type": "string", + "description": "Target schema for variant tables (default public)" + } + } + ] + ], + "output": { + "report": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample1' ]\n" + } + }, + { + "*.load_report.json": { + "type": "file", + "description": "JSON report with loading statistics including variant counts, elapsed time, and throughput metrics", + "pattern": "*.load_report.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample1' ]\n" + } + }, + { + "*.load.log": { + "type": "file", + "description": "Detailed loading log with any warnings or errors", + "pattern": "*.load.log", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + } + ] + } + } + ] + ], + "row_count": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample1' ]\n" + } + }, + { + "ROWS_LOADED": { + "type": "integer", + "description": "Number of variant records successfully loaded" + } + } + ] + ], + "versions_vcfpgloader": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "vcf-pg-loader": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "vcf-pg-loader --version | sed 's/.*version //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "vcf-pg-loader": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "vcf-pg-loader --version | sed 's/.*version //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@Zacharyr41"], + "maintainers": ["@Zacharyr41"] } - ] - ], - "output": { - "reads": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information. e.g. `[ id:'sample1']`" - } - }, - { - "*.{bam,cram}": { - "type": "file", - "description": "Filtered BAM/CRAM file", - "pattern": "*.{bam,cram}", - "ontologies": [ + }, + { + "name": "vcftools", + "path": "modules/nf-core/vcftools/meta.yml", + "type": "module", + "meta": { + "name": "vcftools", + "description": "A set of tools written in Perl and C++ for working with VCF files", + "keywords": ["VCFtools", "VCF", "sort"], + "tools": [ + { + "vcftools": { + "description": "A set of tools written in Perl and C++ for working with VCF files. This package only contains the C++ libraries whereas the package perl-vcftools-vcf contains the perl libraries", + "homepage": "http://vcftools.sourceforge.net/", + "documentation": "http://vcftools.sourceforge.net/man_latest.html", + "licence": ["LGPL"], + "identifier": "biotools:vcftools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "variant_file": { + "type": "file", + "description": "variant input file which can be vcf, vcf.gz, or bcf format.", + "ontologies": [] + } + } + ], { - "edam": "http://edamontology.org/format_2572" + "bed": { + "type": "file", + "description": "bed file which can be used with different arguments in vcftools (optional)", + "ontologies": [] + } }, { - "edam": "http://edamontology.org/format_3462" + "diff_variant_file": { + "type": "file", + "description": "secondary variant file which can be used with the 'diff' suite of tools (optional)", + "ontologies": [] + } } - ] - } - } - ] - ], - "versions_samclip": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "samclip": { - "type": "string", - "description": "The tool name" - } - }, - { - "samclip --version | sed 's/^.*samclip //g'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ], - "versions_samtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "samtools": { - "type": "string", - "description": "The tool name" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "samclip": { - "type": "string", - "description": "The tool name" - } - }, - { - "samclip --version | sed 's/^.*samclip //g'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "samtools": { - "type": "string", - "description": "The tool name" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@emmcauley" - ], - "maintainers": [ - "@emmcauley" - ] - } - }, - { - "name": "samplesheetparser_info", - "path": "modules/nf-core/samplesheetparser/info/meta.yml", - "type": "module", - "meta": { - "name": "samplesheetparser_info", - "description": "Display a structured JSON summary of an Illumina SampleSheet.csv (V1 or V2)\nincluding format version, sample count, lanes, index type, read lengths,\nadapter sequences, experiment name, and instrument platform.\nUseful for logging run metadata or conditional branching in pipelines.\n", - "keywords": [ - "illumina", - "samplesheet", - "metadata", - "bclconvert", - "bcl2fastq", - "genomics" - ], - "tools": [ - { - "samplesheet-parser": { - "description": "Format-agnostic parser for Illumina SampleSheet.csv files.\nSupports IEM V1 (bcl2fastq) and BCLConvert V2 with auto-detection,\nbidirectional conversion, index validation, and Hamming distance checking.\n", - "homepage": "https://github.com/chaitanyakasaraneni/samplesheet-parser", - "documentation": "https://illumina-samplesheet.readthedocs.io", - "tool_dev_url": "https://github.com/chaitanyakasaraneni/samplesheet-parser", - "doi": "10.5281/zenodo.18989694", - "licence": [ - "Apache-2.0" - ], - "identifier": "biotools:samplesheet-parser" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information.\nUse [ id:'run_id' ] to identify the sheet.\n" - } - }, - { - "samplesheet": { - "type": "file", - "description": "Illumina SampleSheet.csv (V1 or V2 format, auto-detected)", - "pattern": "*.{csv,CSV}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "output": { - "json": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*.info.json": { - "type": "file", - "description": "JSON summary with file, format, sample_count, lanes, index_type,\nread_lengths, adapters, experiment_name, and instrument fields.\n", - "pattern": "*.info.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "versions_samplesheetparser": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samplesheet-parser": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samplesheet --version | sed 's/samplesheet-parser //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samplesheet-parser": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samplesheet --version | sed 's/samplesheet-parser //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@chaitanyakasaraneni" - ], - "maintainers": [ - "@chaitanyakasaraneni" - ] - } - }, - { - "name": "samplesheetparser_validate", - "path": "modules/nf-core/samplesheetparser/validate/meta.yml", - "type": "module", - "meta": { - "name": "samplesheetparser_validate", - "description": "Validate an Illumina SampleSheet.csv (V1 or V2) for index, adapter, and\nstructural issues. Format is auto-detected. Exits 0 if valid, 1 if errors\nare found — causing the pipeline to fail early with a clear message rather\nthan discovering demultiplexing problems downstream.\n", - "keywords": [ - "illumina", - "samplesheet", - "validation", - "demultiplexing", - "bclconvert", - "bcl2fastq", - "genomics" - ], - "tools": [ - { - "samplesheet-parser": { - "description": "Format-agnostic parser for Illumina SampleSheet.csv files.\nSupports IEM V1 (bcl2fastq) and BCLConvert V2 with auto-detection,\nbidirectional conversion, index validation, and Hamming distance checking.\n", - "homepage": "https://github.com/chaitanyakasaraneni/samplesheet-parser", - "documentation": "https://illumina-samplesheet.readthedocs.io", - "tool_dev_url": "https://github.com/chaitanyakasaraneni/samplesheet-parser", - "doi": "10.5281/zenodo.18989694", - "licence": [ - "Apache-2.0" - ], - "identifier": "biotools:samplesheet-parser" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information.\nUse [ id:'run_id' ] to identify the sheet.\n" - } - }, - { - "samplesheet": { - "type": "file", - "description": "Illumina SampleSheet.csv (V1 or V2 format)", - "pattern": "*.{csv,CSV}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "output": { - "json": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*.validation.json": { - "type": "file", - "description": "Structured JSON validation report with is_valid, errors, warnings,\nand min_hamming_distance fields.\n", - "pattern": "*.validation.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "versions_samplesheetparser": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samplesheet-parser": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samplesheet --version | sed 's/samplesheet-parser //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samplesheet-parser": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samplesheet --version | sed 's/samplesheet-parser //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@chaitanyakasaraneni" - ], - "maintainers": [ - "@chaitanyakasaraneni" - ] - } - }, - { - "name": "samshee", - "path": "modules/nf-core/samshee/meta.yml", - "type": "module", - "meta": { - "name": "samshee", - "description": "Module to validate illumina® Sample Sheet v2 files.", - "keywords": [ - "samplesheet", - "illumina", - "bclconvert", - "bcl2fastq" - ], - "tools": [ - { - "samshee": { - "description": "A schema-agnostic parser and writer for illumina® sample sheets v2 and similar documents.", - "homepage": "https://github.com/lit-regensburg/samshee", - "documentation": "https://github.com/lit-regensburg/samshee/blob/main/README.md", - "tool_dev_url": "https://github.com/lit-regensburg/samshee", - "licence": [ - "MIT license" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', lane:1 ]\n" - } - }, - { - "samplesheet": { - "type": "file", - "description": "illumina v2 samplesheet", - "pattern": "*.{csv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ], - { - "file_schema_validator": { - "type": "string", - "description": "Optional JSON file used additional samplesheet validation settings" - } - } - ], - "output": { - "samplesheet": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', lane:1 ]\n" - } - }, - { - "*_formatted.csv": { - "type": "file", - "description": "illumina v2 samplesheet", - "ontologies": [] - } - } - ] - ], - "versions_samshee": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samshee": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "0.2.13": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_python": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "python": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python --version | sed -e \"s/Python //g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samshee": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "0.2.13": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "python": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python --version | sed -e \"s/Python //g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@nschcolnicov" - ], - "maintainers": [ - "@nschcolnicov" - ] - }, - "pipelines": [ - { - "name": "demultiplex", - "version": "1.7.1" - } - ] - }, - { - "name": "samtools_addreplacerg", - "path": "modules/nf-core/samtools/addreplacerg/meta.yml", - "type": "module", - "meta": { - "name": "samtools_addreplacerg", - "description": "Adds or replaces read group (RG) tags in BAM/CRAM/SAM files", - "keywords": [ - "addreplacerg", - "bam", - "sam", - "cram" - ], - "tools": [ - { - "samtools": { - "description": "Tools for dealing with SAM, BAM and CRAM files", - "homepage": "http://www.htslib.org", - "documentation": "https://www.htslib.org/doc/samtools-addreplacerg.html", - "tool_dev_url": "https://github.com/samtools/samtools", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "identifier": "biotools:samtools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } - }, - { - "index": { - "type": "file", - "description": "BAM/CRAM/SAM index file", - "pattern": "*.{bai,csi,crai}", - "ontologies": [] - } - }, - { - "read_group": { - "type": "string", - "description": "Read group line to add or replace", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference file the CRAM was created with (optional)", - "pattern": "*.{fasta,fa}", - "ontologies": [] - } - }, - { - "fai": { - "type": "file", - "description": "Index of the reference file the CRAM was created with (optional)", - "pattern": "*.fai", - "ontologies": [] - } - }, - { - "gzi": { - "type": "file", - "description": "Index of the compressed reference file the CRAM was created with (optional)", - "pattern": "*.gzi", - "ontologies": [] - } - } - ] - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.bam": { - "type": "file", - "description": "BAM file with updated RG tags", - "pattern": "${prefix}.bam", - "ontologies": [] - } - } - ] - ], - "cram": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.cram": { - "type": "file", - "description": "CRAM file with updated RG tags", - "pattern": "${prefix}.cram", - "ontologies": [] - } - } - ] - ], - "sam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.sam": { - "type": "file", - "description": "SAM file with updated RG tags", - "pattern": "${prefix}.sam", - "ontologies": [] - } - } - ] - ], - "bai": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.bam.bai": { - "type": "file", - "description": "BAM index file", - "pattern": "${prefix}.bam.bai", - "ontologies": [] - } - } - ] - ], - "csi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.bam.csi": { - "type": "file", - "description": "BAM CSI index file", - "pattern": "${prefix}.bam.csi", - "ontologies": [] - } - } - ] - ], - "crai": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.cram.crai": { - "type": "file", - "description": "CRAM index file", - "pattern": "${prefix}.cram.crai", - "ontologies": [] - } - } - ] - ], - "versions_samtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@sainsachiko" - ], - "maintainers": [ - "@sainsachiko" - ] - } - }, - { - "name": "samtools_ampliconclip", - "path": "modules/nf-core/samtools/ampliconclip/meta.yml", - "type": "module", - "meta": { - "name": "samtools_ampliconclip", - "description": "Clips read alignments where they match BED file defined regions", - "keywords": [ - "amplicon", - "clipping", - "ampliconclip", - "samtools" - ], - "tools": [ - { - "samtools": { - "description": "SAMtools is a set of utilities for interacting with and post-processing\nshort DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.\nThese files are generated as output by short read aligners like 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containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.clipallowed.bam": { - "type": "file", - "description": "Clipped reads BAM file", - "pattern": "*.{bam}", - "ontologies": [] - } - } - ] - ], - "stats": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.clipstats.txt": { - "type": "file", - "description": "Clipping statistics text file", - "pattern": "*.{clipstats.txt}", - "ontologies": [] - } - } - ] - ], - "rejects_bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.cliprejects.bam": { - "type": "file", - "description": "Filtered reads BAM file", - "pattern": "*.{cliprejects.bam}", - "ontologies": [] - } - } - ] - ], - "versions_samtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@bjohnnyd" - ], - "maintainers": [ - "@bjohnnyd", - "@matthdsm" - ] - } - }, - { - "name": "samtools_bam2fq", - "path": "modules/nf-core/samtools/bam2fq/meta.yml", - "type": "module", - "meta": { - "name": "samtools_bam2fq", - "description": "The module uses bam2fq method from samtools to\nconvert a SAM, BAM or CRAM file to FASTQ format\n", - 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"pattern": "*.bcf", + "ontologies": [] + } + } + ] + ], + "frq": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.frq": { + "type": "file", + "description": "Allele frequency for each site (optional)", + "pattern": "*.frq", + "ontologies": [] + } + } + ] + ], + "frq_count": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.frq.count": { + "type": "file", + "description": "Allele counts for each site (optional)", + "pattern": "*.frq.count", + "ontologies": [] + } + } + ] + ], + "idepth": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.idepth": { + "type": "file", + "description": "mean depth per individual (optional)", + "pattern": "*.idepth", + "ontologies": [] + } + } + ] + ], + "ldepth": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.ldepth": { + "type": "file", + "description": "depth per site summed across individuals (optional)", + "pattern": "*.ildepth", + "ontologies": [] + } + } + ] + ], + "ldepth_mean": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.ldepth.mean": { + "type": "file", + "description": "mean depth per site calculated across individuals (optional)", + "pattern": "*.ldepth.mean", + "ontologies": [] + } + } + ] + ], + "gdepth": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.gdepth": { + "type": "file", + "description": "depth for each genotype in vcf file (optional)", + "pattern": "*.gdepth", + "ontologies": [] + } + } + ] + ], + "hap_ld": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.hap.ld": { + "type": "file", + "description": "r2, D, and D’ statistics using phased haplotypes (optional)", + "pattern": "*.hap.ld", + "ontologies": [] + } + } + ] + ], + "geno_ld": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.geno.ld": { + "type": "file", + "description": "squared correlation coefficient between genotypes encoded as 0, 1 and 2 to represent the number of non-reference alleles in each individual (optional)", + "pattern": "*.geno.ld", + "ontologies": [] + } + } + ] + ], + "geno_chisq": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.geno.chisq": { + "type": "file", + "description": "test for genotype independence via the chi-squared statistic (optional)", + "pattern": "*.geno.chisq", + "ontologies": [] + } + } + ] + ], + "list_hap_ld": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.list.hap.ld": { + "type": "file", + "description": "r2 statistics of the sites contained in the provided input file verses all other sites (optional)", + "pattern": "*.list.hap.ld", + "ontologies": [] + } + } + ] + ], + "list_geno_ld": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.list.geno.ld": { + "type": "file", + "description": "r2 statistics of the sites contained in the provided input file verses all other sites (optional)", + "pattern": "*.list.geno.ld", + "ontologies": [] + } + } + ] + ], + "interchrom_hap_ld": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.interchrom.hap.ld": { + "type": "file", + "description": "r2 statistics for sites (haplotypes) on different chromosomes (optional)", + "pattern": "*.interchrom.hap.ld", + "ontologies": [] + } + } + ] + ], + "interchrom_geno_ld": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.interchrom.geno.ld": { + "type": "file", + "description": "r2 statistics for sites (genotypes) on different chromosomes (optional)", + "pattern": "*.interchrom.geno.ld", + "ontologies": [] + } + } + ] + ], + "tstv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.TsTv": { + "type": "file", + "description": "Transition / Transversion ratio in bins of size defined in options (optional)", + "pattern": "*.TsTv", + "ontologies": [] + } + } + ] + ], + "tstv_summary": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.TsTv.summary": { + "type": "file", + "description": "Summary of all Transitions and Transversions (optional)", + "pattern": "*.TsTv.summary", + "ontologies": [] + } + } + ] + ], + "tstv_count": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.TsTv.count": { + "type": "file", + "description": "Transition / Transversion ratio as a function of alternative allele count (optional)", + "pattern": "*.TsTv.count", + "ontologies": [] + } + } + ] + ], + "tstv_qual": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.TsTv.qual": { + "type": "file", + "description": "Transition / Transversion ratio as a function of SNP quality threshold (optional)", + "pattern": "*.TsTv.qual", + "ontologies": [] + } + } + ] + ], + "filter_summary": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.FILTER.summary": { + "type": "file", + "description": "Summary of the number of SNPs and Ts/Tv ratio for each FILTER category (optional)", + "pattern": "*.FILTER.summary", + "ontologies": [] + } + } + ] + ], + "sites_pi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.sites.pi": { + "type": "file", + "description": "Nucleotide divergency on a per-site basis (optional)", + "pattern": "*.sites.pi", + "ontologies": [] + } + } + ] + ], + "windowed_pi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.windowed.pi": { + "type": "file", + "description": "Nucleotide diversity in windows, with window size determined by options (optional)", + "pattern": "*windowed.pi", + "ontologies": [] + } + } + ] + ], + "weir_fst": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.weir.fst": { + "type": "file", + "description": "Fst estimate from Weir and Cockerham’s 1984 paper (optional)", + "pattern": "*.weir.fst", + "ontologies": [] + } + } + ] + ], + "heterozygosity": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.het": { + "type": "file", + "description": "Heterozygosity on a per-individual basis (optional)", + "pattern": "*.het", + "ontologies": [] + } + } + ] + ], + "hwe": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.hwe": { + "type": "file", + "description": "Contains the Observed numbers of Homozygotes and Heterozygotes and the corresponding Expected numbers under HWE (optional)", + "pattern": "*.hwe", + "ontologies": [] + } + } + ] + ], + "tajima_d": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.Tajima.D": { + "type": "file", + "description": "Tajima’s D statistic in bins with size of the specified number in options (optional)", + "pattern": "*.Tajima.D", + "ontologies": [] + } + } + ] + ], + "freq_burden": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.ifreqburden": { + "type": "file", + "description": "Number of variants within each individual of a specific frequency in options (optional)", + "pattern": "*.ifreqburden", + "ontologies": [] + } + } + ] + ], + "lroh": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.LROH": { + "type": "file", + "description": "Long Runs of Homozygosity (optional)", + "pattern": "*.LROH", + "ontologies": [] + } + } + ] + ], + "relatedness": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.relatedness": { + "type": "file", + "description": "Relatedness statistic based on the method of Yang et al, Nature Genetics 2010 (doi:10.1038/ng.608) (optional)", + "pattern": "*.relatedness", + "ontologies": [] + } + } + ] + ], + "relatedness2": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.relatedness2": { + "type": "file", + "description": "Relatedness statistic based on the method of Manichaikul et al., BIOINFORMATICS 2010 (doi:10.1093/bioinformatics/btq559) (optional)", + "pattern": "*.relatedness2", + "ontologies": [] + } + } + ] + ], + "lqual": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.lqual": { + "type": "file", + "description": "per-site SNP quality (optional)", + "pattern": "*.lqual", + "ontologies": [] + } + } + ] + ], + "missing_individual": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.imiss": { + "type": "file", + "description": "Missingness on a per-individual basis (optional)", + "pattern": "*.imiss", + "ontologies": [] + } + } + ] + ], + "missing_site": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.lmiss": { + "type": "file", + "description": "Missingness on a per-site basis (optional)", + "pattern": "*.lmiss", + "ontologies": [] + } + } + ] + ], + "snp_density": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.snpden": { + "type": "file", + "description": "Number and density of SNPs in bins of size defined by option (optional)", + "pattern": "*.snpden", + "ontologies": [] + } + } + ] + ], + "kept_sites": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.kept.sites": { + "type": "file", + "description": "All sites that have been kept after filtering (optional)", + "pattern": "*.kept.sites", + "ontologies": [] + } + } + ] + ], + "removed_sites": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.removed.sites": { + "type": "file", + "description": "All sites that have been removed after filtering (optional)", + "pattern": "*.removed.sites", + "ontologies": [] + } + } + ] + ], + "singeltons": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.singletons": { + "type": "file", + "description": "Location of singletons, and the individual they occur in (optional)", + "pattern": "*.singeltons", + "ontologies": [] + } + } + ] + ], + "indel_hist": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.indel.hist": { + "type": "file", + "description": "Histogram file of the length of all indels (including SNPs) (optional)", + "pattern": "*.indel_hist", + "ontologies": [] + } + } + ] + ], + "hapcount": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.hapcount": { + "type": "file", + "description": "Unique haplotypes within user specified bins (optional)", + "pattern": "*.hapcount", + "ontologies": [] + } + } + ] + ], + "mendel": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.mendel": { + "type": "file", + "description": "Mendel errors identified in trios (optional)", + "pattern": "*.mendel", + "ontologies": [] + } + } + ] + ], + "format": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.FORMAT": { + "type": "file", + "description": "Extracted information from the genotype fields in the VCF file relating to a specified FORMAT identifier (optional)", + "pattern": "*.FORMAT", + "ontologies": [] + } + } + ] + ], + "info": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.INFO": { + "type": "file", + "description": "Extracted information from the INFO field in the VCF file (optional)", + "pattern": "*.INFO", + "ontologies": [] + } + } + ] + ], + "genotypes_matrix": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.012": { + "type": "file", + "description": "Genotypes output as large matrix.\nGenotypes of each individual on a separate line.\nGenotypes are represented as 0, 1 and 2, where the number represent that number of non-reference alleles.\nMissing genotypes are represented by -1 (optional)\n", + "pattern": "*.012", + "ontologies": [] + } + } + ] + ], + "genotypes_matrix_individual": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.012.indv": { + "type": "file", + "description": "Details the individuals included in the main genotypes_matrix file (optional)", + "pattern": "*.012.indv", + "ontologies": [] + } + } + ] + ], + "genotypes_matrix_position": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.012.pos": { + "type": "file", + "description": "Details the site locations included in the main genotypes_matrix file (optional)", + "pattern": "*.012.pos", + "ontologies": [] + } + } + ] + ], + "impute_hap": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.impute.hap": { + "type": "file", + "description": "Phased haplotypes in IMPUTE reference-panel format (optional)", + "pattern": "*.impute.hap", + "ontologies": [] + } + } + ] + ], + "impute_hap_legend": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.impute.hap.legend": { + "type": "file", + "description": "Impute haplotype legend file (optional)", + "pattern": "*.impute.hap.legend", + "ontologies": [] + } + } + ] + ], + "impute_hap_indv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.impute.hap.indv": { + "type": "file", + "description": "Impute haplotype individuals file (optional)", + "pattern": "*.impute.hap.indv", + "ontologies": [] + } + } + ] + ], + "ldhat_sites": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.ldhat.sites": { + "type": "file", + "description": "Output data in LDhat format, sites (optional)", + "pattern": "*.ldhat.sites", + "ontologies": [] + } + } + ] + ], + "ldhat_locs": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.ldhat.locs": { + "type": "file", + "description": "output data in LDhat format, locations (optional)", + "pattern": "*.ldhat.locs", + "ontologies": [] + } + } + ] + ], + "beagle_gl": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.BEAGLE.GL": { + "type": "file", + "description": "Genotype likelihoods for biallelic sites (optional)", + "pattern": "*.BEAGLE.GL", + "ontologies": [] + } + } + ] + ], + "beagle_pl": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.BEAGLE.PL": { + "type": "file", + "description": "Genotype likelihoods for biallelic sites (optional)", + "pattern": "*.BEAGLE.PL", + "ontologies": [] + } + } + ] + ], + "ped": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.ped": { + "type": "file", + "description": "output the genotype data in PLINK PED format (optional)", + "pattern": "*.ped", + "ontologies": [] + } + } + ] + ], + "map_": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.map": { + "type": "file", + "description": "output the genotype data in PLINK PED format (optional)", + "pattern": "*.map", + "ontologies": [] + } + } + ] + ], + "tped": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tped": { + "type": "file", + "description": "output the genotype data in PLINK PED format (optional)", + "pattern": "*.tped", + "ontologies": [] + } + } + ] + ], + "tfam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tfam": { + "type": "file", + "description": "output the genotype data in PLINK PED format (optional)", + "pattern": "*.tfam", + "ontologies": [] + } + } + ] + ], + "diff_sites_in_files": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.diff.sites_in_files": { + "type": "file", + "description": "Sites that are common / unique to each file specified in optional inputs (optional)", + "pattern": "*.diff.sites.in.files", + "ontologies": [] + } + } + ] + ], + "diff_indv_in_files": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.diff.indv_in_files": { + "type": "file", + "description": "Individuals that are common / unique to each file specified in optional inputs (optional)", + "pattern": "*.diff.indv.in.files", + "ontologies": [] + } + } + ] + ], + "diff_sites": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.diff.sites": { + "type": "file", + "description": "Discordance on a site by site basis, specified in optional inputs (optional)", + "pattern": "*.diff.sites", + "ontologies": [] + } + } + ] + ], + "diff_indv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.diff.indv": { + "type": "file", + "description": "Discordance on a individual by individual basis, specified in optional inputs (optional)", + "pattern": "*.diff.indv", + "ontologies": [] + } + } + ] + ], + "diff_discd_matrix": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.diff.discordance.matrix": { + "type": "file", + "description": "Discordance matrix between files specified in optional inputs (optional)", + "pattern": "*.diff.discordance.matrix", + "ontologies": [] + } + } + ] + ], + "diff_switch_error": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.diff.switch": { + "type": "file", + "description": "Switch errors found between sites (optional)", + "pattern": "*.diff.switch", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@Mark-S-Hill"], + "maintainers": ["@Mark-S-Hill"] }, - { - "inputbam": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } - } - ], - { - "split": { - "type": "boolean", - "description": "TRUE/FALSE value to indicate if reads should be separated into\n/1, /2 and if present other, or singleton.\nNote: choosing TRUE will generate 4 different files.\nChoosing FALSE will produce a single file, which will be interleaved in case\nthe input contains paired reads.\n" - } - } - ], - "output": { - "reads": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.fq.gz": { - "type": "file", - "description": "FASTQ files, which will be either a group of 4 files (read_1, read_2, other and singleton)\nor a single interleaved .fq.gz file if the user chooses not to split the reads.\n", - "pattern": "*.fq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "versions_samtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "genomicrelatedness", + "version": "dev" + }, + { + "name": "rnadnavar", + "version": "dev" + }, + { + "name": "sarek", + "version": "3.8.1" + } ] - ] }, - "authors": [ - "@lescai" - ], - "maintainers": [ - "@lescai", - "@matthdsm" - ] - }, - "pipelines": [ { - "name": "rnadnavar", - "version": "dev" + "name": "vclust_align", + "path": "modules/nf-core/vclust/align/meta.yml", + "type": "module", + "meta": { + "name": "vclust_align", + "description": "The align command performs pairwise sequence alignments of viral genomes and provides similarity measures like ANI and coverage (alignment fraction)", + "keywords": ["cluster", "virus", "filter", "contig", "scaffold", "phage"], + "tools": [ + { + "vclust": { + "description": "Fast and accurate tool for calculating ANI and clustering virus genomes and metagenomes.", + "homepage": "https://afproject.org/vclust/", + "documentation": "https://github.com/refresh-bio/vclust/wiki", + "tool_dev_url": "https://github.com/refresh-bio/vclust", + "doi": "10.1038/s41592-025-02701-7", + "licence": ["GPL v3-or-later"], + "identifier": "biotools:vclust" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input fasta file containing sequences needed for filtering", + "pattern": "*.{fasta,fna,fa}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "filter": { + "type": "file", + "description": "Input txt file containing sequences relationships for filtering (generated with vclust prefilter)", + "pattern": "*.txt", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + }, + { + "edam": "http://edamontology.org/format_2082" + } + ] + } + } + ], + { + "save_alignment": { + "type": "boolean", + "default": false, + "description": "Save the pairwise alignments to a blast-like file.\n", + "pattern": "*.aln.tsv" + } + } + ], + "output": { + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}.tsv": { + "type": "file", + "description": "Sorted TSV file", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "ids": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.ids.tsv": { + "type": "file", + "description": "File containing sequence IDs and their number of parts", + "pattern": "*.ids.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "aln": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.aln.tsv": { + "type": "file", + "description": "File similar to the BLASTn tabular output file,\nincludes information on each local alignment between two genomes.\n", + "ontologies": [] + } + } + ] + ], + "versions_vclust": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "vclust": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "vclust --version | sed 's/v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "vclust": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "vclust --version | sed 's/v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@Joon-klaps"], + "maintainers": ["@Joon-klaps"] + } }, { - "name": "sarek", - "version": "3.8.1" - } - ] - }, - { - "name": "samtools_bedcov", - "path": "modules/nf-core/samtools/bedcov/meta.yml", - "type": "module", - "meta": { - "name": "samtools_bedcov", - "description": "reports coverage over regions in a supplied BED file", - "keywords": [ - "bedcov", - "samtools", - "coverage", - "bed", - "bam", - "cram", - "sam", - "regions" - ], - "tools": [ - { - "samtools": { - "description": "Tools for dealing with SAM, BAM and CRAM files", - "homepage": "http://www.htslib.org/", - "documentation": "http://www.htslib.org/doc/samtools-bedcov.html", - "tool_dev_url": "https://github.com/samtools/samtools", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "identifier": "biotools:samtools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "input": { - "type": "file", - "description": "Sorted BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2573" - }, - { - "edam": "http://edamontology.org/format_2572" - }, - { - "edam": "http://edamontology.org/format_3462" - } - ] - } - }, - { - "input_index": { - "type": "file", - "description": "BAM/CRAM index file", - "pattern": "*.{bai,crai}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3327" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'bed']`\n" - } - }, - { - "bed": { - "type": "file", - "description": "Interval BED file", - "pattern": "*.bed", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3003" - } - ] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome file", - "pattern": "*.{fa,fasta}", - "ontologies": [] - } - }, - { - "fasta_index": { - "type": "file", - "description": "Reference genome index file", - "pattern": "*.fai", - "ontologies": [] - } - } - ] - ], - "output": { - "coverage": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "Reports the total read base count (i.e. the sum of per base read depths)\nfor each genomic region specified in the supplied BED file.\nThe regions are output as they appear in the BED file and are 0-based.\nColumns 1-3 are chrom/start/end as per the input BED file, followed by N columns of coverages (for N input BAMs),\nthen (if given -d), N columns of bases-at-depth-X, then (if given -c) N columns of read counts.\n", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_samtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@ToonRosseel" - ], - "maintainers": [ - "@ToonRosseel", - "@matthdsm" - ] - } - }, - { - "name": "samtools_bgzip", - "path": "modules/nf-core/samtools/bgzip/meta.yml", - "type": "module", - "meta": { - "name": "samtools_bgzip", - "description": "DEPRECATED. Use HTSLIB/BGZIPTABIX instead. Converts an arbitrary compressed or uncompressed file to BGZIP", - "keywords": [ - "compression", - "fasta", - "gff", - "vcf", - "bed", - "BGZF", - "gzip", - "bgzip" - ], - "tools": [ - { - "samtools": { - "description": "SAMtools is a set of utilities for interacting with and post-processing\nshort DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.\nThese files are generated as output by short read aligners like BWA.\n", - "homepage": "http://www.htslib.org/", - "documentation": "http://www.htslib.org/doc/samtools.html", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "identifier": "biotools:samtools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "infile": { - "type": "file", - "description": "Input file, compressed or not.", - "pattern": "*.*", - "ontologies": [] - } - } - ], - { - "out_ext": { - "type": "string", - "description": "Extension of the output file. Only used for naming, does not affect the compression.\n" - } - } - ], - "output": { - "output": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "output.gz": { - "type": "map", - "description": "A FASTA file compressed with the BGZF algorithm. It will be\nthe original file if it was already BGZF-compressed.\n", - "pattern": "*.*.gz" - } - } - ] - ], - "versions_samtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@charles-plessy" - ], - "maintainers": [ - "@charles-plessy", - "@matthdsm", - "@itrujnara" - ] - }, - "pipelines": [ - { - "name": "pairgenomealign", - "version": "2.2.3" - } - ] - }, - { - "name": "samtools_calmd", - "path": "modules/nf-core/samtools/calmd/meta.yml", - "type": "module", - "meta": { - "name": "samtools_calmd", - "description": "calculates MD and NM tags", - "keywords": [ - "calmd", - "bam", - "cram" - ], - "tools": [ - { - "samtoolscalmd": { - "description": "SAMtools is a set of utilities for interacting with and post-processing\nshort DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.\nThese files are generated as output by short read aligners like BWA.\n", - "homepage": "http://www.htslib.org/", - "documentation": "http://www.htslib.org/doc/samtools.html", - "tool_dev_url": "https://github.com/samtools/samtools", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "identifier": "biotools:samtools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA ref file", - "pattern": "*.{fasta,fa,fna}", - "ontologies": [] - } - }, - { - "fai": { - "type": "file", - "description": "FASTA ref index file", - "pattern": "*.{fasta,fa,fna}.fai", - "ontologies": [] - } - } - ] - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "Sorted BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } - } - ] - ], - "versions_samtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@JackCurragh" - ], - "maintainers": [ - "@JackCurragh", - "@matthdsm" - ] - } - }, - { - "name": "samtools_cat", - "path": "modules/nf-core/samtools/cat/meta.yml", - "type": "module", - "meta": { - "name": "samtools_cat", - "description": "Concatenate BAM or CRAM file", - "keywords": [ - "merge", - "bam", - "sam", - "cram" - ], - "tools": [ - { - "samtools": { - "description": "SAMtools is a set of utilities for interacting with and post-processing\nshort DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.\nThese files are generated as output by short read aligners like BWA.\n", - "homepage": "http://www.htslib.org/", - "documentation": "http://www.htslib.org/doc/samtools.html", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "identifier": "biotools:samtools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input_files": { - "type": "file", - "description": "BAM/CRAM files", - "pattern": "*.{bam,cram}", - "ontologies": [] - } - } - ] - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.bam": { - "type": "file", - "description": "Concatenated BAM file", - "pattern": "*.{bam}", - "ontologies": [] - } - } - ] - ], - "cram": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.cram": { - "type": "file", - "description": "Concatenated CRAM file", - "pattern": "*.{cram}", - "ontologies": [] - } - } - ] - ], - "versions_samtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@matthdsm" - ], - "maintainers": [ - "@matthdsm" - ] - } - }, - { - "name": "samtools_collate", - "path": "modules/nf-core/samtools/collate/meta.yml", - "type": "module", - "meta": { - "name": "samtools_collate", - "description": "shuffles and groups reads together by their names", - "keywords": [ - "collate", - "bam", - "sam", - "cram" - ], - "tools": [ - { - "samtools": { - "description": "Tools for dealing with SAM, BAM and CRAM files", - "homepage": "http://www.htslib.org", - "documentation": "https://www.htslib.org/doc/samtools-collate.html", - "tool_dev_url": "https://github.com/samtools/samtools", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "identifier": "biotools:samtools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome file", - "pattern": "*.{fa,fasta}", - "ontologies": [] - } - }, - { - "fai": { - "type": "file", - "description": "Reference genome index file", - "pattern": "*.fai", - "ontologies": [] - } - } - ] - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "Sorted BAM", - "pattern": "*.{bam}", - "ontologies": [] - } - } - ] - ], - "cram": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.cram": { - "type": "file", - "description": "Sorted CRAM", - "pattern": "*.{cram}", - "ontologies": [] - } - } - ] - ], - "sam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.sam": { - "type": "file", - "description": "Sorted SAM", - "pattern": "*.{sam}", - "ontologies": [] - } - } - ] - ], - "versions_samtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@priyanka-surana" - ], - "maintainers": [ - "@priyanka-surana", - "@matthdsm" - ] - }, - "pipelines": [ - { - "name": "raredisease", - "version": "3.0.0" - } - ] - }, - { - "name": "samtools_collatefastq", - "path": "modules/nf-core/samtools/collatefastq/meta.yml", - "type": "module", - "meta": { - "name": "samtools_collatefastq", - "description": "The module uses collate and then fastq methods from samtools to\nconvert a SAM, BAM or CRAM file to FASTQ format\n", - "keywords": [ - "bam2fq", - "samtools", - "fastq" - ], - "tools": [ - { - "samtools": { - "description": "Tools for dealing with SAM, BAM and CRAM files", - "homepage": "http://www.htslib.org", - "documentation": "https://www.htslib.org/doc/samtools.html", - "tool_dev_url": "https://github.com/samtools/samtools", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "identifier": "biotools:samtools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome file", - "pattern": "*.{fa,fasta}", - "ontologies": [] - } - }, - { - "fai": { - "type": "file", - "description": "Reference genome index file", - "pattern": "*.fai", - "ontologies": [] - } - } - ], - { - "interleave": { - "type": "boolean", - "description": "If true, the output is a single interleaved paired-end FASTQ\nIf false, the output split paired-end FASTQ\n", - "default": false + "name": "vclust_cluster", + "path": "modules/nf-core/vclust/cluster/meta.yml", + "type": "module", + "meta": { + "name": "vclust_cluster", + "description": "Vclust cluster performs threshold-based clustering by assigning a genome sequence to a cluster if its similarity (e.g., ANI) to the cluster meets or exceeds a user-defined threshold.", + "keywords": ["cluster", "virus", "filter", "contig", "scaffold", "phage"], + "tools": [ + { + "vclust": { + "description": "\"Fast and accurate tool for calculating ANI and clustering virus\ngenomes and metagenomes.\"\n", + "homepage": "https://afproject.org/vclust/", + "documentation": "https://github.com/refresh-bio/vclust/wiki", + "tool_dev_url": "https://github.com/refresh-bio/vclust", + "doi": "10.1038/s41592-025-02701-7", + "licence": ["GPL v3-or-later"], + "identifier": "biotools:vclust" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "tsv": { + "type": "file", + "description": "Sorted TSV file, generated by `vclust align`", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "ids": { + "type": "file", + "description": "TSV file containing sequence IDs and their number of parts, generated by `vclust align`", + "pattern": "*.ids.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + { + "metric": { + "type": "string", + "description": "Similarity metric for clustering choices: 'tani','gani' or 'ani'\n", + "pattern": "tani|gani|ani" + } + }, + { + "tani": { + "type": "float", + "description": "Min. total ANI\n" + } + }, + { + "gani": { + "type": "float", + "description": "Min. global ANI\n" + } + }, + { + "ani": { + "type": "float", + "description": "Min. ANI\n" + } + } + ], + "output": { + "clusters": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "A TSV file with genome identifiers followed by 0-based cluster identifiers.\nThe file includes all input genomes, both clustered and singletons, listed in\nthe same order as the IDs file (sorted by decreasing sequence length). The first genome\nin each cluster is the representative.\n", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.log": { + "type": "file", + "description": "Log file containing the stdout", + "pattern": "*.log", + "ontologies": [] + } + } + ] + ], + "versions_vclust": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "vclust": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "vclust --version | sed 's/v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "vclust": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "vclust --version | sed 's/v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@Joon-Klaps"], + "maintainers": ["@Joon-Klaps"] } - } - ], - "output": { - "fastq": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_{1,2}.fq.gz": { - "type": "file", - "description": "R1 and R2 FASTQ files\n", - "pattern": "*_{1,2}.fq.gz", - "ontologies": [] - } - } - ] - ], - "fastq_interleaved": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_interleaved.fq": { - "type": "file", - "description": "Interleaved paired end FASTQ files\n", - "pattern": "*_interleaved.fq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "fastq_other": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_other.fq.gz": { - "type": "file", - "description": "FASTQ files with reads where the READ1 and READ2 FLAG bits set are either both set or both unset.\n", - "pattern": "*_other.fq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "fastq_singleton": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_singleton.fq.gz": { - "type": "file", - "description": "FASTQ files with singleton reads.\n", - "pattern": "*_singleton.fq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "versions_samtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] }, - "authors": [ - "@lescai", - "@maxulysse", - "@matthdsm" - ] - }, - "pipelines": [ { - "name": "bamtofastq", - "version": "2.2.1" + "name": "vclust_prefilter", + "path": "modules/nf-core/vclust/prefilter/meta.yml", + "type": "module", + "meta": { + "name": "vclust_prefilter", + "description": "The prefilter command creates a pre-alignment filter that reduces the number of genome pairs to be aligned by filtering out dissimilar sequences before the alignment step.", + "keywords": ["cluster", "virus", "filter", "contig", "scaffold", "phage"], + "tools": [ + { + "vclust": { + "description": "Fast and accurate tool for calculating ANI and clustering virus genomes and metagenomes.", + "homepage": "https://afproject.org/vclust/", + "documentation": "https://github.com/refresh-bio/vclust/wiki", + "tool_dev_url": "https://github.com/refresh-bio/vclust", + "doi": "10.1038/s41592-025-02701-7", + "licence": ["GPL v3-or-later"], + "identifier": "biotools:vclust" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input fasta file containing sequences needed for filtering", + "pattern": "*.{fasta,fna,fa}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ] + ], + "output": { + "txt": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "Output text file containing relationships for filtering", + "pattern": "*.txt", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2330" + }, + { + "edam": "http://edamontology.org/format_2082" + } + ] + } + } + ] + ], + "versions_vclust": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "vclust": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "vclust --version | sed 's/v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "vclust": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "vclust --version | sed 's/v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@Joon-Klaps"], + "maintainers": ["@Joon-Klaps"] + } }, { - "name": "hlatyping", - "version": "2.2.0" + "name": "velocyto", + "path": "modules/nf-core/velocyto/meta.yml", + "type": "module", + "meta": { + "name": "velocyto", + "description": "Velocyto is a library for the analysis of RNA velocity. velocyto.py CLI use\n`Path(resolve_path=True)` and breaks the nextflow logic of symbolic links.\nIf in the work dir velocyto find a file named EXACTLY `cellsorted_[ORIGINAL_BAM_NAME]`\nit will skip the samtools sort step.\nCellsorted bam file should be cell sorted with:\n```bash\n samtools sort -t CB -O BAM -o cellsorted_input.bam input.bam\n```\nSee module test for an example with the SAMTOOLS_SORT nf-core module.\nConfig example to cellsort input bam using SAMTOOLS_SORT:\n```groovy\n withName: SAMTOOLS_SORT {\n ext.prefix = { \"cellsorted_${bam.baseName}\" }\n ext.args = '-t CB -O BAM'\n }\n```\nOptional mask must be passed with `ext.args` and option `--mask`\nThis is why I need to stage in the work dir 2 bam files (cellsorted and original).\nSee also [velocyto tutorial](https://velocyto.org/velocyto.py/tutorial/cli.html#notes-on-first-runtime-and-parallelization)\n", + "keywords": ["count", "rnaseq", "rna velocity", "bam"], + "tools": [ + { + "velocyto": { + "description": "A library for the analysis of RNA velocity.", + "homepage": "https://github.com/velocyto-team/velocyto.py", + "documentation": "https://velocyto.org/velocyto.py", + "tool_dev_url": "https://github.com/velocyto-team/velocyto.py", + "doi": "10.1038/s41586-018-0414-6", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "barcodes": { + "type": "file", + "description": "Valid barcodes file, to filter the bam", + "pattern": "*.tsv.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + }, + { + "bam": { + "type": "file", + "description": "Sorted BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}", + "ontologies": [] + } + }, + { + "sorted_bam": { + "type": "file", + "description": "Cell sorted BAM/CRAM/SAM file generated with `samtools sort -t CB -O BAM -o cellsorted_possorted_genome_bam.bam possorted_genome_bam.bam`", + "pattern": "*.bam", + "ontologies": [] + } + } + ], + { + "gtf": { + "type": "file", + "description": "genome annotation file", + "pattern": "*.gtf", + "ontologies": [] + } + } + ], + "output": { + "loom": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.loom": { + "type": "file", + "description": "Loom file with counts divided in spliced/unspliced/ambiguous.", + "pattern": "*.loom", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3913" + } + ] + } + }, + { + "*.velocyto.log": { + "type": "file", + "description": "Loom file with counts divided in spliced/unspliced/ambiguous.", + "pattern": "*.loom", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3913" + } + ] + } + } + ] + ], + "versions_velocyto": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "velocyto": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "velocyto --version | sed 's/^.*version //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "velocyto": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "velocyto --version | sed 's/^.*version //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@tucano"], + "maintainers": ["@tucano"] + } }, { - "name": "rnadnavar", - "version": "dev" + "name": "vembrane_filter", + "path": "modules/nf-core/vembrane/filter/meta.yml", + "type": "module", + "meta": { + "name": "vembrane_filter", + "description": "Filter VCF files with vembrane", + "keywords": ["filter", "vcf", "bcf", "genomics", "variant", "annotation"], + "tools": [ + { + "vembrane": { + "description": "Filter VCF/BCF files with Python expressions.", + "homepage": "https://github.com/vembrane/vembrane/tree/main", + "documentation": "https://github.com/vembrane/vembrane/blob/main/docs/filter.md", + "tool_dev_url": "https://github.com/vembrane/vembrane.git", + "doi": "10.1093/bioinformatics/btac810", + "licence": ["MIT"], + "identifier": "biotools:vembrane/filter" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "Path to the VCF/BCF file to be filtered.\ne.g. 'file.vcf', 'file.vcf.gz', 'file.bcf', 'file.bcf.gz'\n", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", + "ontologies": [] + } + } + ], + { + "expression": { + "type": "string", + "description": "The filter expression can be any valid python expression that evaluates to a value of type bool.\ne.g. 'ANN[\"SYMBOL\"] == \"CDH2\"'\n", + "ontologies": [] + } + } + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.{vcf,bcf,bcf.gz}": { + "type": "file", + "description": "Filtered VCF output file", + "pattern": "*.{vcf,bcf,bcf.gz}", + "ontologies": [] + } + } + ] + ], + "versions_vembrane": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "vembrane": { + "type": "string", + "description": "The tool name" + } + }, + { + "vembrane --version | sed '1!d;s/.* //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "vembrane": { + "type": "string", + "description": "The tool name" + } + }, + { + "vembrane --version | sed '1!d;s/.* //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@trangdo-hsc", "@mkatsanto"], + "maintainers": ["@trangdo-hsc"] + } }, { - "name": "rnafusion", - "version": "4.1.2" + "name": "vembrane_sort", + "path": "modules/nf-core/vembrane/sort/meta.yml", + "type": "module", + "meta": { + "name": "vembrane_sort", + "description": "Sort VCF/BCF files by custom Python expressions for variant prioritization", + "keywords": ["vcf", "bcf", "sort", "genomics", "variant", "prioritization"], + "tools": [ + { + "vembrane": { + "description": "Filter VCF/BCF files with Python expressions", + "homepage": "https://vembrane.github.io/", + "documentation": "https://github.com/vembrane/vembrane/blob/main/docs/sort.md", + "tool_dev_url": "https://github.com/vembrane/vembrane", + "doi": "10.1093/bioinformatics/btac810", + "licence": ["MIT"], + "identifier": "biotools:vembrane", + "args_id": "$args" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF/BCF file to sort", + "pattern": "*.{vcf,bcf,bcf.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + } + ] + } + } + ], + { + "expression": { + "type": "string", + "description": "Python expression (or tuple of expressions) returning orderable values to sort by" + } + } + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.{vcf,bcf,bcf.gz}": { + "type": "file", + "description": "Sorted VCF/BCF file", + "pattern": "*.{vcf,bcf,bcf.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + } + ] + } + } + ] + ], + "versions_vembrane": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "vembrane": { + "type": "string", + "description": "The tool name" + } + }, + { + "vembrane --version | sed '1!d;s/.* //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "vembrane": { + "type": "string", + "description": "The tool name" + } + }, + { + "vembrane --version | sed '1!d;s/.* //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@mkatsanto", "@trangdo-hsc"], + "maintainers": ["@mkatsanto", "@trangdo-hsc"] + } }, { - "name": "sarek", - "version": "3.8.1" - } - ] - }, - { - "name": "samtools_consensus", - "path": "modules/nf-core/samtools/consensus/meta.yml", - "type": "module", - "meta": { - "name": "samtools_consensus", - "description": "Produces a consensus FASTA/FASTQ/PILEUP", - "keywords": [ - "consensus", - "bam", - "fastq", - "fasta", - "pileup" - ], - "tools": [ - { - "samtools": { - "description": "SAMtools is a set of utilities for interacting with and post-processing\nshort DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.\nThese files are generated as output by short read aligners like BWA.\n", - "homepage": "http://www.htslib.org/", - "documentation": "http://www.htslib.org/doc/samtools.html", - "tool_dev_url": "https://github.com/samtools/samtools", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "identifier": "biotools:samtools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "input": { - "type": "file", - "description": "Sorted BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } - }, - { - "index": { - "type": "file", - "description": "BAM/CRAM index file", - "pattern": "*.{bai,crai}", - "ontologies": [] - } - } - ] - ], - "output": { - "fasta": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.fasta": { - "type": "file", - "description": "Consensus FASTA file", - "pattern": "*.{fasta}", - "ontologies": [] - } - } - ] - ], - "fastq": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.fastq": { - "type": "file", - "description": "Consensus FASTQ file", - "pattern": "*.{fastq}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "pileup": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.pileup": { - "type": "file", - "description": "Consensus PILEUP file", - "pattern": "*.{pileup}", - "ontologies": [] - } - } - ] - ], - "versions_samtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@LilyAnderssonLee" - ], - "maintainers": [ - "@LilyAnderssonLee", - "@matthdsm" - ] - } - }, - { - "name": "samtools_convert", - "path": "modules/nf-core/samtools/convert/meta.yml", - "type": "module", - "meta": { - "name": "samtools_convert", - "description": "convert and then index CRAM -> BAM or BAM -> CRAM file", - "keywords": [ - "view", - "index", - "bam", - "cram" - ], - "tools": [ - { - "samtools": { - "description": "SAMtools is a set of utilities for interacting with and post-processing\nshort DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.\nThese files are generated as output by short read aligners like BWA.\n", - "homepage": "http://www.htslib.org/", - "documentation": "http://www.htslib.org/doc/samtools.html", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "identifier": "biotools:samtools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM file", - "pattern": "*.{bam,cram}", - "ontologies": [] - } - }, - { - "index": { - "type": "file", - "description": "BAM/CRAM index file", - "pattern": "*.{bai,crai}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference file to create the CRAM file", - "pattern": "*.{fasta,fa}", - "ontologies": [] - } - }, - { - "fai": { - "type": "file", - "description": "Reference index file to create the CRAM file", - "pattern": "*.{fai}", - "ontologies": [] - } + "name": "vembrane_table", + "path": "modules/nf-core/vembrane/table/meta.yml", + "type": "module", + "meta": { + "name": "vembrane_table", + "description": "Creates tabular (TSV) files from VCF/BCF data with flexible Python expressions", + "keywords": ["vcf", "bcf", "table", "genomics", "variant", "annotation"], + "tools": [ + { + "vembrane": { + "description": "Filter VCF/BCF files with Python expressions", + "homepage": "https://vembrane.github.io/", + "documentation": "https://github.com/vembrane/vembrane/blob/main/docs/table.md", + "tool_dev_url": "https://github.com/vembrane/vembrane", + "doi": "10.1093/bioinformatics/btac810", + "licence": ["MIT"], + "identifier": "biotools:vembrane", + "args_id": "$args" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF/BCF file to extract tabular data from", + "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + } + ] + } + } + ], + { + "expression": { + "type": "string", + "description": "A comma-separated tuple of expressions that define the table column contents" + } + } + ], + "output": { + "table": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "TSV file containing tabular data from VCF/BCF", + "pattern": "*.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_vembrane": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "vembrane": { + "type": "string", + "description": "The tool name" + } + }, + { + "vembrane --version | sed '1!d;s/.* //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "vembrane": { + "type": "string", + "description": "The tool name" + } + }, + { + "vembrane --version | sed '1!d;s/.* //'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@mkatsanto", "@trangdo-hsc"], + "maintainers": ["@mkatsanto", "@trangdo-hsc"] } - ] - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "filtered/converted BAM file", - "pattern": "*{.bam}", - "ontologies": [] - } - } - ] - ], - "cram": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.cram": { - "type": "file", - "description": "filtered/converted CRAM file", - "pattern": "*{cram}", - "ontologies": [] - } - } - ] - ], - "bai": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bai": { - "type": "file", - "description": "filtered/converted BAM index", - "pattern": "*{.bai}", - "ontologies": [] - } - } - ] - ], - "crai": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.crai": { - "type": "file", - "description": "filtered/converted CRAM index", - "pattern": "*{.crai}", - "ontologies": [] - } - } - ] - ], - "versions_samtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] }, - "authors": [ - "@FriederikeHanssen", - "@maxulysse" - ], - "maintainers": [ - "@FriederikeHanssen", - "@maxulysse", - "@matthdsm" - ] - }, - "pipelines": [ { - "name": "drop", - "version": "1.0.0" + "name": "verifybamid_verifybamid", + "path": "modules/nf-core/verifybamid/verifybamid/meta.yml", + "type": "module", + "meta": { + "name": "verifybamid_verifybamid", + "description": "Detecting and estimating inter-sample DNA contamination became a crucial quality assessment step to ensure high quality sequence reads and reliable downstream analysis.", + "keywords": ["qc", "contamination", "bam"], + "tools": [ + { + "verifybamid": { + "description": "verifyBamID is a software that verifies whether the reads in particular file match previously known genotypes for an individual (or group of individuals), and checks whether the reads are contaminated as a mixture of two samples.", + "homepage": "https://genome.sph.umich.edu/wiki/VerifyBamID", + "documentation": "http://genome.sph.umich.edu/wiki/VerifyBamID", + "tool_dev_url": "https://github.com/statgen/verifyBamID", + "doi": "10.1016/j.ajhg.2012.09.004", + "licence": ["GPL v3"], + "identifier": "biotools:verifybamid" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file, a sorted, indexed, base quality recalibrated, and duplication-marked BAM file.\nIt also requires to contain \"@RG\" header lines to annotation different readGroups (sequencing runs and lanes).\nThe SM tag in the \"@RG\" header should match with one of the genotyped sample.\n", + "pattern": "*.bam", + "ontologies": [] + } + }, + { + "bai": { + "type": "file", + "description": "BAM index file BAI", + "pattern": "*.bai", + "ontologies": [] + } + } + ], + { + "refvcf": { + "type": "file", + "description": "The input VCF file contains\n(1) external genotype information and/or\n(2) allele frequency information as AF entry or AC/AN entries in the INFO field.\n", + "pattern": "*.{vcf,vcf.gz}", + "ontologies": [] + } + } + ], + "output": { + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "Detailed summary of the verifyBamID result.", + "pattern": "*.log", + "ontologies": [] + } + } + ] + ], + "selfsm": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.selfSM": { + "type": "file", + "description": "Per-sample statistics describing how well the sample matches to the annotated sample.", + "pattern": "*.selfSM", + "ontologies": [] + } + } + ] + ], + "depthsm": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.depthSM": { + "type": "file", + "description": "The depth distribution of the sequence reads per sample", + "pattern": "*.depthSM", + "ontologies": [] + } + } + ] + ], + "selfrg": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.selfRG": { + "type": "file", + "description": "Per-readGroup statistics describing how well each lane matches to the annotated sample. (available only without --ignoreRG option)", + "pattern": "*.selfRG", + "ontologies": [] + } + } + ] + ], + "depthrg": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.depthRG": { + "type": "file", + "description": "The depth distribution of the sequence reads per readGroup. (available only without --ignoreRG option)", + "pattern": "*.depthRG", + "ontologies": [] + } + } + ] + ], + "bestsm": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bestSM": { + "type": "file", + "description": "Per-sample best-match statistics with best-matching sample among the genotyped sample (available only with --best option)", + "pattern": "*.bestSM", + "ontologies": [] + } + } + ] + ], + "bestrg": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bestRG": { + "type": "file", + "description": "Per-readgroup best-match statistics with best-matching sample among the genotyped sample (available only with --best and without --ignoreRG option)", + "pattern": "*.bestRG", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@manifestoso"], + "maintainers": ["@manifestoso"] + } }, { - "name": "genomicrelatedness", - "version": "dev" + "name": "verifybamid_verifybamid2", + "path": "modules/nf-core/verifybamid/verifybamid2/meta.yml", + "type": "module", + "meta": { + "name": "VERIFYBAMID_VERIFYBAMID2", + "description": "Detecting and estimating inter-sample DNA contamination became a crucial quality assessment step to ensure high quality sequence reads and reliable downstream analysis.", + "keywords": ["contamination", "bam", "verifybamid", "DNA contamination estimation"], + "tools": [ + { + "verifybamid2": { + "description": "A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method.", + "homepage": "http://griffan.github.io/VerifyBamID", + "documentation": "http://griffan.github.io/VerifyBamID", + "tool_dev_url": "https://github.com/Griffan/VerifyBamID", + "doi": "10.1101/gr.246934.118", + "licence": ["MIT"], + "identifier": "biotools:verifybamid" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}", + "ontologies": [] + } + }, + { + "bai": { + "type": "file", + "description": "BAI/CRAI/CSI index file", + "pattern": "*.{bai,crai,csi}", + "ontologies": [] + } + } + ], + [ + { + "svd_ud": { + "type": "file", + "description": ".UD matrix file from SVD result of genotype matrix", + "pattern": "*.UD", + "ontologies": [] + } + }, + { + "svd_mu": { + "type": "file", + "description": ".mu matrix file of genotype matrix", + "pattern": "*.mu", + "ontologies": [] + } + }, + { + "svd_bed": { + "type": "file", + "description": ".Bed file for markers used in this analysis,format(chr\\tpos-1\\tpos\\trefAllele\\taltAllele)[Required]", + "pattern": "*.bed", + "ontologies": [] + } + } + ], + { + "refvcf": { + "type": "file", + "description": "Reference panel VCF with genotype information, for generation of .UD .mu .bed files [Optional]", + "pattern": "*.vcf", + "ontologies": [] + } + }, + { + "references": { + "type": "file", + "description": "reference file [Required]", + "pattern": "*.fasta", + "ontologies": [] + } + } + ], + "output": { + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "Detailed summary of the VerifyBamId2 results", + "pattern": "*.log", + "ontologies": [] + } + } + ] + ], + "ud": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.UD": { + "type": "file", + "description": ".UD matrix file from customized reference vcf input", + "pattern": "*.UD", + "ontologies": [] + } + } + ] + ], + "bed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed": { + "type": "file", + "description": ".Bed file from customized reference marker vcf input", + "pattern": "*.bed", + "ontologies": [] + } + } + ] + ], + "mu": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.mu": { + "type": "file", + "description": ".mu matrix file of genotype matrix from customized reference vcf input", + "pattern": "*.mu", + "ontologies": [] + } + } + ] + ], + "self_sm": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.selfSM": { + "type": "file", + "description": "Shares the same format as legacy VB1 and the key information FREEMIX indicates the estimated contamination level.", + "pattern": "*.selfSM", + "ontologies": [] + } + } + ] + ], + "ancestry": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.Ancestry": { + "type": "file", + "description": "Ancestry information", + "pattern": "*.Ancestry", + "ontologies": [] + } + } + ] + ], + "versions_verifybamid2": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "verifybamid2": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "verifybamid2 --help 2>&1 | sed -n '3s/.*Version://p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "verifybamid2": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "verifybamid2 --help 2>&1 | sed -n '3s/.*Version://p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@manifestoso"], + "maintainers": ["@manifestoso"] + }, + "pipelines": [ + { + "name": "raredisease", + "version": "3.0.0" + } + ] }, { - "name": "rnadnavar", - "version": "dev" + "name": "vg_construct", + "path": "modules/nf-core/vg/construct/meta.yml", + "type": "module", + "meta": { + "name": "vg_construct", + "description": "Constructs a graph from a reference and variant calls or a multiple sequence alignment file", + "keywords": ["vg", "graph", "construct", "fasta", "vcf", "structural variants"], + "tools": [ + { + "vg": { + "description": "Variation graph data structures, interchange formats, alignment, genotyping,\nand variant calling methods.\n", + "homepage": "https://github.com/vgteam/vg", + "documentation": "https://github.com/vgteam/vg/wiki", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "list", + "description": "Either one or more VCF files containing different contigs or a multiple sequence alignment file\n", + "pattern": "*.{vcf.gz,fa,fasta,fna,clustal}" + } + }, + { + "tbis": { + "type": "list", + "description": "The index files for the VCF files", + "pattern": "*.tbi" + } + }, + { + "insertions_fasta": { + "type": "file", + "description": "A FASTA file containing insertion sequences (referred to in the VCF file(s))", + "pattern": "*.{fa,fasta,fna}", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The reference FASTA file (cannot be used in combination with `msa`, but is required when using `vcfs`)", + "pattern": "*.{fa,fasta,fna}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta_fai": { + "type": "file", + "description": "The index of the reference FASTA file", + "pattern": "*.fai", + "ontologies": [] + } + } + ] + ], + "output": { + "graph": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vg": { + "type": "file", + "description": "The constructed graph", + "pattern": "*.vg", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@nvnieuwk"], + "maintainers": ["@nvnieuwk"] + } }, { - "name": "rnafusion", - "version": "4.1.2" + "name": "vg_deconstruct", + "path": "modules/nf-core/vg/deconstruct/meta.yml", + "type": "module", + "meta": { + "name": "vg_deconstruct", + "description": "Deconstruct snarls present in a variation graph in GFA format to variants in VCF format", + "keywords": ["vcf", "gfa", "graph", "pangenome graph", "variation graph", "graph projection to vcf"], + "tools": [ + { + "vg": { + "description": "Variation graph data structures, interchange formats, alignment, genotyping,\nand variant calling methods.\n", + "homepage": "https://github.com/vgteam/vg", + "documentation": "https://github.com/vgteam/vg/wiki", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "gfa": { + "type": "file", + "description": "Variation graph in GFA format", + "pattern": "*.{gfa}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3975" + } + ] + } + } + ], + { + "pb": { + "type": "file", + "description": "Optional snarls file (from vg snarls) to avoid recomputing. Usually ends with \"pb\". See \"vg snarls\".", + "pattern": "*.{pb}", + "ontologies": [] + } + }, + { + "gbwt": { + "type": "file", + "description": "Optional GBWT file (from vg gbwt) so to only consider alt traversals that correspond to GBWT threads FILE.", + "pattern": "*.{gbwt}", + "ontologies": [] + } + } + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf": { + "type": "file", + "description": "Variants in VCF format", + "pattern": "*.{vcf}", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@heuermh, @subwaystation"], + "maintainers": ["@heuermh, @subwaystation"] + } }, { - "name": "rnavar", - "version": "1.2.3" + "name": "vg_index", + "path": "modules/nf-core/vg/index/meta.yml", + "type": "module", + "meta": { + "name": "vg_index", + "description": "write your description here", + "keywords": ["vg", "index", "graph", "structural_variants"], + "tools": [ + { + "vg": { + "description": "Variation graph data structures, interchange formats, alignment, genotyping,\nand variant calling methods.\n", + "homepage": "https://github.com/vgteam/vg", + "documentation": "https://github.com/vgteam/vg/wiki", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "list", + "description": "One or more input graph files created with `vg/construct`", + "pattern": "*.vg" + } + } + ] + ], + "output": { + "xg": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.xg": { + "type": "file", + "description": "File containing a succinct, queryable version of the input graph(s) or read for GCSA or distance indexing", + "pattern": "*.xg", + "ontologies": [] + } + } + ] + ], + "vg_index": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vgi": { + "type": "file", + "description": "An index of the graph(s) created when `--index-sorted-vg` is supplied.", + "pattern": "*.vgi", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@nvnieuwk"], + "maintainers": ["@nvnieuwk"] + } }, { - "name": "sarek", - "version": "3.8.1" - } - ] - }, - { - "name": "samtools_coverage", - "path": "modules/nf-core/samtools/coverage/meta.yml", - "type": "module", - "meta": { - "name": "samtools_coverage", - "description": "produces a histogram or table of coverage per chromosome", - "keywords": [ - "depth", - "samtools", - "bam" - ], - "tools": [ - { - "samtools": { - "description": "SAMtools is a set of utilities for interacting with and post-processing\nshort DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.\nThese files are generated as output by short read aligners like BWA.\n", - "homepage": "http://www.htslib.org/", - "documentation": "http://www.htslib.org/doc/samtools.html", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "identifier": "biotools:samtools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } - }, - { - "input_index": { - "type": "file", - "description": "BAM/CRAM index file", - "pattern": "*.{bai,crai}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome file", - "pattern": "*.{fa,fasta}", - "ontologies": [] - } + "name": "viber", + "path": "modules/nf-core/viber/meta.yml", + "type": "module", + "meta": { + "name": "viber", + "description": "Multisample subclonal deconvolution of cancer genome sequencing data.", + "keywords": ["subclonal deconvolution", "genomics", "cancer evolution"], + "tools": [ + { + "viber": { + "description": "VIBER is a package that implements a variational Bayesian model to fit multi-variate Binomial mixtures.\nThe statistical model is semi-parametric and fit by a variational mean-field approximation to the model posterior.\nThe components are Binomial distributions which can model count data;\nthese can be used to model sequencing counts in the context of cancer, for instance.\nThe package implements methods to fit and visualize clustering results.\n", + "homepage": "https://caravagnalab.github.io/VIBER/", + "documentation": "https://caravagnalab.github.io/VIBER/", + "tool_dev_url": "https://github.com/caravagnalab/VIBER/", + "doi": "10.1038/s41588-020-0675-5", + "licence": ["GPL v3-or-later"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "rds_join": { + "type": "file", + "description": "Either a .rds object of class mCNAqc or a .csv mutations table", + "pattern": "*.{rds,csv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + }, + { + "tumour_samples": { + "type": "list", + "description": "List of tumour sample identifiers for a specific patient" + } + } + ] + ], + "output": { + "viber_rds": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_viber_best_fit.rds": { + "type": "file", + "description": "Best viber fit as an .rds object", + "pattern": "*_viber_best_fit.rds", + "ontologies": [] + } + } + ] + ], + "viber_heuristic_rds": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_viber_best_heuristic_fit.rds": { + "type": "file", + "description": "Cluster-filtering heuristics viber fit as an .rds object", + "pattern": "*_viber_best_heuristic_fit.rds", + "ontologies": [] + } + } + ] + ], + "viber_plots_rds": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_viber_best_fit_plots.rds": { + "type": "file", + "description": "best fit plot", + "pattern": "_viber_best_fit_plots.rds", + "ontologies": [] + } + } + ] + ], + "viber_heuristic_plots_rds": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_viber_best_heuristic_fit_plots.rds": { + "type": "file", + "description": "heuristics fit plot", + "pattern": "*_viber_best_heuristic_fit_plots.rds", + "ontologies": [] + } + } + ] + ], + "viber_report_rds": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_viber_report.rds": { + "type": "file", + "description": "final report plots as a .pdf file", + "pattern": "*_viber_report.rds", + "ontologies": [] + } + } + ] + ], + "viber_report_pdf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_viber_report.pdf": { + "type": "file", + "description": "final report plots as a .pdf file", + "pattern": "*_viber_report.pdf", + "ontologies": [] + } + } + ] + ], + "viber_report_png": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_viber_report.png": { + "type": "file", + "description": "final report plots as a .png file", + "pattern": "*_viber_report.png", + "ontologies": [] + } + } + ] + ], + "versions_viber": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "topics": { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@giorgiagandolfi"], + "maintainers": ["@giorgiagandolfi"] }, - { - "fai": { - "type": "file", - "description": "Reference genome index file", - "pattern": "*.fai", - "ontologies": [] - } - } - ] - ], - "output": { - "coverage": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.txt": { - "type": "file", - "description": "Tabulated text containing the coverage at each position or region or an ASCII-art histogram (with --histogram).", - "pattern": "*.txt", - "ontologies": [] - } - } - ] - ], - "versions_samtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "tumourevo", + "version": "dev" + } ] - ] }, - "authors": [ - "@LouisLeNezet" - ], - "maintainers": [ - "@LouisLeNezet", - "@matthdsm" - ] - }, - "pipelines": [ { - "name": "abotyper", - "version": "dev" + "name": "viennarna_rnacofold", + "path": "modules/nf-core/viennarna/rnacofold/meta.yml", + "type": "module", + "meta": { + "name": "viennarna_rnacofold", + "description": "calculate secondary structures of two RNAs with dimerization", + "keywords": ["RNA", "fasta", "rna_structure"], + "tools": [ + { + "viennarna": { + "description": "calculate secondary structures of two RNAs with dimerization\n\nThe program works much like RNAfold, but allows one to specify two RNA\nsequences which are then allowed to form a dimer structure. RNA sequences\nare read from stdin in the usual format, i.e. each line of input\ncorresponds to one sequence, except for lines starting with > which\ncontain the name of the next sequence. To compute the hybrid structure\nof two molecules, the two sequences must be concatenated using the &\ncharacter as separator. RNAcofold can compute minimum free energy (mfe)\nstructures, as well as partition function (pf) and base pairing\nprobability matrix (using the -p switch) Since dimer formation is\nconcentration dependent, RNAcofold can be used to compute equilibrium\nconcentrations for all five monomer and (homo/hetero)-dimer species,\ngiven input concentrations for the monomers. Output consists of the\nmfe structure in bracket notation as well as PostScript structure\nplots and “dot plot” files containing the pair probabilities, see\nthe RNAfold man page for details. In the dot plots a cross marks\nthe chain break between the two concatenated sequences. The program\nwill continue to read new sequences until a line consisting of the\nsingle character @ or an end of file condition is encountered.\n", + "homepage": "https://www.tbi.univie.ac.at/RNA/", + "documentation": "https://viennarna.readthedocs.io/en/latest/", + "doi": "10.1186/1748-7188-6-26", + "licence": ["custom"], + "identifier": "biotools:viennarna" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "rnacofold_fasta": { + "type": "file", + "description": "A fasta file containing RNA or transcript sequences\n", + "pattern": "*.{fasta,fa}", + "ontologies": [] + } + } + ] + ], + "output": { + "rnacofold_csv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.csv": { + "type": "file", + "description": "The CSV Output of RNAcofold that has the predicted structure and energies", + "pattern": "*.{csv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ] + ], + "rnacofold_ps": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.ps": { + "type": "file", + "description": "The text Output of RNAfold that contains the predicted secondary structure in postscript format", + "pattern": "*.{ps}", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@kokul-atx"], + "maintainers": ["@kokul-atx"] + } }, { - "name": "phaseimpute", - "version": "1.1.0" - } - ] - }, - { - "name": "samtools_cramsize", - "path": "modules/nf-core/samtools/cramsize/meta.yml", - "type": "module", - "meta": { - "name": "samtools_cramsize", - "description": "List CRAM Content-ID and Data-Series sizes", - "keywords": [ - "cram-size", - "cram", - "size" - ], - "tools": [ - { - "samtools": { - "description": "SAMtools is a set of utilities for interacting with and post-processing\nshort DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.\nThese files are generated as output by short read aligners like BWA.\n", - "homepage": "http://www.htslib.org/", - "documentation": "http://www.htslib.org/doc/samtools.html", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "identifier": "biotools:samtools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "cram": { - "type": "file", - "description": "CRAM file", - "pattern": "*.cram", - "ontologies": [] - } - } - ] - ], - "output": { - "size": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.size": { - "type": "file", - "description": "Size information file", - "pattern": "*.size", - "ontologies": [] - } - } - ] - ], - "versions_samtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@limrp" - ] - } - }, - { - "name": "samtools_depth", - "path": "modules/nf-core/samtools/depth/meta.yml", - "type": "module", - "meta": { - "name": "samtools_depth", - "description": "Computes the depth at each position or region.", - "keywords": [ - "depth", - "samtools", - "statistics", - "coverage" - ], - "tools": [ - { - "samtools": { - "description": "Tools for dealing with SAM, BAM and CRAM files; samtools depth – computes the read depth at each position or region", - "homepage": "http://www.htslib.org", - "documentation": "http://www.htslib.org/doc/samtools-depth.html", - "tool_dev_url": "https://github.com/samtools/samtools", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "identifier": "biotools:samtools" - } - } - ], - "input": [ - [ - { - "meta1": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "sorted BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } - }, - { - "index": { - "type": "file", - "description": "BAM/CRAM index file", - "pattern": "*.{bai,crai}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "intervals": { - "type": "file", - "description": "list of positions or regions in specified bed file", - "pattern": "*.{bed}", - "ontologies": [] - } - } - ] - ], - "output": { - "tsv": [ - [ - { - "meta1": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "The output of samtools depth has three columns - the name of the contig or chromosome, the position and the number of reads aligned at that position", - "pattern": "*.{tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_samtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "samtools": { - "type": "string", - "description": "The tool name" - } - }, - { - "samtools version | sed \"1!d;s/.* //\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "samtools": { - "type": "string", - "description": "The tool name" - } - }, - { - "samtools version | sed \"1!d;s/.* //\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@louperelo", - "@nevinwu" - ], - "maintainers": [ - "@louperelo", - "@nevinwu", - "@matthdsm" - ] - }, - "pipelines": [ - { - "name": "phaseimpute", - "version": "1.1.0" - } - ] - }, - { - "name": "samtools_dict", - "path": "modules/nf-core/samtools/dict/meta.yml", - "type": "module", - "meta": { - "name": "samtools_dict", - "description": "Create a sequence dictionary file from a FASTA file", - "keywords": [ - "dict", - "fasta", - "sequence" - ], - "tools": [ - { - "samtools": { - "description": "SAMtools is a set of utilities for interacting with and post-processing\nshort DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.\nThese files are generated as output by short read aligners like BWA.\n", - "homepage": "http://www.htslib.org/", - "documentation": "http://www.htslib.org/doc/samtools.html", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "identifier": "biotools:samtools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA file", - "pattern": "*.{fa,fasta}", - "ontologies": [] - } + "name": "viennarna_rnafold", + "path": "modules/nf-core/viennarna/rnafold/meta.yml", + "type": "module", + "meta": { + "name": "viennarna_rnafold", + "description": "Predict RNA secondary structure using the ViennaRNA RNAfold tools. Calculate minimum free energy secondary structures and partition function of RNAs.", + "keywords": ["RNA", "fasta", "rna_structure"], + "tools": [ + { + "viennarna": { + "description": "Calculate minimum free energy secondary structures and partition function of RNAs\n\nThe program reads RNA sequences, calculates their minimum free energy (mfe) structure and\nprints the mfe structure in bracket notation and its free energy. If not specified differently\nusing commandline arguments, input is accepted from stdin or read from an input file, and\noutput printed to stdout. If the -p option was given it also computes the partition function\n(pf) and base pairing probability matrix, and prints the free energy of the thermodynamic\nensemble, the frequency of the mfe structure in the ensemble, and the ensemble diversity to stdout.\n", + "homepage": "https://www.tbi.univie.ac.at/RNA/", + "documentation": "https://viennarna.readthedocs.io/en/latest/", + "doi": "10.1186/1748-7188-6-26", + "licence": ["custom"], + "identifier": "biotools:viennarna" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "A fasta file containing RNA or transcript sequences\n", + "pattern": "*.{fasta,fa}", + "ontologies": [] + } + } + ] + ], + "output": { + "rnafold_txt": [ + [ + { + "meta": { + "type": "file", + "description": "The text Output of RNAfold that", + "pattern": "*.{fold}", + "ontologies": [] + } + }, + { + "*.fold": { + "type": "file", + "description": "The text Output of RNAfold that", + "pattern": "*.{fold}", + "ontologies": [] + } + } + ] + ], + "rnafold_ps": [ + [ + { + "meta": { + "type": "file", + "description": "The text Output of RNAfold that", + "pattern": "*.{fold}", + "ontologies": [] + } + }, + { + "*.ps": { + "type": "file", + "description": "The text Output of RNAfold that", + "pattern": "*.ss", + "ontologies": [] + } + } + ] + ], + "versions": [ + [ + { + "meta": { + "type": "file", + "description": "The text Output of RNAfold that", + "pattern": "*.{fold}", + "ontologies": [] + } + }, + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + ] + }, + "authors": ["@kokul-atx"], + "maintainers": ["@kokul-atx"] } - ] - ], - "output": { - "dict": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.dict": { - "type": "file", - "description": "FASTA dictionary file", - "pattern": "*.{dict}", - "ontologies": [] - } - } - ] - ], - "versions_samtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "samtools": { - "type": "string", - "description": "The tool name" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "samtools": { - "type": "string", - "description": "The tool name" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] }, - "authors": [ - "@muffato" - ], - "maintainers": [ - "@muffato", - "@matthdsm" - ] - }, - "pipelines": [ { - "name": "fastquorum", - "version": "1.2.0" + "name": "viennarna_rnalfold", + "path": "modules/nf-core/viennarna/rnalfold/meta.yml", + "type": "module", + "meta": { + "name": "viennarna_rnalfold", + "description": "calculate locally stable secondary structures of RNAs", + "keywords": ["RNA", "fasta", "rna_structure"], + "tools": [ + { + "viennarna": { + "description": "calculate locally stable secondary structures of RNAs\n\nCompute locally stable RNA secondary structure with a maximal base pair span.\nFor a sequence of length n and a base pair span of L the algorithm uses only\nO(n+L*L) memory and O(n*L*L) CPU time. Thus it is practical to “scan” very\nlarge genomes for short RNA structures. Output consists of a list of\nsecondary structure components of size <= L, one entry per line. Each\noutput line contains the predicted local structure its energy in\nkcal/mol and the starting position of the local structure.\n", + "homepage": "https://www.tbi.univie.ac.at/RNA/", + "documentation": "https://viennarna.readthedocs.io/en/latest/", + "doi": "10.1186/1748-7188-6-26", + "licence": ["custom"], + "identifier": "biotools:viennarna" + } + } + ], + "input": [ + { + "fasta": { + "type": "file", + "description": "A fasta file containing RNA or transcript sequences\n", + "pattern": "*.{fasta,fa}", + "ontologies": [] + } + } + ], + "output": { + "rnalfold_txt": [ + { + "*.lfold": { + "type": "file", + "description": "The text Output of RNALfold", + "pattern": "*.{lfold}", + "ontologies": [] + } + } + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@kokul-atx"], + "maintainers": ["@kokul-atx"] + } }, { - 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"meta": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA file", - "pattern": "*.{fa,fasta}", - "ontologies": [] - } - }, - { - "fai": { - "type": "file", - "description": "FASTA index file", - "pattern": "*.{fai}", - "ontologies": [] - } - } - ], - { - "get_sizes": { - "type": "boolean", - "description": "use cut to get the sizes of the index (true) or not (false)" + "name": "viralconsensus", + "path": "modules/nf-core/viralconsensus/meta.yml", + "type": "module", + "meta": { + "name": "viralconsensus", + "description": "Fast and memory-efficient viral consensus genome sequence generation from read alignments", + "keywords": ["virus", "genomics", "consensus", "bam", "fasta"], + "tools": [ + { + "viralconsensus": { + "description": "ViralConsensus is a fast and memory-efficient tool for calling viral consensus genome sequences directly from read alignment data.", + "homepage": "https://github.com/niemasd/ViralConsensus", + "documentation": "https://github.com/niemasd/ViralConsensus#usage", + "tool_dev_url": "https://github.com/niemasd/ViralConsensus", + "doi": "10.1093/bioinformatics/btad317", + "licence": ["GPL-3.0-or-later"], + "identifier": "biotools:viralconsensus" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/SAM/CRAM file containing aligned reads", + "pattern": "*.{bam,sam,cram}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'sarscov2' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference genome sequence in FASTA format", + "pattern": "*.{fa,fasta,fna}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ], + { + "primer_bed": { + "type": "file", + "description": "Optional BED file with primer coordinates for trimming", + "pattern": "*.bed", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3003" + } + ] + } + }, + { + "save_pos_counts": { + "type": "boolean", + "description": "Save per-position counts to a TSV file\n" + } + }, + { + "save_ins_counts": { + "type": "boolean", + "description": "Save insertion counts to a JSON file\n" + } + } + ], + "output": { + "fasta": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.consensus.fa": { + "type": "file", + "description": "Consensus genome sequence in FASTA format", + "pattern": "*.consensus.fa", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ] + ], + "pos_counts": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.pos_counts.tsv": { + "type": "file", + "description": "Per-position base counts (optional, enabled via save_pos_counts input)", + "pattern": "*.pos_counts.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "ins_counts": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.ins_counts.json": { + "type": "file", + "description": "Insertion counts (optional, enabled via save_ins_counts input)", + "pattern": "*.ins_counts.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "versions_viralconsensus": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "viralconsensus": { + "type": "string", + "description": "The tool name" + } + }, + { + "viral_consensus --version | sed 's/.*v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "viralconsensus": { + "type": "string", + "description": "The tool name" + } + }, + { + "viral_consensus --version | sed 's/.*v//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@niemasd"], + "maintainers": ["@niemasd", "@lucaspatel"] } - 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} - }, - { - "*.gzi": { - "type": "file", - "description": "Optional gzip index file for compressed inputs", - "pattern": "*.gzi", - "ontologies": [] - } - } - ] - ], - "versions_samtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "samtools": { - "type": "string", - "description": "The tool name" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "samtools": { - "type": "string", - "description": "The tool name" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@drpatelh", - "@ewels", - "@phue" - ], - "maintainers": [ - "@maxulysse", - "@phue", - "@matthdsm" - ] - }, - "pipelines": [ - { - "name": "bamtofastq", - "version": "2.2.1" - }, - { - "name": "callingcards", - "version": "1.0.0" - }, - { - "name": "circdna", - "version": "1.1.0" - }, - { - "name": "circrna", - "version": "dev" - }, - { - "name": "createpanelrefs", - "version": "dev" - }, - { - "name": "cutandrun", - "version": "3.2.2" - }, - { - "name": "fastquorum", - "version": "1.2.0" - }, - { - "name": "genomicrelatedness", - "version": "dev" - }, - { - "name": "mag", - "version": "5.4.2" - }, - { - "name": "methylong", - "version": "2.0.0" - }, - { - "name": "methylseq", - "version": "4.2.0" - }, - { - "name": "nanoseq", - "version": "3.1.0" - }, - { - "name": "oncoanalyser", - "version": "2.3.0" - }, - { - "name": "pacsomatic", - "version": "dev" }, { - "name": "pairgenomealign", - "version": "2.2.3" - }, - { - "name": "pangenome", - "version": "1.1.3" - }, - { - "name": "pathogensurveillance", - "version": "1.1.0" - }, - { - "name": "phaseimpute", - "version": "1.1.0" - }, - { - "name": "radseq", - "version": "dev" - }, - { - "name": "raredisease", - "version": "3.0.0" - }, - { - "name": "references", - "version": "0.1" - }, - { - "name": "rnadnavar", - "version": "dev" - }, - { - "name": "rnafusion", - "version": "4.1.2" - }, - { - "name": "rnaseq", - "version": "3.26.0" + "name": "vireo", + "path": "modules/nf-core/vireo/meta.yml", + "type": "module", + "meta": { + "name": "vireo", + "description": "Use vireo to perform donor deconvolution for multiplexed scRNA-seq data", + "keywords": ["genotype-based demultiplexing", "donor deconvolution", "cellsnp"], + "tools": [ + { + "vireo": { + "description": "vireoSNP - donor deconvolution for multiplexed scRNA-seq data", + "homepage": "https://vireosnp.readthedocs.io/en/latest/", + "documentation": "https://vireosnp.readthedocs.io/en/latest/", + "tool_dev_url": "https://github.com/single-cell-genetics/vireo", + "doi": "10.1186/s13059-019-1865-2", + "licence": ["Apache-2.0"], + "identifier": "biotools:Vireo" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "cell_data": { + "type": "file", + "description": "The cell genotype file in VCF format or cellSNP folder with sparse matrices.", + "pattern": "*.vcf|*/", + "ontologies": [] + } + }, + { + "n_donor": { + "type": "integer", + "description": "Number of donors to demultiplex." + } + }, + { + "donor_file": { + "type": "file", + "description": "The optional donor genotype file in VCF format.", + "pattern": "*.vcf", + "ontologies": [] + } + }, + { + "vartrix_data": { + "type": "file", + "description": "The optional cell genotype files in vartrix outputs.", + "ontologies": [] + } + } + ] + ], + "output": { + "summary": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_summary.tsv": { + "type": "file", + "description": "Summary tsv file of deconvolution result.", + "pattern": "*_summary.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "donor_ids": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_donor_ids.tsv": { + "type": "file", + "description": "Donor assignment with detailed statistics.", + "pattern": "*_donor_ids.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "prob_singlets": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_prob_singlet.tsv.gz": { + "type": "file", + "description": "contains probability of classifing singlets", + "pattern": "*_prob_singlet.tsv.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "prob_doublets": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_prob_doublet.tsv.gz": { + "type": "file", + "description": "contains probability of classifing doublets", + "pattern": "*_prob_doublet.tsv.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "genotype_vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_GT_donors.vireo.vcf.gz": { + "type": "file", + "description": "contains vireo’s inferred donor genotypes at each SNP (only created if `--forceLearnGT` is set in `ext.args`, see n)", + "pattern": "*_GT_donors.vireo.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + } + ] + } + } + ] + ], + "filtered_variants": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_filtered_variants.tsv": { + "type": "file", + "description": "contains the minimal set of discriminatory variants created by `GTbarcode` (only created if `--forceLearnGT` is set in `ext.args`, see the hadge pipeline as an example, and only shows consistent results if `--randSeed` is set)", + "pattern": "*_filtered_variants.tsv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@mari-ga", "@maxozo", "@wxicu", "@Zethson"], + "maintainers": ["@mari-ga", "@maxozo", "@wxicu", "@Zethson"] + } }, { - "name": "rnavar", - "version": "1.2.3" + "name": "virusrecom", + "path": "modules/nf-core/virusrecom/meta.yml", + "type": "module", + "meta": { + "name": "virusrecom", + "description": "Information-theory-based method for recombination detection of viral lineages using weighted information content (WIC).", + "keywords": ["recombination", "virus", "genomics", "phylogenetics"], + "tools": [ + { + "virusrecom": { + "description": "An information-theory-based method for recombination detection of viral lineages.", + "homepage": "https://github.com/ZhijianZhou01/virusrecom", + "documentation": "https://github.com/ZhijianZhou01/virusrecom", + "tool_dev_url": "https://github.com/ZhijianZhou01/virusrecom", + "doi": "10.1093/bib/bbac513", + "licence": ["GPL v3"], + "identifier": "biotools:virusrecom" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "alignment": { + "type": "file", + "description": "Aligned FASTA file containing viral sequences. Use [] when providing iwic input.", + "pattern": "*.{fasta,fa,fna,fas}", + "ontologies": [] + } + }, + { + "mapping": { + "type": "file", + "description": "Tab-separated file mapping sequence names to lineages", + "pattern": "*.{txt,tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, + { + "iwic": { + "type": "file", + "description": "Optional CSV file containing pre-computed WIC values. Use [] to skip.", + "pattern": "*.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ], + { + "query": { + "type": "string", + "description": "Name of the query lineage to test for recombination (e.g. query_recombinant). Use auto to scan all lineages." + } + } + ], + "output": { + "results": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}/": { + "type": "directory", + "description": "Directory containing virusrecom output files including WIC plots and recombination tables" + } + } + ] + ], + "versions_virusrecom": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "virusrecom": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "virusrecom -h 2>&1 | sed -n 's/.*Version: \\([^ ]*\\).*/\\1/p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "virusrecom": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "virusrecom -h 2>&1 | sed -n 's/.*Version: \\([^ ]*\\).*/\\1/p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@haggaikelisha-ai"], + "maintainers": ["@haggaikelisha-ai"] + } }, { - "name": "sammyseq", - "version": "dev" + "name": "vizgenpostprocessing_compiletilesegmentation", + "path": "modules/nf-core/vizgenpostprocessing/compiletilesegmentation/meta.yml", + "type": "module", + "meta": { + "name": "vizgenpostprocessing_compiletilesegmentation", + "description": "The module compiles segmentation tiles using Vizgen's post-processing tool.", + "keywords": ["vpt", "vizgen", "segmentation", "microscopy", "spatial transcriptomics"], + "tools": [ + { + "vizgenpostprocessing": { + "description": "Vizgen's post-processing tool", + "homepage": "https://github.com/Vizgen/vizgen-postprocessing", + "documentation": "https://vizgen.github.io/vizgen-postprocessing", + "tool_dev_url": "https://github.com/Vizgen/vizgen-postprocessing", + "licence": ["Apache-2.0"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample1', single_end:false ]\n" + } + }, + { + "input_images": { + "type": "directory", + "description": "Path to the input images directory to be used for segmentation.\n", + "ontologies": [ + { + "edam": "http://edamontology.org/data_1049" + } + ] + } + }, + { + "segmentation_params": { + "type": "file", + "description": "Path to the segmentation parameters (algorithm specification) JSON\nfile generated by the preparesegmentation module.\n", + "pattern": "*.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ], + { + "algorithm_json": { + "type": "file", + "description": "JSON file containing the algorithm parameters.", + "pattern": "*.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + }, + { + "segmentation_tiles": { + "type": "file", + "description": "Parquet files containing the segmentation results for tiles to compile.\n", + "pattern": "*.parquet", + "ontologies": [] + } + } + ], + "output": { + "mosaic_space": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}/*_mosaic_space.parquet": { + "type": "file", + "description": "Parquet file containing the compiled segmentation results in mosaic space.\n", + "ontologies": [] + } + } + ] + ], + "micron_space": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}/*_micron_space.parquet": { + "type": "file", + "description": "Parquet file containing the compiled segmentation results in micron space.\n", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@mcmero"], + "maintainers": ["@mcmero"] + } }, { - "name": "sarek", - "version": "3.8.1" + "name": "vizgenpostprocessing_preparesegmentation", + "path": "modules/nf-core/vizgenpostprocessing/preparesegmentation/meta.yml", + "type": "module", + "meta": { + "name": "vizgenpostprocessing_preparesegmentation", + "description": "The module prepares the specification JSON file for Vizgen's post-processing tool\ncell segmentation workflow.\n", + "keywords": ["vpt", "vizgen", "segmentation", "microscopy", "spatial transcriptomics"], + "tools": [ + { + "vizgenpostprocessing": { + "description": "Vizgen's post-processing tool", + "homepage": "https://github.com/Vizgen/vizgen-postprocessing", + "documentation": "https://vizgen.github.io/vizgen-postprocessing", + "tool_dev_url": "https://github.com/Vizgen/vizgen-postprocessing", + "licence": ["Apache-2.0"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample1', single_end:false ]\n" + } + }, + { + "input_images": { + "type": "directory", + "description": "Path to the input images directory to be used for segmentation.\n", + "ontologies": [ + { + "edam": "http://edamontology.org/data_1049" + } + ] + } + }, + { + "um_to_mosaic_file": { + "type": "file", + "description": "Path to the micron-to-mosaic pixel transform matrix file.\n", + "pattern": "*.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + } + ], + { + "algorithm_json": { + "type": "file", + "description": "JSON file containing the algorithm specification", + "pattern": "*.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + }, + { + "images_regex": { + "type": "string", + "description": "Can either be blank to match files by MERSCOPE convention, or a\npython formatting string specifying the file name (e.g.,\nimage_{stain}_z{z}.tif), or a regular expression matching the tiff\nfiles to be used (e.g., mosaic_(?P[\\w|-]+)_z(?P[0-9]+).tif)\n", + "ontologies": [ + { + "edam": "http://edamontology.org/data_1352" + } + ] + } + } + ], + "output": { + "segmentation_files": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}/*.json": { + "type": "file", + "description": "Segmentation specification JSON file", + "pattern": "*.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@mcmero"], + "maintainers": ["@mcmero"] + } }, { - "name": "scnanoseq", - "version": "1.2.2" + "name": "vizgenpostprocessing_runsegmentationontile", + "path": "modules/nf-core/vizgenpostprocessing/runsegmentationontile/meta.yml", + "type": "module", + "meta": { + "name": "vizgenpostprocessing_runsegmentationontile", + "description": "The module runs the segmentation algorithm on a specific tile using Vizgen's\npost-processing tool.\n", + "keywords": ["vpt", "vizgen", "segmentation", "microscopy", "spatial transcriptomics"], + "tools": [ + { + "vizgenpostprocessing": { + "description": "Vizgen's post-processing tool", + "homepage": "https://github.com/Vizgen/vizgen-postprocessing", + "documentation": "https://vizgen.github.io/vizgen-postprocessing", + "tool_dev_url": "https://github.com/Vizgen/vizgen-postprocessing", + "licence": ["Apache-2.0"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample1', single_end:false ]\n" + } + }, + { + "input_images": { + "type": "directory", + "description": "Path to the input images directory to be used for segmentation.\n", + "ontologies": [ + { + "edam": "http://edamontology.org/data_1049" + } + ] + } + }, + { + "segmentation_params": { + "type": "file", + "description": "Path to the segmentation parameters (algorithm specification) JSON\nfile generated by the preparesegmentation module.\n", + "pattern": "*.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + }, + { + "tile_index": { + "type": "integer", + "description": "The index of the tile to run the segmentation algorithm on.\n" + } + } + ], + { + "algorithm_json": { + "type": "file", + "description": "JSON file containing the algorithm parameters.", + "pattern": "*.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + }, + { + "custom_weights": { + "type": "directory", + "description": "Directory containing custom weights for the segmentation algorithm.\nMust be defined in the algorithm JSON file under \"custom_weights\"\nas directory name only (not full path).\n" + } + } + ], + "output": { + "segmented_tile": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}/result_tiles/*.parquet": { + "type": "file", + "description": "Parquet file containing the segmentation results for the specified tile.\n", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@mcmero"], + "maintainers": ["@mcmero"] + } }, { - "name": "seqinspector", - "version": "1.0.1" + "name": "vrhyme_extractunbinned", + "path": "modules/nf-core/vrhyme/extractunbinned/meta.yml", + "type": "module", + "meta": { + "name": "vrhyme_extractunbinned", + "description": "Extracting sequences that were unbinnned by vRhyme into a FASTA file", + "keywords": ["bin", "binning", "link", "vrhyme", "extractunbinned"], + "tools": [ + { + "vrhyme": { + "description": "vRhyme functions by utilizing coverage variance comparisons and supervised machine learning classification of sequence features to construct viral metagenome-assembled genomes (vMAGs).", + "homepage": "https://github.com/AnantharamanLab/vRhyme", + "documentation": "https://github.com/AnantharamanLab/vRhyme", + "tool_dev_url": "https://github.com/AnantharamanLab/vRhyme", + "doi": "10.1093/nar/gkac341", + "licence": ["GPL v3 license", "GPL v3"], + "identifier": "biotools:vrhyme" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "membership": { + "type": "file", + "description": "TSV file containing information regarding which bins input sequences were placed information", + "pattern": "*.{tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing information related to the fasta\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA file containing contigs/scaffolds input into vRhyme", + "pattern": "*.{fasta,fna,fa,fasta.gz,fna.gz,fa.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ] + ], + "output": { + "unbinned_sequences": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.fasta": { + "type": "file", + "description": "FASTA file containing unbinned sequences", + "pattern": "*_unbinned_sequences.fasta", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@CarsonJM"], + "maintainers": ["@CarsonJM"] + } }, { - "name": "tfactivity", - "version": "dev" + "name": "vrhyme_linkbins", + "path": "modules/nf-core/vrhyme/linkbins/meta.yml", + "type": "module", + "meta": { + "name": "vrhyme_linkbins", + "description": "Linking bins output by vRhyme to create one sequences per bin", + "keywords": ["bin", "binning", "link", "vrhyme", "linkbins"], + "tools": [ + { + "vrhyme": { + "description": "vRhyme functions by utilizing coverage variance comparisons and supervised machine learning classification of sequence features to construct viral metagenome-assembled genomes (vMAGs).", + "homepage": "https://github.com/AnantharamanLab/vRhyme", + "documentation": "https://github.com/AnantharamanLab/vRhyme", + "tool_dev_url": "https://github.com/AnantharamanLab/vRhyme", + "doi": "10.1093/nar/gkac341", + "licence": ["GPL v3 license", "GPL v3"], + "identifier": "biotools:vrhyme" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "bins": { + "type": "directory", + "description": "Directory file containing bin FASTA files output by vRhyme (each bin having multiple sequences)" + } + } + ] + ], + "output": { + "linked_bins": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_linked_bins.fasta": { + "type": "file", + "description": "FASTA file containing all bins that have been linked by N's", + "pattern": "*_linked_bins.fasta", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@CarsonJM"], + "maintainers": ["@CarsonJM"] + } }, { - 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+ "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "vsearch": { + "type": "string", + "description": "The tool name" + } + }, + { + "vsearch --version 2>&1 | sed -n \"1s/.*v\\([0-9.]*\\).*/\\\\1/p\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ], + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "samtools": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "samtools version | sed '1!d;s/.* //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@mirpedrol"], + "maintainers": ["@mirpedrol"] + }, + "pipelines": [ + { + "name": "ampliseq", + "version": "2.17.0" + }, + { + "name": "crisprseq", + "version": "2.3.0" + }, + { + "name": "viralmetagenome", + "version": "1.1.1" + } + ] }, { - "name": "radseq", - "version": "dev" + "name": "vsearch_dereplicate", + "path": "modules/nf-core/vsearch/dereplicate/meta.yml", + "type": "module", + "meta": { + "name": "vsearch_dereplicate", + "description": "Merge strictly identical sequences contained in filename. Identical sequences are defined as having the same length and the same string of nucleotides (case insensitive, T and U are considered the same).", + "keywords": [ + "vsearch/dereplicate", + "vsearch", + "dereplicate", + "amplicon sequences", + "metagenomics", + "genomics", + "population genetics" + ], + "tools": [ + { + "vsearch": { + "description": "A versatile open source tool for metagenomics (USEARCH alternative)", + "homepage": "https://github.com/torognes/vsearch", + "documentation": "https://github.com/torognes/vsearch/releases/download/v2.31.0/vsearch_manual.pdf", + "tool_dev_url": "https://github.com/torognes/vsearch", + "doi": "10.7717/peerj.2584", + "licence": ["GPL v3-or-later OR BSD-2-clause"], + "identifier": "biotools:vsearch" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'test' ]" + } + }, + { + "fasta": { + "type": "file", + "description": "Sequences to be sorted in FASTA format", + "pattern": "*.{fasta,fa,fasta.gz,fa.gz,.fna,.fna.gz}", + "ontologies": [] + } + } + ] + ], + "output": { + "fasta": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'test']" + } + }, + { + "${prefix}.fasta": { + "type": "file", + "description": "dereplicated fasta", + "pattern": "${prefix}.fasta", + "ontologies": [] + } + } + ] + ], + "clustering": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'test']" + } + }, + { + "${prefix}.uc": { + "type": "file", + "description": "dereplicated derep.uc file", + "pattern": "${prefix}.uc", + "ontologies": [] + } + } + ] + ], + "log": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'test']" + } + }, + { + "${prefix}.log": { + "type": "file", + "description": "a log file of the run", + "pattern": "${prefix}.log", + "ontologies": [] + } + } + ] + ], + "versions_vsearch": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "vsearch": { + "type": "string", + "description": "The tool name" + } + }, + { + "vsearch --version 2>&1 | sed -n \"1s/.*v\\([0-9.]*\\).*/\\\\1/p\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "vsearch": { + "type": "string", + "description": "The tool name" + } + }, + { + "vsearch --version 2>&1 | sed -n \"1s/.*v\\([0-9.]*\\).*/\\\\1/p\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@chriswyatt1"], + "maintainers": ["@chriswyatt1"] + } }, { - "name": "rnaseq", - "version": "3.26.0" + "name": "vsearch_fastqfilter", + "path": "modules/nf-core/vsearch/fastqfilter/meta.yml", + "type": "module", + "meta": { + "name": "vsearch_fastqfilter", + "description": "Performs quality filtering and / or conversion of a FASTQ file to FASTA format.", + "keywords": [ + "vsearch/fastqfilter", + "vsearch", + "fastqfilter", + "amplicon sequences", + "metagenomics", + "genomics", + "population genetics" + ], + "tools": [ + { + "vsearch": { + "description": "VSEARCH is a versatile open-source tool for microbiome analysis, including chimera detection, clustering, dereplication and rereplication, extraction, FASTA/FASTQ/SFF file processing, masking, orienting, pair-wise alignment, restriction site cutting, searching, shuffling, sorting, subsampling, and taxonomic classification of amplicon sequences for metagenomics, genomics, and population genetics. (USEARCH alternative)", + "homepage": "https://github.com/torognes/vsearch", + "documentation": "https://github.com/torognes/vsearch/releases/download/v2.31.0/vsearch_manual.pdf", + "tool_dev_url": "https://github.com/torognes/vsearch", + "doi": "10.7717/peerj.2584", + "licence": ["GPL v3-or-later OR BSD-2-clause"], + "identifier": "biotools:vsearch" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'sample1']" + } + }, + { + "fastq": { + "type": "file", + "description": "FASTQ file to filter", + "pattern": "*.{fastq,fq,fastq.gz,fq.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ] + ], + "output": { + "fasta": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'sample1']" + } + }, + { + "*.fasta": { + "type": "file", + "description": "Filtered FASTA file", + "pattern": "*.fasta", + "ontologies": [] + } + } + ] + ], + "log": [ + { + "*.log": { + "type": "file", + "description": "Log file of the run", + "pattern": "*.log", + "ontologies": [] + } + } + ], + "versions_vsearch": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "vsearch": { + "type": "string", + "description": "The tool name" + } + }, + { + "vsearch --version 2>&1 | sed -n \"1s/.*v\\([0-9.]*\\).*/\\\\1/p\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "vsearch": { + "type": "string", + "description": "The tool name" + } + }, + { + "vsearch --version 2>&1 | sed -n \"1s/.*v\\([0-9.]*\\).*/\\\\1/p\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@FernandoDuarteF"], + "maintainers": ["@FernandoDuarteF"] + } }, { - "name": "taxprofiler", - "version": "2.0.0" - } - ] - }, - { - "name": "samtools_fixmate", - "path": "modules/nf-core/samtools/fixmate/meta.yml", - "type": "module", - "meta": { - "name": "samtools_fixmate", - "description": "Samtools fixmate is a tool that can fill in information (insert size, cigar, mapq) about paired end reads onto the corresponding other read. Also has options to remove secondary/unmapped alignments and recalculate whether reads are proper pairs.", - "keywords": [ - "fixmate", - "samtools", - "insert size", - "repair", - "bam", - "paired", - "read pairs" - ], - "tools": [ - { - "samtools": { - "description": "SAMtools is a set of utilities for interacting with and post-processing\nshort DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.\nThese files are generated as output by short read aligners like BWA.\n", - "homepage": "http://www.htslib.org/", - "documentation": "http://www.htslib.org/doc/samtools.html", - "tool_dev_url": "https://github.com/samtools/samtools", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "identifier": "biotools:samtools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM/SAM file, must be sorted by name, not coordinate", - "pattern": "*.{bam,cram,sam}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - }, - { - "edam": "http://edamontology.org/format_3462" - }, - { - "edam": "http://edamontology.org/format_2573" - } - ] - } - } - ] - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", - "pattern": "*.{bam}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - }, - { - "${prefix}.bam": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", - "pattern": "*.{bam}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - } - ] - ], - "cram": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", - "pattern": "*.{bam}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" + "name": "vsearch_sintax", + "path": "modules/nf-core/vsearch/sintax/meta.yml", + "type": "module", + "meta": { + "name": "vsearch_sintax", + "description": "Taxonomic classification using the sintax algorithm.", + "keywords": ["vsearch", "sintax", "taxonomy"], + "tools": [ + { + "vsearch": { + "description": "VSEARCH is a versatile open-source tool for microbiome analysis, including chimera detection, clustering, dereplication and rereplication, extraction, FASTA/FASTQ/SFF file processing, masking, orienting, pair-wise alignment, restriction site cutting, searching, shuffling, sorting, subsampling, and taxonomic classification of amplicon sequences for metagenomics, genomics, and population genetics. (USEARCH alternative)", + "homepage": "https://github.com/torognes/vsearch", + "documentation": "https://github.com/torognes/vsearch/releases/download/v2.31.0/vsearch_manual.pdf", + "tool_dev_url": "https://github.com/torognes/vsearch", + "doi": "10.7717/peerj.2584", + "licence": ["GPL v3-or-later OR BSD-2-clause"], + "identifier": "biotools:vsearch" + } } - ] - } - }, - { - "${prefix}.cram": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", - "pattern": "*.{cram}", - "ontologies": [ + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing query file information e.g. [ id:'test']" + } + }, + { + "queryfasta": { + "type": "file", + "description": "Query sequences in FASTA or FASTQ format", + "pattern": "*.{fasta,fa,fna,faa,fastq,fq}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ], { - "edam": "http://edamontology.org/format_3462" + "db": { + "type": "file", + "description": "Reference database file in FASTA or UDB format", + "pattern": "*", + "ontologies": [] + } } - ] + ], + "output": { + "tsv": [ + [ + { + "meta": { + "type": "file", + "description": "Results written to tab-delimited file", + "pattern": "*.{tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, + { + "*.tsv": { + "type": "file", + "description": "Results written to tab-delimited file", + "pattern": "*.{tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_vsearch": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "vsearch": { + "type": "string", + "description": "The tool name" + } + }, + { + "vsearch --version 2>&1 | sed -n \"1s/.*v\\([0-9.]*\\).*/\\\\1/p\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "vsearch": { + "type": "string", + "description": "The tool name" + } + }, + { + "vsearch --version 2>&1 | sed -n \"1s/.*v\\([0-9.]*\\).*/\\\\1/p\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@jtangrot"], + "maintainers": ["@jtangrot"] + }, + "pipelines": [ + { + "name": "ampliseq", + "version": "2.17.0" } - } ] - ], - "sam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", - "pattern": "*.{bam}", - "ontologies": [ + }, + { + "name": "vsearch_sort", + "path": "modules/nf-core/vsearch/sort/meta.yml", + "type": "module", + "meta": { + "name": "vsearch_sort", + "description": "Sort fasta entries by decreasing abundance (--sortbysize) or sequence length (--sortbylength).", + "keywords": [ + "vsearch/sort", + "vsearch", + "sort", + "amplicon sequences", + "metagenomics", + "genomics", + "population genetics" + ], + "tools": [ + { + "vsearch": { + "description": "VSEARCH is a versatile open-source tool for microbiome analysis, including chimera detection, clustering, dereplication and rereplication, extraction, FASTA/FASTQ/SFF file processing, masking, orienting, pair-wise alignment, restriction site cutting, searching, shuffling, sorting, subsampling, and taxonomic classification of amplicon sequences for metagenomics, genomics, and population genetics. (USEARCH alternative)", + "homepage": "https://github.com/torognes/vsearch", + "documentation": "https://github.com/torognes/vsearch/releases/download/v2.31.0/vsearch_manual.pdf", + "tool_dev_url": "https://github.com/torognes/vsearch", + "doi": "10.7717/peerj.2584", + "licence": ["GPL v3-or-later OR BSD-2-clause"], + "identifier": "biotools:vsearch" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'test' ]" + } + }, + { + "fasta": { + "type": "file", + "description": "Sequences to be sorted in FASTA format", + "pattern": "*.{fasta,fa,fasta.gz,fa.gz}", + "ontologies": [] + } + } + ], { - "edam": "http://edamontology.org/format_2572" + "sort_arg": { + "type": "string", + "description": "Argument to provide to sort algorithm. Sort by abundance with --sortbysize or by sequence length with --sortbylength.", + "enum": ["--sortbysize", "--sortbylength"] + } } - ] + ], + "output": { + "fasta": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fasta": { + "type": "file", + "description": "Sorted FASTA file", + "pattern": "*.{fasta}", + "ontologies": [] + } + } + ] + ], + "versions_vsearch": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "vsearch": { + "type": "string", + "description": "The tool name" + } + }, + { + "vsearch --version 2>&1 | sed -n \"1s/.*v\\([0-9.]*\\).*/\\\\1/p\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "vsearch": { + "type": "string", + "description": "The tool name" + } + }, + { + "vsearch --version 2>&1 | sed -n \"1s/.*v\\([0-9.]*\\).*/\\\\1/p\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@mirpedrol"], + "maintainers": ["@mirpedrol"] + }, + "pipelines": [ + { + "name": "crisprseq", + "version": "2.3.0" } - }, - { - "${prefix}.sam": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", - "pattern": "*.{sam}", - "ontologies": [ + ] + }, + { + "name": "vsearch_usearchglobal", + "path": "modules/nf-core/vsearch/usearchglobal/meta.yml", + "type": "module", + "meta": { + "name": "vsearch_usearchglobal", + "description": "Compare target sequences to fasta-formatted query sequences using global pairwise alignment.", + "keywords": ["vsearch", "usearch", "alignment", "fasta"], + "tools": [ + { + "vsearch": { + "description": "VSEARCH is a versatile open-source tool for microbiome analysis, including chimera detection, clustering, dereplication and rereplication, extraction, FASTA/FASTQ/SFF file processing, masking, orienting, pair-wise alignment, restriction site cutting, searching, shuffling, sorting, subsampling, and taxonomic classification of amplicon sequences for metagenomics, genomics, and population genetics. (USEARCH alternative)", + "homepage": "https://github.com/torognes/vsearch", + "documentation": "https://github.com/torognes/vsearch/releases/download/v2.31.0/vsearch_manual.pdf", + "tool_dev_url": "https://github.com/torognes/vsearch", + "doi": "10.7717/peerj.2584", + "licence": ["GPL v3-or-later OR BSD-2-clause"], + "identifier": "biotools:vsearch" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'test' ]" + } + }, + { + "queryfasta": { + "type": "file", + "description": "Query sequences in FASTA format", + "pattern": "*.{fasta,fa,fna,faa}", + "ontologies": [] + } + } + ], + { + "db": { + "type": "file", + "description": "Reference database file in FASTA or UDB format", + "pattern": "*", + "ontologies": [] + } + }, + { + "idcutoff": { + "type": "float", + "description": "Reject the sequence match if the pairwise identity is lower than the given id cutoff value (value ranging from 0.0 to 1.0 included)" + } + }, + { + "outoption": { + "type": "string", + "description": "Specify the type of output file to be generated by selecting one of the vsearch output file options", + "pattern": "alnout|biomout|blast6out|mothur_shared_out|otutabout|samout|uc|userout|lcaout" + } + }, { - "edam": "http://edamontology.org/format_2573" + "user_columns": { + "type": "string", + "description": "If using the `userout` option, specify which columns to include in output, with fields separated with `+` (e.g. query+target+id). See USEARCH manual for valid options. For other output options, use an empty string." + } } - ] + ], + "output": { + "aln": [ + [ + { + "meta": { + "type": "file", + "description": "Results in pairwise alignment format", + "pattern": "*.{aln}", + "ontologies": [] + } + }, + { + "*.aln": { + "type": "file", + "description": "Results in pairwise alignment format", + "pattern": "*.{aln}", + "ontologies": [] + } + } + ] + ], + "biom": [ + [ + { + "meta": { + "type": "file", + "description": "Results in pairwise alignment format", + "pattern": "*.{aln}", + "ontologies": [] + } + }, + { + "*.biom": { + "type": "file", + "description": "Results in an OTU table in the biom version 1.0 file format", + "pattern": "*.{biom}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3746" + } + ] + } + } + ] + ], + "lca": [ + [ + { + "meta": { + "type": "file", + "description": "Results in pairwise alignment format", + "pattern": "*.{aln}", + "ontologies": [] + } + }, + { + "*.lca": { + "type": "file", + "description": "Last common ancestor (LCA) information about the hits of each query in tab-separated format", + "pattern": "*.{lca}", + "ontologies": [] + } + } + ] + ], + "mothur": [ + [ + { + "meta": { + "type": "file", + "description": "Results in pairwise alignment format", + "pattern": "*.{aln}", + "ontologies": [] + } + }, + { + "*.mothur": { + "type": "file", + "description": "Results in an OTU table in the mothur ’shared’ tab-separated plain text file format", + "pattern": "*.{mothur}", + "ontologies": [] + } + } + ] + ], + "otu": [ + [ + { + "meta": { + "type": "file", + "description": "Results in pairwise alignment format", + "pattern": "*.{aln}", + "ontologies": [] + } + }, + { + "*.otu": { + "type": "file", + "description": "Results in an OTU table in the classic tab-separated plain text format", + "pattern": "*.{otu}", + "ontologies": [] + } + } + ] + ], + "sam": [ + [ + { + "meta": { + "type": "file", + "description": "Results in pairwise alignment format", + "pattern": "*.{aln}", + "ontologies": [] + } + }, + { + "*.sam": { + "type": "file", + "description": "Results written in sam format", + "pattern": "*.{sam}", + "ontologies": [] + } + } + ] + ], + "tsv": [ + [ + { + "meta": { + "type": "file", + "description": "Results in pairwise alignment format", + "pattern": "*.{aln}", + "ontologies": [] + } + }, + { + "*.tsv": { + "type": "file", + "description": "Results in tab-separated output, columns defined by user", + "pattern": "*.{tsv}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "txt": [ + [ + { + "meta": { + "type": "file", + "description": "Results in pairwise alignment format", + "pattern": "*.{aln}", + "ontologies": [] + } + }, + { + "*.txt": { + "type": "file", + "description": "Tab delimited results in blast-like tabular format", + "pattern": "*.{txt}", + "ontologies": [] + } + } + ] + ], + "uc": [ + [ + { + "meta": { + "type": "file", + "description": "Results in pairwise alignment format", + "pattern": "*.{aln}", + "ontologies": [] + } + }, + { + "*.uc": { + "type": "file", + "description": "Tab delimited results in a uclust-like format with 10 columns", + "pattern": "*.{uc}", + "ontologies": [] + } + } + ] + ], + "versions_vsearch": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "vsearch": { + "type": "string", + "description": "The tool name" + } + }, + { + "vsearch --version 2>&1 | sed -n \"1s/.*v\\([0-9.]*\\).*/\\\\1/p\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "vsearch": { + "type": "string", + "description": "The tool name" + } + }, + { + "vsearch --version 2>&1 | sed -n \"1s/.*v\\([0-9.]*\\).*/\\\\1/p\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@jtangrot"], + "maintainers": ["@jtangrot"] + }, + "pipelines": [ + { + "name": "ampliseq", + "version": "2.17.0" } - } - ] - ], - "versions_samtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "samtools": { - "type": "string", - "description": "The tool name" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "samtools": { - "type": "string", - "description": "The tool name" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@sppearce" - ], - "maintainers": [ - "@sppearce", - "@GallVp", - "@matthdsm" - ] - } - }, - { - "name": "samtools_flagstat", - "path": "modules/nf-core/samtools/flagstat/meta.yml", - "type": "module", - "meta": { - "name": "samtools_flagstat", - "description": "Counts the number of alignments in a BAM/CRAM/SAM file for each FLAG type", - "keywords": [ - "stats", - "mapping", - "counts", - "bam", - "sam", - "cram" - ], - "tools": [ - { - "samtools": { - "description": "SAMtools is a set of utilities for interacting with and post-processing\nshort DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.\nThese files are generated as output by short read aligners like BWA.\n", - "homepage": "http://www.htslib.org/", - "documentation": "http://www.htslib.org/doc/samtools.html", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "identifier": "biotools:samtools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } + }, + { + "name": "vt_decompose", + "path": "modules/nf-core/vt/decompose/meta.yml", + "type": "module", + "meta": { + "name": "vt_decompose", + "description": "decomposes multiallelic variants into biallelic in a VCF file.", + "keywords": ["decompose", "multiallelic", "small variants", "snps", "indels"], + "tools": [ + { + "vt": { + "description": "A tool set for short variant discovery in genetic sequence data", + "homepage": "https://genome.sph.umich.edu/wiki/Vt", + "documentation": "https://genome.sph.umich.edu/wiki/Vt", + "tool_dev_url": "https://github.com/atks/vt", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "vcf": { + "type": "file", + "description": "The VCF file to decompose", + "pattern": "*.vcf(.gz)?", + "ontologies": [] + } + }, + { + "intervals": { + "type": "file", + "description": "The intervals of the variants of decompose", + "pattern": "*.bed", + "ontologies": [] + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "The decomposed VCF file", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@nvnieuwk"], + "maintainers": ["@nvnieuwk"] }, - { - "bai": { - "type": "file", - "description": "Index for BAM/CRAM/SAM file", - "pattern": "*.{bai,crai,sai}", - "ontologies": [] - } - } - ] - ], - "output": { - "flagstat": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.flagstat": { - "type": "file", - "description": "File containing samtools flagstat output", - "pattern": "*.{flagstat}", - "ontologies": [] - } - } - ] - ], - "versions_samtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "rnadnavar", + "version": "dev" + } ] - ] }, - "authors": [ - "@drpatelh" - ], - "maintainers": [ - "@drpatelh", - "@matthdsm" - ] - }, - "pipelines": [ { - "name": "abotyper", - "version": "dev" + "name": "vt_decomposeblocksub", + "path": "modules/nf-core/vt/decomposeblocksub/meta.yml", + "type": "module", + "meta": { + "name": "vt_decomposeblocksub", + "description": "Decomposes biallelic block substitutions into its constituent SNPs.", + "keywords": [ + "decomposeblocksub", + "multiallelic", + "small variants", + "snps", + "indels", + "block substitutions" + ], + "tools": [ + { + "vt": { + "description": "A tool set for short variant discovery in genetic sequence data", + "homepage": "https://genome.sph.umich.edu/wiki/Vt", + "documentation": "https://genome.sph.umich.edu/wiki/Vt", + "tool_dev_url": "https://github.com/atks/vt", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "vcf": { + "type": "file", + "description": "The VCF file to decompose", + "pattern": "*.vcf(.gz)?", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + } + ] + } + }, + { + "index": { + "type": "file", + "description": "The VCF file to decompose", + "pattern": "*.tbi", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3616" + } + ] + } + }, + { + "intervals": { + "type": "file", + "description": "The intervals of the variants of decompose", + "pattern": "*.bed", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3003" + } + ] + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "The decomposed VCF file", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3016" + }, + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@kubranarci"], + "maintainers": ["@kubranarci"] + } }, { - "name": "atacseq", - "version": "2.1.2" + "name": "vt_normalize", + "path": "modules/nf-core/vt/normalize/meta.yml", + "type": "module", + "meta": { + "name": "vt_normalize", + "description": "normalizes variants in a VCF file", + "keywords": ["normalization", "vcf", "snps", "indels"], + "tools": [ + { + "vt": { + "description": "A tool set for short variant discovery in genetic sequence data", + "homepage": "https://genome.sph.umich.edu/wiki/Vt", + "documentation": "https://genome.sph.umich.edu/wiki/Vt", + "tool_dev_url": "https://github.com/atks/vt", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "vcf": { + "type": "file", + "description": "The VCF file to normalize", + "pattern": "*.vcf(.gz)?", + "ontologies": [] + } + }, + { + "tbi": { + "type": "file", + "description": "The tabix index of the VCF file when bgzipped", + "pattern": "*.tbi", + "ontologies": [] + } + }, + { + "intervals": { + "type": "file", + "description": "The intervals of the variants of normalize", + "pattern": "*.bed", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The reference fasta file", + "pattern": "*.{fasta,fn,fna,fa}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference index information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "fai": { + "type": "file", + "description": "The index of the reference fasta file (OPTIONAL)", + "pattern": "*.fai", + "ontologies": [] + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "The normalized VCF file", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "fai": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "${fasta}.fai": { + "type": "file", + "description": "The created index of the reference fasta file (only when the fai wasn't supplied)", + "pattern": "*.fai", + "ontologies": [] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@nvnieuwk"], + "maintainers": ["@nvnieuwk"] + }, + "pipelines": [ + { + "name": "rnadnavar", + "version": "dev" + } + ] }, { - "name": "bamtofastq", - "version": "2.2.1" + "name": "vuegen", + "path": "modules/nf-core/vuegen/meta.yml", + "type": "module", + "meta": { + "name": "vuegen", + "description": "The VueGen nf-core module is designed to automate report generation from outputs produced by other modules, subworkflows, or pipelines. The module integrates the VueGen Python library and customizes it for compatibility with the Nextflow environment. VueGen automates the creation of reports from bioinformatics outputs, supporting formats like PDF, HTML, DOCX, ODT, PPTX, Reveal.js, Jupyter notebooks, and Streamlit web applications.\n", + "keywords": ["reports", "data-visualization", "streamlit", "quarto"], + "tools": [ + { + "vuegen": { + "description": "The VueGen nf-core module is designed to automate report generation from outputs produced by other modules, subworkflows, or pipelines. The module integrates the VueGen Python library and customizes it for compatibility with the Nextflow environment. VueGen automates the creation of reports from bioinformatics outputs, supporting formats like PDF, HTML, DOCX, ODT, PPTX, Reveal.js, Jupyter notebooks, and Streamlit web applications.\n", + "homepage": "https://github.com/Multiomics-Analytics-Group/vuegen", + "documentation": "https://vuegen.readthedocs.io/", + "tool_dev_url": "https://github.com/Multiomics-Analytics-Group/vuegen", + "doi": "10.1101/2025.03.05.641152", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + { + "input_type": { + "type": "string", + "pattern": "^(config|directory)$", + "description": "Specifies whether the input is a configuration file ('config') or a directory ('directory')." + } + }, + { + "input_path": { + "type": "file", + "description": "Path to the input directory or configuration file used by VueGen.", + "ontologies": [] + } + }, + { + "report_type": { + "type": "string", + "pattern": "^(streamlit|html|pdf|docx|odt|revealjs|pptx|jupyter)$", + "description": "The type of report to generate. Options include 'streamlit', 'html', 'pdf', 'docx', 'odt', 'revealjs', 'pptx', and 'jupyter'." + } + } + ], + "output": { + "output_folder": [ + { + "*report": { + "type": "directory", + "description": "The output directory containing the generated report files.\n- If `report_type` is 'streamlit', a 'streamlit_report' directory is created, containing subfolders for each section with Python scripts corresponding to the web application's pages.\n- For other report types, a 'quarto_report' directory is generated, containing a Quarto Markdown (qmd) file that structures the entire report.\n", + "pattern": "*report" + } + } + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@sayalaruano", "@enryH", "@albsantosdel"], + "maintainers": ["@sayalaruano", "@enryH", "@albsantosdel"] + } }, { - "name": "callingcards", - "version": "1.0.0" + "name": "wfmash", + "path": "modules/nf-core/wfmash/meta.yml", + "type": "module", + "meta": { + "name": "wfmash", + "description": "a pangenome-scale aligner", + "keywords": ["long read alignment", "pangenome-scale", "all versus all", "mashmap", "wavefront"], + "tools": [ + { + "wfmash": { + "description": "a pangenome-scale aligner", + "homepage": "https://github.com/waveygang/wfmash", + "documentation": "https://github.com/waveygang/wfmash", + "tool_dev_url": "https://github.com/waveygang/wfmash", + "doi": "10.5281/zenodo.6949373", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta_gz": { + "type": "file", + "description": "BGZIPPED FASTA target file to create the mappings from.", + "pattern": "{fa.gz,fna.gz,fasta.gz}", + "ontologies": [] + } + }, + { + "paf": { + "type": "file", + "description": "Optional inpute file in PAF format to derive the precise alignments for.", + "pattern": "*.{paf}", + "ontologies": [] + } + }, + { + "gzi": { + "type": "file", + "description": "The GZI index of the input FASTA file.", + "pattern": "*.{gzi}", + "ontologies": [] + } + }, + { + "fai": { + "type": "file", + "description": "The FASTA index of the input FASTA file.", + "pattern": "*.{fai}", + "ontologies": [] + } + } + ], + { + "query_self": { + "type": "boolean", + "description": "If set to true, the input FASTA will also be used as the query FASTA." + } + }, + { + "fasta_query_list": { + "type": "file", + "description": "Optional inpute file in FASTA format specifying the query sequences as a list.", + "pattern": "*.{fa,fna,fasta}", + "ontologies": [] + } + } + ], + "output": { + "paf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.paf": { + "type": "file", + "description": "Alignments in PAF format", + "pattern": "*.{paf}", + "ontologies": [] + } + } + ] + ], + "versions_wfmash": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "wfmash": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "wfmash --version 2>&1 | cut -f 1 -d \"-\" | cut -f 2 -d \"v\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "wfmash": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "wfmash --version 2>&1 | cut -f 1 -d \"-\" | cut -f 2 -d \"v\"": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@subwaystation"], + "maintainers": ["@subwaystation"] + }, + "pipelines": [ + { + "name": "pangenome", + "version": "1.1.3" + } + ] }, { - 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"name": "circdna", - "version": "1.1.0" + "name": "wgsim", + "path": "modules/nf-core/wgsim/meta.yml", + "type": "module", + "meta": { + "name": "wgsim", + "description": "simulating sequence reads from a reference genome", + "keywords": ["simulate", "fasta", "reads"], + "tools": [ + { + "wgsim": { + "description": "simulating sequence reads from a reference genome", + "homepage": "https://github.com/lh3/wgsim", + "documentation": "https://github.com/lh3/wgsim", + "tool_dev_url": "https://github.com/lh3/wgsim", + "licence": ["MIT"], + "identifier": "biotools:wgsim" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Genome fasta file", + "pattern": "*.{fa,fasta}", + "ontologies": [] + } + } + ] + ], + "output": { + "fastq": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fastq": { + "type": "file", + "description": "Simulated FASTQ read files", + "pattern": "*.{fastq}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1930" + } + ] + } + } + ] + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@priyanka-surana"], + "maintainers": ["@priyanka-surana"] + } }, { - "name": "circrna", - "version": "dev" + "name": "whamg", + "path": "modules/nf-core/whamg/meta.yml", + "type": "module", + "meta": { + "name": "whamg", + "description": "The wham suite consists of two programs, wham and whamg. wham, the original tool, is a very sensitive method with a high false discovery rate. The second program, whamg, is more accurate and better suited for general structural variant (SV) discovery.", + "keywords": ["whamg", "wham", "vcf", "bam", "variant calling"], + "tools": [ + { + "whamg": { + "description": "Structural variant detection and association testing", + "homepage": "https://github.com/zeeev/wham", + "documentation": "https://github.com/zeeev/wham", + "tool_dev_url": "https://github.com/zeeev/wham", + "doi": "10.1371/journal.pcbi.1004572", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/SAM file", + "pattern": "*.{bam,sam}", + "ontologies": [] + } + }, + { + "bai": { + "type": "file", + "description": "BAM index file", + "pattern": "*.bai", + "ontologies": [] + } + } + ], + { + "fasta": { + "type": "file", + "description": "Reference Fasta file", + "pattern": "*.{fasta,fa}", + "ontologies": [] + } + }, + { + "fasta_fai": { + "type": "file", + "description": "Index of the reference Fasta", + "pattern": "*.fai", + "ontologies": [] + } + } + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "Compressed VCF file", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz.tbi": { + "type": "file", + "description": "Index of the VCF file", + "pattern": "*.vcf.gz.tbi", + "ontologies": [] + } + } + ] + ], + "graph": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "Graph file", + "pattern": "*.txt", + "ontologies": [] + } + } + ] + ], + "versions_whamg": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "whamg": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "whamg 2>&1 | sed -n 's/^Version: v\\([^-]*\\).*/\\1/p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "whamg": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "whamg 2>&1 | sed -n 's/^Version: v\\([^-]*\\).*/\\1/p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@nvnieuwk"], + "maintainers": ["@nvnieuwk"] + } }, { - "name": "cutandrun", - "version": "3.2.2" + "name": "whatshap_haplotag", + "path": "modules/nf-core/whatshap/haplotag/meta.yml", + "type": "module", + "meta": { + "name": "whatshap_haplotag", + "description": "Tag reads by haplotype", + "keywords": ["haplotypes", "tagging", "long-reads", "nanopore", "pacbio"], + "tools": [ + { + "whatshap": { + "description": "WhatsHap is a software for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly.", + "homepage": "https://whatshap.readthedocs.io", + "documentation": "https://whatshap.readthedocs.io", + "tool_dev_url": "https://github.com/whatshap/whatshap", + "doi": "10.1101/085050", + "licence": ["MIT"], + "identifier": "biotools:whatshap" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF file with phased variants (must be gzip-compressed and indexed)", + "pattern": "*.{vcf.gz}", + "ontologies": [] + } + }, + { + "tbi": { + "type": "file", + "description": "VCF index file", + "pattern": "*.{tbi,csi}", + "ontologies": [] + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM file with alignments to be tagged by haplotype", + "pattern": "*.{bam,cram}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + }, + { + "edam": "http://edamontology.org/format_2573" + } + ] + } + }, + { + "bai": { + "type": "file", + "description": "BAM index file", + "pattern": "*.bai", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference file. Must be accompanied by .fai index", + "pattern": "*.{fasta,fa}", + "ontologies": [] + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "fai": { + "type": "file", + "description": "Index for reference file.", + "pattern": "*.fai", + "ontologies": [] + } + } + ], + { + "include_tsv_output": { + "type": "boolean", + "description": "Whether to include TSV output file", + "default": false + } + } + ], + "output": { + "bam": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "BAM/CRAM/SAM file with tagged reads", + "pattern": "*.{bam,cram,sam}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_2572" + }, + { + "edam": "http://edamontology.org/format_2573" + }, + { + "edam": "http://edamontology.org/format_3462" + } + ] + } + } + ] + ], + "tsv": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.{tsv,tsv.gz}": { + "type": "file", + "description": "Write assignments of read names to haplotypes (tab separated) to given output file. If filename ends in .gz, then output is gzipped.", + "pattern": "*.{tsv,tsv.gz}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + } + ] + ], + "versions_whatshap": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "whatshap": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "whatshap --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "whatshap": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "whatshap --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@sofiademmou"], + "maintainers": ["@sofiademmou"] + } }, { - "name": "genomeassembler", - "version": "1.1.0" - }, - { - "name": "hgtseq", - "version": "1.1.0" - }, - { - "name": "hicar", - "version": "1.0.0" - }, - { - "name": "lncpipe", - "version": "dev" - }, - { - "name": "magmap", - "version": "1.0.0" - }, - { - "name": "metatdenovo", - "version": "1.3.0" - }, - { - "name": "methylong", - "version": "2.0.0" - }, - { - "name": "methylseq", - "version": "4.2.0" - }, - { - "name": "nanoseq", - "version": "3.1.0" + "name": "whatshap_phase", + "path": "modules/nf-core/whatshap/phase/meta.yml", + "type": "module", + "meta": { + "name": "whatshap_phase", + "description": "Phase variants in a VCF file using long-read sequencing data", + "keywords": ["phasing", "haplotypes", "vcf", "long-reads", "nanopore", "pacbio"], + "tools": [ + { + "whatshap": { + "description": "WhatsHap is a software for phasing genomic variants using DNA sequencing\nreads, also called read-based phasing or haplotype assembly.\n", + "homepage": "https://whatshap.readthedocs.io/", + "documentation": "https://whatshap.readthedocs.io/", + "tool_dev_url": "https://github.com/whatshap/whatshap", + "doi": "10.1101/085050", + "licence": ["MIT"] + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF file with unphased variants (can be gzipped)", + "pattern": "*.{vcf,vcf.gz}" + } + }, + { + "tbi": { + "type": "file", + "description": "VCF index file (optional but recommended)", + "pattern": "*.{tbi,csi}" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file with aligned reads", + "pattern": "*.bam" + } + }, + { + "bai": { + "type": "file", + "description": "BAM index file (optional but recommended)", + "pattern": "*.bai" + } + }, + { + "pedigree": { + "type": "file", + "description": "Pedigree file to improve phasing of multiple related individuals (optional)", + "pattern": "*.ped" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference genome in FASTA format", + "pattern": "*.{fa,fasta}" + } + }, + { + "fai": { + "type": "file", + "description": "Reference genome index", + "pattern": "*.fai" + } + } + ] + ], + "output": { + "vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "Bgzipped phased VCF file", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.vcf.gz.tbi": { + "type": "file", + "description": "Phased VCF index file", + "pattern": "*.vcf.gz.tbi", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3616" + } + ] + } + } + ] + ], + "versions_whatshap": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "whatshap": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "whatshap --version": { + "type": "string", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "whatshap": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "whatshap --version": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@haidyi"], + "maintainers": ["@haidyi"] + } }, { - 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"name": "rnavar", - "version": "1.2.3" + "name": "wisecondorx_gender", + "path": "modules/nf-core/wisecondorx/gender/meta.yml", + "type": "module", + "meta": { + "name": "wisecondorx_gender", + "description": "Returns the gender of a .npz resulting from convert, based on a Gaussian mixture model trained during the newref phase", + "keywords": ["copy number analysis", "gender determination", "npz"], + "tools": [ + { + "wisecondorx": { + "description": "WIthin-SamplE COpy Number aberration DetectOR, including sex chromosomes", + "homepage": "https://github.com/CenterForMedicalGeneticsGhent/WisecondorX", + "documentation": "https://github.com/CenterForMedicalGeneticsGhent/WisecondorX", + "tool_dev_url": "https://github.com/CenterForMedicalGeneticsGhent/WisecondorX", + "doi": "10.1093/nar/gky1263", + "licence": ["Attribution-NonCommercial-ShareAlike CC BY-NC-SA"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "npz": { + "type": "file", + "description": "Single sample NPZ file (from which to determine the gender)", + "pattern": "*.npz", + "ontologies": [] + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reference": { + "type": "file", + "description": "Reference NPZ file", + "pattern": "*.npz", + "ontologies": [] + } + } + ] + ], + "output": { + "gender": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + } + ], + "versions_wisecondorx": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "wisecondorx": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pip list |& sed -n 's/wisecondorx *//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "wisecondorx": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pip list |& sed -n 's/wisecondorx *//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@nvnieuwk"], + "maintainers": ["@nvnieuwk"] + } }, { - "name": "sammyseq", - "version": "dev" + "name": "wisecondorx_newref", + "path": "modules/nf-core/wisecondorx/newref/meta.yml", + "type": "module", + "meta": { + "name": "wisecondorx_newref", + "description": "Create a new reference using healthy reference samples", + "keywords": ["reference", "copy number alterations", "npz"], + "tools": [ + { + "wisecondorx": { + "description": "WIthin-SamplE COpy Number aberration DetectOR, including sex chromosomes", + "homepage": "https://github.com/CenterForMedicalGeneticsGhent/WisecondorX", + "documentation": "https://github.com/CenterForMedicalGeneticsGhent/WisecondorX", + "tool_dev_url": "https://github.com/CenterForMedicalGeneticsGhent/WisecondorX", + "doi": "10.1093/nar/gky1263", + "licence": ["Attribution-NonCommercial-ShareAlike CC BY-NC-SA"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "inputs": { + "type": "file", + "description": "Multiple NPZ files from healthy patients", + "pattern": "*.{npz}", + "ontologies": [] + } + } + ] + ], + "output": { + "npz": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.npz": { + "type": "file", + "description": "The reference NPZ file", + "pattern": "*.{npz}", + "ontologies": [] + } + } + ] + ], + "versions_wisecondorx": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "wisecondorx": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pip list |& sed -n 's/wisecondorx *//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "wisecondorx": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pip list |& sed -n 's/wisecondorx *//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@nvnieuwk"], + "maintainers": ["@nvnieuwk"] + } }, { - 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A BED file containing blacklist regions (used mainly when the reference is small)", + "pattern": "*.bed", + "ontologies": [] + } + } + ] + ], + "output": { + "aberrations_bed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*_aberrations.bed" + } + }, + { + "*_aberrations.bed": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*_aberrations.bed" + } + } + ] + ], + "bins_bed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*_aberrations.bed" + } + }, + { + "*_bins.bed": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*_bins.bed" + } + } + ] + ], + "segments_bed": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*_aberrations.bed" + } + }, + { + "*_segments.bed": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*_segments.bed" + } + } + ] + ], + "chr_statistics": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*_aberrations.bed" + } + }, + { + "*_statistics.txt": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*_chr_statistics.txt" + } + } + ] + ], + "chr_plots": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*_aberrations.bed" + } + }, + { + "[!genome_wide]*.png": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "[!genome_wide]*.png" + } + } + ] + ], + "genome_plot": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*_aberrations.bed" + } + }, + { + "genome_wide.png": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "genome_wide.png" + } + } + ] + ], + "versions_wisecondorx": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "wisecondorx": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pip list |& sed -n 's/wisecondorx *//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "wisecondorx": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "pip list |& sed -n 's/wisecondorx *//p'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@nvnieuwk"], + "maintainers": ["@nvnieuwk"] + } }, { - "name": "smrnaseq", - "version": "2.4.1" + "name": "wittyer", + "path": "modules/nf-core/wittyer/meta.yml", + "type": "module", + "meta": { + "name": "wittyer", + "description": "A large variant benchmarking tool analogous to hap.py for small variants.", + "keywords": ["structural-variants", "benchmarking", "vcf"], + "tools": [ + { + "wittyer": { + "description": "Illumina tool for large variant benchmarking", + "homepage": "https://github.com/Illumina/witty.er", + "documentation": "https://github.com/Illumina/witty.er", + "tool_dev_url": "https://github.com/Illumina/witty.er", + "licence": ["BSD-2"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "query_vcf": { + "type": "file", + "description": "A VCF with called variants to benchmark against the standard", + "pattern": "*.{vcf}", + "ontologies": [] + } + }, + { + "truth_vcf": { + "type": "file", + "description": "A standard VCF to compare against", + "pattern": "*.{vcf}", + "ontologies": [] + } + }, + { + "bed": { + "type": "file", + "description": "A BED file specifying regions to be included in the analysis (optional)", + "pattern": "*.bed", + "ontologies": [] + } + }, + { + "wittyer_config": { + "type": "file", + "description": "Config file in json format used to specify per variant type settings.\nUsed in place of include bed arguments. (optional)\n", + "pattern": "*.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "output": { + "report": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.json": { + "type": "file", + "description": "Detailed per-sample-pair, per-svtype, per-bin stats", + "pattern": "*.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "bench_vcf": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "Updated query and truth entries merged into one file", + "pattern": "*.vcf.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3989" + } + ] + } + } + ] + ], + "bench_vcf_tbi": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.vcf.gz.tbi": { + "type": "file", + "description": "Index of merged query and truth entries VCF file", + "pattern": "*.vcf.gz.tbi", + "ontologies": [] + } + } + ] + ], + "versions_wittyer": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "wittyer": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "dotnet /opt/Wittyer/Wittyer.dll --version | sed '1!d ; s/witty.er //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "wittyer": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "dotnet /opt/Wittyer/Wittyer.dll --version | sed '1!d ; s/witty.er //'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@famosab"], + "maintainers": ["@famosab"] + }, + "pipelines": [ + { + "name": "variantbenchmarking", + "version": "1.5.0" + } + ] }, { - "name": "viralmetagenome", - "version": "1.1.1" + "name": "xengsort_index", + "path": "modules/nf-core/xengsort/index/meta.yml", + "type": "module", + "meta": { + "name": "xengsort_index", + "description": "Fast lightweight accurate xenograft sorting", + "keywords": ["index", "QC", "reference", "fasta", "xenograft", "sort", "k-mer"], + "tools": [ + { + "xengsort": { + "description": "A fast xenograft read sorter based on space-efficient k-mer hashing", + "homepage": "https://gitlab.com/genomeinformatics/xengsort", + "documentation": "https://gitlab.com/genomeinformatics/xengsort", + "tool_dev_url": "https://gitlab.com/genomeinformatics/xengsort", + "doi": "10.4230/LIPIcs.WABI.2020.4", + "licence": ["MIT"], + "identifier": "" + } + } + ], + "input": [ + { + "host_fasta": { + "type": "file", + "description": "Reference genome fasta file from host, compressed or uncompressed.\n", + "ontologies": [] + } + }, + { + "graft_fasta": { + "type": "file", + "description": "Reference genome fasta file from graft, compressed or uncompressed.\n", + "ontologies": [] + } + }, + { + "index": { + "type": "string", + "description": "File name prefix to store index files.\n" + } + }, + { + "nobjects": { + "type": "string", + "description": "Number of k-mers that will be stored in the hash table. Underscore should be used, i.e for 1000000, it should be typed 1_000_000.\n" + } + }, + { + "mask": { + "type": "string", + "description": "Gapped k-mer mask (quoted string like '#__##_##__#').\n" + } + } + ], + "output": { + "hash": [ + { + "${index}.hash": { + "type": "file", + "description": "File with index hash file.", + "pattern": "*hash", + "ontologies": [] + } + } + ], + "info": [ + { + "${index}.info": { + "type": "file", + "description": "File with index info file.", + "pattern": "*info", + "ontologies": [] + } + } + ], + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + }, + "authors": ["@diegomscoelho"], + "maintainers": ["@diegomscoelho"] + } }, { - "name": "viralrecon", - "version": "3.0.0" - } - ] - }, - { - "name": "samtools_getrg", - "path": "modules/nf-core/samtools/getrg/meta.yml", - "type": "module", - "meta": { - "name": "samtools_getrg", - "description": "filter/convert SAM/BAM/CRAM file", - "deprecated": true, - "keywords": [ - "view", - "bam", - "sam", - "cram", - "readgroup" - ], - "tools": [ - { - "samtools": { - "description": "SAMtools is a set of utilities for interacting with and post-processing\nshort DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.\nThese files are generated as output by short read aligners like BWA.\n", - "homepage": "http://www.htslib.org/", - "documentation": "http://www.htslib.org/doc/samtools.html", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "identifier": "biotools:samtools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } - } - ] - ], - "output": { - "readgroup": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - } - ], - "versions_samtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "samtools": { - "type": "string", - "description": "The tool name" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "samtools": { - "type": "string", - "description": "The tool name" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@matthdsm" - ], - "maintainers": [ - "@matthdsm" - ] - } - }, - { - "name": "samtools_idxstats", - "path": "modules/nf-core/samtools/idxstats/meta.yml", - "type": "module", - "meta": { - "name": "samtools_idxstats", - "description": "Reports alignment summary statistics for a BAM/CRAM/SAM file", - "keywords": [ - "stats", - "mapping", - "counts", - "chromosome", - "bam", - "sam", - "cram" - ], - "tools": [ - { - "samtools": { - "description": "SAMtools is a set of utilities for interacting with and post-processing\nshort DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.\nThese files are generated as output by short read aligners like BWA.\n", - "homepage": "http://www.htslib.org/", - "documentation": "http://www.htslib.org/doc/samtools.html", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "identifier": "biotools:samtools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } + "name": "xeniumranger_import-segmentation", + "path": "modules/nf-core/xeniumranger/import-segmentation/meta.yml", + "type": "module", + "meta": { + "name": "xeniumranger_import_segmentation", + "description": "The xeniumranger import-segmentation module runs `xeniumranger import-segmentation`\nto recompute Xenium Onboard Analysis outputs using external segmentation results.\nIt supports two execution modes mirroring the Xenium Ranger CLI: an image-based\nmode that accepts nuclei and/or cell masks (TIFF/NPY) or GeoJSON polygons together\nwith optional coordinate transforms and unit definitions, and a transcript-based\nmode that ingests Baysor-style transcript assignment CSV files plus visualization\npolygons. Use the image-based inputs when providing label masks or polygons, or\nswitch to the transcript-based inputs when supplying transcript-level assignments\nso the appropriate command-line arguments are passed to Xenium Ranger.\n", + "keywords": [ + "spatial", + "segmentation", + "import segmentation", + "nuclear segmentation", + "cell segmentation", + "xeniumranger", + "imaging" + ], + "tools": [ + { + "xeniumranger": { + "description": "Xenium Ranger is a set of analysis pipelines that process Xenium In Situ Gene Expression data to relabel, resegment, or import new segmentation results from community-developed tools. Xenium Ranger provides flexible off-instrument reanalysis of Xenium In Situ data. Relabel transcripts, resegment cells with the latest 10x segmentation algorithms, or import your own segmentation data to assign transcripts to cells.\n", + "homepage": "https://www.10xgenomics.com/support/software/xenium-ranger/latest", + "documentation": "https://www.10xgenomics.com/support/software/xenium-ranger/latest/getting-started", + "tool_dev_url": "https://www.10xgenomics.com/support/software/xenium-ranger/latest/analysis", + "licence": ["10x Genomics EULA"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing run information\ne.g. [ id:'xenium_sample' ]\n" + } + }, + { + "xenium_bundle": { + "type": "directory", + "description": "Path to the Xenium output bundle generated by the Xenium Onboard Analysis pipeline" + } + }, + { + "transcript_assignment": { + "type": "file", + "optional": true, + "description": "Transcript assignment CSV with cell assignment, such as from Baysor v0.6, (transcript-based mode).\nMutually exclusive with image-based inputs (`nuclei`, `cells`). Required when using\ntranscript-based mode. Passed to `--transcript-assignment`.\n", + "pattern": "*.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + }, + { + "viz_polygons": { + "type": "file", + "optional": true, + "description": "Cell boundary polygons (GeoJSON) for visualization, such as from Baysor v0.6 (transcript-based mode).\nMutually exclusive with image-based inputs (`nuclei`, `cells`). Required when using\n`transcript_assignment`. Passed to `--viz-polygons`.\n", + "pattern": "*.{json,geojson}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + }, + { + "nuclei": { + "type": "file", + "optional": true, + "description": "Nucleus segmentation input as label mask (TIFF/NPY), polygons (GeoJSON), or Xenium Onboard\nAnalysis cells.zarr.zip (image-based mode).\nMutually exclusive with transcript-based inputs\n(`transcript_assignment`, `viz_polygons`). Passed to `--nuclei`.\n", + "pattern": "*.{tif,tiff,npy,json,geojson,zarr.zip}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_4003" + }, + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + }, + { + "cells": { + "type": "file", + "optional": true, + "description": "Cell segmentation input as label mask (TIFF/NPY), polygons (GeoJSON), or Xenium Onboard\nAnalysis cells.zarr.zip (image-based mode).\nMutually exclusive with transcript-based inputs\n(`transcript_assignment`, `viz_polygons`). Passed to `--cells`.\n", + "pattern": "*.{tif,tiff,npy,json,geojson,zarr.zip}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_4003" + }, + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + }, + { + "coordinate_transform": { + "type": "file", + "optional": true, + "description": "Image alignment file containing similarity transform matrix (e.g., `_imagealignment.csv` from\nXenium Explorer). Only used with image-based mode inputs (`nuclei`, `cells`). `units` will be automatically set to \"microns\". Passed to `--coordinate-transform`.\n", + "pattern": "*.csv", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3752" + } + ] + } + }, + { + "units": { + "type": "string", + "optional": true, + "description": "Units for segmentation results. Must be one of two options: \"microns\" (physical space) or\n\"pixels\" (pixel space). Can be used with both image-based and transcript-based modes.\nDefault: \"pixels\". Must be \"microns\" if `coordinate_transform` is used. For Baysor v0.6\ninputs, must be \"microns\". Passed to `--units`.\n", + "enum": ["microns", "pixels"] + } + } + ] + ], + "output": { + "outs": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'test' ]" + } + }, + { + "${prefix}": { + "type": "directory", + "description": "Directory containing the output xenium bundle of Xenium Ranger", + "pattern": "${prefix}" + } + } + ] + ], + "versions_xeniumranger": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "xeniumranger": { + "type": "string", + "description": "The tool name" + } + }, + { + "xeniumranger -V | sed -e 's/.*xenium-//'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "xeniumranger": { + "type": "string", + "description": "The tool name" + } + }, + { + "xeniumranger -V | sed -e 's/.*xenium-//'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@khersameesh24", "@dongzehe"], + "maintainers": ["@khersameesh24", "@dongzehe"] }, - { - "bai": { - "type": "file", - "description": "Index for BAM/CRAM/SAM file", - "pattern": "*.{bai,crai,sai}", - "ontologies": [] - } - } - ] - ], - "output": { - "idxstats": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.idxstats": { - "type": "file", - "description": "File containing samtools idxstats output", - "pattern": "*.{idxstats}", - "ontologies": [] - } - } - ] - ], - "versions_samtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "spatialxe", + "version": "dev" + } ] - ] - }, - "authors": [ - "@drpatelh" - ], - "maintainers": [ - "@drpatelh", - "@matthdsm" - ] - }, - "pipelines": [ - { - "name": "atacseq", - "version": "2.1.2" }, { - "name": "bamtofastq", - "version": "2.2.1" + "name": "xeniumranger_relabel", + "path": "modules/nf-core/xeniumranger/relabel/meta.yml", + "type": "module", + "meta": { + "name": "xeniumranger_relabel", + "description": "The xeniumranger relabel module allows you to change the gene labels applied to decoded transcripts.", + "keywords": ["spatial", "relabel", "gene labels", "transcripts", "xeniumranger"], + "tools": [ + { + "xeniumranger": { + "description": "Xenium Ranger is a set of analysis pipelines that process Xenium In Situ Gene Expression data to relabel, resegment, or import new segmentation results from community-developed tools. Xenium Ranger provides flexible off-instrument reanalysis of Xenium In Situ data. Relabel transcripts, resegment cells with the latest 10x segmentation algorithms, or import your own segmentation data to assign transcripts to cells.\n", + "homepage": "https://www.10xgenomics.com/support/software/xenium-ranger/latest", + "documentation": "https://www.10xgenomics.com/support/software/xenium-ranger/latest/getting-started", + "tool_dev_url": "https://www.10xgenomics.com/support/software/xenium-ranger/latest/analysis", + "licence": ["10x Genomics EULA"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing run information\ne.g. [ id:'xenium_bundle_path' ]\n" + } + }, + { + "xenium_bundle": { + "type": "directory", + "description": "Path to the xenium output bundle generated by the Xenium Onboard Analysis pipeline" + } + }, + { + "panel": { + "type": "file", + "description": "Path to the gene panel file", + "pattern": "*.json", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3464" + } + ] + } + } + ] + ], + "output": { + "outs": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'test' ]" + } + }, + { + "${prefix}": { + "type": "directory", + "description": "Directory containing the output xenium bundle of Xenium Ranger", + "pattern": "${prefix}" + } + } + ] + ], + "versions_xeniumranger": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "xeniumranger": { + "type": "string", + "description": "The tool name" + } + }, + { + "xeniumranger -V | sed -e 's/.*xenium-//'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "xeniumranger": { + "type": "string", + "description": "The tool name" + } + }, + { + "xeniumranger -V | sed -e 's/.*xenium-//'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@khersameesh24", "@dongzehe"], + "maintainers": ["@khersameesh24", "@dongzehe"] + }, + "pipelines": [ + { + "name": "spatialxe", + "version": "dev" + } + ] }, { - "name": "callingcards", - "version": "1.0.0" + "name": "xeniumranger_rename", + "path": "modules/nf-core/xeniumranger/rename/meta.yml", + "type": "module", + "meta": { + "name": "xeniumranger_rename", + "description": "The xeniumranger rename module allows you to change the sample region_name and cassette_name throughout all the Xenium Onboard Analysis output files that contain this information.", + "keywords": ["spatial", "rename", "gene labels", "transcripts", "xeniumranger"], + "tools": [ + { + "xeniumranger": { + "description": "Xenium Ranger is a set of analysis pipelines that process Xenium In Situ Gene Expression data to relabel, resegment, or import new segmentation results from community-developed tools. Xenium Ranger provides flexible off-instrument reanalysis of Xenium In Situ data. Relabel transcripts, resegment cells with the latest 10x segmentation algorithms, or import your own segmentation data to assign transcripts to cells.\n", + "homepage": "https://www.10xgenomics.com/support/software/xenium-ranger/latest", + "documentation": "https://www.10xgenomics.com/support/software/xenium-ranger/latest/getting-started", + "tool_dev_url": "https://www.10xgenomics.com/support/software/xenium-ranger/latest/analysis", + "licence": ["10x Genomics EULA"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'test' ]" + } + }, + { + "xenium_bundle": { + "type": "directory", + "description": "Path to the xenium output bundle generated by the Xenium Onboard Analysis pipeline" + } + }, + { + "region_name": { + "type": "string", + "description": "New region name" + } + }, + { + "cassette_name": { + "type": "string", + "description": "New cassette name" + } + } + ] + ], + "output": { + "outs": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'test' ]" + } + }, + { + "${prefix}": { + "type": "directory", + "description": "Directory containing the output xenium bundle of Xenium Ranger", + "pattern": "${prefix}" + } + } + ] + ], + "versions_xeniumranger": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "xeniumranger": { + "type": "string", + "description": "The tool name" + } + }, + { + "xeniumranger -V | sed -e 's/.*xenium-//'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "xeniumranger": { + "type": "string", + "description": "The tool name" + } + }, + { + "xeniumranger -V | sed -e 's/.*xenium-//'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@khersameesh24", "@dongzehe"], + "maintainers": ["@khersameesh24", "@dongzehe"] + } }, { - "name": "chipseq", - "version": "2.1.0" + "name": "xeniumranger_resegment", + "path": "modules/nf-core/xeniumranger/resegment/meta.yml", + "type": "module", + "meta": { + "name": "xeniumranger_resegment", + "description": "The xeniumranger resegment module allows you to generate a new segmentation of the morphology image space by rerunning the Xenium Onboard Analysis (XOA) segmentation algorithms with modified parameters.", + "keywords": ["spatial", "resegment", "morphology", "segmentation", "xeniumranger"], + "tools": [ + { + "xeniumranger": { + "description": "Xenium Ranger is a set of analysis pipelines that process Xenium In Situ Gene Expression data to relabel, resegment, or import new segmentation results from community-developed tools. Xenium Ranger provides flexible off-instrument reanalysis of Xenium In Situ data. Relabel transcripts, resegment cells with the latest 10x segmentation algorithms, or import your own segmentation data to assign transcripts to cells.\n", + "homepage": "https://www.10xgenomics.com/support/software/xenium-ranger/latest", + "documentation": "https://www.10xgenomics.com/support/software/xenium-ranger/latest/getting-started", + "tool_dev_url": "https://www.10xgenomics.com/support/software/xenium-ranger/latest/analysis", + "licence": ["10x Genomics EULA"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing run information\ne.g. [ id:'xenium_experiment' ]\n" + } + }, + { + "xenium_bundle": { + "type": "directory", + "description": "Path to the xenium output bundle generated by the Xenium Onboard Analysis pipeline" + } + } + ] + ], + "output": { + "outs": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "${prefix}": { + "type": "directory", + "description": "Directory containing the output xenium bundle of Xenium Ranger", + "pattern": "${prefix}" + } + } + ] + ], + "versions_xeniumranger": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "xeniumranger": { + "type": "string", + "description": "The tool name" + } + }, + { + "xeniumranger -V | sed -e 's/.*xenium-//'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "xeniumranger": { + "type": "string", + "description": "The tool name" + } + }, + { + "xeniumranger -V | sed -e 's/.*xenium-//'": { + "type": "string", + "description": "The command used to generate the version of the tool" + } + } + ] + ] + }, + "authors": ["@khersameesh24", "@dongzehe"], 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"xz --version | sed '1!d;s/\\([^0-9.]*\\)//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@leoisl"], + "maintainers": ["@leoisl"] + } }, { - "name": "circrna", - "version": "dev" + "name": "xz_decompress", + "path": "modules/nf-core/xz/decompress/meta.yml", + "type": "module", + "meta": { + "name": "xz_decompress", + "description": "Decompresses files with xz.", + "keywords": ["xz", "decompression", "compression"], + "tools": [ + { + "xz": { + "description": "xz is a general-purpose data compression tool with command line syntax similar to gzip and bzip2.", + "homepage": "https://tukaani.org/xz/", + "documentation": "https://tukaani.org/xz/man/xz.1.html", + "tool_dev_url": "https://github.com/tukaani-project/xz", + "licence": ["GNU LGPLv2.1", "GNU GPLv2", "GNU GPLv3"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample 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name of the process" + } + }, + { + "xz": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "xz --version | sed '1!d;s/\\([^0-9.]*\\)//g'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@leoisl"], + "maintainers": ["@leoisl"] + }, + "pipelines": [ + { + "name": "coproid", + "version": "2.0.1" + }, + { + "name": "viralmetagenome", + "version": "1.1.1" + } + ] }, { - "name": "cutandrun", - "version": "3.2.2" + "name": "yahs", + "path": "modules/nf-core/yahs/meta.yml", + "type": "module", + "meta": { + "name": "yahs", + "description": "Performs assembly scaffolding using YaHS", + "keywords": ["scaffolding", "assembly", "yahs", "hic"], + "tools": [ + { + "yahs": { + "description": "YaHS, yet another Hi-C scaffolding tool.", + "homepage": "https://github.com/c-zhou/yahs", + "documentation": "https://github.com/c-zhou/yahs", + "tool_dev_url": "https://github.com/c-zhou/yahs", + "doi": "10.1093/bioinformatics/btac808", + "licence": ["MIT"], + "identifier": "biotools:yahs" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA reference file", + "pattern": "*.{fasta,fa}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + }, + { + "fai": { + "type": "file", + "description": "index of the reference file", + "pattern": "*.{fai}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, + { + "hic_map": { + "type": "file", + "description": "BED file containing coordinates of read alignments", + "pattern": "*.{bed,bam,bin}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3003" + }, + { + "edam": "http://edamontology.org/format_2572" + } + ] + } + }, + { + "agp": { + "type": "file", + "description": "Optional AGP file describing a set of 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+ } + ] + ], + "initial_break_agp": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "${prefix}_{inital,no}_break*.agp": { + "type": "file", + "description": "AGP file describing initial contig breaks", + "pattern": "${prefix}_{inital,no}_break*.agp", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3693" + } + ] + } + } + ] + ], + "round_agp": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "${prefix}_r*_*.agp": { + "type": "file", + "description": "AGP file describing intermediate rounds of scaffolding", + "pattern": "${prefix}_{initial,no}_break*.agp", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3693" + } + ] + } + } + ] + ], + "binary": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + 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"string", + "description": "The name of the process" + } + }, + { + "yahs": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "yahs --version 2>&1": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@ksenia-krasheninnikova"], + "maintainers": ["@ksenia-krasheninnikova", "@yy5"] + } }, { - "name": "drop", - "version": "1.0.0" + "name": "yak_count", + "path": "modules/nf-core/yak/count/meta.yml", + "type": "module", + "meta": { + "name": "yak_count", + "description": "a tool to build k-mer hash table for fasta and fastq files", + "keywords": ["kmer", "fastq", "sequence", "count", "assembly"], + "tools": [ + { + "yak": { + "description": "Yet another k-mer analyzer", + "homepage": "https://github.com/lh3/yak", + "documentation": "https://github.com/lh3/yak/blob/master/README.md", + "tool_dev_url": "https://github.com/lh3/yak", + "licence": ["MIT"], + "identifier": "" + } + } + ], + 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"ontologies": [ + { + "edam": "http://edamontology.org/format_3750" + } + ] + } + } + ] + ], + "versions_yte": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "yte": { + "type": "string", + "description": "The tool name" + } + }, + { + "1.9.4": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The process the versions were collected from" + } + }, + { + "yte": { + "type": "string", + "description": "The tool name" + } + }, + { + "1.9.4": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@famosab"], + "maintainers": ["@famosab"] + }, + "pipelines": [ + { + "name": "sarek", + "version": "3.8.1" + } + ] }, { - "name": "lncpipe", - "version": "dev" - }, + "name": "zip", + "path": "modules/nf-core/zip/meta.yml", + "type": "module", + "meta": { + "name": "zip", + "description": "Compress file lists to produce ZIP archive files", + "keywords": ["unzip", "decompression", "zip", "archiving"], + "tools": [ + { + "unzip": { + "description": "p7zip is a quick port of 7z.exe and 7za.exe (command line version of 7zip, see www.7-zip.org) for Unix.", + "homepage": "https://sourceforge.net/projects/p7zip/", + "documentation": "https://sourceforge.net/projects/p7zip/", + "tool_dev_url": "https://sourceforge.net/projects/p7zip\"", + "licence": ["LGPL-2.1-or-later"], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "files": { + "type": "file", + "description": "File or list of files to be zipped", + "ontologies": [] + } + } + ] + ], + "output": { + "zipped_archive": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.zip": { + "type": "file", + "description": "ZIP file", + "pattern": "*.zip", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3987" + } + ] + } + } + ] + ], + "versions_zip": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "zip": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "7za i 2>&1 | grep 'p7zip Version' | sed 's/.*p7zip Version //; s/(.*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "topics": { + "versions": [ + [ + { + "${task.process}": { + "type": "string", + "description": "The name of the process" + } + }, + { + "zip": { + "type": "string", + "description": "The name of the tool" + } + }, + { + "7za i 2>&1 | grep 'p7zip Version' | sed 's/.*p7zip Version //; s/(.*//'": { + "type": "eval", + "description": "The expression to obtain the version of the tool" + } + } + ] + ] + }, + "authors": ["@jfy133", "@pinin4fjords"], + "maintainers": ["@jfy133", "@pinin4fjords", "@JoseEspinosa"] + }, + "pipelines": [ + { + "name": "differentialabundance", + "version": "1.5.0" + }, + { + "name": "tfactivity", + "version": "dev" + } + ] + } + ], + "subworkflows": [ { - "name": "magmap", - "version": "1.0.0" + "name": "abundance_differential_filter", + "path": "subworkflows/nf-core/abundance_differential_filter/meta.yml", + "type": "subworkflow", + "meta": { + "name": "abundance_differential_filter", + "description": "A subworkflow for filtering differential abundance results", + "keywords": ["differential", "abundance", "expression", "count matrix", "fold-change"], + "components": [ + "limma/differential", + "deseq2/differential", + "propr/propd", + "custom/filterdifferentialtable", + "variancepartition/dream" + ], + "input": [ + { + "ch_input": { + "description": "Channel with input data for differential analysis", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata map" + } + }, + { + "counts": { + "type": "file", + "description": "Count matrix file" + } + }, + { + "analysis_method": { + "type": "value", + "description": "Analysis method (deseq2, limma, or propd)" + } + }, + { + "fc_threshold": { + "type": "value", + "description": "Fold change threshold for filtering" + } + }, + { + "stat_threshold": { + "type": "value", + "description": "Threshold for filtering the significance statistics\n(eg. adjusted p-values in the case of deseq2 or limma,\nweighted connectivity in the case of propd)\n" + } + } + ] + } + }, + { + "ch_samplesheet": { + "description": "Channel with sample information", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata map" + } + }, + { + "samplesheet": { + "type": "file", + "description": "Sample information file" + } + } + ] + } + }, + { + "ch_transcript_lengths": { + "description": "Channel with transcript length information", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata map" + } + }, + { + "transcript_lengths": { + "type": "file", + "description": "Transcript length information file" + } + } + ] + } + }, + { + "ch_control_features": { + "description": "Channel with control features information", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata map" + } + }, + { + "control_features": { + "type": "file", + "description": "Control features information file" + } + } + ] + } + }, + { + "ch_contrasts": { + "description": "Channel with contrast information", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata map" + } + }, + { + "meta_contrast": { + "type": "map", + "description": "Map with all the contrast info, such as contrast\nid, variable, reference, target, etc.\n" + } + }, + { + "variable": { + "type": "list", + "description": "List of contrast variable" + } + }, + { + "reference": { + "type": "list", + "description": "List of reference level" + } + }, + { + "target": { + "type": "list", + "description": "List of target level" + } + }, + { + "formula": { + "type": "list", + "description": "List of contrast formula" + } + }, + { + "comparison": { + "type list": null, + "description": "List of contrast comparison" + } + } + ] + } + } + ], + "output": [ + { + "versions": { + "description": "Channel containing software versions file", + "structure": [ + { + "versions.yml": { + "type": "file", + "description": "File containing versions of the software used" + } + } + ] + } + }, + { + "results_genewise": { + "description": "Channel containing unfiltered differential analysis results", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata map" + } + }, + { + "results": { + "type": "file", + "description": "Unfiltered differential analysis results file", + "pattern": "*.{csv,tsv}" + } + } + ] + } + }, + { + "results_genewise_filtered": { + "description": "Channel containing filtered differential analysis results", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata map" + } + }, + { + "filtered_results": { + "type": "file", + "description": "Filtered differential analysis results file", + "pattern": "*.{csv,tsv}" + } + } + ] + } + }, + { + "adjacency": { + "description": "Channel containing the adjacency matrix suited for downstream graph-based functional analysis", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata map" + } + }, + { + "adjacency_matrix": { + "type": "file", + "description": "Adjacency matrix file", + "pattern": "*.{csv,tsv}" + } + } + ] + } + }, + { + "normalised_matrix": { + "description": "Channel containing normalised count matrix", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata map" + } + }, + { + "matrix": { + "type": "file", + "description": "Normalised count matrix file", + "pattern": "*.{csv,tsv}" + } + } + ] + } + }, + { + "variance_stabilised_matrix": { + "description": "Channel containing variance stabilised count matrix (DESeq2 only)", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata map" + } + }, + { + "matrices": { + "type": "list", + "description": "A list of variance stabilised count matrix files", + "pattern": "*.{csv,tsv}" + } + } + ] + } + }, + { + "model": { + "description": "Channel containing statistical model object from differential analysis", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata map" + } + }, + { + "model": { + "type": "file", + "description": "Statistical model object file", + "pattern": "*.rds" + } + } + ] + } + }, + { + "plots": { + "description": "Channel containing plots from differential analysis", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata map" + } + }, + { + "plots": { + "type": "file", + "description": "Plot file", + "pattern": "*.{png,pdf}" + } + } + ] + } + }, + { + "other": { + "description": "Channel containing other outputs from differential analysis", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata map" + } + }, + { + "other_files": { + "type": "file", + "description": "Other output file from differential analysis", + "pattern": "*.{rds,tsv,log}" + } + } + ] + } + } + ], + "authors": ["@pinin4fjords", "@bjlang", "@caraiz2001", "@suzannejin", "@delfiterradas", "@sofiromano"], + "maintainers": ["@pinin4fjords", "@suzannejin"] + } }, { - "name": "metatdenovo", - "version": "1.3.0" + "name": "archive_extract", + "path": "subworkflows/nf-core/archive_extract/meta.yml", + "type": "subworkflow", + "meta": { + "name": "archive_extract", + "description": "Extract archive(s) from any format\nCurrently supported format are .gz, .tar.gz, .zip\n", + "keywords": ["archive", "gzip", "tar", "zip"], + "components": ["gunzip", "untar", "unzip"], + "input": [ + { + "archive": { + "description": "Channel with archive to extract", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata map" + } + }, + { + "archive": { + "type": "file", + "description": "Structure: [path(archive)]\nFile containing the archive to extract\n", + "pattern": "*{.tar.gz, .gz, .zip}" + } + } + ] + } + } + ], + "output": [ + { + "extracted": { + "description": "Channel with extracted archive", + "structure": [ + { + "meta": null, + "type": "map", + "description": "Metadata map" + }, + { + "*": null, + "type": "file", + "description": "Structure: [path]\nFolder or file(s) extracted\n" + } + ] + } + }, + { + "not_extracted": { + "description": "Channel with any not extracted (ie not recognized) archive", + "structure": [ + { + "meta": null, + "type": "map", + "description": "Metadata map" + }, + { + "*": null, + "type": "file", + "description": "Structure: [path]\nFile(s) not extracted\n" + } + ] + } + }, + { + "versions": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ], + "authors": ["@maxulysse"], + "maintainers": ["@maxulysse"] + } }, { - "name": "methylseq", - "version": "4.2.0" - }, - { - "name": "nanoseq", - "version": "3.1.0" - }, - { - "name": "nascent", - "version": "2.3.0" - }, - { - "name": "pacsomatic", - "version": "dev" - }, - { - "name": "phageannotator", - "version": "dev" - }, - { - "name": "radseq", - "version": "dev" - }, - { - "name": "riboseq", - "version": "1.2.0" - }, - { - "name": "rnadnavar", - "version": "dev" - }, - { - "name": "rnafusion", - "version": "4.1.2" - }, - { - "name": "rnaseq", - "version": "3.26.0" - }, - { - "name": "rnasplice", - "version": "1.0.4" - }, - { - "name": "rnavar", - "version": "1.2.3" - }, - { - "name": "sammyseq", - "version": "dev" - }, - { - "name": "scnanoseq", - "version": "1.2.2" - }, - { - "name": "smrnaseq", - "version": "2.4.1" - }, - { - "name": "ssds", - "version": "dev" - }, - { - "name": "viralmetagenome", - "version": "1.1.1" + "name": "bam_cnv_wisecondorx", + "path": "subworkflows/nf-core/bam_cnv_wisecondorx/meta.yml", + "type": "subworkflow", + "meta": { + "name": "bam_cnv_wisecondorx", + "description": "A subworkflow for calling CNVs using WisecondorX", + "keywords": ["cnv", "bam", "bed", "cram", "plots", "genomics"], + "components": ["wisecondorx/convert", "wisecondorx/predict"], + "input": [ + { + "ch_bam": { + "description": "An input channel containing BAM/CRAM files and their indices\nStructure: [ val(meta), path(bam), path(bai) ]\n" + } + }, + { + "ch_fasta": { + "description": "A channel containing the reference FASTA file\nStructure: [ val(meta2), path(fasta) ]\n" + } + }, + { + "ch_fai": { + "description": "A channel containing the index of the reference FASTA file\nStructure: [ val(meta3), path(fai) ]\n" + } + }, + { + "ch_ref": { + "description": "A channel containing WisecondorX reference created with `WisecondorX newref`\nStructure: [ val(meta4), path(reference) ]\n" + } + }, + { + "ch_blacklist": { + "description": "An optional channel containing a BED file with regions to mask from the analysis\nStructure: [ val(meta5), path(blacklist) ]\n" + } + } + ], + "output": [ + { + "aberrations_bed": { + "description": "A channel containing the BED files with CNV aberrations\nStructure: [ val(meta), path(bed) ]\n" + } + }, + { + "bins_bed": { + "description": "A channel containing the BED files with the used bins\nStructure: [ val(meta), path(bed) ]\n" + } + }, + { + "segments_bed": { + "description": "A channel containing the segment BED files\nStructure: [ val(meta), path(bed) ]\n" + } + }, + { + "chr_statistics": { + "description": "A channel containing TXT files with chromosome statistics\nStructure: [ val(meta), path(txt) ]\n" + } + }, + { + "chr_plots": { + "description": "A channel containing lists of chromosome plots\nStructure: [ val(meta), [ path(png), path(png), ... ] ]\n" + } + }, + { + "genome_plot": { + "description": "A channel containing the plots of the whole genomes\nStructure: [ val(meta), path(png) ]\n" + } + }, + { + "versions": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ], + "authors": ["@nvnieuwk"], + "maintainers": ["@nvnieuwk"] + } }, { - "name": "viralrecon", - "version": "3.0.0" - } - ] - }, - { - "name": "samtools_import", - "path": "modules/nf-core/samtools/import/meta.yml", - "type": "module", - "meta": { - "name": "samtools_import", - "description": "converts FASTQ files to unmapped SAM/BAM/CRAM", - "keywords": [ - "import", - "fastq", - "bam", - "sam", - "cram" - ], - "tools": [ - { - "samtools": { - "description": "SAMtools is a set of utilities for interacting with and post-processing\nshort DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.\nThese files are generated as output by short read aligners like BWA.\n", - "homepage": "http://www.htslib.org/", - "documentation": "http://www.htslib.org/doc/samtools.html", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "identifier": "biotools:samtools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "reads": { - "type": "file", - "description": "fastq data to be converted to SAM/BAM/CRAM", - "pattern": "*.{fastq,fq,fastq.gz,fq.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "output": { - "sam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*.sam": { - "type": "file", - "description": "SAM file", - "pattern": "*.sam", - "ontologies": [] - } - } - ] - ], - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "Unaligned BAM file", - "pattern": "*.bam", - "ontologies": [] - } - } - ] - ], - "cram": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*.cram": { - "type": "file", - "description": "Unaligned CRAM file", - "pattern": "*.cram", - "ontologies": [] - } - } - ] - ], - "versions_samtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "samtools": { - "type": "string", - "description": "The tool name" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "samtools": { - "type": "string", - "description": "The tool name" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@matthdsm" - ], - "maintainers": [ - "@matthdsm" - ] - }, - "pipelines": [ - { - "name": "methylong", - "version": "2.0.0" - } - ] - }, - { - "name": "samtools_index", - "path": "modules/nf-core/samtools/index/meta.yml", - "type": "module", - "meta": { - "name": "samtools_index", - "description": "Index SAM/BAM/CRAM file", - "keywords": [ - "index", - "bam", - "sam", - "cram" - ], - "tools": [ - { - "samtools": { - "description": "SAMtools is a set of utilities for interacting with and post-processing\nshort DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.\nThese files are generated as output by short read aligners like BWA.\n", - "homepage": "http://www.htslib.org/", - "documentation": "http://www.htslib.org/doc/samtools.html", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "identifier": "biotools:samtools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + "name": "bam_create_som_pon_gatk", + "path": "subworkflows/nf-core/bam_create_som_pon_gatk/meta.yml", + "type": "subworkflow", + "meta": { + "name": "bam_create_som_pon_gatk", + "description": "Perform variant calling on a set of normal samples using mutect2 panel of normals mode. Group them into a genomicsdbworkspace using genomicsdbimport, then use this to create a panel of normals using createsomaticpanelofnormals.", + "keywords": [ + "gatk4", + "mutect2", + "genomicsdbimport", + "createsomaticpanelofnormals", + "variant_calling", + "genomicsdb_workspace", + "panel_of_normals" + ], + "components": [ + "gatk4/mutect2", + "gatk4/genomicsdbimport", + "gatk4/createsomaticpanelofnormals", + "gatk4/mergevcfs", + "gatk4/mergemutectstats" + ], + "input": [ + { + "ch_input": { + "type": "list", + "description": "An input channel containing the following files:\n- input: One or more BAM/CRAM files\n- input_index: The index/indices from the BAM/CRAM file(s)\nStructure: [ meta, path(input), path(input_index) ]\n" + } + }, + { + "ch_fasta": { + "type": "list", + "description": "Reference fasta file\nStructure: [ meta, path(fasta) ]\n" + } + }, + { + "ch_fai": { + "type": "list", + "description": "Reference fasta file index\nStructure: [ meta, path(fai) ]\n" + } + }, + { + "ch_dict": { + "type": "list", + "description": "GATK sequence dictionary\nStructure: [ meta, path(dict) ]\n" + } + }, + { + "ch_intervals_gendb": { + "type": "file", + "description": "Interval file used for GenomicsDBImport", + "pattern": "*.{bed,interval_list}" + } + }, + { + "ch_intervals_num": { + "type": "list", + "description": "Intervals channel for scatter and gather strategy. Each item is a tuple of\nan interval file and the total number of intervals. Use [ [], 0 ] if no intervals.\nStructure: [ path(intervals), val(num_intervals) ]\n" + } + } + ], + "output": [ + { + "mutect2_vcf": { + "type": "list", + "description": "List of compressed vcf files to be used to make the gendb workspace", + "pattern": "[ *.vcf.gz ]" + } + }, + { + "mutect2_index": { + "type": "list", + "description": "List of indexes of mutect2_vcf files", + "pattern": "[ *vcf.gz.tbi ]" + } + }, + { + "mutect2_stats": { + "type": "list", + "description": "List of stats files that pair with mutect2_vcf files", + "pattern": "[ *vcf.gz.stats ]" + } + }, + { + "genomicsdb": { + "type": "directory", + "description": "Directory containing the files that compose the genomicsdb workspace.", + "pattern": "path/name_of_workspace" + } + }, + { + "pon_vcf": { + "type": "file", + "description": "Panel of normal as compressed vcf file", + "pattern": "*.vcf.gz" + } + }, + { + "pon_index": { + "type": "file", + "description": "Index of pon_vcf file", + "pattern": "*vcf.gz.tbi" + } + } + ], + "authors": ["@GCJMackenzie"], + "maintainers": ["@GCJMackenzie", "@maxulysse"] }, - { - "input": { - "type": "file", - "description": "input file", - "ontologies": [] - } - } - ] - ], - "output": { - "index": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.{bai,csi,crai}": { - "type": "file", - "description": "BAM/CRAM/SAM index file", - "pattern": "*.{bai,csi,crai}", - "ontologies": [] - } - } - ] - ], - "versions_samtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "createpanelrefs", + "version": "dev" + } ] - ] }, - "authors": [ - "@drpatelh", - "@ewels", - "@maxulysse" - ], - "maintainers": [ - "@ewels", - "@maxulysse", - "@matthdsm" - ] - }, - "pipelines": [ { - "name": "alleleexpression", - "version": "dev" - }, - { - "name": "atacseq", - "version": "2.1.2" - }, - { - "name": "bacass", - "version": "2.6.0" - }, - { - "name": "bamtofastq", - "version": "2.2.1" - }, - { - "name": "callingcards", - "version": "1.0.0" - }, - { - "name": "chipseq", - "version": "2.1.0" - }, - { - "name": "circdna", - "version": "1.1.0" - }, - { - "name": "circrna", - "version": "dev" - }, - { - "name": "coproid", - "version": "2.0.1" - }, - { - "name": "createpanelrefs", - "version": "dev" - }, - { - "name": "crisprseq", - "version": "2.3.0" - }, - { - "name": "cutandrun", - "version": "3.2.2" - }, - { - "name": "dartseq", - "version": "dev" - }, - { - "name": "drop", - "version": "1.0.0" - }, - { - "name": "evexplorer", - "version": "dev" - }, - { - "name": "genomeassembler", - "version": "1.1.0" - }, - { - "name": "genomicrelatedness", - "version": "dev" - }, - { - "name": "hgtseq", - "version": "1.1.0" - }, - { - "name": "hicar", - "version": "1.0.0" - }, - { - "name": "lncpipe", - "version": "dev" - }, - { - "name": "mag", - "version": "5.4.2" - }, - { - "name": "magmap", - "version": "1.0.0" - }, - { - "name": "metatdenovo", - "version": "1.3.0" - }, - { - "name": "methylong", - "version": "2.0.0" - }, - { - "name": "methylseq", - "version": "4.2.0" - }, - { - "name": "nanoseq", - "version": "3.1.0" - }, - { - "name": "nascent", - "version": "2.3.0" - }, - { - "name": "pacsomatic", - "version": "dev" - }, - { - "name": "pacvar", - "version": "1.0.1" - }, - { - "name": "panoramaseq", - "version": "dev" - }, - { - "name": "pathogensurveillance", - "version": "1.1.0" - }, - { - "name": "phageannotator", - "version": "dev" - }, - { - "name": "phaseimpute", - "version": "1.1.0" - }, - { - "name": "radseq", - "version": "dev" - }, - { - "name": "raredisease", - "version": "3.0.0" - }, - { - "name": "readsimulator", - "version": "1.0.1" - }, - { - "name": "riboseq", - "version": "1.2.0" - }, - { - "name": "rnadnavar", - "version": "dev" - }, - { - "name": "rnafusion", - "version": "4.1.2" - }, - { - "name": "rnaseq", - "version": "3.26.0" - }, - { - "name": "rnasplice", - "version": "1.0.4" - }, - { - "name": "rnavar", - "version": "1.2.3" - }, - { - "name": "sammyseq", - "version": "dev" - }, - { - "name": "sarek", - "version": "3.8.1" - }, - { - "name": "scnanoseq", - "version": "1.2.2" - }, - { - "name": "seqinspector", - "version": "1.0.1" - }, - { - "name": "smrnaseq", - "version": "2.4.1" - }, - { - "name": "ssds", - "version": "dev" - }, - { - "name": "taxprofiler", - "version": "2.0.0" - }, - { - "name": "tbanalyzer", - "version": "dev" - }, - { - "name": "variantcatalogue", - "version": "dev" - }, - { - "name": "viralintegration", - "version": "0.1.1" - }, - { - "name": "viralmetagenome", - "version": "1.1.1" - }, - { - "name": "viralrecon", - "version": "3.0.0" - } - ] - }, - { - "name": "samtools_markdup", - "path": "modules/nf-core/samtools/markdup/meta.yml", - "type": "module", - "meta": { - "name": "samtools_markdup", - "description": "mark duplicate alignments in a coordinate sorted file", - "keywords": [ - "bam", - "duplicates", - "markduplicates", - "samtools" - ], - "tools": [ - { - "samtools": { - "description": "Tools for dealing with SAM, BAM and CRAM files", - "homepage": "http://www.htslib.org", - "documentation": "https://www.htslib.org/doc/samtools-markdup.html", - "tool_dev_url": "https://github.com/samtools/samtools", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "identifier": "biotools:samtools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome file", - "pattern": "*.{fa,fasta}", - "ontologies": [] - } - }, - { - "fai": { - "type": "file", - "description": "Reference genome index file", - "pattern": "*.fai", - "ontologies": [] - } - } - ] - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "BAM file", - "pattern": "*{.bam}", - "ontologies": [] - } - } - ] - ], - "cram": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.cram": { - "type": "file", - "description": "CRAM file", - "pattern": "*{.cram}", - "ontologies": [] - } - } - ] - ], - "sam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.sam": { - "type": "file", - "description": "SAM file", - "pattern": "*{.sam}", - "ontologies": [] - } - } - ] - ], - "versions_samtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "samtools": { - "type": "string", - "description": "The tool name" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "samtools": { - "type": "string", - "description": "The tool name" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@priyanka-surana" - ], - "maintainers": [ - "@priyanka-surana", - "@matthdsm" - ] - } - }, - { - "name": "samtools_merge", - "path": "modules/nf-core/samtools/merge/meta.yml", - "type": "module", - "meta": { - "name": "samtools_merge", - "description": "Merge BAM or CRAM file", - "keywords": [ - "merge", - "bam", - "sam", - "cram" - ], - "tools": [ - { - "samtools": { - "description": "SAMtools is a set of utilities for interacting with and post-processing\nshort DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.\nThese files are generated as output by short read aligners like BWA.\n", - "homepage": "http://www.htslib.org/", - "documentation": "http://www.htslib.org/doc/samtools.html", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "identifier": "biotools:samtools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input_files": { - "type": "file", - "description": "BAM/CRAM file", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } - }, - { - "index_files": { - "type": "file", - "description": "BAI/CRAI/CSI index file", - "pattern": "*.{bai,crai,csi}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference file the CRAM was created with (optional)", - "pattern": "*.{fasta,fa}", - "ontologies": [] - } - }, - { - "fai": { - "type": "file", - "description": "Index of the reference file the CRAM was created with (optional)", - "pattern": "*.fai", - "ontologies": [] - } + "name": "bam_dedup_stats_samtools_umicollapse", + "path": "subworkflows/nf-core/bam_dedup_stats_samtools_umicollapse/meta.yml", + "type": "subworkflow", + "meta": { + "name": "bam_dedup_stats_samtools_umicollapse", + "description": "umicollapse, index BAM file and run samtools stats, flagstat and idxstats", + "keywords": ["umi", "dedup", "index", "bam", "sam", "cram"], + "components": [ + "umicollapse", + "samtools/index", + "samtools/stats", + "samtools/idxstats", + "samtools/flagstat", + "bam_stats_samtools" + ], + "input": [ + { + "ch_bam_bai": { + "description": "input BAM file\nStructure: [ val(meta), path(bam), path(bai) ]\n" + } + } + ], + "output": [ + { + "bam": { + "description": "Umi deduplicated BAM/SAM file\nStructure: [ val(meta), path(bam) ]\n" + } + }, + { + "bai": { + "description": "Umi deduplicated BAM/SAM samtools index\nStructure: [ val(meta), path(bai) ]\n" + } + }, + { + "csi": { + "description": "CSI samtools index\nStructure: [ val(meta), path(csi) ]\n" + } + }, + { + "dedupstats": { + "description": "File containing umicollapse deduplication stats\nStructure: [ val(meta), path(stats) ]\n" + } + }, + { + "stats": { + "description": "File containing samtools stats output\nStructure: [ val(meta), path(stats) ]\n" + } + }, + { + "flagstat": { + "description": "File containing samtools flagstat output\nStructure: [ val(meta), path(flagstat) ]\n" + } + }, + { + "idxstats": { + "description": "File containing samtools idxstats output\nStructure: [ val(meta), path(idxstats) ]\n" + } + }, + { + "versions": { + "description": "Files containing software versions\nStructure: [ path(versions.yml) ]\n" + } + } + ], + "authors": ["@MatthiasZepper"], + "maintainers": ["@MatthiasZepper"] }, - { - "gzi": { - "type": "file", - "description": "Index of the compressed reference file the CRAM was created with (optional)", - "pattern": "*.gzi", - "ontologies": [] - } - } - ] - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.bam": { - "type": "file", - "description": "BAM file", - "pattern": "*.{bam}", - "ontologies": [] - } - } - ] - ], - "cram": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.cram": { - "type": "file", - "description": "CRAM file", - "pattern": "*.{cram}", - "ontologies": [] - } - } - ] - ], - "index": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.{bai,crai,csi}": { - "type": "file", - "description": "BAM index file (optional)", - "pattern": "*.{bai,crai,csi}", - "ontologies": [] - } - } - ] - ], - "versions_samtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "samtools": { - "type": "string", - "description": "The tool name" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "samtools": { - "type": "string", - "description": "The tool name" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } + "pipelines": [ + { + "name": "lncpipe", + "version": "dev" + }, + { + "name": "riboseq", + "version": "1.2.0" + }, + { + "name": "rnaseq", + "version": "3.26.0" + } ] - ] - }, - "authors": [ - "@yuukiiwa", - "@maxulysse", - "@FriederikeHanssen", - "@ramprasadn" - ], - "maintainers": [ - "@yuukiiwa", - "@maxulysse", - "@FriederikeHanssen", - "@ramprasadn", - "@matthdsm" - ] - }, - "pipelines": [ - { - "name": "bamtofastq", - "version": "2.2.1" - }, - { - "name": "callingcards", - "version": "1.0.0" - }, - { - "name": "coproid", - "version": "2.0.1" - }, - { - "name": "fastquorum", - "version": "1.2.0" - }, - { - "name": "genomicrelatedness", - "version": "dev" - }, - { - "name": "hicar", - "version": "1.0.0" - }, - { - "name": "nascent", - "version": "2.3.0" - }, - { - "name": "phaseimpute", - "version": "1.1.0" - }, - { - "name": "radseq", - "version": "dev" - }, - { - "name": "raredisease", - "version": "3.0.0" - }, - { - "name": "rnadnavar", - "version": "dev" - }, - { - "name": "rnavar", - "version": "1.2.3" - }, - { - "name": "sarek", - "version": "3.8.1" }, { - "name": "scnanoseq", - "version": "1.2.2" - }, - { - "name": "tbanalyzer", - "version": "dev" - } - ] - }, - { - "name": "samtools_mpileup", - "path": "modules/nf-core/samtools/mpileup/meta.yml", - "type": "module", - "meta": { - "name": "samtools_mpileup", - "description": "Generate text pileup output for one or multiple BAM files. Each input file produces a separate group of pileup columns in the output.", - "keywords": [ - "mpileup", - "bam", - "sam", - "cram" - ], - "tools": [ - { - "samtools": { - "description": "SAMtools is a set of utilities for interacting with and post-processing\nshort DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.\nThese files are generated as output by short read aligners like BWA.\n", - "homepage": "http://www.htslib.org/", - "documentation": "http://www.htslib.org/doc/samtools.html", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "identifier": "biotools:samtools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } - }, - { - "index": { - "type": "file", - "description": "CSI/BAI/CRAI file. Optional. Only required when using the '-r' parameter.", - "pattern": "*.{bai,crai,csi}", - "ontologies": [] - } - }, - { - "intervals": { - "type": "file", - "description": "Interval FILE. Optional.", - "pattern": "*.bed", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA reference file. Optional.", - "pattern": "*.{fasta,fa,fna}", - "ontologies": [] - } + "name": "bam_dedup_stats_samtools_umitools", + "path": "subworkflows/nf-core/bam_dedup_stats_samtools_umitools/meta.yml", + "type": "subworkflow", + "meta": { + "name": "bam_dedup_stats_samtools_umitools", + "description": "UMI-tools dedup, index BAM file and run samtools stats, flagstat and idxstats", + "keywords": ["umi", "dedup", "index", "bam", "sam", "cram"], + "components": [ + "umitools/dedup", + "samtools/index", + "samtools/view", + "samtools/stats", + "samtools/idxstats", + "samtools/flagstat", + "bam_stats_samtools" + ], + "input": [ + { + "ch_bam_bai": { + "description": "input BAM file\nStructure: [ val(meta), path(bam), path(bai) ]\n" + } + }, + { + "val_get_dedup_stats": { + "type": "boolean", + "description": "Generate output stats when running \"umi_tools dedup\"\n" + } + }, + { + "val_primary_only": { + "type": "boolean", + "description": "Filter to primary alignments (SAM flag 0x900) before running UMI-tools dedup.\nWhen true, secondary and supplementary alignments are removed so that dedup\nstatistics reflect only primary alignments.\n" + } + } + ], + "output": [ + { + "bam": { + "description": "Umi deduplicated BAM/SAM file\nStructure: [ val(meta), path(bam) ]\n" + } + }, + { + "bai": { + "description": "Umi deduplicated BAM/SAM samtools index\nStructure: [ val(meta), path(bai) ]\n" + } + }, + { + "csi": { + "description": "CSI samtools index\nStructure: [ val(meta), path(csi) ]\n" + } + }, + { + "deduplog": { + "description": "UMI-tools deduplication log\nStructure: [ val(meta), path(log) ]\n" + } + }, + { + "stats": { + "description": "File containing samtools stats output\nStructure: [ val(meta), path(stats) ]\n" + } + }, + { + "flagstat": { + "description": "File containing samtools flagstat output\nStructure: [ val(meta), path(flagstat) ]\n" + } + }, + { + "idxstats": { + "description": "File containing samtools idxstats output\nStructure: [ val(meta), path(idxstats) ]\n" + } + }, + { + "versions": { + "description": "Files containing software versions\nStructure: [ path(versions.yml) ]\n" + } + } + ], + "authors": ["@drpatelh", "@KamilMaliszArdigen"], + "maintainers": ["@drpatelh", "@KamilMaliszArdigen"] }, - { - "fai": { - "type": "file", - "description": "FAI file. Optional. Only required (recommended) when using the '-f' parameter.", - "pattern": "*.{fai}", - "ontologies": [] - } - } - ] - ], - "output": { - "mpileup": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.mpileup.gz": { - "type": "file", - "description": "mpileup file", - "pattern": "*.{mpileup}", - "ontologies": [] - } - } - ] - ], - "versions_samtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "samtools": { - "type": "string", - "description": "The tool name" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "samtools": { - "type": "string", - "description": "The tool name" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } + "pipelines": [ + { + "name": "lncpipe", + "version": "dev" + }, + { + "name": "nascent", + "version": "2.3.0" + }, + { + "name": "riboseq", + "version": "1.2.0" + }, + { + "name": "rnaseq", + "version": "3.26.0" + } ] - ] }, - "authors": [ - "@drpatelh", - "@joseespinosa" - ], - "maintainers": [ - "@joseespinosa", - "@krannich479", - "@matthdsm" - ] - }, - "pipelines": [ { - "name": "abotyper", - "version": "dev" + "name": "bam_dedup_umi", + "path": "subworkflows/nf-core/bam_dedup_umi/meta.yml", + "type": "subworkflow", + "meta": { + "name": "bam_dedup_umi", + "description": "BAM deduplication with UMI processing for both genome and transcriptome alignments", + "keywords": ["deduplication", "UMI", "BAM", "genome", "transcriptome", "umicollapse", "umitools"], + "components": [ + "umitools/prepareforrsem", + "samtools/sort", + "bam_dedup_stats_samtools_umicollapse", + "bam_dedup_stats_samtools_umitools", + "bam_sort_stats_samtools" + ], + "input": [ + { + "ch_genome_bam": { + "description": "Channel with genome BAM files", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata map" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file", + "pattern": "*.bam" + } + }, + { + "bai": { + "type": "file", + "description": "BAM index file", + "pattern": "*.bai" + } + } + ] + } + }, + { + "ch_fasta_fai": { + "description": "Channel with genome FASTA file and index", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata map" + } + }, + { + "fasta": { + "type": "file", + "description": "Genome FASTA file", + "pattern": "*.{fa,fna,fasta}" + } + }, + { + "fai": { + "type": "file", + "description": "Genome FASTA index file", + "pattern": "*.fai" + } + } + ] + } + }, + { + "umi_dedup_tool": { + "description": "UMI deduplication tool to use", + "structure": [ + { + "value": { + "type": "string", + "description": "Either 'umicollapse' or 'umitools'" + } + } + ] + } + }, + { + "umitools_dedup_stats": { + "description": "Whether to generate UMI-tools deduplication stats", + "structure": [ + { + "value": { + "type": "boolean", + "description": "True or False" + } + } + ] + } + }, + { + "bam_csi_index": { + "description": "Whether to generate CSI index", + "structure": [ + { + "value": { + "type": "boolean", + "description": "True or False" + } + } + ] + } + }, + { + "ch_transcriptome_bam": { + "description": "Channel with transcriptome BAM files", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata map" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file", + "pattern": "*.bam" + } + } + ] + } + }, + { + "ch_transcript_fasta_fai": { + "description": "Channel with transcript FASTA file and index", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata map" + } + }, + { + "fasta": { + "type": "file", + "description": "Transcript FASTA file", + "pattern": "*.{fa,fasta}" + } + }, + { + "fai": { + "type": "file", + "description": "Transcript FASTA index file", + "pattern": "*.fai" + } + } + ] + } + }, + { + "umitools_dedup_primary_only": { + "description": "Whether to filter to primary alignments before UMI-tools dedup", + "structure": [ + { + "value": { + "type": "boolean", + "description": "When true, secondary and supplementary alignments (SAM flag 0x900) are\nremoved before running UMI-tools dedup so that dedup statistics reflect\nonly primary alignments.\n" + } + } + ] + } + } + ], + "output": [ + { + "bam": { + "description": "Channel containing deduplicated genome BAM files", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata map" + } + }, + { + "bam": { + "type": "file", + "description": "Deduplicated BAM file", + "pattern": "*.bam" + } + } + ] + } + }, + { + "bai": { + "description": "Channel containing indexed BAM (BAI) files", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata map" + } + }, + { + "bai": { + "type": "file", + "description": "BAM index file", + "pattern": "*.bai" + } + } + ] + } + }, + { + "csi": { + "description": "Channel containing CSI files (if bam_csi_index is true)", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata map" + } + }, + { + "csi": { + "type": "file", + "description": "CSI index file", + "pattern": "*.csi" + } + } + ] + } + }, + { + "dedup_log": { + "description": "Channel containing deduplication log files", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata map" + } + }, + { + "log": { + "type": "file", + "description": "Deduplication log file", + "pattern": "*.log" + } + } + ] + } + }, + { + "stats": { + "description": "Channel containing BAM statistics files", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata map" + } + }, + { + "stats": { + "type": "file", + "description": "BAM statistics file", + "pattern": "*.stats" + } + } + ] + } + }, + { + "flagstat": { + "description": "Channel containing flagstat files", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata map" + } + }, + { + "flagstat": { + "type": "file", + "description": "Flagstat file", + "pattern": "*.flagstat" + } + } + ] + } + }, + { + "idxstats": { + "description": "Channel containing idxstats files", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata map" + } + }, + { + "idxstats": { + "type": "file", + "description": "Idxstats file", + "pattern": "*.idxstats" + } + } + ] + } + }, + { + "genome_stats": { + "description": "Channel containing BAM statistics for the genome-aligned BAM only (transcriptome excluded)", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata map" + } + }, + { + "stats": { + "type": "file", + "description": "BAM statistics file", + "pattern": "*.stats" + } + } + ] + } + }, + { + "genome_flagstat": { + "description": "Channel containing flagstat for the genome-aligned BAM only", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata map" + } + }, + { + "flagstat": { + "type": "file", + "description": "Flagstat file", + "pattern": "*.flagstat" + } + } + ] + } + }, + { + "genome_idxstats": { + "description": "Channel containing idxstats for the genome-aligned BAM only", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata map" + } + }, + { + "idxstats": { + "type": "file", + "description": "Idxstats file", + "pattern": "*.idxstats" + } + } + ] + } + }, + { + "per_sample_mqc_bundle": { + "description": "Per-sample MultiQC-feeding outputs (genome-side only: genomic dedup log,\ngenome stats, flagstat, idxstats) joined on meta. Transcriptome stats\nexcluded (MultiQC can't disambiguate them from genome stats).\n", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata map" + } + }, + { + "files": { + "type": "file", + "description": "List of MultiQC-relevant files for the sample" + } + } + ] + } + }, + { + "multiqc_files": { + "description": "Channel containing files for MultiQC", + "structure": [ + { + "file": { + "type": "file", + "description": "File for MultiQC" + } + } + ] + } + }, + { + "transcriptome_bam": { + "description": "Channel containing deduplicated transcriptome BAM files", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata map" + } + }, + { + "bam": { + "type": "file", + "description": "Deduplicated transcriptome BAM file", + "pattern": "*.bam" + } + } + ] + } + }, + { + "versions": { + "description": "Channel containing software versions file", + "structure": [ + { + "versions": { + "type": "file", + "description": "File containing versions of the software used", + "pattern": "versions.yml" + } + } + ] + } + } + ], + "authors": ["@pinin4fjords"], + "maintainers": ["@pinin4fjords"] + }, + "pipelines": [ + { + "name": "lncpipe", + "version": "dev" + }, + { + "name": "riboseq", + "version": "1.2.0" + }, + { + "name": "rnaseq", + "version": "3.26.0" + } + ] }, { - "name": "rnadnavar", - "version": "dev" + "name": "bam_docounts_contamination_angsd", + "path": "subworkflows/nf-core/bam_docounts_contamination_angsd/meta.yml", + "type": "subworkflow", + "meta": { + "name": "bam_docounts_contamination_angsd", + "description": "Calculate contamination of the X-chromosome with ANGSD", + "keywords": ["angsd", "bam", "contamination", "docounts"], + "components": ["angsd/docounts", "angsd/contamination"], + "input": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM or CRAM file", + "pattern": "*.{bam,cram}" + } + }, + { + "bai": { + "type": "file", + "description": "BAM/SAM samtools index", + "pattern": "*.{bai,csi}" + } + }, + { + "hapmap_file": { + "type": "file", + "description": "Hapmap file" + } + } + ], + "output": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\n" + } + }, + { + "txt": { + "type": "file", + "description": "Contamination estimation file", + "pattern": "*.txt" + } + }, + { + "versions": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ], + "authors": ["@scarlhoff"], + "maintainers": ["@scarlhoff"] + } }, { - "name": "sarek", - "version": "3.8.1" - } - ] - }, - { - "name": "samtools_quickcheck", - "path": "modules/nf-core/samtools/quickcheck/meta.yml", - "type": "module", - "meta": { - "name": "samtools_quickcheck", - "description": "Quickly check that input files appear to be intact. Checks that beginning of the file contains a valid header (all formats) containing at least one target sequence and then seeks to the end of the file and checks that an end-of-file (EOF) is present and intact (BAM and CRAM only). Alignment records are not checked. The quickcheck module returns a non-zero EXIT_CODE if any input files don't have a valid header or are missing an EOF block. Otherwise EXIT_CODE is zero.", - "keywords": [ - "check", - "quickcheck", - "sam", - "bam", - "cram" - ], - "tools": [ - { - "samtools": { - "description": "Tools for dealing with SAM, BAM and CRAM files", - "homepage": "https://www.htslib.org/", - "documentation": "https://www.htslib.org/doc/samtools-quickcheck.html", - "tool_dev_url": "https://github.com/samtools/", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "identifier": "biotools:samtools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" - } - }, - { - "bam": { - "type": "file", - "description": "sequence_trace file", - "pattern": "*.{cram,sam,bam}", - "ontologies": [ - { - "edam": "http://edamontology.org/data_0924" - }, - { - "edam": "http://edamontology.org/format_3462" - }, - { - "edam": "http://edamontology.org/format_2573" - }, - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - } - ] - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" - } - }, - { - "bam": { - "type": "file", - "description": "sequence_trace file", - "pattern": "*.{cram,sam,bam}", - "ontologies": [ + "name": "bam_impute_quilt", + "path": "subworkflows/nf-core/bam_impute_quilt/meta.yml", + "type": "subworkflow", + "meta": { + "name": "BAM_IMPUTE_QUILT", + "description": "Subworkflow to impute BAM files using QUILT software.\nVariants location to impute are obtain through the tsv file given\n", + "keywords": ["BAM", "imputation", "quilt"], + "components": ["gawk", "quilt/quilt", "bcftools/index", "glimpse2/ligate"], + "input": [ + { + "ch_input": { + "description": "Channel with input data", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata map" + } + }, + { + "file": { + "type": "file", + "description": "List of input BAM files", + "pattern": "*.bam" + } + }, + { + "index": { + "type": "file", + "description": "List of input index file", + "pattern": "*.{bai,csi}" + } + }, + { + "bampaths": { + "type": "file", + "description": "File containing the list of BAM/CRAM files to be phased.\nOne file per line.\n", + "pattern": "*.{txt,tsv}" + } + }, + { + "bamnames": { + "type": "file", + "description": "File containing the sample names of each BAM files listed in bampaths.\nOne file per line.\n", + "pattern": "*.{txt,tsv}" + } + } + ] + } + }, + { + "ch_hap_legend": { + "description": "Channel with reference panel variants data", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata map that will be combined with the input data map\nNeed to have the \"chr\" as chromosome name and \"id\" as panel name\n" + } + }, + { + "hap": { + "type": "file", + "description": "Panel VCF haplotypes files by chromosomes", + "pattern": "*.hap[.gz]+" + } + }, + { + "legend": { + "type": "file", + "description": "Panel VCF legend files by chromosomes", + "pattern": "*.legend[.gz]+" + } + }, + { + "posfile": { + "type": "file", + "description": "Position to impute variants file in TSV format (chromosome, position, ref, alt)" + } + } + ] + } + }, + { + "ch_chunks": { + "description": "Channel with chromosome chunks data", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata map with chromosome information" + } + }, + { + "chr": { + "type": "string", + "description": "Chromosome name" + } + }, + { + "start": { + "type": "integer", + "description": "Start position of the chunk" + } + }, + { + "end": { + "type": "integer", + "description": "End position of the chunk" + } + } + ] + } + }, { - "edam": "http://edamontology.org/data_0924" + "ch_map": { + "description": "Channel with genetic map data", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata map with chromosome information\n" + } + }, + { + "map": { + "type": "file", + "description": "Stitch format genetic map files", + "pattern": "*.map" + } + } + ] + } }, { - "edam": "http://edamontology.org/format_3462" + "ch_fasta": { + "description": "Channel with reference genome data", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata map" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA file of the reference genome", + "pattern": "*.fa[sta]+" + } + }, + { + "fai": { + "type": "file", + "description": "FASTA index file of the reference genome", + "pattern": "*.fai" + } + } + ] + } }, { - "edam": "http://edamontology.org/format_2573" + "n_gen": { + "type": "integer", + "description": "Number of generations since founding or mixing" + } }, { - "edam": "http://edamontology.org/format_2572" + "buffer": { + "type": "integer", + "description": "Buffer of region to perform imputation over" + } } - ] - } - }, - { - "EXIT_CODE": { - "type": "string", - "description": "Exit code (0 for success, non-zero otherwise) that is the result of the format check.", - "ontologies": [] - } - } - ] - ], - "versions_samtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@Krannich479" - ], - "maintainers": [ - "@Krannich479", - "@matthdsm" - ] - } - }, - { - "name": "samtools_reheader", - "path": "modules/nf-core/samtools/reheader/meta.yml", - "type": "module", - "meta": { - "name": "samtools_reheader", - "description": "Replace the header in the bam file with the header generated by the command.\nThis command is much faster than replacing the header with a BAM→SAM→BAM conversion.\n", - "keywords": [ - "reheader", - "cram", - "bam", - "genomics" - ], - "tools": [ - { - "samtools": { - "description": "SAMtools is a set of utilities for interacting with and post-processing\nshort DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.\nThese files are generated as output by short read aligners like BWA.\n", - "homepage": "http://www.htslib.org/", - "documentation": "http://www.htslib.org/doc/samtools.html", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "identifier": "biotools:samtools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM file to be reheaded", - "pattern": "*.{bam,cram}", - "ontologies": [] - } - }, - { - "bai": { - "type": "file", - "description": "BAM/CRAM index file to be reheaded", - "pattern": "*.{bai,crai,csi}", - "ontologies": [] - } + ], + "output": [ + { + "vcf_index": { + "description": "Channel with imputed VCF files", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata map combined with the posfile, chunks and map data map.\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF imputed file", + "pattern": "*.{vcf,bcf,vcf.gz}" + } + }, + { + "index": { + "type": "file", + "description": "VCF index file", + "pattern": "*.{tbi,csi}" + } + } + ] + } + } + ], + "authors": ["@louislenezet"], + "maintainers": ["@louislenezet"] } - ] - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "Reheaded BAM/CRAM file", - "pattern": "*.{bam,cram}", - "ontologies": [] - } - } - ] - ], - "versions_samtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "samtools": { - "type": "string", - "description": "The tool name" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "samtools": { - "type": "string", - "description": "The tool name" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The command used to generate the version of the tool" - } - } - ] - ] }, - "authors": [ - "@louislenezet" - ], - "maintainers": [ - "@louislenezet", - "@matthdsm" - ] - }, - "pipelines": [ { - "name": "phaseimpute", - "version": "1.1.0" - }, - { - "name": "tfactivity", - "version": "dev" - } - ] - }, - { - "name": "samtools_samples", - "path": "modules/nf-core/samtools/samples/meta.yml", - "type": "module", - "meta": { - "name": "samtools_samples", - "description": "Write sample names and path to reference genome of an alignment to a text file.\n", - "keywords": [ - "samples", - "bam", - "cram", - "genomics" - ], - "tools": [ - { - "samtools": { - "description": "SAMtools is a set of utilities for interacting with and post-processing\nshort DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.\nThese files are generated as output by short read aligners like BWA.\n", - "homepage": "http://www.htslib.org/", - "documentation": "http://www.htslib.org/doc/samtools.html", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "identifier": "biotools:samtools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" - } - }, - { - "bam": { - "type": "file", - "description": "alignment file", - "pattern": "*.{bam,sam,cram}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - }, - { - "edam": "http://edamontology.org/format_2573" - }, - { - "edam": "http://edamontology.org/format_3462" - } - ] - } - }, - { - "bai": { - "type": "file", - "description": "index file for the alignment", - "pattern": "*.{bai,crai}" - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information." - } - }, - { - "fasta": { - "type": "file", - "description": "reference genome file (optional)", - "pattern": "*.{fasta,fa,fna}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - }, - { - "fai": { - "type": "file", - "description": "index file for the reference genome (optional)", - "pattern": "*.fai" - } - } - ] - ], - "output": { - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" - } - }, - { - "*.tsv": { - "type": "file", - "description": "tab-separated file containing sample names, BAM filename and optionally reference genome path", - "pattern": "*.tsv" - } - } - ] - ], - "versions_samtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "samtools": { - "type": "string", - "description": "The tool name" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "samtools": { - "type": "string", - "description": "The tool name" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@Schmytzi" - ], - "maintainers": [ - "@Schmytzi", - "@matthdsm" - ] - } - }, - { - "name": "samtools_sormadup", - "path": "modules/nf-core/samtools/sormadup/meta.yml", - "type": "module", - "meta": { - "name": "samtools_sormadup", - "description": "Collate/Fixmate/Sort/Markdup SAM/BAM/CRAM file", - "keywords": [ - "cat", - "collate", - "fixmate", - "sort", - "markduplicates", - "bam", - "sam", - "cram", - "multi-tool" - ], - "tools": [ - { - "samtools_cat": { - "description": "SAMtools is a set of utilities for interacting with and post-processing\nshort DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.\nThese files are generated as output by short read aligners like BWA.\n", - "homepage": "http://www.htslib.org/", - "documentation": "http://www.htslib.org/doc/samtools.html", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "args_id": "$args", - "identifier": "biotools:samtools" - } - }, - { - "samtools_collate": { - "description": "SAMtools is a set of utilities for interacting with and post-processing\nshort DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.\nThese files are generated as output by short read aligners like BWA.\n", - "homepage": "http://www.htslib.org/", - "documentation": "http://www.htslib.org/doc/samtools.html", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "args_id": "$args2", - "identifier": "biotools:samtools" - } - }, - { - "samtools_fixmate": { - "description": "SAMtools is a set of utilities for interacting with and post-processing\nshort DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.\nThese files are generated as output by short read aligners like BWA.\n", - "homepage": "http://www.htslib.org/", - "documentation": "http://www.htslib.org/doc/samtools.html", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "args_id": "$args3", - "identifier": "biotools:samtools" - } - }, - { - "samtools_sort": { - "description": "SAMtools is a set of utilities for interacting with and post-processing\nshort DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.\nThese files are generated as output by short read aligners like BWA.\n", - "homepage": "http://www.htslib.org/", - "documentation": "http://www.htslib.org/doc/samtools.html", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "args_id": "$args4", - "identifier": "biotools:samtools" - } - }, - { - "samtools_markdup": { - "description": "SAMtools is a set of utilities for interacting with and post-processing\nshort DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.\nThese files are generated as output by short read aligners like BWA.\n", - "homepage": "http://www.htslib.org/", - "documentation": "http://www.htslib.org/doc/samtools.html", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "args_id": "$args5", - "identifier": "biotools:samtools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM/SAM files", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome file", - "pattern": "*.{fasta,fa,fna}", - "ontologies": [] - } - }, - { - "fai": { - "type": "file", - "description": "Reference genome index file", - "pattern": "*.fai", - "ontologies": [] - } - } - ] - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "Sorted and duplicate marked BAM file", - "pattern": "*.bam", - "ontologies": [] - } - } - ] - ], - "cram": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.cram": { - "type": "file", - "description": "Sorted and duplicate marked CRAM file", - "pattern": "*.cram", - "ontologies": [] - } - } - ] - ], - "csi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.csi": { - "type": "file", - "description": "Sorted and duplicate marked BAM index file", - "pattern": "*.csi", - "ontologies": [] - } - } - ] - ], - "crai": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.crai": { - "type": "file", - "description": "Sorted and duplicate marked CRAM index file", - "pattern": "*.crai", - "ontologies": [] - } - } - ] - ], - "metrics": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.metrics": { - "type": "file", - "description": "Duplicate metrics file", - "pattern": "*.metrics", - "ontologies": [] - } - } - ] - ], - "versions_samtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "samtools": { - "type": "string", - "description": "The tool name" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "samtools": { - "type": "string", - "description": "The tool name" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@matthdsm" - ], - "maintainers": [ - "@matthdsm" - ] - } - }, - { - "name": "samtools_sort", - "path": "modules/nf-core/samtools/sort/meta.yml", - "type": "module", - "meta": { - "name": "samtools_sort", - "description": "Sort SAM/BAM/CRAM file", - "keywords": [ - "sort", - "bam", - "sam", - "cram" - ], - "tools": [ - { - "samtools": { - "description": "SAMtools is a set of utilities for interacting with and post-processing\nshort DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.\nThese files are generated as output by short read aligners like BWA.\n", - "homepage": "http://www.htslib.org/", - "documentation": "http://www.htslib.org/doc/samtools.html", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "identifier": "biotools:samtools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM/SAM file(s)", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome FASTA file", - "pattern": "*.{fa,fasta,fna}", - "optional": true, - "ontologies": [] - } - }, - { - "fai": { - "type": "file", - "description": "Reference genome FASTA index file", - "pattern": "*.{fai}", - "optional": true, - "ontologies": [] - } - } - ], - { - "index_format": { - "type": "string", - "description": "Index format to use (optional)", - "pattern": "bai|csi|crai" + "name": "bam_impute_quilt2", + "path": "subworkflows/nf-core/bam_impute_quilt2/meta.yml", + "type": "subworkflow", + "meta": { + "name": "bam_impute_quilt2", + "description": "Impute low-coverage BAM or CRAM inputs with QUILT2 and ligate chunked outputs per chromosome. 'regionout' key will be used to store temporarily the region and therefore shouldn't be used in the meta maps.\n", + "keywords": ["bam", "cram", "imputation", "quilt", "quilt2", "vcf"], + "components": ["quilt/quilt2", "glimpse2/ligate", "bcftools/index"], + "input": [ + { + "ch_input": { + "description": "Channel with target sequencing data and optional rename files.\n", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata map for the input batch." + } + }, + { + "bam_or_cram": { + "type": "file", + "description": "Input BAM or CRAM file, or a list of BAM or CRAM files.", + "pattern": "*.{bam,cram}" + } + }, + { + "index": { + "type": "file", + "description": "Index for the BAM or CRAM input.", + "pattern": "*.{bai,crai}" + } + }, + { + "bampaths": { + "type": "file", + "description": "Optional text file listing BAM or CRAM paths to impute.\nOne file per line.\n", + "pattern": "*.{txt,tsv}" + } + }, + { + "bamnames": { + "type": "file", + "description": "Optional text file listing sample names in the same order as `bampaths`.\nOne file per line.\n", + "pattern": "*.{txt,tsv}" + } + } + ] + } + }, + { + "ch_reference_panel": { + "description": "Channel with phased reference panel VCFs per chromosome.\n", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata map that will be combined with the input metadata.\nMust include `id` for the panel name and `chr` for the chromosome.\n" + } + }, + { + "vcf": { + "type": "file", + "description": "Reference panel VCF or BCF.", + "pattern": "*.{vcf,vcf.gz,bcf}" + } + }, + { + "index": { + "type": "file", + "description": "Index for the reference panel VCF or BCF.", + "pattern": "*.{tbi,csi}" + } + } + ] + } + }, + { + "ch_chunks": { + "description": "Channel with optional imputation chunks per chromosome.\n", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata map with the panel id and chromosome." + } + }, + { + "chr": { + "type": "string", + "description": "Chromosome name." + } + }, + { + "start": { + "type": "integer", + "description": "Start position of the chunk." + } + }, + { + "end": { + "type": "integer", + "description": "End position of the chunk." + } + } + ] + } + }, + { + "ch_map": { + "description": "Channel with optional genetic maps per chromosome.\n", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata map with the panel id and chromosome." + } + }, + { + "map": { + "type": "file", + "description": "Genetic map used by QUILT2.", + "pattern": "*.{txt,map}{,gz}" + } + } + ] + } + }, + { + "ch_fasta": { + "description": "Channel with optional reference FASTA data, required for CRAM inputs.\n", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata map for the reference genome." + } + }, + { + "fasta": { + "type": "file", + "description": "Reference genome FASTA.", + "pattern": "*.{fa,fasta}" + } + }, + { + "fai": { + "type": "file", + "description": "FASTA index file.", + "pattern": "*.fai" + } + } + ] + } + }, + { + "n_gen": { + "type": "integer", + "description": "Number of generations since founding or mixing." + } + }, + { + "buffer": { + "type": "integer", + "description": "Buffer of region to perform imputation over." + } + } + ], + "output": [ + { + "vcf_index": { + "description": "Imputed and indexed VCFs after ligating chunked outputs per chromosome.\n", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata map combined from the input batch and panel metadata." + } + }, + { + "vcf": { + "type": "file", + "description": "Imputed VCF file.", + "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}" + } + }, + { + "index": { + "type": "file", + "description": "Index for the imputed VCF or BCF file.", + "pattern": "*.{tbi,csi}" + } + } + ] + } + } + ], + "authors": ["@atrigila"], + "maintainers": ["@atrigila"] } - } - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.bam": { - "type": "file", - "description": "Sorted BAM file", - "pattern": "*.{bam}", - "ontologies": [] - } - } - ] - ], - "cram": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.cram": { - "type": "file", - "description": "Sorted CRAM file", - "pattern": "*.{cram}", - "ontologies": [] - } - } - ] - ], - "sam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.sam": { - "type": "file", - "description": "Sorted SAM file", - "pattern": "*.{sam}", - "ontologies": [] - } - } - ] - ], - "index": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.${extension}.{crai,csi,bai}": { - "type": "file", - "description": "CRAM index file (optional)", - "pattern": "*.{crai,csi,bai}", - "ontologies": [] - } - } - ] - ], - "versions_samtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "samtools": { - "type": "string", - "description": "The tool name" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "samtools": { - "type": "string", - "description": "The tool name" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@drpatelh", - "@ewels", - "@matthdsm" - ], - "maintainers": [ - "@drpatelh", - "@ewels", - "@matthdsm" - ] - }, - "pipelines": [ - { - "name": "alleleexpression", - "version": "dev" - }, - { - "name": "atacseq", - "version": "2.1.2" - }, - { - "name": "bacass", - "version": "2.6.0" - }, - { - "name": "callingcards", - "version": "1.0.0" - }, - { - "name": "chipseq", - "version": "2.1.0" - }, - { - "name": "circdna", - "version": "1.1.0" - }, - { - "name": "circrna", - "version": "dev" - }, - { - "name": "coproid", - "version": "2.0.1" - }, - { - "name": "cutandrun", - "version": "3.2.2" - }, - { - "name": "dartseq", - "version": "dev" - }, - { - "name": "evexplorer", - "version": "dev" - }, - { - "name": "genomeassembler", - "version": "1.1.0" - }, - { - "name": "hgtseq", - "version": "1.1.0" - }, - { - "name": "hicar", - "version": "1.0.0" - }, - { - "name": "lncpipe", - "version": "dev" - }, - { - "name": "magmap", - "version": "1.0.0" - }, - { - "name": "metatdenovo", - "version": "1.3.0" - }, - { - "name": "methylong", - "version": "2.0.0" - }, - { - "name": "methylseq", - "version": "4.2.0" - }, - { - "name": "nanoseq", - "version": "3.1.0" - }, - { - "name": "nascent", - "version": "2.3.0" - }, - { - "name": "oncoanalyser", - "version": "2.3.0" - }, - { - "name": "pacsomatic", - "version": "dev" - }, - { - "name": "pacvar", - "version": "1.0.1" - }, - { - "name": "panoramaseq", - "version": "dev" - }, - { - "name": "phageannotator", - "version": "dev" - }, - { - "name": "radseq", - "version": "dev" - }, - { - "name": "raredisease", - "version": "3.0.0" - }, - { - "name": "riboseq", - "version": "1.2.0" - }, - { - "name": "rnadnavar", - "version": "dev" }, { - "name": "rnafusion", - "version": "4.1.2" - }, - { - "name": "rnaseq", - "version": "3.26.0" - }, - { - "name": "rnasplice", - "version": "1.0.4" - }, - { - "name": "rnavar", - "version": "1.2.3" - }, - { - "name": "sammyseq", - "version": "dev" - }, - { - "name": "scnanoseq", - "version": "1.2.2" - }, - { - "name": "smrnaseq", - "version": "2.4.1" - }, - { - "name": "viralintegration", - "version": "0.1.1" + "name": "bam_impute_stitch", + "path": "subworkflows/nf-core/bam_impute_stitch/meta.yml", + "type": "subworkflow", + "meta": { + "name": "BAM_IMPUTE_STITCH", + "description": "Subworkflow to impute BAM files using STITCH software.\nVariants location to impute are obtain through the legend file given\n", + "keywords": ["BAM", "imputation", "stitch"], + "components": ["stitch", "bcftools/index", "glimpse2/ligate"], + "input": [ + { + "ch_input": { + "description": "Channel with input data", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata map" + } + }, + { + "file": { + "type": "file", + "description": "List of input BAM files", + "pattern": "*.bam" + } + }, + { + "index": { + "type": "file", + "description": "List of input index file", + "pattern": "*.{bai,csi}" + } + }, + { + "bampaths": { + "type": "file", + "description": "File containing the list of BAM/CRAM files to be phased.\nOne file per line.\n", + "pattern": "*.{txt,tsv}" + } + }, + { + "bamnames": { + "type": "file", + "description": "File containing the sample names of each BAM files listed in bampaths.\nOne file per line.\n", + "pattern": "*.{txt,tsv}" + } + } + ] + } + }, + { + "ch_posfile": { + "description": "Channel with position to call variants by chromosomes", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata map with chromosome information\n" + } + }, + { + "tsv": { + "type": "file", + "description": "Position to impute variants file in TSV format (chromosome, position, ref, alt)" + } + } + ] + } + }, + { + "ch_chunks": { + "description": "Channel with chromosome chunks data", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata map with chromosome information" + } + }, + { + "chr": { + "type": "string", + "description": "Chromosome name" + } + }, + { + "start": { + "type": "integer", + "description": "Start position of the chunk" + } + }, + { + "end": { + "type": "integer", + "description": "End position of the chunk" + } + } + ] + } + }, + { + "ch_map": { + "description": "Channel with genetic map data", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata map with chromosome information\n" + } + }, + { + "map": { + "type": "file", + "description": "Stitch format genetic map files", + "pattern": "*.map" + } + } + ] + } + }, + { + "ch_fasta": { + "description": "Channel with reference genome data", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata map" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA file of the reference genome", + "pattern": "*.fa[sta]+" + } + }, + { + "fai": { + "type": "file", + "description": "FASTA index file of the reference genome", + "pattern": "*.fai" + } + } + ] + } + }, + { + "k_val": { + "type": "integer", + "description": "K value for STITCH imputation" + } + }, + { + "n_gen": { + "type": "integer", + "description": "Number of generations for STITCH imputation" + } + }, + { + "buffer": { + "type": "integer", + "description": "Buffer size around each chunk for STITCH imputation" + } + }, + { + "seed": { + "type": "integer", + "description": "Random seed for STITCH imputation" + } + } + ], + "output": [ + { + "vcf_index": { + "description": "Channel with imputed VCF files", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata map combined with the posfile, chunks and map data map.\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF imputed file", + "pattern": "*.{vcf,bcf,vcf.gz}" + } + }, + { + "index": { + "type": "file", + "description": "VCF index file", + "pattern": "*.{tbi,csi}" + } + } + ] + } + }, + { + "versions": { + "description": "Channel containing software versions file", + "structure": [ + { + "versions.yml": { + "type": "file", + "description": "File containing versions of the software used" + } + } + ] + } + } + ], + "authors": ["@louislenezet"], + "maintainers": ["@louislenezet"] + } }, { - "name": "viralrecon", - "version": "3.0.0" - } - ] - }, - { - "name": "samtools_splitheader", - "path": "modules/nf-core/samtools/splitheader/meta.yml", - "type": "module", - "meta": { - "name": "samtools_splitheader", - "description": "Extract header lines from a SAM/BAM/CRAM file into separate files depending on type", - "keywords": [ - "view", - "bam", - "sam", - "cram", - "readgroup", - "program", - "sequence", - "header" - ], - "tools": [ - { - "samtools": { - "description": "SAMtools is a set of utilities for interacting with and post-processing\nshort DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.\nThese files are generated as output by short read aligners like BWA.\n", - "homepage": "http://www.htslib.org/", - "documentation": "http://www.htslib.org/doc/samtools.html", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "identifier": "biotools:samtools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2573" - }, - { - "edam": "http://edamontology.org/format_2572" - }, - { - "edam": "http://edamontology.org/format_3462" - } - ] - } - } - ] - ], - "output": { - "readgroup": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_readgroups.txt": { - "type": "file", - "description": "Text file containing read group (@RG) lines from SAM header\n", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3462" - } - ] - } - } - ] - ], - "programs": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_programs.txt": { - "type": "file", - "description": "Text file containing program (@PG) lines from SAM header\n", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3462" - } - ] - } - } - ] - ], - "sequences": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_sequences.txt": { - "type": "file", - "description": "Text file containing sequence (@SQ) lines from SAM header\n", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3462" - } - ] - } - } - ] - ], - "versions_samtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "samtools": { - "type": "string", - "description": "The tool name" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "samtools": { - "type": "string", - "description": "The tool name" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@matthdsm", - "@prototaxites" - ], - "maintainers": [ - "@matthdsm", - "@prototaxites" - ] - } - }, - { - "name": "samtools_stats", - "path": "modules/nf-core/samtools/stats/meta.yml", - "type": "module", - "meta": { - "name": "samtools_stats", - "description": "Produces comprehensive statistics from SAM/BAM/CRAM file", - "keywords": [ - "statistics", - "counts", - "bam", - "sam", - "cram" - ], - "tools": [ - { - "samtools": { - "description": "SAMtools is a set of utilities for interacting with and post-processing\nshort DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.\nThese files are generated as output by short read aligners like BWA.\n", - "homepage": "http://www.htslib.org/", - "documentation": "http://www.htslib.org/doc/samtools.html", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "identifier": "biotools:samtools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM file from alignment", - "pattern": "*.{bam,cram}", - "ontologies": [] - } - }, - { - "input_index": { - "type": "file", - "description": "BAI/CRAI file from alignment", - "pattern": "*.{bai,crai}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference file the CRAM was created with (optional)", - "pattern": "*.{fasta,fa,fna}", - "ontologies": [] - } + "name": "bam_markduplicates_picard", + "path": "subworkflows/nf-core/bam_markduplicates_picard/meta.yml", + "type": "subworkflow", + "meta": { + "name": "bam_markduplicates_picard", + "description": "Picard MarkDuplicates, index BAM file and run samtools stats, flagstat and idxstats", + "keywords": ["markduplicates", "bam", "sam", "cram"], + "components": [ + "picard/markduplicates", + "samtools/index", + "samtools/stats", + "samtools/idxstats", + "samtools/flagstat", + "bam_stats_samtools" + ], + "input": [ + { + "ch_reads": { + "description": "Sequence reads in BAM/CRAM/SAM format\nStructure: [ val(meta), path(reads) ]\n" + } + }, + { + "ch_fasta_fai": { + "description": "Reference genome fasta file required for CRAM input\nStructure: [ path(fasta), path(fai) ]\n" + } + } + ], + "output": [ + { + "bam": { + "description": "processed BAM/SAM file\nStructure: [ val(meta), path(bam) ]\n" + } + }, + { + "bai": { + "description": "BAM/SAM samtools index\nStructure: [ val(meta), path(bai) ]\n" + } + }, + { + "cram": { + "description": "processed CRAM file\nStructure: [ val(meta), path(cram) ]\n" + } + }, + { + "crai": { + "description": "CRAM samtools index\nStructure: [ val(meta), path(crai) ]\n" + } + }, + { + "csi": { + "description": "CSI samtools index\nStructure: [ val(meta), path(csi) ]\n" + } + }, + { + "stats": { + "description": "File containing samtools stats output\nStructure: [ val(meta), path(stats) ]\n" + } + }, + { + "flagstat": { + "description": "File containing samtools flagstat output\nStructure: [ val(meta), path(flagstat) ]\n" + } + }, + { + "idxstats": { + "description": "File containing samtools idxstats output\nStructure: [ val(meta), path(idxstats) ]\n" + } + }, + { + "per_sample_mqc_bundle": { + "description": "Per-sample MultiQC-feeding outputs (stats, flagstat, idxstats, metrics) joined on meta.\nStructure: [ val(meta), list(files) ]\n" + } + }, + { + "versions": { + "description": "Files containing software versions\nStructure: [ path(versions.yml) ]\n" + } + } + ], + "authors": ["@dmarron", "@drpatelh"], + "maintainers": ["@dmarron", "@drpatelh"] }, - 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"pattern": "*.{txt,list}", - "ontologies": [] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + "name": "bam_methyldackel", + "path": "subworkflows/nf-core/bam_methyldackel/meta.yml", + "type": "subworkflow", + "meta": { + "name": "bam_methyldackel", + "description": "Performs methylation quantification based on negative readout of C to T conversion of 3-letter genome alignments using Methyldackel.", + "keywords": ["3-letter genome", "methylation", "5mC", "methylseq", "bisulphite", "bisulfite", "bam"], + "components": ["methyldackel/extract", "methyldackel/mbias"], + "input": [ + { + "ch_bam": { + "type": "file", + "description": "BAM alignment files\nStructure: [ val(meta), path(bam) ]\n", + "pattern": "*.bam" + } + }, + { + "ch_bai": { + "type": "file", + "description": "BAM index files\nStructure: [ val(meta), path(bai) ]\n", + "pattern": "*.bai" + } + }, + { + "ch_fasta": { + "type": "file", + "description": "Structure: [ val(meta), path(fasta) ]\n", + "pattern": "*.{fa,fa.gz}" + } + }, + { + "ch_fasta_index": { + "type": "file", + "description": "Structure: [ val(meta), path(fasta index) ]\n" + } + } + ], + "output": [ + { + "methydackel_extract_bedgraph": { + "type": "file", + "description": "bedGraph file, containing per-base methylation metrics\nStructure: [ val(meta), path(bedgraph) ]\n", + "pattern": "*.bedGraph" + } + }, + { + "methydackel_extract_methylkit": { + "type": "file", + "description": "methylKit file, containing per-base methylation metrics\nStructure: [ val(meta), path(methylKit) ]\n", + "pattern": "*.methylKit" + } + }, + { + "methydackel_mbias": { + "type": "file", + "description": "Text file containing methylation bias\nStructure: [ val(meta), path(mbias) ]\n", + "pattern": "*.{txt}" + } + } + ], + "authors": ["@eduard-watchmaker"], + "maintainers": ["@eduard-watchmaker"] }, - { - "bed": { - "type": "file", - "description": "Optional BED file for filtering alignments by genomic region (-L)", - "pattern": "*.{bed}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3003" - } - ] - } - } - ], - { - "index_format": { - "type": "string", - "description": "Index format, used together with ext.args = '--write-index'", - "pattern": "bai|csi|crai" - } - } - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.bam": { - "type": "file", - "description": "optional filtered/converted BAM file", - "pattern": "*.{bam}", - "ontologies": [] - } - } - ] - ], - "cram": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.cram": { - "type": "file", - "description": "optional filtered/converted CRAM file", - "pattern": "*.{cram}", - "ontologies": [] - } - } - ] - ], - "sam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.sam": { - "type": "file", - "description": "optional filtered/converted SAM file", - "pattern": "*.{sam}", - "ontologies": [] - } - } - ] - ], - "bai": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.${file_type}.bai": { - "type": "file", - "description": "optional BAM file index", - "pattern": "*.{bai}", - "ontologies": [] - } - } - ] - ], - "csi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.${file_type}.csi": { - "type": "file", - "description": "optional tabix BAM file index", - "pattern": "*.{csi}", - "ontologies": [] - } - } - ] - ], - "crai": [ - 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"@priyanka-surana", - "@matthdsm" - ] - }, - "pipelines": [ - { - "name": "alleleexpression", - "version": "dev" - }, - { - "name": "bamtofastq", - "version": "2.2.1" - }, - { - "name": "circdna", - "version": "1.1.0" - }, - { - "name": "circrna", - "version": "dev" - }, - { - "name": "createpanelrefs", - "version": "dev" - }, - { - "name": "cutandrun", - "version": "3.2.2" - }, - { - "name": "hgtseq", - "version": "1.1.0" - }, - { - "name": "hicar", - "version": "1.0.0" - }, - { - "name": "hlatyping", - "version": "2.2.0" - }, - { - "name": "phaseimpute", - "version": "1.1.0" - }, - { - "name": "radseq", - "version": "dev" - }, - { - "name": "raredisease", - "version": "3.0.0" - }, - { - "name": "rnadnavar", - "version": "dev" - }, - { - "name": "rnaseq", - "version": "3.26.0" - }, - { - "name": "sammyseq", - "version": "dev" }, { - "name": "sarek", - "version": "3.8.1" - }, - { - "name": "scnanoseq", - "version": "1.2.2" + "name": "bam_ngscheckmate", + "path": "subworkflows/nf-core/bam_ngscheckmate/meta.yml", + "type": "subworkflow", + "meta": { + "name": "bam_ngscheckmate", + "description": "Take a set of bam files and run NGSCheckMate to determine whether samples match with each other, using a set of SNPs.", + "keywords": ["ngscheckmate", "qc", "bam", "snp"], + "components": ["bcftools/mpileup", "ngscheckmate/ncm"], + "input": [ + { + "meta1": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM files for each sample", + "pattern": "*.{bam}" + } + }, + { + "meta2": { + "type": "map", + "description": "Groovy Map containing bed file information\ne.g. [ id:'sarscov2' ]\n" + } + }, + { + "snp_bed": { + "type": "file", + "description": "BED file containing the SNPs to analyse. NGSCheckMate provides some default ones for hg19/hg38.", + "pattern": "*.{bed}" + } + }, + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference genome meta information\ne.g. [ id:'sarscov2' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "fasta file for the genome", + "pattern": "*.{fasta}" + } + }, + { + "fai": { + "type": "file", + "description": "fasta file index for the genome", + "pattern": "*.{fai}" + } + } + ], + "output": [ + { + "pdf": { + "type": "file", + "description": "A pdf containing a dendrogram showing how the samples match up", + "pattern": "*.{pdf}" + } + }, + { + "corr_matrix": { + "type": "file", + "description": "A text file containing the correlation matrix between each sample", + "pattern": "*corr_matrix.txt" + } + }, + { + "matched": { + "type": "file", + "description": "A txt file containing only the samples that match with each other", + "pattern": "*matched.txt" + } + }, + { + "all": { + "type": "file", + "description": "A txt file containing all the sample comparisons, whether they match or not", + "pattern": "*all.txt" + } + }, + { + "vcf": { + "type": "file", + "description": "vcf files for each sample giving the SNP calls", + "pattern": "*.vcf" + } + }, + { + "versions": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ], + "authors": ["@SPPearce"], + "maintainers": ["@SPPearce"] + }, + "pipelines": [ + { + "name": "sarek", + "version": "3.8.1" + } + ] }, { - "name": "ssds", - "version": "dev" + "name": "bam_qc_picard", + "path": "subworkflows/nf-core/bam_qc_picard/meta.yml", + "type": "subworkflow", + "meta": { + "name": "bam_qc_picard", + "description": "Produces comprehensive statistics from BAM file", + "keywords": ["statistics", "counts", "hs_metrics", "wgs_metrics", "bam", "sam", "cram"], + "components": ["picard/collectmultiplemetrics", "picard/collectwgsmetrics", "picard/collecthsmetrics"], + "input": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + }, + { + "bai": { + "type": "file", + "description": "BAM/CRAM/SAM file index", + "pattern": "*.{bai,crai,sai}" + } + }, + { + "bait_intervals": { + "type": "optional file", + "description": "An interval list or bed file that contains the locations of the baits used.", + "pattern": "baits.{interval_list,bed,bed.gz}" + } + }, + { + "target_intervals": { + "type": "optional file", + "description": "An interval list or bed file that contains the locations of the targets.", + "pattern": "targets.{interval_list,bed,bed.gz}" + } + }, + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "optional file", + "description": "Reference fasta file", + "pattern": "*.{fasta,fa,fna}" + } + }, + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta_fai": { + "type": "optional file", + "description": "Reference fasta file index", + "pattern": "*.{fasta,fa,fna}.fai" + } + }, + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta_dict": { + "type": "optional file", + "description": "Reference fasta sequence dictionary", + "pattern": "*.{dict}" + } + } + ], + "output": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "coverage_metrics": { + "type": "file", + "description": "Alignment metrics files generated by picard CollectHsMetrics or CollectWgsMetrics", + "pattern": "*_metrics.txt" + } + }, + { + "multiple_metrics": { + "type": "file", + "description": "Alignment metrics files generated by picard CollectMultipleMetrics", + "pattern": "*_{metrics}" + } + }, + { + "versions": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ], + "authors": ["@matthdsm"], + "maintainers": ["@matthdsm"] + } }, { - "name": "taxprofiler", - "version": "2.0.0" - }, - { - "name": "viralrecon", - "version": "3.0.0" - } - ] - }, - { - "name": "savana_classify", - "path": "modules/nf-core/savana/classify/meta.yml", - "type": "module", - "meta": { - "name": "savana_classify", - "description": "Classify structural variants using SAVANA", - "keywords": [ - "classify", - "structural variants", - "somatic", - "germline", - "genomics" - ], - "tools": [ - { - "savana": { - "description": "SAVANA: a somatic structural variant caller for long-read data.", - "homepage": "https://github.com/cortes-ciriano-lab/savana", - "documentation": "https://github.com/cortes-ciriano-lab/savana", - "tool_dev_url": "https://github.com/cortes-ciriano-lab/savana", - "doi": "10.1038/s41592-025-02708-0", - "licence": [ - "Apache-2.0" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "vcf": { - "type": "file", - "description": "Input VCF file", - "pattern": "*{.vcf,vcf.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - }, - { - "edam": "http://edamontology.org/format_3615" - } - ] - } - } - ] - ], - "output": { - "classified_vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Sample information" - } - }, - { - "${prefix}.classified.vcf": { - "type": "file", - "description": "VCF containing information about variant classification in the INFO field", - "pattern": "*.classified.vcf", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - } - ] - } - } - ] - ], - "somatic_vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Sample information" - } - }, - { - "${prefix}.classified.somatic.vcf": { - "type": "file", - "description": "VCF containing variants classified as somatic", - "pattern": "*.classified.somatic.vcf", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - } - ] - } - } - ] - ], - "germline_vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Sample information" - } - }, - { - "${prefix}.classified.germline.vcf": { - "type": "file", - "description": "VCF containing variants classified as germline", - "pattern": "*.classified.germline.vcf", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - } - ] - } - } - ] - ], - "somatic_bedpe": [ - [ - { - "meta": { - "type": "map", - "description": "Sample information" - } - }, - { - "${prefix}.classified.somatic.bedpe": { - "type": "file", - "description": "Variants classified as somatic in BEDPE format", - "pattern": "*.classified.somatic.bedpe", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3003" - } - ] - } - } - ] - ], - "legacy_vcfs": [ - [ - { - "meta": { - "type": "map", - "description": "Sample information" - } - }, - { - "${prefix}.classified.{strict,lenient}.vcf": { - "type": "file", - "description": "Legacy strict/lenient VCFs", - "pattern": "*.classified.{strict,lenient}.vcf", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - } - ] - } - } - ] - ], - "versions_savana": [ - [ - { - "${task.process}": { - "type": "string", - "description": "Process name" - } - }, - { - "savana": { - "type": "string", - "description": "Name of the tool" - } - }, - { - "python -c \"import importlib.metadata as m; print(m.version('savana'))\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "Process name" - } - }, - { - "savana": { - "type": "string", - "description": "Name of the tool" - } - }, - { - "python -c \"import importlib.metadata as m; print(m.version('savana'))\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@manascripts" - ], - "maintainers": [ - "@manascripts" - ] - } - }, - { - "name": "sawfish_discover", - "path": "modules/nf-core/sawfish/discover/meta.yml", - "type": "module", - "meta": { - "name": "sawfish_discover", - "description": "SV candidate discovery from PacBio HiFi data", - "keywords": [ - "sawfish", - "structural-variant calling", - "CNV calling", - "Pacbio" - ], - "tools": [ - { - "sawfish": { - "description": "Joint structural variant and copy number variant caller for HiFi sequencing data", - "homepage": "https://github.com/PacificBiosciences/sawfish", - "documentation": "https://github.com/PacificBiosciences/sawfish/tree/main/docs", - "doi": "10.1093/bioinformatics/btaf136", - "licence": [ - "Pacific Biosciences Software License (https://github.com/PacificBiosciences/sawfish/blob/main/LICENSE.md)" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM/CRAM file", - "pattern": "*.{bam,cram}", - "ontologies": [] - } - }, - { - "bai": { - "type": "file", - "description": "Index of BAM/CAM file", - "pattern": "*.{bai,crai}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'fasta' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome in FASTA format", - "pattern": "*.{fasta,fa}", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing additional information\ne.g. [ id:'cn' ]\n" - } - }, - { - "expected_cn_bed": { - "type": "file", - "description": "Expected copy number BED file", - "pattern": "*.bed", - "ontologies": [] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing additional information\ne.g. [ id:'maf' ]\n" - } - }, - { - "maf_vcf": { - "type": "file", - "description": "Variant file used to generate minor allele frequency track for this sample,\nin VCF or BCF format.\n", - "pattern": "*.{vcf.gz,bcf.gz}", - "ontologies": [] - } - } - ], - [ - { - "meta5": { - "type": "map", - "description": "Groovy Map containing additional information\ne.g. [ id:'cnv' ]\n" - } - }, - { - "cnv_exclude_regions_bed": { - "type": "file", - "description": "BED file containing regions to exclude from CNV calling", - "pattern": "*.bed", - "ontologies": [] - } - } - ] - ], - "output": { - "assembly_regions": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "${prefix}/assembly.regions.bed": { - "type": "file", - "description": "Assembly regions BED file", - "pattern": "*.bed", - "ontologies": [] - } - } - ] - ], - "candidate_sv_bcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "${prefix}/candidate.sv.bcf": { - "type": "file", - "description": "Candidate SV BCF file", - "pattern": "*.bcf", - "ontologies": [] - } - } - ] - ], - "candidate_sv_bcf_csi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "${prefix}/candidate.sv.bcf.csi": { - "type": "file", - "description": "Candidate SV BCF CSI file", - "pattern": "*.csi", - "ontologies": [] - } - } - ] - ], - "contig_alignment_bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "${prefix}/contig.alignment.bam": { - "type": "file", - "description": "Contig alignment BAM file", - "pattern": "*.bam", - "ontologies": [] - } - } - ] - ], - "contig_alignment_bam_csi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "${prefix}/contig.alignment.bam.csi": { - "type": "file", - "description": "Contig alignment BAM CSI file", - "pattern": "*.csi", - "ontologies": [] - } - } - ] - ], - "copynum_bedgraph": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "${prefix}/copynum.bedgraph": { - "type": "file", - "description": "Copy number BEDGraph file", - "pattern": "*.bedgraph", - "optional": true, - "ontologies": [] - } - } - ] - ], - "copynum_mpack": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "${prefix}/copynum.mpack": { - "type": "file", - "description": "Copy number mpack file", - "pattern": "*.mpack", - "optional": true, - "ontologies": [] - } - } - ] - ], - "debug_breakpoint_clusters": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "${prefix}/debug.breakpoint_clusters.bed": { - "type": "file", - "description": "Debug breakpoint clusters BED file", - "pattern": "*.bed", - "ontologies": [] - } - } - ] - ], - "debug_cluster_refinement": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "${prefix}/debug.cluster.refinement.txt": { - "type": "file", - "description": "Debug cluster refinement text file", - "pattern": "*.txt", - "ontologies": [] - } - } - ] - ], - "discover_settings": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "${prefix}/discover.settings.json": { - "type": "file", - "description": "Discover settings JSON file", - "pattern": "*.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "genome_gclevels": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "${prefix}/genome.gclevels.mpack": { - "type": "file", - "description": "Genome GC levels mpack file", - "pattern": "*.mpack", - "optional": true, - "ontologies": [] - } - } - ] - ], - "max_depth": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "${prefix}/max.depth.bed": { - "type": "file", - "description": "Max depth BED file", - "pattern": "*.bed", - "ontologies": [] - } - } - ] - ], - "run_stats": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "${prefix}/run.stats.json": { - "type": "file", - "description": "Run statistics JSON file", - "pattern": "*.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "sample_gcbias": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "${prefix}/sample.gcbias.mpack": { - "type": "file", - "description": "Sample GC bias mpack file", - "pattern": "*.mpack", - "optional": true, - "ontologies": [] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "${prefix}/sawfish.log": { - "type": "file", - "description": "Sawfish log file", - "pattern": "*.log", - "ontologies": [] - } - } - ] - ], - "depth_mpack": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "${prefix}/depth.mpack": { - "type": "file", - "description": "Depth mpack file", - "pattern": "*.mpack", - "ontologies": [] - } - } - ] - ], - "maf_mpack": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "${prefix}/maf.mpack": { - "type": "file", - "description": "MAF mpack file", - "pattern": "*.mpack", - "optional": true, - "ontologies": [] - } - } - ] - ], - "expected_cn": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "${prefix}/expected.copy.number.bed": { - "type": "file", - "description": "Expected copy number BED file", - "pattern": "*.bed", - "optional": true, - "ontologies": [] - } - } - ] - ], - "discover_dir": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "${prefix}": { - "type": "directory", - "description": "Directory containing all discover output files", - "ontologies": [] - } - } - ] - ], - "versions_sawfish": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "sawfish": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "sawfish --version | sed 's/.* //g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "sawfish": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "sawfish --version | sed 's/.* //g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@padraicc" - ], - "maintainers": [ - "@padraicc" - ] - } - }, - { - "name": "sawfish_jointcall", - "path": "modules/nf-core/sawfish/jointcall/meta.yml", - "type": "module", - "meta": { - "name": "sawfish_jointcall", - "description": "Joint calling of structural variants from multiple samples using Sawfish", - "keywords": [ - "sawfish", - "structural-variant calling", - "joint calling", - "CNV calling", - "Pacbio" - ], - "tools": [ - { - "sawfish": { - "description": "Joint structural variant and copy number variant caller for HiFi sequencing data", - "homepage": "https://github.com/PacificBiosciences/sawfish", - "documentation": "https://github.com/PacificBiosciences/sawfish/tree/main/docs", - "doi": "10.1093/bioinformatics/btaf136", - "licence": [ - "Pacific Biosciences Software License (https://github.com/PacificBiosciences/sawfish/blob/main/LICENSE.md)" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "sample_dirs": { - "type": "directory", - "description": "Sample directories from sawfish discover step", - "pattern": "*_discover_dir/", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'fasta' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome in FASTA format", - "pattern": "*.{fasta,fa}", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "bams": { - "type": "file", - "description": "Sorted BAM/CRAM file", - "pattern": "*.{bam,cram}", - "ontologies": [] - } - }, - { - "bais": { - "type": "file", - "description": "Index of BAM/CAM file", - "pattern": "*.{bai,crai}", - "ontologies": [] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing additional information\ne.g. [ id:'csv' ]\n" - } + "name": "bam_qc_rnaseq", + "path": "subworkflows/nf-core/bam_qc_rnaseq/meta.yml", + "type": "subworkflow", + "meta": { + "name": "bam_qc_rnaseq", + "description": "Run post-alignment QC tools on RNA-seq BAM files including library complexity\nestimation (Preseq), biotype QC (featureCounts), RNA-seq-specific QC metrics\n(Qualimap), duplicate rate analysis (dupRadar), and comprehensive RSeQC analysis.\n", + "keywords": [ + "rnaseq", + "bam", + "qc", + "quality_control", + "preseq", + "qualimap", + "dupradar", + "rseqc", + "featurecounts", + "biotype" + ], + "components": [ + "preseq/lcextrap", + "qualimap/rnaseq", + "dupradar", + "subread/featurecounts", + "custom/multiqccustombiotype", + "samtools/sort", + "bam_rseqc" + ], + "input": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false, strandedness:'reverse' ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "Coordinate-sorted BAM file aligned to the genome", + "pattern": "*.{bam}" + } + }, + { + "bai": { + "type": "file", + "description": "Index for the genome-aligned BAM file", + "pattern": "*.{bai}" + } + }, + { + "gtf": { + "type": "file", + "description": "GTF annotation file", + "pattern": "*.{gtf}" + } + }, + { + "gene_bed": { + "type": "file", + "description": "BED12 file for the reference gene model", + "pattern": "*.{bed}" + } + }, + { + "fasta_fai": { + "type": "file", + "description": "Tuple of FASTA and FAI files for samtools sort\n[ val(meta), path(fasta), path(fai) ]\n" + } + }, + { + "biotypes_header": { + "type": "file", + "description": "Header file for biotype counts MultiQC section", + "pattern": "*.{txt}" + } + }, + { + "tools": { + "type": "list", + "description": "List of QC tools to run. Top-level tools: 'preseq', 'biotype_qc', 'qualimap',\n'dupradar'. RSeQC modules use an 'rseqc_' prefix: 'rseqc_bam_stat',\n'rseqc_inner_distance', 'rseqc_infer_experiment', 'rseqc_junction_annotation',\n'rseqc_junction_saturation', 'rseqc_read_distribution', 'rseqc_read_duplication',\n'rseqc_tin'. Pass an empty list to skip all.\n" + } + }, + { + "biotype": { + "type": "string", + "description": "GTF attribute for biotype grouping (e.g. \"gene_type\" or \"gene_biotype\").\nOnly used when 'biotype_qc' is in tools. Set to empty string to skip biotype QC.\n" + } + } + ], + "output": [ + { + "multiqc_files": { + "type": "file", + "description": "Collected MultiQC-compatible output files from all enabled tools" + } + }, + { + "preseq_lc_extrap": { + "type": "file", + "description": "Preseq library complexity extrapolation curve", + "pattern": "*.lc_extrap.txt" + } + }, + { + "preseq_log": { + "type": "file", + "description": "Preseq log file", + "pattern": "*.log" + } + }, + { + "featurecounts_counts": { + "type": "file", + "description": "featureCounts count matrix", + "pattern": "*.featureCounts.txt" + } + }, + { + "featurecounts_summary": { + "type": "file", + "description": "featureCounts summary statistics", + "pattern": "*.featureCounts.txt.summary" + } + }, + { + "biotype_tsv": { + "type": "file", + "description": "Biotype counts formatted for MultiQC bargraph", + "pattern": "*biotype_counts_mqc.tsv" + } + }, + { + "biotype_rrna": { + "type": "file", + "description": "rRNA percentage for MultiQC general stats", + "pattern": "*biotype_counts_rrna_mqc.tsv" + } + }, + { + "qualimap_results": { + "type": "directory", + "description": "Qualimap RNA-seq QC results directory" + } + }, + { + "dupradar_multiqc": { + "type": "file", + "description": "dupRadar MultiQC-compatible output", + "pattern": "*_mqc.txt" + } + }, + { + "inferexperiment_txt": { + "type": "file", + "description": "RSeQC infer_experiment results (for strandedness detection)", + "pattern": "*.infer_experiment.txt" + } + }, + { + "bamstat_txt": { + "type": "file", + "description": "RSeQC bam_stat report", + "pattern": "*.bam_stat.txt" + } + }, + { + "readdistribution_txt": { + "type": "file", + "description": "RSeQC read_distribution report", + "pattern": "*.read_distribution.txt" + } + }, + { + "tin_txt": { + "type": "file", + "description": "RSeQC TIN results summary", + "pattern": "*.txt" + } + }, + { + "per_sample_mqc_bundle": { + "type": "tuple", + "description": "Per-sample MultiQC-feeding outputs (Preseq, biotype TSV, Qualimap,\ndupRadar, and RSeQC bamstat/inferexperiment/innerdistance_freq/\njunctionannotation_log/junctionsaturation_rscript/readdistribution/\nreadduplication_pos/tin) joined on meta.\nStructure: [ val(meta), list(files) ]\n" + } + } + ], + "authors": ["@pinin4fjords"], + "maintainers": ["@pinin4fjords"] }, - { - "sample_csv": { - "type": "file", - "description": "CSV file listing sample sawfish discover output and the sample bam file used with sawfish discover", - "ontologies": [] - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "*/*_genotyped.sv.vcf.gz": { - "type": "file", - "description": "Joint called variants in compressed VCF format", - "pattern": "*_genotyped.sv.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "*/*_genotyped.sv.vcf.gz.tbi": { - "type": "file", - "description": "Tabix index for the joint called VCF file", - "pattern": "*_genotyped.sv.vcf.gz.tbi", - "ontologies": [] - } - } - ] - ], - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "*/contig.alignment.bam": { - "type": "file", - "description": "Contig alignment BAM file", - "pattern": "*.bam", - "ontologies": [] - } - } - ] - ], - "bam_index": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "*/contig.alignment.bam.csi": { - "type": "file", - "description": "Contig alignment BAM index file", - "pattern": "*.csi", - "ontologies": [] - } - } - ] - ], - "stats": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "*/run.stats.json": { - "type": "file", - "description": "Run statistics JSON file", - "pattern": "*.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "depth_bw": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "*/samples/*/depth.bw": { - "type": "file", - "description": "Sample depth BigWig file", - "pattern": "*.bw", - "ontologies": [] - } - } - ] - ], - "copynum_bedgraph": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "*/samples/*/copynum.bedgraph": { - "type": "file", - "description": "Sample copy number BEDGraph file", - "pattern": "*.bedgraph", - "ontologies": [] - } - } - ] - ], - "gc_bias_corrected_depth_bw": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "*/samples/*/gc_bias_corrected_depth.bw": { - "type": "file", - "description": "Sample GC bias BigWig file", - "pattern": "*.bw", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3006" - } - ] - } - } - ] - ], - "copynum_summary": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "*/samples/*/copynum.summary.json": { - "type": "file", - "description": "Sample copy number summary JSON file", - "pattern": "*.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "maf_bw": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "*/samples/*/maf.bw": { - "type": "file", - "description": "Sample SNV MAF BigWig file", - "pattern": "*.bw", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3006" - } - ] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "*/sawfish.log": { - "type": "file", - "description": "Sawfish log file", - "pattern": "*.log", - "ontologies": [] - } - } - ] - ], - "versions_sawfish": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "sawfish": { - "type": "string", - "description": "The tool name" - } - }, - { - "sawfish --version | sed \"s/.* //g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "sawfish": { - "type": "string", - "description": "The tool name" - } - }, - { - "sawfish --version | sed \"s/.* //g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "rnaseq", + "version": "3.26.0" + } ] - ] - }, - "authors": [ - "@padraicc" - ], - "maintainers": [ - "@padraicc" - ] - } - }, - { - "name": "scanpy_filter", - "path": "modules/nf-core/scanpy/filter/meta.yml", - "type": "module", - "meta": { - "name": "scanpy_filter", - "description": "Filter cells and genes in single-cell RNA-seq data using Scanpy", - "keywords": [ - "filter", - "quality-control", - "scanpy", - "single-cell", - "preprocessing" - ], - "tools": [ - { - "scanpy": { - "description": "Single-Cell Analysis in Python", - "homepage": "https://scanpy.readthedocs.io", - "documentation": "https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pp.filter_cells.html", - "tool_dev_url": "https://github.com/scverse/scanpy", - "doi": "10.1186/s13059-017-1382-0", - "licence": [ - "BSD-3-Clause" - ] - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "h5ad": { - "type": "file", - "description": "AnnData object in h5ad format", - "pattern": "*.{h5ad}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3590" - } - ] - } - } - ], - [ - { - "min_genes": { - "type": "integer", - "description": "Minimum number of genes expressed per cell" - } - } - ], - [ - { - "min_cells": { - "type": "integer", - "description": "Minimum number of cells expressing each gene" - } - } - ], - [ - { - "min_counts_gene": { - "type": "integer", - "description": "Minimum number of counts per gene" - } - } - ], - [ - { - "min_counts_cell": { - "type": "integer", - "description": "Minimum number of counts per cell" - } - } - ], - [ - { - "max_mito_percentage": { - "type": "integer", - "description": "Maximum percentage of mitochondrial genes per cell" - } - } - ], - [ - { - "symbol_col": { - "type": "string", - "description": "Column name of the gene symbols in the `var` of the AnnData object. Use `index` if the gene symbols are the row names." - } - } - ] - ], - "output": { - "h5ad": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.h5ad": { - "type": "file", - "description": "Filtered AnnData object", - "pattern": "*.h5ad", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3590" - } - ] - } - } - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - } - ] - }, - "authors": [ - "@nictru" - ], - "maintainers": [ - "@nictru" - ] - } - }, - { - "name": "scanpy_hashsolo", - "path": "modules/nf-core/scanpy/hashsolo/meta.yml", - "type": "module", - "meta": { - "name": "SCANPY_HASHSOLO", - "description": "Probabilistic demultiplexing of cell hashing data", - "keywords": [ - "anndata", - "single-cell", - "hashing", - "demultiplexing", - "scanpy" - ], - "tools": [ - { - "scanpy": { - "description": "Single-cell analysis in Python. Scales to >100M cells.", - "homepage": "https://github.com/scverse/scanpy", - "documentation": "https://scanpy.readthedocs.io/en/stable/generated/scanpy.external.pp.hashsolo.html", - "tool_dev_url": "https://github.com/scverse/scanpy", - "doi": "10.1186/s13059-017-1382-0", - "licence": [ - "BSD-3" - ], - "identifier": "biotools:scanpy" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "data": { - "type": "file", - "description": "A directory in 10x Genomics format containing `matrix.mtx.gz`, `features.tsv.gz`, `barcodes.tsv.gz` (hashing count matrix), or an AnnData (`.h5ad`) file with hashing counts stored in `.obs`.\n", - "ontologies": [ - { - "edam": "http://edamontology.org/data_3917" - } - ] - } + }, + { + "name": "bam_rseqc", + "path": "subworkflows/nf-core/bam_rseqc/meta.yml", + "type": "subworkflow", + "meta": { + "name": "bam_rseqc", + "description": "Subworkflow to run multiple commands in the RSeqC package", + "keywords": [ + "rnaseq", + "experiment", + "inferexperiment", + "bamstat", + "innerdistance", + "junctionannotation", + "junctionsaturation", + "readdistribution", + "readduplication", + "tin" + ], + "components": [ + "rseqc", + "rseqc/tin", + "rseqc/readduplication", + "rseqc/readdistribution", + "rseqc/junctionsaturation", + "rseqc/junctionannotation", + "rseqc/innerdistance", + "rseqc/inferexperiment", + "rseqc/bamstat" + ], + "input": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file to calculate statistics", + "pattern": "*.{bam}" + } + }, + { + "bai": { + "type": "file", + "description": "Index for input BAM file", + "pattern": "*.{bai}" + } + }, + { + "bed": { + "type": "file", + "description": "BED file for the reference gene model", + "pattern": "*.{bed}" + } + }, + { + "rseqc_modules": { + "type": "list", + "description": "List of rseqc modules to run\ne.g. [ 'bam_stat', 'infer_experiment' ]\n" + } + } + ], + "output": [ + { + "bamstat_txt": { + "type": "file", + "description": "bam statistics report", + "pattern": "*.bam_stat.txt" + } + }, + { + "innerdistance_all": { + "type": "file", + "description": "All the output files from RSEQC_INNERDISTANCE", + "pattern": "*.{txt,pdf,R}" + } + }, + { + "innerdistance_distance": { + "type": "file", + "description": "the inner distances", + "pattern": "*.inner_distance.txt" + } + }, + { + "innerdistance_freq": { + "type": "file", + "description": "frequencies of different insert sizes", + "pattern": "*.inner_distance_freq.txt" + } + }, + { + "innerdistance_mean": { + "type": "file", + "description": "mean/median values of inner distances", + "pattern": "*.inner_distance_mean.txt" + } + }, + { + "innerdistance_pdf": { + "type": "file", + "description": "distribution plot of inner distances", + "pattern": "*.inner_distance_plot.pdf" + } + }, + { + "innerdistance_rscript": { + "type": "file", + "description": "script to reproduce the plot", + "pattern": "*.inner_distance_plot.R" + } + }, + { + "inferexperiment_txt": { + "type": "file", + "description": "infer_experiment results report", + "pattern": "*.infer_experiment.txt" + } + }, + { + "junctionannotation_all": { + "type": "file", + "description": "All the output files from RSEQC_JUNCTIONANNOTATION", + "pattern": "*.{bed,xls,pdf,R,log}" + } + }, + { + "junctionannotation_bed": { + "type": "file", + "description": "bed file of annotated junctions", + "pattern": "*.junction.bed" + } + }, + { + "junctionannotation_interact_bed": { + "type": "file", + "description": "Interact bed file", + "pattern": "*.Interact.bed" + } + }, + { + "junctionannotation_xls": { + "type": "file", + "description": "xls file with junction information", + "pattern": "*.xls" + } + }, + { + "junctionannotation_pdf": { + "type": "file", + "description": "junction plot", + "pattern": "*.junction.pdf" + } + }, + { + "junctionannotation_events_pdf": { + "type": "file", + "description": "events plot", + "pattern": "*.events.pdf" + } + }, + { + "junctionannotation_rscript": { + "type": "file", + "description": "Rscript to reproduce the plots", + "pattern": "*.r" + } + }, + { + "junctionannotation_log": { + "type": "file", + "description": "Log file generated by tool", + "pattern": "*.log" + } + }, + { + "junctionsaturation_all": { + "type": "file", + "description": "All the output files from RSEQC_JUNCTIONSATURATION", + "pattern": "*.{pdf,R}" + } + }, + { + "junctionsaturation_pdf": { + "type": "file", + "description": "Junction saturation report", + "pattern": "*.pdf" + } + }, + { + "junctionsaturation_rscript": { + "type": "file", + "description": "Junction saturation R-script", + "pattern": "*.r" + } + }, + { + "readdistribution_txt": { + "type": "file", + "description": "the read distribution report", + "pattern": "*.read_distribution.txt" + } + }, + { + "readduplication_all": { + "type": "file", + "description": "All the output files from RSEQC_READDUPLICATION", + "pattern": "*.{xls,pdf,R}" + } + }, + { + "readduplication_seq_xls": { + "type": "file", + "description": "Read duplication rate determined from mapping position of read", + "pattern": "*seq.DupRate.xls" + } + }, + { + "readduplication_pos_xls": { + "type": "file", + "description": "Read duplication rate determined from sequence of read", + "pattern": "*pos.DupRate.xls" + } + }, + { + "readduplication_pdf": { + "type": "file", + "description": "plot of duplication rate", + "pattern": "*.pdf" + } + }, + { + "readduplication_rscript": { + "type": "file", + "description": "script to reproduce the plot", + "pattern": "*.R" + } + }, + { + "tin_txt": { + "type": "file", + "description": "TXT file containing tin.py results summary", + "pattern": "*.txt" + } + }, + { + "versions": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ], + "authors": ["@drpatelh", "@kevinmenden"], + "maintainers": ["@drpatelh", "@kevinmenden"] }, - { - "cell_hashing_columns": { - "type": "list", - "description": "Groovy list (`['hash_1', 'hash_2']`) of `.obs` columns that contain cell hashing counts.\nCan be `[]` if the data is in 10x Genomics format, as the columns are derived from the input.\n" - } - } - ] - ], - "output": { - "assignment": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*_assignment_hashsolo.csv": { - "type": "file", - "description": "CSV file containing hashsolo assignment results\n", - "pattern": "*_assignment_hashsolo.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "h5ad": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*_hashsolo.h5ad": { - "type": "file", - "description": "Processed AnnData object containing hashsolo results\n", - "pattern": "*_hashsolo.h5ad", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3590" - } - ] - } - } - ] - ], - "params": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n", - "pattern": "*_params_hashsolo.csv" - } - }, - { - "*_params_hashsolo.csv": { - "type": "file", - "description": "CSV file containing parameters used in hashsolo analysis\n", - "pattern": "*_params_hashsolo.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } + "pipelines": [ + { + "name": "callingcards", + "version": "1.0.0" + }, + { + "name": "nascent", + "version": "2.3.0" + }, + { + "name": "rnaseq", + "version": "3.26.0" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@seohyonkim", - "@LuisHeinzlmeier" - ], - "maintainers": [ - "@seohyonkim", - "@LuisHeinzlmeier" - ] - } - }, - { - "name": "scanpy_pca", - "path": "modules/nf-core/scanpy/pca/meta.yml", - "type": "module", - "meta": { - "name": "scanpy_pca", - "description": "Perform principal component analysis (PCA) on single-cell RNA-seq data using Scanpy", - "keywords": [ - "pca", - "principal-component-analysis", - "scanpy", - "single-cell", - "dimensionality-reduction" - ], - "tools": [ - { - "scanpy": { - "description": "Single-Cell Analysis in Python", - "homepage": "https://scanpy.readthedocs.io", - "documentation": "https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pp.pca.html", - "tool_dev_url": "https://github.com/scverse/scanpy", - "doi": "10.1186/s13059-017-1382-0", - "licence": [ - "BSD-3-Clause" - ] - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } + }, + { + "name": "bam_sort_stats_samtools", + "path": "subworkflows/nf-core/bam_sort_stats_samtools/meta.yml", + "type": "subworkflow", + "meta": { + "name": "bam_sort_stats_samtools", + "description": "Sort SAM/BAM/CRAM file", + "keywords": ["sort", "bam", "sam", "cram"], + "components": [ + "samtools/sort", + "samtools/index", + "samtools/stats", + "samtools/idxstats", + "samtools/flagstat", + "bam_stats_samtools" + ], + "input": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference genome fasta file", + "pattern": "*.{fasta,fa}" + } + } + ], + "output": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "Sorted BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + }, + { + "bai": { + "type": "file", + "description": "BAM/CRAM/SAM index file", + "pattern": "*.{bai,crai,sai}" + } + }, + { + "crai": { + "type": "file", + "description": "BAM/CRAM/SAM index file", + "pattern": "*.{bai,crai,sai}" + } + }, + { + "stats": { + "type": "file", + "description": "File containing samtools stats output", + "pattern": "*.{stats}" + } + }, + { + "flagstat": { + "type": "file", + "description": "File containing samtools flagstat output", + "pattern": "*.{flagstat}" + } + }, + { + "idxstats": { + "type": "file", + "description": "File containing samtools idxstats output", + "pattern": "*.{idxstats}" + } + }, + { + "versions": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ], + "authors": ["@drpatelh", "@ewels"], + "maintainers": ["@drpatelh", "@ewels"] }, - { - "h5ad": { - "type": "file", - "description": "AnnData object in h5ad format", - "pattern": "*.{h5ad}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3590" - } - ] - } - } - ], - { - "key_added": { - "type": "string", - "description": "Key to add to obsm with PCA coordinates, usually 'X_pca'\n" - } - } - ], - "output": { - "h5ad": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.h5ad": { - "type": "file", - "description": "AnnData object with PCA coordinates added", - "pattern": "*.h5ad", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3590" - } - ] - } - } - ] - ], - "obsm": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "X_*.pkl": { - "type": "file", - "description": "Pickle file containing PCA coordinates matrix", - "pattern": "X_*.pkl", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3553" - } - ] - } - } + "pipelines": [ + { + "name": "atacseq", + "version": "2.1.2" + }, + { + "name": "chipseq", + "version": "2.1.0" + }, + { + "name": "circrna", + "version": "dev" + }, + { + "name": "cutandrun", + "version": "3.2.2" + }, + { + "name": "genomeassembler", + "version": "1.1.0" + }, + { + "name": "lncpipe", + "version": "dev" + }, + { + "name": "magmap", + "version": "1.0.0" + }, + { + "name": "metatdenovo", + "version": "1.3.0" + }, + { + "name": "methylseq", + "version": "4.2.0" + }, + { + "name": "nascent", + "version": "2.3.0" + }, + { + "name": "pacsomatic", + "version": "dev" + }, + { + "name": "phageannotator", + "version": "dev" + }, + { + "name": "riboseq", + "version": "1.2.0" + }, + { + "name": "rnadnavar", + "version": "dev" + }, + { + "name": "rnafusion", + "version": "4.1.2" + }, + { + "name": "rnaseq", + "version": "3.26.0" + }, + { + "name": "rnasplice", + "version": "1.0.4" + }, + { + "name": "rnavar", + "version": "1.2.3" + }, + { + "name": "sammyseq", + "version": "dev" + }, + { + "name": "scnanoseq", + "version": "1.2.2" + }, + { + "name": "smrnaseq", + "version": "2.4.1" + }, + { + "name": "viralrecon", + "version": "3.0.0" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@nictru" - ], - "maintainers": [ - "@nictru" - ] - } - }, - { - "name": "scanpy_scrublet", - "path": "modules/nf-core/scanpy/scrublet/meta.yml", - "type": "module", - "meta": { - "name": "scanpy_scrublet", - "description": "Detect doublets in single-cell RNA-seq data using Scrublet via Scanpy", - "keywords": [ - "scrublet", - "doublet-detection", - "scanpy", - "single-cell" - ], - "tools": [ - { - "scanpy": { - "description": "Single-Cell Analysis in Python", - "homepage": "https://scanpy.readthedocs.io", - "documentation": "https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pp.scrublet.html", - "tool_dev_url": "https://github.com/scverse/scanpy", - "doi": "10.1186/s13059-017-1382-0", - "licence": [ - "BSD-3-Clause" - ], - "identifier": "biotools:scanpy" + }, + { + "name": "bam_split_by_region", + "path": "subworkflows/nf-core/bam_split_by_region/meta.yml", + "type": "subworkflow", + "meta": { + "name": "bam_split_by_region", + "description": "Split the reads in the input bam by specified genomic region.", + "keywords": ["split", "bam", "sam", "cram", "index"], + "components": ["samtools/view", "samtools/index"], + "input": [ + { + "ch_bam": { + "description": "The input channel of this subworkflow containing:\n- meta: Groovy Map containing sample information => doesn't have a field called 'genomic_region'\n- bam: BAM/CRAM/SAM file\n- bai: Index for BAM/CRAM/SAM file\n- regions_file: A file containing the genomic regions used to separate the reads in the\n input bam. This should be a BED or TSV file containing either a single\n column of chromosome names, two columns (chromosome name and position),\n or three columns (chromosome name, start position, and end position).\nStructure: [ val(meta), path(bam), path(bai), path(regions_file) ]\n" + } + } + ], + "output": [ + { + "bam_bai": { + "description": "BAM/CRAM/SAM file, the meta contains a new 'genomic_region' field with the included regions\nStructure: [ val(meta), path(bam), path(bai) ]\n" + } + }, + { + "versions": { + "description": "Files containing software versions\nStructure: [ path(versions.yml) ]\n" + } + } + ], + "authors": ["@TCLamnidis"], + "maintainers": ["@TCLamnidis"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } + }, + { + "name": "bam_stats_mirna_mirtop", + "path": "subworkflows/nf-core/bam_stats_mirna_mirtop/meta.yml", + "type": "subworkflow", + "meta": { + "name": "bam_stats_mirna_mirtop", + "description": "mirtop is a command line tool to annotate miRNAs and isomiRs and compute general statistics using the mirGFF3 format.", + "keywords": ["miRNA", "isomirs", "bam", "stats"], + "components": ["mirtop/gff", "mirtop/counts", "mirtop/export", "mirtop/stats"], + "input": [ + { + "ch_bam": { + "type": "file", + "description": "The input channel containing the BAM/CRAM/SAM files\nStructure: [ val(meta), path(bam) ]\n", + "pattern": "*.{bam/cram/sam}" + } + }, + { + "ch_hairpin": { + "type": "file", + "description": "Input channel containing the hairpin fasta file\nStructure: [ val(meta), path(fasta) ]\n", + "pattern": "*.{fasta,fa}" + } + }, + { + "ch_gtf_species": { + "type": "file", + "description": "Input channel containing the species gtf and the name of species in miRbase format\nStructure: [ val(meta), path(gtf), val(species)]\n", + "pattern": "*.{gtf}" + } + } + ], + "output": [ + { + "rawdata_tsv": { + "type": "file", + "description": "Channel containing isomiRs compatible files\nStructure: [ val(meta), path(tsv) ]\n", + "pattern": "*.tsv" + } + }, + { + "stats_txt": { + "type": "file", + "description": "Channel containing TXT file with a table with different statistics for each type of isomiRs: total counts, average counts, total sequences.\nStructure: [ val(meta), path(txt) ]\n", + "pattern": "*.txt" + } + }, + { + "stats_log": { + "type": "file", + "description": "Channel containing log files in JSON format with the same information as stats_txt\nStructure: [ val(meta), path(log) ]\n", + "pattern": "*.log" + } + }, + { + "versions": { + "type": "file", + "description": "File containing software versions\nStructure: [ path(versions.yml) ]\n", + "pattern": "versions.yml" + } + } + ], + "authors": ["@atrigila"], + "maintainers": ["@atrigila"] }, - { - "h5ad": { - "type": "file", - "description": "AnnData object in h5ad format", - "pattern": "*.{h5ad}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3590" - } - ] - } - } - ], - { - "batch_col": { - "type": "string", - "description": "Optional column name in adata.obs containing batch information\nIf provided and contains multiple batches, will be used as batch_key parameter\n" - } - } - ], - "output": { - "h5ad": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.h5ad": { - "type": "file", - "description": "AnnData object with doublets removed", - "pattern": "*.h5ad", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3590" - } - ] - } - } - ] - ], - "predictions": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.pkl": { - "type": "file", - "description": "Pickle file containing doublet predictions", - "pattern": "*.pkl", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3553" - } - ] - } - } + "pipelines": [ + { + "name": "smrnaseq", + "version": "2.4.1" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@nictru" - ], - "maintainers": [ - "@nictru" - ] - }, - "pipelines": [ - { - "name": "scdownstream", - "version": "dev" - } - ] - }, - { - "name": "scds", - "path": "modules/nf-core/scds/meta.yml", - "type": "module", - "meta": { - "name": "scds", - "description": "Module to use scds for doublet scoring", - "keywords": [ - "doublet", - "single-cell", - "transcriptomics" - ], - "tools": [ - { - "scds": { - "description": "scds is an in-silico doublet annotation tool for single cell RNA sequencing data", - "homepage": "https://www.bioconductor.org/packages/release/bioc/html/scds.html", - "documentation": "https://www.bioconductor.org/packages/release/bioc/vignettes/scds/inst/doc/scds.html", - "tool_dev_url": "https://github.com/kostkalab/scds", - "doi": "10.1093/bioinformatics/btz698", - "licence": [ - "MIT" - ], - "identifier": "biotools:scds" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } + }, + { + "name": "bam_stats_samtools", + "path": "subworkflows/nf-core/bam_stats_samtools/meta.yml", + "type": "subworkflow", + "meta": { + "name": "bam_stats_samtools", + "description": "Produces comprehensive statistics from SAM/BAM/CRAM file", + "keywords": ["statistics", "counts", "bam", "sam", "cram"], + "components": ["samtools/stats", "samtools/idxstats", "samtools/flagstat"], + "input": [ + { + "ch_bam_bai": { + "description": "The input channel containing the BAM/CRAM and it's index\nStructure: [ val(meta), path(bam), path(bai) ]\n" + } + }, + { + "ch_fasta": { + "description": "Reference genome fasta file\nStructure: [ path(fasta) ]\n" + } + } + ], + "output": [ + { + "stats": { + "description": "File containing samtools stats output\nStructure: [ val(meta), path(stats) ]\n" + } + }, + { + "flagstat": { + "description": "File containing samtools flagstat output\nStructure: [ val(meta), path(flagstat) ]\n" + } + }, + { + "idxstats": { + "description": "File containing samtools idxstats output\nStructure: [ val(meta), path(idxstats)]\n" + } + }, + { + "versions": { + "description": "Files containing software versions\nStructure: [ path(versions.yml) ]\n" + } + } + ], + "authors": ["@drpatelh"], + "maintainers": ["@drpatelh"] }, - { - "rds": { - "type": "file", - "description": "RDS file containing filtered data (without empty droplets) in SingleCellExperiment format", - "pattern": "*.rds", - "ontologies": [] - } - } - ] - ], - "output": { - "rds": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.rds": { - "type": "file", - "description": "RDS file containing doublet scores in SingleCellExperiment format", - "pattern": "*.rds", - "ontologies": [] - } - } - ] - ], - "predictions": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.csv": { - "type": "file", - "description": "CSV file containing doublet scores", - "pattern": "*.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } + "pipelines": [ + { + "name": "atacseq", + "version": "2.1.2" + }, + { + "name": "callingcards", + "version": "1.0.0" + }, + { + "name": "chipseq", + "version": "2.1.0" + }, + { + "name": "circdna", + "version": "1.1.0" + }, + { + "name": "circrna", + "version": "dev" + }, + { + "name": "cutandrun", + "version": "3.2.2" + }, + { + "name": "genomeassembler", + "version": "1.1.0" + }, + { + "name": "lncpipe", + "version": "dev" + }, + { + "name": "magmap", + "version": "1.0.0" + }, + { + "name": "metatdenovo", + "version": "1.3.0" + }, + { + "name": "methylseq", + "version": "4.2.0" + }, + { + "name": "nascent", + "version": "2.3.0" + }, + { + "name": "pacsomatic", + "version": "dev" + }, + { + "name": "phageannotator", + "version": "dev" + }, + { + "name": "riboseq", + "version": "1.2.0" + }, + { + "name": "rnadnavar", + "version": "dev" + }, + { + "name": "rnafusion", + "version": "4.1.2" + }, + { + "name": "rnaseq", + "version": "3.26.0" + }, + { + "name": "rnasplice", + "version": "1.0.4" + }, + { + "name": "rnavar", + "version": "1.2.3" + }, + { + "name": "sammyseq", + "version": "dev" + }, + { + "name": "scnanoseq", + "version": "1.2.2" + }, + { + "name": "smrnaseq", + "version": "2.4.1" + }, + { + "name": "viralmetagenome", + "version": "1.1.1" + }, + { + "name": "viralrecon", + "version": "3.0.0" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software version", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@cakirb" - ], - "maintainers": [ - "@cakirb" - ] - } - }, - { - "name": "scimap_mcmicro", - "path": "modules/nf-core/scimap/mcmicro/meta.yml", - "type": "module", - "meta": { - "name": "scimap_mcmicro", - "description": "SCIMAP is a suite of tools that enables spatial single-cell analyses", - "keywords": [ - "sort", - "spatial", - "single cell" - ], - "tools": [ - { - "scimap": { - "description": "Scimap is a scalable toolkit for analyzing spatial molecular data.", - "homepage": "https://scimap.xyz/", - "documentation": "https://scimap.xyz/All%20Functions/A.%20Pre%20Processing/sm.pp.mcmicro_to_scimap/", - "tool_dev_url": "https://github.com/labsyspharm/scimap", - "licence": [ - "MIT License" - ], - "identifier": "biotools:SCIMAP" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + }, + { + "name": "bam_stringtie_merge", + "path": "subworkflows/nf-core/bam_stringtie_merge/meta.yml", + "type": "subworkflow", + "meta": { + "name": "bam_stringtie_merge", + "description": "Assemble transcripts from sorted BAM alignments using StringTie, then merge per-sample transcript GTFs into a unified annotation.\n", + "keywords": ["rna-seq", "transcript-assembly", "transcript-merge", "stringtie", "gtf"], + "components": ["stringtie/stringtie", "stringtie/merge"], + "input": [ + { + "bam_sorted": { + "type": "file", + "description": "Sorted alignment files.\nStructure: [ val(meta), path(bam) ]\n", + "pattern": "*.bam" + } + }, + { + "ch_chrgtf": { + "type": "file", + "description": "Reference gene annotation (GTF) for guided assembly and merge.\nStructure: [ val(meta), path(gtf) ]\n", + "pattern": "*.gtf" + } + } + ], + "output": [ + { + "stringtie_gtf": { + "type": "file", + "description": "Merged transcript annotation produced by StringTie --merge.\nStructure: [ val(meta), path(gtf) ]\n", + "pattern": "*.gtf" + } + }, + { + "versions": { + "type": "file", + "description": "File containing software versions for the subworkflow components.\nStructure: [ path(versions.yml) ]\n", + "pattern": "versions.yml" + } + } + ], + "authors": ["@atrigila", "@rannick", "@nvnieuwk"], + "maintainers": ["@atrigila", "@rannick", "@nvnieuwk"] }, - { - "cellbyfeature": { - "type": "file", - "description": "CSV file with cell by feature table", - "pattern": "*.{csv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "output": { - "csv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.csv": { - "type": "file", - "description": "Sorted CSV file", - "pattern": "*.{csv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "h5ad": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.h5ad": { - "type": "file", - "description": "Sorted H5AD file", - "pattern": "*.{h5ad}", - "ontologies": [] - } - } + "pipelines": [ + { + "name": "rnafusion", + "version": "4.1.2" + }, + { + "name": "rnaseq", + "version": "3.26.0" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@luiskuhn" - ], - "maintainers": [ - "@luiskuhn" - ] - }, - "pipelines": [ - { - "name": "mcmicro", - "version": "dev" - } - ] - }, - { - "name": "scimap_spatiallda", - "path": "modules/nf-core/scimap/spatiallda/meta.yml", - "type": "module", - "meta": { - "name": "scimap_spatiallda", - "description": "SpatialLDA uses an LDA based approach for the identification of cellular neighborhoods, using cell type identities.", - "keywords": [ - "spatial_neighborhoods", - "scimap", - "spatial_omics" - ], - "tools": [ - { - "scimap": { - "description": "Scimap is a scalable toolkit for analyzing spatial molecular data. The underlying framework is generalizable to spatial datasets mapped to XY coordinates. The package uses the anndata framework making it easy to integrate with other popular single-cell analysis toolkits. It includes preprocessing, phenotyping, visualization, clustering, spatial analysis and differential spatial testing. The Python-based implementation efficiently deals with large datasets of millions of cells.", - "homepage": "https://scimap.xyz/", - "documentation": "https://scimap.xyz/tutorials/1-scimap-tutorial-getting-started/", - "tool_dev_url": "https://github.com/labsyspharm/scimap", - "doi": "10.5281/zenodo.7854095", - "licence": [ - "MIT licence" - ], - "identifier": "biotools:SCIMAP" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "phenotyped": { - "type": "file", - "description": "Phenotyped CSV file, it must contain the columns, sampleID, X, Y and Phenotype.", - "pattern": "*.{csv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "output": { - "spatial_lda_output": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - 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"ontologies": [] - } - } - ] - ], - "multi_bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/${prefix}.mult.bed": { - "type": "file", - "description": "Bed file containing all splice events predicted\nin the split read alignments.\n (optional, only if -S flag is set in task.ext.args)\n", - "pattern": "*.mult.bed", - "ontologies": [] - } - } - ] - ], - "single_bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/${prefix}.sngl.bed": { - "type": "file", - "description": "Bed file containing all single splice events predicted\nin the split read alignments.\n (optional, only if -S flag is set in task.ext.args)\n", - "pattern": "*.sngl.bed", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - 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Files with non-standard\nextensions are automatically renamed to .fa for SEGUL compatibility.\n", - "pattern": "*.{fa,fas,fasta,nex,nexus,phy,phylip,aln,alnfaa,clipkit,trimal,msa}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1921" - }, - { - "edam": "http://edamontology.org/format_1929" - }, - { - "edam": "http://edamontology.org/format_1912" - }, - { - "edam": "http://edamontology.org/format_1997" - } - ] - } - } - ] - ], - "output": { - "trimmed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}/trimmed_alignments/*": { - "type": "file", - "description": "Trimmed alignment files.", - "pattern": "*.{fas,nex,phy}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1921" - } - ] - } - } - ] - ], - "summary": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}/trimming_summary.csv": { - "type": "file", - "description": "CSV summary with per-alignment trimming statistics.", - "pattern": "*.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "versions_segul": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "segul": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "segul --version | sed 's/segul //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "segul": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "segul --version | sed 's/segul //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@eparisis" - ], - "maintainers": [ - "@eparisis" - 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"description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "*.vcf.gz": { - "type": "file", - "description": "compressed vcf file containing the recalibrated variants.", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "*.tbi": { - "type": "file", - "description": "Index of recalibrated vcf file.", - "pattern": "*vcf.gz.tbi", - "ontologies": [] - } - } - ] - ], - "versions_sentieon": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "sentieon": { - "type": "string", - "description": "The tool name" - } - }, - { - "sentieon driver --version | sed \"s/.*-//g\"": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - 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} - }, - { - "fai": { - "type": "file", - "description": "Index of the genome fasta file [required]", - "pattern": "*.fai", - "ontologies": [] - } - } - ], - [ - { - "meta5": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "interval": { - "type": "file", - "description": "BED file of genome regions to draw coverage from", - "pattern": "*.bed", - "ontologies": [] - } - } - ] - ], - "output": { - "metrics": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.variant_calling_detail_metrics": { - "type": "file", - "description": "Metrics file from VCF\n", - "pattern": "*.variant_calling_detail_metrics", - "ontologies": [] - } - } - ] - ], - "summary": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.variant_calling_summary_metrics": { - "type": "file", - "description": "Summary of VCF metrics\n", - "pattern": "*.collectvcmetrics.txt", - "ontologies": [] - } - } - ] - ], - "versions_sentieon": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "sentieon": { - "type": "string", - "description": "The tool name" - } - }, - { - "sentieon driver --version | sed \"s/.*-//g\"": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "sentieon": { - "type": "string", - "description": "The tool name" - } - }, - { - "sentieon driver --version | sed \"s/.*-//g\"": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@adamrtalbot" - ], - "maintainers": [ - "@adamrtalbot" - ] - } - }, - { - "name": "sentieon_coveragemetrics", - "path": "modules/nf-core/sentieon/coveragemetrics/meta.yml", - "type": "module", - "meta": { - "name": "sentieon_coveragemetrics", - "description": "Accelerated implementation of the GATK DepthOfCoverage tool.", - "keywords": [ - "coverage", - "sentieon", - "genomics" - ], - "tools": [ - { - "sentieon": { - "description": "Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads.\nOur software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.\n", - "homepage": "https://www.sentieon.com/", - "documentation": "https://www.sentieon.com/", - "licence": [ - "Commercial (requires license for use; redistribution allowed)" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } - }, - { - "bai": { - "type": "file", - "description": "BAM/CRAM/SAM file index", - "pattern": "*.{bai,crai}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "interval": { - "type": "file", - "description": "BED file of genome regions to draw coverage from", - "pattern": "*.bed", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Genome fasta file", - "pattern": "*.{fa,fasta}", - "ontologies": [] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "fai": { - "type": "file", - "description": "Index of the genome fasta file", - "pattern": "*.fai", - "ontologies": [] - } - } - ], - [ - { - "meta5": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "gene_list": { - "type": "file", - "description": "RefSeq file used to aggregate the results", - "pattern": "*", - "ontologies": [] - } - } - ] - ], - "output": { - "per_locus": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "${prefix}": { - "type": "file", - "description": "The per locus coverage with no partition.", - "pattern": "${sample_id}", - "ontologies": [] - } - } - ] - ], - "sample_summary": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "${prefix}.${partitions_output}_summary": { - "type": "file", - "description": "The summary for PARTITION_GROUP sample, aggregated over all bases.", - "pattern": "${sample_id}.sample_summary", - "ontologies": [] - } - } - ] - ], - "statistics": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "${prefix}.${partitions_output}_interval_statistics": { - "type": "file", - "description": "The statistics for PARTITION_GROUP library, aggregated by interval.", - "pattern": "${sample_id}_interval_statistics", - "ontologies": [] - } - } - ] - ], - "coverage_counts": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "${prefix}.${partitions_output}_cumulative_coverage_counts": { - "type": "file", - "description": "Contains the histogram of loci with depth larger than x.", - "pattern": "${sample_id}_cumulative_coverage_counts", - "ontologies": [] - } - } - ] - ], - "coverage_proportions": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "${prefix}.${partitions_output}_cumulative_coverage_proportions": { - "type": "file", - "description": "Contains the normalized histogram of loci with depth larger than x.", - "pattern": "${sample_id}_cumulative_coverage_proportions", - "ontologies": [] - } - } - ] - ], - "interval_summary": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "${prefix}.${partitions_output}_interval_summary": { - "type": "file", - "description": "The summary for PARTITION_GROUP library, aggregated by interval.", - "pattern": "${sample_id}_interval_summary", - "ontologies": [] - } - } - ] - ], - "versions_sentieon": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "sentieon": { - "type": "string", - "description": "The tool name" - } - }, - { - "sentieon driver --version | sed \"s/.*-//g\"": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "sentieon": { - "type": "string", - "description": "The tool name" - } - }, - { - "sentieon driver --version | sed \"s/.*-//g\"": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@adamrtalbot" - ], - "maintainers": [ - "@adamrtalbot" - ] - } - }, - { - "name": "sentieon_datametrics", - "path": "modules/nf-core/sentieon/datametrics/meta.yml", - "type": "module", - "meta": { - "name": "sentieon_datametrics", - "description": "Collects multiple quality metrics from a bam file", - "keywords": [ - "metrics", - "bam", - "sentieon" - ], - "tools": [ - { - "sentieon": { - "description": "Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads.\nOur software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.\n", - "homepage": "https://www.sentieon.com/", - "documentation": "https://www.sentieon.com/", - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } - }, - { - "bai": { - "type": "file", - "description": "Index of th sorted BAM/CRAM/SAM file", - "pattern": "*.{bai,crai,sai}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Genome fasta file", - "pattern": "*.{fa,fasta}", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "fai": { - "type": "file", - "description": "Index of the genome fasta file", - "pattern": "*.fai", - "ontologies": [] - } - } - ], - { - "plot_results": { - "type": "boolean", - "description": "Boolean to determine whether plots should be generated", - "pattern": "true or false" - } - } - ], - "output": { - "mq_metrics": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*mq_metrics.txt": { - "type": "file", - "description": "File containing the information about mean base quality score for each sequencing cycle", - "pattern": "*.txt", - "ontologies": [] - } - } - ] - ], - "qd_metrics": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*qd_metrics.txt": { - "type": "file", - "description": "File containing the information about number of bases with a specific base quality score", - "pattern": "*.txt", - "ontologies": [] - } - } - ] - ], - "gc_summary": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*gc_summary.txt": { - "type": "file", - "description": "File containing the information about GC bias in the reference and the sample", - "pattern": "*.txt", - "ontologies": [] - } - } - ] - ], - "gc_metrics": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*gc_metrics.txt": { - "type": "file", - "description": "File containing the information about GC bias in the reference and the sample", - "pattern": "*.txt", - "ontologies": [] - } - } - ] - ], - "aln_metrics": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*aln_metrics.txt": { - "type": "file", - "description": "File containing the statistics about the alignment of the reads", - "pattern": "*.txt", - "ontologies": [] - } - } - ] - ], - "is_metrics": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*is_metrics.txt": { - "type": "file", - "description": "File containing the information about statistical distribution of insert sizes", - "pattern": "*.txt", - "ontologies": [] - } - } - ] - ], - "mq_plot": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*mq_metrics.pdf": { - "type": "file", - "description": "PDF containing plot of mean base quality scores", - "pattern": "*.pdf", - "ontologies": [] - } - } - ] - ], - "qd_plot": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*qd_metrics.pdf": { - "type": "file", - "description": "PDF containing plot of specific base quality score", - "pattern": "*.pdf", - "ontologies": [] - } - } - ] - ], - "is_plot": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*is_metrics.pdf": { - "type": "file", - "description": "PDF containing plot of insert sizes", - "pattern": "*.pdf", - "ontologies": [] - } - } - ] - ], - "gc_plot": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*gc_metrics.pdf": { - "type": "file", - "description": "PDF containing plot of GC bias", - "pattern": "*.pdf", - "ontologies": [] - } - } - ] - ], - "versions_sentieon": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "sentieon": { - "type": "string", - "description": "The tool name" - } - }, - { - "sentieon driver --version | sed \"s/.*-//g\"": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "sentieon": { - "type": "string", - "description": "The tool name" - } - }, - { - "sentieon driver --version | sed \"s/.*-//g\"": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@ramprasadn" - ], - "maintainers": [ - "@ramprasadn" - ] - }, - "pipelines": [ - { - "name": "raredisease", - "version": "3.0.0" - } - ] - }, - { - "name": "sentieon_dedup", - "path": "modules/nf-core/sentieon/dedup/meta.yml", - "type": "module", - "meta": { - "name": "sentieon_dedup", - "description": "Runs the sentieon tool LocusCollector followed by Dedup. LocusCollector collects read information that is used by Dedup which in turn marks or removes duplicate reads.", - "keywords": [ - "mem", - "dedup", - "map", - "bam", - "cram", - "sentieon" - ], - "tools": [ - { - "sentieon": { - "description": "Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads.\nOur software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.\n", - "homepage": "https://www.sentieon.com/", - "documentation": "https://www.sentieon.com/", - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file.", - "pattern": "*.bam", - "ontologies": [] - } - }, - { - "bai": { - "type": "file", - "description": "BAI file", - "pattern": "*.bai", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Genome fasta file", - "pattern": "*.{fa,fasta}", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta_fai": { - "type": "file", - "description": "The index of the FASTA reference.", - "pattern": "*.fai", - "ontologies": [] - } + "name": "bam_subsampledepth_samtools", + "path": "subworkflows/nf-core/bam_subsampledepth_samtools/meta.yml", + "type": "subworkflow", + "meta": { + "name": "bam_subsampledepth_samtools", + "description": "Subsample a BAM/CRAM/SAM file using samtools to a given mean depth", + "keywords": ["subsample", "bam", "sam", "cram"], + "components": ["samtools/depth", "samtools/view", "gawk"], + "input": [ + { + "ch_bam": { + "type": "file", + "description": "The input channel containing the BAM/CRAM/SAM files and their indexes.\nStructure: [ val(meta), path(bam), path(bai) ]\n", + "pattern": "*.{bam,cram,sam}" + } + }, + { + "ch_depth": { + "type": "float", + "description": "Target depth to downsample each input of ch_bam to.\nStructure: [ val(meta), val(depth) ]\nThe meta map will be combined to the meta map of the ch_bam channel.\n" + } + }, + { + "ch_fasta": { + "type": "file", + "description": "The reference genome channel containing the fasta files and its index\nStructure: [ val(meta), path(fasta), path(fai) ]\n", + "pattern": "*.{fa(sta)?}" + } + } + ], + "output": [ + { + "bam_subsampled": { + "type": "file", + "description": "Channel containing subsampled BAM/CRAM/SAM files and their indexes.\ndepth and subsample_fraction parameter will be added to the meta map.\nThe later will be used to set the `--subsample` parameter in SAMTOOLS/VIEW command.\nStructure: [ val(meta), path(bam), path(csi) ]\n", + "pattern": "*.{bam,cram,sam}" + } + } + ], + "authors": ["@louislenezet"], + "maintainers": ["@louislenezet"] } - ] - ], - "output": { - "cram": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.cram": { - "type": "file", - "description": "CRAM file", - "pattern": "*.cram", - "ontologies": [] - } - } - ] - ], - "crai": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.crai": { - "type": "file", - "description": "CRAM index file", - "pattern": "*.crai", - "ontologies": [] - } - } - ] - ], - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "BAM file.", - "pattern": "*.bam", - "ontologies": [] - } - } - ] - ], - "bai": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bai": { - "type": "file", - "description": "BAI file", - "pattern": "*.bai", - "ontologies": [] - } - } - ] - ], - "score": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.score": { - "type": "file", - "description": "The score file indicates which reads LocusCollector finds are likely duplicates.", - "pattern": "*.score", - "ontologies": [] - } - } - ] - ], - "metrics": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.metrics": { - "type": "file", - "description": "Output file containing Dedup metrics incl. histogram data.", - "pattern": "*.metrics", - "ontologies": [] - } - } - ] - ], - "metrics_multiqc_tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.metrics.multiqc.tsv": { - "type": "file", - "description": "Output tsv-file containing Dedup metrics excl. histogram data.", - "pattern": "*.metrics.multiqc.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_sentieon": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "sentieon": { - "type": "string", - "description": "The tool name" - } - }, - { - "sentieon driver --version | sed \"s/.*-//g\"": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "sentieon": { - "type": "string", - "description": "The tool name" - } - }, - { - "sentieon driver --version | sed \"s/.*-//g\"": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@asp8200" - ], - "maintainers": [ - "@asp8200" - ] - }, - "pipelines": [ - { - "name": "raredisease", - "version": "3.0.0" }, { - "name": "sarek", - "version": "3.8.1" - } - ] - }, - { - "name": "sentieon_dnamodelapply", - "path": "modules/nf-core/sentieon/dnamodelapply/meta.yml", - "type": "module", - "meta": { - "name": "sentieon_dnamodelapply", - "description": "modifies the input VCF file by adding the MLrejected FILTER to the variants", - "keywords": [ - "dnamodelapply", - "vcf", - "filter", - "sentieon" - ], - "tools": [ - { - "sentieon": { - "description": "Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads.\nOur software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.\n", - "homepage": "https://www.sentieon.com/", - "documentation": "https://www.sentieon.com/", - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "vcf": { - "type": "file", - "description": "INPUT VCF file", - "pattern": "*.{vcf,vcf.gz}", - "ontologies": [] - } - }, - { - "idx": { - "type": "file", - "description": "Index of the input VCF file", - "pattern": "*.{tbi}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Genome fasta file", - "pattern": "*.{fa,fasta}", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "fai": { - "type": "file", - "description": "Index of the genome fasta file", - "pattern": "*.fai", - "ontologies": [] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. `[ id:'test' ]`\n" - } + "name": "bam_taps_conversion", + "path": "subworkflows/nf-core/bam_taps_conversion/meta.yml", + "type": "subworkflow", + "meta": { + "name": "bam_taps_conversion", + "description": "Uses rastair to assess C->T conversion as a readout for methylation in a genome-wide basis", + "keywords": [ + "TAPS conversion", + "Methylation analysis", + "Molecular bias (MBIAS)", + "mCtoT", + "rastair", + "4-letter genome" + ], + "components": ["rastair/mbias", "rastair/call", "rastair/methylkit", "rastair/mbiasparser"], + "input": [ + { + "ch_fasta": { + "type": "file", + "description": "Reference genome fasta file\nStructure: [ [:], path(fasta) ]\n", + "pattern": "*.{fa,fasta}" + } + }, + { + "ch_fasta_index": { + "type": "file", + "description": "Reference genome index file\nStructure: [ val(meta), path(fai) ]\n", + "pattern": "*.fai" + } + }, + { + "ch_bam": { + "type": "file", + "description": "BAM alignment files\nStructure: [ val(meta), path(bam) ]\n", + "pattern": "*.bam" + } + }, + { + "ch_bai": { + "type": "file", + "description": "BAM index files\nStructure: [ val(meta), path(bai) ]\n", + "pattern": "*.bai" + } + } + ], + "output": [ + { + "mbias": { + "type": "file", + "description": "File describing the molecular bias (MBIAS) of the TAPS conversion\nStructure: [ val(meta), path(mbias) ]\n", + "pattern": "*.txt" + } + }, + { + "call": { + "type": "file", + "description": "Rastair call output files (similar to bed format, genome-wide)\nStructure: [ val(meta), path(call) ]\n", + "pattern": "*.txt" + } + }, + { + "methylkit": { + "type": "file", + "description": "Rastair call output files in MethylKit format (similar to bed format, genome-wide)\nStructure: [ val(meta), path(methylkit) ]\n", + "pattern": "*.gz" + } + }, + { + "versions": { + "type": "file", + "description": "File containing software versions\nStructure: [ path(versions.yml) ]\n", + "pattern": "versions.yml" + } + } + ], + "authors": ["@eduard-watchmaker"], + "maintainers": ["@eduard-watchmaker"] }, - { - "ml_model": { - "type": "file", - "description": "machine learning model file", - "pattern": "*.model", - "ontologies": [] - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*.vcf.gz": { - "type": "file", - "description": "INPUT VCF file", - "pattern": "*.{vcf,vcf.gz}", - "ontologies": [] - } - } - ] - ], - "tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*.vcf.gz.tbi": { - "type": "file", - "description": "Index of the input VCF file", - "pattern": "*.{tbi}", - "ontologies": [] - } - } - ] - ], - "versions_sentieon": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "sentieon": { - "type": "string", - "description": "The tool name" - } - }, - { - "sentieon driver --version | sed \"s/.*-//g\"": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "sentieon": { - "type": "string", - "description": "The tool name" - } - }, - { - "sentieon driver --version | sed \"s/.*-//g\"": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } + "pipelines": [ + { + "name": "methylseq", + "version": "4.2.0" + } ] - ] }, - "authors": [ - "@ramprasadn" - ], - "maintainers": [ - "@ramprasadn" - ] - }, - "pipelines": [ { - "name": "raredisease", - "version": "3.0.0" + "name": "bam_telomere_estimation", + "path": "subworkflows/nf-core/bam_telomere_estimation/meta.yml", + "type": "subworkflow", + "meta": { + "name": "bam_telomere_estimation", + "description": "Estimate telomere length and content from aligned reads using telseq, telogator2, and telomerehunter", + "keywords": ["telomere", "telseq", "telogator2", "telomerehunter", "bam", "cram"], + "components": ["telseq", "telogator2", "telomerehunter", "custom/summarisetelomereestimation"], + "input": [ + { + "ch_reads": { + "type": "file", + "description": "Channel of aligned reads with data type and optional index.\nStructure: [ val(meta), val(data_type), path(reads), path(reads_index) ]\ndata_type: 'short' routes to telseq, 'long' routes to telogator2.\nThe calling pipeline is responsible for determining the sequencing type.\nReads must be indexed. bed is an optional exome BED for telseq ([] if not needed).\n" + } + }, + { + "ch_control": { + "type": "file", + "description": "Channel of control/normal BAM files for telomerehunter.\nStructure: [ val(meta), path(control_bam), path(control_bai) ]\nPass Channel.empty() if not needed.\n" + } + }, + { + "ch_fasta": { + "type": "file", + "description": "Reference genome FASTA with index.\nStructure: [ val(meta2), path(fasta), path(fai) ]\n" + } + }, + { + "ch_cytoband": { + "type": "file", + "description": "Optional cytoband file for telomerehunter.\nStructure: [ path(cytoband) ]\nWhen not provided ([[]] / empty), telomerehunter uses its bundled hg19 cytoband.\nMust be supplied for hg38 data to avoid an IndexError caused by\nchromosomes that are longer in hg38 than hg19.\n" + } + }, + { + "run_telomerehunter": { + "type": "boolean", + "description": "Enable telomerehunter content profiling" + } + }, + { + "length_estimator": { + "type": "string", + "description": "Global override for length estimation tool. If set, all samples\nuse this tool regardless of per-sample data_type.\nValues: 'short', 'long', or null.\n" + } + } + ], + "output": [ + { + "length_tsv": { + "type": "file", + "description": "Raw telomere length TSV from telseq or telogator2.\nStructure: [ val(meta), path(tsv) ]\n" + } + }, + { + "content_tsv": { + "type": "file", + "description": "Raw telomere content TSV from telomerehunter (empty if not run).\nStructure: [ val(meta), path(tsv) ]\n" + } + }, + { + "summary": { + "type": "file", + "description": "Normalised summary combining length and content per sample.\nStructure: [ val(meta), path(tsv) ]\n" + } + }, + { + "telomerehunter_tumor": { + "type": "directory", + "description": "Telomerehunter tumor analysis directory (empty if not run).\nStructure: [ val(meta), path(dir) ]\n" + } + }, + { + "telomerehunter_control": { + "type": "directory", + "description": "Telomerehunter control analysis directory (empty if not run).\nStructure: [ val(meta), path(dir) ]\n" + } + }, + { + "telogator2_plots": { + "type": "file", + "description": "Telogator2 allele and violin plots.\nStructure: [ val(meta), path(*.png) ]\n" + } + }, + { + "telogator2_stats": { + "type": "file", + "description": "Telogator2 QC statistics.\nStructure: [ val(meta), path(stats.txt) ]\n" + } + } + ], + "authors": ["@pinin4fjords"], + "maintainers": ["@pinin4fjords"] + } }, { - "name": "sarek", - "version": "3.8.1" - } - ] - }, - { - "name": "sentieon_dnascope", - "path": "modules/nf-core/sentieon/dnascope/meta.yml", - "type": "module", - "meta": { - "name": "sentieon_dnascope", - "description": "DNAscope algorithm performs an improved version of Haplotype variant calling.", - "keywords": [ - "dnascope", - "sentieon", - "variant_calling" - ], - "tools": [ - { - "sentieon": { - "description": "Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads.\nOur software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.\n", - "homepage": "https://www.sentieon.com/", - "documentation": "https://www.sentieon.com/", - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file.", - "pattern": "*.bam", - "ontologies": [] - } - }, - { - "bai": { - "type": "file", - "description": "BAI file", - "pattern": "*.bai", - "ontologies": [] - } - }, - { - "intervals": { - "type": "file", - "description": "bed or interval_list file containing interval in the reference that will be used in the analysis", - "pattern": "*.{bed,interval_list}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing meta information for fasta.\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Genome fasta file", - "pattern": "*.{fa,fasta}", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing meta information for fasta index.\n" - } - }, - { - "fai": { - "type": "file", - "description": "Index of the genome fasta file", - "pattern": "*.fai", - "ontologies": [] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing meta information for dbsnp.\n" - } - }, - { - "dbsnp": { - "type": "file", - "description": "Single Nucleotide Polymorphism database (dbSNP) file", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ], - [ - { - "meta5": { - "type": "map", - "description": "Groovy Map containing meta information for dbsnp_tbi.\n" - } - }, - { - "dbsnp_tbi": { - "type": "file", - "description": "Index of the Single Nucleotide Polymorphism database (dbSNP) file", - "pattern": "*.vcf.gz.tbi", - "ontologies": [] - } - } - ], - [ - { - "meta6": { - "type": "map", - "description": "Groovy Map containing meta information for machine learning model for Dnascope.\n" - } - }, - { - "ml_model": { - "type": "file", - "description": "machine learning model file", - "pattern": "*.model", - "ontologies": [] - } - } - ], - { - "pcr_indel_model": { - "type": "string", - "description": "Controls the option pcr_indel_model for Dnascope.\nThe possible options are \"NONE\" (used for PCR free samples), and \"HOSTILE\", \"AGGRESSIVE\" and \"CONSERVATIVE\".\nSee Sentieons documentation for further explanation.\n" - } - }, - { - "emit_vcf": { - "type": "string", - "description": "Controls the vcf output from Dnascope.\nPossible options are \"all\", \"confident\" and \"variant\".\nSee Sentieons documentation for further explanation.\n" - } - }, - { - "emit_gvcf": { - "type": "boolean", - "description": "If true, the haplotyper will output a gvcf" + "name": "bam_tumor_normal_somatic_variant_calling_gatk", + "path": "subworkflows/nf-core/bam_tumor_normal_somatic_variant_calling_gatk/meta.yml", + "type": "subworkflow", + "meta": { + "name": "bam_tumor_normal_somatic_variant_calling_gatk", + "description": "Perform variant calling on a paired tumor normal set of samples using mutect2 tumor normal mode.\nf1r2 output of mutect2 is run through learnreadorientationmodel to get the artifact priors.\nRun the input bam files through getpileupsummarries and then calculatecontamination to get the contamination and segmentation tables.\nFilter the mutect2 output vcf using filtermutectcalls, artifact priors and the contamination & segmentation tables for additional filtering.\n", + "keywords": [ + "gatk4", + "mutect2", + "learnreadorientationmodel", + "getpileupsummaries", + "calculatecontamination", + "filtermutectcalls", + "variant_calling", + "tumor_only", + "filtered_vcf" + ], + "components": [ + "gatk4/mutect2", + "gatk4/learnreadorientationmodel", + "gatk4/getpileupsummaries", + "gatk4/calculatecontamination", + "gatk4/filtermutectcalls" + ], + "input": [ + { + "ch_input": { + "description": "The tumor and normal BAM files, in that order, also able to take CRAM as an input\nCan contain an optional list of sample headers contained in the normal sample input file.\nStructure: [ val(meta), path(input), path(input_index), val(which_norm) ]\n" + } + }, + { + "ch_fasta": { + "description": "The reference fasta file\nStructure: [ path(fasta) ]\n" + } + }, + { + "ch_fai": { + "description": "Index of reference fasta file\nStructure: [ path(fai) ]\n" + } + }, + { + "ch_dict": { + "description": "GATK sequence dictionary\nStructure: [ path(dict) ]\n" + } + }, + { + "ch_alleles": { + "description": "VCF file to be used for force calling of alleles.\nStructure: [ path(alleles) ]\n" + } + }, + { + "ch_alleles_tbi": { + "description": "Index of VCF file of alleles for force calling.\nStructure: [ path(alleles_tbi) ]\n" + } + }, + { + "ch_germline_resource": { + "description": "Population vcf of germline sequencing, containing allele fractions.\nStructure: [ path(germline_resources) ]\n" + } + }, + { + "ch_germline_resource_tbi": { + "description": "Index file for the germline resource.\nStructure: [ path(germline_resources_tbi) ]\n" + } + }, + { + "ch_panel_of_normals": { + "description": "Vcf file to be used as a panel of normals.\nStructure: [ path(panel_of_normals) ]\n" + } + }, + { + "ch_panel_of_normals_tbi": { + "description": "Index for the panel of normals.\nStructure: [ path(panel_of_normals_tbi) ]\n" + } + }, + { + "ch_interval_file": { + "description": "File containing intervals.\nStructure: [ path(interval_files) ]\n" + } + } + ], + "output": [ + { + "mutect2_vcf": { + "description": "Compressed vcf file to be used for variant_calling.\nStructure: [ val(meta), path(vcf) ]\n" + } + }, + { + "mutect2_tbi": { + "description": "Indexes of the mutect2_vcf file\nStructure: [ val(meta), path(tbi) ]\n" + } + }, + { + "mutect2_stats": { + "description": "Stats files for the mutect2 vcf\nStructure: [ val(meta), path(stats) ]\n" + } + }, + { + "mutect2_f1r2": { + "description": "File containing information to be passed to LearnReadOrientationModel.\nStructure: [ val(meta), path(f1r2) ]\n" + } + }, + { + "artifact_priors": { + "description": "File containing artifact-priors to be used by filtermutectcalls.\nStructure: [ val(meta), path(artifact_priors) ]\n" + } + }, + { + "pileup_table_tumor": { + "description": "File containing the tumor pileup summary table, kept separate as calculatecontamination needs them individually specified.\nStructure: [ val(meta), path(table) ]\n" + } + }, + { + "pileup_table_normal": { + "description": "File containing the normal pileup summary table, kept separate as calculatecontamination needs them individually specified.\nStructure: [ val(meta), path(table) ]\n" + } + }, + { + "contamination_table": { + "description": "File containing the contamination table.\nStructure: [ val(meta), path(table) ]\n" + } + }, + { + "segmentation_table": { + "description": "Output table containing segmentation of tumor minor allele fractions.\nStructure: [ val(meta), path(table) ]\n" + } + }, + { + "filtered_vcf": { + "description": "File containing filtered mutect2 calls.\nStructure: [ val(meta), path(vcf) ]\n" + } + }, + { + "filtered_tbi": { + "description": "Tbi file that pairs with filtered vcf.\nStructure: [ val(meta), path(tbi) ]\n" + } + }, + { + "filtered_stats": { + "description": "File containing statistics of the filtermutectcalls run.\nStructure: [ val(meta), path(stats) ]\n" + } + } + ], + "authors": ["@GCJMackenzie"], + "maintainers": ["@GCJMackenzie"] } - } - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.unfiltered.vcf.gz": { - "type": "file", - "description": "Compressed VCF file", - "pattern": "*.unfiltered.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "vcf_tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.unfiltered.vcf.gz.tbi": { - "type": "file", - "description": "Index of VCF file", - "pattern": "*.unfiltered.vcf.gz.tbi", - "ontologies": [] - } - } - ] - ], - "gvcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.g.vcf.gz": { - "type": "file", - "description": "Compressed GVCF file", - "pattern": "*.g.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "gvcf_tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.g.vcf.gz.tbi": { - "type": "file", - "description": "Index of GVCF file", - "pattern": "*.g.vcf.gz.tbi", - "ontologies": [] - } - } - ] - ], - "versions_sentieon": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "sentieon": { - "type": "string", - "description": "The tool name" - } - }, - { - "sentieon driver --version | sed \"s/.*-//g\"": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "sentieon": { - "type": "string", - "description": "The tool name" - } - }, - { - "sentieon driver --version | sed \"s/.*-//g\"": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] }, - "authors": [ - "@ramprasadn" - ], - "maintainers": [ - "@ramprasadn" - ] - }, - "pipelines": [ { - "name": "raredisease", - "version": "3.0.0" + "name": "bam_tumor_normal_somatic_variant_calling_strelka", + "path": "subworkflows/nf-core/bam_tumor_normal_somatic_variant_calling_strelka/meta.yml", + "type": "subworkflow", + "meta": { + "name": "bam_tumor_normal_somatic_variant_calling_strelka", + "description": "Perform variant calling on a paired tumor normal set of samples using strelka somatic mode.\nf1r2 output of mutect2 is run through learnreadorientationmodel to get the artifact priors.\nRun the input bam files through getpileupsummarries and then calculatecontamination to get the contamination and segmentation tables.\nFilter the mutect2 output vcf using filtermutectcalls, artifact priors and the contamination & segmentation tables for additional filtering.\n", + "keywords": ["strelka", "variant_calling", "filtered_vcf"], + "components": ["gatk4/mergevcfs", "strelka/somatic"], + "input": [ + { + "ch_cram": { + "description": "The normal and tumor CRAM files, in that order.\nStructure: [ meta, normal_cram, normal_crai, tumor_cram, tumor_crai, manta_vcf, manta_tbi ] manta* are optional\n" + } + }, + { + "ch_dict": { + "description": "GATK sequence dictionary, optional\nStructure: [ meta, dict ]\n" + } + }, + { + "ch_fasta": { + "type": "file", + "description": "reference fasta file", + "pattern": ".{fa,fa.gz,fasta,fasta.gz}" + } + }, + { + "ch_fasta_fai": { + "type": "file", + "description": "reference fasta file index", + "pattern": "*.{fa,fasta}.fai" + } + }, + { + "ch_intervals": { + "description": "Intervals to be used for variant calling.\nStructure: [ interval.bed.gz, interval.bed.gz.tbi, num_intervals ] or [ [], [], 0 ] if no intervals\n" + } + } + ], + "output": [ + { + "versions": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + }, + { + "vcf": { + "type": "file", + "description": "Compressed vcf files for indels and snvs, in that order.\nStructure: [ val(meta), path(vcf), path(vcf) ]\n", + "pattern": "*.{vcf.gz}" + } + } + ], + "authors": ["@famosab"], + "maintainers": ["@famosab"] + } }, { - "name": "sarek", - "version": "3.8.1" - } - ] - }, - { - "name": "sentieon_gvcftyper", - "path": "modules/nf-core/sentieon/gvcftyper/meta.yml", - "type": "module", - "meta": { - "name": "sentieon_gvcftyper", - "description": "Perform joint genotyping on one or more samples pre-called with Sentieon's Haplotyper.\n", - "keywords": [ - "joint genotyping", - "genotype", - "gvcf" - ], - "tools": [ - { - "sentieon": { - "description": "Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads.\nOur software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.\n", - "homepage": "https://www.sentieon.com/", - "documentation": "https://www.sentieon.com/", - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "gvcfs": { - "type": "file", - "description": "gVCF(.gz) file\n", - "pattern": "*.{vcf,vcf.gz}", - "ontologies": [] - } - }, - { - "tbis": { - "type": "file", - "description": "index of gvcf file\n", - "pattern": "*.tbi", - "ontologies": [] - } - }, - { - "intervals": { - "type": "file", - "description": "Interval file with the genomic regions included in the library (optional)", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference fasta file", - "pattern": "*.fasta", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fai": { - "type": "file", - "description": "Reference fasta index file", - "pattern": "*.fai", - "ontologies": [] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "dbsnp": { - "type": "file", - "description": "dbSNP VCF file", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ], - [ - { - "meta5": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "dbsnp_tbi": { - "type": "file", - "description": "dbSNP VCF index file", - "pattern": "*.tbi", - "ontologies": [] - } - } - ] - ], - "output": { - "vcf_gz": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.vcf.gz": { - "type": "file", - "description": "VCF file", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "vcf_gz_tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.vcf.gz.tbi": { - "type": "file", - "description": "VCF index file", - "pattern": "*.vcf.gz.tbi", - "ontologies": [] - } - } - ] - ], - "versions_sentieon": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "sentieon": { - "type": "string", - "description": "The tool name" - } - }, - { - "sentieon driver --version | sed \"s/.*-//g\"": { - "type": "eval", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "sentieon": { - "type": "string", - "description": "The tool name" - } - }, - { - "sentieon driver --version | sed \"s/.*-//g\"": { - "type": "eval", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@asp8200" - ], - "maintainers": [ - "@asp8200" - ] - }, - "pipelines": [ - { - "name": "sarek", - "version": "3.8.1" - } - ] - }, - { - "name": "sentieon_haplotyper", - "path": "modules/nf-core/sentieon/haplotyper/meta.yml", - "type": "module", - "meta": { - "name": "sentieon_haplotyper", - "description": "Runs Sentieon's haplotyper for germline variant calling.", - "keywords": [ - "sentieon", - "haplotypecaller", - "haplotype" - ], - "tools": [ - { - "sentieon": { - "description": "Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads.\nOur software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.\n", - "homepage": "https://www.sentieon.com/", - "documentation": "https://www.sentieon.com/", - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM file from alignment", - "pattern": "*.{bam,cram}", - "ontologies": [] - } - }, - { - "input_index": { - "type": "file", - "description": "BAI/CRAI file from alignment", - "pattern": "*.{bai,crai}", - "ontologies": [] - } - }, - { - "intervals": { - "type": "file", - "description": "Bed file with the genomic regions included in the library (optional)", - "ontologies": [] - } - }, - { - "recal_table": { - "type": "file", - "description": "Recalibration table from sentieon/qualcal (optional)", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Genome fasta file", - "pattern": "*.{fa,fasta}", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fai": { - "type": "file", - "description": "The index of the FASTA reference.", - "pattern": "*.fai", - "ontologies": [] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "dbsnp": { - "type": "file", - "description": "VCF file containing known sites (optional)", - "ontologies": [] - } - } - ], - [ - { - "meta5": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "dbsnp_tbi": { - "type": "file", - "description": "VCF index of dbsnp (optional)", - "ontologies": [] - } - } - ], - { - "emit_vcf": { - "type": "string", - "description": "Controls the vcf output from the haplotyper.\nIf emit_vcf is set to \"all\" then the haplotyper will output a vcf generated by the haplotyper in emit-mode \"all\".\nIf emit_vcf is set to \"confident\" then the haplotyper will output a vcf generated by the haplotyper in emit-mode \"confident\".\nIf emit_vcf is set to \"variant\" then the haplotyper will output a vcf generated by the haplotyper in emit_mode \"confident\".\n" - } - }, - { - "emit_gvcf": { - "type": "boolean", - "description": "If true, the haplotyper will output a gvcf" - } - } - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.unfiltered.vcf.gz": { - "type": "file", - "description": "Compressed VCF file", - "pattern": "*.unfiltered.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "vcf_tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.unfiltered.vcf.gz.tbi": { - "type": "file", - "description": "Index of VCF file", - "pattern": "*.unfiltered.vcf.gz.tbi", - "ontologies": [] - } - } - ] - ], - "gvcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.g.vcf.gz": { - "type": "file", - "description": "Compressed GVCF file", - "pattern": "*.g.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "gvcf_tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.g.vcf.gz.tbi": { - "type": "file", - "description": "Index of GVCF file", - "pattern": "*.g.vcf.gz.tbi", - "ontologies": [] - } - } - ] - ], - "versions_sentieon": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "sentieon": { - "type": "string", - "description": "The tool name" - } - }, - { - "sentieon driver --version | sed \"s/.*-//g\"": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "sentieon": { - "type": "string", - "description": "The tool name" - } - }, - { - "sentieon driver --version | sed \"s/.*-//g\"": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@asp8200" - ], - "maintainers": [ - "@asp8200" - ] - }, - "pipelines": [ - { - "name": "sarek", - "version": "3.8.1" - } - ] - }, - { - "name": "sentieon_hsmetrics", - "path": "modules/nf-core/sentieon/hsmetrics/meta.yml", - "type": "module", - "meta": { - "name": "sentieon_hsmetrics", - "description": "Collects hybrid-selection (HS) metrics for a SAM or BAM file.", - "keywords": [ - "metrics", - "bam", - "sentieon" - ], - "tools": [ - { - "sentieon": { - "description": "Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads.\nOur software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.\n", - "homepage": "https://www.sentieon.com/", - "documentation": "https://www.sentieon.com/", - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - }, - { - "bai": { - "type": "file", - "description": "Index of the BAM/CRAM/SAM file", - "pattern": "*.{bai,crai,sai}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3327" - } - ] - } - }, - { - "bait_intervals": { - "type": "file", - "description": "An interval file that contains the locations of the baits used.", - "pattern": "*.{interval_list,bed,bed.gz}", - "ontologies": [] - } - }, - { - "target_intervals": { - "type": "file", - "description": "An interval file that contains the locations of the targets.", - "pattern": "*.{interval_list,bed,bed.gz}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Genome fasta file", - "pattern": "*.{fa,fasta}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "fai": { - "type": "file", - "description": "Index of the genome fasta file", - "pattern": "*.fai", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3326" - } - ] - } - } - ] - ], - "output": { - "metrics": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*.txt": { - "type": "file", - "description": "Alignment metrics related to how many reads overlap the target/bait regions.", - "pattern": "*.txt", - "ontologies": [] - } - } - ] - ], - "versions_sentieon": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "sentieon": { - "type": "string", - "description": "The tool name" - } - }, - { - "sentieon driver --version | sed 's/.*-//g'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "sentieon": { - "type": "string", - "description": "The tool name" - } - }, - { - "sentieon driver --version | sed 's/.*-//g'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@sppearce" - ], - "maintainers": [ - "@sppearce" - ] - } - }, - { - "name": "sentieon_qualcal", - "path": "modules/nf-core/sentieon/qualcal/meta.yml", - "type": "module", - "meta": { - "name": "sentieon_qualcal", - "description": "Generate recalibration table and optionally perform base quality recalibration", - "keywords": [ - "base quality score recalibration", - "bqsr", - "sentieon" - ], - "tools": [ - { - "sentieon": { - "description": "Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads.\nOur software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.\n", - "homepage": "https://www.sentieon.com/", - "documentation": "https://www.sentieon.com/", - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM file from alignment", - "pattern": "*.{bam,cram}", - "ontologies": [] - } - }, - { - "input_index": { - "type": "file", - "description": "BAI/CRAI file from alignment", - "pattern": "*.{bai,crai}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference fasta file", - "pattern": "*.fasta", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fai": { - "type": "file", - "description": "Index of reference fasta file", - "pattern": "*.fasta.fai", - "ontologies": [] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "known_sites": { - "type": "file", - "description": "VCF files with known sites for indels / snps (optional)", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ], - [ - { - "meta5": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "known_sites_tbi": { - "type": "file", - "description": "Tabix index of the known_sites (optional)", - "pattern": "*.vcf.gz.tbi", - "ontologies": [] - } - } - ], - [ - { - "meta6": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "recalibration_table": { - "type": "file", - "description": "File containing recalibration values (optional)", - "pattern": "*.table", - "ontologies": [] - } - } - ], - { - "generate_recalibrated_bams": { - "type": "boolean", - "description": "If truem, writes recalibrated bams to disc" - } - } - ], - "output": { - "table": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.table": { - "type": "file", - "description": "Pre Recalibration table (optional)", - "pattern": "*.table", - "ontologies": [] - } - } - ] - ], - "table_post": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.table.post": { - "type": "file", - "description": "Post recalibration table (optional)", - "pattern": "*.table.post", - "ontologies": [] - } - } - ] - ], - "recal_alignment": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.{cram,bam}": { - "type": "file", - "description": "Recalibrated input files (optional)", - "pattern": "*.{bam,cram}", - "ontologies": [] - } - } - ] - ], - "csv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.csv": { - "type": "file", - "description": "Recalibration results output file used for plotting. (optional)", - "pattern": "*.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "pdf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.pdf": { - "type": "file", - "description": "PDF file containing graphs (optional)", - "pattern": "*.pdf", - "ontologies": [] - } - } - ] - ], - "versions_sentieon": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "sentieon": { - "type": "string", - "description": "The tool name" - } - }, - { - "sentieon driver --version | sed \"s/.*-//g\"": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@FriederikeHanssen" - ], - "maintainers": [ - "@FriederikeHanssen" - ], - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "sentieon": { - "type": "string", - "description": "The tool name" - } - }, - { - "sentieon driver --version | sed \"s/.*-//g\"": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - } - } - }, - { - "name": "sentieon_readwriter", - "path": "modules/nf-core/sentieon/readwriter/meta.yml", - "type": "module", - "meta": { - "name": "sentieon_readwriter", - "description": "Merges BAM files, and/or convert them into cram files. Also, outputs the result of applying the Base Quality Score Recalibration to a file.", - "keywords": [ - "merge", - "convert", - "readwriter", - "sentieon" - ], - "tools": [ - { - "sentieon": { - "description": "Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads.\nOur software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.\n", - "homepage": "https://www.sentieon.com/", - "documentation": "https://www.sentieon.com/", - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM file.", - "pattern": "*.{bam,cram}", - "ontologies": [] - } - }, - { - "index": { - "type": "file", - "description": "BAI/CRAI file.", - "pattern": "*.{bai,crai}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Genome fasta file", - "pattern": "*.{fa,fasta}", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" - } - }, - { - "fai": { - "type": "file", - "description": "The index of the FASTA reference.", - "pattern": "*.fai", - "ontologies": [] - } - } - ] - ], - "output": { - "output": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}": { - "type": "file", - "description": "BAM/CRAM file. Depends on how ext.prefix is set. BAM \"ext.prefix = .bam\", CRAM \"ext.prefix = .cram\". Defaults to cram", - "pattern": "*.{bam,cram}", - "ontologies": [] - } - } - ] - ], - "index": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.${index}": { - "type": "file", - "description": "BAM/CRAM index file", - "pattern": "*.{bai,crai}", - "ontologies": [] - } - } - ] - ], - "output_index": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}": { - "type": "file", - "description": "BAM/CRAM file. Depends on how ext.prefix is set. BAM \"ext.prefix = .bam\", CRAM \"ext.prefix = .cram\". Defaults to cram", - "pattern": "*.{bam,cram}", - "ontologies": [] - } - }, - { - "${prefix}.${index}": { - "type": "file", - "description": "BAM/CRAM index file", - "pattern": "*.{bai,crai}", - "ontologies": [] - } - } - ] - ], - "versions_sentieon": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "sentieon": { - "type": "string", - "description": "The tool name" - } - }, - { - "sentieon driver --version | sed \"s/.*-//g\"": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "sentieon": { - "type": "string", - "description": "The tool name" - } - }, - { - "sentieon driver --version | sed \"s/.*-//g\"": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@ramprasadn" - ], - "maintainers": [ - "@ramprasadn" - ] - }, - "pipelines": [ - { - "name": "raredisease", - "version": "3.0.0" - } - ] - }, - { - "name": "sentieon_rsemcalculateexpression", - "path": "modules/nf-core/sentieon/rsemcalculateexpression/meta.yml", - "type": "module", - "meta": { - "name": "sentieon_rsemcalculateexpression", - "description": "Calculate expression with RSEM", - "keywords": [ - "rsem", - "expression", - "quantification", - "sentieon" - ], - "tools": [ - { - "rseqc": { - "description": "RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome\n", - "homepage": "https://github.com/deweylab/RSEM", - "documentation": "https://github.com/deweylab/RSEM", - "doi": "10.1186/1471-2105-12-323", - "licence": [ - "GPL-3.0-or-later" - ], - "identifier": "biotools:rsem" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "Input reads for quantification", - "pattern": "*.fastq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ], - { - "index": { - "type": "file", - "description": "RSEM index", - "pattern": "rsem/*", - "ontologies": [] - } - } - ], - "output": { - "counts_gene": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.genes.results": { - "type": "file", - "description": "Expression counts on gene level", - "pattern": "*.genes.results", - "ontologies": [] - } - } - ] - ], - "counts_transcript": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.isoforms.results": { - "type": "file", - "description": "Expression counts on transcript level", - "pattern": "*.isoforms.results", - "ontologies": [] - } - } - ] - ], - "stat": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.stat": { - "type": "file", - "description": "RSEM statistics", - "pattern": "*.stat", - "ontologies": [] - } - } - ] - ], - "logs": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.log": { - "type": "file", - "description": "RSEM logs", - "pattern": "*.log", - "ontologies": [] - } - } - ] - ], - "bam_star": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.STAR.genome.bam": { - "type": "file", - "description": "BAM file generated by STAR (optional)", - "pattern": "*.STAR.genome.bam", - "ontologies": [] - } - } - ] - ], - "bam_genome": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "${prefix}.genome.bam": { - "type": "file", - "description": "Genome BAM file (optional)", - "pattern": "*.genome.bam", - "ontologies": [] - } - } - ] - ], - "bam_transcript": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "${prefix}.transcript.bam": { - "type": "file", - "description": "Transcript BAM file (optional)", - "pattern": "*.transcript.bam", - "ontologies": [] - } - } - ] - ], - "versions_rsem": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "rsem": { - "type": "string", - "description": "The tool name" - } - }, - { - "rsem-calculate-expression --version | sed -e \"s/Current version: RSEM v//g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_star": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "star": { - "type": "string", - "description": "The tool name" - } - }, - { - "STAR --version | sed -e \"s/STAR_//g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_sentieon": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "sentieon": { - "type": "string", - "description": "The tool name" - } - }, - { - "sentieon driver --version 2>&1 | sed -e \"s/sentieon-genomics-//g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "rsem": { - "type": "string", - "description": "The tool name" - } - }, - { - "rsem-calculate-expression --version | sed -e \"s/Current version: RSEM v//g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "star": { - "type": "string", - "description": "The tool name" - } - }, - { - "STAR --version | sed -e \"s/STAR_//g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "sentieon": { - "type": "string", - "description": "The tool name" - } - }, - { - "sentieon driver --version 2>&1 | sed -e \"s/sentieon-genomics-//g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@FriederikeHanssen" - ], - "maintainers": [ - "@FriederikeHanssen" - ] - }, - "pipelines": [ - { - "name": "rnaseq", - "version": "3.26.0" - } - ] - }, - { - "name": "sentieon_rsempreparereference", - "path": "modules/nf-core/sentieon/rsempreparereference/meta.yml", - "type": "module", - "meta": { - "name": "sentieon_rsempreparereference", - "description": "Prepare a reference genome for RSEM", - "keywords": [ - "rsem", - "genome", - "index", - "sentieon" - ], - "tools": [ - { - "rseqc": { - "description": "RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome\n", - "homepage": "https://github.com/deweylab/RSEM", - "documentation": "https://github.com/deweylab/RSEM", - "doi": "10.1186/1471-2105-12-323", - "licence": [ - "GPL-3.0-or-later" - ], - "identifier": "biotools:rsem" - } - } - ], - "input": [ - { - "fasta": { - "type": "file", - "description": "The Fasta file of the reference genome", - "pattern": "*.{fasta,fa}", - "ontologies": [] - } - }, - { - "gtf": { - "type": "file", - "description": "The GTF file of the reference genome", - "pattern": "*.gtf", - "ontologies": [] - } - } - ], - "output": { - "index": [ - { - "rsem": { - "type": "directory", - "description": "RSEM index directory", - "pattern": "rsem" - } - } - ], - "transcript_fasta": [ - { - "*transcripts.fa": { - "type": "file", - "description": "Fasta file of transcripts", - "pattern": "rsem/*transcripts.fa", - "ontologies": [] - } - } - ], - "versions_rsem": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "rsem": { - "type": "string", - "description": "The tool name" - } - }, - { - "rsem-calculate-expression --version | sed -e \"s/Current version: RSEM v//g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_star": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "star": { - "type": "string", - "description": "The tool name" - } - }, - { - "STAR --version | sed -e \"s/STAR_//g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_sentieon": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "sentieon": { - "type": "string", - "description": "The tool name" - } - }, - { - "sentieon driver --version 2>&1 | sed -e \"s/sentieon-genomics-//g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "rsem": { - "type": "string", - "description": "The tool name" - } - }, - { - "rsem-calculate-expression --version | sed -e \"s/Current version: RSEM v//g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "star": { - "type": "string", - "description": "The tool name" - } - }, - { - "STAR --version | sed -e \"s/STAR_//g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "sentieon": { - "type": "string", - "description": "The tool name" - } - }, - { - "sentieon driver --version 2>&1 | sed -e \"s/sentieon-genomics-//g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@FriederikeHanssen" - ], - "maintainers": [ - "@FriederikeHanssen" - ] - }, - "pipelines": [ - { - "name": "rnaseq", - "version": "3.26.0" - } - ] - }, - { - "name": "sentieon_staralign", - "path": "modules/nf-core/sentieon/staralign/meta.yml", - "type": "module", - "meta": { - "name": "sentieon_staralign", - "description": "Align reads to a reference genome using Sentieon STAR", - "keywords": [ - "align", - "fasta", - "genome", - "reference" - ], - "tools": [ - { - "sentieon": { - "description": "Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads.\nOur software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.\n", - "homepage": "https://www.sentieon.com/", - "documentation": "https://www.sentieon.com/", - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "index": { - "type": "directory", - "description": "STAR genome index", - "pattern": "star" - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "gtf": { - "type": "file", - "description": "Annotation GTF file", - "pattern": "*.{gtf}", - "ontologies": [] - } - } - ], - { - "star_ignore_sjdbgtf": { - "type": "boolean", - "description": "Ignore annotation GTF file" - } - } - ], - "output": { - "log_final": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*Log.final.out": { - "type": "file", - "description": "STAR final log file", - "pattern": "*Log.final.out", - "ontologies": [] - } - } - ] - ], - "log_out": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*Log.out": { - "type": "file", - "description": "STAR lot out file", - "pattern": "*Log.out", - "ontologies": [] - } - } - ] - ], - "log_progress": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*Log.progress.out": { - "type": "file", - "description": "STAR log progress file", - "pattern": "*Log.progress.out", - "ontologies": [] - } - } - ] - ], - "versions_star": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "star": { - "type": "string", - "description": "The tool name" - } - }, - { - "sentieon STAR --version | sed -e \"s/STAR_//g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_sentieon": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "sentieon": { - "type": "string", - "description": "The tool name" - } - }, - { - "sentieon driver --version 2>&1 | sed -e \"s/sentieon-genomics-//g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*d.out.bam": { - "type": "file", - "description": "Output BAM file containing read alignments", - "pattern": "*.{bam}", - "ontologies": [] - } - } - ] - ], - "bam_sorted": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.sortedByCoord.out.bam": { - "type": "file", - "description": "Sorted BAM file of read alignments (optional)", - "pattern": "*sortedByCoord.out.bam", - "ontologies": [] - } - } - ] - ], - "bam_sorted_aligned": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.Aligned.sortedByCoord.out.bam": { - "type": "file", - "description": "Sorted BAM file of read alignments (optional)", - "pattern": "*.Aligned.sortedByCoord.out.bam", - "ontologies": [] - } - } - ] - ], - "bam_transcript": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*toTranscriptome.out.bam": { - "type": "file", - "description": "Output BAM file of transcriptome alignment (optional)", - "pattern": "*toTranscriptome.out.bam", - "ontologies": [] - } - } - ] - ], - "bam_unsorted": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*Aligned.unsort.out.bam": { - "type": "file", - "description": "Unsorted BAM file of read alignments (optional)", - "pattern": "*Aligned.unsort.out.bam", - "ontologies": [] - } - } - ] - ], - "fastq": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*fastq.gz": { - "type": "file", - "description": "Unmapped FastQ files (optional)", - "pattern": "*fastq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "tab": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tab": { - "type": "file", - "description": "STAR output tab file(s) (optional)", - "pattern": "*.tab", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "spl_junc_tab": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.SJ.out.tab": { - "type": "file", - "description": "STAR output splice junction tab file", - "pattern": "*.SJ.out.tab", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "read_per_gene_tab": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.ReadsPerGene.out.tab": { - "type": "file", - "description": "STAR output read per gene tab file", - "pattern": "*.ReadsPerGene.out.tab", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "junction": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.out.junction": { - "type": "file", - "description": "STAR chimeric junction output file (optional)", - "pattern": "*.out.junction", - "ontologies": [] - } - } - ] - ], - "sam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.out.sam": { - "type": "file", - "description": "STAR output SAM file(s) (optional)", - "pattern": "*.out.sam", - "ontologies": [] - } - } - ] - ], - "wig": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.wig": { - "type": "file", - "description": "STAR output wiggle format file(s) (optional)", - "pattern": "*.wig", - "ontologies": [] - } - } - ] - ], - "bedgraph": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bg": { - "type": "file", - "description": "STAR output bedGraph format file(s) (optional)", - "pattern": "*.bg", - "ontologies": [] - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "star": { - "type": "string", - "description": "The tool name" - } - }, - { - "sentieon STAR --version | sed -e \"s/STAR_//g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "sentieon": { - "type": "string", - "description": "The tool name" - } - }, - { - "sentieon driver --version 2>&1 | sed -e \"s/sentieon-genomics-//g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@FriederikeHanssen" - ], - "maintainers": [ - "@FriederikeHanssen" - ] - }, - "pipelines": [ - { - "name": "rnaseq", - "version": "3.26.0" - } - ] - }, - { - "name": "sentieon_tnfilter", - "path": "modules/nf-core/sentieon/tnfilter/meta.yml", - "type": "module", - "meta": { - "name": "sentieon_tnfilter", - "description": "Filters the raw output of sentieon/tnhaplotyper2.\n", - "keywords": [ - "tnfilter", - "filter", - "sentieon", - "tnhaplotyper2", - "vcf" - ], - "tools": [ - { - "sentieon": { - "description": "Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads.\nOur software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.\n", - "homepage": "https://www.sentieon.com/", - "documentation": "https://www.sentieon.com/", - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "compressed vcf file from tnhaplotyper2", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - }, - { - "vcf_tbi": { - "type": "file", - "description": "Tabix index of vcf file", - "pattern": "*vcf.gz.tbi", - "ontologies": [] - } - }, - { - "stats": { - "type": "file", - "description": "Stats file that pairs with output vcf file", - "pattern": "*vcf.gz.stats", - "ontologies": [] - } - }, - { - "contamination": { - "type": "file", - "description": "the location and file name of the file containing the contamination information produced by ContaminationModel.", - "pattern": "*.contamination_data.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - }, - { - "segments": { - "type": "file", - "description": "the location and file name of the file containing the tumor segments information produced by ContaminationModel.", - "pattern": "*.segments", - "ontologies": [] - } - }, - { - "orientation_priors": { - "type": "file", - "description": "the location and file name of the file containing the orientation bias information produced by OrientationBias.", - "pattern": "*.orientation_data.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference fasta file", - "pattern": "*.fasta", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" - } - }, - { - "fai": { - "type": "file", - "description": "Index of reference fasta file", - "pattern": "*.fasta.fai", - "ontologies": [] - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "file", - "description": "file containing filtered tnhaplotyper2 calls.", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - }, - { - "*.vcf.gz": { - "type": "file", - "description": "file containing filtered tnhaplotyper2 calls.", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "tbi": [ - [ - { - "meta": { - "type": "file", - "description": "file containing filtered tnhaplotyper2 calls.", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - }, - { - "*.vcf.gz.tbi": { - "type": "file", - "description": "tbi file that pairs with vcf.", - "pattern": "*.vcf.gz.tbi", - "ontologies": [] - } - } - ] - ], - "stats": [ - [ - { - "meta": { - "type": "file", - "description": "file containing filtered tnhaplotyper2 calls.", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - }, - { - "*.vcf.gz.stats": { - "type": "file", - "description": "file containing statistics of the tnfilter run.", - "pattern": "*.stats", - "ontologies": [] - } - } - ] - ], - "versions_sentieon": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "sentieon": { - "type": "string", - "description": "The tool name" - } - }, - { - "sentieon driver --version | sed \"s/.*-//g\"": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "sentieon": { - "type": "string", - "description": "The tool name" - } - }, - { - "sentieon driver --version | sed \"s/.*-//g\"": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@asp8200" - ] - } - }, - { - "name": "sentieon_tnhaplotyper2", - "path": "modules/nf-core/sentieon/tnhaplotyper2/meta.yml", - "type": "module", - "meta": { - "name": "sentieon_tnhaplotyper2", - "description": "Tnhaplotyper2 performs somatic variant calling on the tumor-normal matched pairs.", - "keywords": [ - "tnseq", - "tnhaplotyper2", - "sentieon", - "variant_calling" - ], - "tools": [ - { - "sentieon": { - "description": "Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads.\nOur software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.\n", - "homepage": "https://www.sentieon.com/", - "documentation": "https://www.sentieon.com/", - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information.\ne.g. [ id:'test' ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM file(s) from alignment", - "pattern": "*.{bam,cram}", - "ontologies": [] - } - }, - { - "input_index": { - "type": "file", - "description": "BAI/CRAI file(s) from alignment", - "pattern": "*.{bai,crai}", - "ontologies": [] - } - }, - { - "intervals": { - "type": "file", - "description": "Bed file with the genomic regions included in the library (optional)", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" - } - }, - { - "dict": { - "type": "file", - "description": "GATK sequence dictionary", - "pattern": "*.dict", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Genome fasta file", - "pattern": "*.{fa,fasta}", - "ontologies": [] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" - } - }, - { - "fai": { - "type": "file", - "description": "Index of the genome fasta file", - "pattern": "*.fai", - "ontologies": [] - } - } - ], - [ - { - "meta5": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" - } - }, - { - "germline_resource": { - "type": "file", - "description": "Population vcf of germline sequencing, containing allele fractions.", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ], - [ - { - "meta6": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" - } - }, - { - "germline_resource_tbi": { - "type": "file", - "description": "Index file for the germline resource.", - "pattern": "*.vcf.gz.tbi", - "ontologies": [] - } - } - ], - [ - { - "meta7": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" - } - }, - { - "panel_of_normals": { - "type": "file", - "description": "vcf file to be used as a panel of normals.", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ], - [ - { - "meta8": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" - } - }, - { - "panel_of_normals_tbi": { - "type": "file", - "description": "Index for the panel of normals.", - "pattern": "*.vcf.gz.tbi", - "ontologies": [] - } - } - ], - { - "emit_orientation_data": { - "type": "boolean", - "description": "If true, the module will run the sentieon algorithm TNhaplotyper2 followed by the sentieon algorithm OrientationBias." - } - }, - { - "emit_contamination_data": { - "type": "boolean", - "description": "If true, the module will run the sentieon algorithm TNhaplotyper2 followed by the sentieon algorithm ContaminationModel." - } - } - ], - "output": { - "orientation_data": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.orientation_data.tsv": { - "type": "file", - "description": "TSV file from Sentieon's algorithm OrientationBias", - "pattern": "*.orientation_data.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "contamination_data": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.contamination_data.tsv": { - "type": "file", - "description": "TSV file from Sentieon's algorithm ContaminationModel", - "pattern": "*.contamination_data.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "contamination_segments": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.segments": { - "type": "file", - "description": "Tumour segments file from Sentieon's algorithm ContaminationModel", - "pattern": "*.segments", - "ontologies": [] - } - } - ] - ], - "stats": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.stats": { - "type": "file", - "description": "Stats file from Sentieon's algorithm", - "pattern": "*.stats", - "ontologies": [] - } - } - ] - ], - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.vcf.gz": { - "type": "file", - "description": "VCF file", - "pattern": "*.{vcf.gz}", - "ontologies": [] - } - } - ] - ], - "index": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.vcf.gz.tbi": { - "type": "file", - "description": "Index of the VCF file", - "pattern": "*.vcf.gz.tbi", - "ontologies": [] - } - } - ] - ], - "versions_sentieon": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "sentieon": { - "type": "string", - "description": "The tool name" - } - }, - { - "sentieon driver --version | sed \"s/.*-//g\"": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "sentieon": { - "type": "string", - "description": "The tool name" - } - }, - { - "sentieon driver --version | sed \"s/.*-//g\"": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@asp8200" - ], - "maintainers": [ - "@asp8200" - ] - } - }, - { - "name": "sentieon_tnscope", - "path": "modules/nf-core/sentieon/tnscope/meta.yml", - "type": "module", - "meta": { - "name": "sentieon_tnscope", - "description": "TNscope algorithm performs somatic variant calling on the tumor-normal matched pair or the tumor only data, using a Haplotyper algorithm.", - "keywords": [ - "tnscope", - "sentieon", - "variant_calling" - ], - "tools": [ - { - "sentieon": { - "description": "Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads.\nOur software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.\n", - "homepage": "https://www.sentieon.com/", - "documentation": "https://www.sentieon.com/", - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information.\ne.g. [ id:'test' ]\n" - } - }, - { - "input": { - "type": "file", - "description": "One or more BAM or CRAM files.", - "pattern": "*.{bam,cram}", - "ontologies": [] - } - }, - { - "input_index": { - "type": "file", - "description": "Indices for the input files", - "pattern": "*.{bai,crai}", - "ontologies": [] - } - }, - { - "intervals": { - "type": "file", - "description": "bed or interval_list file containing interval in the reference that will be used in the analysis. Only recommended for large WGS data, else the overhead may not be worth the additional parallelisation.", - "pattern": "*.{bed,interval_list}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Genome fasta file", - "pattern": "*.{fa,fasta}", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" - } - }, - { - "fai": { - "type": "file", - "description": "Index of the genome fasta file", - "pattern": "*.fai", - "ontologies": [] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" - } - }, - { - "dbsnp": { - "type": "file", - "description": "Single Nucleotide Polymorphism database (dbSNP) file", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ], - [ - { - "meta5": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" - } - }, - { - "dbsnp_tbi": { - "type": "file", - "description": "Index of the Single Nucleotide Polymorphism database (dbSNP) file", - "pattern": "*.vcf.gz.tbi", - "ontologies": [] - } - } - ], - [ - { - "meta6": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" - } - }, - { - "pon": { - "type": "file", - "description": "Single Nucleotide Polymorphism database (dbSNP) file", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } + "name": "bam_tumor_only_somatic_variant_calling_gatk", + "path": "subworkflows/nf-core/bam_tumor_only_somatic_variant_calling_gatk/meta.yml", + "type": "subworkflow", + "meta": { + "name": "bam_tumor_only_somatic_variant_calling_gatk", + "description": "Perform variant calling on a single tumor sample using mutect2 tumor only mode.\nRun the input bam file through getpileupsummarries and then calculatecontaminationto get the contamination and segmentation tables.\nFilter the mutect2 output vcf using filtermutectcalls and the contamination & segmentation tables for additional filtering.\n", + "keywords": [ + "gatk4", + "mutect2", + "getpileupsummaries", + "calculatecontamination", + "filtermutectcalls", + "variant_calling", + "tumor_only", + "filtered_vcf" + ], + "components": [ + "gatk4/mutect2", + "gatk4/getpileupsummaries", + "gatk4/calculatecontamination", + "gatk4/filtermutectcalls" + ], + "input": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "input": { + "type": "list", + "description": "list containing one BAM file, also able to take CRAM as an input", + "pattern": "[ *.{bam/cram} ]" + } + }, + { + "input_index": { + "type": "list", + "description": "list containing one BAM file indexe, also able to take CRAM index as an input", + "pattern": "[ *.{bam.bai/cram.crai} ]" + } + }, + { + "fasta": { + "type": "file", + "description": "The reference fasta file", + "pattern": "*.fasta" + } + }, + { + "fai": { + "type": "file", + "description": "Index of reference fasta file", + "pattern": "*.fasta.fai" + } + }, + { + "dict": { + "type": "file", + "description": "GATK sequence dictionary", + "pattern": "*.dict" + } + }, + { + "alleles": { + "type": "file", + "description": "vcf file to be used to force-call alleles.", + "pattern": "*.vcf.gz" + } + }, + { + "alleles_tbi": { + "type": "file", + "description": "Index file for alleles to be force-called.", + "pattern": "*.vcf.gz.tbi" + } + }, + { + "germline_resource": { + "type": "file", + "description": "Population vcf of germline sequencing, containing allele fractions.", + "pattern": "*.vcf.gz" + } + }, + { + "germline_resource_tbi": { + "type": "file", + "description": "Index file for the germline resource.", + "pattern": "*.vcf.gz.tbi" + } + }, + { + "panel_of_normals": { + "type": "file", + "description": "vcf file to be used as a panel of normals.", + "pattern": "*.vcf.gz" + } + }, + { + "panel_of_normals_tbi": { + "type": "file", + "description": "Index for the panel of normals.", + "pattern": "*.vcf.gz.tbi" + } + }, + { + "interval_file": { + "type": "file", + "description": "File containing intervals.", + "pattern": "*.interval_list" + } + } + ], + "output": [ + { + "mutect2_vcf": { + "type": "file", + "description": "Compressed vcf file to be used for variant_calling.", + "pattern": "[ *.vcf.gz ]" + } + }, + { + "mutect2_tbi": { + "type": "file", + "description": "Indexes of the mutect2_vcf file", + "pattern": "[ *vcf.gz.tbi ]" + } + }, + { + "mutect2_stats": { + "type": "file", + "description": "Stats files for the mutect2 vcf", + "pattern": "[ *vcf.gz.stats ]" + } + }, + { + "pileup_table": { + "type": "file", + "description": "File containing the pileup summary table.", + "pattern": "*.pileups.table" + } + }, + { + "contamination_table": { + "type": "file", + "description": "File containing the contamination table.", + "pattern": "*.contamination.table" + } + }, + { + "segmentation_table": { + "type": "file", + "description": "Output table containing segmentation of tumor minor allele fractions.", + "pattern": "*.segmentation.table" + } + }, + { + "filtered_vcf": { + "type": "file", + "description": "file containing filtered mutect2 calls.", + "pattern": "*.vcf.gz" + } + }, + { + "filtered_tbi": { + "type": "file", + "description": "tbi file that pairs with filtered vcf.", + "pattern": "*.vcf.gz.tbi" + } + }, + { + "filtered_stats": { + "type": "file", + "description": "file containing statistics of the filtermutectcalls run.", + "pattern": "*.filteringStats.tsv" + } + } + ], + "authors": ["@GCJMackenzie"], + "maintainers": ["@GCJMackenzie"] } - ], - [ - { - "meta7": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" - } - }, - { - "pon_tbi": { - "type": "file", - "description": "Index of the Single Nucleotide Polymorphism database (dbSNP) file", - "pattern": "*.vcf.gz.tbi", - "ontologies": [] - } + }, + { + "name": "bam_variant_calling_mpileup_bcftools", + "path": "subworkflows/nf-core/bam_variant_calling_mpileup_bcftools/meta.yml", + "type": "subworkflow", + "meta": { + "name": "BAM_VARIANT_CALLING_MPILEUP_BCFTOOLS", + "description": "Subworkflow to compute genotype likelihoods from BAM files using\nbcftools/mpileup and bcftools/call variants by chromosomes.\nThe resulting VCF files are then merged by chromosomes and\nannotated with bcftools/annotate to give an ID for each variants.\nDuring samples merging and region concatenation, all metadata will\nbe preserved and stored in the key `metas` at each step.\n", + "keywords": ["BAM", "genotype likelihoods", "bcftools"], + "components": [ + "gawk", + "tabix/bgzip", + "bcftools/mpileup", + "bcftools/merge", + "bcftools/annotate", + "bcftools/concat", + "vcf_gather_bcftools" + ], + "input": [ + { + "ch_bam": { + "description": "Channel with input data", + "structure": [ + { + "meta": null, + "type": "map", + "description": "Metadata map" + }, + { + "bam": null, + "type": "file", + "description": "Input BAM file", + "pattern": "*.bam" + }, + { + "index": null, + "type": "file", + "description": "Input BAM index file", + "pattern": "*.{bai,csi}" + } + ] + } + }, + { + "ch_posfile": { + "description": "Channel with position to call variants by chromosomes", + "structure": [ + { + "meta": null, + "type": "map", + "description": "Metadata map that will be combined with the input data map\n" + }, + { + "posfile": null, + "type": "file", + "description": "Region to extract from the BAM file in the format \"CHR\\tPOS\\tREF,ALT\"" + } + ] + } + }, + { + "ch_fasta": { + "description": "Channel with reference genome data", + "structure": [ + { + "meta": null, + "type": "map", + "description": "Metadata map" + }, + { + "fasta": null, + "type": "file", + "description": "FASTA file of the reference genome", + "pattern": "*.fa[sta]+" + }, + { + "fai": null, + "type": "file", + "description": "FASTA index file of the reference genome", + "pattern": "*.fai" + } + ] + } + }, + { + "meta_sample_merge_key": { + "type": "list", + "description": "List of keys that define the sample.\nAll file sharing the same values for these keys will be merged together.\ne.g. [ \"id\" ]\n" + } + }, + { + "meta_sample_merge_value": { + "description": "Shared value that will be set to `meta_sample_merge_key` for all samples to be merged together.\ne.g. \"all_samples\"\n" + } + }, + { + "meta_region_gather_keys": { + "type": "list", + "description": "List of keys to be used to gather the VCF files by region with vcf_gather_bcftools.\nAll file sharing the same values for these keys will be gathered together.\ne.g. [ \"id\", \"panel_id\" ]\n" + } + }, + { + "sort_region_gather": { + "type": "boolean", + "description": "Whether to sort the VCF files by region after concatenation with\nvcf_gather_bcftools.\n" + } + }, + { + "annotate": { + "type": "boolean", + "description": "Whether to annotate the merged VCF file with bcftools/annotate to give\nan ID for each variants\n" + } + } + ], + "output": [ + { + "multiqc_files": { + "description": "Channel containing stat files of bcftools mpileup and call", + "type": "file" + } + }, + { + "vcf_index": { + "description": "Channel with one VCF files by chromosomes", + "structure": [ + { + "meta": null, + "type": "map", + "description": "Metadata map combined with the ch_posfile data map.\n" + }, + { + "vcf": null, + "type": "file", + "description": "VCF file with all individuals merged by chromosomes", + "pattern": "*.{vcf,bcf,vcf.gz}" + }, + { + "index": null, + "type": "file", + "description": "VCF index file", + "pattern": "*.{tbi,csi}" + } + ] + } + } + ], + "authors": ["@louislenezet"], + "maintainers": ["@louislenezet"] } - ], - [ - { - "meta8": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" - } - }, - { - "cosmic": { - "type": "file", - "description": "Catalogue of Somatic Mutations in Cancer (COSMIC) VCF file.", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } + }, + { + "name": "bam_variant_calling_sort_freebayes_bcftools", + "path": "subworkflows/nf-core/bam_variant_calling_sort_freebayes_bcftools/meta.yml", + "type": "subworkflow", + "meta": { + "name": "bam_variant_calling_sort_freebayes_bcftools", + "description": "Call variants using freebayes, then sort and index", + "keywords": ["variant", "sort", "index", "bam", "cram", "vcf"], + "components": ["freebayes", "bcftools/sort", "bcftools/index"], + "input": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "input1": { + "type": "file", + "description": "BAM/CRAM/SAM file;", + "pattern": "*.{bam,cram,sam}" + } + }, + { + "index1": { + "type": "file", + "description": "Index BAI/CRAI/CSI file", + "pattern": "*.{bai,crai,csi}" + } + }, + { + "input2": { + "type": "file", + "description": "BAM/CRAM/SAM file; used to run variant calling with pair (normal vs tumor)", + "pattern": "*.{bam,cram,sam}" + } + }, + { + "index2": { + "type": "file", + "description": "Index BAI/CRAI/CSI file", + "pattern": "*.{bai,crai,csi}" + } + }, + { + "bed": { + "type": "file", + "description": "Optional - Limit analysis to targets listed in this BED-format FILE.", + "pattern": "*.bed" + } + }, + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "reference fasta file", + "pattern": ".{fa,fa.gz,fasta,fasta.gz}" + } + }, + { + "fai": { + "type": "file", + "description": "reference fasta file index", + "pattern": "*.{fa,fasta}.fai" + } + }, + { + "samples": { + "type": "file", + "description": "Optional - Limit analysis to samples listed (one per line) in the FILE.", + "pattern": "*.txt" + } + }, + { + "populations": { + "type": "file", + "description": "Optional - Each line of FILE should list a sample and a population which it is part of.", + "pattern": "*.txt" + } + }, + { + "cnv": { + "type": "file", + "description": "A copy number map BED file, which has either a sample-level ploidy:\nsample_name copy_number\nor a region-specific format:\nseq_name start end sample_name copy_number\n", + "pattern": "*.bed" + } + } + ], + "output": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "Sorted VCF file", + "pattern": "*.{vcf.gz}" + } + }, + { + "csi": { + "type": "file", + "description": "Default VCF file index file", + "pattern": "*.csi" + } + }, + { + "tbi": { + "type": "file", + "description": "Alternative VCF file index file (activated with -t parameter)", + "pattern": "*.tbi" + } + } + ], + "authors": ["@priyanka-surana", "@FriederikeHanssen", "@ramprasadn"], + "maintainers": ["@priyanka-surana", "@FriederikeHanssen", "@ramprasadn"] } - ], - [ - { - "meta9": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" - } + }, + { + "name": "bam_variant_demix_boot_freyja", + "path": "subworkflows/nf-core/bam_variant_demix_boot_freyja/meta.yml", + "type": "subworkflow", + "meta": { + "name": "bam_variant_demix_boot_freyja", + "description": "Recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset (BAM aligned to the Hu-1 reference)", + "keywords": ["bam", "variants", "cram"], + "components": ["freyja/variants", "freyja/demix", "freyja/update", "freyja/boot"], + "input": [ + { + "ch_bam": { + "type": "file", + "description": "Structure: [ val(meta), path(bam) ]\nGroovy Map containing sample information e.g. [ id:'test', single_end:false ] and sorted BAM file\n" + } + }, + { + "ch_fasta": { + "type": "file", + "description": "Structure: [ val(meta), path(fasta) ]\nGroovy Map containing sample information e.g. [ id:'test', single_end:false ] and the fasta reference used for the sorted BAM file\n" + } + }, + { + "val_repeats": { + "type": "integer", + "description": "Number of bootstrap repeats to perform" + } + }, + { + "val_db_name": { + "type": "string", + "description": "Name of the dir where UShER's files will be stored" + } + }, + { + "ch_barcodes": { + "type": "file", + "description": "Structure: path(barcodes)\nFile containing lineage defining barcodes\n" + } + }, + { + "ch_lineages_meta": { + "type": "file", + "description": "Structure: path(lineages_meta)\nFile containing lineage metadata that correspond to barcodes\n" + } + }, + { + "ch_lineages_topology": { + "type": "file", + "description": "Structure: path(lineages_topology)\nFile containing lineage topology information that correspond to barcodes\n" + } + } + ], + "output": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "variants": { + "type": "file", + "description": "Structure: [ val(meta), path(variants) ]\nFile containing identified variants in a gff-like format\n" + } + }, + { + "depths": { + "type": "file", + "description": "Structure: [ val(meta), path(variants) ]\nFile containing depth of the variants\n" + } + }, + { + "demix": { + "type": "file", + "description": "Structure: [ val(meta), path(demix) ]\na tsv file that includes the lineages present, their corresponding abundances, and summarization by constellation\n" + } + }, + { + "lineages": { + "type": "file", + "description": "Structure: [ val(meta), path(lineages) ]\na csv file that includes the lineages present and their corresponding abundances\n" + } + }, + { + "summarized": { + "type": "file", + "description": "Structure: [ val(meta), path(lineages) ]\na csv file that includes the lineages present but summarized by constellation and their corresponding abundances\n" + } + }, + { + "barcodes": { + "type": "file", + "description": "File containing lineage defining barcodes" + } + }, + { + "lineages_meta": { + "type": "file", + "description": "File containing lineage topology information that correspond to barcodes" + } + }, + { + "lineages_topology": { + "type": "file", + "description": "File containing lineage metadata that correspond to barcodes" + } + } + ], + "authors": ["@Joon-Klaps"], + "maintainers": ["@Joon-Klaps"] }, - { - "cosmic_tbi": { - "type": "file", - "description": "Index of the Catalogue of Somatic Mutations in Cancer (COSMIC) VCF file.", - "pattern": "*.vcf.gz.tbi", - "ontologies": [] - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" - } - }, - { - "*.vcf.gz": { - "type": "file", - "description": "VCF file", - "pattern": "*.{vcf.gz}", - "ontologies": [] - } - } - ] - ], - "index": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" - } - }, - { - "*.vcf.gz.tbi": { - "type": "file", - "description": "Index of the VCF file", - "pattern": "*.vcf.gz.tbi", - "ontologies": [] - } - } - ] - ], - "versions_sentieon": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "sentieon": { - "type": "string", - "description": "The tool name" - } - }, - { - "sentieon driver --version | sed \"s/.*-//g\"": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "sentieon": { - "type": "string", - "description": "The tool name" - } - }, - { - "sentieon driver --version | sed \"s/.*-//g\"": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } + "pipelines": [ + { + "name": "viralrecon", + "version": "3.0.0" + } ] - ] - }, - "authors": [ - "@ramprasadn" - ], - "maintainers": [ - "@ramprasadn" - ] - }, - "pipelines": [ - { - "name": "sarek", - "version": "3.8.1" - } - ] - }, - { - "name": "sentieon_varcal", - "path": "modules/nf-core/sentieon/varcal/meta.yml", - "type": "module", - "meta": { - "name": "sentieon_varcal", - "description": "Module for Sentieons VarCal. The VarCal algorithm calculates the Variant Quality Score Recalibration (VQSR).\nVarCal builds a recalibration model for scoring variant quality.\nhttps://support.sentieon.com/manual/usages/general/#varcal-algorithm\n", - "keywords": [ - "sentieon", - "varcal", - "variant recalibration" - ], - "tools": [ - { - "sentieon": { - "description": "Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads.\nOur software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.\n", - "homepage": "https://www.sentieon.com/", - "documentation": "https://www.sentieon.com/", - "identifier": "" + }, + { + "name": "bam_vcf_impute_glimpse2", + "path": "subworkflows/nf-core/bam_vcf_impute_glimpse2/meta.yml", + "type": "subworkflow", + "meta": { + "name": "bam_vcf_impute_glimpse2", + "description": "Impute VCF/BCF files, but also CRAM and BAM files with Glimpse2", + "keywords": ["glimpse", "chunk", "phase", "ligate", "split_reference"], + "components": [ + "glimpse2/chunk", + "glimpse2/phase", + "glimpse2/ligate", + "glimpse2/splitreference", + "bcftools/index" + ], + "input": [ + { + "ch_input": { + "type": "file", + "description": "Target dataset in CRAM, BAM or VCF/BCF format.\nIndex file of the input file.\nFile containing the list of files to be imputed and their sample names (for CRAM/BAM input).\nFile with sample names and ploidy information.\nStructure: [ meta, file, index, bamlist, ploidy ]\n" + } + }, + { + "ch_ref": { + "type": "file", + "description": "Reference panel of haplotypes in VCF/BCF format.\nIndex file of the Reference panel file.\nTarget region, usually a full chromosome (e.g. chr20:1000000-2000000 or chr20).\nThe file could possibly be without GT field (for efficiency reasons a file containing only the positions is recommended).\nStructure: [ meta, vcf, csi, region ]\n" + } + }, + { + "ch_chunks": { + "type": "string", + "description": "Channel containing the chunking regions for each chromosome.\nStructure: [ meta, region with buffer, region without buffer ]\n" + } + }, + { + "ch_map": { + "type": "file", + "description": "Genetic map file for each chromosome.\nStructure: [ meta, gmap ]\n" + } + }, + { + "ch_fasta": { + "type": "file", + "description": "Reference genome in fasta format.\nReference genome index in fai format\nStructure: [ meta, fasta, fai ]\n" + } + }, + { + "chunk": { + "type": "boolean", + "description": "Whether to perform chunking of the input data before imputation." + } + }, + { + "chunk_model": { + "type": "string", + "description": "Chunking model to use.\nOptions: \"sequential\", \"recursive\"\n" + } + }, + { + "splitreference": { + "type": "boolean", + "description": "Whether to split the reference panel and convert it to binary files before imputation." + } + } + ], + "output": [ + { + "ch_chunks": { + "type": "string", + "description": "Channel containing the chunking regions for each chromosome.\nStructure: [ meta, region with buffer, region without buffer ]\n" + } + }, + { + "ch_vcf_index": { + "type": "file", + "description": "Output VCF/BCF file for the merged regions.\nIndex file of the output VCF/BCF file.\nStructure: [ val(meta), variants, index ]\n" + } + } + ], + "authors": ["@LouisLeNezet"], + "maintainers": ["@LouisLeNezet"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "input vcf file containing the variants to be recalibrated", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } + }, + { + "name": "bcl_demultiplex", + "path": "subworkflows/nf-core/bcl_demultiplex/meta.yml", + "type": "subworkflow", + "meta": { + "name": "bcl_demultiplex", + "description": "Demultiplex Illumina BCL data using bcl-convert or bcl2fastq", + "keywords": ["bcl", "bclconvert", "bcl2fastq", "demultiplex", "fastq"], + "components": ["bcl2fastq", "bclconvert", "multiqcsav"], + "input": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'string', lane: int ]\n" + } + }, + { + "samplesheet": { + "type": "file", + "description": "CSV file containing information about samples to be demultiplexed in Illumina SampleSheet format\n" + } + }, + { + "flowcell": { + "type": "file", + "description": "Directory or tar archive containing Illumina BCL data, sequencer output directory" + } + }, + { + "demultiplexer": { + "type": "string", + "description": "Which demultiplexer to use, bcl2fastq or bclconvert" + } + } + ], + "output": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "fastq": { + "type": "file", + "description": "Demultiplexed fastq files", + "pattern": "*.fastq.gz" + } + }, + { + "reports": { + "type": "file", + "description": "Demultiplexing reports", + "pattern": "Reports/*" + } + }, + { + "interop": { + "type": "file", + "description": "InterOp files", + "pattern": "InterOp/*" + } + }, + { + "stats": { + "type": "file", + "description": "Demultiplexing statistics (bcl2fastq only)", + "pattern": "Stats/*" + } + }, + { + "logs": { + "type": "file", + "description": "Demultiplexing logs (bclconvert only)", + "pattern": "Logs/*" + } + }, + { + "versions": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ], + "authors": ["@matthdsm"], + "maintainers": ["@matthdsm"] }, - { - "tbi": { - "type": "file", - "description": "tbi file matching with -vcf", - "pattern": "*.vcf.gz.tbi", - "ontologies": [] - } - } - ], - { - "resource_vcf": { - "type": "file", - "description": "all resource vcf files that are used with the corresponding '--resource' label", - "pattern": "*.vcf.gz", - "ontologies": [ + "pipelines": [ { - "edam": "http://edamontology.org/format_3989" + "name": "demultiplex", + "version": "1.7.1" } - ] - } - }, - { - "resource_tbi": { - "type": "file", - "description": "all resource tbi files that are used with the corresponding '--resource' label", - "pattern": "*.vcf.gz.tbi", - "ontologies": [] - } - }, - { - "labels": { - "type": "string", - "description": "necessary arguments for Sentieon's VarCal. Specified to directly match the resources provided. More information can be found at https://support.sentieon.com/manual/usages/general/#varcal-algorithm" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference fasta file", - "pattern": "*.fasta", - "ontologies": [] - } - }, - { - "fai": { - "type": "file", - "description": "Index of reference fasta file", - "pattern": "fasta.fai", - "ontologies": [] - } - } - ], - "output": { - "recal": [ - [ - { - "meta": { - "type": "file", - "description": "Output recal file used by ApplyVQSR", - "pattern": "*.recal", - "ontologies": [] - } - }, - { - "*.recal": { - "type": "file", - "description": "Output recal file used by ApplyVQSR", - "pattern": "*.recal", - "ontologies": [] - } - } ] - ], - "idx": [ - [ - { - "meta": { - "type": "file", - "description": "Output recal file used by ApplyVQSR", - "pattern": "*.recal", - "ontologies": [] - } - }, - { - "*.idx": { - "type": "file", - "description": "Index file for the recal output file", - "pattern": "*.idx", - "ontologies": [] - } - } - ] - ], - "tranches": [ - [ - { - "meta": { - "type": "file", - "description": "Output recal file used by ApplyVQSR", - "pattern": "*.recal", - "ontologies": [] - } - }, - { - "*.tranches": { - "type": "file", - "description": "Output tranches file used by ApplyVQSR", - "pattern": "*.tranches", - "ontologies": [] - } - } - ] - ], - "plots": [ - [ - { - "meta": { - "type": "file", - "description": "Output recal file used by ApplyVQSR", - "pattern": "*.recal", - "ontologies": [] - } - }, - { - "*plots.R": { - "type": "file", - "description": "Optional output rscript file to aid in visualization of the input data and learned model.", - "pattern": "*plots.R", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3999" - } - ] - } - } - ] - ], - "versions_sentieon": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "sentieon": { - "type": "string", - "description": "The tool name" - } - }, - { - "sentieon driver --version | sed \"s/.*-//g\"": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@asp8200" - ], - "maintainers": [ - "@asp8200" - ], - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "sentieon": { - "type": "string", - "description": "The tool name" - } - }, - { - "sentieon driver --version | sed \"s/.*-//g\"": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - } - }, - "pipelines": [ + }, { - "name": "sarek", - "version": "3.8.1" - } - ] - }, - { - "name": "sentieon_wgsmetrics", - "path": "modules/nf-core/sentieon/wgsmetrics/meta.yml", - "type": "module", - "meta": { - "name": "sentieon_wgsmetrics", - "description": "Collects whole genome quality metrics from a bam file", - "keywords": [ - "metrics", - "bam", - "sentieon" - ], - "tools": [ - { - "sentieon": { - "description": "Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads.\nOur software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.\n", - "homepage": "https://www.sentieon.com/", - "documentation": "https://www.sentieon.com/", - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } - }, - { - "bai": { - "type": "file", - "description": "Index of th sorted BAM/CRAM/SAM file", - "pattern": "*.{bai,crai,sai}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Genome fasta file", - "pattern": "*.{fa,fasta}", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "fai": { - "type": "file", - "description": "Index of the genome fasta file", - "pattern": "*.fai", - "ontologies": [] - } + "name": "bed_scatter_bedtools", + "path": "subworkflows/nf-core/bed_scatter_bedtools/meta.yml", + "type": "subworkflow", + "meta": { + "name": "bed_scatter_bedtools", + "description": "Scatters inputted BED files by the amount specified.\nThe configuration in nextflow.config should be added to your modules.config for the subworkflow to work.\n", + "keywords": ["bed", "scatter", "bedtools"], + "components": ["bedtools/split"], + "input": [ + { + "ch_bed": { + "description": "The input channel containing the BED file and an integer stating the amount of files it should be split into\nStructure: [ val(meta), path(bed), val(scatter_count) ]\n" + } + } + ], + "output": [ + { + "scattered_beds": { + "description": "One channel entry per scattered BED file (all BED files from the same source are transposed but contain the same meta)\nStructure: [ val(meta), path(bed), val(scatter_count) ]\n" + } + } + ], + "authors": ["@nvnieuwk"], + "maintainers": ["@nvnieuwk"] } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. `[ id:'test' ]`\n" - } + }, + { + "name": "bedgraph_bedclip_bedgraphtobigwig", + "path": "subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/meta.yml", + "type": "subworkflow", + "meta": { + "name": "bedgraph_bedclip_bedgraphtobigwig", + "description": "Convert bedgraph to bigwig with clip", + "keywords": ["bedgraph", "bigwig", "clip", "conversion"], + "components": ["ucsc/bedclip", "ucsc/bedgraphtobigwig"], + "input": [ + { + "bedgraph": { + "type": "file", + "description": "bedGraph file which should be converted", + "pattern": "*.bedGraph" + } + }, + { + "sizes": { + "type": "file", + "description": "File with chromosome sizes", + "pattern": "*.sizes" + } + } + ], + "output": [ + { + "bigwig": { + "type": "file", + "description": "bigWig coverage file relative to genes on the input file", + "pattern": ".bigWig" + } + }, + { + "bedgraph": { + "type": "file", + "description": "bedGraph file after clipping", + "pattern": "*.bedGraph" + } + }, + { + "versions": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ], + "authors": ["@drpatelh", "@KamilMaliszArdigen"], + "maintainers": ["@drpatelh", "@KamilMaliszArdigen"] }, - { - "intervals_list": { - "type": "file", - "description": "intervals", - "ontologies": [] - } - } - ] - ], - "output": { - "wgs_metrics": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*.txt": { - "type": "file", - "description": "File containing the information about mean base quality score for each sequencing cycle", - "pattern": "*.txt", - "ontologies": [] - } - } - ] - ], - "versions_sentieon": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "sentieon": { - "type": "string", - "description": "The tool name" - } - }, - { - "sentieon driver --version | sed \"s/.*-//g\"": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } + "pipelines": [ + { + "name": "rnaseq", + "version": "3.26.0" + }, + { + "name": "rnasplice", + "version": "1.0.4" + } ] - ] - }, - "authors": [ - "@ramprasadn" - ], - "maintainers": [ - "@ramprasadn" - ], - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "sentieon": { - "type": "string", - "description": "The tool name" - } - }, - { - "sentieon driver --version | sed \"s/.*-//g\"": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - } - }, - "pipelines": [ + }, { - "name": "raredisease", - "version": "3.0.0" - } - ] - }, - { - "name": "seq2hla", - "path": "modules/nf-core/seq2hla/meta.yml", - "type": "module", - "meta": { - "name": "seq2hla", - "description": "Precision HLA typing and expression from RNA-seq data using seq2HLA", - "keywords": [ - "hla", - "typing", - "rna-seq", - "genomics", - "immunogenetics" - ], - "tools": [ - { - "seq2hla": { - "description": "Precision HLA typing and expression from next-generation RNA sequencing data", - "homepage": "https://github.com/TRON-Bioinformatics/seq2HLA", - "documentation": "https://github.com/TRON-Bioinformatics/seq2HLA#readme", - "tool_dev_url": "https://github.com/TRON-Bioinformatics/seq2HLA", - "doi": "10.1186/s13073-015-0240-5", - "licence": [ - "MIT" - ], - "identifier": "biotools:seq2HLA" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "reads": { - "type": "file", - "description": "Paired-end FASTQ files for RNA-seq data", - "pattern": "*.{fastq.gz,fq.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "output": { - "class1_genotype_2d": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*ClassI-class.HLAgenotype2digits": { - "type": "file", - "description": "HLA Class I 2-digit genotype results", - "pattern": "*ClassI-class.HLAgenotype2digits", - "ontologies": [] - } - } - ] - ], - "class2_genotype_2d": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*ClassII.HLAgenotype2digits": { - "type": "file", - "description": "HLA Class II 2-digit genotype results", - "pattern": "*ClassII.HLAgenotype2digits", - "ontologies": [] - } - } - ] - ], - "class1_genotype_4d": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*ClassI-class.HLAgenotype4digits": { - "type": "file", - "description": "HLA Class I 4-digit genotype results", - "pattern": "*ClassI-class.HLAgenotype4digits", - "ontologies": [] - } - } - ] - ], - "class2_genotype_4d": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*ClassII.HLAgenotype4digits": { - "type": "file", - "description": "HLA Class II 4-digit genotype results", - "pattern": "*ClassII.HLAgenotype4digits", - "ontologies": [] - } - } - ] - ], - "class1_bowtielog": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*ClassI-class.bowtielog": { - "type": "file", - "description": "HLA Class I Bowtie alignment log", - "pattern": "*ClassI-class.bowtielog", - "ontologies": [] - } - } - ] - ], - "class2_bowtielog": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*ClassII.bowtielog": { - "type": "file", - "description": "HLA Class II Bowtie alignment log", - "pattern": "*ClassII.bowtielog", - "ontologies": [] - } - } - ] - ], - "class1_expression": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*ClassI-class.expression": { - "type": "file", - "description": "HLA Class I expression results", - "pattern": "*ClassI-class.expression", - "ontologies": [] - } - } - ] - ], - "class2_expression": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*ClassII.expression": { - "type": "file", - "description": "HLA Class II expression results", - "pattern": "*ClassII.expression", - "ontologies": [] - } - } - ] - ], - "class1_nonclass_genotype_2d": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*ClassI-nonclass.HLAgenotype2digits": { - "type": "file", - "description": "HLA Class I non-classical 2-digit genotype results", - "pattern": "*ClassI-nonclass.HLAgenotype2digits", - "ontologies": [] - } - } - ] - ], - "ambiguity": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.ambiguity": { - "type": "file", - "description": "HLA typing ambiguity results", - "pattern": "*.ambiguity", - "ontologies": [] - } - } - ] - ], - "class1_nonclass_genotype_4d": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*ClassI-nonclass.HLAgenotype4digits": { - "type": "file", - "description": "HLA Class I non-classical 4-digit genotype results", - "pattern": "*ClassI-nonclass.HLAgenotype4digits", - "ontologies": [] - } - } - ] - ], - "class1_nonclass_bowtielog": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*ClassI-nonclass.bowtielog": { - "type": "file", - "description": "HLA Class I non-classical Bowtie alignment log", - "pattern": "*ClassI-nonclass.bowtielog", - "ontologies": [] - } - } - ] - ], - "class1_nonclass_expression": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*ClassI-nonclass.expression": { - "type": "file", - "description": "HLA Class I non-classical expression results", - "pattern": "*ClassI-nonclass.expression", - "ontologies": [] - } - } - ] - ], - "versions_seq2hla": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "seq2hla": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "seq2HLA --version | sed 's/seq2HLA.py //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "seq2hla": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "seq2HLA --version | sed 's/seq2HLA.py //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@FriederikeHanssen" - ], - "maintainers": [ - "@FriederikeHanssen" - ] - }, - "pipelines": [ - { - "name": "rnavar", - "version": "1.2.3" - } - ] - }, - { - "name": "seqcluster_collapse", - "path": "modules/nf-core/seqcluster/collapse/meta.yml", - "type": "module", - "meta": { - "name": "seqcluster_collapse", - "description": "Seqcluster collapse reduces computational complexity by collapsing identical sequences in a FASTQ file.", - "keywords": [ - "smrnaseq", - "cluster", - "mirna" - ], - "tools": [ - { - "seqcluster": { - "description": "Small RNA analysis from NGS data. Seqcluster generates a list of clusters of small RNA sequences, their genome location, their annotation and the abundance in all the sample of the project.", - "homepage": "https://github.com/lpantano/seqcluster", - "documentation": "https://github.com/lpantano/seqcluster", - "tool_dev_url": "https://github.com/lpantano/seqcluster", - "doi": "10.1093/bioinformatics/btr527", - "licence": [ - "MIT" - ], - "identifier": "biotools:seqcluster" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "fastq": { - "type": "file", - "description": "FASTQ file", - "pattern": "*.{fastq.gz}", - "ontologies": [] - } - } - ] - ], - "output": { - "fastq": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.fastq.gz": { - "type": "file", - "description": "FASTQ file", - "pattern": "*.{fastq.gz}", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@atrigila" - ], - "maintainers": [ - "@atrigila" - ] - }, - "pipelines": [ - { - "name": "smrnaseq", - "version": "2.4.1" - } - ] - }, - { - "name": "seqfu_check", - "path": "modules/nf-core/seqfu/check/meta.yml", - "type": "module", - "meta": { - "name": "seqfu_check", - "description": "Evaluates the integrity of DNA FASTQ files", - "keywords": [ - "check", - "seqfu", - "fastq" - ], - "tools": [ - { - "seqfu": { - "description": "A general-purpose program to manipulate and parse information from FASTQ files", - "homepage": "https://telatin.github.io/seqfu2/", - "documentation": "https://telatin.github.io/seqfu2/tools/check.html#usage", - "tool_dev_url": "https://github.com/telatin/seqfu2", - "doi": "10.3390/bioengineering8050059", - "licence": [ - "MIT" - ], - "identifier": "biotools:seqfu" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" - } - }, - { - "reads": { - "type": "file", - "description": "Either fastq file(s) or directory containing fastq files to be checked", - "pattern": "*.{fq,fastq}[.gz]", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1931" - } - ] - } - } - ] - ], - "output": { - "check": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" - } - }, - { - "${prefix}.tsv": { - "type": "file", - "description": "Tab-separated output file with basic sequence statistics.\n", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_seqfu": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "seqfu": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "seqfu version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "seqfu": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "seqfu version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@kornkv", - "@mrozon-zip" - ], - "maintainers": [ - "@kornkv", - "@mrozon-zip", - "@vagkaratzas" - ] - } - }, - { - "name": "seqfu_derep", - "path": "modules/nf-core/seqfu/derep/meta.yml", - "type": "module", - "meta": { - "name": "seqfu_derep", - "description": "Dereplicate FASTX sequences, removing duplicate sequences and printing the number of identical sequences in the sequence header. Can dereplicate already dereplicated FASTA files, summing the numbers found in the headers.", - "keywords": [ - "dereplicate", - "fasta", - "uniques" - ], - "tools": [ - { - "seqfu": { - "description": "DNA sequence utilities for FASTX files", - "homepage": "https://telatin.github.io/seqfu2/", - "documentation": "https://telatin.github.io/seqfu2/", - "tool_dev_url": "https://telatin.github.io/seqfu2/tools/derep.html", - "doi": "10.3390/bioengineering8050059", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:seqfu" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "fastas": { - "type": "file", - "description": "Input files (mainly FASTA, FASTQ supported)", - "pattern": "*.{fa,fna,faa,fasta,fq,fastq}[.gz]", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "output": { - "fasta": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*_derep.fasta.gz": { - "type": "file", - "description": "dereplicated file (FASTA format)", - "pattern": "*.{fasta.gz}", - "ontologies": [] - } - } - ] - ], - "versions_seqfu": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "seqfu": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "seqfu version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "seqfu": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "seqfu version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@telatin" - ], - "maintainers": [ - "@telatin" - ] - } - }, - { - "name": "seqfu_stats", - "path": "modules/nf-core/seqfu/stats/meta.yml", - "type": "module", - "meta": { - "name": "seqfu_stats", - "description": "Statistics for FASTA or FASTQ files", - "keywords": [ - "seqfu", - "stats", - "n50" - ], - "tools": [ - { - "seqfu": { - "description": "Cross-platform compiled suite of tools to manipulate and inspect FASTA and FASTQ files", - "homepage": "https://telatin.github.io/seqfu2/", - "documentation": "https://telatin.github.io/seqfu2/", - "tool_dev_url": "https://github.com/telatin/seqfu2", - "doi": "10.3390/bioengineering8050059", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:seqfu" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "files": { - "type": "file", - "description": "One or more FASTA or FASTQ files", - "pattern": "*.{fasta,fastq,fasta.gz,fastq.gz,fq,fq.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } + "name": "cache_download_ensemblvep_snpeff", + "path": "subworkflows/nf-core/cache_download_ensemblvep_snpeff/meta.yml", + "type": "subworkflow", + "meta": { + "name": "cache_download_ensemblvep_snpeff", + "description": "downlad annotation cache for snpeff and ensemblvep", + "keywords": ["ensemblvep", "snpeff", "download", "annotation", "cache"], + "components": ["ensemblvep/download", "snpeff/download"], + "input": [ + { + "ensemblvep_info": { + "description": "All information necessary to download the cache\nStructure: [ val(meta), val(ensemblvep_genome), val(ensemblvep_species), val(ensemblvep_cache_version) ]\n" + } + }, + { + "snpeff_info": { + "description": "All information necessary to download the cache\nStructure: [ val(meta), val(snpeff_db) ]\n" + } + }, + { + "ensemblvep_preflight_check": { + "description": "Whether to check that the expected cache file is listed in the Ensembl CHECKSUMS file before downloading\nStructure: val(true/false)\n" + } + } + ], + "output": [ + { + "ensemblvep_cache": { + "description": "Path to ensemblvep cache\nStructure: [ val(meta), path(cache) ]\n" + } + }, + { + "snpeff_cache": { + "description": "Path to snpeff cache\nStructure: [ val(meta), path(cache) ]\n" + } + } + ], + "authors": ["@maxulysse"], + "maintainers": ["@maxulysse"] } - ] - ], - "output": { - "stats": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "Tab-separated output file with basic sequence statistics.", - "pattern": "*.{tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "multiqc": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*_mqc.txt": { - "type": "file", - "description": "MultiQC ready table", - "pattern": "*.{_mqc.txt}", - "ontologies": [] - } - } - ] - ], - "versions_seqfu": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "seqfu": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "seqfu version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "seqfu": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "seqfu version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] }, - "authors": [ - "@telatin" - ], - "maintainers": [ - "@telatin" - ] - }, - "pipelines": [ { - "name": "proteinannotator", - "version": "1.1.0" + "name": "deepvariant", + "path": "subworkflows/nf-core/deepvariant/meta.yml", + "type": "subworkflow", + "meta": { + "name": "deepvariant", + "description": "DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data", + "keywords": ["variant calling", "machine learning", "neural network"], + "components": [ + "deepvariant/makeexamples", + "deepvariant/callvariants", + "deepvariant/postprocessvariants" + ], + "input": [ + { + "ch_input": { + "type": "list", + "description": "Input aligned reads in bam or cram format, with index, and optional intervals BED file\nStructure: [ val(meta), path(bam_or_cram), path(bai_or_crai), path(intervals_bed) ]\n" + } + }, + { + "ch_fasta": { + "type": "file", + "description": "Reference genome\nStructure: [ val(meta2), path(fasta) ]\n" + } + }, + { + "ch_fai": { + "type": "string", + "description": "Reference genome index in fai format\nStructure: [ val(meta3), path(fai) ]\n" + } + }, + { + "ch_gzi": { + "type": "string", + "description": "Reference genome index in gzi format (either gzi or fai should be used)\nStructure: [ val(meta4), val(gzi) ]\n" + } + }, + { + "ch_par_bed": { + "type": "string", + "description": "bed file of pseudoautosomal regions (optional)\nStructure: [ val(meta5), val(par_bed) ]\n", + "pattern": "*.bed" + } + } + ], + "output": [ + { + "vcf": { + "type": "file", + "description": "Variant calls\nStructure: [ val(meta), path(vcf) ]\n", + "pattern": "*.vcf.gz" + } + }, + { + "vcf_tbi": { + "type": "file", + "description": "Index for variant call file\nStructure: [ val(meta), path(vcf_tbi) ]\n", + "pattern": "*.tbi" + } + }, + { + "gvcf": { + "type": "file", + "description": "Variant call file with genomic coverage information\nStructure: [ val(meta), path(gvcf) ]\n", + "pattern": "*.g.vcf.gz" + } + }, + { + "gvcf_tbi": { + "type": "file", + "description": "Index for the GVCF.\nStructure: [ val(meta), path(gvcf_tbi) ]\n", + "pattern": "*.tbi" + } + }, + { + "versions": { + "type": "file", + "description": "File containing software versions\nStructure: path(versions.yml)\n", + "pattern": "versions.yml" + } + } + ], + "authors": ["@abhi18av", "@ramprasadn", "@fa2k"], + "maintainers": ["@abhi18av", "@ramprasadn", "@fa2k"] + } }, { - "name": "proteinfamilies", - "version": "2.3.0" + "name": "dia_proteomics_analysis", + "path": "subworkflows/nf-core/dia_proteomics_analysis/meta.yml", + "type": "subworkflow", + "meta": { + "name": "dia_proteomics_analysis", + "description": "Complete DIA-NN proteomics analysis pipeline including in-silico library generation,\npreliminary analysis, empirical library assembly, individual analysis, and final quantification.\nThis subworkflow combines DIA-NN modules with quantms-utils for comprehensive\ndata-independent acquisition (DIA) proteomics data processing.\n", + "keywords": ["diann", "proteomics", "dia", "quantification", "spectral library", "quantms-utils"], + "tools": [ + { + "diann": { + "description": "DIA-NN is a universal software for data-independent acquisition (DIA) proteomics data processing.\nIt uses deep learning to predict spectral libraries and perform peptide identification and quantification.\n", + "homepage": "https://github.com/vdemichev/DiaNN", + "documentation": "https://github.com/vdemichev/DiaNN", + "tool_dev_url": "https://github.com/vdemichev/DiaNN", + "doi": "10.1038/s41592-020-01009-0", + "licence": ["https://github.com/vdemichev/DiaNN/blob/1.8.1/LICENSE.txt"], + "identifier": "biotools:diann" + } + }, + { + "quantms-utils": { + "description": "quantms-utils is a Python package with scripts and functions for quantitative proteomics data analysis.\nProvides utilities for DIA-NN configuration, mzML statistics, and format conversion to mzTab.\n", + "homepage": "https://github.com/bigbio/quantms-utils", + "documentation": "https://github.com/bigbio/quantms-utils", + "tool_dev_url": "https://github.com/bigbio/quantms-utils", + "licence": ["MIT"], + "identifier": "biotools:quantms-utils" + } + } + ], + "components": [ + "diann", + "quantmsutils/dianncfg", + "quantmsutils/mzmlstatistics", + "quantmsutils/diann2mztab" + ], + "input": [ + { + "ch_input": { + "type": "channel", + "description": "Channel containing tuples of meta maps, mass spectrometry files, and search parameters.\nStructure: [meta, ms_file, enzyme, fixed_mods, variable_mods, precursor_tolerance,\nfragment_tolerance, precursor_tolerance_unit, fragment_tolerance_unit]\ne.g. `[[id:'sample1'], file('sample1.mzML'), 'Trypsin', 'Carbamidomethyl (C)',\n'Oxidation (M)', 10, 20, 'ppm', 'ppm']`\nNote: For Thermo RAW file conversion to mzML, the ThermoRawFileParser module is available\nin nf-core/modules and can be used upstream of this subworkflow.\n", + "pattern": "*.{mzML,mzml}" + } + }, + { + "ch_searchdb": { + "type": "channel", + "description": "Channel containing tuples of meta maps and protein sequence database in FASTA format.\nStructure: [meta, fasta]\ne.g. `[[id:'uniprot_human'], file('uniprot_human.fasta')]`\n", + "pattern": "*.{fasta,fa}" + } + }, + { + "ch_expdesign": { + "type": "channel", + "description": "Channel containing tuples of meta maps and experimental design files.\nStructure: [meta, expdesign]\ne.g. `[[id:'experiment1'], file('design.tsv')]`\n", + "pattern": "*.tsv" + } + }, + { + "random_preanalysis": { + "type": "tuple", + "description": "Tuple controlling random sampling for preliminary analysis.\nStructure: [boolean, integer, integer] for [enable_random, n_samples, seed]\ne.g. `[true, 5, 42]` to randomly sample 5 files with seed 42\nSet to null or [false, null, null] to use all files\n" + } + }, + { + "wf_scan_window": { + "type": "integer", + "description": "Scan window parameter for DIA-NN individual analysis.\nOnly used if wf_scan_window_automatic is false.\n" + } + }, + { + "wf_mass_acc_automatic": { + "type": "boolean", + "description": "If true, use automatic mass accuracy settings extracted from DIA-NN preliminary analysis log.\nIf false, use user-provided precursor_tolerance and fragment_tolerance from ch_input.\n" + } + }, + { + "wf_scan_window_automatic": { + "type": "boolean", + "description": "If true, use automatic scan window settings extracted from DIA-NN preliminary analysis log.\nIf false, use user-provided wf_scan_window parameter.\n" + } + }, + { + "wf_diann_debug": { + "type": "boolean", + "description": "Enable DIA-NN debug output mode for troubleshooting.\n" + } + }, + { + "wf_pg_level": { + "type": "string", + "description": "Protein group level for DIA-NN analysis.\nOptions: 'genes', 'proteins', etc.\n" + } + }, + { + "ch_speclib_in": { + "type": "channel", + "description": "Optional channel containing pre-generated spectral library file.\nIf provided, skips in-silico library generation.\nApplied to all samples in the workflow.\nStructure: path(speclib)\ne.g. `file('pregenerated.speclib')`\n", + "pattern": "*.{speclib,tsv}" + } + }, + { + "ch_empirical_library_in": { + "type": "channel", + "description": "Optional channel containing pre-generated empirical library file.\nIf provided, skips preliminary analysis and empirical library assembly.\nApplied to all samples in the workflow.\nStructure: path(empirical_library)\ne.g. `file('empirical_library.speclib')`\n", + "pattern": "*.speclib" + } + }, + { + "ch_empirical_log_in": { + "type": "channel", + "description": "Optional channel containing assembly log from pre-generated empirical library.\nRequired if ch_empirical_library_in is provided (for extracting mass accuracy settings).\nStructure: path(assembly_log)\ne.g. `file('assembly.log')`\n", + "pattern": "*.log" + } + } + ], + "output": [ + { + "versions": { + "description": "File containing software versions", + "structure": [ + { + "versions": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] + } + }, + { + "diann_report": { + "description": "Main DIA-NN report in TSV format containing quantification results", + "structure": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing experiment and search database information" + } + }, + { + "report": { + "type": "file", + "description": "Main DIA-NN report in TSV format", + "pattern": "*.tsv" + } + } + ] + } + }, + { + "diann_report_parquet": { + "description": "Main DIA-NN report in Parquet format containing quantification results", + "structure": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing experiment and search database information" + } + }, + { + "report": { + "type": "file", + "description": "Main DIA-NN report in Parquet format", + "pattern": "*.parquet" + } + } + ] + } + }, + { + "mzml_statistics": { + "description": "Statistics extracted from mzML files", + "structure": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "statistics": { + "type": "file", + "description": "mzML statistics in parquet format", + "pattern": "*_ms_info.parquet" + } + } + ] + } + }, + { + "msstats_in": { + "description": "MSstats-compatible input file for statistical analysis", + "structure": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing experiment and search database information" + } + }, + { + "msstats": { + "type": "file", + "description": "MSstats input file", + "pattern": "*_msstats_in.csv" + } + } + ] + } + }, + { + "out_triqler": { + "description": "Triqler-compatible input file for protein quantification with uncertainty", + "structure": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing experiment and search database information" + } + }, + { + "triqler": { + "type": "file", + "description": "Triqler input file", + "pattern": "*_triqler_in.tsv" + } + } + ] + } + }, + { + "final_result": { + "description": "Final quantification results in mzTab format", + "structure": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing experiment and search database information" + } + }, + { + "mztab": { + "type": "file", + "description": "Final results in mzTab format (standard proteomics exchange format)", + "pattern": "*.mzTab" + } + } + ] + } + } + ], + "authors": ["@daichengxin", "@wanghong", "@pinin4fjords", "@DongzeHE"], + "maintainers": ["@daichengxin", "@pinin4fjords", "@DongzeHE"] + } }, { - "name": "seqinspector", - "version": "1.0.1" - } - ] - }, - { - "name": "seqkit_concat", - "path": "modules/nf-core/seqkit/concat/meta.yml", - "type": "module", - "meta": { - "name": "seqkit_concat", - "description": "Concatenating multiple uncompressed sequence files together", - "keywords": [ - "concat", - "fasta", - "fastq", - "merge" - ], - "tools": [ - { - "seqkit": { - "description": "Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen.\n", - "homepage": "https://github.com/shenwei356/seqkit", - "documentation": "https://bioinf.shenwei.me/seqkit/", - "tool_dev_url": "https://github.com/shenwei356/seqkit", - "doi": "10.1371/journal.pone.0163962", - "licence": [ - "MIT" - ], - "identifier": "biotools:seqkit" + "name": "differential_functional_enrichment", + "path": "subworkflows/nf-core/differential_functional_enrichment/meta.yml", + "type": "subworkflow", + "meta": { + "name": "differential_functional_enrichment", + "description": "Run functional analysis on differential abundance analysis output", + "keywords": [ + "functional analysis", + "functional enrichment", + "differential", + "over-representation analysis" + ], + "components": [ + "gprofiler2/gost", + "gsea/gsea", + "decoupler/decoupler", + "propr/grea", + "custom/tabulartogseagct", + "custom/tabulartogseacls", + "custom/tabulartogseachip" + ], + "input": [ + { + "ch_input": { + "description": "Channel with the input data for functional analysis.", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata map" + } + }, + { + "input": { + "type": "file", + "description": "Input file. This should be the DE statistics obtained from the DE modules,\nor the normalized abundance matrix (in the case of running GSEA).\n" + } + }, + { + "genesets": { + "type": "file", + "description": "Gene sets database. Currently all methods support GMT format.\n" + } + }, + { + "background": { + "type": "file", + "description": "Background features for functional analysis.\nFor the moment, it is only required for gprofiler2.\n" + } + }, + { + "analysis_method": { + "type": "value", + "description": "Analysis method (gprofiler2, gsea, decoupler or grea)" + } + } + ] + } + }, + { + "ch_contrasts": { + "description": "Channel with contrast information", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata map" + } + }, + { + "meta_contrast": { + "type": "map", + "description": "Map with all the contrast info, such as contrast\nid, variable, reference, target, etc.\n" + } + }, + { + "variable": { + "type": "list", + "description": "List of contrast variable" + } + }, + { + "reference": { + "type": "list", + "description": "List of reference level" + } + }, + { + "target": { + "type": "list", + "description": "List of target level" + } + }, + { + "formula": { + "type": "list", + "description": "List of contrast formula" + } + }, + { + "comparison": { + "type": "list", + "description": "List of contrast comparison" + } + } + ] + } + }, + { + "ch_samplesheet": { + "description": "Channel with sample information", + "structure": [ + { + "meta_exp": { + "type": "map", + "description": "Experiment metadata map" + } + }, + { + "samplesheet": { + "type": "file", + "description": "Sample information file", + "pattern": "*.{csv,tsv}" + } + } + ] + } + }, + { + "ch_featuresheet": { + "description": "Channel with features information", + "structure": [ + { + "meta_exp": { + "type": "map", + "description": "Experiment metadata map" + } + }, + { + "features": { + "type": "file", + "description": "Features information file", + "pattern": "*.{csv,tsv}" + } + }, + { + "features_id": { + "type": "value", + "description": "Features id column" + } + }, + { + "features_symbol": { + "type": "value", + "description": "Features symbol column" + } + } + ] + } + } + ], + "output": [ + { + "versions": { + "type": "file", + "description": "File containing software versions\nStructure: [ path(versions.yml) ]\n", + "pattern": "versions.yml" + } + }, + { + "gprofiler2_all_enrich": { + "description": "Channel containing the main enrichment table output from gprofiler2", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata map" + } + }, + { + "all_enrich": { + "type": "file", + "description": "Table listing all enriched pathways that were found by gprofiler2.\nIt can be empty, if none is found.\n", + "pattern": "*.gprofiler2.all_enriched_pathways.tsv" + } + } + ] + } + }, + { + "gprofiler2_sub_enrich": { + "description": "Channel containing the secondary enrichment table output from gprofiler2.", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata map" + } + }, + { + "sub_enrich": { + "type": "file", + "description": "Table listing enriched pathways that were found from one particular source.\nNote that it will only be created if any were found.\n", + "pattern": "*.gprofiler2.*.sub_enriched_pathways.tsv" + } + } + ] + } + }, + { + "gprofiler2_plot_html": { + "description": "Channel containing the html report generated from gprofiler2.", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata map" + } + }, + { + "plot_html": { + "type": "file", + "description": "HTML file; interactive Manhattan plot of all enriched pathways.\nNote that this file will only be generated if enriched pathways were found.\n", + "pattern": "*.gprofiler2.gostplot.html" + } + } + ] + } + }, + { + "gprofiler2_artifacts": { + "description": "Channel containing additional gprofiler2 artifacts.", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata map" + } + }, + { + "artifact": { + "type": "file", + "description": "Additional outputs from gprofiler2, including gost results (RDS),\nfiltered GMT files, R session logs, and PNG plot files.\n", + "pattern": "*.{rds,gmt,log,png}" + } + } + ] + } + }, + { + "gsea_report": { + "description": "Channel containing all the output from GSEA needed for further reporting.", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata map" + } + }, + { + "reports_ref": { + "type": "file", + "description": "Main TSV results report file for the reference group.", + "pattern": "*gsea_report_for_${reference}.tsv" + } + }, + { + "reports_target": { + "type": "file", + "description": "Main TSV results report file for the target group.", + "pattern": "*gsea_report_for_${target}.tsv" + } + } + ] + } + }, + { + "gsea_artifacts": { + "description": "Channel containing additional GSEA output artifacts.", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata map" + } + }, + { + "artifact": { + "type": "file", + "description": "Additional files generated by GSEA, including reports, plots, archives,\nand supporting HTML/TSV outputs.\n", + "pattern": "*.{rpt,html,tsv,png,zip}" + } + } + ] + } + }, + { + "decoupler_dc_estimate": { + "description": "Channel containing decoupler estimate results.", + "structure": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end ]\n" + } + }, + { + "estimate_files": { + "type": "file", + "description": "Files containing the estimation results of the enrichment(s)\n", + "pattern": "*estimate_decoupler.tsv" + } + } + ] + } + }, + { + "decoupler_dc_pvals": { + "description": "Channel containing decoupler pvals results.", + "structure": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end ]\n" + } + }, + { + "pvals_files": { + "type": "file", + "description": "Files containing the p-values associated to the estimation\nresults of the enrichment(s)\n", + "pattern": "*pvals_decoupler.tsv" + } + } + ] + } + }, + { + "decoupler_png": { + "description": "Channel containing decoupler png results.", + "structure": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end ]\n" + } + }, + { + "plot_files": { + "type": "file", + "description": "Files containing the plots associated to the estimation\nresults of the enrichment(s)\n", + "pattern": "*estimate_decoupler_plot.png" + } + } + ] + } + }, + { + "grea_results": { + "description": "Channel containing the output from GREA.", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata map" + } + }, + { + "results": { + "type": "file", + "description": "Main TSV results file.", + "pattern": "*.grea.tsv" + } + } + ] + } + } + ], + "authors": ["@suzannejin", "@bjlang", "@caraiz2001"], + "maintainers": ["@suzannejin", "@pinin4fjords"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } + }, + { + "name": "faa_seqfu_seqkit", + "path": "subworkflows/nf-core/faa_seqfu_seqkit/meta.yml", + "type": "subworkflow", + "meta": { + "name": "faa_seqfu_seqkit", + "description": "Subworkflow that optionally preprocesses amino acid FASTA sequences\n(seqkit seq/replace/rmdup), computes sequence statistics before and\nafter preprocessing using seqfu stats, and exports MultiQC-compatible\nstatistics and software versions.\n", + "keywords": ["fasta", "protein", "preprocessing", "statistics", "quality check"], + "components": ["seqfu/stats", "seqkit/seq", "seqkit/rmdup", "seqkit/replace"], + "input": [ + { + "ch_fasta": { + "type": "file", + "description": "Amino acid sequences fasta file.\nStructure: [ val(meta), [ path(fasta) ] ]\n" + } + }, + { + "skip_preprocessing": { + "type": "boolean", + "description": "If true, skip seqkit-based preprocessing steps and only compute\ninitial sequence statistics.\n" + } + } + ], + "output": [ + { + "fasta": { + "type": "file", + "description": "Contains the final amino acid FASTA file\n(either preprocessed or original if preprocessing is skipped).\n" + } + }, + { + "multiqc_files": { + "type": "file", + "description": "Statistics file for MultiQC.\n" + } + }, + { + "versions": { + "type": "file", + "description": "Versions file containing the software versions used in the workflow.\n" + } + } + ], + "authors": ["@vagkaratzas"], + "maintainers": ["@vagkaratzas"] }, - { - "input": { - "type": "file", - "description": "Sequence file in fasta/q format", - "pattern": "*.{fasta,fastq,fa,fq,fas,fna,faa}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "output": { - "fastx": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.{fasta,fastq,fa,fq,fas,fna,faa}": { - "type": "file", - "description": "A concatenated sequence file", - "pattern": "*.{fasta,fastq,fa,fq,fas,fna,faa}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "versions_seqkit": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "seqkit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "seqkit version | sed 's/^.*v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "seqkit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "seqkit version | sed 's/^.*v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "proteinannotator", + "version": "1.1.0" + }, + { + "name": "proteinfamilies", + "version": "2.3.0" + } ] - ] - }, - "authors": [ - "@DLBPointon" - ], - "maintainers": [ - "@DLBPointon" - ] - } - }, - { - "name": "seqkit_fq2fa", - "path": "modules/nf-core/seqkit/fq2fa/meta.yml", - "type": "module", - "meta": { - "name": "seqkit_fq2fa", - "description": "Convert FASTQ to FASTA format", - "keywords": [ - "fastq", - "fasta", - "convert" - ], - "tools": [ - { - "seqkit": { - "description": "Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen.", - "homepage": "https://github.com/shenwei356/seqkit", - "documentation": "https://bioinf.shenwei.me/seqkit/", - "doi": "10.1371/journal.pone.0163962", - "licence": [ - "MIT" - ], - "identifier": "biotools:seqkit" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } + }, + { + "name": "fasta_binning_concoct", + "path": "subworkflows/nf-core/fasta_binning_concoct/meta.yml", + "type": "subworkflow", + "meta": { + "name": "fasta_binning_concoct", + "description": "Runs the CONCOCT workflow of contig binning", + "keywords": ["concoct", "binning", "metagenomics", "contigs"], + "components": [ + "concoct/cutupfasta", + "concoct/concoctcoveragetable", + "concoct/concoct", + "concoct/mergecutupclustering", + "concoct/extractfastabins" + ], + "input": [ + { + "ch_fasta": { + "type": "file", + "description": "Structure: [ val(meta), path(fasta)]\nFile containing raw assembled contigs in FASTA format.\n" + } + }, + { + "ch_bam": { + "type": "file", + "description": "Structure: [ val(meta), path(bam), path(bai)]\nBAM and associated index files file representing reads mapped against each\ncontig in ch_fasta. Meta must be identical between ch_fasta and ch_bam entries.\n" + } + } + ], + "output": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "coverage_table": { + "type": "file", + "description": "Structure: [ val(meta), path(tsv)]\n(Sub)contig coverage table\n" + } + }, + { + "original_csv": { + "type": "file", + "description": "Structure: [ val(meta), path(csv) ]\nOriginal CONCOCT GT1000 output\n" + } + }, + { + "raw_clustering_csv": { + "type": "file", + "description": "Structure: [ val(meta), path(csv) ]\nCSV containing information which subcontig is assigned to which cluster\n" + } + }, + { + "pca_original": { + "type": "file", + "description": "Structure: [ val(meta), path(csv) ]\nCSV file containing untransformed PCA component values\n" + } + }, + { + "pca_transformed": { + "type": "file", + "description": "Structure: [ val(meta), path(csv) ]\nCSV file transformed PCA component values\n" + } + }, + { + "cluster_table": { + "type": "file", + "description": "Structure: [ val(meta), path(csv) ]\nCSV file containing final cluster assignments of original input contigs\n" + } + }, + { + "bin": { + "type": "file", + "description": "Structure: [ val(meta), path(fasta) ]\nFASTA files containing CONCOCT predicted bin clusters, named numerically\nby CONCOCT cluster ID\n" + } + }, + { + "versions": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ], + "authors": ["@jfy133"], + "maintainers": ["@jfy133"] }, - { - "fastq": { - "type": "file", - "description": "Sequence file in fastq format", - "pattern": "*.{fastq,fq}.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "output": { - "fasta": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*.fa.gz": { - "type": "file", - "description": "Sequence file in fasta format", - "pattern": "*.{fasta,fa}.gz", - "ontologies": [] - } - } - ] - ], - "versions_seqkit": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "seqkit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "seqkit version | sed 's/^.*v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "seqkit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "seqkit version | sed 's/^.*v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "mag", + "version": "5.4.2" + } ] - ] }, - "authors": [ - "@d-jch" - ] - }, - "pipelines": [ { - "name": "funcprofiler", - "version": "dev" + "name": "fasta_build_add_kraken2", + "path": "subworkflows/nf-core/fasta_build_add_kraken2/meta.yml", + "type": "subworkflow", + "meta": { + "name": "fasta_build_add_kraken2", + "description": "KRAKEN2 build custom database subworkflow", + "keywords": ["metagenomics", "kraken2", "database", "build", "custom"], + "components": ["kraken2/add", "kraken2/build"], + "input": [ + { + "ch_fasta": { + "type": "file", + "description": "Channel containing a meta with a list of FASTAs to be built\nStructure: [ val(meta), [ fasta1, fasta2, fasta3 ] ]\n", + "pattern": "*.{fasta,fa,fna}" + } + }, + { + "ch_taxonomy_names": { + "type": "file", + "description": "Channel containing a NCBI-style taxdump names file\nStructure: [ names.dmp ]\n", + "pattern": "names.dmp" + } + }, + { + "ch_taxonomy_nodes": { + "type": "file", + "description": "Channel containing a NCBI-style taxdump nodes file\nStructure: [ nodes.dmp ]\n", + "pattern": "nodes.dmp" + } + }, + { + "ch_accession2taxid": { + "type": "file", + "description": "Channel containing a NCBI-style taxdump accession2taxid (acc2tax) file\nStructure: [ accession2taxid_file ]\n", + "pattern": "*.accession2taxid" + } + }, + { + "val_cleanintermediate": { + "type": "boolean", + "description": "Boolean flag whether to clean up intermediate files after build or not\nStructure: [ val_cleanintermediate ]\n", + "pattern": "true|false" + } + }, + { + "ch_custom_seqid2taxid": { + "type": "file", + "description": "Optional custom or prebuilt seqid2taxid text file. If not provided, it will be generated by kraken2-build.\n", + "pattern": "seqid2taxid.map" + } + } + ], + "output": [ + { + "db": { + "type": "directory", + "description": "Channel containing KRAKEN2 database directory.\nUse publishDir in a modules.conf file to change default name for user\nStructure: [ val(meta), path(db) ]\n", + "pattern": "kraken2-database/" + } + }, + { + "db_separated": { + "type": "file", + "description": "Channel containing a list of KRAKEN2 database directory files as separate elements of a tuple.\nUse publishDir in a modules.conf file to change default name for user\nStructure: [ val(meta), path(k2d_files), path(map_files), path(added_files), path(taxonomy_files) ]\n", + "pattern": "kraken2-database/" + } + }, + { + "versions": { + "type": "file", + "description": "File containing software versions\nStructure: [ path(versions.yml) ]\n", + "pattern": "versions.yml" + } + } + ], + "authors": ["@jfy133"], + "maintainers": ["@jfy133"] + } }, { - "name": "smrnaseq", - "version": "2.4.1" - } - ] - }, - { - "name": "seqkit_fx2tab", - "path": "modules/nf-core/seqkit/fx2tab/meta.yml", - "type": "module", - "meta": { - "name": "seqkit_fx2tab", - "description": "Convert FASTA/Q to tabular format, and provide various information, like sequence length, GC content/GC skew.", - "keywords": [ - "fasta", - "fastq", - "text", - "tabular", - "convert" - ], - "tools": [ - { - "seqkit": { - "description": "Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen.\n", - "homepage": "https://github.com/shenwei356/seqkit", - "documentation": "https://bioinf.shenwei.me/seqkit/", - "doi": "10.1371/journal.pone.0163962", - "licence": [ - "MIT" - ], - "identifier": "biotools:seqkit" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fastx": { - "type": "file", - "description": "Sequence file in fasta/q format", - "pattern": "*.{fasta,fastq,fa,fq,fas,fna,faa}[.gz,.zst]", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "output": { - "text": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.txt*": { - "type": "file", - "description": "Text file in tabular format", - "pattern": "*.txt[.gz,.zstd,.zst]", - "ontologies": [] - } - } - ] - ], - "versions_seqkit": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "seqkit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "seqkit version | sed 's/^.*v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "seqkit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "seqkit version | sed 's/^.*v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@heuermh" - ], - "maintainers": [ - "@heuermh" - ] - }, - "pipelines": [ - { - "name": "circrna", - "version": "dev" - } - ] - }, - { - "name": "seqkit_grep", - "path": "modules/nf-core/seqkit/grep/meta.yml", - "type": "module", - "meta": { - "name": "seqkit_grep", - "description": "Select sequences from a large file based on name/ID", - "keywords": [ - "filter", - "seqkit", - "subseq", - "grep" - ], - "tools": [ - { - "seqkit": { - "description": "Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen.", - "homepage": "https://bioinf.shenwei.me/seqkit/usage/", - "documentation": "https://bioinf.shenwei.me/seqkit/usage/", - "tool_dev_url": "https://github.com/shenwei356/seqkit/", - "doi": "10.1371/journal.pone.0163962", - "licence": [ - "MIT" - ], - "identifier": "biotools:seqkit" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]\n" - } + "name": "fasta_build_add_kraken2_bracken", + "path": "subworkflows/nf-core/fasta_build_add_kraken2_bracken/meta.yml", + "type": "subworkflow", + "meta": { + "name": "fasta_build_add_kraken2_bracken", + "description": "KRAKEN2 and BRACKEN build custom database subworkflow", + "keywords": ["metagenomics", "kraken2", "database", "build", "custom", "bracken"], + "components": ["kraken2/add", "kraken2/build", "bracken/build"], + "input": [ + { + "ch_fasta": { + "type": "file", + "description": "Channel containing a meta with a list of FASTAs to be built\nStructure: [ val(meta), [ fasta1, fasta2, fasta3 ] ]\n", + "pattern": "*.{fasta,fa,fna}" + } + }, + { + "ch_taxonomy_names": { + "type": "file", + "description": "Channel containing a NCBI-style taxdump names file\nStructure: [ names.dmp ]\n", + "pattern": "names.dmp" + } + }, + { + "ch_taxonomy_nodes": { + "type": "file", + "description": "Channel containing a NCBI-style taxdump nodes file\nStructure: [ nodes.dmp ]\n", + "pattern": "nodes.dmp" + } + }, + { + "ch_accession2taxid": { + "type": "file", + "description": "Channel containing a NCBI-style taxdump accession2taxid (acc2tax) file\nStructure: [ accession2taxid_file ]\n", + "pattern": "*.accession2taxid" + } + }, + { + "val_cleanintermediates": { + "type": "boolean", + "description": "Boolean flag whether to clean up intermediate files after build or not.\nIf val_runbrackenbuild set, will be ignored as BRACKEN requires intermediate files.\nStructure: [ val_cleanintermediate ]\n", + "pattern": "true|false" + } + }, + { + "ch_custom_seqid2taxid": { + "type": "file", + "description": "Optional custom or prebuilt seqid2taxid text file. If not provided, it will be generated by kraken2-build.\n", + "pattern": "seqid2taxid.map" + } + }, + { + "val_runbrackenbuild": { + "type": "boolean", + "description": "Boolean flag whether to additionally insert required BRACKEN database files into KRAKEN2 directory.\nNote any changes for k-mer or read lengths must come via Nextflow config `ext.args`.\nStructure: [ val_runbrackenbuild ]\n", + "pattern": "true|false" + } + } + ], + "output": [ + { + "db": { + "type": "directory", + "description": "Channel containing KRAKEN2 (and BRACKEN) database directory files.\nUse publishDir in a modules.conf file to change default name for user\nStructure: [ val(meta), path(db) ]\n", + "pattern": "bracken-database/" + } + }, + { + "db_separated": { + "type": "file", + "description": "Channel containing a list of KRAKEN2 (and BRACKEN) database directory files as separate elements of a tuple.\nUse publishDir in a modules.conf file to change default name for user\nStructure: [ val(meta), path(k2d_files), path(map_files), path(added_files), path(taxonomy_files) ]\n" + } + }, + { + "versions": { + "type": "file", + "description": "File containing software versions\nStructure: [ path(versions.yml) ]\n", + "pattern": "versions.yml" + } + } + ], + "authors": ["@jfy133"], + "maintainers": ["@jfy133"] }, - { - "sequence": { - "type": "file", - "description": "Fasta or fastq file containing sequences to be filtered\n", - "pattern": "*.{fa,fna,faa,fasta,fq,fastq}[.gz]", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ], - { - "pattern": { - "type": "file", - "description": "pattern file (one record per line). If no pattern is given, a string can be specified within the args using '-p pattern_string'\n", - "pattern": "*.{txt,tsv}", - "ontologies": [ + "pipelines": [ { - "edam": "http://edamontology.org/format_3475" + "name": "createtaxdb", + "version": "3.0.0" } - ] - } - } - ], - "output": { - "filter": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.{fa,fq,fa.gz,fq.gz}": { - "type": "file", - "description": "Fasta or fastq file containing the filtered sequences. Will be gzipped if the input file was gzipped.\n" - } - } - ] - ], - "versions_seqkit": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "seqkit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "seqkit version | sed \"s/seqkit v//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "seqkit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "seqkit version | sed \"s/seqkit v//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@Joon-Klaps" - ], - "maintainers": [ - "@Joon-Klaps" - ] - }, - "pipelines": [ - { - "name": "smrnaseq", - "version": "2.4.1" - } - ] - }, - { - "name": "seqkit_head", - "path": "modules/nf-core/seqkit/head/meta.yml", - "type": "module", - "meta": { - "name": "seqkit_head", - "description": "Subset FASTA/FASTQ files to some number of sequences", - "keywords": [ - "filter", - "subset", - "reads", - "fasta", - "fastq", - "seqkit" - ], - "tools": [ - { - "seqkit": { - "description": "A cross-platform and ultrafast toolkit for FASTA/Q file manipulation", - "homepage": "https://bioinf.shenwei.me/seqkit/", - "documentation": "https://bioinf.shenwei.me/seqkit/usage/", - "tool_dev_url": "https://github.com/shenwei356/seqkit", - "doi": "10.1371/journal.pone.0163962", - "licence": [ - "MIT" - ], - "identifier": "biotools:seqkit" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "fastqs": { - "type": "file", - "description": "FASTA or FASTQ files to subset", - "pattern": "*.{fa,fasta,fq,fastq}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - }, - { - "seq_count": { - "type": "integer", - "description": "The number of sequences to include in the subset" - } - } - ] - ], - "output": { - "subset": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "${prefix}_subset_*": { - "type": "file", - "description": "Subset FASTA/FASTQ files", - "pattern": "*.{fa,fasta,fq,fastq}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "versions_seqkit": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "seqkit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "seqkit version | sed 's/^.*v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "seqkit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "seqkit version | sed 's/^.*v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@zachary-foster" - ], - "maintainers": [ - "@zachary-foster" - ] - }, - "pipelines": [ - { - "name": "pathogensurveillance", - "version": "1.1.0" - } - ] - }, - { - "name": "seqkit_pair", - "path": "modules/nf-core/seqkit/pair/meta.yml", - "type": "module", - "meta": { - "name": "seqkit_pair", - "description": "match up paired-end reads from two fastq files", - "keywords": [ - "seqkit", - "pair", - "fastq" - ], - "tools": [ - { - "seqkit": { - "description": "Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen.", - "homepage": "https://bioinf.shenwei.me/seqkit/usage/", - "documentation": "https://bioinf.shenwei.me/seqkit/usage/", - "tool_dev_url": "https://github.com/shenwei356/seqkit/", - "doi": "10.1371/journal.pone.0163962", - "licence": [ - "MIT" - ], - "identifier": "biotools:seqkit" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input paired-end FastQ files.\n", - "ontologies": [] - } - } - ] - ], - "output": { - "reads": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.paired.fastq.gz": { - "type": "file", - "description": "Paired fastq reads", - "pattern": "*.paired.fastq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "unpaired_reads": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.unpaired.fastq.gz": { - "type": "file", - "description": "Unpaired reads (optional)", - "pattern": "*.unpaired.fastq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "versions_seqkit": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "seqkit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "seqkit version | sed 's/^.*v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "seqkit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "seqkit version | sed 's/^.*v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@sateeshperi", - "@mjcipriano", - "@hseabolt" - ], - "maintainers": [ - "@sateeshperi", - "@mjcipriano", - "@hseabolt" - ] - } - }, - { - "name": "seqkit_replace", - "path": "modules/nf-core/seqkit/replace/meta.yml", - "type": "module", - "meta": { - "name": "seqkit_replace", - "description": "Use seqkit to find/replace strings within sequences and sequence headers", - "keywords": [ - "seqkit", - "replace", - "sequence", - "sequence headers", - "fasta" - ], - "tools": [ - { - "seqkit": { - "description": "Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen.", - "homepage": "https://bioinf.shenwei.me/seqkit/usage/", - "documentation": "https://bioinf.shenwei.me/seqkit/usage/", - "tool_dev_url": "https://github.com/shenwei356/seqkit/", - "doi": "10.1371/journal.pone.016396", - "identifier": "biotools:seqkit" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fastx": { - "type": "file", - "description": "fasta/q file", - "pattern": "*.{fasta,fastq,fa,fq,fas,fna,faa}*", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "output": { - "fastx": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.fast*": { - "type": "file", - "description": "fasta/q file with replaced values", - "pattern": "*.{fasta,fastq,fa,fq,fas,fna,faa}*", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "versions_seqkit": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "seqkit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "seqkit version | sed 's/^.*v//'": { - "type": "eval", - "description": "The expression to obtain the version of seqkit" - } - } ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "seqkit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "seqkit version | sed 's/^.*v//'": { - "type": "eval", - "description": "The expression to obtain the version of seqkit" - } - } - ] - ] - }, - "authors": [ - "@mjcipriano" - ], - "maintainers": [ - "@mjcipriano" - ] - }, - "pipelines": [ - { - "name": "proteinannotator", - "version": "1.1.0" }, { - "name": "proteinfamilies", - "version": "2.3.0" + "name": "fasta_classify_catpack", + "path": "subworkflows/nf-core/fasta_classify_catpack/meta.yml", + "type": "subworkflow", + "meta": { + "name": "fasta_classify_catpack", + "description": "Taxonomic classification of binned MAGs and contigs using CAT/BAT (CAT_pack).", + "keywords": ["metagenomics", "taxonomy", "classification", "bins", "MAGs", "contigs", "CAT", "BAT"], + "components": [ + "catpack/addnames", + "catpack/bins", + "catpack/contigs", + "catpack/download", + "catpack/prepare", + "catpack/summarise", + "untar" + ], + "input": [ + { + "ch_bins": { + "type": "file", + "description": "Channel containing binned MAG FASTA files.\nStructure: [ val(meta), path(fasta) ]\n", + "pattern": "*.{fa,fasta,fna}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + }, + { + "ch_contigs": { + "type": "file", + "description": "Channel containing contig FASTA files. Provide channel.empty() to skip\ncontig classification.\nStructure: [ val(meta), path(fasta) ]\n", + "pattern": "*.{fa,fasta,fna}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + }, + { + "ch_cat_db": { + "type": "directory", + "description": "Channel containing a pre-built CAT/BAT database. Can be a directory with db/ and tax/\nsubdirectories, or a .tar.gz archive of such a directory. Provide channel.empty() to\ntrigger automatic database download using ch_cat_db_download_id. Supplying both\nch_cat_db and ch_cat_db_download_id will cause a runtime error.\nStructure: [ val(meta), path(db) ]\n", + "ontologies": [ + { + "edam": "http://edamontology.org/data_1049" + } + ] + } + }, + { + "ch_cat_db_download_id": { + "type": "string", + "description": "Channel containing the database identifier to download via CATPACK_DOWNLOAD (e.g. 'nr').\nOnly used when ch_cat_db is channel.empty(). Provide channel.empty() when supplying a\npre-built database via ch_cat_db. Supplying both inputs will cause a runtime error.\nStructure: [ val(meta), val(db_id) ]\n" + } + }, + { + "run_summarise": { + "type": "boolean", + "description": "Whether to run CATPACK_SUMMARISE on the classification outputs. Requires\next.args = \"--only_official\" to be set on CATPACK_ADDNAMES_BINS and\nCATPACK_ADDNAMES_CONTIGS in the pipeline configuration, as CATPACK_SUMMARISE\nrequires official-rank headers in its input.\n" + } + }, + { + "bin_suffix": { + "type": "string", + "description": "File extension of the bin FASTA files passed to CATPACK_BINS (e.g. '.fa').\n" + } + } + ], + "output": [ + { + "bin2classification": { + "type": "file", + "description": "Raw per-bin taxonomic classification file produced by CATPACK_BINS, before human-readable\nnames are added by CATPACK_ADDNAMES. Useful for downstream tools that consume the raw\nCAT_pack output directly.\nStructure: [ val(meta), path(txt) ]\n", + "pattern": "*.bin2classification.txt", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, + { + "bat_classification": { + "type": "file", + "description": "Per-bin taxonomic classification with human-readable names added by CATPACK_ADDNAMES.\nStructure: [ val(meta), path(txt) ]\n", + "pattern": "*.txt", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, + { + "bat_summary": { + "type": "file", + "description": "Summary of bin classifications produced by CATPACK_SUMMARISE. Empty channel when\nrun_summarise is false.\nStructure: [ val(meta), path(txt) ]\n", + "pattern": "*.txt", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, + { + "contig2classification": { + "type": "file", + "description": "Raw per-contig taxonomic classification file produced by CATPACK_CONTIGS, before\nhuman-readable names are added by CATPACK_ADDNAMES. Empty channel when ch_contigs\nis channel.empty(). Useful for downstream tools that consume the raw CAT_pack output directly.\nStructure: [ val(meta), path(txt) ]\n", + "pattern": "*.contig2classification.txt", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, + { + "contigs_classification": { + "type": "file", + "description": "Per-contig taxonomic classification with human-readable names added by CATPACK_ADDNAMES.\nEmpty channel when ch_contigs is channel.empty().\nStructure: [ val(meta), path(txt) ]\n", + "pattern": "*.txt", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, + { + "contigs_summary": { + "type": "file", + "description": "Summary of contig classifications produced by CATPACK_SUMMARISE. Empty channel when\nch_contigs is channel.empty() or run_summarise is false.\nStructure: [ val(meta), path(txt) ]\n", + "pattern": "*.txt", + "ontologies": [ + { + "edam": "http://edamontology.org/format_3475" + } + ] + } + }, + { + "versions": { + "type": "file", + "description": "Channel containing software versions.\nStructure: versions\n" + } + } + ], + "authors": ["@mberacochea", "@dialvarezs"], + "maintainers": [ + "@mberacochea", + "@dialvarezs", + "@jfy133", + "@prototaxites", + "@dialvarezs", + "@d4straub", + "@muabnezor" + ] + }, + "pipelines": [ + { + "name": "seqsubmit", + "version": "dev" + } + ] }, { - "name": "rnaseq", - "version": "3.26.0" + "name": "fasta_clean_fcs", + "path": "subworkflows/nf-core/fasta_clean_fcs/meta.yml", + "type": "subworkflow", + "meta": { + "name": "fasta_clean_fcs", + "description": "Foreign Contamination Screen (FCS) is a tool suite for identifying and removing contaminant sequences in genome assemblies", + "keywords": ["contamination screening", "cleaning", "assemblies", "fasta"], + "components": ["fcs/fcsadaptor", "fcsgx/rungx"], + "input": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\nwith taxonomy ID of the expected organism\ne.g. [ id:'test', taxid:'id' ]\n" + } + }, + { + "assembly": { + "type": "file", + "description": "assembly fasta file", + "pattern": "*.{fasta,fa}" + } + }, + { + "database": { + "type": "directory", + "description": "Directory containing the FCS-GX database" + } + }, + { + "ramdisk_path": { + "type": "string", + "description": "Path to RAM disk for improved performance (optional)" + } + } + ], + "output": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "versions": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + }, + { + "fcsadaptor_cleaned_assembly": { + "type": "file", + "description": "Cleaned assembly in fasta format", + "pattern": "*.{cleaned_sequences.fa.gz}" + } + }, + { + "fcsadaptor_report": { + "type": "file", + "description": "Report of identified adaptors", + "pattern": "*.{fcs_adaptor_report.txt}" + } + }, + { + "fcsadaptor_log": { + "type": "file", + "description": "Log file", + "pattern": "*.{fcs_adaptor.log}" + } + }, + { + "fcsadaptor_pipeline_args": { + "type": "file", + "description": "Run arguments", + "pattern": "*.{pipeline_args.yaml}" + } + }, + { + "fcsadaptor_skipped_trims": { + "type": "file", + "description": "Skipped trim information", + "pattern": "*.{skipped_trims.jsonl}" + } + }, + { + "fcs_gx_report": { + "type": "file", + "description": "Report containing the contig identifier and recommended action (EXCLUDE, TRIM, FIX, REVIEW)", + "pattern": "*.fcs_gx_report.txt" + } + }, + { + "fcsgx_taxonomy_report": { + "type": "file", + "description": "Report containing the contig identifier and mapped contaminant species", + "pattern": "*.taxonomy.rpt" + } + } + ], + "authors": ["@scorreard"], + "maintainers": ["@scorreard"] + } }, { - "name": "smrnaseq", - "version": "2.4.1" - } - ] - }, - { - "name": "seqkit_rmdup", - "path": "modules/nf-core/seqkit/rmdup/meta.yml", - "type": "module", - "meta": { - "name": "seqkit_rmdup", - "description": "Transforms sequences (extract ID, filter by length, remove gaps, reverse complement...)", - "keywords": [ - "genomics", - "fasta", - "fastq", - "remove", - "duplicates" - ], - "tools": [ - { - "seqkit": { - "description": "A cross-platform and ultrafast toolkit for FASTA/Q file manipulation", - "homepage": "https://bioinf.shenwei.me/seqkit/", - "documentation": "https://bioinf.shenwei.me/seqkit/usage/", - "tool_dev_url": "https://github.com/shenwei356/seqkit", - "doi": "10.1371/journal.pone.0163962", - "licence": [ - "MIT" - ], - "identifier": "biotools:seqkit" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } + "name": "fasta_consensus_autocycler", + "path": "subworkflows/nf-core/fasta_consensus_autocycler/meta.yml", + "type": "subworkflow", + "meta": { + "name": "fasta_consensus_autocycler", + "description": "Generate consensus assemblies and assembly graphs from grouped contig FASTA files using autocycler", + "keywords": ["autocycler", "consensus", "assembly", "fasta"], + "components": [ + "autocycler/compress", + "autocycler/cluster", + "autocycler/trim", + "autocycler/resolve", + "autocycler/combine" + ], + "input": [ + { + "ch_grouped_contigs": { + "type": "file", + "description": "The input channel containing grouped contig FASTA files\nStructure: [ val(meta), [ fasta, fasta, ... ] ]\n", + "pattern": "*.{fasta,fa,fna}" + } + } + ], + "output": [ + { + "consensus_assembly": { + "type": "file", + "description": "Channel containing consensus assembly FASTA files\nStructure: [ val(meta), path(fasta) ]\n", + "pattern": "*/consensus_assembly.fasta" + } + }, + { + "consensus_assembly_graph": { + "type": "file", + "description": "Channel containing consensus assembly graphs\nStructure: [ val(meta), path(gfa) ]\n", + "pattern": "*/consensus_assembly.gfa" + } + } + ], + "authors": ["@dwells-eit"], + "maintainers": ["@dwells-eit"] }, - { - "fastx": { - "type": "file", - "description": "Input fasta/fastq file", - "pattern": "*.{fsa,fas,fa,fasta,fastq,fq,fsa.gz,fas.gz,fa.gz,fasta.gz,fastq.gz,fq.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "output": { - "fastx": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}.${extension}": { - "type": "file", - "description": "Output fasta/fastq file", - "pattern": "*.{fasta,fasta.gz,fastq,fastq.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.log": { - "type": "file", - "description": "Log containing information regarding removed duplicates", - "pattern": "*.log", - "ontologies": [] - } - } - ] - ], - "versions_seqkit": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "seqkit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "seqkit version | sed 's/^.*v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "seqkit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "seqkit version | sed 's/^.*v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "bacass", + "version": "2.6.0" + } ] - ] - }, - "authors": [ - "@GallVp" - ], - "maintainers": [ - "@GallVp" - ] - }, - "pipelines": [ - { - "name": "proteinannotator", - "version": "1.1.0" }, { - "name": "proteinfamilies", - "version": "2.3.0" - } - ] - }, - { - "name": "seqkit_sample", - "path": "modules/nf-core/seqkit/sample/meta.yml", - "type": "module", - "meta": { - "name": "seqkit_sample", - "description": "Sample sequences from FASTA/FASTQ files by number or proportion", - "keywords": [ - "genomics", - "fasta", - "fastq", - "sample", - "subset", - "seqkit" - ], - "tools": [ - { - "seqkit": { - "description": "A cross-platform and ultrafast toolkit for FASTA/Q file manipulation", - "homepage": "https://bioinf.shenwei.me/seqkit/", - "documentation": "https://bioinf.shenwei.me/seqkit/usage/", - "tool_dev_url": "https://github.com/shenwei356/seqkit", - "doi": "10.1371/journal.pone.0163962", - "licence": [ - "MIT" - ], - "identifier": "biotools:seqkit" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "fastx": { - "type": "file", - "description": "Input FASTA or FASTQ file", - "pattern": "*.{fsa,fas,fa,fasta,fastq,fq}{,.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "output": { - "fastx": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}.${extension}": { - "type": "file", - "description": "Sampled output FASTA or FASTQ file", - "pattern": "*.{fasta,fasta.gz,fastq,fastq.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "versions_seqkit": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "seqkit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "seqkit version | sed 's/^.*v//'": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "seqkit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "seqkit version | sed 's/^.*v//'": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@emmcauley" - ], - "maintainers": [ - "@emmcauley" - ] - } - }, - { - "name": "seqkit_sana", - "path": "modules/nf-core/seqkit/sana/meta.yml", - "type": "module", - "meta": { - "name": "seqkit_sana", - "description": "Sanitize broken single line FASTQ files", - "keywords": [ - "fastq", - "quality check", - "skip malformed", - "parser" - ], - "tools": [ - { - "seqkit": { - "description": "A cross-platform and ultrafast toolkit for FASTA/Q file manipulation.", - "homepage": "https://bioinf.shenwei.me/seqkit", - "documentation": "https://bioinf.shenwei.me/seqkit", - "tool_dev_url": "https://github.com/shenwei356/seqkit", - "doi": "10.1371/journal.pone.0163962", - "licence": [ - "MIT" - ], - "identifier": "biotools:seqkit" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information. e.g. [ id:'sample1']" - } - }, - { - "reads": { - "type": "file", - "description": "One line for each sequence and quality value", - "pattern": "*.{fq,fastq}{,.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "output": { - "reads": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information. e.g. [ id:'sample1']" - } - }, - { - "${prefix}${extension}": { - "type": "file", - "description": "Parsed fastq file without malformed entries/lines", - "pattern": "*.${extension}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information. e.g. [ id:'sample1']" - } - }, - { - "${prefix}.log": { - "type": "file", - "description": "Log file produced by the seqkit/sana software", - "pattern": "*.log", - "ontologies": [] - } - } - ] - ], - "versions_seqkit": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "seqkit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "seqkit version | sed 's/^.*v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "seqkit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "seqkit version | sed 's/^.*v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@vagkaratzas" - ], - "maintainers": [ - "@vagkaratzas" - ] - } - }, - { - "name": "seqkit_seq", - "path": "modules/nf-core/seqkit/seq/meta.yml", - "type": "module", - "meta": { - "name": "seqkit_seq", - "description": "Transforms sequences (extract ID, filter by length, remove gaps, reverse complement...)", - "keywords": [ - "genomics", - "fasta", - "fastq", - "transform", - "filter", - "gaps", - "complement" - ], - "tools": [ - { - "seqkit": { - "description": "A cross-platform and ultrafast toolkit for FASTA/Q file manipulation", - "homepage": "https://bioinf.shenwei.me/seqkit/", - "documentation": "https://bioinf.shenwei.me/seqkit/usage/", - "tool_dev_url": "https://github.com/shenwei356/seqkit", - "doi": "10.1371/journal.pone.0163962", - "licence": [ - "MIT" - ], - "identifier": "biotools:seqkit" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } + "name": "fasta_explore_search_plot_tidk", + "path": "subworkflows/nf-core/fasta_explore_search_plot_tidk/meta.yml", + "type": "subworkflow", + "meta": { + "name": "fasta_explore_search_plot_tidk", + "description": "Uses Telomere Identification toolKit (TIDK) to identify the frequency of telomeric repeats\nalong a sliding window for each sequence in the input fasta file. Results are presented in\nTSV and SVG formats. The user can specify an a priori sequence for identification.\nPossible a posteriori sequences are also explored and the most frequent sequence is\nused for identification similar to the a priori sequence. seqkit/seq and seqkit/sort modules are\nalso included to filter out small sequences and sort sequences by length.\n", + "keywords": ["genomics", "telomere", "repeat", "search", "plot"], + "components": ["seqkit/seq", "seqkit/sort", "tidk/explore", "tidk/plot", "tidk/search"], + "input": [ + { + "ch_fasta": { + "type": "file", + "description": "Input assembly\nStructure: [ val(meta), path(fasta) ]\n", + "pattern": "*.{fsa/fa/fasta}" + } + }, + { + "ch_apriori_sequence": { + "type": "string", + "description": "A priori sequence\nStructure: [ val(meta), val(sequence) ]\n" + } + } + ], + "output": [ + { + "apriori_tsv": { + "type": "file", + "description": "Frequency table for the identification of the a priori sequence\nStructure: [ val(meta), path(tsv) ]\n", + "pattern": "*.tsv" + } + }, + { + "apriori_svg": { + "type": "file", + "description": "Frequency graph for the identification of the a priori sequence\nStructure: [ val(meta), path(svg) ]\n", + "pattern": "*.svg" + } + }, + { + "aposteriori_sequence": { + "type": "file", + "description": "The most frequent a posteriori sequence\nStructure: [ val(meta), path(txt) ]\n", + "pattern": "*.txt" + } + }, + { + "aposteriori_tsv": { + "type": "file", + "description": "Frequency table for the identification of the a aposteriori sequence\nStructure: [ val(meta), path(tsv) ]\n", + "pattern": "*.tsv" + } + }, + { + "aposteriori_svg": { + "type": "file", + "description": "Frequency graph for the identification of the a aposteriori sequence\nStructure: [ val(meta), path(svg) ]\n", + "pattern": "*.svg" + } + }, + { + "versions": { + "type": "file", + "description": "File containing software versions\nStructure: [ path(versions.yml) ]\n", + "pattern": "versions.yml" + } + } + ], + "authors": ["@GallVp"], + "maintainers": ["@GallVp"] }, - { - "fastx": { - "type": "file", - "description": "Input fasta/fastq file", - "pattern": "*.{fsa,fas,fa,fasta,fastq,fq,fsa.gz,fas.gz,fa.gz,fasta.gz,fastq.gz,fq.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "output": { - "fastx": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}.*": { - "type": "file", - "description": "Output fasta/fastq file", - "pattern": "*.{fasta,fasta.gz,fastq,fastq.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "versions_seqkit": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "seqkit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "seqkit version | sed 's/^.*v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "seqkit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "seqkit version | sed 's/^.*v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "genomeqc", + "version": "dev" + } ] - ] - }, - "authors": [ - "@GallVp" - ], - "maintainers": [ - "@GallVp" - ] - }, - "pipelines": [ - { - "name": "funcscan", - "version": "3.0.0" - }, - { - "name": "genomeqc", - "version": "dev" }, { - "name": "proteinannotator", - "version": "1.1.0" - }, - { - "name": "proteinfamilies", - "version": "2.3.0" - } - ] - }, - { - "name": "seqkit_sliding", - "path": "modules/nf-core/seqkit/sliding/meta.yml", - "type": "module", - "meta": { - "name": "seqkit_sliding", - "description": "Use seqkit to generate sliding windows of input fasta", - "keywords": [ - "seqkit", - "sliding", - "windows" - ], - "tools": [ - { - "seqkit": { - "description": "Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen.", - "homepage": "https://bioinf.shenwei.me/seqkit/usage/", - "documentation": "https://bioinf.shenwei.me/seqkit/usage/", - "tool_dev_url": "https://github.com/shenwei356/seqkit/", - "doi": "10.1371/journal.pone.016396", - "identifier": "biotools:seqkit" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fastx": { - "type": "file", - "description": "fasta/q file", - "pattern": "*.{fasta,fastq,fa,fq,fas,fna,faa}*", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "output": { - "fastx": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.fast*": { - "type": "file", - "description": "fasta/q window file", - "pattern": "*.{fasta,fastq,fa,fq,fas,fna,faa}*", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "versions_seqkit": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "seqkit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "seqkit version | sed 's/^.*v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "seqkit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "seqkit version | sed 's/^.*v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@DLBPointon" - ], - "maintainers": [ - "@DLBPointon" - ] - }, - "pipelines": [ - { - "name": "pathogensurveillance", - "version": "1.1.0" - } - ] - }, - { - "name": "seqkit_sort", - "path": "modules/nf-core/seqkit/sort/meta.yml", - "type": "module", - "meta": { - "name": "seqkit_sort", - "description": "Sorts sequences by id/name/sequence/length", - "keywords": [ - "genomics", - "fasta", - "fastq", - "sort" - ], - "tools": [ - { - "seqkit": { - "description": "A cross-platform and ultrafast toolkit for FASTA/Q file manipulation", - "homepage": "https://bioinf.shenwei.me/seqkit/", - "documentation": "https://bioinf.shenwei.me/seqkit/usage/", - "tool_dev_url": "https://github.com/shenwei356/seqkit", - "doi": "10.1371/journal.pone.0163962", - "licence": [ - "MIT" - ], - "identifier": "biotools:seqkit" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "fastx": { - "type": "file", - "description": "Input fasta/fastq file", - "pattern": "*.{fsa,fas,fa,fasta,fastq,fq,fsa.gz,fas.gz,fa.gz,fasta.gz,fastq.gz,fq.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "output": { - "fastx": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}.*": { - "type": "file", - "description": "Output fasta/fastq file", - "pattern": "*.{fasta.gz,fastq.gz}", - "ontologies": [] - } - } - ] - ], - "versions_seqkit": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "seqkit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "seqkit version | sed 's/^.*v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "seqkit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "seqkit version | sed 's/^.*v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@GallVp" - ], - "maintainers": [ - "@GallVp" - ] - }, - "pipelines": [ - { - "name": "genomeqc", - "version": "dev" - } - ] - }, - { - "name": "seqkit_split2", - "path": "modules/nf-core/seqkit/split2/meta.yml", - "type": "module", - "meta": { - "name": "seqkit_split2", - "description": "Split single or paired-end fastq.gz files", - "keywords": [ - "split", - "fastq", - "seqkit" - ], - "tools": [ - { - "seqkit": { - "description": "Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen.\n", - "homepage": "https://github.com/shenwei356/seqkit", - "documentation": "https://bioinf.shenwei.me/seqkit/", - "doi": "10.1371/journal.pone.0163962", - "licence": [ - "MIT" - ], - "identifier": "biotools:seqkit" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "FastQ files", - "pattern": "*.{f[aq].gz/fast[aq].gz}", - "ontologies": [] - } - } - ] - ], - "output": { - "reads": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/*": { - "type": "file", - "description": "Split fastq files", - "pattern": "*.{f[aq][.gz]/fast[aq][.gz]}", - "ontologies": [] - } - } - ] - ], - "versions_seqkit": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "seqkit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "seqkit version | sed 's/^.*v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "seqkit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "seqkit version | sed 's/^.*v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@FriederikeHanssen", - "@heuermh" - ], - "maintainers": [ - "@FriederikeHanssen", - "@heuermh" - ] - }, - "pipelines": [ - { - "name": "callingcards", - "version": "1.0.0" - } - ] - }, - { - "name": "seqkit_stats", - "path": "modules/nf-core/seqkit/stats/meta.yml", - "type": "module", - "meta": { - "name": "seqkit_stats", - "description": "simple statistics of FASTA/Q files", - "keywords": [ - "seqkit", - "fasta", - "stats" - ], - "tools": [ - { - "seqkit": { - "description": "Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen.", - "homepage": "https://bioinf.shenwei.me/seqkit/usage/", - "documentation": "https://bioinf.shenwei.me/seqkit/usage/", - "tool_dev_url": "https://github.com/shenwei356/seqkit/", - "doi": "10.1371/journal.pone.0163962", - "licence": [ - "MIT" - ], - "identifier": "biotools:seqkit" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "Either FASTA or FASTQ files.\n", - "pattern": "*.{fa,fna,faa,fasta,fq,fastq}[.gz]", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } + "name": "fasta_gxf_busco_plot", + "path": "subworkflows/nf-core/fasta_gxf_busco_plot/meta.yml", + "type": "subworkflow", + "meta": { + "name": "fasta_gxf_busco_plot", + "description": "Runs BUSCO for input assemblies and their annotations in GFF/GFF3/GTF format, and creates summary plots using `BUSCO/generate_plot.py` script\n", + "keywords": ["genome", "annotation", "busco", "plot"], + "components": ["busco/busco", "busco/generateplot", "gffread"], + "input": [ + { + "ch_fasta": { + "type": "file", + "description": "Channel containing FASTA files\nStructure:[ val(meta), fasta ]\n", + "pattern": "*.{fa,faa,fsa,fas,fasta}(.gz)?" + } + }, + { + "ch_gxf": { + "type": "file", + "description": "Channel containing GFF/GFF3/GTF files\nStructure:[ val(meta2), gxf ]\n", + "pattern": "*.{gff,gff3,gtf}" + } + }, + { + "val_mode": { + "type": "string", + "description": "String containing BUSCO mode to apply to ch_fasta files\nStructure:val(mode)\n" + } + }, + { + "val_lineages": { + "type": "array", + "description": "Array of strings representing BUSCO lineage datasets\nStructure:[ val(lineage) ]\n" + } + }, + { + "val_busco_lineages_path": { + "type": "path", + "description": "Path where BUSCO lineages are located or downloaded if not already there. If this input is `[]`,\nBUSCO will download the datasets in the task work directory\nStructure:val(busco_lineages_path)\n" + } + }, + { + "val_busco_config": { + "type": "path", + "description": "Path to BUSCO config. It is optional and can be set to `[]`\nStructure:val(busco_config)\n" + } + }, + { + "val_busco_cleanup": { + "type": "boolean", + "description": "Flag to indicate if intermediate BUSCO files should be removed\nStructure:val(busco_cleanup)\n" + } + } + ], + "output": [ + { + "assembly_batch_summary": { + "type": "file", + "description": "Channel containing BUSCO batch summaries corresponding to fasta files\nStructure: [ val(meta), txt ]\n", + "pattern": "*.txt" + } + }, + { + "assembly_short_summaries_txt": { + "type": "file", + "description": "Channel containing BUSCO short summaries corresponding to fasta files\nStructure: [ val(meta), txt ]\n", + "pattern": "*.txt" + } + }, + { + "assembly_short_summaries_json": { + "type": "file", + "description": "Channel containing BUSCO short summaries corresponding to fasta files\nStructure: [ val(meta), json ]\n", + "pattern": "*.json" + } + }, + { + "assembly_full_table": { + "description": "Channel containing complete results in a tabular format with scores and lengths of BUSCO matches,\nand coordinates (for genome mode) or gene/protein IDs (for transcriptome or protein modes)\nStructure: [ val(meta), tsv ]\n", + "pattern": "*.tsv" + } + }, + { + "assembly_plot_summary_txt": { + "type": "file", + "description": "Channel containing BUSCO short summaries corresponding to fasta files renamed to include lineage in sample id\nStructure: [ txt ]\n", + "pattern": "*.txt" + } + }, + { + "assembly_png": { + "type": "file", + "description": "Channel containing summary plot for assemblies\nStructure: png\n", + "pattern": "*.png" + } + }, + { + "annotation_batch_summary": { + "type": "file", + "description": "Channel containing BUSCO batch summaries corresponding to annotation files\nStructure: [ val(meta), txt ]\n", + "pattern": "*.txt" + } + }, + { + "annotation_short_summaries_txt": { + "type": "file", + "description": "Channel containing BUSCO short summaries corresponding to annotation files\nStructure: [ val(meta), txt ]\n", + "pattern": "*.txt" + } + }, + { + "annotation_short_summaries_json": { + "type": "file", + "description": "Channel containing BUSCO short summaries corresponding to annotation files\nStructure: [ val(meta), json ]\n", + "pattern": "*.json" + } + }, + { + "annotation_full_table": { + "description": "Channel containing complete results in a tabular format with scores and lengths of BUSCO matches,\nprotein IDs in protein mode\nStructure: [ val(meta), tsv ]\n", + "pattern": "*.tsv" + } + }, + { + "annotation_plot_summary_txt": { + "type": "file", + "description": "Channel containing BUSCO short summaries corresponding to annotation files renamed to include lineage in sample id\nStructure: [ txt ]\n", + "pattern": "*.txt" + } + }, + { + "annotation_png": { + "type": "file", + "description": "Channel containing summary plot for annotations\nStructure: png\n", + "pattern": "*.png" + } + }, + { + "versions": { + "type": "file", + "description": "File containing software versions\nStructure: [ path(versions.yml) ]\n", + "pattern": "versions.yml" + } + } + ], + "authors": ["@GallVp"], + "maintainers": ["@GallVp", "@FernandoDuarteF"] } - ] - ], - "output": { - "stats": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "Tab-separated output file with basic sequence statistics.\n", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_seqkit": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "seqkit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "seqkit version | sed 's/^.*v//'": { - "type": "eval", - "description": "The expression to obtain the version of seqkit" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "seqkit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "seqkit version | sed 's/^.*v//'": { - "type": "eval", - "description": "The expression to obtain the version of seqkit" - } - } - ] - ] - }, - "authors": [ - "@Midnighter", - "@heuermh" - ], - "maintainers": [ - "@Midnighter", - "@heuermh" - ] - }, - "pipelines": [ - { - "name": "circrna", - "version": "dev" }, { - "name": "mag", - "version": "5.4.2" - }, - { - "name": "pathogensurveillance", - "version": "1.1.0" - }, - { - "name": "rnaseq", - "version": "3.26.0" - } - ] - }, - { - "name": "seqkit_tab2fx", - "path": "modules/nf-core/seqkit/tab2fx/meta.yml", - "type": "module", - "meta": { - "name": "seqkit_tab2fx", - "description": "Convert tabular format (first two/three columns) to FASTA/Q format.", - "keywords": [ - "fasta", - "fastq", - "text", - "tabular", - "convert" - ], - "tools": [ - { - "seqkit": { - "description": "Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen.\n", - "homepage": "https://github.com/shenwei356/seqkit", - "documentation": "https://bioinf.shenwei.me/seqkit/", - "doi": "10.1371/journal.pone.0163962", - "licence": [ - "MIT" - ], - "identifier": "biotools:seqkit" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "text": { - "type": "file", - "description": "Text file in tabular format", - "pattern": "*.txt[.gz,.zst]", - "ontologies": [] - } - } - ] - ], - "output": { - "fastx": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.f*": { - "type": "file", - "description": "Sequence file in fasta/q format", - "pattern": "*.{fa,fq}[.gz,.zst]", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "versions_seqkit": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "seqkit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "seqkit version | sed 's/^.*v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "seqkit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "seqkit version | sed 's/^.*v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@heuermh" - ], - "maintainers": [ - "@heuermh" - ] - } - }, - { - "name": "seqkit_translate", - "path": "modules/nf-core/seqkit/translate/meta.yml", - "type": "module", - "meta": { - "name": "seqkit_translate", - "description": "Translate DNA/RNA to protein sequence", - "keywords": [ - "seqkit", - "translate", - "protein" - ], - "tools": [ - { - "seqkit": { - "description": "A cross-platform and ultrafast toolkit for FASTA/Q file manipulation", - "homepage": "https://bioinf.shenwei.me/seqkit/", - "documentation": "https://bioinf.shenwei.me/seqkit/usage/", - "tool_dev_url": "https://github.com/shenwei356/seqkit", - "doi": "10.1371/journal.pone.0163962", - "licence": [ - "MIT" - ], - "identifier": "biotools:seqkit" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "fastx": { - "type": "file", - "description": "Input fasta/fastq file", - "pattern": "*.{fna,fsa,fas,fa,fasta,fastq,fq}[.gz]", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "output": { - "fastx": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}.*": { - "type": "file", - "description": "Translated fasta/fastq file", - "pattern": "*.{fna,fsa,fas,fa,fasta,fastq,fq}[.gz]", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "versions_seqkit": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "seqkit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "seqkit version | sed 's/^.*v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "seqkit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "seqkit version | sed 's/^.*v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@delfiterradas" - ], - "maintainers": [ - "@delfiterradas" - ] - } - }, - { - "name": "seqsero2", - "path": "modules/nf-core/seqsero2/meta.yml", - "type": "module", - "meta": { - "name": "seqsero2", - "description": "Salmonella serotype prediction from reads and assemblies", - "keywords": [ - "fasta", - "fastq", - "salmonella", - "sertotype" - ], - "tools": [ - { - "seqsero2": { - "description": "Salmonella serotype prediction from genome sequencing data", - "homepage": "https://github.com/denglab/SeqSero2", - "documentation": "https://github.com/denglab/SeqSero2", - "tool_dev_url": "https://github.com/denglab/SeqSero2", - "doi": "10.1128/AEM.01746-19", - "licence": [ - "GPL v2" - ], - "identifier": "biotools:SeqSero2" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "seqs": { - "type": "file", - "description": "FASTQ or FASTA formatted sequences", - "pattern": "*.{fq.gz,fastq.gz,fna.gz,fna,fasta.gz,fasta,fa.gz,fa}", - "ontologies": [] - } - } - ] - ], - "output": { - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "results/*_log.txt": { - "type": "file", - "description": "A log of serotype antigen results", - "pattern": "*_log.txt", - "ontologies": [] - } - } - ] - ], - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "results/*_result.tsv": { - "type": "file", - "description": "Tab-delimited summary of the SeqSero2 results", - "pattern": "*_result.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "txt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "results/*_result.txt": { - "type": "file", - "description": "Detailed summary of the SeqSero2 results", - "pattern": "*_result.txt", - "ontologies": [] - } - } - ] - ], - "versions_seqsero2": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "seqsero2": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "SeqSero2_package.py --version 2>&1 | sed 's/^.*SeqSero2_package.py //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "seqsero2": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "SeqSero2_package.py --version 2>&1 | sed 's/^.*SeqSero2_package.py //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@rpetit3" - ], - "maintainers": [ - "@rpetit3" - ] - } - }, - { - "name": "seqtk_comp", - "path": "modules/nf-core/seqtk/comp/meta.yml", - "type": "module", - "meta": { - "name": "seqtk_comp", - "description": "Computes sequence statistics from FASTQ or FASTA files", - "keywords": [ - "seqtk", - "comp", - "fastx" - ], - "tools": [ - { - "seqtk_comp": { - "description": "Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format.\nThe seqtk comp command computes base composition, sequence length, and GC content for quality control.\n", - "homepage": "https://github.com/lh3/seqtk", - "documentation": "https://docs.csc.fi/apps/seqtk/", - "tool_dev_url": "https://github.com/lh3/seqtk", - "licence": [ - "MIT" - ], - "identifier": "biotools:seqtk" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample1' ]\n" - } - }, - { - "fastx": { - "type": "file", - "description": "A FASTQ or FASTA file", - "pattern": "*.{fastq,fq,fasta,fa,fas,fna}{,.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "output": { - "seqtk_stats": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample1', single_end:false ]\n" - } - }, - { - "*.seqtk_stats.tsv": { - "type": "file", - "description": "The output TSV file summarizing sequence statistics with columns for sequence name, length, counts of A, C, G, T, and N bases, and GC content percentage.\"", - "pattern": "*.seqtk_stats.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_seqtk": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "seqtk": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "seqtk 2>&1 | sed -n 's/^Version: //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "seqtk": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "seqtk 2>&1 | sed -n 's/^Version: //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@sainsachiko" - ], - "maintainers": [ - "@sainsachiko" - ] - } - }, - { - "name": "seqtk_cutn", - "path": "modules/nf-core/seqtk/cutn/meta.yml", - "type": "module", - "meta": { - "name": "seqtk_cutn", - "description": "Generates a BED file containing genomic locations of lengths of N.", - "keywords": [ - "cut", - "fasta", - "seqtk" - ], - "tools": [ - { - "seqtk": { - "description": "Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. Seqtk mergepe command merges pair-end reads into one interleaved file.", - "homepage": "https://github.com/lh3/seqtk", - "documentation": "https://docs.csc.fi/apps/seqtk/", - "tool_dev_url": "https://github.com/lh3/seqtk", - "licence": [ - "MIT" - ], - "identifier": "biotools:seqtk" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "A single fasta file to be split.", - "pattern": "*.{fasta}", - "ontologies": [] - } - } - ] - ], - "output": { - "bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bed": { - "type": "file", - "description": "The output bed which summarised locations of cuts", - "pattern": "*.{bed}", - "ontologies": [] - } - } - ] - ], - "versions_seqtk": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "seqtk": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "seqtk 2>&1 | sed -n 's/^Version: //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "seqtk": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "seqtk 2>&1 | sed -n 's/^Version: //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@DLBPointon" - ], - "maintainers": [ - "@DLBPointon" - ] - }, - "pipelines": [ - { - "name": "pairgenomealign", - "version": "2.2.3" - } - ] - }, - { - "name": "seqtk_mergepe", - "path": "modules/nf-core/seqtk/mergepe/meta.yml", - "type": "module", - "meta": { - "name": "seqtk_mergepe", - "description": "Interleave pair-end reads from FastQ files", - "keywords": [ - "interleave", - "merge", - "fastx" - ], - "tools": [ - { - "seqtk": { - "description": "Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. Seqtk mergepe command merges pair-end reads into one interleaved file.", - "homepage": "https://github.com/lh3/seqtk", - "documentation": "https://docs.csc.fi/apps/seqtk/", - "tool_dev_url": "https://github.com/lh3/seqtk", - "licence": [ - "MIT" - ], - "identifier": "biotools:seqtk" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + "name": "fasta_hmmsearch_rank_fastas", + "path": "subworkflows/nf-core/fasta_hmmsearch_rank_fastas/meta.yml", + "type": "subworkflow", + "meta": { + "name": "fasta_hmmsearch_rank_fastas", + "description": "Run hmmsearch and output separate fasta files for top scoring hits to each profile", + "keywords": ["hmmer", "search", "rank", "fasta"], + "components": ["hmmer/hmmsearch", "hmmer/hmmrank", "seqtk/subseq"], + "input": [ + { + "ch_hmms": { + "type": "file", + "description": "The input channel containing hmm profiles\nStructure: [ val(meta), path(hmm) ]\n", + "pattern": "*.{hmm}" + } + }, + { + "ch_fasta": { + "type": "file", + "description": "The input channel containing sequences to be searched and ranked\n" + } + } + ], + "output": [ + { + "hmmrank": { + "type": "file", + "description": "Channel containing the TSV file from ranking hmmsearch hits\nStructure: [ val(meta), path(hmmrank) ]\n", + "pattern": "*.hmmrank.tsv.gz" + } + }, + { + "bai": { + "type": "file", + "description": "Channel containing subsets of sequences\nStructure: [ val(meta), path(fasta) ]\n", + "pattern": "*.fa.gz" + } + } + ], + "authors": ["@erikrikarddaniel"], + "maintainers": ["@erikrikarddaniel"] }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,respectively.", - "pattern": "*.{fastq.gz}", - "ontologies": [] - } - } - ] - ], - "output": { - "reads": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.fastq.gz": { - "type": "file", - "description": "If single-end reads, the output is the same as the input, 1 FastQ file for each read. If pair-end reads, the read pairs will be interleaved and output as 1 FastQ file for each read pair.", - "pattern": "*.{fastq.gz}", - "ontologies": [] - } - } - ] - ], - "versions_seqtk": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "seqtk": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "seqtk 2>&1 | sed -n 's/^Version: //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "seqtk": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "seqtk 2>&1 | sed -n 's/^Version: //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "ampliseq", + "version": "2.17.0" + }, + { + "name": "phyloplace", + "version": "2.0.0" + } ] - ] - }, - "authors": [ - "@emnilsson" - ], - "maintainers": [ - "@emnilsson" - ] - }, - "pipelines": [ - { - "name": "mag", - "version": "5.4.2" }, { - "name": "metatdenovo", - "version": "1.3.0" - } - ] - }, - { - "name": "seqtk_rename", - "path": "modules/nf-core/seqtk/rename/meta.yml", - "type": "module", - "meta": { - "name": "seqtk_rename", - "description": "Rename sequence names in FASTQ or FASTA files.", - "keywords": [ - "rename", - "fastx", - "header" - ], - "tools": [ - { - "seqtk": { - "description": "Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. The seqtk rename command renames sequence names.", - "homepage": "https://github.com/lh3/seqtk", - "documentation": "https://docs.csc.fi/apps/seqtk/", - "tool_dev_url": "https://github.com/lh3/seqtk", - "licence": [ - "MIT" - ], - "identifier": "biotools:seqtk" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "sequences": { - "type": "file", - "description": "A FASTQ or FASTA file", - "pattern": "*.{fastq.gz, fastq, fq, fq.gz, fasta, fastq.gz, fa, fa.gz, fas, fas.gz, fna, fna.gz}", - "ontologies": [] - } - } - ] - ], - "output": { - "sequences": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.gz": { - "type": "file", - "description": "FASTQ/FASTA file containing renamed sequences", - "pattern": "*.{fastq.gz, fasta.gz}", - "ontologies": [] - } - } - ] - ], - "versions_seqtk": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "seqtk": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "seqtk 2>&1 | sed -n 's/^Version: //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "seqtk": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "seqtk 2>&1 | sed -n 's/^Version: //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@hseabolt", - "@mjcipriano", - "@sateeshperi" - ], - "maintainers": [ - "@hseabolt", - "@mjcipriano", - "@sateeshperi" - ] - } - }, - { - "name": "seqtk_sample", - "path": "modules/nf-core/seqtk/sample/meta.yml", - "type": "module", - "meta": { - "name": "seqtk_sample", - "description": "Subsample reads from FASTQ files", - "keywords": [ - "sample", - "fastx", - "reads" - ], - "tools": [ - { - "seqtk": { - "description": "Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. Seqtk sample command subsamples sequences.", - "homepage": "https://github.com/lh3/seqtk", - "documentation": "https://docs.csc.fi/apps/seqtk/", - "tool_dev_url": "https://github.com/lh3/seqtk", - "licence": [ - "MIT" - ], - "identifier": "biotools:seqtk" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files", - "pattern": "*.{fastq.gz}", - "ontologies": [] - } + "name": "fasta_index_bismark_bwameth", + "path": "subworkflows/nf-core/fasta_index_bismark_bwameth/meta.yml", + "type": "subworkflow", + "meta": { + "name": "fasta_index_bismark_bwameth", + "description": "Generate index files from reference fasta for bismark and bwameth", + "keywords": ["bismark", "bwameth", "prepare genome", "index"], + "components": ["untar", "gunzip", "bismark/genomepreparation", "bwameth/index", "samtools/faidx"], + "input": [ + { + "fasta_fai": { + "type": "file", + "description": "Reference genome\nStructure: [ val(meta), path(fasta), path(fai) ]\n", + "pattern": "*.{fa/fa.gz,fai}" + } + }, + { + "bismark_index": { + "type": "file", + "description": "Bismark genome index files\nStructure: [ val(meta), path(bismark_index) ]\n" + } + }, + { + "bwameth_index": { + "type": "file", + "description": "Bwameth genome index files\nStructure: [ val(meta), path(bwameth_index) ]\n" + } + }, + { + "aligner": { + "type": "string", + "description": "Aligner name (bismark, bismark_hisat, or bwameth)\n" + } + }, + { + "use_mem2": { + "type": "boolean", + "description": "Build a mem2 index when bwameth is chosen as an aligner, and an index path is not supplied\n" + } + } + ], + "output": [ + { + "fasta_fai": { + "type": "file", + "description": "Reference genome\nStructure: [ val(meta), path(fasta), path(fai) ]\n", + "pattern": "*.{fa/fa.gz,fai}" + } + }, + { + "bismark_index": { + "type": "file", + "description": "Bismark genome index files\nStructure: [ val(meta), path(bismark_index) ]\npattern: \"BismarkIndex\"\n" + } + }, + { + "bwameth_index": { + "type": "file", + "description": "Bwameth genome index files\nStructure: [ val(meta), path(bwameth_index) ]\npattern: \"index\"\n" + } + }, + { + "versions": { + "type": "file", + "description": "File containing software versions\nStructure: [ path(versions.yml) ]\n", + "pattern": "versions.yml" + } + } + ], + "authors": ["@sateeshperi", "dcarrillox"], + "maintainers": ["@sateeshperi", "@dcarrillox"] }, - { - "sample_size": { - "type": "float", - "description": "Fraction (<1.0) or number (>=1) of reads to sample." - } - } - ] - ], - "output": { - "reads": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.fastq.gz": { - "type": "file", - "description": "Subsampled FastQ files", - "pattern": "*.{fastq.gz}", - "ontologies": [] - } - } - ] - ], - "versions_seqtk": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "seqtk": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "seqtk 2>&1 | sed -n 's/^Version: //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "seqtk": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "seqtk 2>&1 | sed -n 's/^Version: //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "methylseq", + "version": "4.2.0" + } ] - ] - }, - "authors": [ - "@kaurravneet4123", - "@sidorov-si", - "@adamrtalbot" - ], - "maintainers": [ - "@kaurravneet4123", - "@sidorov-si", - "@adamrtalbot" - ] - }, - "pipelines": [ - { - "name": "demultiplex", - "version": "1.7.1" - }, - { - "name": "panoramaseq", - "version": "dev" - }, - { - "name": "pathogensurveillance", - "version": "1.1.0" }, { - "name": "raredisease", - "version": "3.0.0" + "name": "fasta_index_dna", + "path": "subworkflows/nf-core/fasta_index_dna/meta.yml", + "type": "subworkflow", + "meta": { + "name": "fasta_index_dna", + "description": "Generate aligner index for a reference genome.\nPlease note, this workflow requires input CHANNELS. Input values will cause errors\n", + "keywords": ["fasta", "index", "bowtie2", "bwamem", "bwamem2", "dragmap", "snapaligner"], + "components": ["bowtie2/build", "bwa/index", "bwamem2/index", "dragmap/hashtable", "snapaligner/index"], + "input": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference genome fasta file" + } + }, + { + "meta2": { + "type": "map", + "description": "Groovy Map containing altliftover information\ne.g. [ id:'test' ]\n" + } + }, + { + "altliftover": { + "type": "file", + "description": "Sam formatted liftover file for the reference genome alt contigs\nSee: https://github.com/lh3/bwa/blob/master/README-alt.md\nDownload from: https://sourceforge.net/projects/bio-bwa/files/bwakit\n" + } + }, + { + "val_aligner": { + "type": "string", + "description": "Aligner to use for alignment", + "enum": ["bowtie2", "bwa", "bwamem2", "dragmap", "snap"] + } + } + ], + "output": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "index": { + "type": "file", + "description": "aligner index" + } + }, + { + "versions": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ], + "authors": ["@matthdsm", "@ramprasadn"], + "maintainers": ["@matthdsm", "@ramprasadn"] + } }, { - "name": "seqinspector", - "version": "1.0.1" - } - ] - }, - { - "name": "seqtk_seq", - "path": "modules/nf-core/seqtk/seq/meta.yml", - "type": "module", - "meta": { - "name": "seqtk_seq", - "description": "Common transformation operations on FASTA or FASTQ files.", - "keywords": [ - "seq", - "filter", - "transformation" - ], - "tools": [ - { - "seqtk": { - "description": "Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. The seqtk seq command enables common transformation operations on FASTA or FASTQ files.", - "homepage": "https://github.com/lh3/seqtk", - "documentation": "https://docs.csc.fi/apps/seqtk/", - "tool_dev_url": "https://github.com/lh3/seqtk", - "licence": [ - "MIT" - ], - "identifier": "biotools:seqtk" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } + "name": "fasta_index_methylseq", + "path": "subworkflows/nf-core/fasta_index_methylseq/meta.yml", + "type": "subworkflow", + "meta": { + "name": "fasta_index_methylseq", + "description": "Generate index files from reference fasta for bismark, bwameth and bwamem aligners", + "keywords": ["bismark", "bwameth", "bwamem", "prepare genome", "index"], + "components": [ + "untar", + "gunzip", + "bismark/genomepreparation", + "bwameth/index", + "bwa/index", + "samtools/faidx" + ], + "input": [ + { + "fasta": { + "type": "file", + "description": "Reference genome\nStructure: [ val(meta), path(fasta) ]\n", + "pattern": "*.{fa/fa.gz}" + } + }, + { + "fasta_index": { + "type": "file", + "description": "Reference genome index file\nStructure: [ val(meta), path(fasta) ]\n", + "pattern": "*.fai" + } + }, + { + "bismark_index": { + "type": "file", + "description": "Bismark genome index files\nStructure: [ val(meta), path(bismark_index) ]\n" + } + }, + { + "bwameth_index": { + "type": "file", + "description": "Bwameth genome index files\nStructure: [ val(meta), path(bwameth_index) ]\n" + } + }, + { + "bwamem_index": { + "type": "file", + "description": "Bwamem genome index files\nStructure: [ val(meta), path(bwamem_index) ]\n" + } + }, + { + "aligner": { + "type": "string", + "description": "Aligner name (bismark, bismark_hisat, bwameth, or bwamem)\n" + } + }, + { + "collecthsmetrics": { + "type": "boolean", + "description": "Whether to run picard collecthsmetrics tool\n" + } + }, + { + "use_mem2": { + "type": "boolean", + "description": "Build a mem2 index when bwameth is chosen as an aligner, and an index path is not supplied\n" + } + } + ], + "output": [ + { + "fasta": { + "type": "file", + "description": "Reference genome\nStructure: [ val(meta), path(fasta) ]\n", + "pattern": "*.fa" + } + }, + { + "fasta_index": { + "type": "file", + "description": "Reference genome index file\nStructure: [ val(meta), path(fasta) ]\n", + "pattern": "*.fai" + } + }, + { + "bismark_index": { + "type": "file", + "description": "Bismark genome index files\nStructure: [ val(meta), path(bismark_index) ]\npattern: \"BismarkIndex\"\n" + } + }, + { + "bwameth_index": { + "type": "file", + "description": "Bwameth genome index files\nStructure: [ val(meta), path(bwameth_index) ]\npattern: \"index\"\n" + } + }, + { + "bwamem_index": { + "type": "file", + "description": "Bwamem genome index files\nStructure: [ val(meta), path(bwamem_index) ]\npattern: \"index\"\n" + } + }, + { + "versions": { + "type": "file", + "description": "File containing software versions\nStructure: [ path(versions.yml) ]\n", + "pattern": "versions.yml" + } + } + ], + "authors": ["@sateeshperi", "@dcarrillox", "@eduard.watchmaker"], + "maintainers": ["@sateeshperi", "@dcarrillox", "@eduard.watchmaker"] }, - { - "fastx": { - "type": "file", - "description": "A FASTQ or FASTA file", - "pattern": "*.{fastq.gz, fastq, fq, fq.gz, fasta, fastq.gz, fa, fa.gz, fas, fas.gz, fna, fna.gz}", - "ontologies": [] - } - } - ] - ], - "output": { - "fastx": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.gz": { - "type": "file", - "description": "FASTQ/FASTA file containing renamed sequences", - "pattern": "*.{fastq.gz, fasta.gz}", - "ontologies": [] - } - } - ] - ], - "versions_seqtk": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "seqtk": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "seqtk 2>&1 | sed -n 's/^Version: //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "seqtk": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "seqtk 2>&1 | sed -n 's/^Version: //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "methylseq", + "version": "4.2.0" + } ] - ] - }, - "authors": [ - "@hseabolt", - "@mjcipriano", - "@sateeshperi" - ], - "maintainers": [ - "@hseabolt", - "@mjcipriano", - "@sateeshperi" - ] - }, - "pipelines": [ - { - "name": "crisprseq", - "version": "2.3.0" - }, - { - "name": "metatdenovo", - "version": "1.3.0" }, { - "name": "radseq", - "version": "dev" - } - ] - }, - { - "name": "seqtk_subseq", - "path": "modules/nf-core/seqtk/subseq/meta.yml", - "type": "module", - "meta": { - "name": "seqtk_subseq", - "description": "Select only sequences that match the filtering condition", - "keywords": [ - "filtering", - "selection", - "fastx" - ], - "tools": [ - { - "seqtk": { - "description": "Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format", - "homepage": "https://github.com/lh3/seqtk", - "documentation": "https://docs.csc.fi/apps/seqtk/", - "tool_dev_url": "https://github.com/lh3/seqtk", - "licence": [ - "MIT" - ], - "identifier": "biotools:seqtk" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } + "name": "fasta_newick_epang_gappa", + "path": "subworkflows/nf-core/fasta_newick_epang_gappa/meta.yml", + "type": "subworkflow", + "meta": { + "name": "fasta_newick_epang_gappa", + "description": "Run phylogenetic placement with a number of query sequences plus a reference alignment and phylogeny. Used in nf-core/phyloplace.", + "keywords": ["phylogenetic placement", "phylogenetics", "alignment", "fasta", "newick"], + "components": [ + "hmmer/hmmbuild", + "hmmer/hmmalign", + "hmmer/eslalimask", + "hmmer/eslreformat", + "clustalo/align", + "mafft/align", + "epang/place", + "epang/split", + "gappa/examinegraft", + "gappa/examineassign", + "gappa/examineheattree" + ], + "input": [ + { + "ch_pp_data": { + "type": "map", + "description": "Structure: [\n meta: val(meta),\n data: [\n alignmethod: 'hmmer',\n queryseqfile: path(\"*.faa\"),\n refseqfile: path(\"*.alnfaa\"),\n refphylogeny: path(\"*.newick\"),\n model: \"LG\",\n taxonomy: path(\"*.tsv\")\n ]\n]\n" + } + }, + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "queryseqfile": { + "type": "file", + "description": "Fasta file with query sequences", + "pattern": "*.{faa,fna,fa,fasta,fa,faa.gz,fna.gz,fa.gz,fasta.gz,fa.gz}" + } + }, + { + "refseqfile": { + "type": "file", + "description": "File with reference sequences; aligned unless an hmmfile is provided", + "pattern": "*.{faa,fna,fa,fasta,fa,phy,aln,alnfaa,alnfna,alnfa,mfa,faa.gz,fna.gz,fa.gz,fasta.gz,fa.gz,phy.gz,aln.gz,alnfaa.gz,alnfna.gz,alnfa.gz,mfa.gz}" + } + }, + { + "refphylogeny": { + "type": "file", + "description": "Newick file with reference phylogenetic tree", + "pattern": "*.{newick,tree}" + } + }, + { + "hmmfile": { + "type": "file", + "description": "HMM file to use for alignment; implies that refseqfile is not aligned. Optional.", + "pattern": "*.{hmm,HMM,hmm.gz,HMM.gz}" + } + }, + { + "model": { + "type": "string", + "description": "Phylogenetic model to use in placement, e.g. 'LG+F' or 'GTR+I+F'" + } + }, + { + "alignmethod": { + "type": "string", + "description": "Method used for alignment, 'hmmer', 'clustalo' or 'mafft'" + } + } + ], + "output": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "epang": { + "type": "directory", + "description": "All output from EPA-NG", + "pattern": "*" + } + }, + { + "jplace": { + "type": "file", + "description": "jplace file from EPA-NG", + "pattern": "*.jplace" + } + }, + { + "grafted_phylogeny": { + "type": "file", + "description": "Newick file with query sequences placed in reference tree", + "pattern": "*.newick" + } + }, + { + "taxonomy_profile": { + "type": "file", + "description": "Tab separated file with taxonomy information from classification", + "pattern": "*.tsv" + } + }, + { + "taxonomy_per_query": { + "type": "file", + "description": "Tab separated file with taxonomy information per query from classification", + "pattern": "*.tsv" + } + }, + { + "heattree": { + "type": "file", + "description": "Heattree in SVG format", + "pattern": "*.svg" + } + } + ], + "authors": ["@erikrikarddaniel"], + "maintainers": ["@erikrikarddaniel"] }, - { - "sequences": { - "type": "file", - "description": "FASTQ/FASTA file", - "pattern": "*.{fq,fq.gz,fa,fa.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ], - { - "filter_list": { - "type": "file", - "description": "BED file or a text file with a list of sequence names", - "pattern": "*.{bed,lst}", - "ontologies": [] - } - } - ], - "output": { - "sequences": [ - [ - { - "meta": { - "type": "file", - "description": "FASTQ/FASTA file", - "pattern": "*.{fq.gz,fa.gz}", - "ontologies": [] - } - }, - { - "*.gz": { - "type": "file", - "description": "FASTQ/FASTA file", - "pattern": "*.{fq.gz,fa.gz}", - "ontologies": [] - } - } - ] - ], - "versions_seqtk": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "seqtk": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "seqtk 2>&1 | sed -n 's/^Version: //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "seqtk": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "seqtk 2>&1 | sed -n 's/^Version: //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "ampliseq", + "version": "2.17.0" + }, + { + "name": "phyloplace", + "version": "2.0.0" + } ] - ] }, - "authors": [ - "@sidorov-si" - ], - "maintainers": [ - "@sidorov-si" - ] - }, - "pipelines": [ { - "name": "ampliseq", - "version": "2.17.0" + "name": "fasta_vclust_prefilter_align_cluster", + "path": "subworkflows/nf-core/fasta_vclust_prefilter_align_cluster/meta.yml", + "type": "subworkflow", + "meta": { + "name": "fasta_vclust_prefilter_align_cluster", + "description": "Subworkflow that runs a three-stage VCLUST pipeline: 1) create a prefilter\nof candidate sequence pairs with `vclust prefilter`, 2) compute pairwise\nalignments and similarity metrics with `vclust align`, and 3) generate\nthreshold-based clusters with `vclust cluster`.\n", + "keywords": ["fasta", "vclust", "cluster", "prefilter", "align"], + "components": ["vclust/prefilter", "vclust/align", "vclust/cluster"], + "input": [ + { + "ch_fasta": { + "type": "file", + "description": "Input channel containing FASTA files to cluster. Each entry is a two-item\ntuple: [ val(meta), path(fasta) ] where `meta` is a Groovy map (e.g.\n[ id:'sample1' ]) and `fasta` is the path to the FASTA file.\n", + "pattern": "*.{fasta,fna,fa}" + } + }, + { + "save_alignment": { + "type": "boolean", + "description": "Whether to save pairwise alignments produced by `vclust align`.\n", + "default": false + } + }, + { + "metric": { + "type": "string", + "description": "Similarity metric to use for clustering. Allowed values: 'tani', 'gani',\nor 'ani'.\n", + "enum": ["tani", "gani", "ani"] + } + }, + { + "tani": { + "type": "float", + "description": "Minimum total ANI threshold.\n" + } + }, + { + "gani": { + "type": "float", + "description": "Minimum global ANI threshold.\n" + } + }, + { + "ani": { + "type": "float", + "description": "Minimum ANI threshold.\n" + } + } + ], + "output": [ + { + "versions": { + "type": "file", + "description": "File containing software versions used by the subworkflow", + "pattern": "versions.yml" + } + }, + { + "fasta": { + "type": "file", + "description": "Input FASTA file forwarded from the workflow. Each output is associated\nwith its input sample/meta tuple.\n", + "pattern": "*.{fasta,fna,fa}" + } + }, + { + "clusters": { + "type": "file", + "description": "TSV file containing clustering assignments produced by `vclust cluster`.\nFormat: genome identifier followed by 0-based cluster identifier.\n", + "pattern": "*.tsv" + } + }, + { + "alignment": { + "type": "file", + "description": "Optional pairwise alignment file(s) produced by `vclust align`.", + "pattern": "*.aln.tsv" + } + }, + { + "ids": { + "type": "file", + "description": "IDs file produced by `vclust align` mapping sequence IDs and part counts.", + "pattern": "*.ids.tsv" + } + } + ], + "authors": ["@Joon-Klaps"], + "maintainers": ["@Joon-Klaps"] + } }, { - "name": "phyloplace", - "version": "2.0.0" - } - ] - }, - { - "name": "seqtk_trim", - "path": "modules/nf-core/seqtk/trim/meta.yml", - "type": "module", - "meta": { - "name": "seqtk_trim", - "description": "Trim low quality bases from FastQ files", - "keywords": [ - "trimfq", - "fastq", - "seqtk" - ], - "tools": [ - { - "seqtk": { - "description": "Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format", - "homepage": "https://github.com/lh3/seqtk", - "documentation": "https://docs.csc.fi/apps/seqtk/", - "tool_dev_url": "https://github.com/lh3/seqtk", - "licence": [ - "MIT" - ], - "identifier": "biotools:seqtk" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files", - "pattern": "*.{fastq.gz}", - "ontologies": [] - } + "name": "fastq_align_bamcmp_bwa", + "path": "subworkflows/nf-core/fastq_align_bamcmp_bwa/meta.yml", + "type": "subworkflow", + "meta": { + "name": "fastq_align_bamcmp_bwa", + "description": "Align reads to two different reference genomes using bwa, then use bamcmp to keep only reads that align better to the first genome, then sort with samtools", + "keywords": ["bam", "cram", "bamcmp", "contamination", "align"], + "components": [ + "bamcmp", + "bwa/mem", + "bwa/align", + "samtools/sort", + "samtools/index", + "samtools/stats", + "samtools/idxstats", + "samtools/flagstat", + "bam_sort_stats_samtools" + ], + "input": [ + { + "ch_reads": { + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\nStructure: [ val(meta), [ path(reads) ] ]\n" + } + }, + { + "ch_primary_index": { + "description": "BWA genome index files for the primary species.\nStructure: [ val(meta2), path(primary_index) ]\n" + } + }, + { + "ch_contaminant_index": { + "description": "BWA genome index files for the contamination species.\nStructure: [ val(meta3), path(contaminant_index) ]\n" + } + }, + { + "val_sort_bam": { + "type": "boolean", + "description": "If true sort resulting primary bam files.", + "pattern": "true|false" + } + }, + { + "ch_primary_fasta_fai": { + "type": "file", + "description": "Optional reference fasta file for the primary genome. This only needs to be given if val_sort_bam = true\nStructure: [ path(fasta), path(fai) ]\n" + } + } + ], + "output": [ + { + "bam": { + "description": "BAM file, sorted by samtools if requested\nStructure: [ val(meta), path(bam) ]\n" + } + }, + { + "contaminant_bam": { + "description": "BAM file of the reads that map better to the contamination genome. Sorted by queryname.\nStructure: [ val(meta), path(bam) ]\n" + } + }, + { + "bai": { + "description": "BAI index of the ordered BAM file\nStructure: [ val(meta), path(bai) ]\n" + } + }, + { + "csi": { + "description": "CSI index of the ordered BAM file\nStructure: [ val(meta), path(csi) ]\n" + } + }, + { + "stats": { + "description": "File containing samtools stats output\nStructure: [ val(meta), path(stats) ]\n" + } + }, + { + "flagstat": { + "description": "File containing samtools flagstat output\nStructure: [ val(meta), path(flagstat) ]\n" + } + }, + { + "idxstats": { + "description": "File containing samtools idxstats output\nStructure: [ val(meta), path(idxstats) ]\n" + } + }, + { + "unfiltered_stats": { + "description": "File containing samtools stats output for primary unfiltered alignment.\nStructure: [ val(meta), path(stats) ]\n" + } + }, + { + "unfiltered_flagstat": { + "description": "File containing samtools flagstat output for primary unfiltered alignment.\nStructure: [ val(meta), path(flagstat) ]\n" + } + }, + { + "unfiltered_idxstats": { + "description": "File containing samtools idxstats output for primary unfiltered alignment.\nStructure: [ val(meta), path(idxstats) ]\n" + } + }, + { + "versions": { + "description": "Files containing software versions\nStructure: [ path(versions.yml) ]\n" + } + } + ], + "authors": ["@sppearce"], + "maintainers": ["@sppearce"] } - ] - ], - "output": { - "reads": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.fastq.gz": { - "type": "file", - "description": "Filtered FastQ files", - "pattern": "*.{fastq.gz}", - "ontologies": [] - } - } - ] - ], - "versions_seqtk": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "seqtk": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "seqtk 2>&1 | sed -n 's/^Version: //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "seqtk": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "seqtk 2>&1 | sed -n 's/^Version: //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] }, - "authors": [ - "@laramiellindsey" - ] - }, - "pipelines": [ { - "name": "demo", - "version": "1.1.0" - } - ] - }, - { - "name": "sequali", - "path": "modules/nf-core/sequali/meta.yml", - "type": "module", - "meta": { - "name": "sequali", - "description": "Sequence quality metrics for FASTQ and uBAM files.", - "keywords": [ - "quality_control", - "qc", - "preprocessing" - ], - "tools": [ - { - "sequali": { - "description": "Fast sequencing quality metrics", - "homepage": "https://github.com/rhpvorderman/sequali", - "documentation": "https://sequali.readthedocs.io/en/latest/", - "tool_dev_url": "https://github.com/rhpvorderman/sequali", - "doi": "10.5281/zenodo.10854010", - "licence": [ - "AGPL v3-or-later" - ], - "identifier": "biotools:sequali" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "reads": { - "type": "file", - "description": "Input FASTQ(s) or uBAM file. The format is autodetected and compressed formats are supported.", - "pattern": "*.{fastq,fq,fastq.gz,fq.gz,bam}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "output": { - "html": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.html": { - "type": "file", - "description": "HTML output file.", - "pattern": "*.{html}", - "ontologies": [] - } - } - ] - ], - "json": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.json": { - "type": "file", - "description": "JSON output file.", - "pattern": "*.{json}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "versions_sequali": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "sequali": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "sequali --version |& sed '1!d ; s/sequali //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "sequali": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "sequali --version |& sed '1!d ; s/sequali //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@irliampa", - "@DarkoCucin" - ], - "maintainers": [ - "@irliampa", - "@DarkoCucin" - ] - } - }, - { - "name": "sequencetools_pileupcaller", - "path": "modules/nf-core/sequencetools/pileupcaller/meta.yml", - "type": "module", - "meta": { - "name": "sequencetools_pileupcaller", - "description": "PileupCaller is a tool to create genotype calls from bam files using read-sampling methods", - "keywords": [ - "genotyping", - "mpileup", - "random draw", - "pseudohaploid", - "pseudodiploid", - "freqsum", - "plink", - "bed", - "eigenstrat" - ], - "tools": [ - { - "sequencetools": { - "description": "Tools for population genetics on sequencing data", - "homepage": "https://github.com/stschiff/sequenceTools", - "documentation": "https://github.com/stschiff/sequenceTools#readme", - "tool_dev_url": "https://github.com/stschiff/sequenceTools", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "mpileup": { - "type": "file", - "description": "samtools mpileup output.", - "ontologies": [] - } - } - ], - { - "snpfile": { - "type": "file", - "description": "Eigenstrat format .snp file of the sites in the mpileup file to call genotypes on.\nOnly alleles matching the Ref and Alt alleles of the provided snp file will be called.\n", - "ontologies": [] - } - }, - { - "sample_names_fn": { - "type": "file", - "description": "File containing the sample names", - "ontologies": [] - } - } - ], - "output": { - "eigenstrat": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.geno": { - "type": "file", - "description": "A tuple containing the output Eigenstrat-formatted geno, snp and ind files.", - "pattern": "*.{geno,snp,ind}.txt", - "ontologies": [] - } - }, - { - "*.snp": { - "type": "file", - "description": "A tuple containing the output Eigenstrat-formatted geno, snp and ind files.", - "pattern": "*.{geno,snp,ind}.txt", - "ontologies": [] - } - }, - { - "*.ind": { - "type": "file", - "description": "A tuple containing the output Eigenstrat-formatted geno, snp and ind files.", - "pattern": "*.{geno,snp,ind}.txt", - "ontologies": [] - } - } - ] - ], - "plink": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bed": { - "type": "file", - "description": "A tuple containing the output Plink-formatted bed, bim and fam files.", - "pattern": "*.{bed,bim,fam}", - "ontologies": [] - } - }, - { - "*.bim": { - "type": "file", - "description": "A tuple containing the output Plink-formatted bed, bim and fam files.", - "pattern": "*.{bed,bim,fam}", - "ontologies": [] - } - }, - { - "*.fam": { - "type": "file", - "description": "A tuple containing the output Plink-formatted bed, bim and fam files.", - "pattern": "*.{bed,bim,fam}", - "ontologies": [] - } - } - ] - ], - "freqsum": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.freqsum.gz": { - "type": "file", - "description": "The output freqsum-formatted file.", - "pattern": "*.freqsum.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@TCLamnidis" - ], - "maintainers": [ - "@TCLamnidis" - ] - } - }, - { - "name": "sequenzautils_bam2seqz", - "path": "modules/nf-core/sequenzautils/bam2seqz/meta.yml", - "type": "module", - "meta": { - "name": "sequenzautils_bam2seqz", - "description": "Sequenza-utils bam2seqz process BAM and Wiggle files to produce a seqz file", - "keywords": [ - "sequenzautils", - "copy number", - "bam2seqz" - ], - "tools": [ - { - "sequenzautils": { - "description": "Sequenza-utils provides 3 main command line programs to transform common NGS file format - such as FASTA, BAM - to input files for the Sequenza R package. The program - bam2seqz - process a paired set of BAM/pileup files (tumour and matching normal), and GC-content genome-wide information, to extract the common positions with A and B alleles frequencies.", - "homepage": "https://sequenza-utils.readthedocs.io/en/latest/index.html", - "documentation": "https://sequenza-utils.readthedocs.io/en/latest/index.html", - "doi": "10.1093/annonc/mdu479", - "licence": [ - "GPL-3.0-or-later" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "normalbam": { - "type": "file", - "description": "BAM file from the reference/normal sample", - "pattern": "*.{bam}", - "ontologies": [] - } - }, - { - "tumourbam": { - "type": "file", - "description": "BAM file from the tumour sample", - "pattern": "*.{bam}", - "ontologies": [] - } - } - ], - { - "fasta": { - "type": "file", - "description": "Reference FASTA file", - "pattern": "*.{fasta}", - "ontologies": [] - } - }, - { - "wigfile": { - "type": "file", - "description": "GC content wiggle file", - "pattern": "*.{wig.gz}", - "ontologies": [] - } - } - ], - "output": { - "seqz": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.gz": { - "type": "file", - "description": "Seqz file", - "pattern": "*.{seqz.gz}", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@kaurravneet4123" - ], - "maintainers": [ - "@kaurravneet4123" - ] - } - }, - { - "name": "sequenzautils_gcwiggle", - "path": "modules/nf-core/sequenzautils/gcwiggle/meta.yml", - "type": "module", - "meta": { - "name": "sequenzautils_gcwiggle", - "description": "Sequenza-utils gc_wiggle computes the GC percentage across the sequences, and returns a file in the UCSC wiggle format, given a fasta file and a window size.", - "keywords": [ - "sequenzautils", - "copy number", - "gc_wiggle" - ], - "tools": [ - { - "sequenzautils": { - "description": "Sequenza-utils provides 3 main command line programs to transform common NGS file format - such as FASTA, BAM - to input files for the Sequenza R package. The program -gc_wiggle- takes fasta file as an input, computes GC percentage across the sequences and returns a file in the UCSC wiggle format.", - "homepage": "https://sequenza-utils.readthedocs.io/en/latest/index.html", - "documentation": "https://sequenza-utils.readthedocs.io/en/latest/index.html", - "doi": "10.1093/annonc/mdu479", - "licence": [ - "GPL-3.0-or-later" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA file", - "pattern": "*.{fasta}", - "ontologies": [] - } - } - ] - ], - "output": { - "wig": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.wig.gz": { - "type": "file", - "description": "GC Wiggle track file", - "pattern": "*.{wig.gz}", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@kaurravneet4123" - ], - "maintainers": [ - "@kaurravneet4123" - ] - } - }, - { - "name": "seqwish_induce", - "path": "modules/nf-core/seqwish/induce/meta.yml", - "type": "module", - "meta": { - "name": "seqwish_induce", - "description": "Induce a variation graph in GFA format from alignments in PAF format", - "keywords": [ - "induce", - "paf", - "gfa", - "graph", - "variation graph" - ], - "tools": [ - { - "seqwish": { - "description": "seqwish implements a lossless conversion from pairwise alignments between\nsequences to a variation graph encoding the sequences and their alignments.\n", - "homepage": "https://github.com/ekg/seqwish", - "documentation": "https://github.com/ekg/seqwish", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "paf": { - "type": "list", - "description": "comma-separated PAF file(s) of alignments, single entry allowed", - "pattern": "[*.{paf,paf.gz},*.{paf,paf.gz},...]" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA file used to generate alignments", - "pattern": "*.{fa,fa.gz,fasta,fasta.gz}", - "ontologies": [] - } - } - ] - ], - "output": { - "gfa": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.gfa": { - "type": "file", - "description": "Variation graph in GFA 1.0 format", - "pattern": "*.{gfa}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3975" - } - ] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@heuermh" - ], - "maintainers": [ - "@heuermh" - ] - }, - "pipelines": [ - { - "name": "pangenome", - "version": "1.1.3" - } - ] - }, - { - "name": "seroba_run", - "path": "modules/nf-core/seroba/run/meta.yml", - "type": "module", - "meta": { - "name": "seroba_run", - "description": "Determine Streptococcus pneumoniae serotype from Illumina paired-end reads", - "keywords": [ - "fastq", - "serotype", - "Streptococcus pneumoniae" - ], - "tools": [ - { - "seroba": { - "description": "SeroBA is a k-mer based pipeline to identify the Serotype from Illumina NGS reads for given references.", - "homepage": "https://sanger-pathogens.github.io/seroba/", - "documentation": "https://sanger-pathogens.github.io/seroba/", - "tool_dev_url": "https://github.com/sanger-pathogens/seroba", - "doi": "10.1099/mgen.0.000186", - "licence": [ - "GPL v3" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "Input Illunina paired-end FASTQ files", - "pattern": "*.{fq.gz,fastq.gz}", - "ontologies": [] - } - } - ] - ], - "output": { - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/${prefix}.tsv": { - "type": "file", - "description": "The predicted serotype in tab-delimited format", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "txt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/detailed_serogroup_info.txt": { - "type": "file", - "description": "A detailed description of the predicted serotype", - "pattern": "*.txt", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@rpetit3" - ], - "maintainers": [ - "@rpetit3" - ] - } - }, - { - "name": "severus", - "path": "modules/nf-core/severus/meta.yml", - "type": "module", - "meta": { - "name": "severus", - "description": "Severus is a somatic structural variation (SV) caller for long reads (both PacBio and ONT)", - "keywords": [ - "structural", - "variation", - "somatic", - "germline", - "long-read" - ], - "tools": [ - { - "severus": { - "description": "A tool for somatic structural variant calling using long reads", - "homepage": "https://github.com/KolmogorovLab/Severus", - "documentation": "https://github.com/KolmogorovLab/Severus", - "tool_dev_url": "https://github.com/KolmogorovLab/Severus", - "doi": "10.1101/2024.03.22.24304756", - "licence": [ - "BSD-3-clause" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "target_input": { - "type": "file", - "description": "path to one or multiple target BAM/CRAM files (e.g. tumor, must be indexed)", - "pattern": "*.{bam,cram}", - "ontologies": [] - } - }, - { - "target_index": { - "type": "file", - "description": "path to one or multiple target BAM/CRAM index files", - "pattern": "*.{bai,crai,csi}", - "ontologies": [] - } - }, - { - "control_input": { - "type": "file", - "description": "path to the control BAM/CRAM file (e.g. normal, must be indexed)", - "pattern": "*.{bam,cram}", - "ontologies": [] - } - }, - { - "control_index": { - "type": "file", - "description": "path to the control BAM/CRAM file index", - "pattern": "*.{bai,crai,csi}", - "ontologies": [] - } - }, - { - "vcf": { - "type": "file", - "description": "path to vcf file used for phasing (if using haplotype specific SV calling", - "pattern": "*.{vcf,vcf.gz}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing tandem repeat regions information\ne.g. `[ id:'hg38']`\n" - } + "name": "fastq_align_bowtie2", + "path": "subworkflows/nf-core/fastq_align_bowtie2/meta.yml", + "type": "subworkflow", + "meta": { + "name": "fastq_align_bowtie2", + "description": "Align reads to a reference genome using bowtie2 then sort with samtools", + "keywords": ["align", "fasta", "genome", "reference"], + "components": [ + "bowtie2/align", + "samtools/sort", + "samtools/index", + "samtools/stats", + "samtools/idxstats", + "samtools/flagstat", + "bam_sort_stats_samtools" + ], + "input": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "ch_reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" + } + }, + { + "ch_index": { + "type": "file", + "description": "Bowtie2 genome index files", + "pattern": "*.ebwt" + } + }, + { + "save_unaligned": { + "type": "boolean", + "description": "Save reads that do not map to the reference (true) or discard them (false)\n(default: false)\n" + } + }, + { + "sort_bam": { + "type": "boolean", + "description": "Use samtools sort (true) or samtools view (false)\n", + "default": false + } + }, + { + "ch_fasta_fai": { + "type": "file", + "description": "Reference fasta file and index", + "pattern": "*.{fasta,fa},*.{fai,fai}" + } + } + ], + "output": [ + { + "bam": { + "type": "file", + "description": "Output BAM file containing read alignments", + "pattern": "*.{bam}" + } + }, + { + "fastq": { + "type": "file", + "description": "Unaligned FastQ files", + "pattern": "*.fastq.gz" + } + }, + { + "log": { + "type": "file", + "description": "Alignment log", + "pattern": "*.log" + } + } + ], + "authors": ["@drpatelh"], + "maintainers": ["@drpatelh"] }, - { - "bed": { - "type": "file", - "description": "path to bed file for tandem repeat regions (must be ordered)", - "pattern": "*.bed", - "ontologies": [] - } - } - ] - ], - "output": { - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\n" - } - }, - { - "${prefix}/severus.log": { - "type": "file", - "description": "log file\n", - "pattern": "${prefix}/severus.log", - "ontologies": [] - } - } - ] - ], - "read_qual": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\n" - } - }, - { - "${prefix}/read_qual.txt": { - "type": "file", - "description": "txt file containing read quality information\n", - "pattern": "${prefix}/read_qual.txt", - "ontologies": [] - } - } - ] - ], - "breakpoints_double": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\n" - } - }, - { - "${prefix}/breakpoints_double.csv": { - "type": "file", - "description": "Detailed info about the detected breakpoints for all samples in text format, intended for an advanced user.\n", - "pattern": "${prefix}/breakpoints_double.csv", - "ontologies": [] - } - } - ] - ], - "read_alignments": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\n" - } - }, - { - "${prefix}/read_alignments": { - "type": "file", - "description": "A directory containing read alignments in BAM format for all samples, intended for an advanced user.\n", - "pattern": "${prefix}/read_alignments", - "ontologies": [] - } - } - ] - ], - "read_ids": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\n" - } - }, - { - "${prefix}/read_ids.csv": { - "type": "file", - "description": "Contains supporting read IDs for each SV\n", - "pattern": "${prefix}/read_ids.csv", - "ontologies": [] - } - } - ] - ], - "collapsed_dup": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\n" - } - }, - { - "${prefix}/severus_collaped_dup.bed": { - "type": "file", - "description": "BED file containing collapsed duplications\n", - "pattern": "${prefix}/severus_collaped_dup", - "ontologies": [] - } - } - ] - ], - "loh": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\n" - } - }, - { - "${prefix}/severus_LOH.bed": { - "type": "file", - "description": "BED file containing loss of heterozygosity information\n", - "pattern": "${prefix}/severus_LOH.bed", - "ontologies": [] - } - } - ] - ], - "all_vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\n" - } - }, - { - "${prefix}/all_SVs/severus_all.vcf": { - "type": "map", - "description": "VCF file containing somatic and germline structural variants\n", - "pattern": "${prefix}/all_SVs/severus_all.vcf", - "ontologies": [] - } - } - ] - ], - "all_breakpoints_clusters_list": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\n" - } - }, - { - "${prefix}/all_SVs/breakpoints_clusters_list.tsv": { - "type": "file", - "description": "a TSV containing a list of all breakpoint clusters\n", - "pattern": "${prefix}/all_SVs/breakpoints_clusters_list.tsv", - "ontologies": [] - } - } - ] - ], - "all_breakpoints_clusters": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\n" - } - }, - { - "${prefix}/all_SVs/breakpoints_clusters.tsv": { - "type": "file", - "description": "TSV file listing meta information in breakpoint clusters\n", - "pattern": "${prefix}/all_SVs/breakpoints_clusters.tsv", - "ontologies": [] - } - } - ] - ], - "all_plots": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\n" - } - }, - { - "${prefix}/all_SVs/plots/severus*.html": { - "type": "file", - "description": "HTML files containing plots for all SVs\n", - "pattern": "${prefix}/all_SVs/plots/severus*.html", - "ontologies": [] - } - } - ] - ], - "somatic_vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\n" - } - }, - { - "${prefix}/somatic_SVs/severus_somatic.vcf": { - "type": "file", - "description": "VCF file containing somatic structural variants (SV)\n", - "pattern": "${prefix}/somatic_SVs/severus_all.vcf", - "ontologies": [] - } - } - ] - ], - "somatic_breakpoints_clusters_list": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\n" - } - }, - { - "${prefix}/somatic_SVs/breakpoints_clusters_list.tsv": { - "type": "file", - "description": "TSV file containing full list of somatic breakpoint clusters\n", - "pattern": "${prefix}/somatic_SVs/breakpoints_clusters_list.tsv", - "ontologies": [] - } - } - ] - ], - "somatic_breakpoints_clusters": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\n" - } - }, - { - "${prefix}/somatic_SVs/breakpoints_clusters.tsv": { - "type": "file", - "description": "TSV file containing meta information of somatic breakpoint clusters\n", - "pattern": "${prefix}/somatic_SVs/breakpoints_clusters.tsv", - "ontologies": [] - } - } - ] - ], - "somatic_plots": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\n" - } - }, - { - "${prefix}/somatic_SVs/plots/severus*.html": { - "type": "file", - "description": "HTML files containing plots for somatic SVs\n", - "pattern": "${prefix}/somatic_SVs/plots/severus*.html", - "ontologies": [] - } - } - ] - ], - "versions_severus": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "severus": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "severus --version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "severus": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "severus --version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "atacseq", + "version": "2.1.2" + }, + { + "name": "chipseq", + "version": "2.1.0" + }, + { + "name": "nascent", + "version": "2.3.0" + }, + { + "name": "phageannotator", + "version": "dev" + }, + { + "name": "viralrecon", + "version": "3.0.0" + } ] - ] - }, - "authors": [ - "@fellen31" - ], - "maintainers": [ - "@fellen31" - ] - }, - "pipelines": [ - { - "name": "pacsomatic", - "version": "dev" - } - ] - }, - { - "name": "sexdeterrmine", - "path": "modules/nf-core/sexdeterrmine/meta.yml", - "type": "module", - "meta": { - "name": "sexdeterrmine", - "description": "Calculate the relative coverage on the Gonosomes vs Autosomes from the output of samtools depth, with error bars.", - "keywords": [ - "sex determination", - "genetic sex", - "relative coverage", - "ancient dna" - ], - "tools": [ - { - "sexdeterrmine": { - "description": "A python script carry out calculate the relative coverage of X and Y chromosomes, and their associated error bars, out of capture data.", - "homepage": "https://github.com/TCLamnidis/Sex.DetERRmine", - "documentation": "https://github.com/TCLamnidis/Sex.DetERRmine/README.md", - "tool_dev_url": "https://github.com/TCLamnidis/Sex.DetERRmine", - "doi": "10.1038/s41467-018-07483-5", - "licence": [ - "GPL v3" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + }, + { + "name": "fastq_align_bwa", + "path": "subworkflows/nf-core/fastq_align_bwa/meta.yml", + "type": "subworkflow", + "meta": { + "name": "fastq_align_bwa", + "description": "Align reads to a reference genome using bwa then sort with samtools", + "keywords": ["align", "fasta", "genome", "reference"], + "components": [ + "bwa/mem", + "bwa/align", + "samtools/sort", + "samtools/index", + "samtools/stats", + "samtools/idxstats", + "samtools/flagstat", + "bam_sort_stats_samtools" + ], + "input": [ + { + "ch_reads": { + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\nStructure: [ val(meta), [ path(reads) ] ]\n" + } + }, + { + "ch_index": { + "description": "BWA genome index files\nStructure: [ val(meta), path(index) ]\n" + } + }, + { + "val_sort_bam": { + "type": "boolean", + "description": "If true bwa modules sort resulting bam files", + "pattern": "true|false" + } + }, + { + "ch_fasta_fai": { + "type": "file", + "description": "Optional reference fasta file and index. This only needs to be given if val_sort_bam = true.\nStructure: [ val(meta), path(fasta), path(fai) ]\n" + } + } + ], + "output": [ + { + "bam_orig": { + "description": "BAM file produced by bwa\nStructure: [ val(meta), path(bam) ]\n" + } + }, + { + "bam": { + "description": "BAM file ordered by samtools\nStructure: [ val(meta), path(bam) ]\n" + } + }, + { + "bai": { + "description": "BAI index of the ordered BAM file\nStructure: [ val(meta), path(bai) ]\n" + } + }, + { + "csi": { + "description": "CSI index of the ordered BAM file\nStructure: [ val(meta), path(csi) ]\n" + } + }, + { + "stats": { + "description": "File containing samtools stats output\nStructure: [ val(meta), path(stats) ]\n" + } + }, + { + "flagstat": { + "description": "File containing samtools flagstat output\nStructure: [ val(meta), path(flagstat) ]\n" + } + }, + { + "idxstats": { + "description": "File containing samtools idxstats output\nStructure: [ val(meta), path(idxstats) ]\n" + } + } + ], + "authors": ["@JoseEspinosa"], + "maintainers": ["@JoseEspinosa"] }, - { - "depth": { - "type": "file", - "description": "Output from samtools depth (with header)", - "pattern": "*", - "ontologies": [] - } - } - ], - { - "sample_list_file": { - "type": "file", - "description": "File containing the list of samples to be processed.", - "ontologies": [] - } - } - ], - "output": { - "json": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.json": { - "type": "file", - "description": "JSON formatted table of relative coverages on the X and Y, with associated error bars.", - "pattern": "*.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "TSV table of relative coverages on the X and Y, with associated error bars.", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } + "pipelines": [ + { + "name": "atacseq", + "version": "2.1.2" + }, + { + "name": "chipseq", + "version": "2.1.0" + }, + { + "name": "methylseq", + "version": "4.2.0" + }, + { + "name": "nascent", + "version": "2.3.0" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@TCLamnidis" - ], - "maintainers": [ - "@TCLamnidis" - ] - } - }, - { - "name": "sgdemux", - "path": "modules/nf-core/sgdemux/meta.yml", - "type": "module", - "meta": { - "name": "sgdemux", - "description": "Demultiplex bgzip'd fastq files", - "keywords": [ - "demultiplex", - "fastq", - "bgzip" - ], - "tools": [ - { - "sgdemux": { - "description": "Tool for demultiplexing sequencing data generated on Singular Genomics' sequencing instruments.", - "homepage": "https://github.com/Singular-Genomics/singular-demux", - "documentation": "https://github.com/Singular-Genomics/singular-demux#sgdemux", - "licence": [ - "For Singular G4™ Sequencing Platform only" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "sample_sheet": { - "type": "file", - "description": "sample_sheet file (either a Singular Genomics sample sheet, or a two column csv with Sample_Barcode and Sample_ID)", - "pattern": "*.{csv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } + }, + { + "name": "fastq_align_bwaaln", + "path": "subworkflows/nf-core/fastq_align_bwaaln/meta.yml", + "type": "subworkflow", + "meta": { + "name": "fastq_align_bwaaln", + "description": "Align FASTQ files against reference genome with the bwa aln short-read aligner producing a sorted and indexed BAM files", + "keywords": ["bwa", "aln", "fasta", "bwa", "align", "map"], + "components": ["bwa/aln", "bwa/sampe", "bwa/samse", "samtools/index"], + "input": [ + { + "ch_reads": { + "description": "Structure: [ val(meta), path(fastq) ]\nOne or two FASTQ files for single or paired end data respectively.\nNote: the subworkflow adds a new meta ID `meta.id_index` that _must_\nbe used in `prefix` to ensure unique file names. See the associated\nnextflow.config file.\n" + } + }, + { + "ch_index": { + "description": "Structure: [ val(meta), path(index) ]\nA directory containing bwa aln reference indices as from `bwa index`\nContains files ending in extensions such as .amb, .ann, .bwt etc.\n" + } + } + ], + "output": [ + { + "bam": { + "description": "Structure: [ val(meta), path(bam) ]\nSorted BAM/CRAM/SAM file\nNote: the subworkflow adds a new meta ID `meta.id_index` that _must_\nbe used in `prefix` to ensure unique file names. See the associated\nnextflow.config file.\n" + } + }, + { + "bai": { + "description": "Structure: [ val(meta), path(bai) ]\nBAM/CRAM/SAM samtools index file\n" + } + }, + { + "csi": { + "description": "Structure: [ val(meta), path(csi) ]\nBAM/CRAM/SAM samtools index file for larger references\n" + } + }, + { + "versions": { + "description": "Files containing software versions\nStructure: [ path(versions.yml) ]\n" + } + } + ], + "authors": ["@jfy133"], + "maintainers": ["@jfy133"] }, - { - "fastqs_dir": { - "type": "directory", - "description": "Input directory containing bgzipped (not gzip) FASTQ files" - } - } - ] - ], - "output": { - "sample_fastq": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/*_R*.fastq.gz": { - "type": "file", - "description": "Demultiplexed per-sample FASTQ files", - "pattern": "${prefix}/*_R*.fastq.gz", - "ontologies": [] - } - } - ] - ], - "metrics": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/metrics.tsv": { - "type": "file", - "description": "Demultiplexing summary stats; control_reads_omitted failing_reads_omitted, total_templates\n", - "pattern": "${prefix}/metrics.tsv", - "ontologies": [] - } - } - ] - ], - "most_frequent_unmatched": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/most_frequent_unmatched.tsv": { - "type": "file", - "description": "File containing approx. counts of barcodes that did not match the expected barcodes\n", - "pattern": "${prefix}/most_frequence_unmatched.tsv", - "ontologies": [] - } - } - ] - ], - "per_project_metrics": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/per_project_metrics.tsv": { - "type": "file", - "description": "Summary metrics for samples in the same project", - "pattern": "${prefix}/per_project_metrics.tsv", - "ontologies": [] - } - } - ] - ], - "per_sample_metrics": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/per_sample_metrics.tsv": { - "type": "file", - "description": "Summary metrics for each sample", - "pattern": "${prefix}/per_sample_metrics.tsv", - "ontologies": [] - } - } - ] - ], - "sample_barcode_hop_metrics": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/sample_barcode_hop_metrics.tsv": { - "type": "file", - "description": "File output for dual-indexed runs with barcodes which are unexpected combinations of\nexpected barcodes e.g. expected barcodes = AA-TT/GG-CC and observed barcodes = AA-CC/GG-TT\n", - "pattern": "${prefix}/sample_barcode_hop_metrics/tsv", - "ontologies": [] - } - } - ] - ], - "versions_sgdemux": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "sgdemux": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "sgdemux --version | cut -d \" \" -f2": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "sgdemux": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "sgdemux --version | cut -d \" \" -f2": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "callingcards", + "version": "1.0.0" + }, + { + "name": "sammyseq", + "version": "dev" + } ] - ] - }, - "authors": [ - "@nh13", - "@sam-white04" - ], - "maintainers": [ - "@nh13", - "@sam-white04" - ] - }, - "pipelines": [ - { - "name": "demultiplex", - "version": "1.7.1" - } - ] - }, - { - "name": "shapeit5_ligate", - "path": "modules/nf-core/shapeit5/ligate/meta.yml", - "type": "module", - "meta": { - "name": "shapeit5_ligate", - "description": "Ligate multiple phased BCF/VCF files into a single whole chromosome file.\nTypically run to ligate multiple chunks of phased common variants.\n", - "keywords": [ - "ligate", - "haplotype", - "shapeit" - ], - "tools": [ - { - "shapeit5": { - "description": "Fast and accurate method for estimation of haplotypes (phasing)", - "homepage": "https://odelaneau.github.io/shapeit5/", - "documentation": "https://odelaneau.github.io/shapeit5/docs/documentation", - "tool_dev_url": "https://github.com/odelaneau/shapeit5", - "doi": "10.1101/2022.10.19.512867", - "licence": [ - "MIT" - ], - "identifier": "biotools:shapeit5" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input_list": { - "type": "file", - "description": "VCF/BCF files containing genotype probabilities (GP field).\nThe files should be ordered by genomic position.\n", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", - "ontologies": [] - } + }, + { + "name": "fastq_align_chromap", + "path": "subworkflows/nf-core/fastq_align_chromap/meta.yml", + "type": "subworkflow", + "meta": { + "name": "fastq_align_chromap", + "description": "Align high throughput chromatin profiles using Chromap then sort with samtools", + "keywords": [ + "align", + "fasta", + "genome", + "reference", + "chromatin profiles", + "chip-seq", + "atac-seq", + "hic" + ], + "components": [ + "chromap/chromap", + "samtools/sort", + "samtools/index", + "samtools/stats", + "samtools/idxstats", + "samtools/flagstat", + "bam_sort_stats_samtools" + ], + "input": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "ch_reads": { + "type": "file", + "description": "Structure: [val(meta), path(reads)]\nList of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" + } + }, + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "ch_index": { + "type": "file", + "description": "Structure: [val(meta2), path(index)]\nChromap genome index files\n", + "pattern": "*.index" + } + }, + { + "ch_fasta_fai": { + "type": "file", + "description": "Structure: [val(meta2), path(fasta), path(fai)]\nReference fasta file and index\n", + "pattern": "*.{fasta,fa},*.fai" + } + }, + { + "ch_barcodes": { + "type": "file", + "description": "Structure: [path(barcodes)]\nCell barcode files\n" + } + }, + { + "ch_whitelist": { + "type": "file", + "description": "Structure: [path(whitelist)]\nCell barcode whitelist file\n" + } + }, + { + "ch_chr_order": { + "type": "file", + "description": "Structure: [path(chr_order)]\nCustom chromosome order\n" + } + }, + { + "ch_pairs_chr_order": { + "type": "file", + "description": "Structure: [path(pairs_chr_order)]\nNatural chromosome order for pairs flipping\n" + } + } + ], + "output": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file", + "pattern": "*.bam" + } + }, + { + "bai": { + "type": "file", + "description": "BAM index (currently only for snapaligner)", + "pattern": "*.bai" + } + }, + { + "stats": { + "type": "file", + "description": "File containing samtools stats output", + "pattern": "*.{stats}" + } + }, + { + "flagstat": { + "type": "file", + "description": "File containing samtools flagstat output", + "pattern": "*.{flagstat}" + } + }, + { + "idxstats": { + "type": "file", + "description": "File containing samtools idxstats output", + "pattern": "*.{idxstats}" + } + }, + { + "versions": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ], + "authors": ["@JoseEspinosa"], + "maintainers": ["@JoseEspinosa"] }, - { - "input_list_index": { - "type": "file", - "description": "VCF/BCF files index.", - "pattern": "*.csi", - "ontologies": [] - } - } - ], - { - "suffix_": { - "type": "string", - "description": "Output format", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" - } - } - ], - "output": { - "merged_variants": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.{vcf,bcf,vcf.gz,bcf.gz}": { - "type": "file", - "description": "Output VCF/BCF file for the merged regions.\nPhased information (HS field) is updated accordingly for the full region.\n", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", - "ontologies": [] - } - } - ] - ], - "versions_shapeit5": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "shapeit5": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "SHAPEIT5_ligate | sed \"5!d;s/^.*Version *: //; s/ .*$//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "shapeit5": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "SHAPEIT5_ligate | sed \"5!d;s/^.*Version *: //; s/ .*$//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "atacseq", + "version": "2.1.2" + }, + { + "name": "chipseq", + "version": "2.1.0" + } ] - ] - }, - "authors": [ - "@louislenezet" - ], - "maintainers": [ - "@louislenezet" - ] - }, - "pipelines": [ - { - "name": "phaseimpute", - "version": "1.1.0" - } - ] - }, - { - "name": "shapeit5_phasecommon", - "path": "modules/nf-core/shapeit5/phasecommon/meta.yml", - "type": "module", - "meta": { - "name": "shapeit5_phasecommon", - "description": "Tool to phase common sites, typically SNP array data, or the first step of WES/WGS data.", - "keywords": [ - "phasing", - "haplotype", - "shapeit" - ], - "tools": [ - { - "shapeit5": { - "description": "Fast and accurate method for estimation of haplotypes (phasing)", - "homepage": "https://odelaneau.github.io/shapeit5/", - "documentation": "https://odelaneau.github.io/shapeit5/docs/documentation", - "tool_dev_url": "https://github.com/odelaneau/shapeit5", - "doi": "10.1101/2022.10.19.512867 ", - "licence": [ - "MIT" - ], - "identifier": "biotools:shapeit5" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "Target dataset in VCF/BCF format defined at all variable positions.\nThe file could possibly be without GT field (for efficiency reasons a file containing only the positions is recommended).\n", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", - "ontologies": [] - } - }, - { - "input_index": { - "type": "file", - "description": "Index file of the input VCF/BCF file containing genotype likelihoods.", - "pattern": "*.{vcf.gz.csi,bcf.gz.csi}", - "ontologies": [] - } - }, - { - "pedigree": { - "type": "file", - "description": "Pedigree information in the following format: offspring father mother.\n", - "pattern": "*.{txt, tsv}", - "ontologies": [] - } - }, - { - "region": { - "type": "string", - "description": "Target region, usually a full chromosome (e.g. chr20:1000000-2000000 or chr20).\nFor chrX, please treat PAR and non-PAR regions as different choromosome in order to avoid mixing ploidy.\n", - "pattern": "chrXX:leftBufferPosition-rightBufferPosition" - } - }, - { - "reference": { - "type": "file", - "description": "Reference panel of haplotypes in VCF/BCF format.", - "pattern": "*.{vcf.gz,bcf.gz}", - "ontologies": [] - } - }, - { - "reference_index": { - "type": "file", - "description": "Index file of the Reference panel file.", - "pattern": "*.{vcf.gz.csi,bcf.gz.csi}", - "ontologies": [] - } - }, - { - "scaffold": { - "type": "file", - "description": "Scaffold of haplotypes in VCF/BCF format.", - "pattern": "*.{vcf.gz,bcf.gz}", - "ontologies": [] - } - }, - { - "scaffold_index": { - "type": "file", - "description": "Index file of the scaffold file.", - "pattern": "*.{vcf.gz.csi,bcf.gz.csi}", - "ontologies": [] - } + }, + { + "name": "fastq_align_dedup_bismark", + "path": "subworkflows/nf-core/fastq_align_dedup_bismark/meta.yml", + "type": "subworkflow", + "meta": { + "name": "fastq_align_dedup_bismark", + "description": "Align BS-Seq reads to a reference genome using bismark, deduplicate and sort", + "keywords": [ + "bismark", + "3-letter genome", + "map", + "methylation", + "5mC", + "methylseq", + "bisulphite", + "bisulfite", + "bam" + ], + "components": [ + "bismark/align", + "samtools/sort", + "samtools/index", + "bismark/deduplicate", + "bismark/methylationextractor", + "bismark/coverage2cytosine", + "bismark/report", + "bismark/summary" + ], + "input": [ + { + "ch_reads": { + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\nStructure: [ val(meta), [ path(reads) ] ]\n", + "pattern": "*.{fastq,fastq.gz}" + } + }, + { + "ch_fasta_fai": { + "type": "file", + "description": "Structure: [ val(meta), path(fasta), path(fai) ]\n", + "pattern": "*.{fa,fa.gz}" + } + }, + { + "ch_bismark_index": { + "description": "Bismark genome index files\nStructure: [ val(meta), path(index) ]\n", + "pattern": "BismarkIndex" + } + }, + { + "skip_deduplication": { + "type": "boolean", + "description": "Skip deduplication of aligned reads\n" + } + }, + { + "cytosine_report": { + "type": "boolean", + "description": "Produce coverage2cytosine reports that relates methylation calls back to genomic cytosine contexts\n" + } + } + ], + "output": [ + { + "bam": { + "type": "file", + "description": "Channel containing aligned or deduplicated BAM files.\nStructure: [ val(meta), path(bam) ]\n", + "pattern": "*.bam" + } + }, + { + "bai": { + "type": "file", + "description": "Channel containing aligned or deduplicated BAM index files.\nStructure: [ val(meta), path(bam.bai) ]\n", + "pattern": "*.bai" + } + }, + { + "coverage2cytosine_coverage": { + "type": "file", + "description": "Channel containing coverage information from coverage2cytosine.\nStructure: [ val(meta), path(coverage.txt) ]\n", + "pattern": "*.cov.gz" + } + }, + { + "coverage2cytosine_report": { + "type": "file", + "description": "Channel containing report from coverage2cytosine summarizing cytosine methylation coverage.\nStructure: [ val(meta), path(report.txt) ]\n", + "pattern": "*report.txt.gz" + } + }, + { + "coverage2cytosine_summary": { + "type": "file", + "description": "Channel containing summary information from coverage2cytosine.\nStructure: [ val(meta), path(summary.txt) ]\n", + "pattern": "*cytosine_context_summary.txt" + } + }, + { + "methylation_bedgraph": { + "type": "file", + "description": "Channel containing methylation data in bedGraph format.\nStructure: [ val(meta), path(methylation.bedgraph) ]\n", + "pattern": "*.bedGraph.gz" + } + }, + { + "methylation_calls": { + "type": "file", + "description": "Channel containing methylation call data.\nStructure: [ val(meta), path(calls.txt) ]\n", + "pattern": "*.txt.gz" + } + }, + { + "methylation_coverage": { + "type": "file", + "description": "Channel containing methylation coverage data.\nStructure: [ val(meta), path(coverage.txt) ]\n", + "pattern": "*.cov.gz" + } + }, + { + "methylation_report": { + "type": "file", + "description": "Channel containing methylation report detailing methylation patterns.\nStructure: [ val(meta), path(report.txt) ]\n", + "pattern": "*_splitting_report.txt" + } + }, + { + "methylation_mbias": { + "type": "file", + "description": "Channel containing M-bias report showing methylation bias across read positions.\nStructure: [ val(meta), path(mbias.txt) ]\n", + "pattern": "*.M-bias.txt" + } + }, + { + "bismark_report": { + "type": "file", + "description": "Channel containing Bismark report with mapping and methylation statistics.\nStructure: [ val(meta), path(bismark_report.txt) ]\n", + "pattern": "*report.{html,txt}" + } + }, + { + "bismark_summary": { + "type": "file", + "description": "Channel containing Bismark summary report.\nStructure: [ val(meta), path(bismark_summary.txt) ]\n", + "pattern": "*report.{html,txt}" + } + }, + { + "multiqc": { + "type": "file", + "description": "Channel containing files for MultiQC input (reports, alignment reports, methylation reports).\nStructure: [ path(files) ]\n", + "pattern": "*.{html,txt}" + } + }, + { + "versions": { + "type": "file", + "description": "File containing software versions.\nStructure: [ path(versions.yml) ]\n", + "pattern": "versions.yml" + } + } + ], + "authors": ["@sateeshperi"], + "maintainers": ["@sateeshperi"] }, - { - "map": { - "type": "file", - "description": "File containing the genetic map in Glimpse format.", - "pattern": "*.gmap", - "ontologies": [] - } - } - ] - ], - "output": { - "phased_variant": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.{bcf,graph,bh}": { - "type": "file", - "description": "Phased variant dataset in BCF, GRAPH or XCF binary format.", - "pattern": "*.{bcf,graph,bh}", - "ontologies": [] - } - } - ] - ], - "versions_shapeit5": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "shapeit5": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "SHAPEIT5_phase_common | sed \"5!d;s/^.*Version *: //; s/ .*$//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "shapeit5": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "SHAPEIT5_phase_common | sed \"5!d;s/^.*Version *: //; s/ .*$//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "methylseq", + "version": "4.2.0" + } ] - ] - }, - "authors": [ - "@LouisLeNezet" - ], - "maintainers": [ - "@LouisLeNezet" - ] - }, - "pipelines": [ - { - "name": "phaseimpute", - "version": "1.1.0" - } - ] - }, - { - "name": "shapeit5_phaserare", - "path": "modules/nf-core/shapeit5/phaserare/meta.yml", - "type": "module", - "meta": { - "name": "shapeit5_phaserare", - "description": "Tool to phase rare variants onto a scaffold of common variants (output of phase_common / ligate).\nRequire feature AVX2.\n", - "keywords": [ - "phasing", - "rare variants", - "haplotype", - "shapeit" - ], - "tools": [ - { - "shapeit5": { - "description": "Fast and accurate method for estimation of haplotypes (phasing)", - "homepage": "https://odelaneau.github.io/shapeit5/", - "documentation": "https://odelaneau.github.io/shapeit5/docs/documentation", - "tool_dev_url": "https://github.com/odelaneau/shapeit5", - "doi": "10.1101/2022.10.19.512867 ", - "licence": [ - "MIT" - ], - "identifier": "biotools:shapeit5" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "Genotypes to be phased in plain VCF/BCF format.\n", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", - "ontologies": [] - } - }, - { - "input_index": { - "type": "file", - "description": "Index file of the input_plain VCF/BCF file containing genotype likelihoods.", - "pattern": "*.{vcf.gz.csi,bcf.gz.csi}", - "ontologies": [] - } - }, - { - "pedigree": { - "type": "file", - "description": "Pedigree information in the following format: offspring father mother.\n", - "pattern": "*.{txt, tsv}", - "ontologies": [] - } - }, - { - "input_region": { - "type": "string", - "description": "Region to be considered in --input-plain (e.g. chr20:1000000-2000000 or chr20).\nFor chrX, please treat PAR and non-PAR regions as different choromosome in order to avoid mixing ploidy.\n", - "pattern": "chrXX:leftBufferPosition-rightBufferPosition" - } - }, - { - "scaffold": { - "type": "file", - "description": "Scaffold of haplotypes in VCF/BCF format.", - "pattern": "*.{vcf.gz,bcf.gz}", - "ontologies": [] - } - }, - { - "scaffold_index": { - "type": "file", - "description": "Index file of the scaffold file.", - "pattern": "*.{vcf.gz.csi,bcf.gz.csi}", - "ontologies": [] - } - }, - { - "scaffold_region": { - "type": "string", - "description": "Region to be considered in --scaffold (e.g. chr20:1000000-2000000 or chr20).\n", - "pattern": "chrXX:leftBufferPosition-rightBufferPosition" - } + }, + { + "name": "fastq_align_dedup_bwamem", + "path": "subworkflows/nf-core/fastq_align_dedup_bwamem/meta.yml", + "type": "subworkflow", + "meta": { + "name": "fastq_align_dedup_bwamem", + "description": "Performs alignment of DNA or TAPS-treated reads using bwamem or parabricks/fq2bam, sort and deduplicate", + "keywords": ["bwamem", "alignment", "map", "5mC", "methylseq", "DNA", "fastq", "bam"], + "components": [ + "parabricks/fq2bam", + "samtools/index", + "picard/addorreplacereadgroups", + "picard/markduplicates", + "bam_sort_stats_samtools", + "fastq_align_bwa" + ], + "input": [ + { + "ch_reads": { + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\nStructure: [ val(meta), [ path(reads) ] ]\n", + "pattern": "*.{fastq,fastq.gz}" + } + }, + { + "ch_fasta": { + "type": "file", + "description": "Structure: [ val(meta), path(fasta) ]\n", + "pattern": "*.{fa,fa.gz}" + } + }, + { + "ch_fasta_index": { + "type": "file", + "description": "Structure: [ val(meta), path(fasta index) ]\n" + } + }, + { + "ch_bwamem_index": { + "type": "directory", + "description": "Bwa-mem genome index files\nStructure: [ val(meta), path(index) ]\n", + "pattern": "Bwa-memIndex" + } + }, + { + "skip_deduplication": { + "type": "boolean", + "description": "Skip deduplication of aligned reads\n" + } + }, + { + "use_gpu": { + "type": "boolean", + "description": "Use GPU for alignment\n" + } + }, + { + "output_fmt": { + "type": "string", + "description": "Output format for the alignment. Options are 'bam' or 'cram'", + "pattern": "{bam,cram}" + } + }, + { + "interval_file": { + "type": "file", + "description": "Structure: [ val(meta), path(interval file) ]\n", + "pattern": "*.{bed,intervals}" + } + }, + { + "known_sites": { + "type": "file", + "description": "Structure: [ val(meta), path(known sites) ]\n", + "pattern": "*.{vcf,vcf.gz}" + } + } + ], + "output": [ + { + "bam": { + "type": "file", + "description": "Channel containing BAM files\nStructure: [ val(meta), path(bam) ]\n", + "pattern": "*.bam" + } + }, + { + "bai": { + "type": "file", + "description": "Channel containing indexed BAM (BAI) files\nStructure: [ val(meta), path(bai) ]\n", + "pattern": "*.bai" + } + }, + { + "samtools_flagstat": { + "type": "file", + "description": "File containing samtools flagstat output\nStructure: [ val(meta), path(flagstat) ]\n", + "pattern": "*.flagstat" + } + }, + { + "samtools_idxstats": { + "type": "file", + "description": "File containing samtools idxstats output\nStructure: [ val(meta), path(idxstats) ]\n", + "pattern": "*.idxstats" + } + }, + { + "samtools_stats": { + "type": "file", + "description": "File containing samtools stats output\nStructure: [ val(meta), path(stats) ]\n", + "pattern": "*.{stats}" + } + }, + { + "picard_metrics": { + "type": "file", + "description": "Duplicate metrics file generated by picard\nStructure: [ val(meta), path(metrics) ]\n", + "pattern": "*.{metrics.txt}" + } + }, + { + "multiqc": { + "type": "file", + "description": "Channel containing files for MultiQC input (metrics, stats, flagstat, idxstats).\nStructure: [ path(file) ]\n", + "pattern": "*{.txt,.stats,.flagstat,.idxstats}" + } + } + ], + "authors": ["@eduard-watchmaker"], + "maintainers": ["@eduard-watchmaker"] }, - { - "map": { - "type": "file", - "description": "File containing the genetic map in Glimpse format.", - "pattern": "*.gmap", - "ontologies": [] - } - } - ], - { - "output_suffix": { - "type": "string", - "description": "Module output format", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" - } - } - ], - "output": { - "phased_variant": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.{vcf,bcf,vcf.gz,bcf.gz}": { - "type": "file", - "description": "Phased variants in VCF/BCF format.", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", - "ontologies": [] - } - } - ] - ], - "versions_shapeit5": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "shapeit5": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "SHAPEIT5_phase_rare | sed \"5!d;s/^.*Version *: //; s/ .*$//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "shapeit5": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "SHAPEIT5_phase_rare | sed \"5!d;s/^.*Version *: //; s/ .*$//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "methylseq", + "version": "4.2.0" + } ] - ] - }, - "authors": [ - "@LouisLeNezet" - ], - "maintainers": [ - "@LouisLeNezet" - ], - "requirement": "AVX2" - } - }, - { - "name": "shapeit5_switch", - "path": "modules/nf-core/shapeit5/switch/meta.yml", - "type": "module", - "meta": { - "name": "shapeit5_switch", - "description": "Program to compute switch error rate and genotyping error rate given simulated or trio data.", - "keywords": [ - "error", - "phasing", - "genotype", - "switch" - ], - "tools": [ - { - "shapeit5": { - "description": "Fast and accurate method for estimation of haplotypes (phasing)", - "homepage": "https://odelaneau.github.io/shapeit5/", - "documentation": "https://odelaneau.github.io/shapeit5/docs/documentation", - "tool_dev_url": "https://github.com/odelaneau/shapeit5", - "doi": "10.1101/2022.10.19.512867 ", - "licence": [ - "MIT" - ], - "identifier": "biotools:shapeit5" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "estimate": { - "type": "file", - "description": "Imputed data.", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", - "ontologies": [] - } - }, - { - "estimate_index": { - "type": "file", - "description": "Index file of the freq VCF/BCF file.", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", - "ontologies": [] - } - }, - { - "region": { - "type": "string", - "description": "Target region used for imputation, including left and right buffers (e.g. chr20:1000000-2000000).", - "pattern": "chrXX:leftBufferPosition-rightBufferPosition" - } - }, - { - "pedigree": { - "type": "file", - "description": "Pedigree information in the following format: offspring father mother.\n", - "pattern": "*.{txt, tsv}", - "ontologies": [] - } - }, - { - "truth": { - "type": "file", - "description": "Validation dataset called at the same positions as the imputed file.", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", - "ontologies": [] - } - }, - { - "truth_index": { - "type": "file", - "description": "Index file of the truth VCF/BCF file.", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", - "ontologies": [] - } - }, - { - "freq": { - "type": "file", - "description": "File containing allele frequencies at each site.", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", - "ontologies": [] - } + }, + { + "name": "fastq_align_dedup_bwameth", + "path": "subworkflows/nf-core/fastq_align_dedup_bwameth/meta.yml", + "type": "subworkflow", + "meta": { + "name": "fastq_align_dedup_bwameth", + "description": "Performs alignment of BS-Seq reads using bwameth or parabricks/fq2bammeth, sort and deduplicate", + "keywords": [ + "bwameth", + "alignment", + "3-letter genome", + "map", + "methylation", + "5mC", + "methylseq", + "bisulphite", + "bisulfite", + "fastq", + "bam" + ], + "components": [ + "bwameth/align", + "parabricks/fq2bammeth", + "samtools/sort", + "samtools/index", + "samtools/flagstat", + "samtools/stats", + "picard/markduplicates" + ], + "input": [ + { + "ch_reads": { + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\nStructure: [ val(meta), [ path(reads) ] ]\n", + "pattern": "*.{fastq,fastq.gz}" + } + }, + { + "ch_fasta_fai": { + "type": "file", + "description": "Structure: [ val(meta), path(fasta), path(fai) ]\n", + "pattern": "*.{fa,fa.gz}" + } + }, + { + "ch_bwameth_index": { + "description": "Bwa-meth genome index files\nStructure: [ val(meta), path(index) ]\n", + "pattern": "Bwa-methIndex" + } + }, + { + "skip_deduplication": { + "type": "boolean", + "description": "Skip deduplication of aligned reads\n" + } + }, + { + "use_gpu": { + "type": "boolean", + "description": "Use GPU for alignment\n" + } + } + ], + "output": [ + { + "bam": { + "type": "file", + "description": "Channel containing BAM files\nStructure: [ val(meta), path(bam) ]\n", + "pattern": "*.bam" + } + }, + { + "bai": { + "type": "file", + "description": "Channel containing indexed BAM (BAI) files\nStructure: [ val(meta), path(bai) ]\n", + "pattern": "*.bai" + } + }, + { + "samtools_flagstat": { + "type": "file", + "description": "File containing samtools flagstat output\nStructure: [ val(meta), path(flagstat) ]\n", + "pattern": "*.flagstat" + } + }, + { + "samtools_stats": { + "type": "file", + "description": "File containing samtools stats output\nStructure: [ val(meta), path(stats) ]\n", + "pattern": "*.{stats}" + } + }, + { + "picard_metrics": { + "type": "file", + "description": "Duplicate metrics file generated by picard\nStructure: [ val(meta), path(metrics) ]\n", + "pattern": "*.{metrics.txt}" + } + }, + { + "multiqc": { + "type": "file", + "description": "Channel containing files for MultiQC input (metrics, stats, flagstat).\nStructure: [ path(files) ]\n", + "pattern": "*.{txt,stats,flagstat}" + } + }, + { + "versions": { + "type": "file", + "description": "File containing software versions\nStructure: [ path(versions.yml) ]\n", + "pattern": "versions.yml" + } + } + ], + "authors": ["@sateeshperi"], + "maintainers": ["@sateeshperi", "@gallvp", "@eduard-watchmaker"] }, - { - "freq_index": { - "type": "file", - "description": "Index file of the freq VCF/BCF file.", - "pattern": "*.{vcf.gz.csi,bcf.gz.csi}", - "ontologies": [] - } - } - ] - ], - "output": { - "errors": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.txt.gz": { - "type": "file", - "description": "Estimates errors from the phased file.", - "pattern": "*.txt.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "versions_shapeit5": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "shapeit5": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "SHAPEIT5_switch | sed \"5!d;s/^.*Version *: //; s/ .*$//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "shapeit5": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "SHAPEIT5_switch | sed \"5!d;s/^.*Version *: //; s/ .*$//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "methylseq", + "version": "4.2.0" + } ] - ] - }, - "authors": [ - "@LouisLeNezet" - ], - "maintainers": [ - "@LouisLeNezet" - ] - } - }, - { - "name": "shasta", - "path": "modules/nf-core/shasta/meta.yml", - "type": "module", - "meta": { - "name": "shasta", - "description": "The goal of the Shasta long read assembler is to rapidly produce accurate assembled sequence using DNA reads generated by Oxford Nanopore flow cells as input. Please note Assembler is design to focus on speed, so assembly may be considered somewhat non-deterministic as final assembly may vary across executions. See https://github.com/chanzuckerberg/shasta/issues/296.", - "keywords": [ - "nanopore", - "de-novo", - "assembly", - "longread" - ], - "tools": [ - { - "shasta": { - "description": "Rapidly produce accurate assembled sequence using as input DNA reads generated by Oxford Nanopore flow cells.", - "homepage": "https://chanzuckerberg.github.io/shasta/index.html", - "documentation": "https://chanzuckerberg.github.io/shasta/index.html", - "tool_dev_url": "https://github.com/chanzuckerberg/shasta", - "doi": "10.1038/s41587-020-0503-6", - "licence": [ - "MIT" - ], - "identifier": "biotools:shasta" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + }, + { + "name": "fastq_align_dna", + "path": "subworkflows/nf-core/fastq_align_dna/meta.yml", + "type": "subworkflow", + "meta": { + "name": "fastq_align_dna", + "description": "Align fastq files to a reference genome", + "keywords": ["fastq", "bam", "sort", "bwamem", "bwamem2", "dragmap", "snapaligner", "strobealign"], + "components": [ + "bowtie2/align", + "bwa/mem", + "bwamem2/mem", + "dragmap/align", + "snapaligner/align", + "strobealign" + ], + "input": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" + } + }, + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "index": { + "type": "file", + "description": "Aligner genome index files", + "pattern": "Directory containing aligner index" + } + }, + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference genome in fasta format", + "pattern": "*.{fa, fasta, fna}" + } + }, + { + "aligner": { + "type": "string", + "description": "Aligner to use for alignment", + "enum": ["bowtie2", "bwa", "bwamem2", "dragmap", "snap", "strobealign"] + } + }, + { + "sort_bam": { + "type": "boolean", + "description": "sort output" + } + } + ], + "output": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file", + "pattern": "*.bam" + } + }, + { + "bam_index": { + "type": "file", + "description": "BAM index (currently only for snapaligner)", + "pattern": "*.{bai, csi}" + } + }, + { + "report": { + "type": "file", + "description": "Alignment report (currently only for dragmap)", + "pattern": "*.txt" + } + }, + { + "versions": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ], + "authors": ["@matthdsm"], + "maintainers": ["@matthdsm"] }, - { - "reads": { - "type": "file", - "description": "Input file in FASTQ format.", - "pattern": "*.{fastq,fastq.gz,fq,fq.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ], - { - "model": { - "type": "string", - "description": "Shasta assembly configuration model name\n(e.g. 'Nanopore-Oct2021', 'Nanopore-Dec2019')\n" - } - } - ], - "output": { - "assembly": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_Assembly.fasta.gz": { - "type": "file", - "description": "Assembled FASTA file", - "pattern": "${prefix}_Assembly.fasta.gz", - "ontologies": [] - } - } - ] - ], - "gfa": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_Assembly.gfa.gz": { - "type": "file", - "description": "Repeat graph", - "pattern": "${prefix}_Assembly.gfa.gz", - "ontologies": [] - } - } - ] - ], - "results": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "ShastaRun/": { - "type": "directory", - "description": "Resulting assembly directory", - "pattern": "ShastaRun" - } - } - ] - ], - "versions_shasta": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "shasta": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "shasta --version | sed -n '1s/.* //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "sammyseq", + "version": "dev" + } ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "shasta": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "shasta --version | sed -n '1s/.* //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@fmalmeida" - ], - "maintainers": [ - "@fmalmeida" - ] - } - }, - { - "name": "shasum", - "path": "modules/nf-core/shasum/meta.yml", - "type": "module", - "meta": { - "name": "shasum", - "description": "Print SHA256 (256-bit) checksums.", - "keywords": [ - "checksum", - "sha256", - "256 bit" - ], - "tools": [ - { - "md5sum": { - "description": "Create an SHA256 (256-bit) checksum.", - "homepage": "https://www.gnu.org", - "documentation": "https://linux.die.net/man/1/shasum", - "licence": [ - "GPLv3+" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "file": { - "type": "file", - "description": "Any file", - "pattern": "*.*", - "ontologies": [] - } - } - ] - ], - "output": { - "checksum": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.sha256": { - "type": "file", - "description": "File containing checksum", - "pattern": "*.sha256", - "ontologies": [] - } - } - ] - ], - "versions_sha256sum": [ - [ - { - "${task.process}": { - "type": "string", - "description": "Process name" - } - }, - { - "sha256sum": { - "type": "string", - "description": "Tool name" - } - }, - { - "sha256sum --version 2>&1 | head -n 1 | sed 's/.* //'": { - "type": "eval", - "description": "Software version" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "Process name" - } - }, - { - "sha256sum": { - "type": "string", - "description": "Tool name" - } - }, - { - "sha256sum --version 2>&1 | head -n 1 | sed 's/.* //'": { - "type": "eval", - "description": "Software version" - } - } - ] - ] - }, - "authors": [ - "@matthdsm" - ], - "maintainers": [ - "@matthdsm" - ] - } - }, - { - "name": "shigapass", - "path": "modules/nf-core/shigapass/meta.yml", - "type": "module", - "meta": { - "name": "shigapass", - "description": "ShigaPass is an in silico tool used to predict Shigella serotypes and to differentiate between Shigella, EIEC (Enteroinvasive E. coli), and non Shigella/EIEC using assembled whole genomes.", - "keywords": [ - "bacteria", - "shigella", - "stec" - ], - "tools": [ - { - "shigapass": { - "description": "ShigaPass is an in silico tool used to predict Shigella serotypes", - "homepage": "https://github.com/imanyass/ShigaPass", - "documentation": "https://github.com/imanyass/ShigaPass", - "tool_dev_url": "https://github.com/imanyass/ShigaPass", - "licence": [ - "GPL v3" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA, GenBank or EMBL formatted file. Note that the standard input for ShigaPass is a file of file paths - here for paralellisation a fasta file is required.", - "pattern": "*.{fa,fasta,fna,fa.gz,fasta.gz,fna.gz}", - "ontologies": [] - } - } - ] - ], - "output": { - "report": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.tsv": { - "type": "file", - "description": "Tab-delimited report of results", - "pattern": "${prefix}.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "flex_tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_ShigaPass_Flex_summary.tsv": { - "type": "file", - "description": "Tab-delimited report of results", - "pattern": "*_ShigaPass_Flex_summary.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - 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"description": "The name of the process" - } - }, - { - "shinyngs": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "Rscript -e \"library(shinyngs); cat(as.character(packageVersion('shinyngs')))\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "lncpipe", + "version": "dev" + }, + { + "name": "nascent", + "version": "2.3.0" + }, + { + "name": "rnadnavar", + "version": "dev" + }, + { + "name": "rnaseq", + "version": "3.26.0" + } ] - ] - }, - "authors": [ - "@pinin4fjords" - ], - "maintainers": [ - "@pinin4fjords" - ] - }, - "pipelines": [ - { - "name": "differentialabundance", - "version": "1.5.0" - } - ] - }, - { - "name": "shinyngs_validatefomcomponents", - "path": "modules/nf-core/shinyngs/validatefomcomponents/meta.yml", - "type": "module", - "meta": { - "name": "shinyngs_validatefomcomponents", - "description": "validate consistency of feature and sample annotations with matrices and contrasts", - "keywords": [ - "expression", - "features", - "observations", - "validation" - ], - "tools": [ - { - "shinyngs": { - "description": "Provides Shiny applications for various array and NGS applications. Currently very RNA-seq centric, with plans for expansion.", - "homepage": "https://github.com/pinin4fjords/shinyngs", - "documentation": "https://rawgit.com/pinin4fjords/shinyngs/master/vignettes/shinyngs.html", - "tool_dev_url": "https://github.com/pinin4fjords/shinyngs", - "licence": [ - "AGPL v3" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing information on experiment, at a minimum an id.\ne.g. [ id:'test' ]\n" - } - }, - { - "sample": { - "type": "file", - "description": "CSV-format sample sheet with sample metadata\n", - "ontologies": [] - } - }, - { - "assay_files": { - "type": "file", - "description": "List of TSV-format matrix files representing different measures for the same samples (e.g. raw and normalised).\n", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing information on features.\ne.g. [ id:'test' ]\n" - } - }, - { - "feature_meta": { - "type": "file", - "description": "TSV-format feature (e.g. gene) metadata\n", - "ontologies": [] - } + }, + { + "name": "fastq_align_mapad", + "path": "subworkflows/nf-core/fastq_align_mapad/meta.yml", + "type": "subworkflow", + "meta": { + "name": "fastq_align_mapad", + "description": "Align FASTQ files against reference genome with the mapAD aDNA short-read aligner producing a sorted and indexed BAM files", + "keywords": ["sort", "fastq", "bam", "mapad", "align", "map"], + "components": [ + "mapad/map", + "samtools/sort", + "samtools/index", + "samtools/stats", + "samtools/idxstats", + "samtools/flagstat", + "bam_sort_stats_samtools" + ], + "input": [ + { + "ch_reads": { + "description": "List of input FASTQ file\nStructure: [ val(meta), path(reads) ]\n" + } + }, + { + "ch_index": { + "description": "mapAD genome index files\nStructure: [ val(meta), path(index) ]\n" + } + }, + { + "ch_fasta_fai": { + "type": "file", + "description": "Reference fasta file and index\nStructure: [ val(meta), path(fasta), path(fai) ]\n" + } + }, + { + "val_mismatch_parameter": { + "type": "float", + "description": "`bwa aln` compatible allowed-mismatches parameter\n" + } + }, + { + "val_double_stranded_library": { + "type": "boolean", + "description": "If true, `--library` is set to `double_stranded`\n", + "pattern": "true|false" + } + }, + { + "val_five_prime_overhang": { + "type": "float", + "description": "5' overhang parameter (global overhang parameter\nif `val_double_stranded_library` is set to `true`)\n" + } + }, + { + "val_three_prime_overhang": { + "type": "float", + "description": "3' overhang parameter (ignored if\n`val_double_stranded_library` is set to `true`)\n" + } + }, + { + "val_deam_rate_double_stranded": { + "type": "float", + "description": "`-d` parameter. Specifies the expected deamination\nrate in double-stranded stems of the reads.\n" + } + }, + { + "val_deam_rate_single_stranded": { + "type": "float", + "description": "`-s` parameter. Specifies the expected deamination\nrate in single-stranded overhangs of the reads.\n" + } + }, + { + "val_indel_rate": { + "type": "float", + "description": "`-i` parameter. Specifies the expected rate of InDels.\n" + } + } + ], + "output": [ + { + "bam_unsorted": { + "description": "BAM file produced by mapAD\nStructure: [ val(meta), path(bam) ]\n" + } + }, + { + "bam": { + "description": "BAM file sorted by samtools\nStructure: [ val(meta), path(bam) ]\n" + } + }, + { + "bai": { + "description": "BAI index of the sorted BAM file\nStructure: [ val(meta), path(bai) ]\n" + } + }, + { + "csi": { + "description": "CSI index of the sorted BAM file\nStructure: [ val(meta), path(csi) ]\n" + } + }, + { + "stats": { + "description": "File containing samtools stats output\nStructure: [ val(meta), path(stats) ]\n" + } + }, + { + "flagstat": { + "description": "File containing samtools flagstat output\nStructure: [ val(meta), path(flagstat) ]\n" + } + }, + { + "idxstats": { + "description": "File containing samtools idxstats output\nStructure: [ val(meta), path(idxstats) ]\n" + } + }, + { + "versions": { + "description": "Files containing software versions\nStructure: [ path(versions.yml) ]\n" + } + } + ], + "authors": ["@jch-13"] } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing information on contrasts.\ne.g. [ id:'test' ]\n" - } + }, + { + "name": "fastq_align_star", + "path": "subworkflows/nf-core/fastq_align_star/meta.yml", + "type": "subworkflow", + "meta": { + "name": "fastq_align_star", + "description": "Align reads to a reference genome using bowtie2 then sort with samtools", + "keywords": ["align", "fasta", "genome", "reference"], + "components": [ + "star/align", + "samtools/sort", + "samtools/index", + "samtools/stats", + "samtools/idxstats", + "samtools/flagstat", + "bam_sort_stats_samtools" + ], + "input": [ + { + "ch_reads": { + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\nStructure: [ val(meta), [ path(reads) ] ]\n" + } + }, + { + "ch_index": { + "type": "directory", + "description": "STAR genome index", + "pattern": "star" + } + }, + { + "ch_gtf": { + "type": "file", + "description": "GTF file used to set the splice junctions with the --sjdbGTFfile flag\n", + "pattern": "*.gtf" + } + }, + { + "val_star_ignore_sjdbgtf": { + "type": "boolean", + "description": "If true the --sjdbGTFfile flag is set\n", + "pattern": "true|false" + } + }, + { + "ch_fasta_fai": { + "type": "file", + "description": "Reference genome fasta file and index", + "pattern": "*.{fasta,fa,fna,fai}" + } + }, + { + "ch_transcripts_fasta_fai": { + "type": "file", + "description": "Optional reference genome fasta file and index", + "pattern": "*.{fasta,fa,fna,fai}" + } + } + ], + "output": [ + { + "orig_bam": { + "description": "Output BAM file containing read alignments\nStructure: [ val(meta), path(bam) ]\n" + } + }, + { + "log_final": { + "description": "STAR final log file\nStructure: [ val(meta), path(log_final) ]\n" + } + }, + { + "log_out": { + "description": "STAR log out file\nStructure: [ val(meta), path(log_out) ]\n" + } + }, + { + "log_progress": { + "description": "STAR log progress file\nStructure: [ val(meta), path(log_progress) ]\n" + } + }, + { + "bam_sorted": { + "description": "Sorted BAM file of read alignments (optional)\nStructure: [ val(meta), path(bam) ]\n" + } + }, + { + "orig_bam_transcript": { + "description": "Output BAM file of transcriptome alignment (optional)\nStructure: [ val(meta), path(bam) ]\n" + } + }, + { + "fastq": { + "description": "Unmapped FastQ files (optional)\nStructure: [ val(meta), path(fastq) ]\n" + } + }, + { + "tab": { + "description": "STAR output tab file(s) (optional)\nStructure: [ val(meta), path(tab) ]\n" + } + }, + { + "bam": { + "description": "BAM file ordered by samtools\nStructure: [ val(meta), path(bam) ]\n" + } + }, + { + "bai": { + "description": "BAI index of the ordered BAM file\nStructure: [ val(meta), path(bai) ]\n" + } + }, + { + "stats": { + "description": "File containing samtools stats output\nStructure: [ val(meta), path(stats) ]\n" + } + }, + { + "flagstat": { + "description": "File containing samtools flagstat output\nStructure: [ val(meta), path(flagstat) ]\n" + } + }, + { + "idxstats": { + "description": "File containing samtools idxstats output\nStructure: [ val(meta), path(idxstats) ]\n" + } + }, + { + "bam_transcript": { + "description": "Transcriptome-level BAM file ordered by samtools (optional)\nStructure: [ val(meta), path(bam) ]\n" + } + }, + { + "bai_transcript": { + "description": "Transcriptome-level BAI index of the ordered BAM file (optional)\nStructure: [ val(meta), path(bai) ]\n" + } + }, + { + "stats_transcript": { + "description": "Transcriptome-level file containing samtools stats output (optional)\nStructure: [ val(meta), path(stats) ]\n" + } + }, + { + "flagstat_transcript": { + "description": "Transcriptome-level file containing samtools flagstat output (optional)\nStructure: [ val(meta), path(flagstat) ]\n" + } + }, + { + "idxstats_transcript": { + "description": "Transcriptome-level file containing samtools idxstats output (optional)\nStructure: [ val(meta), path(idxstats) ]\n" + } + }, + { + "versions": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ], + "authors": ["@JoseEspinosa"], + "maintainers": ["@JoseEspinosa"] }, - { - "contrasts": { - "type": "file", - "description": "CSV-format file with four columns identifying the sample sheet variable, reference level, treatment level, and optionally a comma-separated list of covariates used as blocking factors.\n", - "ontologies": [] - } - } - ] - ], - "output": { - "sample_meta": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing information on experiment.\ne.g. [ id:'test' ]\n" - } - }, - { - "*/*.sample_metadata.tsv": { - "type": "file", - "description": "File containing validated sample metadata", - "pattern": "/*.sample_metadata.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "feature_meta": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing information on experiment.\ne.g. [ id:'test' ]\n" - } - }, - { - "*/*.feature_metadata.tsv": { - "type": "file", - "description": "File containing validated feature metadata", - "pattern": "/*.feature_metadata.tsv", - "optional": true, - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "assays": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing information on experiment.\ne.g. [ id:'test' ]\n" - } - }, - { - "*/*.assay.tsv": { - "type": "file", - "description": "Files containing validated matrices", - "pattern": "/*.assay.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "contrasts": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing information on experiment.\ne.g. [ id:'test' ]\n" - } - }, - { - "*/*.contrasts_file.tsv": { - "type": "file", - "description": "Files containing validated matrices", - "pattern": "/*.contrasts_file.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_shinyngs": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "shinyngs": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "Rscript -e \"library(shinyngs); cat(as.character(packageVersion('shinyngs')))\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "shinyngs": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "Rscript -e \"library(shinyngs); cat(as.character(packageVersion('shinyngs')))\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "lncpipe", + "version": "dev" + }, + { + "name": "nascent", + "version": "2.3.0" + }, + { + "name": "riboseq", + "version": "1.2.0" + }, + { + "name": "rnadnavar", + "version": "dev" + }, + { + "name": "rnafusion", + "version": "4.1.2" + }, + { + "name": "rnavar", + "version": "1.2.3" + } ] - ] - }, - "authors": [ - "@pinin4fjords" - ], - "maintainers": [ - "@pinin4fjords" - ] - }, - "pipelines": [ - { - "name": "differentialabundance", - "version": "1.5.0" - } - ] - }, - { - "name": "shovill", - "path": "modules/nf-core/shovill/meta.yml", - "type": "module", - "meta": { - "name": "shovill", - "description": "Assemble bacterial isolate genomes from Illumina paired-end reads", - "keywords": [ - "bacterial", - "assembly", - "illumina" - ], - "tools": [ - { - "shovill": { - "description": "Microbial assembly pipeline for Illumina paired-end reads", - "homepage": "https://github.com/tseemann/shovill", - "documentation": "https://github.com/tseemann/shovill/blob/master/README.md", - "licence": [ - "GPL v2" - ], - "identifier": "biotools:shovill" + }, + { + "name": "fastq_complexity_filter", + "path": "subworkflows/nf-core/fastq_complexity_filter/meta.yml", + "type": "subworkflow", + "meta": { + "name": "fastq_complexity_filter", + "description": "Perform low-complexity filtering of FASTQ reads using a selectable tool.\nOne of PRINSEQ++, BBDuk, or fastp is executed based on the provided tool name.\nOnly complexity filtering is applied; no adapter trimming, read merging, or\nquality trimming is performed.\n", + "keywords": ["fastq", "complexity filtering", "low complexity", "entropy", "qc"], + "components": ["prinseqplusplus", "bbmap/bbduk", "fastp"], + "input": [ + { + "ch_reads": { + "type": "file", + "description": "Input channel containing sample metadata and FASTQ reads.\nStructure: [ val(meta), path(fastq) ]\n", + "pattern": "*.{fastq,fastq.gz}" + } + }, + { + "val_complexity_filter_tool": { + "type": "string", + "description": "Complexity filtering tool to use.\nMust be one of: 'prinseqplusplus', 'bbduk', or 'fastp'.\n" + } + } + ], + "output": [ + { + "filtered_reads": { + "type": "file", + "description": "Channel containing complexity-filtered FASTQ reads.\nStructure: [ val(meta), path(fastq) ]\n", + "pattern": "*.{fastq,fastq.gz}" + } + }, + { + "logfile": { + "type": "file", + "description": "Tool-specific log files, when available.\nStructure: [ val(meta), path(log) ]\n", + "pattern": "*.log" + } + }, + { + "report": { + "type": "file", + "description": "HTML report generated by fastp. Empty for other tools.\nStructure: [ val(meta), path(html) ]\n", + "pattern": "*.html" + } + }, + { + "multiqc_files": { + "type": "file", + "description": "Files emitted for MultiQC aggregation (e.g. fastp JSON reports,\nBBDuk logs).\nStructure: [ path(file) ]\n", + "pattern": "*.{json,log}" + } + }, + { + "versions": { + "type": "file", + "description": "File containing software versions\nStructure: [ path(versions.yml) ]\n", + "pattern": "versions.yml" + } + } + ], + "authors": ["@vagkaratzas"], + "maintainers": ["@vagkaratzas"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + }, + { + "name": "fastq_contam_seqtk_kraken", + "path": "subworkflows/nf-core/fastq_contam_seqtk_kraken/meta.yml", + "type": "subworkflow", + "meta": { + "name": "FASTQ_CONTAM_SEQTK_KRAKEN", + "description": "Produces a contamination report from FastQ input after subsampling", + "keywords": ["statistics", "fastq", "contamination"], + "components": ["kraken2/kraken2", "seqtk/sample"], + "input": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively" + } + }, + { + "sample_size": { + "type": "string", + "description": "Number of reads to subsample for contamination detection." + } + } + ], + "output": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "report": { + "type": "file", + "description": "Kraken2 contamination report", + "pattern": "*.txt" + } + }, + { + "versions": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ], + "authors": ["@apeltzer"], + "maintainers": ["@apeltzer"] }, - 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"type": "file", - "description": "Full log file for bug reporting", - "pattern": "shovill.log", - "ontologies": [] - } - } - ] - ], - "raw_contigs": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "{skesa,spades,megahit,velvet}.fasta": { - "type": "file", - "description": "Raw assembly produced by the assembler (SKESA, SPAdes, MEGAHIT, or Velvet)", - "pattern": "{skesa,spades,megahit,velvet}.fasta", - "ontologies": [] - } - } - ] - ], - "gfa": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "contigs.{fastg,gfa,LastGraph}": { - "type": "file", - "description": "Assembly graph produced by MEGAHIT, SPAdes, or Velvet", - "pattern": "contigs.{fastg,gfa,LastGraph}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3975" - } - ] - } - } - ] - ], - "versions_shovill": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "shovill": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "shovill --version 2>&1 | sed \"s/^.*shovill //\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "shovill": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "shovill --version 2>&1 | sed \"s/^.*shovill //\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "demultiplex", + "version": "1.7.1" + } ] - ] - }, - "authors": [ - "@rpetit3", - "@eit-maxlcummins" - ], - "maintainers": [ - "@rpetit3" - ] - } - }, - { - "name": "sickle", - "path": "modules/nf-core/sickle/meta.yml", - "type": "module", - "meta": { - "name": "sickle", - "description": "A windowed adaptive trimming tool for FASTQ files using quality", - "keywords": [ - "fastq", - "sliding window", - "trimming" - ], - "tools": [ - { - "sickle": { - "description": "a tool that determines clipping of reads on 3' end and 5'end based on base quality ", - "homepage": "https://github.com/najoshi/sickle", - "tool_dev_url": "https://github.com/najoshi/sickle", - "licence": [ - "MIT License" - ], - "identifier": "biotools:sickle" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively. File of forward reads must be supplied first and reverse reads as the second e.g. [\"read.1.fastq.gz\",\"read.2.fastq.gz\"]", - "pattern": "*.{fq,fastq,fq.gz,fastq.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - }, - { - "qual_type": { - "type": "string", - "description": "sickle needs a base quality values, which could be either illumina, solexa or sanger", - "pattern": "illumina or solexa or sanger" - } + }, + { + "name": "fastq_create_umi_consensus_fgbio", + "path": "subworkflows/nf-core/fastq_create_umi_consensus_fgbio/meta.yml", + "type": "subworkflow", + "meta": { + "name": "fastq_create_umi_consensus_fgbio", + "description": "This workflow uses the suite FGBIO to identify and remove UMI tags from FASTQ reads\nconvert them to unmapped BAM file, map them to the reference genome,\nand finally use the mapped information to group UMIs and generate consensus reads in each group\n", + "keywords": ["fgbio", "umi", "samblaster", "samtools", "bwa"], + "components": [ + "bwa/index", + "bwa/mem", + "bwamem2/mem", + "bwamem2/index", + "fgbio/fastqtobam", + "fgbio/groupreadsbyumi", + "fgbio/callmolecularconsensusreads", + "fgbio/callduplexconsensusreads", + "fgbio/filterconsensusreads", + "samblaster", + "samtools/bam2fq", + "samtools/sort", + "samtools/index", + "samtools/fastq", + "fgbio/zipperbams" + ], + "input": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "reads": { + "type": "list", + "description": "list umi-tagged reads", + "pattern": "[ *.{fastq.gz/fq.gz} ]" + } + }, + { + "fasta_fai_dict": { + "type": "file", + "description": "The reference fasta file, index and dictionary", + "pattern": "*.{fa,fasta,fna,fai,dict}" + } + }, + { + "bwa_index": { + "type": "file", + "description": "The reference genome bwa index files", + "pattern": "*.{fa,fasta,fna,amb,ann,bwt,pac,sa}" + } + }, + { + "groupreadsbyumi_strategy": { + "type": "string", + "description": "Defines the UMI assignment strategy.", + "Required argument": "defines the UMI assignment strategy.", + "enum": ["Identity", "Edit", "Adjacency", "Paired"] + } + }, + { + "aligner": { + "type": "string", + "description": "The aligner to use for mapping the reads to the reference genome. Options are bwa-mem and bwamem2.", + "enum": ["bwa-mem", "bwamem2"] + } + }, + { + "duplex": { + "type": "boolean", + "description": "Whether the library contains duplex UMIs." + } + }, + { + "min_reads": { + "type": "integer", + "description": "One integer (for non-duplex) or a string of up-to three space-separated numbers for duplex sequencing" + } + }, + { + "min_baseq": { + "type": "integer", + "description": "Minimum base quality for bases to be considered in consensus calling." + } + }, + { + "max_base_error_rate": { + "type": "integer", + "description": "Maximum base error rate for consensus building" + } + } + ], + "output": [ + { + "ubam": { + "type": "file", + "description": "unmapped bam file", + "pattern": "*.bam" + } + }, + { + "groupbam": { + "type": "file", + "description": "mapped bam file, where reads are grouped by UMI tag", + "pattern": "*.bam" + } + }, + { + "consensusbam": { + "type": "file", + "description": "mapped bam file, where reads are created as consensus of those\nbelonging to the same UMI group\n", + "pattern": "*.bam" + } + }, + { + "mappedconsensusbam": { + "type": "file", + "description": "mapped bam file, where reads are created as consensus of those\nbelonging to the same UMI group and filtered for minimum base quality and maximum error rate\n", + "pattern": "*.bam" + } + } + ], + "authors": ["@lescai"], + "maintainers": ["@lescai"] } - ] - ], - "output": { - "single_trimmed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false, qual:'Illumina' ]\n" - } - }, - { - "*.se.trimmed.fastq.gz": { - "type": "file", - "description": "Single end trimmed reads", - "pattern": "*.se.trimmed.fastq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "paired_trimmed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false, qual:'Illumina' ]\n" - } - }, - { - "*.pe{1,2}.trimmed.fastq.gz": { - "type": "file", - "description": "Paired end trimmed reads", - "pattern": "*.pe{1,2}.trimmed.fastq.gz", - "ontologies": [] - } - } - ] - ], - "singleton_trimmed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false, qual:'Illumina' ]\n" - } - }, - { - "*.singleton.trimmed.fastq.gz": { - "type": "file", - "description": "Singleton trimmed reads", - "pattern": "*.singleton.trimmed.fastq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false, qual:'Illumina' ]\n" - } - }, - { - "*.log": { - "type": "file", - "description": "log file", - "pattern": "*.log", - "ontologies": [] - } - } - ] - ], - "versions_sickle": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "sickle": { - "type": "string", - "description": "The tool name" - } - }, - { - "sickle --version 2>&1 | head -1 | sed \"s/sickle version //\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "sickle": { - "type": "string", - "description": "The tool name" - } - }, - { - "sickle --version 2>&1 | head -1 | sed \"s/sickle version //\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@BioInf2305" - ], - "maintainers": [ - "@BioInf2305" - ] - } - }, - { - "name": "sigprofiler", - "path": "modules/nf-core/sigprofiler/meta.yml", - "type": "module", - "meta": { - "name": "sigprofiler", - "description": "mutational signature deconvolution of cancer cells", - "keywords": [ - "mutational signatures", - "SBSs, DBSs, IDs", - "cancer genomics" - ], - "tools": [ - { - "sigprofilermatrixgenerator": { - "description": "Sigprofilermatrixgenerator is a Python-based tool. It creates mutational matrices for all types of somatic mutations (SBS, DBS, and IDs)", - "documentation": "https://osf.io/s93d5/wiki/home/", - "tool_dev_url": "https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/tree/master/SigProfilerMatrixGenerator", - "doi": "10.1186/s12864-019-6041-2", - "licence": [ - "BSD-2-clause" - ], - "identifier": "biotools:sigprofilermatrixgenerator" + }, + { + "name": "fastq_decontaminate_deacon", + "path": "subworkflows/nf-core/fastq_decontaminate_deacon/meta.yml", + "type": "subworkflow", + "meta": { + "name": "fastq_decontaminate_deacon", + "description": "Decontaminate FastQ files by filtering reads that match a reference genome using Deacon\n", + "keywords": [ + "filter", + "index", + "fasta", + "fastq", + "genome", + "reference", + "minimizer", + "decontamination" + ], + "components": ["deacon/index", "deacon/filter"], + "input": [ + { + "ch_fasta_reads": { + "type": "file", + "description": "Input genome fasta file and a list of FastQ files of size 1 and 2 for single-end and paired-end data, respectively.\nStructure: [ val(meta), path(fasta), [ path(reads) ] ]\n" + } + } + ], + "output": [ + { + "index": { + "type": "file", + "description": "Deacon minimizer index file\nStructure: [ val(meta), path(index) ]\n", + "pattern": ".idx" + } + }, + { + "fastq_filtered": { + "type": "file", + "description": "List of output filtered FastQ files of size 1 and 2 for single-end and paired-end data, respectively.\nStructure: [ val(meta), path(${prefix}*.fq) ]\n", + "pattern": "*.fq" + } + }, + { + "summary": { + "type": "file", + "description": "JSON file containing summary of results.\nStructure: [ val(meta), path(${prefix}.json) ]\n", + "pattern": "*.json" + } + }, + { + "versions": { + "type": "file", + "description": "File containing software versions\nStructure: [ path(versions.yml) ]\n", + "pattern": "versions.yml" + } + } + ], + "authors": ["@Baksic-Ivan", "@Omer0191"], + "maintainers": ["@Baksic-Ivan", "@Omer0191"] } - }, - { - "sigprofilerextractor": { - "description": "SigProfilerExtractor is a Python-based tool. It allows de novo extraction of mutational signatures from data generated in a matrix format, identification of the number of operative mutational signatures, and their activities in each sample.", - "documentation": "https://osf.io/t6j7u/wiki/home/", - "tool_dev_url": "https://github.com/AlexandrovLab/SigProfilerExtractor", - "doi": "10.1016/j.xgen.2022.100179 ", - "licence": [ - "BSD-2-clause" - ], - "identifier": "biotools:sigprofilerextractor" + }, + { + "name": "fastq_decontaminate_deacon_hostile", + "path": "subworkflows/nf-core/fastq_decontaminate_deacon_hostile/meta.yml", + "type": "subworkflow", + "meta": { + "name": "fastq_decontaminate_deacon_hostile", + "description": "Decontaminate FastQ files by filtering reads that match a reference genome using Deacon or Hostile", + "keywords": [ + "hostile", + "deacon", + "filter", + "index", + "fasta", + "fastq", + "genome", + "reference", + "minimizer", + "decontamination" + ], + "components": [ + "hostile/fetch", + "hostile/clean", + "deacon/index", + "deacon/filter", + "fastq_fetch_clean_hostile", + "fastq_index_filter_deacon" + ], + "input": [ + { + "ch_reads": { + "type": "file", + "description": "List of FastQ files of size 1 and 2 for single-end and paired-end data, respectively.\nStructure: [ val(meta), [ path(reads) ] ]\n" + } + }, + { + "ch_fasta": { + "type": "file", + "description": "Input genome fasta file used by Deacon. Meta must match the meta of ch_reads.\nStructure: [ val(meta), [ path(fasta) ] ]\n" + } + }, + { + "ch_reference": { + "type": "directory", + "description": "Directory containing index file(s) corresponding to the preferred aligner (bowtie2 short reads or minimap for long reads) used by Hostile.\nNote that single end data is assumed to be long reads. If you have single-end short read you must supply both the BowTie2\nindices AND explicitly specify `--aligner bowtie2`\n" + } + }, + { + "index_name": { + "type": "string", + "description": "Name of the reference genome index to download for Hostile fetch if the reference is not provided." + } + }, + { + "decontaminator": { + "type": "string", + "description": "Name of the deacontamination tool to use.", + "enum": ["deacon", "hostile"] + } + } + ], + "output": [ + { + "fastq_filtered": { + "type": "file", + "description": "List of output filtered FastQ files of size 1 and 2 for single-end and paired-end data, respectively.\nStructure: [ val(meta), path(${prefix}*.fq.gz) ]\n", + "pattern": "*.fq.gz" + } + }, + { + "reference": { + "type": "channel", + "description": "Channel containing reference name and directory with index files for Hostile.\nStructure: [ val(reference_name), path(reference_dir) ]\n" + } + }, + { + "json": { + "type": "channel", + "description": "Channel containing sample metadata and Hostile cleaning log in JSON format.\nStructure: [ val(meta), path(*.json) ]\n", + "pattern": "*.json" + } + }, + { + "index": { + "type": "file", + "description": "Deacon minimizer index file.\nStructure: [ val(meta), path(index) ]\n", + "pattern": ".idx" + } + }, + { + "summary": { + "type": "file", + "description": "JSON file containing summary of results.\nStructure: [ val(meta), path(${prefix}.json) ]\n", + "pattern": "*.json" + } + } + ], + "authors": ["@Baksic-Ivan"], + "maintainers": ["@Baksic-Ivan"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } + }, + { + "name": "fastq_download_prefetch_fasterqdump_sratools", + "path": "subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/meta.yml", + "type": "subworkflow", + "meta": { + "name": "fastq_download_prefetch_fasterqdump_sratools", + "description": "Download FASTQ sequencing reads from the NCBI's Sequence Read Archive (SRA).", + "keywords": ["SRA", "NCBI", "sequencing", "fastq", "prefetch", "fasterq-dump"], + "components": ["custom/sratoolsncbisettings", "sratools/prefetch", "sratools/fasterqdump"], + "input": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]\n" + } + }, + { + "id": { + "type": "string", + "description": "SRA run identifier.\n" + } + }, + { + "certificate": { + "type": "file", + "description": "Path to a JWT cart file used to access protected dbGAP data on SRA using the sra-toolkit\n", + "pattern": "*.cart" + } + } + ], + "output": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "Extracted FASTQ file or files if the sequencing reads are paired-end.", + "pattern": "*.fastq.gz" + } + }, + { + "versions": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ], + "authors": ["@Midnighter", "@drpatelh"], + "maintainers": ["@Midnighter", "@drpatelh"] }, - { - "tsv_list": { - "type": "file", - "description": "joint tsv file with validated mutations by CNAqc", - "pattern": "*.{tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - { - "genome": { - "type": "string", - "description": "Reference genome name to use with SigProfiler (e.g. \"GRCh37\", \"GRCh38\")", - "ontologies": [] - } - }, - { - "genome_installed_path": { - "type": "file", - "description": "path to installed reference genome (optional)", - "ontologies": [] - } - } - ], - "output": { - "results_sigprofiler": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test' ]" - } - }, - { - "results/*": { - "type": "directory", - "description": "folder with saved output results", - "pattern": "results/*", - "ontologies": [] - } - } + "pipelines": [ + { + "name": "fetchngs", + "version": "1.12.0" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] }, - "authors": [ - "@kdavydzenka" - ] - }, - "pipelines": [ { - "name": "tumourevo", - "version": "dev" - } - ] - }, - { - "name": "simpleaf_index", - "path": "modules/nf-core/simpleaf/index/meta.yml", - "type": "module", - "meta": { - "name": "simpleaf_index", - "description": "Indexing of transcriptome for gene expression quantification using SimpleAF", - "keywords": [ - "indexing", - "transcriptome", - "gene expression", - "SimpleAF" - ], - "tools": [ - { - "simpleaf": { - "description": "SimpleAF is a tool for quantification of gene expression from RNA-seq data\n", - "homepage": "https://github.com/COMBINE-lab/simpleaf", - "licence": [ - "BSD-3-Clause" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing information on genome_fasta and genome_gtf\n" - } - }, - { - "genome_fasta": { - "type": "file", - "description": "FASTA file containing the genome sequence. It must be provided together with the corresponding genome_gtf file.\nWhen another input set is provided, it must be empty (provided as []).\n", - "ontologies": [] - } - }, - { - "genome_gtf": { - "type": "file", - "description": "GTF file containing gene annotations. It must be provided together with its corresponding genome_fasta file.\nWhen another input set rather than genome_fasta + genome_gtf is provided, it must be empty (provided as []).\n", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing information on transcript_fasta\n" - } - }, - { - "transcript_fasta": { - "type": "file", - "description": "FASTA file containing the transcript sequences to build index directly on.\nWhen another input set is provided, it must be empty (provided as []).\n", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing information on probe_csv.\n" - } - }, - { - "probe_csv": { - "type": "file", - "description": "CSV file containing the reference probe sequences to build index directly on.\nWhen another input set is provided, it must be empty (provided as []).\n", - "ontologies": [] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing information on feature_csv.\n" - } - }, - { - "feature_csv": { - "type": "file", - "description": "CSV file containing the reference feature barcodes to build index directly on.\nWhen another input set is provided, it must be empty (provided as []).\n", - "ontologies": [] - } - } - ] - ], - "output": { - "index": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing information on the index generated by simpleaf\n" - } - }, - { - "${prefix}/index": { - "type": "map", - "description": "Groovy Map containing information on the index generated by simpleaf\n" - } - } - ] - ], - "ref": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing information on the index generated by simpleaf\n" - } - }, - { - "${prefix}/ref": { - "type": "map", - "description": "Groovy Map containing information on the transcriptomic reference constructed by simpleaf.\n" - } - } - ] - ], - "t2g": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing information on the index generated by simpleaf\n" - } - }, - { - "${prefix}/ref/{t2g,t2g_3col}.tsv": { - "type": "file", - "description": "Path to the tsv file containing the transcript-to-gene mapping information generated by simpleaf. This is used as --t2g-map when invoking simpleaf quant.\n", - "ontologies": [] - } - } - ] - ], - "versions_alevin_fry": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "alevin-fry": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "alevin-fry --version | sed 's/alevin-fry //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_piscem": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "piscem": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "piscem --version | sed 's/piscem //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_simpleaf": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "simpleaf": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "ALEVIN_FRY_HOME=. simpleaf --version | sed 's/simpleaf //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "alevin-fry": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "alevin-fry --version | sed 's/alevin-fry //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "piscem": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "piscem --version | sed 's/piscem //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "simpleaf": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "ALEVIN_FRY_HOME=. simpleaf --version | sed 's/simpleaf //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@fmalmeida", - "@maxulysse", - "@Khajidu", - "@apeltzer", - "@pinin4fjords", - "@dongzehe" - ], - "maintainers": [ - "@fmalmeida", - "@maxulysse", - "@Khajidu", - "@apeltzer", - "@pinin4fjords", - "@dongzehe" - ] - }, - "pipelines": [ - { - "name": "scrnaseq", - "version": "4.1.0" - } - ] - }, - { - "name": "simpleaf_quant", - "path": "modules/nf-core/simpleaf/quant/meta.yml", - "type": "module", - "meta": { - "name": "simpleaf_quant", - "description": "simpleaf is a program to simplify and customize the running and configuration of single-cell processing with alevin-fry.", - "keywords": [ - "quantification", - "gene expression", - "SimpleAF" - ], - "tools": [ - { - "simpleaf": { - "description": "SimpleAF is a program to simplify and customize the running and configuration of single-cell processing with alevin-fry.\n", - "homepage": "https://github.com/COMBINE-lab/simpleaf", - "licence": [ - "BSD-3-Clause" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "chemistry": { - "type": "string", - "description": "Chemistry used for library preparation. It can be a string describing the specific chemistry or the geometry of the barcode, UMI, and mappable read. For example, \"10xv2\" and \"10xv3\" will apply the appropriate settings for 10x Chromium v2 and v3 protocols, respectively. Alternatively, you can provide a general geometry string if your chemistry is not pre-registered. For example, instead of \"10xv2\", you could use \"1{b[16]u[10]x:}2{r:}\", or instead of \"10xv3\", you could use \"1{b[16]u[12]x:}2{r:}\". Details at https://hackmd.io/@PI7Og0l1ReeBZu_pjQGUQQ/rJMgmvr13\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files for paired-end data.\nReads should be grouped by pairs.\nFor example, [ [R1_1.fastq.gz, R2_1.fastq.gz], [R1_2.fastq.gz, R2_2.fastq.gz] ]\n", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing index information\ne.g. [ tool:'piscem' ]\n" - } - }, - { - "index": { - "type": "directory", - "description": "Folder containing the index files. For a *salmon* index that is not generated by simpleaf to be taken, '--no-piscem' MUST be specified in ext.args." - } - }, - { - "txp2gene": { - "type": "file", - "description": "File mapping transcripts to genes. It can be either a two-column TSV file for a standard transcriptomic index containing the transcript-to-gene ID mapping information, or a three-column TSV file for an augmented transcriptomic index with the third column representing the splicing status of each transcript.\n", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing txp2gene information\ne.g. [ mode:'usa' ]\n" - } - }, - { - "cell_filter": { - "type": "string", - "enum": [ - "knee", - "forced-cells", - "explicit-pl", - "expect-cells", - "unfiltered-pl" - ], - "description": "Cell filtering mode. Possible values are 'usa' and 'whitelist'. 'usa' will use the default cell filtering mode, while 'whitelist' will use the whitelist file provided in the 'whitelist' input.\n" - } - }, - { - "number_cb": { - "type": "integer", - "description": "Number of cell barcodes to use for cell filtering. Set as empty ('[]') unless 'cell_filter' is set to 'forced-cells' or 'expect-cells'.\n" - } - }, - { - "cb_list": { - "type": "file", - "description": "File containing a list of cell barcodes to use for cell filtering. Set as empty ('[]') unless 'cell_filter' is set to 'unfiltered-pl' or 'explicit-pl'.\n", - "ontologies": [] - } - } - ], - { - "resolution": { - "type": "string", - "description": "UMI resolution (https://alevin-fry.readthedocs.io/en/latest/quant.html). Possible values are 'cr-like', 'cr-like-em', 'parsimony', 'parsimony-em', 'parsimony-gene', and 'parsimony-gene-em'.\n" - } - }, - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing existing mapping results.\ne.g. [ tool:'piscem' ]\n" - } - }, - { - "map_dir": { - "type": "directory", - "description": "Folder containing the existing mapping results. It must be generated by simpleaf or alevin-fry, and contain the mapping file named map.rad." - } - } - ] - ], - "output": { - "map": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", - "pattern": "simpleaf/af_map" - } - }, - { - "${prefix}/af_map": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - } - ] - ], - "quant": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", - "pattern": "simpleaf/af_map" - } - }, - { - "${prefix}/af_quant": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - } - ] - ], - "versions_alevin_fry": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "alevin-fry": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "alevin-fry --version | sed 's/alevin-fry //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_piscem": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "piscem": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "piscem --version | sed 's/piscem //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_simpleaf": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "simpleaf": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "ALEVIN_FRY_HOME=. simpleaf --version | sed 's/simpleaf //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "alevin-fry": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "alevin-fry --version | sed 's/alevin-fry //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "piscem": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "piscem --version | sed 's/piscem //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "simpleaf": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "ALEVIN_FRY_HOME=. simpleaf --version | sed 's/simpleaf //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@fmalmeida", - "@maxulysse", - "@Khajidu", - "@apeltzer", - "@pinin4fjords", - "@dongzehe" - ], - "maintainers": [ - "@fmalmeida", - "@maxulysse", - "@Khajidu", - "@apeltzer", - "@pinin4fjords", - "@dongzehe" - ] - }, - "pipelines": [ - { - "name": "scrnaseq", - "version": "4.1.0" - } - ] - }, - { - "name": "singlem_dbdownload", - "path": "modules/nf-core/singlem/dbdownload/meta.yml", - "type": "module", - "meta": { - "name": "singlem_dbdownload", - "description": "Download the SingleM metapackage database used for metagenome profiling", - "keywords": [ - "metagenomics", - "database", - "download", - "profiling", - "singlem", - "metapackage" - ], - "tools": [ - { - "singlem": { - "description": "SingleM is a tool for profiling shotgun metagenomes. It determines the relative\nabundance of bacterial and archaeal taxa in a sample and can also profile dsDNA\nphages. It has particular strength in dealing with novel lineages and is suitable\nfor tasks such as assessing eukaryotic contamination, finding bias in genome\nrecovery, and lineage-targeted MAG recovery.\n", - "homepage": "https://wwood.github.io/singlem", - "documentation": "https://wwood.github.io/singlem", - "tool_dev_url": "https://github.com/wwood/singlem", - "doi": "10.1038/s41587-024-02492-w", - "licence": [ - "GPL-3.0-or-later" - ], - "identifier": "biotools:singlem" - } - } - ], - "output": { - "singlem_database": [ - { - "*.smpkg.zb": { - "type": "file", - "description": "SingleM metapackage database file used for taxonomic profiling", - "pattern": "*.smpkg.zb", - "ontologies": [ - { - "edam": "http://edamontology.org/data_0955" - } - ] - } - } - ], - "versions_singlem": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "singlem": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "singlem --version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "singlem": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "singlem --version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@TheGreatJack" - ], - "maintainers": [ - "@TheGreatJack" - ] - } - }, - { - "name": "sistr", - "path": "modules/nf-core/sistr/meta.yml", - "type": "module", - "meta": { - "name": "sistr", - "description": "Serovar prediction of salmonella assemblies", - "keywords": [ - "bacteria", - "fasta", - "salmonella" - ], - "tools": [ - { - "sistr": { - "description": "Salmonella In Silico Typing Resource (SISTR) commandline tool for serovar prediction", - "homepage": "https://github.com/phac-nml/sistr_cmd", - "documentation": "https://github.com/phac-nml/sistr_cmd", - "tool_dev_url": "https://github.com/phac-nml/sistr_cmd", - "doi": "10.1371/journal.pone.0147101", - "licence": [ - "Apache-2.0" - ], - "identifier": "biotools:SISTR" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Nucleotide or protein sequences in FASTA format", - "pattern": "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}", - "ontologies": [] - } - } - ] - ], - "output": { - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tab": { - "type": "file", - "description": "SISTR serovar prediction", - "pattern": "*.{tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "allele_fasta": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*-allele.fasta": { - "type": "file", - "description": "FASTA file destination of novel cgMLST alleles", - "pattern": "*.{fasta}", - "ontologies": [] - } - } - ] - ], - "allele_json": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*-allele.json": { - "type": "file", - "description": "Allele sequences and info to JSON", - "pattern": "*.{json}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "cgmlst_csv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*-cgmlst.csv": { - "type": "file", - "description": "CSV file destination for cgMLST allelic profiles", - "pattern": "*.{csv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "versions_sistr": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "sistr": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "sistr --version 2>&1 | sed \"s/^.*sistr_cmd //; s/ .*\\$//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "sistr": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "sistr --version 2>&1 | sed \"s/^.*sistr_cmd //; s/ .*\\$//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@rpetit3" - ], - "maintainers": [ - "@rpetit3" - ] - } - }, - { - "name": "ska_distance", - "path": "modules/nf-core/ska/distance/meta.yml", - "type": "module", - "meta": { - "name": "ska_distance", - "description": "Calculate pairwise distances and basic clustering from SKA sketches", - "keywords": [ - "genomics", - "metagenomics", - "kmer", - "split_kmers", - "distance", - "clustering" - ], - "tools": [ - { - "ska": { - "description": "SKA (Split Kmer Analysis)", - "homepage": "https://github.com/simonrharris/SKA", - "documentation": "https://github.com/simonrharris/SKA/wiki", - "tool_dev_url": "https://github.com/simonrharris/SKA", - "doi": "10.1101/453142", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "sketch_files": { - "type": "file", - "description": "SKA sketch files", - "pattern": "*.skf", - "ontologies": [] - } - }, - { - "sketch_list": { - "type": "file", - "description": "List of SKA sketch files", - "pattern": "*.txt", - "ontologies": [] - } - } - ] - ], - "output": { - "distances": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*distances.tsv": { - "type": "file", - "description": "Pairwise distance table", - "pattern": "*distance.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "cluster_list": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*clusters.tsv": { - "type": "file", - "description": "List of samples and their clusters", - "pattern": "*clusters.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "cluster_files": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*cluster*.txt": { - "type": "file", - "description": "Cluster files", - "pattern": "*cluster*.txt", - "ontologies": [] - } - } - ] - ], - "dot": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.dot": { - "type": "file", - "description": "DOT file for visualization", - "pattern": "*.dot", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@itrujnara" - ], - "maintainers": [ - "@itrujnara" - ] - } - }, - { - "name": "ska_fasta", - "path": "modules/nf-core/ska/fasta/meta.yml", - "type": "module", - "meta": { - "name": "ska_fasta", - "description": "Create genome sketch using split k-mers", - "keywords": [ - "genomics", - "metagenomics", - "kmer", - "split_kmers", - "sketch" - ], - "tools": [ - { - "ska": { - "description": "SKA (Split Kmer Analysis)", - "homepage": "https://github.com/simonrharris/SKA", - "documentation": "https://github.com/simonrharris/SKA/wiki", - "tool_dev_url": "https://github.com/simonrharris/SKA", - "doi": "10.1101/453142", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "fastas": { - "type": "file", - "description": "FASTA files with contigs/reads", - "pattern": "*.fa(sta)", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - }, - { - "fasta_list": { - "type": "file", - "description": "List of FASTA files with contigs/reads", - "pattern": "*.txt", - "ontologies": [] - } - } - ] - ], - "output": { - "skf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } - }, - { - "*.skf": { - "type": "file", - "description": "File containing genome sketch", - "pattern": "*.skf", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@itrujnara" - ], - "maintainers": [ - "@itrujnara" - ] - } - }, - { - "name": "skani_dist", - "path": "modules/nf-core/skani/dist/meta.yml", - "type": "module", - "meta": { - "name": "skani_dist", - "description": "Simple ANI calculation between reference and query genomes.", - "keywords": [ - "skani", - "metagenomics", - "genome", - "alignment", - "sketch", - "distance", - "dist" - ], - "tools": [ - { - "skani": { - "description": "skani is a fast and robust tool for calculating ANI between metagenome assembled genomes and contigs.", - "homepage": "https://github.com/bluenote-1577/skani", - "documentation": "https://github.com/bluenote-1577/skani/wiki", - "tool_dev_url": "https://github.com/bluenote-1577/skani", - "doi": "10.1038/s41592-023-02018-3", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "query": { - "type": "file", - "description": "FASTA/skani sketch file to be used as query.\n", - "pattern": "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,sketch}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "reference": { - "type": "file", - "description": "FASTA/skani sketch file to be used as reference.\n", - "pattern": "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,sketch}", - "ontologies": [] - } - } - ] - ], - "output": { - "dist": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}.tsv": { - "type": "file", - "description": "TSV file containing ANI and AF between query and reference as calculated by skani.\npattern: \"*.tsv\"\n", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@CarsonJM" - ], - "maintainers": [ - "@CarsonJM" - ] - } - }, - { - "name": "skani_search", - "path": "modules/nf-core/skani/search/meta.yml", - "type": "module", - "meta": { - "name": "skani_search", - "description": "Memory-efficient ANI database queries with skani.", - "keywords": [ - "skani", - "metagenomics", - "genome", - "alignment", - "search" - ], - "tools": [ - { - "skani": { - "description": "skani is a fast and robust tool for calculating ANI between metagenome assembled genomes and contigs.", - "homepage": "https://github.com/bluenote-1577/skani", - "documentation": "https://github.com/bluenote-1577/skani/wiki", - "tool_dev_url": "https://github.com/bluenote-1577/skani", - "doi": "10.1038/s41592-023-02018-3", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - 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"keywords": [ - "gfa", - "graph", - "pangenome", - "variation graph", - "POA" - ], - "tools": [ - { - "smoothxg": { - "description": "smoothxg linearizes and simplifies variation graphs using blocked partial\norder alignment.\n", - "homepage": "https://github.com/pangenome/smoothxg", - "documentation": "https://github.com/pangenome/smoothxg", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "gfa": { - "type": "file", - "description": "Variation graph in GFA 1.0 format", - "pattern": "*.{gfa}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3975" - } - ] - } - } - ] - ], - "output": { - "gfa": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*smoothxg.gfa": { - "type": "file", - "description": "Linearized and simplified graph in GFA 1.0 format", - "pattern": "*.smoothxg.{gfa}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3975" - } - ] - } - } - ] - ], - "maf": [ - { - "*.maf": { - "type": "file", - "description": "write the multiple sequence alignments (MSAs) in MAF format in this file (optional)", - "pattern": "*.{maf}", - "ontologies": [] - } - } - ], - "versions_smoothxg": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "smoothxg": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "smoothxg --version 2>&1 | sed 's/^v//; s/-.*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "smoothxg": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "smoothxg --version 2>&1 | sed 's/^v//; s/-.*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@heuermh, @subwaystation" - ], - "maintainers": [ - "@heuermh, @subwaystation" - ] - }, - "pipelines": [ - { - "name": "pangenome", - "version": "1.1.3" - } - ] - }, - { - "name": "smoove_call", - "path": "modules/nf-core/smoove/call/meta.yml", - "type": "module", - "meta": { - "name": "smoove_call", - "description": "smoove simplifies and speeds calling and genotyping SVs for short reads. It also improves specificity by removing many spurious alignment signals that are indicative of low-level noise and often contribute to spurious calls. Developed by Brent Pedersen.", - "keywords": [ - "structural variants", - "SV", - "vcf", - "wgs" - ], - "tools": [ - { - "smoove": { - "description": "structural variant calling and genotyping with existing tools, but, smoothly", - "homepage": "https://github.com/brentp/smoove", - "documentation": "https://brentp.github.io/post/smoove/", - "tool_dev_url": "https://github.com/brentp/smoove", - "licence": [ - "Apache-2.0" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM file", - "pattern": "*.{bam,cram}", - "ontologies": [] - } - }, - { - "index": { - "type": "file", - "description": "Index of BAM/CRAM file", - "pattern": "*.{bai,crai}", - "ontologies": [] - } - }, - { - "exclude_beds": { - "type": "file", - "description": "A BED file containing the regions to exclude from the SV calling", - "pattern": "*.bed", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference fasta file", - "pattern": "*.{fasta,fna,fa}", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fai": { - "type": "file", - "description": "Index of reference fasta file", - "pattern": "*.fai", - "ontologies": [] - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.vcf.gz": { - "type": "file", - "description": "Compressed VCF file", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "versions_smoove": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "smoove": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "smoove -v |& sed -n 's/smoove version: *//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "smoove": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "smoove -v |& sed -n 's/smoove version: *//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@scorreard", - "@nvnieuwk" - ], - "maintainers": [ - "@scorreard", - "@nvnieuwk" - ] - } - }, - { - "name": "snakemake", - "path": "modules/nf-core/snakemake/meta.yml", - "type": "module", - "meta": { - "name": "snakemake", - "description": "The Snakemake workflow management system is a tool to create reproducible and scalable data analyses. This module runs a simple Snakemake pipeline based on input snakefile. Expect many limitations.\"", - "keywords": [ - "snakemake", - "workflow", - "workflow_mode" - ], - "tools": [ - { - "snakemake": { - "description": "A popular workflow management system aiming at full in-silico reproducibility.", - "homepage": "https://snakemake.readthedocs.io/en/stable/", - "documentation": "https://snakemake.readthedocs.io/en/stable/", - "tool_dev_url": "https://github.com/snakemake/snakemake", - "doi": "10.1093/bioinformatics/bty350", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "inputs": { - "type": "file", - "description": "Any input file required by Snakemake", - "pattern": "*", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Meta information for Snakefile\ne.g. [ id: 'snakefile' ]\n" - } - }, - { - "snakefile": { - "type": "file", - "description": "Snakefile to use with Snakemake. This is required for proper execution of Snakemake.\n", - "ontologies": [] - } - } - ] - ], - "output": { - "outputs": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "[!.snakemake|versions.yml]**": { - "type": "file", - "description": "Any file generated by Snakemake, excluding the inputs, hidden files and Snakemake log directory (.snakemake). This is set to optional because Snakemake can be used to run arbitrary commands, and we cannot know what files will be generated.\n", - "ontologies": [] - } - } - ] - ], - "snakemake_dir": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - ".snakemake": { - "type": "directory", - "description": "Hidden directory containing Snakemake execution logs and metadata", - "pattern": ".snakemake", - "ontologies": [] - } - } - ] - ], - "versions_snakemake": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "snakemake": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "snakemake --version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "snakemake": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "snakemake --version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@adamrtalbot" - ], - "maintainers": [ - "@adamrtalbot" - ] - } - }, - { - "name": "snapaligner_align", - "path": "modules/nf-core/snapaligner/align/meta.yml", - "type": "module", - "meta": { - "name": "snapaligner_align", - "description": "Performs fastq alignment to a fasta reference using SNAP", - "keywords": [ - "alignment", - "map", - "fastq", - "bam", - "sam" - ], - "tools": [ - { - "snapaligner": { - "description": "Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data", - "homepage": "http://snap.cs.berkeley.edu", - "documentation": "https://1drv.ms/b/s!AhuEg_0yZD86hcpblUt-muHKYsG8fA?e=R8ogug", - "tool_dev_url": "https://github.com/amplab/snap", - "doi": "10.1101/2021.11.23.469039", - "licence": [ - "Apache v2" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input fastq files of size 2 for paired fastq or 1 for bam or single fastq", - "pattern": "*.{fastq.gz,fq.gz,fastq,fq,bam}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "index": { - "type": "file", - "description": "List of SNAP genome index files", - "pattern": "{Genome,GenomeIndex,GenomeIndexHash,OverflowTable}", - "ontologies": [] - } - } - ] - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "Aligned BAM file", - "pattern": "*.{bam}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - } - ] - ], - "bai": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bai": { - "type": "file", - "description": "Optional aligned BAM file index", - "pattern": "*.{bai}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - } - ] - ], - "versions_snapaligner": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "snap-aligner": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "snap-aligner 2>&1 | sed 's/^.*version //;s/.\\$//;q'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "snap-aligner": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "snap-aligner 2>&1 | sed 's/^.*version //;s/.\\$//;q'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@matthdsm" - ], - "maintainers": [ - "@matthdsm", - "@delfiterradas", - "@sofiromano" - ] - }, - "pipelines": [ - { - "name": "sammyseq", - "version": "dev" - } - ] - }, - { - "name": "snapaligner_index", - "path": "modules/nf-core/snapaligner/index/meta.yml", - "type": "module", - "meta": { - "name": "snapaligner_index", - "description": "Create a SNAP index for reference genome", - "keywords": [ - "index", - "fasta", - "genome", - "reference" - ], - "tools": [ - { - "snapaligner": { - "description": "Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data", - "homepage": "http://snap.cs.berkeley.edu", - "documentation": "https://1drv.ms/b/s!AhuEg_0yZD86hcpblUt-muHKYsG8fA?e=R8ogug", - "tool_dev_url": "https://github.com/amplab/snap", - "doi": "10.1101/2021.11.23.469039", - "licence": [ - "Apache v2" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input genome fasta file", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - }, - { - "altcontigfile": { - "type": "file", - "description": "Optional file with a list of alt contig names, one per line.", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - }, - { - "nonaltcontigfile": { - "type": "file", - "description": "Optional file that contains a list of contigs (one per line) that will not be marked ALT regardless of size.", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - }, - { - "altliftoverfile": { - "type": "file", - "description": "Optional file containing ALT-to-REF mappings (SAM format). e.g., hs38DH.fa.alt from bwa-kit.", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - ], - "output": { - "index": [ - [ - { - "meta": { - "type": "file", - "description": "SNAP genome index files", - "pattern": "{Genome,GenomeIndex,GenomeIndexHash,OverflowTable}", - "ontologies": [] - } - }, - { - "snap/*": { - "type": "file", - "description": "SNAP genome index files", - "pattern": "{Genome,GenomeIndex,GenomeIndexHash,OverflowTable}", - "ontologies": [] - } - } - ] - ], - "versions_snapaligner": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "snap-aligner": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "snap-aligner 2>&1 | sed 's/^.*version //;s/.\\$//;q'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "snap-aligner": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "snap-aligner 2>&1 | sed 's/^.*version //;s/.\\$//;q'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@matthdsm" - ], - "maintainers": [ - "@matthdsm" - ] - } - }, - { - "name": "sniffles", - "path": "modules/nf-core/sniffles/meta.yml", - "type": "module", - "meta": { - "name": "sniffles", - "description": "structural-variant calling with sniffles", - "keywords": [ - "sniffles", - "structural-variant calling", - "long-read" - ], - "tools": [ - { - "sniffles": { - "description": "a fast structural variant caller for long-read sequencing", - "homepage": "https://github.com/fritzsedlazeck/Sniffles", - "documentation": "https://github.com/fritzsedlazeck/Sniffles#readme", - "tool_dev_url": "https://github.com/fritzsedlazeck/Sniffles", - "licence": [ - "MIT" - ], - "identifier": "biotools:sniffles" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "input": { - "type": "file", - "description": "A single .bam/.cram file - OR - one or more .snf files - OR - a single .tsv file containing a list of .snf files and optional sample ids as input", - "pattern": "*.{bam,cram,snf,tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - }, - { - "index": { - "type": "file", - "description": "Index of BAM/CAM file", - "pattern": "*.{bai,crai}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'fasta' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference database in FASTA format\n", - "ontologies": [] - } + "name": "fastq_extract_kraken_krakentools", + "path": "subworkflows/nf-core/fastq_extract_kraken_krakentools/meta.yml", + "type": "subworkflow", + "meta": { + "name": "fastq_extract_kraken_krakentools", + "description": "Extract classified Kraken2 reads by taxonomic id", + "keywords": [ + "classify", + "metagenomics", + "fastq", + "db", + "kraken2", + "krakentools", + "extract", + "extractreads" + ], + "components": ["kraken2/kraken2", "krakentools/extractkrakenreads"], + "input": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "ch_reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" + } + }, + { + "ch_db": { + "type": "directory", + "description": "Kraken2 database" + } + }, + { + "val_taxid": { + "type": "string", + "description": "A string of one or more of taxonomic IDs (e.g. from NCBI Taxonomy) separated by spaces" + } + } + ], + "output": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "report": { + "type": "file", + "description": "Kraken2 report containing stats about classified\nand not classified reads.\n" + } + }, + { + "extracted_kraken2_reads": { + "type": "file", + "description": "FASTQ or FASTA file of just reads assigned to the requested taxonomic IDs.\n", + "pattern": "*.{fastq.gz,fasta.gz}" + } + }, + { + "versions": { + "type": "file", + "description": "File containing software versions\nStructure: [ path(versions.yml) ]\n", + "pattern": "versions.yml" + } + } + ], + "authors": ["@MarieLataretu"], + "maintainers": ["@MarieLataretu"] } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing tandem repeat information\ne.g. [ id:'hg38' ]\n" - } + }, + { + "name": "fastq_fastqc_umitools_fastp", + "path": "subworkflows/nf-core/fastq_fastqc_umitools_fastp/meta.yml", + "type": "subworkflow", + "meta": { + "name": "fastq_fastqc_umitools_fastp", + "description": "Read QC, UMI extraction and trimming", + "keywords": ["fastq", "fastqc", "qc", "UMI", "trimming", "fastp"], + "components": ["fastqc", "umitools/extract", "fastp"], + "input": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" + } + }, + { + "skip_fastqc": { + "type": "boolean", + "description": "Skip fastqc process\n" + } + }, + { + "with_umi": { + "type": "boolean", + "description": "With or without umi detection\n" + } + }, + { + "skip_umi_extract": { + "type": "boolean", + "description": "With or without umi extrection\n" + } + }, + { + "umi_discard_read": { + "type": "integer", + "description": "Discard R1 / R2 if required\n" + } + }, + { + "skip_trimming": { + "type": "boolean", + "description": "Allows to skip FastP execution\n" + } + }, + { + "adapter_fasta": { + "type": "file", + "description": "Fasta file of adapter sequences\n" + } + }, + { + "save_trimmed_fail": { + "type": "boolean", + "description": "Save trimmed fastqs of failed samples\n" + } + }, + { + "save_merged": { + "type": "boolean", + "description": "Save merged fastqs\n" + } + }, + { + "min_trimmed_reads": { + "type": "integer", + "description": "Inputs with fewer than this reads will be filtered out of the \"reads\" output channel\n" + } + } + ], + "output": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "Extracted FASTQ files. | For single-end reads, pattern is \\${prefix}.umi_extract.fastq.gz. | For paired-end reads, pattern is \\${prefix}.umi_extract_{1,2}.fastq.gz.\n", + "pattern": "*.{fastq.gz}" + } + }, + { + "fastqc_html": { + "type": "file", + "description": "FastQC report", + "pattern": "*_{fastqc.html}" + } + }, + { + "fastqc_zip": { + "type": "file", + "description": "FastQC report archive", + "pattern": "*_{fastqc.zip}" + } + }, + { + "log": { + "type": "file", + "description": "Logfile for umi_tools", + "pattern": "*.{log}" + } + }, + { + "trim_json": { + "type": "file", + "description": "FastP Trimming report", + "pattern": "*.{fastp.json}" + } + }, + { + "trim_html": { + "type": "file", + "description": "FastP Trimming report", + "pattern": "*.{fastp.html}" + } + }, + { + "log": { + "type": "file", + "description": "Logfile FastP", + "pattern": "*.{fastp.log}" + } + }, + { + "trim_reads_fail": { + "type": "file", + "description": "Trimmed fastq files failing QC", + "pattern": "*.{fastq.gz}" + } + }, + { + "trim_reads_merged": { + "type": "file", + "description": "Trimmed and merged fastq files", + "pattern": "*.{fastq.gz}" + } + }, + { + "trim_read_count": { + "type": "integer", + "description": "Number of reads after trimming" + } + }, + { + "fastqc_trim_html": { + "type": "file", + "description": "FastQC report", + "pattern": "*_{fastqc.html}" + } + }, + { + "fastqc_trim_zip": { + "type": "file", + "description": "FastQC report archive", + "pattern": "*_{fastqc.zip}" + } + }, + { + "adapter_seq": { + "type": "string", + "description": "Adapter Sequence found in read1\n" + } + }, + { + "versions": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ], + "authors": ["@robsyme"], + "maintainers": ["@robsyme"] }, - 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"aln": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.aln": { - "type": "file", - "description": "A core SNP alignment in FASTA format", - "pattern": "*.aln", - "ontologies": [] - } - } - ] - ], - "full_aln": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.full.aln": { - "type": "file", - "description": "A whole genome SNP alignment (includes invariant sites)", - "pattern": "*.full.aln", - "ontologies": [] - } - } - ] - ], - "tab": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.tab": { - "type": "file", - "description": "Tab-separated columnar list of core SNP sites with alleles but NO annotations", - "pattern": "*.tab", - "ontologies": [ - 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"pattern": "*.{fq,fastq,fq.gz,fastq.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ], - { - "reference": { - "type": "file", - "description": "Reference genome in FASTA format", - "pattern": "*.{fasta,fna,fa}", - "ontologies": [] - } - } - ], - "output": { - "tab": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/${prefix}.tab": { - "type": "file", - "description": "A simple tab-separated summary of all the variants", - "pattern": "*.tab", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "csv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/${prefix}.csv": { - "type": "file", - "description": "A comma-separated version of the .tab file", - "pattern": "*.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "html": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/${prefix}.html": { - "type": "file", - "description": "A HTML version of the .tab file", - "pattern": "*.html", - "ontologies": [] - } - } - ] - ], - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/${prefix}.vcf": { - "type": "file", - "description": "The final annotated variants in VCF format", - "pattern": "*.vcf", - "ontologies": [] - } - } - ] - ], - "bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/${prefix}.bed": { - "type": "file", - "description": "The variants in BED format", - "pattern": "*.bed", - "ontologies": [] - } - } - ] - ], - "gff": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/${prefix}.gff": { - "type": "file", - "description": "The variants in GFF3 format", - "pattern": "*.gff", - "ontologies": [] - } - } - ] - ], - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/${prefix}.bam": { - "type": "file", - "description": "The alignments in BAM format. Includes unmapped, multimapping reads. 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} - }, - { - "${prefix}/${prefix}.vcf.gz.csi": { - "type": "file", - "description": "Index for the .vcf.gz via bcftools index", - "pattern": "*.vcf.gz.csi", - "ontologies": [] - } - } - ] - ], - "txt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}/${prefix}.txt": { - "type": "file", - "description": "Tab-separated columnar list of statistics", - "pattern": "*.txt", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@rpetit3", - "@delfiterradas" - ], - "maintainers": [ - "@rpetit3" - ] - } - }, - { - "name": "snpdists", - "path": "modules/nf-core/snpdists/meta.yml", - "type": "module", - "meta": { - "name": "snpdists", - "description": "Pairwise SNP distance matrix from a FASTA sequence alignment", - "keywords": [ - "snp", - "dist", - "distance", - "matrix" - ], - "tools": [ - { - "snpdists": { - "description": "Convert a FASTA alignment to SNP distance matrix", - "homepage": "https://github.com/tseemann/snp-dists", - "documentation": "https://github.com/tseemann/snp-dists", - "tool_dev_url": "https://github.com/tseemann/snp-dists", - "licence": [ - "GPL v3" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "alignment": { - "type": "file", - "description": "The input FASTA sequence alignment file", - "pattern": "*.{fasta,fasta.gz}", - "ontologies": [] - } - } - ] - ], - "output": { - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "The output TSV file containing SNP distance matrix", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_snpdists": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "snpdists": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "snp-dists -v 2>&1 | sed \"s/snp-dists //;\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "snpdists": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "snp-dists -v 2>&1 | sed \"s/snp-dists //;\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@abhi18av" - ], - "maintainers": [ - "@abhi18av" - ] - }, - "pipelines": [ - { - "name": "tbanalyzer", - "version": "dev" - } - ] - }, - { - "name": "snpeff_download", - "path": "modules/nf-core/snpeff/download/meta.yml", - "type": "module", - "meta": { - "name": "snpeff_download", - "description": "Genetic variant annotation and functional effect prediction toolbox", - "keywords": [ - "annotation", - "effect prediction", - "snpeff", - "variant", - "vcf" - ], - "tools": [ - { - "snpeff": { - "description": "SnpEff is a variant annotation and effect prediction tool.\nIt annotates and predicts the effects of genetic variants on genes and proteins (such as amino acid changes).\n", - "homepage": "https://pcingola.github.io/SnpEff/", - "documentation": "https://pcingola.github.io/SnpEff/se_introduction/", - "licence": [ - "MIT" - ], - "identifier": "biotools:snpeff" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "snpeff_db": { - "type": "string", - "description": "SnpEff database name", - "ontologies": [] - } - } - ] - ], - "output": { - "cache": [ - [ - { - "meta": { - "type": "file", - "description": "snpEff cache\n", - "ontologies": [] - } - }, - { - "snpeff_cache": { - "type": "file", - "description": "snpEff cache\n", - "ontologies": [] - } - } - ] - ], - "versions_snpeff": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "snpeff": { - "type": "string", - "description": "The tool name" - } - }, - { - "snpEff -version 2>&1 | cut -f 2 -d '\t'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "snpeff": { - "type": "string", - "description": "The tool name" - } - }, - { - "snpEff -version 2>&1 | cut -f 2 -d '\t'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@maxulysse" - ], - "maintainers": [ - "@maxulysse" - ] - }, - "pipelines": [ - { - "name": "rnavar", - "version": "1.2.3" - }, - { - "name": "sarek", - "version": "3.8.1" }, { - "name": "tbanalyzer", - "version": "dev" - } - ] - }, - { - "name": "snpeff_snpeff", - "path": "modules/nf-core/snpeff/snpeff/meta.yml", - "type": "module", - "meta": { - "name": "snpeff_snpeff", - "description": "Genetic variant annotation and functional effect prediction toolbox", - "keywords": [ - "annotation", - "effect prediction", - "snpeff", - "variant", - "vcf" - ], - "tools": [ - { - "snpeff": { - "description": "SnpEff is a variant annotation and effect prediction tool.\nIt annotates and predicts the effects of genetic variants on genes and proteins (such as amino acid changes).\n", - "homepage": "https://pcingola.github.io/SnpEff/", - "documentation": "https://pcingola.github.io/SnpEff/se_introduction/", - "licence": [ - "MIT" - ], - "identifier": "biotools:snpeff" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "vcf to annotate\n", - "ontologies": [] - } - } - ], - { - "db": { - "type": "string", - "description": "which db to annotate with\n" - } - }, - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + "name": "fastq_fastqc_umitools_trimgalore", + "path": "subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/meta.yml", + "type": "subworkflow", + "meta": { + "name": "fastq_fastqc_umitools_trimgalore", + "description": "Read QC, UMI extraction and trimming", + "keywords": ["fastq", "fastqc", "qc", "UMI", "trimming", "trimgalore"], + "components": ["fastqc", "umitools/extract", "trimgalore"], + "input": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" + } + }, + { + "skip_fastqc": { + "type": "boolean", + "description": "Skip fastqc process\n" + } + }, + { + "with_umi": { + "type": "boolean", + "description": "With or without umi detection\n" + } + }, + { + "skip_umi_extract": { + "type": "boolean", + "description": "With or without umi extrection\n" + } + }, + { + "skip_trimming": { + "type": "boolean", + "description": "Allows to skip trimgalore execution\n" + } + }, + { + "umi_discard_read": { + "type": "integer", + "description": "Discard R1 / R2 if required\n" + } + }, + { + "min_trimmed_reads": { + "type": "integer", + "description": "Inputs with fewer than this reads will be filtered out of the \"reads\" output channel\n" + } + } + ], + "output": [ + { + "reads": { + "type": "file", + "description": "Extracted FASTQ files. | For single-end reads, pattern is \\${prefix}.umi_extract.fastq.gz. |\n\n\n\n For paired-end reads, pattern is \\${prefix}.umi_extract_{1,2}.fastq.gz.\n", + "pattern": "*.{fastq.gz}" + } + }, + { + "fastqc_html": { + "type": "file", + "description": "FastQC report", + "pattern": "*_{fastqc.html}" + } + }, + { + "fastqc_zip": { + "type": "file", + "description": "FastQC report archive", + "pattern": "*_{fastqc.zip}" + } + }, + { + "log": { + "type": "file", + "description": "Logfile for umi_tools", + "pattern": "*.{log}" + } + }, + { + "trim_unpaired": { + "type": "file", + "description": "FastQ files containing unpaired reads from read 1 or read 2\n", + "pattern": "*unpaired*.fq.gz" + } + }, + { + "trim_html": { + "type": "file", + "description": "FastQC report (optional)", + "pattern": "*_{fastqc.html}" + } + }, + { + "trim_zip": { + "type": "file", + "description": "FastQC report archive (optional)", + "pattern": "*_{fastqc.zip}" + } + }, + { + "trim_log": { + "type": "file", + "description": "Trim Galore! trimming report", + "pattern": "*_{report.txt}" + } + }, + { + "trim_read_count": { + "type": "integer", + "description": "Number of reads remaining after trimming for all input samples" + } + }, + { + "versions": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ], + "authors": ["@drpatelh", "@KamilMaliszArdigen"], + "maintainers": ["@drpatelh", "@KamilMaliszArdigen"] }, - { - "cache": { - "type": "file", - "description": "path to snpEff cache (optional)\n", - "ontologies": [] - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "file", - "description": "annotated vcf\n", - "pattern": "*.ann.vcf", - "ontologies": [] - } - }, - { - "*.ann.vcf": { - "type": "file", - "description": "annotated vcf\n", - "pattern": "*.ann.vcf", - "ontologies": [] - } - } - ] - ], - "report": [ - [ - { - "meta": { - "type": "file", - "description": "annotated vcf\n", - "pattern": "*.ann.vcf", - "ontologies": [] - } - }, - { - "${task.process}": { - "type": "string", - "description": "The process" - } - }, - { - "snpeff": { - "type": "string", - "description": "The tool name" - } - }, - { - "*.csv": { - "type": "file", - "description": "snpEff report csv file", - "pattern": "*.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "summary_html": [ - [ - { - "meta": { - "type": "file", - "description": "annotated vcf\n", - "pattern": "*.ann.vcf", - "ontologies": [] - } - }, - { - "${task.process}": { - "type": "string", - "description": "The process" - } - }, - { - "snpeff": { - "type": "string", - "description": "The tool name" - } - }, - { - "*.html": { - "type": "file", - "description": "snpEff summary statistics in html file", - "pattern": "*.html", - "ontologies": [] - } - } - ] - ], - "genes_txt": [ - [ - { - "meta": { - "type": "file", - "description": "annotated vcf\n", - "pattern": "*.ann.vcf", - "ontologies": [] - } - }, - { - "${task.process}": { - "type": "string", - "description": "The process" - } - }, - { - "snpeff": { - "type": "string", - "description": "The tool name" - } - }, - { - "*.genes.txt": { - "type": "file", - "description": "txt (tab separated) file having counts of the number of variants affecting each transcript and gene", - "pattern": "*.genes.txt", - "ontologies": [] - } - } - ] - ], - "versions_snpeff": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "snpeff": { - "type": "string", - "description": "The tool name" - } - }, - { - "snpEff -version 2>&1 | cut -f 2 -d '\t'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "multiqc_files": [ - [ - { - "meta": { - "type": "file", - "description": "annotated vcf\n", - "pattern": "*.ann.vcf", - "ontologies": [] - } - }, - { - "${task.process}": { - "type": "string", - "description": "The process" - } - }, - { - "snpeff": { - "type": "string", - "description": "The tool name" - } - }, - { - "*.csv": { - "type": "file", - "description": "snpEff report csv file", - "pattern": "*.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ], - [ - { - "meta": { - "type": "file", - "description": "annotated vcf\n", - "pattern": "*.ann.vcf", - "ontologies": [] - } - }, - { - "${task.process}": { - "type": "string", - "description": "The process" - } - }, - { - "snpeff": { - "type": "string", - "description": "The tool name" - } - }, - { - "*.html": { - "type": "file", - "description": "snpEff summary statistics in html file", - "pattern": "*.html", - "ontologies": [] - } - } - ], - [ - { - "meta": { - "type": "file", - "description": "annotated vcf\n", - "pattern": "*.ann.vcf", - "ontologies": [] - } - }, - { - "${task.process}": { - "type": "string", - "description": "The process" - } - }, - { - "snpeff": { - "type": "string", - "description": "The tool name" - } - }, - { - "*.genes.txt": { - "type": "file", - "description": "txt (tab separated) file having counts of the number of variants affecting each transcript and gene", - "pattern": "*.genes.txt", - "ontologies": [] - } - } - ] - ], - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "snpeff": { - "type": "string", - "description": "The tool name" - } - }, - { - "snpEff -version 2>&1 | cut -f 2 -d '\t'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } + "pipelines": [ + { + "name": "atacseq", + "version": "2.1.2" + }, + { + "name": "chipseq", + "version": "2.1.0" + }, + { + "name": "lncpipe", + "version": "dev" + }, + { + "name": "riboseq", + "version": "1.2.0" + }, + { + "name": "rnaseq", + "version": "3.26.0" + }, + { + "name": "rnasplice", + "version": "1.0.4" + } ] - ] - }, - "authors": [ - "@maxulysse" - ], - "maintainers": [ - "@maxulysse" - ] - }, - "pipelines": [ - { - "name": "rnavar", - "version": "1.2.3" - }, - { - "name": "sarek", - "version": "3.8.1" }, { - "name": "tbanalyzer", - "version": "dev" + "name": "fastq_fetch_clean_hostile", + "path": "subworkflows/nf-core/fastq_fetch_clean_hostile/meta.yml", + "type": "subworkflow", + "meta": { + "name": "fastq_fetch_clean_hostile", + "description": "Downloads required reference genomes for hostile and removes host reads from short-read FASTQ sequencing files", + "keywords": ["hostile", "decontamination", "human removal", "download", "host removal", "clean"], + "components": ["hostile/fetch", "hostile/clean"], + "input": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "reads": { + "type": "file", + "description": "Input FASTQ files for hostile cleaning", + "pattern": "*.{fastq,fastq.gz,fq,fq.gz}" + } + }, + { + "reference_name": { + "type": "string", + "description": "Name of the reference to align against and thus remove mapped reads to." + } + }, + { + "reference_dir": { + "type": "directory", + "description": "Directory containing index file(s) corresponding to the preferred aligner (bowtie2 short reads or minimap for long reads).\nNote that single end data is assumed to be long reads. If you have single-end short read you must supply both the BowTie2\nindices AND explicitly specify `--aligner bowtie2`\n" + } + }, + { + "index_name": { + "type": "string", + "description": "Name of the reference genome index to download for hostile fetch if the reference is not provided." + } + } + ], + "output": [ + { + "reference": { + "type": "channel", + "description": "Channel containing reference name and directory with index files for Hostile.\nStructure: [ val(reference_name), path(reference_dir) ]\n" + } + }, + { + "fastq": { + "type": "file", + "description": "Channel containing sample metadata and cleaned FASTQ files.\nStructure: [ val(meta), path(*.fastq.gz) ]\n", + "pattern": "*.{fastq,fq,fastq.gz,fq.gz}" + } + }, + { + "json": { + "type": "channel", + "description": "Channel containing sample metadata and Hostile cleaning log in JSON format.\nStructure: [ val(meta), path(*.json) ]\n", + "pattern": "*.json" + } + }, + { + "versions": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ], + "authors": ["@maia-munteanu"], + "maintainers": ["@maia-munteanu", "@vagkaratzas"] + } }, { - "name": "viralmetagenome", - "version": "1.1.1" - } - ] - }, - { - "name": "snpsift_annmem", - "path": "modules/nf-core/snpsift/annmem/meta.yml", - "type": "module", - "meta": { - "name": "snpsift_annmem", - "description": "Annotate VCF files using pre-built SnpSift annMem databases.\nEnriches input VCF records by querying memory-optimized indexed dataframes for high-performance annotation.\n", - "keywords": [ - "vcf", - "annotation", - "snpsift", - "variant", - "database" - ], - "tools": [ - { - "snpsift": { - "description": "Genetic variant annotations and functional effect prediction toolbox", - "homepage": "https://pcingola.github.io/SnpEff/snpsift/annotate_mem/", - "documentation": "https://pcingola.github.io/SnpEff/snpsift/annotate_mem/", - "tool_dev_url": "https://github.com/pcingola/SnpSift", - "doi": "10.3389/fgene.2012.00035", - "licence": [ - "MIT" - ], - "identifier": "biotools:snpsift" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF file to annotate", - "pattern": "*.{vcf,vcf.gz}", - "ontologies": [] - } - }, - { - "vcf_tbi": { - "type": "file", - "description": "Tabix index for input VCF (optional)", - "pattern": "*.tbi", - "ontologies": [] - } - } - ], - [ - { - "db_vcf": { - "type": "file", - "description": "VCF database file(s) for annotation.\nCan provide multiple databases for multi-database annotation.\n", - "pattern": "*.{vcf,vcf.gz}", - "ontologies": [] - } - }, - { - "db_vcf_tbi": { - "type": "file", - "description": "Tabix index for database VCF file(s)", - "pattern": "*.tbi", - "ontologies": [] - } - }, - { - "db_vardb": { - "type": "directory", - "description": "Pre-built .snpsift.vardb directory (used instead of db_vcf if provided)", - "pattern": "*.snpsift.vardb" - } - }, - { - "db_fields": { - "type": "list", - "description": "INFO field names to annotate with.\nCan be a list or a single string.\n" - } - }, - { - "db_prefixes": { - "type": "string", - "description": "Prefix to add to annotated field names" - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "*.vcf.gz": { - "type": "file", - "description": "Annotated VCF file", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "*.vcf.gz.tbi": { - "type": "file", - "description": "Tabix index for annotated VCF", - "pattern": "*.vcf.gz.tbi", - "ontologies": [] - } - } - ] - ], - "versions_snpsift": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "snpsift": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "SnpSift -version 2>&1 | grep -oE '[0-9]+\\.[0-9]+[a-z]?'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "snpsift": { - "type": "string", - "description": "The tool name" - } - }, - { - "SnpSift -version 2>&1 | grep -oE '[0-9]+\\.[0-9]+[a-z]?'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@friederike-hanssen" - ], - "maintainers": [ - "@friederike-hanssen" - ] - }, - "pipelines": [ - { - "name": "sarek", - "version": "3.8.1" - } - ] - }, - { - "name": "snpsift_annmemcreate", - "path": "modules/nf-core/snpsift/annmemcreate/meta.yml", - "type": "module", - "meta": { - "name": "snpsift_annmemcreate", - "description": "Create memory-optimized SnpSift vardb databases from VCF files for use with SnpSift annMem annotation.\nConverts VCF files (e.g. ClinVar, dbSNP, Cosmic) into indexed dataframes for fast lookup.\n", - "keywords": [ - "vcf", - "annotation", - "snpsift", - "variant", - "database" - ], - "tools": [ - { - "snpsift": { - "description": "Genetic variant annotations and functional effect prediction toolbox", - "homepage": "https://pcingola.github.io/SnpEff/snpsift/annotate_mem/", - "documentation": "https://pcingola.github.io/SnpEff/snpsift/annotate_mem/", - "tool_dev_url": "https://github.com/pcingola/SnpSift", - "doi": "10.3389/fgene.2012.00035", - "licence": [ - "MIT" - ], - "identifier": "biotools:snpsift" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "db_vcf": { - "type": "file", - "description": "VCF file to build the database from", - "pattern": "*.{vcf,vcf.gz}", - "ontologies": [] - } - }, - { - "db_vcf_tbi": { - "type": "file", - "description": "Tabix index for the database VCF file (optional)", - "pattern": "*.tbi", - "ontologies": [] - } - }, - { - "db_fields": { - "type": "list", - "description": "INFO field names to include in the database.\nCan be a list or a single string.\n" - } - } - ] - ], - "output": { - "database": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "*.snpsift.vardb": { - "type": "directory", - "description": "SnpSift vardb directory containing indexed dataframes", - "pattern": "*.snpsift.vardb" - } - } - ] - ], - "versions_snpsift": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "snpsift": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "SnpSift -version 2>&1 | grep -oE '[0-9]+\\.[0-9]+[a-z]?'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - 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"@nvnieuwk" - ] - } - }, - { - "name": "somalier_relate", - "path": "modules/nf-core/somalier/relate/meta.yml", - "type": "module", - "meta": { - "name": "somalier_relate", - "description": "Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs", - "keywords": [ - "relatedness", - "QC", - "bam", - "cram", - "vcf", - "gvcf", - "ancestry", - "identity", - "kinship", - "informative sites", - "family" - ], - "tools": [ - { - "somalier": { - "description": "Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs", - "homepage": "https://github.com/brentp/somalier", - "documentation": "https://github.com/brentp/somalier/blob/master/README.md", - "tool_dev_url": "https://github.com/brentp/somalier", - "doi": "10.1186/s13073-020-00761-2", - "licence": [ - "MIT" - ], - "identifier": "biotools:somalier" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "extract": { - "type": "file", - "description": "extract file(s) from Somalier extract", - "pattern": "*.somalier", - "ontologies": [] - } + "name": "fastq_find_mirna_mirdeep2", + "path": "subworkflows/nf-core/fastq_find_mirna_mirdeep2/meta.yml", + "type": "subworkflow", + "meta": { + "name": "fastq_find_mirna_mirdeep2", + "description": "This subworkflow identifies miRNAs from FASTQ files using miRDeep2. The workflow converts FASTQ to FASTA, processes and replaces any whitespace in sequence IDs, builds a Bowtie index of the genome, and then maps reads using miRDeep2 mapper before identifying known and novel miRNAs.\n", + "keywords": ["miRNA", "FASTQ", "FASTA", "Bowtie", "miRDeep2"], + "components": [ + "seqkit/fq2fa", + "seqkit/replace", + "bowtie/build", + "mirdeep2/mapper", + "mirdeep2/mirdeep2" + ], + "input": [ + { + "ch_reads": { + "type": "file", + "description": "The input channel containing the FASTQ files to process and identify miRNAs.\nStructure: [ val(meta), path(fastq) ]\n", + "pattern": "*.fastq.gz" + } + }, + { + "ch_genome_fasta": { + "type": "file", + "description": "The input channel containing the genome FASTA files used to build the Bowtie index.\nStructure: [ val(meta), path(fasta) ]\n", + "pattern": "*.fa" + } + }, + { + "ch_mirna_mature_hairpin": { + "type": "file", + "description": "The input channel containing the mature and hairpin miRNA sequences for miRNA identification.\nStructure: [ val(meta), path(mature_fasta), path(hairpin_fasta) ]\n", + "pattern": "*.fa" + } + } + ], + "output": [ + { + "outputs": { + "type": "file", + "description": "The output channel containing the BED, CSV, and HTML files with the identified miRNAs.\nStructure: [ val(meta), path(bed), path(csv), path(html) ]\n", + "pattern": "*.{bed,csv,html}" + } + }, + { + "versions": { + "type": "file", + "description": "File containing software versions\nStructure: [ path(versions.yml) ]\n", + "pattern": "versions.yml" + } + } + ], + "authors": ["@atrigila"], + "maintainers": ["@atrigila"] }, - { - "ped": { - "type": "file", - "description": "optional path to a ped or fam file indicating the expected relationships among samples", - "pattern": "*.{ped,fam}", - "ontologies": [] - } - } - ], - { - "sample_groups": { - "type": "file", - "description": "optional path to expected groups of samples such as tumor normal pairs specified as comma-separated groups per line", - "pattern": "*.{txt,csv}", - "ontologies": [ + "pipelines": [ { - "edam": "http://edamontology.org/format_3752" + "name": "smrnaseq", + "version": "2.4.1" } - ] - } - } - ], - "output": { - "html": [ - [ - { - "meta": { - "type": "file", - "description": "html file", - "pattern": "*.html", - "ontologies": [] - } - }, - { - "*.html": { - "type": "file", - "description": "html file", - "pattern": "*.html", - "ontologies": [] - } - } - ] - ], - "pairs_tsv": [ - [ - { - "meta": { - "type": "file", - "description": "html file", - "pattern": "*.html", - "ontologies": [] - } - }, - { - "*.pairs.tsv": { - "type": "file", - "description": "tsv file with output stats for pairs of samples", - "pattern": "*.pairs.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "samples_tsv": [ - [ - { - "meta": { - "type": "file", - "description": "html file", - "pattern": "*.html", - "ontologies": [] - } - }, - { - "*.samples.tsv": { - "type": "file", - "description": "tsv file with sample-level information", - "pattern": "*.samples.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_somalier": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "somalier": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "somalier 2>&1 | sed -n 's/.*version: \\([0-9.]*\\).*/\\1/p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "somalier": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "somalier 2>&1 | sed -n 's/.*version: \\([0-9.]*\\).*/\\1/p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@ashotmarg", - "@nvnieuwk" - ], - "maintainers": [ - "@ashotmarg", - "@nvnieuwk" - ] - } - }, - { - "name": "sortmerna", - "path": "modules/nf-core/sortmerna/meta.yml", - "type": "module", - "meta": { - "name": "sortmerna", - "description": "Local sequence alignment tool for filtering, mapping and clustering.", - "keywords": [ - "filtering", - "mapping", - "clustering", - "rRNA", - "ribosomal RNA" - ], - "tools": [ - { - "SortMeRNA": { - "description": "The core algorithm is based on approximate seeds and allows for sensitive analysis of NGS reads. The main application of SortMeRNA is filtering rRNA from metatranscriptomic data. SortMeRNA takes as input files of reads (fasta, fastq, fasta.gz, fastq.gz) and one or multiple rRNA database file(s), and sorts apart aligned and rejected reads into two files. Additional applications include clustering and taxonomy assignation available through QIIME v1.9.1. SortMeRNA works with Illumina, Ion Torrent and PacBio data, and can produce SAM and BLAST-like alignments.", - "homepage": "https://hpc.nih.gov/apps/sortmeRNA.html", - "documentation": "https://github.com/biocore/sortmerna/wiki/", - "licence": [ - "GPL-3.0-or-later" - ], - "identifier": "biotools:sortmerna" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "fastas": { - "type": "file", - "description": "Path to reference file(s)\n", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing index information\ne.g. [ id:'test' ]\n" - } - }, - { - "index": { - "type": "directory", - "description": "Path to index directory of a previous sortmerna run\n" - } - } - ] - ], - "output": { - "reads": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ], or reference information from an\nindexing-only run\n" - } - }, - { - "*non_rRNA.fastq.gz": { - "type": "file", - "description": "The filtered fastq reads", - "pattern": "*fastq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ], or reference information from an\nindexing-only run\n" - } - }, - { - "*.log": { - "type": "file", - "description": "SortMeRNA log file", - "pattern": "*sortmerna.log", - "ontologies": [] - } - } - ] - ], - "index": [ - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "idx": { - "type": "directory", - "description": "Path to index directory generated by sortmern\n" - } - } ] - ], - "versions_sortmerna": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "sortmerna": { - "type": "string", - "description": "The tool name" - } - }, - { - "sortmerna --version 2>&1 | grep -oE \"[0-9]+\\.[0-9]+\\.[0-9]+\" | head -1": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "sortmerna": { - "type": "string", - "description": "The tool name" - } - }, - { - "sortmerna --version 2>&1 | grep -oE \"[0-9]+\\.[0-9]+\\.[0-9]+\" | head -1": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] }, - "authors": [ - "@drpatelh", - "@mashehu" - ], - "maintainers": [ - "@drpatelh", - "@mashehu" - ] - }, - "pipelines": [ { - "name": "denovotranscript", - "version": "1.2.1" + "name": "fastq_index_filter_deacon", + "path": "subworkflows/nf-core/fastq_index_filter_deacon/meta.yml", + "type": "subworkflow", + "meta": { + "name": "fastq_index_filter_deacon", + "description": "Decontaminate FastQ files by filtering reads that match a reference genome using Deacon\n", + "keywords": [ + "filter", + "index", + "fasta", + "fastq", + "genome", + "reference", + "minimizer", + "decontamination" + ], + "components": ["deacon/index", "deacon/filter"], + "input": [ + { + "ch_fasta_reads": { + "type": "file", + "description": "Input genome fasta file and a list of FastQ files of size 1 and 2 for single-end and paired-end data, respectively.\nStructure: [ val(meta), path(fasta), [ path(reads) ] ]\n" + } + } + ], + "output": [ + { + "index": { + "type": "file", + "description": "Deacon minimizer index file\nStructure: [ val(meta), path(index) ]\n", + "pattern": ".idx" + } + }, + { + "fastq_filtered": { + "type": "file", + "description": "List of output filtered FastQ files of size 1 and 2 for single-end and paired-end data, respectively.\nStructure: [ val(meta), path(${prefix}*.fq) ]\n", + "pattern": "*.fq.gz" + } + }, + { + "summary": { + "type": "file", + "description": "JSON file containing summary of results.\nStructure: [ val(meta), path(${prefix}.json) ]\n", + "pattern": "*.json" + } + } + ], + "authors": ["@Baksic-Ivan", "@Omer0191"], + "maintainers": ["@Baksic-Ivan", "@Omer0191"] + } }, { - "name": "lncpipe", - "version": "dev" + "name": "fastq_ngscheckmate", + "path": "subworkflows/nf-core/fastq_ngscheckmate/meta.yml", + "type": "subworkflow", + "meta": { + "name": "fastq_ngscheckmate", + "description": "Take a set of fastq files and run NGSCheckMate to determine whether samples match with each other, using a set of SNPs.", + "keywords": ["ngscheckmate", "qc", "fastq", "snp"], + "components": ["ngscheckmate/fastq", "ngscheckmate/vafncm"], + "input": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "fastq": { + "type": "file", + "description": "Single or pair of fastq files", + "pattern": "*.{fastq.gz}" + } + }, + { + "meta2": { + "type": "map", + "description": "Groovy Map containing snp_pt file information\ne.g. [ id:'sarscov2' ]\n" + } + }, + { + "snp_bed": { + "type": "file", + "description": "Binary PT file containing the SNPs to analyse. NGSCheckMate provides one for human samples.", + "pattern": "*.{bed}" + } + } + ], + "output": [ + { + "pdf": { + "type": "file", + "description": "A pdf containing a dendrogram showing how the samples match up", + "pattern": "*.{pdf}" + } + }, + { + "corr_matrix": { + "type": "file", + "description": "A text file containing the correlation matrix between each sample", + "pattern": "*corr_matrix.txt" + } + }, + { + "matched": { + "type": "file", + "description": "A txt file containing only the samples that match with each other", + "pattern": "*matched.txt" + } + }, + { + "all": { + "type": "file", + "description": "A txt file containing all the sample comparisons, whether they match or not", + "pattern": "*all.txt" + } + }, + { + "vcf": { + "type": "file", + "description": "vcf files for each sample giving the SNP calls", + "pattern": "*.vcf" + } + }, + { + "versions": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ], + "authors": ["@SPPearce"], + "maintainers": ["@SPPearce"] + } }, { - "name": "references", - "version": "0.1" + "name": "fastq_preprocess", + "path": "subworkflows/nf-core/fastq_preprocess/meta.yml", + "type": "subworkflow", + "meta": { + "name": "fastq_preprocess", + "description": "Subworkflow that preprocesses FASTQ files", + "keywords": ["fasta", "seqkit", "preprocessing"], + "components": [ + "fastq_sanitise_seqkit", + "seqkit/sana", + "seqkit/pair", + "seqkit/seq", + "seqkit/replace", + "seqkit/rmdup" + ], + "input": [ + { + "ch_reads": { + "type": "channel", + "description": "Channel containing sample metadata and FASTQ files.\nStructure: [ val(meta), [ fastq ] ]\nWhere meta is a map containing at least:\n- id: sample identifier\n- single_end: boolean indicating if data is single-end (true) or paired-end (false)\n", + "pattern": "*.{fastq,fastq.gz,fq,fq.gz}" + } + }, + { + "skip_seqkit_sana_pair": { + "type": "boolean", + "description": "If true, skips the seqkit_sana_pair subworkflow.\n" + } + }, + { + "skip_seqkit_seq": { + "type": "boolean", + "description": "If true, skips the seqkit_seq process.\n" + } + }, + { + "skip_seqkit_replace": { + "type": "boolean", + "description": "If true, skips the seqkit_replace process.\n" + } + }, + { + "skip_seqkit_rmdup": { + "type": "boolean", + "description": "If true, skips the seqkit_rmdup process.\n" + } + } + ], + "output": [ + { + "reads": { + "type": "channel", + "description": "Channel containing filtered FASTQ files.\nStructure: [ val(meta), [ fastq ] ]\n", + "pattern": "*.{fastq,fastq.gz,fq,fq.gz}" + } + }, + { + "versions": { + "type": "file", + "description": "File containing software versions\nStructure: [ path(versions.yml) ]\n", + "pattern": "versions.yml" + } + } + ], + "authors": ["@maia-munteanu"], + "maintainers": ["@maia-munteanu", "@vagkaratzas"] + } }, { - "name": "riboseq", - "version": "1.2.0" + "name": "fastq_preprocess_seqkit", + "path": "subworkflows/nf-core/fastq_preprocess_seqkit/meta.yml", + "type": "subworkflow", + "meta": { + "name": "fastq_preprocess_seqkit", + "description": "Subworkflow that preprocesses FASTQ files", + "keywords": ["fastq", "seqkit", "preprocessing"], + "components": [ + "fastq_sanitise_seqkit", + "seqkit/sana", + "seqkit/pair", + "seqkit/seq", + "seqkit/replace", + "seqkit/rmdup" + ], + "input": [ + { + "ch_reads": { + "type": "channel", + "description": "Channel containing sample metadata and FASTQ files.\nStructure: [ val(meta), [ fastq ] ]\nWhere meta is a map containing at least:\n- id: sample identifier\n- single_end: boolean indicating if data is single-end (true) or paired-end (false)\n", + "pattern": "*.{fastq,fastq.gz,fq,fq.gz}" + } + }, + { + "skip_seqkit_sana_pair": { + "type": "boolean", + "description": "If true, skips the seqkit_sana_pair subworkflow.\n" + } + }, + { + "skip_seqkit_seq": { + "type": "boolean", + "description": "If true, skips the seqkit_seq process.\n" + } + }, + { + "skip_seqkit_replace": { + "type": "boolean", + "description": "If true, skips the seqkit_replace process.\n" + } + }, + { + "skip_seqkit_rmdup": { + "type": "boolean", + "description": "If true, skips the seqkit_rmdup process.\n" + } + } + ], + "output": [ + { + "reads": { + "type": "channel", + "description": "Channel containing filtered FASTQ files.\nStructure: [ val(meta), [ fastq ] ]\n", + "pattern": "*.{fastq,fastq.gz,fq,fq.gz}" + } + }, + { + "versions": { + "type": "file", + "description": "File containing software versions\nStructure: [ path(versions.yml) ]\n", + "pattern": "versions.yml" + } + } + ], + "authors": ["@maia-munteanu"], + "maintainers": ["@maia-munteanu", "@vagkaratzas"] + } }, { - "name": "rnaseq", - "version": "3.26.0" - } - ] - }, - { - "name": "souporcell", - "path": "modules/nf-core/souporcell/meta.yml", - "type": "module", - "meta": { - "name": "souporcell", - "description": "souporcell is a method for clustering mixed-genotype scRNAseq experiments by individual.", - "keywords": [ - "clustering", - "mixed-genotype", - "genomics" - ], - "tools": [ - { - "souporcell": { - "description": "Clustering scRNAseq by genotypes.", - "homepage": "https://github.com/wheaton5/souporcell", - "documentation": "https://demultiplexing-doublet-detecting-docs.readthedocs.io/en/latest/Souporcell.html", - "tool_dev_url": "https://github.com/wheaton5/souporcell", - "doi": "10.1101/699637v1", - "licence": [ - "MIT" - ], - "identifier": "biotools:souporcell" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "A BAM file from cellranger containing single-cell RNA-seq alignments.", - "pattern": "*.bam", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - }, - { - "barcodes": { - "type": "file", - "description": "A barcode or whitelist TSV file from cellranger identifying individual cell barcodes.", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - }, - { - "clusters": { - "type": "integer", - "description": "Number of clusters." - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "A reference fasta file.", - "pattern": "*.fasta", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ], - "output": { - "clusters": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*/clusters.tsv": { - "type": "file", - "description": "TSV file listing cell barcodes with singlet/doublet status, assigned cluster, and per-cluster log-loss metrics", - "pattern": "clusters.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*/cluster_genotypes.vcf": { - "type": "file", - "description": "A `vcf` with genotypes for each cluster for each variant in the input `vcf` from freebayes.", - "pattern": "cluster_genotypes.vcf", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - } - ] - } - } - ] - ], - "ambient_rna": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*/ambient_rna.txt": { - "type": "file", - "description": "Contains the ambient RNA percentage detected", - "pattern": "ambient_rna.txt", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2330" - } - ] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@seohyonkim", - "@LuisHeinzlmeier" - ], - "maintainers": [ - "@seohyonkim", - "@LuisHeinzlmeier" - ] - } - }, - { - "name": "soupx", - "path": "modules/nf-core/soupx/meta.yml", - "type": "module", - "meta": { - "name": "soupx", - "description": "Estimation and removal of cell free mRNA contamination in droplet based single cell RNA-seq data.\n\nThe filtered counts are preprocessed with Seurat (LogNormalize, PCA, kNN graph, clustering) to\nprovide cluster assignments to SoupX, which then estimates per-cluster contamination and adjusts\ncounts. The adjusted counts are written to the output H5AD as an `ambient` layer.\n", - "keywords": [ - "single-cell", - "transcriptomics", - "ambient" - ], - "tools": [ - { - "soupx": { - "description": "Estimation and removal of cell free mRNA contamination in droplet based single cell RNA-seq data", - "documentation": "https://rawcdn.githack.com/constantAmateur/SoupX/204b602418df12e9fdb4b68775a8b486c6504fe4/inst/doc/pbmcTutorial.html", - "tool_dev_url": "https://github.com/constantAmateur/SoupX", - "doi": "10.1093/gigascience/giaa151", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "h5ad_filtered": { - "type": "file", - "description": "filtered H5AD file (after CellRanger filtering)", - "pattern": "*.h5ad", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3590" - } - ] - } - }, - { - "h5ad_raw": { - "type": "file", - "description": "raw H5AD file (before CellRanger filtering)", - "pattern": "*.h5ad", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3590" - } - ] - } - } - ], - { - "npcs": { - "type": "integer", - "description": "Number of principal components for Seurat PCA (also controls FindNeighbors dims = 1:npcs).\n" - } - }, - { - "cluster_algorithm": { - "type": "integer", - "description": "Seurat FindClusters algorithm identifier passed to `FindClusters(algorithm = ...)`.\nValid values:\n - 1: louvain\n - 2: louvain_multilevel\n - 3: slm\n - 4: leiden\n" - } - } - ], - "output": { - "h5ad": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.h5ad": { - "type": "file", - "description": "H5AD anndata object with ambient RNA removed", - "pattern": "*.h5ad", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3590" - } - ] - } - } - ] - ], - "versions_soupx": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "topics": { - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@LeonHafner" - ], - "maintainers": [ - "@LeonHafner", - "@nictru" - ] - } - }, - { - "name": "sourcepredict", - "path": "modules/nf-core/sourcepredict/meta.yml", - "type": "module", - "meta": { - "name": "sourcepredict", - "description": "Classifies and predicts the origin of metagenomic samples", - "keywords": [ - "source tracking", - "metagenomics", - "machine learning" - ], - "tools": [ - { - "sourcepredict": { - "description": "Classification and prediction of the origin of metagenomic samples.", - "homepage": "https://github.com/maxibor/sourcepredict", - "documentation": "https://sourcepredict.readthedocs.io/en/latest/index.html", - "tool_dev_url": "https://github.com/maxibor/sourcepredict", - "doi": "10.21105/joss.01540", - "licence": [ - "GPL v3-or-later" - ], - "identifier": "biotools:sourcepredict" + "name": "fastq_qc_stats", + "path": "subworkflows/nf-core/fastq_qc_stats/meta.yml", + "type": "subworkflow", + "meta": { + "name": "fastq_qc_stats", + "description": "Generate statistics for short read sequencing data using multiple tools", + "keywords": ["fastq", "qc", "fastqc", "seqfu", "seqkit", "seqtk"], + "components": ["fastqc", "seqfu/check", "seqfu/stats", "seqkit/stats", "seqtk/comp"], + "input": [ + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" + } + }, + { + "skip_fastqc": { + "type": "boolean", + "description": "Skip fastqc process\n" + } + }, + { + "skip_seqfu_check": { + "type": "boolean", + "description": "Skip seqfu_check process\n" + } + }, + { + "skip_seqfu_stats": { + "type": "boolean", + "description": "Skip seqfu_stats process\n" + } + }, + { + "skip_seqkit_stats": { + "type": "boolean", + "description": "Skip seqkit_stats process\n" + } + }, + { + "skip_seqtk_comp": { + "type": "boolean", + "description": "Skip seqtk_comp process\n" + } + } + ], + "output": [ + { + "fastqc_html": { + "type": "file", + "description": "FastQC report", + "pattern": "*_fastqc.html" + } + }, + { + "fastqc_zip": { + "type": "file", + "description": "FastQC report archive", + "pattern": "*_fastqc.zip" + } + }, + { + "seqfu_check": { + "type": "file", + "description": "seqfu check tsv report", + "pattern": "*.tsv" + } + }, + { + "seqfu_stats": { + "type": "file", + "description": "seqfu stats tsv report", + "pattern": "*.tsv" + } + }, + { + "seqfu_multiqc": { + "type": "file", + "description": "seqfu stats MultiQC report", + "pattern": "*_mqc.txt" + } + }, + { + "seqkit_stats": { + "type": "file", + "description": "seqkit stats report", + "pattern": "*.tsv" + } + }, + { + "versions": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ], + "authors": ["@pablo-scd"], + "maintainers": ["@pablo-scd", "@vagkaratzas"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } + }, + { + "name": "fastq_qc_trim_filter_setstrandedness", + "path": "subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/meta.yml", + "type": "subworkflow", + "meta": { + "name": "fastq_qc_trim_filter_setstrandedness", + "description": "Performs linting, quality control, trimming, filtering, and strandedness determination on RNA-seq FASTQ files, preparing them for downstream analysis.", + "keywords": ["fastq", "rnaseq", "rrna", "trimming", "subsample", "strandedness"], + "components": [ + "bbmap/bbsplit", + "cat/fastq", + "fastqc", + "fq/lint", + "fastq_remove_rrna", + "fastq_subsample_fq_salmon", + "fastq_fastqc_umitools_trimgalore", + "fastq_fastqc_umitools_fastp" + ], + "input": [ + { + "ch_reads": { + "description": "Channel with input FastQ files", + "structure": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'test' ]" + } + }, + { + "reads": { + "type": "file", + "description": "FastQ files", + "pattern": "*.{fq,fastq},{,.gz}" + } + } + ] + } + }, + { + "ch_fasta": { + "description": "Channel with genome sequence in fasta format", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata for the fasta file" + } + }, + { + "fasta": { + "type": "file", + "description": "Genome fasta file", + "pattern": "*.{fa,fasta}" + } + } + ] + } + }, + { + "ch_transcript_fasta": { + "description": "Channel with transcriptome sequence in fasta format", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata for the transcript fasta file" + } + }, + { + "fasta": { + "type": "file", + "description": "Transcript fasta file", + "pattern": "*.{fa,fasta}" + } + } + ] + } + }, + { + "ch_gtf": { + "description": "Channel with features in GTF format", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata for the GTF file" + } + }, + { + "gtf": { + "type": "file", + "description": "GTF file", + "pattern": "*.gtf" + } + } + ] + } + }, + { + "ch_salmon_index": { + "description": "Directory containing Salmon index", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata for the Salmon index" + } + }, + { + "index": { + "type": "directory", + "description": "Salmon index directory" + } + } + ] + } + }, + { + "ch_sortmerna_index": { + "description": "Directory containing sortmerna index", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata for the SortMeRNA index" + } + }, + { + "index": { + "type": "directory", + "description": "SortMeRNA index directory" + } + } + ] + } + }, + { + "ch_bowtie2_index": { + "description": "Directory containing bowtie2 index for rRNA removal", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata for the Bowtie2 index" + } + }, + { + "index": { + "type": "directory", + "description": "Bowtie2 index directory" + } + } + ] + } + }, + { + "ch_bbsplit_index": { + "description": "Path to directory or tar.gz archive for pre-built BBSplit index", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata for the BBSplit index" + } + }, + { + "index": { + "type": "file", + "description": "BBSplit index directory or tar.gz archive", + "pattern": "{*,*.tar.gz}" + } + } + ] + } + }, + { + "ch_rrna_fastas": { + "description": "Channel containing one or more FASTA files containing rRNA sequences for use with SortMeRNA or Bowtie2", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata for the rRNA fasta files" + } + }, + { + "fasta": { + "type": "file", + "description": "rRNA fasta files", + "pattern": "*.{fa,fasta}" + } + } + ] + } + }, + { + "skip_bbsplit": { + "type": "boolean", + "description": "Whether to skip BBSplit for removal of non-reference genome reads" + } + }, + { + "skip_fastqc": { + "type": "boolean", + "description": "Whether to skip FastQC" + } + }, + { + "skip_trimming": { + "type": "boolean", + "description": "Whether to skip trimming" + } + }, + { + "skip_umi_extract": { + "type": "boolean", + "description": "Skip the UMI extraction from the read in case the UMIs have been moved to the headers in advance of the pipeline run" + } + }, + { + "skip_linting": { + "type": "boolean", + "description": "Whether to skip linting of FastQ files" + } + }, + { + "make_salmon_index": { + "type": "boolean", + "description": "Whether to create salmon index before running salmon quant" + } + }, + { + "make_sortmerna_index": { + "type": "boolean", + "description": "Whether to create sortmerna index before running sortmerna" + } + }, + { + "make_bowtie2_index": { + "type": "boolean", + "description": "Whether to create bowtie2 index before running bowtie2 for rRNA removal" + } + }, + { + "trimmer": { + "type": "string", + "description": "Specifies the trimming tool to use", + "enum": ["trimgalore", "fastp"] + } + }, + { + "min_trimmed_reads": { + "type": "integer", + "description": "Minimum number of trimmed reads below which samples are removed from further processing" + } + }, + { + "save_trimmed": { + "type": "boolean", + "description": "Save the trimmed FastQ files in the results directory?" + } + }, + { + "fastp_merge": { + "type": "boolean", + "description": "For FASTP, save merged fastqs stitching together read1 and read2 for paired end reads\n" + } + }, + { + "remove_ribo_rna": { + "type": "boolean", + "description": "Enable the removal of reads derived from ribosomal RNA" + } + }, + { + "ribo_removal_tool": { + "type": "string", + "description": "Specifies the rRNA removal tool to use", + "enum": ["sortmerna", "ribodetector", "bowtie2"] + } + }, + { + "with_umi": { + "type": "boolean", + "description": "Enable UMI-based read deduplication" + } + }, + { + "umi_discard_read": { + "type": "integer", + "description": "After UMI barcode extraction discard either R1 or R2 by setting this parameter to 1 or 2, respectively" + } + }, + { + "stranded_threshold": { + "type": "float", + "min": 0.5, + "description": "The fraction of stranded reads that must be assigned to a strandedness for confident assignment. Must be at least 0.5." + } + }, + { + "unstranded_threshold": { + "type": "float", + "description": "The difference in fraction of stranded reads assigned to 'forward' and 'reverse' below which a sample is classified as 'unstranded'." + } + } + ], + "output": [ + { + "reads": { + "description": "Preprocessed fastq reads", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata for the preprocessed reads" + } + }, + { + "reads": { + "type": "file", + "description": "Preprocessed FastQ files", + "pattern": "*.{fq,fastq},{,.gz}" + } + } + ] + } + }, + { + "multiqc_files": { + "description": "MultiQC-compatible output files from tools used in preprocessing", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata for the MultiQC files" + } + }, + { + "mqc": { + "type": "file", + "description": "MultiQC-compatible files", + "pattern": "*" + } + } + ] + } + }, + { + "trim_read_count": { + "description": "Number of reads remaining after trimming for all input samples", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata for the trim read count" + } + }, + { + "count": { + "type": "integer", + "description": "Number of reads after trimming" + } + } + ] + } + }, + { + "lint_log": { + "description": "Log files from FastQ linting", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata for the lint log" + } + }, + { + "log": { + "type": "file", + "description": "FastQ lint log file", + "pattern": "*.log" + } + } + ] + } + }, + { + "fastqc_filtered_html": { + "description": "FastQC report HTML files for filtered reads (after BBSplit and/or rRNA removal)", + "structure": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "html": { + "type": "file", + "description": "FastQC report HTML file", + "pattern": "*.html" + } + } + ] + } + }, + { + "fastqc_filtered_zip": { + "description": "FastQC report ZIP files for filtered reads (after BBSplit and/or rRNA removal)", + "structure": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "zip": { + "type": "file", + "description": "FastQC report ZIP file", + "pattern": "*.zip" + } + } + ] + } + }, + { + "per_sample_mqc_bundle": { + "description": "Per-sample MultiQC-feeding outputs (FastQC raw/trim/filtered zips,\ntrim log/JSON, UMI log, BBSplit stats, SortMeRNA log, RiboDetector\nlog, SeqKit stats, Bowtie2 log) joined on meta.\n", + "structure": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "files": { + "type": "file", + "description": "List of MultiQC-relevant files for the sample" + } + } + ] + } + } + ], + "authors": ["@pinin4fjords"], + "maintainers": ["@pinin4fjords"] }, - { - "kraken_parse": { - "type": "file", - "description": "Sink TAXID count table in csv format", - "pattern": "*.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ], - { - "sources": { - "type": "file", - "description": "Sources TAXID count table in csv format. Default can be downloaded from https://raw.githubusercontent.com/maxibor/sourcepredict/master/data/modern_gut_microbiomes_sources.csv", - "pattern": "*.csv", - "ontologies": [ + "pipelines": [ { - "edam": "http://edamontology.org/format_3752" - } - ] - } - }, - { - "labels": { - "type": "file", - "description": "Labels for the sources table in csv format. Default can be downloaded from https://raw.githubusercontent.com/maxibor/sourcepredict/master/data/modern_gut_microbiomes_labels.csv", - "pattern": "*.csv", - "ontologies": [ + "name": "lncpipe", + "version": "dev" + }, + { + "name": "riboseq", + "version": "1.2.0" + }, { - "edam": "http://edamontology.org/format_3752" + "name": "rnaseq", + "version": "3.26.0" } - ] - } - }, - { - "taxa_sqlite": { - "type": "file", - "description": "taxa.sqlite file downloaded with ete3 toolkit", - "pattern": "taxa.sqlite", - "ontologies": [] - } - }, - { - "taxa_sqlite_traverse_pkl": { - "type": "file", - "description": "taxa.sqlite.traverse.pkl file downloaded with ete3 toolkit", - "pattern": "taxa.sqlite.traverse.pkl", - "ontologies": [] - } - } - ], - "output": { - "report": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.sourcepredict.csv": { - "type": "file", - "description": "Table containing the predicted proportion of each source in each sample", - "pattern": "*.sourcepredict.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "versions_sourcepredict": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "sourcepredict": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python -c \"import sourcepredict; print(sourcepredict.__version__)\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_python": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "python": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python -V | sed \"s/Python //g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_sklearn": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "sklearn": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python -c \"import sklearn; print(sklearn.__version__)\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "sourcepredict": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python -c \"import sourcepredict; print(sourcepredict.__version__)\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "python": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python -V | sed \"s/Python //g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "sklearn": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python -c \"import sklearn; print(sklearn.__version__)\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@MeriamOs" - ], - "maintainers": [ - "@MeriamOs" - ] - }, - "pipelines": [ - { - "name": "coproid", - "version": "2.0.1" - } - ] - }, - { - "name": "sourmash_compare", - "path": "modules/nf-core/sourmash/compare/meta.yml", - "type": "module", - "meta": { - "name": "sourmash_compare", - "description": "Compare many FracMinHash signatures generated by sourmash sketch.", - "keywords": [ - "compare", - "FracMinHash sketch", - "containment", - "sourmash", - "metagenomics", - "genomics", - "kmer" - ], - "tools": [ - { - "sourmash": { - "description": "Compute and compare FracMinHash signatures for DNA and protein data sets.", - "homepage": "https://sourmash.readthedocs.io/", - "documentation": "https://sourmash.readthedocs.io/", - "tool_dev_url": "https://github.com/sourmash-bio/sourmash", - "doi": "10.21105/joss.00027", - "licence": [ - "BSD-3-clause" - ], - "identifier": "biotools:sourmash" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "signatures": { - "type": "file", - "description": "Files containing signatures (hash sketches) of samples", - "pattern": "*.{sig}", - "ontologies": [] - } - } - ], - { - "file_list": { - "type": "file", - "description": "An optional file specifying a list of file paths that should be appended to the input signatures.\n", - "ontologies": [] - } - }, - { - "save_numpy_matrix": { - "type": "boolean", - "description": "If true, output will contain a (dis)similarity matrix numpy binary format.\nAt least one of save_numpy_matrix or save_csv is required.\n" - } - }, - { - "save_csv": { - "type": "boolean", - "description": "If true, output will contain a (dis)similarity matrix in CSV format\nAt least one of save_numpy_matrix or save_csv is required.\n" - } - } - ], - "output": { - "matrix": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*comp.npy": { - "type": "file", - "description": "An optional (dis)similarity matrix numpy binary format", - "pattern": "*.comp", - "ontologies": [] - } - } - ] - ], - "labels": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*comp.npy.labels.txt": { - "type": "file", - "description": "A text file that specifies the labels in the output numpy_matrix", - "pattern": "*.comp.labels.txt", - "ontologies": [] - } - } - ] - ], - "csv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*comp.csv": { - "type": "file", - "description": "An optional (dis)similarity matrix in CSV format", - "pattern": "*.comp.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "versions_sourmash": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "sourmash": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "sourmash --version 2>&1 | sed 's/^sourmash //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "sourmash": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "sourmash --version 2>&1 | sed 's/^sourmash //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@taylorreiter" - ], - "maintainers": [ - "@taylorreiter" - ] - }, - "pipelines": [ - { - "name": "pathogensurveillance", - "version": "1.1.0" - } - ] - }, - { - "name": "sourmash_gather", - "path": "modules/nf-core/sourmash/gather/meta.yml", - "type": "module", - "meta": { - "name": "sourmash_gather", - "description": "Search a metagenome sourmash signature against one or many reference databases and return the minimum set of genomes that contain the k-mers in the metagenome.", - "keywords": [ - "FracMinHash sketch", - "signature", - "kmer", - "containment", - "sourmash", - "genomics", - "metagenomics", - "taxonomic classification", - "taxonomic profiling" - ], - "tools": [ - { - "sourmash": { - "description": "Compute and compare FracMinHash signatures for DNA data sets.", - "homepage": "https://sourmash.readthedocs.io/", - "documentation": "https://sourmash.readthedocs.io/", - "tool_dev_url": "https://github.com/sourmash-bio/sourmash", - "doi": "10.21105/joss.00027", - "licence": [ - "BSD-3-clause" - ], - "identifier": "biotools:sourmash" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "signature": { - "type": "file", - "description": "File containing signatures (hash sketches) of a sample", - "pattern": "*.{sig}", - "ontologies": [] - } - } - ], - { - "database": { - "type": "file", - "description": "database", - "ontologies": [] - } - }, - { - "save_unassigned": { - "type": "boolean", - "description": "If true, output will contain a file that is a sourmash signature containing the unassigned hashes from the query\n" - } - }, - { - "save_matches_sig": { - "type": "boolean", - "description": "If true, output will contain a file that is a sourmash signature composed of the FracMinHash sketches that were matched in the database and that matched the query\n" - } - }, - { - "save_prefetch": { - "type": "boolean", - "description": "If true, output will contain a file with all prefetch-matched signatures from the database\n" - } - }, - { - "save_prefetch_csv": { - "type": "boolean", - "description": "If true, output will contain a csv file with the names of all prefetch-matched signatures\n" - } - } - ], - "output": { - "result": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.csv.gz": { - "type": "file", - "description": "Table with signatures classified as belonging to any of the genomes\nin the sourmash database(s).\n", - "pattern": "*{csv.gz}", - "ontologies": [] - } - } - ] - ], - "unassigned": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_unassigned.sig.zip": { - "type": "file", - "description": "A FracMinHash sketch containing hashes (k-mers) that did not match to any of the genomes\nin the sourmash database(s).\n", - "pattern": "*{sig.zip}", - "ontologies": [] - } - } - ] - ], - "matches": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_matches.sig.zip": { - "type": "file", - "description": "A signature containing FracMinHash sketches of genomes\nin the sourmash database.\n", - "pattern": "*{sig.zip}", - "ontologies": [] - } - } - ] - ], - "prefetch": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_prefetch.sig.zip": { - "type": "file", - "description": "All prefetch-matched signatures from the database.\n", - "pattern": "*{sig.zip}", - "ontologies": [] - } - } - ] - ], - "prefetchcsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_prefetch.csv.gz": { - "type": "file", - "description": "The names of all prefetch-matched signatures from the database in CSV format.\n", - "pattern": "*{csv.gz}", - "ontologies": [] - } - } - ] - ], - "versions_sourmash": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "sourmash": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "sourmash --version 2>&1 | sed 's/^sourmash //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "sourmash": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "sourmash --version 2>&1 | sed 's/^sourmash //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@vmikk", - "@taylorreiter" - ], - "maintainers": [ - "@vmikk", - "@taylorreiter" - ] - }, - "pipelines": [ - { - "name": "magmap", - "version": "1.0.0" - } - ] - }, - { - "name": "sourmash_index", - "path": "modules/nf-core/sourmash/index/meta.yml", - "type": "module", - "meta": { - "name": "sourmash_index", - "description": "Create a database of sourmash signatures (a group of FracMinHash sketches) to be used as references.", - "keywords": [ - "signatures", - "sourmash", - "genomics", - "metagenomics", - "mapping", - "kmer" - ], - "tools": [ - { - "sourmash": { - "description": "Compute and compare FracMinHash signatures for DNA data sets.", - "homepage": "https://sourmash.readthedocs.io/", - "documentation": "https://sourmash.readthedocs.io/", - "tool_dev_url": "https://github.com/sourmash-bio/sourmash", - "doi": "10.21105/joss.00027", - "licence": [ - "BSD-3-clause" - ], - "identifier": "biotools:sourmash" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "signatures": { - "type": "file", - "description": "Files containing signature (hash sketches) of reference genomes", - "pattern": "*.{sig}", - "ontologies": [] - } - } - ], - { - "ksize": { - "type": "integer", - "description": "ksize value" - } - } - ], - "output": { - "signature_index": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.sbt.zip": { - "type": "file", - "description": "Database of signatures", - "pattern": "*.{sbt.zip}", - "ontologies": [] - } - } - ] - ], - "versions_sourmash": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "sourmash": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "sourmash --version 2>&1 | sed 's/^sourmash //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "sourmash": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "sourmash --version 2>&1 | sed 's/^sourmash //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@emnilsson" - ], - "maintainers": [ - "@emnilsson" - ] - }, - "pipelines": [ - { - "name": "createtaxdb", - "version": "3.0.0" - }, - { - "name": "magmap", - "version": "1.0.0" - } - ] - }, - { - "name": "sourmash_sketch", - "path": "modules/nf-core/sourmash/sketch/meta.yml", - "type": "module", - "meta": { - "name": "sourmash_sketch", - "description": "Create a signature (a group of FracMinHash sketches) of a sequence using sourmash", - "keywords": [ - "hash sketch", - "sourmash", - "genomics", - "metagenomics", - "taxonomic classification", - "taxonomic profiling", - "kmer" - ], - "tools": [ - { - "sourmash": { - "description": "Compute and compare FracMinHash signatures for DNA and protein data sets.", - "homepage": "https://sourmash.readthedocs.io/", - "documentation": "https://sourmash.readthedocs.io/", - "tool_dev_url": "https://github.com/sourmash-bio/sourmash", - "doi": "10.21105/joss.00027", - "licence": [ - "BSD-3-clause" - ], - "identifier": "biotools:sourmash" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "library": { - "type": "file", - "description": "One or more FASTA or FASTQ file(s) containing (genomic, transcriptomic, or proteomic) sequence data", - "pattern": "*.{fna,fa,fasta,fastq,fq,faa}.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "output": { - "signatures": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.sig": { - "type": "file", - "description": "FracMinHash signature of the given sequence", - "pattern": "*.{sig}", - "ontologies": [] - } - } ] - ], - "versions_sourmash": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "sourmash": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "sourmash --version 2>&1 | sed 's/^sourmash //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "sourmash": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "sourmash --version 2>&1 | sed 's/^sourmash //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@Midnighter" - ], - "maintainers": [ - "@Midnighter" - ] - }, - "pipelines": [ - { - "name": "createtaxdb", - "version": "3.0.0" }, { - "name": "magmap", - "version": "1.0.0" - }, - { - "name": "pathogensurveillance", - "version": "1.1.0" - } - ] - }, - { - "name": "sourmash_taxannotate", - "path": "modules/nf-core/sourmash/taxannotate/meta.yml", - "type": "module", - "meta": { - "name": "sourmash_taxannotate", - "description": "Annotate list of metagenome members (based on sourmash signature matches) with taxonomic information.", - "keywords": [ - "fracminhash sketch", - "signature", - "kmer", - "containment", - "sourmash", - "genomics", - "metagenomics", - "taxonomic classification", - "taxonomic profiling" - ], - "tools": [ - { - "sourmash": { - "description": "Compute and compare FracMinHash signatures for DNA data sets.", - "homepage": "https://sourmash.readthedocs.io/", - "documentation": "https://sourmash.readthedocs.io/", - "tool_dev_url": "https://github.com/sourmash-bio/sourmash", - "doi": "10.21105/joss.00027", - "licence": [ - "BSD-3-clause" - ], - "identifier": "biotools:sourmash" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "gather_results": { - "type": "file", - "description": "Mandatory table with signatures classified as belonging to any of the genomes\nin the sourmash database(s), result of `sourmash gather` command.\n", - "ontologies": [] - } - } - ], - { - "taxonomy": { - "type": "file", - "description": "One or more databases with lineages (in CSV format, Mandatory)", - "ontologies": [] - } - } - ], - "output": { - "result": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.with-lineages.csv.gz": { - "type": "file", - "description": "Table with signatures classified as belonging to any of the genomes\nin the sourmash database(s) with an additional 'lineage' column\ncontaining the taxonomic information for each database match.\n", - "pattern": "*{csv.gz}", - "ontologies": [] - } - } - ] - ], - "versions_sourmash": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "sourmash": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "sourmash --version 2>&1 | sed 's/^sourmash //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "sourmash": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "sourmash --version 2>&1 | sed 's/^sourmash //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@vmikk", - "@taylorreiter" - ], - "maintainers": [ - "@vmikk", - "@taylorreiter" - ] - } - }, - { - "name": "spaceranger_count", - "path": "modules/nf-core/spaceranger/count/meta.yml", - "type": "module", - "meta": { - "name": "spaceranger_count", - "description": "Module to use the 10x Space Ranger pipeline to process 10x spatial transcriptomics data", - "keywords": [ - "align", - "count", - "spatial", - "spaceranger", - "imaging" - ], - "tools": [ - { - "spaceranger": { - "description": "Visium Spatial Gene Expression is a next-generation molecular profiling solution for classifying tissue\nbased on total mRNA. Space Ranger is a set of analysis pipelines that process Visium Spatial Gene Expression\ndata with brightfield and fluorescence microscope images. Space Ranger allows users to map the whole\ntranscriptome in formalin fixed paraffin embedded (FFPE) and fresh frozen tissues to discover novel\ninsights into normal development, disease pathology, and clinical translational research. Space Ranger provides\npipelines for end to end analysis of Visium Spatial Gene Expression experiments.\n", - "homepage": "https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger", - "documentation": "https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger", - "tool_dev_url": "https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger", - "licence": [ - "10x Genomics EULA" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', slide:'10L13-020', area: 'B1']\n\n`id`, `slide` and `area` are mandatory information!\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", - "pattern": "${Sample_Name}_S1_L00${Lane_Number}_${I1,I2,R1,R2}_001.fastq.gz", - "ontologies": [] - } - }, - { - "image": { - "type": "file", - "description": "Brightfield tissue H&E image in JPEG or TIFF format.", - "pattern": "*.{tif,tiff,jpg,jpeg}", - "ontologies": [] - } - }, - { - "slide": { - "type": "string", - "description": "Visium slide ID used for the sample." - } - }, - { - "area": { - "type": "string", - "description": "Visium slide capture area used for the sample." - } - }, - { - "cytaimage": { - "type": "file", - "description": "CytAssist instrument captured eosin stained Brightfield tissue image with fiducial\nframe in TIFF format. The size of this image is set at 3k in both dimensions and this image should\nnot be modified any way before passing it as input to either Space Ranger or Loupe Browser.\n", - "pattern": "*.{tif,tiff}", - "ontologies": [] - } - }, - { - "darkimage": { - "type": "file", - "description": "Optional for dark background fluorescence microscope image input. Multi-channel, dark-background fluorescence\nimage as either a single, multi-layer TIFF file or as multiple TIFF or JPEG files.\n", - "pattern": "*.{tif,tiff,jpg,jpeg}", - "ontologies": [] - } - }, - { - "colorizedimage": { - "type": "file", - "description": "Required for color composite fluorescence microscope image input.\nA color composite of one or more fluorescence image channels saved as a single-page,\nsingle-file color TIFF or JPEG.\n", - "pattern": "*.{tif,tiff,jpg,jpeg}", - "ontologies": [] - } - }, - { - "alignment": { - "type": "file", - "description": "OPTIONAL - Path to manual image alignment.", - "pattern": "*.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } + "name": "fastq_remove_rrna", + "path": "subworkflows/nf-core/fastq_remove_rrna/meta.yml", + "type": "subworkflow", + "meta": { + "name": "fastq_remove_rrna", + "description": "Remove ribosomal RNA reads from FASTQ files using SortMeRNA, RiboDetector, or Bowtie2", + "keywords": ["fastq", "rrna", "ribosomal", "filter", "sortmerna", "ribodetector", "bowtie2"], + "components": [ + "bowtie2/align", + "bowtie2/build", + "ribodetector", + "samtools/fastq", + "samtools/view", + "seqkit/replace", + "seqkit/stats", + "sortmerna" + ], + "input": [ + { + "ch_reads": { + "type": "file", + "description": "List of FastQ files of size 1 and 2 for single-end and paired-end data, respectively.\n", + "structure": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]" + } + }, + { + "reads": { + "type": "file", + "description": "FastQ files", + "pattern": "*.{fq,fastq}{,.gz}" + } + } + ] + } + }, + { + "ch_rrna_fastas": { + "type": "file", + "description": "Channel containing one or more FASTA files with rRNA sequences for use with SortMeRNA or Bowtie2.\nNot required for RiboDetector which uses built-in models.\n", + "structure": [ + { + "fasta": { + "type": "file", + "description": "rRNA reference fasta files", + "pattern": "*.{fa,fasta}{,.gz}" + } + } + ] + } + }, + { + "ch_sortmerna_index": { + "type": "directory", + "description": "Pre-built SortMeRNA index directory. Optional - can be built on-the-fly if make_sortmerna_index is true.\n", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata for the SortMeRNA index" + } + }, + { + "index": { + "type": "directory", + "description": "SortMeRNA index directory" + } + } + ] + } + }, + { + "ch_bowtie2_index": { + "type": "directory", + "description": "Pre-built Bowtie2 index directory. Optional - can be built on-the-fly if make_bowtie2_index is true.\n", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata for the Bowtie2 index" + } + }, + { + "index": { + "type": "directory", + "description": "Bowtie2 index directory" + } + } + ] + } + }, + { + "ribo_removal_tool": { + "type": "string", + "description": "Specifies the rRNA removal tool to use", + "enum": ["sortmerna", "ribodetector", "bowtie2"] + } + }, + { + "make_sortmerna_index": { + "type": "boolean", + "description": "Whether to create SortMeRNA index before running SortMeRNA" + } + }, + { + "make_bowtie2_index": { + "type": "boolean", + "description": "Whether to create Bowtie2 index before running Bowtie2 for rRNA removal" + } + } + ], + "output": [ + { + "reads": { + "type": "file", + "description": "FASTQ files with rRNA reads removed.\n", + "structure": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "reads": { + "type": "file", + "description": "Filtered FastQ files", + "pattern": "*.{fq,fastq}{,.gz}" + } + } + ] + } + }, + { + "multiqc_files": { + "type": "file", + "description": "Log files from the rRNA removal tool, compatible with MultiQC.\n", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata for the log files" + } + }, + { + "log": { + "type": "file", + "description": "Tool-specific log files", + "pattern": "*.log" + } + } + ] + } + } + ], + "authors": ["@pinin4fjords"], + "maintainers": ["@pinin4fjords"] }, - { - "slidefile": { - "type": "file", - "description": "OPTIONAL - Path to slide specifications.", - "pattern": "*.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ], - { - "reference": { - "type": "directory", - "description": "Folder containing all the reference indices needed by Space Ranger" - } - }, - { - "probeset": { - "type": "file", - "description": "OPTIONAL - Probe set specification.", - "pattern": "*.csv", - "ontologies": [ + "pipelines": [ { - "edam": "http://edamontology.org/format_3752" + "name": "rnaseq", + "version": "3.26.0" } - ] - } - } - ], - "output": { - "outs": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "outs/**": { - "type": "file", - "description": "Files containing the outputs of Space Ranger, see official 10X Genomics documentation for a complete list", - "pattern": "outs/*", - "ontologies": [] - } - } - ] - ], - "versions_spaceranger": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "spaceranger": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "spaceranger -V | sed \"s/spaceranger spaceranger-//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "spaceranger": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "spaceranger -V | sed \"s/spaceranger spaceranger-//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] }, - "authors": [ - "@grst" - ], - "maintainers": [ - "@grst", - "@fasterius" - ] - }, - "pipelines": [ { - "name": "sopa", - "version": "dev" - }, - { - "name": "spatialvi", - "version": "dev" - } - ] - }, - { - "name": "spaceranger_mkgtf", - "path": "modules/nf-core/spaceranger/mkgtf/meta.yml", - "type": "module", - "meta": { - "name": "spaceranger_mkgtf", - "description": "Module to build a filtered GTF needed by the 10x Genomics Space Ranger tool. Uses the spaceranger mkgtf command.", - "keywords": [ - "reference", - "mkref", - "index", - "spaceranger" - ], - "tools": [ - { - "spaceranger": { - "description": "Visium Spatial Gene Expression is a next-generation molecular profiling solution for classifying tissue\nbased on total mRNA. Space Ranger is a set of analysis pipelines that process Visium Spatial Gene Expression\ndata with brightfield and fluorescence microscope images. Space Ranger allows users to map the whole\ntranscriptome in formalin fixed paraffin embedded (FFPE) and fresh frozen tissues to discover novel\ninsights into normal development, disease pathology, and clinical translational research. Space Ranger provides\npipelines for end to end analysis of Visium Spatial Gene Expression experiments.\n", - "homepage": "https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger", - "documentation": "https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger", - "tool_dev_url": "https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger", - "licence": [ - "10x Genomics EULA" - ], - "identifier": "" - } - } - ], - "input": [ - { - "gtf": { - "type": "file", - "description": "The reference GTF transcriptome file", - "pattern": "*.gtf", - "ontologies": [] - } - } - ], - "output": { - "gtf": [ - { - "*.gtf": { - "type": "directory", - "description": "The filtered GTF transcriptome file", - "pattern": "*.filtered.gtf" - } - } - ], - "versions_spaceranger": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "spaceranger": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "spaceranger -V | sed \"s/spaceranger spaceranger-//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "spaceranger": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "spaceranger -V | sed \"s/spaceranger spaceranger-//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@grst" - ], - "maintainers": [ - "@grst", - "@fasterius" - ] - } - }, - { - "name": "spaceranger_mkref", - "path": "modules/nf-core/spaceranger/mkref/meta.yml", - "type": "module", - "meta": { - "name": "spaceranger_mkref", - "description": "Module to build the reference needed by the 10x Genomics Space Ranger tool. Uses the spaceranger mkref command.", - "keywords": [ - "reference", - "mkref", - "index", - "spaceranger" - ], - "tools": [ - { - "spaceranger": { - "description": "Visium Spatial Gene Expression is a next-generation molecular profiling solution for classifying tissue\nbased on total mRNA. Space Ranger is a set of analysis pipelines that process Visium Spatial Gene Expression\ndata with brightfield and fluorescence microscope images. Space Ranger allows users to map the whole\ntranscriptome in formalin fixed paraffin embedded (FFPE) and fresh frozen tissues to discover novel\ninsights into normal development, disease pathology, and clinical translational research. Space Ranger provides\npipelines for end to end analysis of Visium Spatial Gene Expression experiments.\n", - "homepage": "https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger", - "documentation": "https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger", - "tool_dev_url": "https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger", - "licence": [ - "10x Genomics EULA" - ], - "identifier": "" - } - } - ], - "input": [ - { - "fasta": { - "type": "file", - "description": "Reference genome FASTA file", - "pattern": "*.{fasta,fa}", - "ontologies": [] - } - }, - { - "gtf": { - "type": "file", - "description": "Reference transcriptome GTF file", - "pattern": "*.gtf", - "ontologies": [] - } - }, - { - "reference_name": { - "type": "string", - "description": "The name to give the new reference folder", - "pattern": "str" + "name": "fastq_removeadapters_merge", + "path": "subworkflows/nf-core/fastq_removeadapters_merge/meta.yml", + "type": "subworkflow", + "meta": { + "name": "fastq_removeadapters_merge", + "description": "Remove adapters and merge reads based on various module choices", + "keywords": ["adapters", "removal", "short reads", "merge", "trim"], + "components": [ + "trimmomatic", + "cutadapt", + "trimgalore", + "bbmap/bbduk", + "leehom", + "fastp", + "adapterremoval", + "cat/fastq" + ], + "input": [ + { + "ch_input_reads": { + "type": "file", + "description": "List of FastQ files of size 1 and 2 for single-end and paired-end data, respectively.\nStructure: [ val(meta), [ path(reads) ] ]\n" + } + }, + { + "val_adapter_tool": { + "type": "string", + "description": "Choose one of the available adapter removal and/or merging tools\n", + "enum": [ + "trimmomatic", + "cutadapt", + "trimgalore", + "bbduk", + "leehom", + "fastp", + "adapterremoval" + ] + } + }, + { + "ch_custom_adapters_file": { + "type": "file", + "description": "Optional reference files, containing adapter and/or contaminant sequences for removal.\nIn fasta format for bbmap/bbduk and fastp, or in text format for AdapterRemoval (one adapter per line).\n" + } + }, + { + "val_save_merged": { + "type": "boolean", + "description": "Specify true to output merged reads instead\nUsed by fastp and adapterremoval\n" + } + }, + { + "val_fastp_discard_trimmed_pass": { + "type": "boolean", + "description": "Used only by fastp.\nSpecify true to not write any reads that pass trimming thresholds from the fastp process.\nThis can be used to use fastp for the output report only.\n" + } + }, + { + "val_fastp_save_trimmed_fail": { + "type": "boolean", + "description": "Used only by fastp.\nSpecify true to save files that failed to pass fastp trimming thresholds\n" + } + } + ], + "output": [ + { + "processed_reads": { + "type": "file", + "description": "Structure: [ val(meta), path(fastq.gz) ]\nThe trimmed/modified single or paired end or merged fastq reads\n", + "pattern": "*.fastq.gz" + } + }, + { + "discarded_reads": { + "type": "file", + "description": "Structure: [ val(meta), path(fastq.gz) ]\nThe discarded reads\n", + "pattern": "*.fastq.gz" + } + }, + { + "logfile": { + "type": "file", + "description": "Execution log file\n(trimmomatic {log}, trimgalore {txt}, fastp {log})\n", + "pattern": "*.{log,txt}" + } + }, + { + "report": { + "type": "file", + "description": "Execution report\n(trimmomatic {summary}, trimgalore {html,zip}, fastp {html})\n", + "pattern": "*.{summary,html,zip}" + } + }, + { + "versions": { + "type": "file", + "description": "File containing software versions\nStructure: [ path(versions.yml) ]\n", + "pattern": "versions.yml" + } + }, + { + "multiqc_files": { + "type": "file", + "description": "MultiQC-compatible output files from tools used in preprocessing\n(trimmomatic, cutadapt, bbduk, leehom, fastp, adapterremoval)\n" + } + } + ], + "authors": ["@kornkv", "@vagkaratzas"], + "maintainers": ["@kornkv", "@vagkaratzas"] } - } - ], - "output": { - "reference": [ - { - "${reference_name}": { - "type": "directory", - "description": "Folder containing all the reference indices needed by Space Ranger" - } + }, + { + "name": "fastq_sanitise_seqkit", + "path": "subworkflows/nf-core/fastq_sanitise_seqkit/meta.yml", + "type": "subworkflow", + "meta": { + "name": "fastq_sanitise_seqkit", + "description": "Filters and reports malformed FASTQ sequences with seqkit/sana,\nand then pairs any paired-end files using seqkit/pair\n", + "keywords": [ + "fastq", + "quality control", + "filtering", + "malformed", + "pairing", + "seqkit", + "preprocessing" + ], + "components": ["seqkit/sana", "seqkit/pair"], + "input": [ + { + "ch_reads": { + "type": "channel", + "description": "Channel containing sample metadata and FASTQ files.\nStructure: [ val(meta), [ fastq ] ]\nWhere meta is a map containing at least:\n- id: sample identifier\n- single_end: boolean indicating if data is single-end (true) or paired-end (false)\n", + "pattern": "*.{fastq,fastq.gz,fq,fq.gz}" + } + } + ], + "output": [ + { + "reads": { + "type": "channel", + "description": "Channel containing filtered (i.e., non-malformed) and paired FASTQ files.\nFor single-end data: returns filtered reads\nFor paired-end data: returns properly paired reads and any unpaired reads\nStructure: [ val(meta), [ fastq ] ]\n", + "pattern": "*.{fastq,fastq.gz,fq,fq.gz}" + } + }, + { + "versions": { + "type": "file", + "description": "File containing software versions\nStructure: [ path(versions.yml) ]\n", + "pattern": "versions.yml" + } + } + ], + "authors": ["@vagkaratzas"], + "maintainers": ["@vagkaratzas"] } - ], - "versions_spaceranger": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "spaceranger": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "spaceranger -V | sed \"s/spaceranger spaceranger-//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "spaceranger": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "spaceranger -V | sed \"s/spaceranger spaceranger-//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@grst" - ], - "maintainers": [ - "@grst", - "@fasterius" - ] - } - }, - { - "name": "spades", - "path": "modules/nf-core/spades/meta.yml", - "type": "module", - "meta": { - "name": "spades", - "description": "Assembles a small genome (bacterial, fungal, viral)", - "keywords": [ - "genome", - "assembly", - "genome assembler", - "small genome", - "de novo assembler" - ], - "tools": [ - { - "spades": { - "description": "SPAdes (St. Petersburg genome assembler) is intended for both standard isolates and single-cell MDA bacteria assemblies.", - "homepage": "http://cab.spbu.ru/files/release3.15.0/manual.html", - "documentation": "http://cab.spbu.ru/files/release3.15.0/manual.html", - "tool_dev_url": "https://github.com/ablab/spades", - "doi": "10.1089/cmb.2012.0021", - "licence": [ - "GPL v2" - ], - "identifier": "" + }, + { + "name": "fastq_shortreads_preprocess_qc", + "path": "subworkflows/nf-core/fastq_shortreads_preprocess_qc/meta.yml", + "type": "subworkflow", + "meta": { + "name": "fastq_shortreads_preprocess_qc", + "description": "Quality check and preprocessing subworkflow of Illumina short reads\nthat can do: quality check of input reads and generate statistics,\npreprocess and validate reads, barcode removal, remove adapters and merge reads,\nfilter by sequence complexity, deduplicate reads, remove host contamination,\nconcatenate reads and generate statistics for post-processing reads.\nWARNING: requires at least the process configurations from the nextflow.config\nto be added to the modules.config in the pipeline in order to work as intended.\n", + "keywords": [ + "fastq", + "illumina", + "short", + "reads", + "qc", + "stats", + "preprocessing", + "barcoding", + "adapters", + "merge", + "complexity", + "deduplication", + "host", + "decontamination" + ], + "components": [ + "fastq_qc_stats", + "fastqc", + "seqfu/check", + "seqfu/stats", + "seqkit/stats", + "seqtk/comp", + "fastq_preprocess_seqkit", + "fastq_sanitise_seqkit", + "seqkit/sana", + "seqkit/pair", + "seqkit/seq", + "seqkit/replace", + "seqkit/rmdup", + "umitools/extract", + "fastq_removeadapters_merge", + "trimmomatic", + "cutadapt", + "trimgalore", + "bbmap/bbduk", + "leehom", + "fastp", + "adapterremoval", + "cat/fastq", + "fastq_complexity_filter", + "prinseqplusplus", + "bbmap/clumpify", + "fastq_decontaminate_deacon_hostile", + "fastq_index_filter_deacon", + "fastq_fetch_clean_hostile", + "hostile/fetch", + "hostile/clean", + "bowtie2/build", + "deacon/filter", + "deacon/index" + ], + "input": [ + { + "ch_reads": { + "type": "file", + "description": "List of FastQ files of size 1 and 2 for single-end and paired-end data, respectively.\nStructure: [ val(meta), [ path(reads) ] ]\n", + "pattern": "*.fastq.gz" + } + }, + { + "skip_fastqc": { + "type": "boolean", + "description": "Skip FastQC quality control step\n" + } + }, + { + "skip_seqfu_check": { + "type": "boolean", + "description": "Skip SeqFu check step\n" + } + }, + { + "skip_seqfu_stats": { + "type": "boolean", + "description": "Skip SeqFu statistics step\n" + } + }, + { + "skip_seqkit_stats": { + "type": "boolean", + "description": "Skip SeqKit statistics step\n" + } + }, + { + "skip_seqtk_comp": { + "type": "boolean", + "description": "Skip SeqTk composition analysis step\n" + } + }, + { + "skip_seqkit_sana_pair": { + "type": "boolean", + "description": "Skip SeqKit sanitize and pair step\n" + } + }, + { + "skip_seqkit_seq": { + "type": "boolean", + "description": "Skip SeqKit sequence processing step\n" + } + }, + { + "skip_seqkit_replace": { + "type": "boolean", + "description": "Skip SeqKit replace step\n" + } + }, + { + "skip_seqkit_rmdup": { + "type": "boolean", + "description": "Skip SeqKit remove duplicates step\n" + } + }, + { + "skip_umitools_extract": { + "type": "boolean", + "description": "Skip UMI-tools extract barcoding step\n" + } + }, + { + "val_umi_discard_read": { + "type": "integer", + "description": "Discard R1 or R2 after UMI extraction (0 = keep both, 1 = discard R1, 2 = discard R2)\n" + } + }, + { + "skip_adapterremoval": { + "type": "boolean", + "description": "Skip the adapter removal and merge subworkflow completely\n" + } + }, + { + "val_adapter_tool": { + "type": "string", + "description": "Choose one of the available adapter removal and/or merging tools\n", + "enum": [ + "trimmomatic", + "cutadapt", + "trimgalore", + "bbduk", + "leehom", + "fastp", + "adapterremoval" + ] + } + }, + { + "ch_custom_adapters_file": { + "type": "file", + "description": "Optional reference files, containing adapter and/or contaminant sequences for removal.\nIn fasta format for bbmap/bbduk and fastp, or in text format for AdapterRemoval (one adapter per line).\n" + } + }, + { + "val_save_merged": { + "type": "boolean", + "description": "Specify true to output merged reads instead\nUsed by fastp and adapterremoval\n" + } + }, + { + "val_fastp_discard_trimmed_pass": { + "type": "boolean", + "description": "Used only by fastp.\nSpecify true to not write any reads that pass trimming thresholds from the fastp process.\nThis can be used to use fastp for the output report only.\n" + } + }, + { + "val_fastp_save_trimmed_fail": { + "type": "boolean", + "description": "Used only by fastp.\nSpecify true to save files that failed to pass fastp trimming thresholds\n" + } + }, + { + "skip_complexity_filtering": { + "type": "boolean", + "description": "Skip PRINSEQ++ complexity filtering step\n" + } + }, + { + "val_complexity_filter_tool": { + "type": "string", + "description": "Complexity filtering tool to use.\nMust be one of: 'prinseqplusplus', 'bbduk', or 'fastp'.\n" + } + }, + { + "skip_deduplication": { + "type": "boolean", + "description": "Skip BBMap Clumpify deduplication step\n" + } + }, + { + "skip_decontamination": { + "type": "boolean", + "description": "Skip host decontamination step\n" + } + }, + { + "ch_decontamination_fasta": { + "type": "file", + "description": "Reference genome FASTA file for decontamination (optional)\nStructure: [ val(meta), [ path(fasta) ] ]\n", + "pattern": "*.{fasta,fa,fna}" + } + }, + { + "ch_decontamination_reference": { + "type": "directory", + "description": "Pre-built reference index directory for decontamination (optional)\nStructure: [ val(reference_name), path(reference_dir) ]\n" + } + }, + { + "val_decontamination_index_name": { + "type": "string", + "description": "Name for the decontamination index (optional)\n" + } + }, + { + "val_decontamination_tool": { + "type": "string", + "description": "Decontamination tool to use ('hostile' or 'deacon')\n" + } + }, + { + "skip_final_concatenation": { + "type": "boolean", + "description": "Skip final FASTQ concatenation step\n" + } + } + ], + "output": [ + { + "reads": { + "type": "file", + "description": "Channel containing processed short reads\nStructure: [ val(meta), path(reads) ]\n", + "pattern": "*.fastq.gz" + } + }, + { + "pre_stats_fastqc_html": { + "type": "file", + "description": "FastQC HTML reports for pre-processing reads\nStructure: [ val(meta), path(html) ]\n", + "pattern": "*.html" + } + }, + { + "pre_stats_fastqc_zip": { + "type": "file", + "description": "FastQC ZIP archives for pre-processing reads\nStructure: [ val(meta), path(zip) ]\n", + "pattern": "*.zip" + } + }, + { + "pre_stats_seqfu_check": { + "type": "file", + "description": "SeqFu check results for pre-processing reads\nStructure: [ val(meta), path(check) ]\n" + } + }, + { + "pre_stats_seqfu_stats": { + "type": "file", + "description": "SeqFu statistics for pre-processing reads\nStructure: [ val(meta), path(stats) ]\n" + } + }, + { + "pre_stats_seqfu_multiqc": { + "type": "file", + "description": "SeqFu MultiQC-compatible stats for pre-processing reads\nStructure: [ val(meta), path(multiqc) ]\n" + } + }, + { + "pre_stats_seqkit_stats": { + "type": "file", + "description": "SeqKit statistics for pre-processing reads\nStructure: [ val(meta), path(stats) ]\n" + } + }, + { + "pre_stats_seqtk_stats": { + "type": "file", + "description": "SeqTk composition statistics for pre-processing reads\nStructure: [ val(meta), path(stats) ]\n" + } + }, + { + "post_stats_fastqc_html": { + "type": "file", + "description": "FastQC HTML reports for post-processing reads\nStructure: [ val(meta), path(html) ]\n", + "pattern": "*.html" + } + }, + { + "post_stats_fastqc_zip": { + "type": "file", + "description": "FastQC ZIP archives for post-processing reads\nStructure: [ val(meta), path(zip) ]\n", + "pattern": "*.zip" + } + }, + { + "post_stats_seqfu_check": { + "type": "file", + "description": "SeqFu check results for post-processing reads\nStructure: [ val(meta), path(check) ]\n" + } + }, + { + "post_stats_seqfu_stats": { + "type": "file", + "description": "SeqFu statistics for post-processing reads\nStructure: [ val(meta), path(stats) ]\n" + } + }, + { + "post_stats_seqfu_multiqc": { + "type": "file", + "description": "SeqFu MultiQC-compatible stats for post-processing reads\nStructure: [ val(meta), path(multiqc) ]\n" + } + }, + { + "post_stats_seqkit_stats": { + "type": "file", + "description": "SeqKit statistics for post-processing reads\nStructure: [ val(meta), path(stats) ]\n" + } + }, + { + "post_stats_seqtk_stats": { + "type": "file", + "description": "SeqTk composition statistics for post-processing reads\nStructure: [ val(meta), path(stats) ]\n" + } + }, + { + "umi_log": { + "type": "file", + "description": "UMI-tools extract log file\nStructure: [ val(meta), path(log) ]\n" + } + }, + { + "adapterremoval_discarded_reads": { + "type": "file", + "description": "Reads discarded during adapter removal or merging\nStructure: [ val(meta), path(fastq) ]\n", + "pattern": "*.fastq.gz" + } + }, + { + "adapterremoval_logfile": { + "type": "file", + "description": "Adapter removal execution log file\n(trimmomatic {log}, trimgalore {txt}, fastp {log})\nStructure: [ val(meta), path({log,txt}) ]\n" + } + }, + { + "adapterremoval_report": { + "type": "file", + "description": "Adapter removal report\n(trimmomatic {summary}, trimgalore {html,zip}, fastp {html})\nStructure: [ val(meta), path({summary,html,zip}) ]\n" + } + }, + { + "complexity_filter_log": { + "type": "file", + "description": "Log file from complexity filtering\nStructure: [ val(meta), path(log) ]\n" + } + }, + { + "complexity_filter_report": { + "type": "file", + "description": "Report generated by complexity filtering\nHTML report generated by fastp. Empty for other tools.\nStructure: [ val(meta), path(html) ]\n" + } + }, + { + "clumpify_log": { + "type": "file", + "description": "BBMap Clumpify log file\nStructure: [ val(meta), path(log) ]\n" + } + }, + { + "hostile_reference": { + "type": "file", + "description": "Hostile reference files used for decontamination\nStructure: [ val(reference_name), path(reference_dir) ]\n" + } + }, + { + "hostile_json": { + "type": "file", + "description": "Hostile JSON report\nStructure: [ val(meta), path(json) ]\n" + } + }, + { + "deacon_index": { + "type": "directory", + "description": "Deacon index directory\nStructure: [ val(meta), path(index) ]\n" + } + }, + { + "deacon_summary": { + "type": "file", + "description": "Deacon decontamination summary file\nStructure: [ val(meta), path(log) ]\n" + } + }, + { + "multiqc_files": { + "type": "file", + "description": "MultiQC compatible files for aggregated reporting\nStructure: [ path(files) ]\n" + } + }, + { + "versions": { + "type": "file", + "description": "File containing software versions\nStructure: [ path(versions.yml) ]\n", + "pattern": "versions.yml" + } + } + ], + "authors": ["@vagkaratzas"], + "maintainers": ["@vagkaratzas"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "illumina": { - "type": "file", - "description": "List of input FastQ (Illumina or PacBio CCS reads) files\nof size 1 and 2 for single-end and paired-end data,\nrespectively. This input data type is required.\n", - "ontologies": [] - } - }, - { - "pacbio": { - "type": "file", - "description": "List of input PacBio CLR FastQ files of size 1.\n", - "ontologies": [] - } + }, + { + "name": "fastq_subsample_fq_salmon", + "path": "subworkflows/nf-core/fastq_subsample_fq_salmon/meta.yml", + "type": "subworkflow", + "meta": { + "name": "fastq_subsample_fq_salmon", + "description": "Subsample fastq", + "keywords": ["fastq", "subsample", "strandedness"], + "components": ["fq/subsample", "salmon/quant", "salmon/index"], + "input": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "ch_reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" + } + }, + { + "ch_genome_fasta": { + "type": "file", + "description": "Genome fasta file", + "pattern": "Path to genome sequence in fasta format" + } + }, + { + "ch_transcript_fasta": { + "type": "file", + "description": "Transcript fasta file", + "pattern": "Path to transcript sequence in fasta format" + } + }, + { + "ch_gtf": { + "type": "file", + "description": "GTF features file", + "pattern": "Path features in GTF format" + } + }, + { + "ch_index": { + "type": "file", + "description": "Salmon index files", + "pattern": "Directory containing Salmon index" + } + }, + { + "make_index": { + "type": "boolean", + "description": "Whether to create salmon index before running salmon quant" + } + } + ], + "output": [ + { + "index": { + "type": "directory", + "description": "Directory containing salmon index", + "pattern": "salmon" + } + }, + { + "reads": { + "type": "file", + "description": "Subsampled fastq reads.", + "pattern": "*.{fq,fastq}{,.gz}" + } + }, + { + "results": { + "type": "directory", + "description": "Folder containing the quantification results for a specific sample", + "pattern": "${prefix}" + } + }, + { + "json_info": { + "type": "file", + "description": "File containing meta information from Salmon quant\nWhich could be used to infer strandedness among other things\n", + "pattern": "*info.json" + } + } + ], + "authors": ["@robsyme", "@drpatelh"], + "maintainers": ["@robsyme", "@drpatelh"] }, - { - "nanopore": { - "type": "file", - "description": "List of input FastQ files of size 1, originating from Oxford Nanopore technology.\n", - "ontologies": [] - } - } - ], - { - "yml": { - "type": "file", - "description": "Path to yml file containing read information.\nThe raw FASTQ files listed in this YAML file MUST be supplied to the respective illumina/pacbio/nanopore input channel(s) _in addition_ to this YML.\nFile entries in this yml must contain only the file name and no paths.\n", - "pattern": "*.{yml,yaml}", - "ontologies": [ + "pipelines": [ + { + "name": "lncpipe", + "version": "dev" + }, + { + "name": "riboseq", + "version": "1.2.0" + }, { - "edam": "http://edamontology.org/format_3750" + "name": "rnaseq", + "version": "3.26.0" } - ] - } - }, - { - "hmm": { - "type": "file", - "description": "File or directory with amino acid HMMs for Spades HMM-guided mode.", - "ontologies": [] - } - } - ], - "output": { - "scaffolds": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", - "pattern": "*.fa.gz" - } - }, - { - "*.scaffolds.fa.gz": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", - "pattern": "*.fa.gz" - } - } - ] - ], - "contigs": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", - "pattern": "*.fa.gz" - } - }, - { - "*.contigs.fa.gz": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", - "pattern": "*.fa.gz" - } - } - ] - ], - "transcripts": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", - "pattern": "*.fa.gz" - } - }, - { - "*.transcripts.fa.gz": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", - "pattern": "*.fa.gz" - } - } - ] - ], - "gene_clusters": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", - "pattern": "*.fa.gz" - } - }, - { - "*.gene_clusters.fa.gz": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", - "pattern": "*.fa.gz" - } - } ] - ], - "gfa": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", - "pattern": "*.fa.gz" - } - }, - { - "*.assembly.gfa.gz": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", - "pattern": "*.gfa.gz" - } - } - ] - ], - "warnings": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", - "pattern": "*.fa.gz" - } - }, - { - "*.warnings.log": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", - "pattern": "*.fa.gz" - } - }, - { - "*.spades.log": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", - "pattern": "*.spades.log" - } - } - ] - ], - "versions_spades": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "spades": { - "type": "string", - "description": "The tool name" - } - }, - { - "spades.py --version 2>&1 | sed -n 's/^.*SPAdes genome assembler v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "spades": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "spades.py --version 2>&1 | sed -n 's/^.*SPAdes genome assembler v//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] }, - "authors": [ - "@JoseEspinosa", - "@drpatelh", - "@d4straub" - ], - "maintainers": [ - "@JoseEspinosa", - "@drpatelh", - "@d4straub" - ] - }, - "pipelines": [ { - "name": "denovotranscript", - "version": "1.2.1" + "name": "fastq_taxonomic_profile_metaphlan", + "path": "subworkflows/nf-core/fastq_taxonomic_profile_metaphlan/meta.yml", + "type": "subworkflow", + "meta": { + "name": "fastq_taxonomic_profile_metaphlan", + "description": "Subworkflow to taxonomically classify metagenomic sequencing data using MetaPhlAn", + "keywords": ["metaphlan", "metagenomics", "database", "classification", "merge", "profiles"], + "components": ["metaphlan/makedb", "metaphlan/metaphlan", "metaphlan/mergemetaphlantables"], + "input": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:‘test’, single_end:false ]\n" + } + }, + { + "ch_fastq": { + "type": "file", + "description": "The input channel containing the FASTQ files\nStructure: [ val(meta), path(fastqs) ]\n", + "pattern": "*.{fastq/fastq.gz}" + } + } + ], + "output": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:‘test’, single_end:false ]\n" + } + }, + { + "versions": { + "type": "file", + "description": "File containing software versions\nStructure: [ path(versions.yml) ]\n", + "pattern": "versions.yml" + } + }, + { + "txt": { + "type": "file", + "description": "Combined MetaPhlAn table\nStructure: [ val(meta), path(txt) ]\n", + "pattern": "*.txt" + } + } + ], + "authors": ["@LaurenGonsalves", "@hhayden01", "@ErikLHendrickson", "@CarsonJM"], + "maintainers": ["@LaurenGonsalves", "@CarsonJM"] + } }, { - "name": "mag", - "version": "5.4.2" + "name": "fastq_trim_fastp_fastqc", + "path": "subworkflows/nf-core/fastq_trim_fastp_fastqc/meta.yml", + "type": "subworkflow", + "meta": { + "name": "fastq_trim_fastp_fastqc", + "description": "Read QC, fastp trimming and read qc", + "keywords": ["qc", "quality_control", "adapters", "trimming", "fastq"], + "components": ["fastqc", "fastp"], + "input": [ + { + "ch_reads": { + "type": "file", + "description": "Structure: [ val(meta), path (reads) ]\nGroovy Map containing sample information\ne.g. [ id:'test', single_end:false ], List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively. If you wish to run interleaved paired-end data, supply as single-end data\nbut with `--interleaved_in` in your `modules.conf`'s `ext.args` for the module.\n" + } + }, + { + "ch_adapter_fasta": { + "type": "file", + "description": "Structure: path(adapter_fasta)\nFile in FASTA format containing possible adapters to remove.\n" + } + }, + { + "val_save_trimmed_fail": { + "type": "boolean", + "description": "Structure: val(save_trimmed_fail)\nSpecify true to save files that failed to pass trimming thresholds ending in `*.fail.fastq.gz`\n" + } + }, + { + "val_discard_trimmed_pass": { + "type": "boolean", + "description": "Structure: val(discard_trimmed)\nSpecify true to not write any reads that pass trimming thresholds.\nThis can be used to use fastp for the output report only.\n" + } + }, + { + "val_save_merged": { + "type": "boolean", + "description": "Structure: val(save_merged)\nSpecify true to save all merged reads to the a file ending in `*.merged.fastq.gz`\n" + } + }, + { + "val_skip_fastqc": { + "type": "boolean", + "description": "Structure: val(skip_fastqc)\nskip the fastqc process if true\n" + } + }, + { + "val_skip_fastp": { + "type": "boolean", + "description": "Structure: val(skip_fastp)\nskip the fastp process if true\n" + } + } + ], + "output": [ + { + "meta": { + "type": "string", + "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]" + } + }, + { + "reads": { + "type": "file", + "description": "Structure: [ val(meta), path(reads) ]\nThe trimmed/modified/unmerged fastq reads\n" + } + }, + { + "trim_json": { + "type": "file", + "description": "Structure: [ val(meta), path(trim_json) ]\nResults in JSON format\n" + } + }, + { + "trim_html": { + "type": "file", + "description": "Structure: [ val(meta), path(trim_html) ]\nResults in HTML format\n" + } + }, + { + "trim_log": { + "type": "file", + "description": "Structure: [ val(meta), path(trim_log) ]\nfastq log file\n" + } + }, + { + "trim_reads_fail": { + "type": "file", + "description": "Structure: [ val(meta), path(trim_reads_fail) ]\nReads the failed the preprocessing\n" + } + }, + { + "trim_reads_merged": { + "type": "file", + "description": "Structure: [ val(meta), path(trim_reads_merged) ]\nReads that were successfully merged\n" + } + }, + { + "fastqc_raw_html": { + "type": "file", + "description": "Structure: [ val(meta), path(fastqc_raw_html) ]\nRaw fastQC report\n" + } + }, + { + "fastqc_raw_zip": { + "type": "file", + "description": "Structure: [ val(meta), path(fastqc_raw_zip) ]\nRaw fastQC report archive\n" + } + }, + { + "fastqc_trim_html": { + "type": "file", + "description": "Structure: [ val(meta), path(fastqc_trim_html) ]\nTrimmed fastQC report\n" + } + }, + { + "fastqc_trim_zip": { + "type": "file", + "description": "Structure: [ val(meta), path(fastqc_trim_zip) ]\nTrimmed fastQC report archive\n" + } + }, + { + "versions": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ], + "authors": ["@Joon-Klaps"], + "maintainers": ["@Joon-Klaps"] + }, + "pipelines": [ + { + "name": "bacass", + "version": "2.6.0" + }, + { + "name": "denovotranscript", + "version": "1.2.1" + } + ] }, { - "name": "metatdenovo", - "version": "1.3.0" + "name": "gtf_hybridmerge_gffcompare", + "path": "subworkflows/nf-core/gtf_hybridmerge_gffcompare/meta.yml", + "type": "subworkflow", + "meta": { + "name": "gtf_hybridmerge_gffcompare", + "description": "Build a hybrid GTF by classifying a novel-transcript GTF against a reference\nannotation with gffcompare, filtering the resulting annotated GTF down to a\nuser-supplied set of class codes (e.g. \"u\" for novel intergenic), optionally\nsubtracting features that overlap a user-supplied blacklist BED, and merging\nthe survivors into an annotation backbone GTF. Gene rows missing from the\nbackbone for surviving novel transcripts are synthesised with coordinates\nspanning the union of their child transcripts so the output is a\nself-consistent GTF.\n\nInput format scope: standard GTF2 with `gene_id` / `transcript_id`\nattributes in column 9 and `gene` / `transcript` (and child `exon` etc.)\nfeature types in column 3. GFF3 dialects (Parent= / ID= attributes) and\nprokaryotic GTFs without transcript rows are out of scope.\n\nResource sizing: GAWK steps hold the full input in memory under\n`process_single`. Fine for annotation-scale GTFs; for >~500 MB inputs\noverride `memory` / `cpus` directly via `withName`.\n", + "keywords": ["gtf", "annotation", "novel-transcripts", "gffcompare", "merge", "hybrid"], + "components": ["gffcompare", "gawk", "bedtools/intersect"], + "input": [ + { + "ch_novel_gtf": { + "type": "file", + "description": "Channel of novel-transcript GTFs (e.g. output of a StringTie merge or\na user-supplied annotation of unannotated transcribed regions) that\nwill be classified against the reference annotation. The subworkflow\nis designed for a single novel-vs-single-backbone build; if a caller\nhas multiple novel GTFs (one per sample, say) they should be merged\nbefore the call - the meta swap at the concat step adopts the\nbackbone meta and would collapse multiple emissions to the same id.\nStructure: [ val(meta), path(novel_gtf) ]\n", + "pattern": "*.{gtf,gff,gff3}" + } + }, + { + "ch_reference_gtf": { + "type": "file", + "description": "Channel containing the reference annotation GTF used by gffcompare to\ncompute class codes for every novel transcript. This drives which\ntranscripts survive the class-code filter, so callers usually want\nthe most complete annotation available here (not a subset such as a\ncanonical-only backbone).\nStructure: [ val(meta), path(reference_gtf) ]\n", + "pattern": "*.{gtf,gff,gff3}" + } + }, + { + "ch_backbone_gtf": { + "type": "file", + "description": "Channel containing the annotation GTF that surviving novel transcripts\nare merged into. The output is the concatenation of this backbone and\nthe filtered novel transcripts; missing gene rows are synthesised. For\ncallers that only have one annotation, pass the same channel as\nch_reference_gtf; callers that want the novel transcripts grafted onto\na reduced annotation (e.g. canonical-only) pass the reduced GTF here.\nStructure: [ val(meta), path(backbone_gtf) ]\n", + "pattern": "*.{gtf,gff,gff3}" + } + }, + { + "val_class_codes": { + "type": "string", + "description": "Single-element value channel carrying the gffcompare class codes to\nkeep, either as a comma-separated string (\"u\" or \"u,j,i\") or a List\n([\"u\", \"j\"]). Class codes describe how each novel transcript relates\nto the reference: \"u\" is intergenic (unknown), \"j\" is a multi-exon\nalternative splice junction, \"i\" is fully within a reference intron,\netc. See the gffcompare documentation for the full list.\n" + } + }, + { + "ch_blacklist_bed": { + "type": "file", + "description": "Optional channel containing a BED file of regions to exclude. Novel\ntranscripts overlapping these regions are dropped via `bedtools\nintersect -v` (the bundled `nextflow.config` sets `ext.args = '-v'`\non `BEDTOOLS_INTERSECT`; consumers can override in their own\n`modules.config` if they want strand-aware subtraction with `-v -s`,\nor positive overlap, etc.). Useful for rRNA loci, repeats, or any\nother interval set the caller wants kept out of the final hybrid GTF.\nPass `channel.empty()` to skip the intersect step entirely.\nStructure: [ val(meta), path(blacklist_bed) ]\n", + "pattern": "*.{bed}" + } + } + ], + "output": [ + { + "hybrid_gtf": { + "type": "file", + "description": "The hybrid GTF: the backbone annotation concatenated with surviving\nnovel transcripts, with synthesised gene rows for any novel gene_id\nnot already present in the backbone. Comment lines (`#`) are stripped.\nThe emitted meta is the backbone's meta (`ch_backbone_gtf`), not the\nnovel input's, so downstream channels keyed on the backbone's\nidentity can `.join()` against this output directly.\nStructure: [ val(meta), path(hybrid_gtf) ]\n", + "pattern": "*.gtf" + } + }, + { + "gffcompare_stats": { + "type": "file", + "description": "gffcompare summary statistics file. Useful for QC reporting of the\nclassification step.\nStructure: [ val(meta), path(stats) ]\n", + "pattern": "*.stats" + } + }, + { + "gffcompare_tracking": { + "type": "file", + "description": "gffcompare per-transcript tracking file, mapping every novel transcript\nto its best match in the reference annotation.\nStructure: [ val(meta), path(tracking) ]\n", + "pattern": "*.tracking" + } + }, + { + "gffcompare_loci": { + "type": "file", + "description": "gffcompare loci file, listing each locus covered by the novel and\nreference transcripts.\nStructure: [ val(meta), path(loci) ]\n", + "pattern": "*.loci" + } + }, + { + "versions": { + "type": "file", + "description": "Software versions are emitted via the `versions` topic channel by the\nupstream gffcompare, gawk, and bedtools modules; no separate output is\nemitted from this subworkflow.\n" + } + } + ], + "authors": ["@pinin4fjords"], + "maintainers": ["@pinin4fjords"] + } }, { - "name": "pathogensurveillance", - "version": "1.1.0" + "name": "h5ad_removebackground_barcodes_cellbender_anndata", + "path": "subworkflows/nf-core/h5ad_removebackground_barcodes_cellbender_anndata/meta.yml", + "type": "subworkflow", + "meta": { + "name": "h5ad_removebackground_barcodes_cellbender_anndata", + "description": "Use cellbender for empty droplet removal", + "keywords": ["scdownstream", "cellbender", "anndata"], + "components": ["cellbender/removebackground", "anndata/barcodes"], + "input": [ + { + "ch_unfiltered": { + "type": "file", + "description": "The input channel containing the unfiltered AnnData file to process\nand remove background noise and empty droplets\nStructure: [ val(meta), path(h5ad) ]\n", + "pattern": "*.h5ad" + } + } + ], + "output": [ + { + "h5ad": { + "description": "Background and empty droplet removed AnnData file containing cells with\nbarcodes exceeding 0.5 posterior cell probability determined by the\ncellbender's remove-background\nStructure: [ val(meta), path(h5ad) ]\n", + "pattern": "*.h5ad" + } + }, + { + "versions": { + "type": "file", + "description": "File containing software versions\n", + "pattern": "versions.yml" + } + } + ], + "authors": ["@nictru", "@chaochaowong"], + "maintainers": ["@nictru"] + }, + "pipelines": [ + { + "name": "scdownstream", + "version": "dev" + }, + { + "name": "scrnaseq", + "version": "4.1.0" + } + ] }, { - "name": "viralmetagenome", - "version": "1.1.1" + "name": "homer_groseq", + "path": "subworkflows/nf-core/homer_groseq/meta.yml", + "type": "subworkflow", + "meta": { + "name": "homer_groseq", + "description": "Basic process of trying to analyze GRO-Seq data with HOMER. From the [GRO-Seq Analysis Tutorial](http://homer.ucsd.edu/homer/ngs/groseq/groseq.html).", + "keywords": ["homer", "groseq", "nascent"], + "components": [ + "unzip", + "homer/maketagdirectory", + "homer/makeucscfile", + "homer/findpeaks", + "homer/pos2bed" + ], + "input": [ + { + "bam": { + "description": "list of BAM files, also able to take SAM and BED as input", + "pattern": "[ *.{bam/sam/bed} ]" + } + }, + { + "fasta": { + "type": "file", + "description": "The reference fasta file", + "pattern": "*.fasta" + } + }, + { + "uniqmap": { + "type": "file", + "description": "Optional HOMER uniqmap", + "pattern": "*.zip" + } + } + ], + "output": [ + { + "tagdir": { + "type": "directory", + "description": "The \"Tag Directory\"", + "pattern": "*_tagdir" + } + }, + { + "bed_graph": { + "type": "file", + "description": "The UCSC bed graph", + "pattern": "*.bedGraph.gz" + } + }, + { + "peaks": { + "type": "file", + "description": "The found peaks", + "pattern": "*.peaks.txt" + } + }, + { + "bed": { + "type": "file", + "description": "A BED file of the found peaks", + "pattern": "*.bed" + } + }, + { + "versions": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ], + "authors": ["@edmundmiller"], + "maintainers": ["@edmundmiller"] + }, + "pipelines": [ + { + "name": "nascent", + "version": "2.3.0" + } + ] }, { - "name": "viralrecon", - "version": "3.0.0" - } - ] - }, - { - "name": "sparsesignatures", - "path": "modules/nf-core/sparsesignatures/meta.yml", - "type": "module", - "meta": { - "name": "sparse_signatures", - "description": "mutational signature deconvolution of cancer cells", - "keywords": [ - "mutational signatures", - "SBS", - "bs genome reference" - ], - "tools": [ - { - "sparsesignatures": { - "description": "SparseSignatures is an R-based computational framework which performs de novo extraction, inference, interpretation, or deconvolution of mutational counts of a large number of patients.", - "documentation": "https://www.bioconductor.org/packages/release/bioc/html/SparseSignatures.html", - "tool_dev_url": "https://github.com/danro9685/SparseSignatures/tree/master?tab=readme-ov-file", - "doi": "10.1371/journal.pcbi.1009119", - "licence": [ - "Apache-2.0" - ], - "identifier": "biotools:sparsesignatures" - } - }, - { - "bsgenome.hsapiens.1000genomes.hs37d5": { - "description": "Reference Genome Sequence (hs37d5), based on NCBI GRCh37", - "documentation": "https://bioconductor.org/packages/3.8/data/annotation/html/BSgenome.Hsapiens.1000genomes.hs37d5.html", - "doi": "10.1038/s41467-022-29271-y", - "licence": [ - "Artistic-2.0" - ], - "identifier": "biotools:bsgenome.hsapiens.1000genomes.hs37d5" + "name": "mafft_align", + "path": "subworkflows/nf-core/mafft_align/meta.yml", + "type": "subworkflow", + "meta": { + "name": "mafft_align", + "description": "Prepare channels for running MAFFT/align", + "keywords": ["msa", "mafft", "align"], + "components": ["mafft/align"], + "input": [ + { + "ch_fasta": { + "type": "file", + "description": "The input channel containing the FASTA files\n", + "pattern": "*.{bam/cram/sam}", + "structure": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input sequences in FASTA format", + "pattern": "*.{fa,fasta}", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1929" + } + ] + } + } + ] + ] + } + } + ], + "output": [ + { + "alignment": { + "type": "file", + "description": "Channel containing the alignment file in fasta format.", + "structure": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" + } + }, + { + "*.aln.gz": { + "type": "file", + "description": "Alignment file, in FASTA format.", + "pattern": "*.aln.gz", + "ontologies": [ + { + "edam": "http://edamontology.org/format_1984" + } + ] + } + } + ] + ] + } + } + ], + "authors": ["@mirpedrol"], + "maintainers": ["@mirpedrol", "@luisas", "@JoseEspinosa"] } - }, - { - "bsgenome.hsapiens.ucsc.hg38": { - "description": "Full genomic sequences for Homo sapiens (UCSC genome hg38)", - "documentation": "https://bioconductor.org/packages/3.16/data/annotation/html/BSgenome.Hsapiens.UCSC.hg38.html", - "doi": "10.18129/B9.bioc.BSgenome.Hsapiens.UCSC.hg38", - "licence": [ - "Artistic-2.0" - ], - "identifier": "biotools:bsgenome.hsapiens.ucsc.hg38" + }, + { + "name": "mmseqs_contig_taxonomy", + "path": "subworkflows/nf-core/mmseqs_contig_taxonomy/meta.yml", + "type": "subworkflow", + "meta": { + "name": "mmseqs_contig_taxonomy", + "description": "Assign taxonomy to contigs using the MMseqs2 workflow.", + "keywords": ["metagenomics", "database", "contigs", "mmsesq2", "taxonomy"], + "components": ["mmseqs/databases", "mmseqs/createdb", "mmseqs/taxonomy", "mmseqs/createtsv"], + "input": [ + { + "contigs": { + "type": "file", + "description": "Channel containing each fasta in nucleotide format as a distinct element with meta.\nStructure: [ val(meta), path(fasta) ]\n", + "pattern": "*.{fasta,fa,fna}" + } + }, + { + "mmseqs_databases": { + "type": "string", + "description": "Channel containing a database created by mmseqs2 databases.\nStructure: [ path(mmseqsdb) ]\n", + "pattern": "*/mmseqs/database" + } + }, + { + "databases_id": { + "type": "string", + "description": "Channel containing the ID of a database made available by developers of mmseqs2. Please refer to https://github.com/soedinglab/MMseqs2/wiki#downloading-databases for possible IDs to use.\nStructure: [ val(id) ]\n" + } + } + ], + "output": [ + { + "taxonomy": { + "type": "file", + "description": "Channel containing the tab separated file with all assigned taxonomy.\nStructure: [ val(meta), path(tsv) ]\n", + "pattern": "*.tsv" + } + }, + { + "db_mmseqs": { + "type": "directory", + "description": "Channel containing the mmseqs database directory. Useful for when the databases is downloaded in the pipeline.\nStructure: [ path(outputdir) ]\n", + "pattern": "*/mmseqs_database" + } + }, + { + "db_taxonomy": { + "type": "directory", + "description": "Channel containing the database containing the taxonomic classification for each input fasta file.\nStructure: [ path(outputdir) ]\n", + "pattern": "*/sample_taxonomy" + } + }, + { + "db_contig": { + "type": "directory", + "description": "Channel containing the database containing the mmseqs format of each input fasta file.\nStructure: [ path(outputdir) ]\n", + "pattern": "*/sample_db" + } + } + ], + "authors": ["@darcy220606"], + "maintainers": ["@darcy220606"] } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample1' ]\n" - } + }, + { + "name": "mmseqs_fasta_cluster", + "path": "subworkflows/nf-core/mmseqs_fasta_cluster/meta.yml", + "type": "subworkflow", + "meta": { + "name": "MMSEQS_FASTA_CLUSTER", + "description": "Subworkflow that generates a clustering TSV file from a set of amino acid sequence within a FASTA file.", + "keywords": ["fasta", "sequences", "cluster", "linclust", "mmseqs"], + "components": ["mmseqs/createdb", "mmseqs/cluster", "mmseqs/linclust", "mmseqs/createtsv"], + "input": [ + { + "sequences": { + "type": "file", + "description": "Fasta file containing sequences for clustering.\n" + } + }, + { + "clustering_tool": { + "type": "string", + "description": "Clustering algorithm of MMSeqs to use for cluster generation. 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} - }, - { - "splitubam --version | sed 's/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "Name of the process" - } - }, - { - "splitubam": { - "type": "string", - "description": "Name of the tool" - } - }, - { - "splitubam --version | sed 's/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@fellen31" - ], - "maintainers": [ - "@fellen31" - ] - } - }, - { - "name": "spotiflow", - "path": "modules/nf-core/spotiflow/meta.yml", - "type": "module", - "meta": { - "name": "spotiflow", - "description": "Spotiflow, accurate and efficient spot detection with stereographic flow.", - "keywords": [ - "imaging", - "image", - "microscopy", - "transcriptomics", - "spatial", - "spot", - "detection" - ], - "tools": [ - { - "spotiflow": { - "description": "Spotiflow allows for accurate and efficient spot detection with stereographic flow", - 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"versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@migueLib" - ], - "maintainers": [ - "@migueLib" - ] - } - }, - { - "name": "spring_compress", - "path": "modules/nf-core/spring/compress/meta.yml", - "type": "module", - "meta": { - "name": "spring_compress", - "description": "Fast, efficient, lossless compression of FASTQ files.", - "keywords": [ - "FASTQ", - "compression", - "lossless" - ], - "tools": [ - { - "spring": { - "description": "SPRING is a compression tool for Fastq files (containing up to 4.29 Billion reads)", - "homepage": "https://github.com/shubhamchandak94/Spring", - "documentation": "https://github.com/shubhamchandak94/Spring/blob/master/README.md", - "tool_dev_url": "https://github.com/shubhamchandak94/Spring", - "doi": "10.1093/bioinformatics/bty1015", - "licence": [ - 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} - }, - { - "spring": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "1.1.1": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "spring": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "1.1.1": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@xec-cm" - ], - "maintainers": [ - "@xec-cm" - ] - } - }, - { - "name": "spring_decompress", - "path": "modules/nf-core/spring/decompress/meta.yml", - "type": "module", - "meta": { - "name": "spring_decompress", - "description": "Fast, efficient, lossless decompression of FASTQ files.", - "keywords": [ - "FASTQ", - "decompression", - "lossless" - ], - "tools": [ - { - "spring": { - "description": "SPRING is a compression tool for Fastq files (containing up to 4.29 Billion reads)", - 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} - }, - { - "*.fastq.gz": { - "type": "file", - "description": "Decompressed FASTQ file(s).", - "pattern": "*.{fastq.gz}", - "ontologies": [] - } - } - ] - ], - "versions_spring": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "spring": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "1.1.1": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "spring": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "1.1.1": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@xec-cm" - ], - "maintainers": [ - "@xec-cm" - ] - }, - "pipelines": [ - { - "name": "genomicrelatedness", - "version": "dev" - }, - { - 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"pattern": "*/*.sra" - } - } - ], - { - "ncbi_settings": { - "type": "file", - "description": "An NCBI user settings file.\n", - "pattern": "*.mkfg", - "ontologies": [] - } - }, - { - "certificate": { - "type": "file", - "description": "Path to a JWT cart file used to access protected dbGAP data on SRA using the sra-toolkit\n", - "pattern": "*.cart", - "ontologies": [] - } - } - ], - "output": { - "reads": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.fastq.gz": { - "type": "file", - "description": "Extracted FASTQ file or files if the sequencing reads are paired-end.", - "pattern": "*.fastq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "versions_sratools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "sratools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "prefetch --version 2>&1 | grep -Eo '[0-9.]+'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_pigz": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pigz": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pigz --version 2>&1 | sed 's/pigz //g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "sratools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "prefetch --version 2>&1 | grep -Eo '[0-9.]+'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pigz": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pigz --version 2>&1 | sed 's/pigz //g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@Midnighter" - ], - "maintainers": [ - "@Midnighter", - "@gallvp" - ] - }, - "pipelines": [ - { - "name": "fetchngs", - "version": "1.12.0" - }, - { - "name": "pathogensurveillance", - "version": "1.1.0" - } - ] - }, - { - "name": "sratools_prefetch", - "path": "modules/nf-core/sratools/prefetch/meta.yml", - "type": "module", - "meta": { - "name": "sratools_prefetch", - "description": "Download sequencing data from the NCBI Sequence Read Archive (SRA).", - "keywords": [ - "sequencing", - "fastq", - "prefetch" - ], - "tools": [ - { - "sratools": { - "description": "SRA Toolkit and SDK from NCBI", - "homepage": "https://github.com/ncbi/sra-tools", - "documentation": "https://github.com/ncbi/sra-tools/wiki", - "tool_dev_url": "https://github.com/ncbi/sra-tools", - "licence": [ - "Public Domain" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]\n" - } - }, - { - "id": { - "type": "string", - "description": "A string denoting an SRA id.\n" - } - } - ], - { - "ncbi_settings": { - "type": "file", - "description": "An NCBI user settings file.\n", - "pattern": "*.mkfg", - "ontologies": [] - } - }, - { - "certificate": { - "type": "file", - "description": "Path to a JWT cart file used to access protected dbGAP data on SRA using the sra-toolkit\n", - "pattern": "*.cart", - "ontologies": [] - } - } - ], - "output": { - "sra": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${id}": { - "type": "directory", - "description": "Directory containing SRA data files", - "pattern": "*/*.sra", - "ontologies": [] - } - } - ] - ], - "versions_sratools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "sratools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "prefetch --version 2>&1 | grep -Eo '[0-9.]+'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_curl": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "curl": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "curl --version | sed '1!d;s/^curl //; s/ .*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "sratools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "prefetch --version 2>&1 | grep -Eo '[0-9.]+'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "curl": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "curl --version | sed '1!d;s/^curl //; s/ .*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@Midnighter" - ], - "maintainers": [ - "@Midnighter", - "@gallvp" - ] - }, - "pipelines": [ - { - "name": "fetchngs", - "version": "1.12.0" - } - ] - }, - { - "name": "srst2_srst2", - "path": "modules/nf-core/srst2/srst2/meta.yml", - "type": "module", - "meta": { - "name": "srst2_srst2", - "description": "Short Read Sequence Typing for Bacterial Pathogens is a program designed to take Illumina sequence data,\na MLST database and/or a database of gene sequences (e.g. resistance genes, virulence genes, etc)\nand report the presence of STs and/or reference genes.\n", - "keywords": [ - "mlst", - "typing", - "illumina" - ], - "tools": [ - { - "srst2": { - "description": "Short Read Sequence Typing for Bacterial Pathogens", - "homepage": "http://katholt.github.io/srst2/", - "documentation": "https://github.com/katholt/srst2/blob/master/README.md", - "tool_dev_url": "https://github.com/katholt/srst2", - "doi": "10.1186/s13073-014-0090-6", - "licence": [ - "BSD" - ], - "identifier": "biotools:srst2" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\nid: should be the identification number or sample name\nsingle_end: should be true for single end data and false for paired in data\ndb: should be either 'gene' to use the --gene_db option or \"mlst\" to use the --mlst_db option\ne.g. [ id:'sample', single_end:false , db:'gene']\n" - } - }, - { - "fastq_s": { - "type": "file", - "description": "input FastQ files", - "pattern": "*.{fq,fastq,fq.gz,fastq.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - }, - { - "db": { - "type": "file", - "description": "Database in FASTA format", - "pattern": "*.fasta", - "ontologies": [] - } - } - ], - { - "db_type": { - "type": "string", - "description": "Type of database to use, either 'gene' or 'mlst'" - } - } - ], - "output": { - "gene_results": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample', single_end:false ]\n" - } - }, - { - "*_genes_*_results.txt": { - "type": "file", - "description": "SRST2 gene results", - "pattern": "*_genes_*_results.txt", - "ontologies": [] - } - } - ] - ], - "fullgene_results": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample', single_end:false ]\n" - } - }, - { - "*_fullgenes_*_results.txt": { - "type": "file", - "description": "SRST2 full gene results", - "pattern": "*_fullgenes_*_results.txt", - "ontologies": [] - } - } - ] - ], - "mlst_results": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample', single_end:false ]\n" - } - }, - { - "*_mlst_*_results.txt": { - "type": "file", - "description": "SRST2 MLST results", - "pattern": "*_mlst_*_results.txt", - "ontologies": [] - } - } - ] - ], - "pileup": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample', single_end:false ]\n" - } - }, - { - "*.pileup": { - "type": "file", - "description": "SAMtools pileup file", - "pattern": "*.pileup", - "ontologies": [] - } - } - ] - ], - "sorted_bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample', single_end:false ]\n" - } - }, - { - "*.sorted.bam": { - "type": "file", - "description": "Sorted BAM file", - "pattern": "*.sorted.bam", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@jvhagey" - ], - "maintainers": [ - "@jvhagey" - ] - } - }, - { - "name": "ssuissero", - "path": "modules/nf-core/ssuissero/meta.yml", - "type": "module", - "meta": { - "name": "ssuissero", - "description": "Serotype prediction of Streptococcus suis assemblies", - "keywords": [ - "bacteria", - "fasta", - "streptococcus" - ], - "tools": [ - { - "ssuissero": { - "description": "Rapid Streptococcus suis serotyping pipeline for Nanopore Data", - "homepage": "https://github.com/jimmyliu1326/SsuisSero", - "documentation": "https://github.com/jimmyliu1326/SsuisSero", - "tool_dev_url": "https://github.com/jimmyliu1326/SsuisSero", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Assembly in FASTA format", - "pattern": "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}", - "ontologies": [] - } - } - ] - ], - "output": { - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "Tab-delimited serotype prediction", - "pattern": "*.{tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_ssuissero": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "ssuissero": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "1.0.1": { - "type": "string", - "description": "The version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "ssuissero": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "1.0.1": { - "type": "string", - "description": "The version of the tool" - } - } - ] - ] - }, - "authors": [ - "@rpetit3" - ], - "maintainers": [ - "@rpetit3" - ] - } - }, - { - "name": "stacks_refmap", - "path": "modules/nf-core/stacks/refmap/meta.yml", - "type": "module", - "meta": { - "name": "stacks_refmap", - "description": "ref_map.pl script from Stacks for the analysis of RAD-seq data when a reference genome is available.", - "keywords": [ - "rad-seq", - "gbs", - "variant-calling", - "population-genomics", - "genomics" - ], - "tools": [ - { - "stacks": { - "description": "Stacks is a software pipeline for building loci from short-read sequences.", - "homepage": "https://catchenlab.life.illinois.edu/stacks/", - "documentation": "https://catchenlab.life.illinois.edu/stacks/manual/", - "tool_dev_url": "http://groups.google.com/group/stacks-users", - "doi": "10.1111/mec.12354", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:stacks" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]" - } - }, - { - "bams": { - "type": "file", - "description": "BAM alignment files from individual samples", - "pattern": "*.bam", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - } - ], - { - "popmap": { - "type": "file", - "description": "Tab-delimited population map file", - "pattern": "*.tsv", - "ontologies": [ + "pipelines": [ + { + "name": "proteinfamilies", + "version": "2.3.0" + }, { - "edam": "http://edamontology.org/format_3475" + "name": "viralmetagenome", + "version": "1.1.1" } - ] - } - } - ], - "output": { - "catalog_calls": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]" - } - }, - { - "catalog.calls": { - "type": "file", - "description": "Stacks catalog calls output file", - "pattern": "catalog.calls", - "ontologies": [] - } - } - ] - ], - "catalog_chrs": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]" - } - }, - { - "catalog.chrs.tsv": { - "type": "file", - "description": "Stacks catalog chrs output file", - "pattern": "catalog.chrs.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "catalog_fa": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]" - } - }, - { - "catalog.fa.gz": { - "type": "file", - "description": "Stacks catalog fasta output file", - "pattern": "catalog.fa.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "gstacks_log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]" - } - }, - { - "gstacks.log": { - "type": "file", - "description": "Stacks gstacks log output file", - "pattern": "gstacks.log", - "ontologies": [] - } - } - ] - ], - "gstacks_log_distribs": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]" - } - }, - { - "gstacks.log.distribs": { - "type": "file", - "description": "Stacks gstacks log distribs output file", - "pattern": "gstacks.log.distribs", - "ontologies": [] - } - } - ] - ], - "haplotypes": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]" - } - }, - { - "populations.haplotypes.tsv": { - "type": "file", - "description": "Stacks haplotypes output file", - "pattern": "populations.haplotypes.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "hapstats": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]" - } - }, - { - "populations.hapstats.tsv": { - "type": "file", - "description": "Stacks hapstats output file", - "pattern": "populations.hapstats.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "sumstats": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]" - } - }, - { - "populations.sumstats.tsv": { - "type": "file", - "description": "Stacks populations sumstats output file", - "pattern": "populations.sumstats.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "sumstats_summary": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]" - } - }, - { - "populations.sumstats_summary.tsv": { - "type": "file", - "description": "Stacks populations sumstats summary output file", - "pattern": "populations.sumstats_summary.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "populations_log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]" - } - }, - { - "populations.log": { - "type": "file", - "description": "Stacks populations log output file", - "pattern": "populations.log", - "ontologies": [] - } - } - ] - ], - "populations_log_distribs": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]" - } - }, - { - "populations.log.distribs": { - "type": "file", - "description": "Stacks populations log distribs output file", - "pattern": "populations.log.distribs", - "ontologies": [] - } - } - ] - ], - "ref_map_log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]" - } - }, - { - "ref_map.log": { - "type": "file", - "description": "Stacks ref_map log output file", - "pattern": "ref_map.log", - "ontologies": [] - } - } - ] - ], - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]" - } - }, - { - "populations.snps.vcf": { - "type": "file", - "description": "Stacks populations vcf output file", - "pattern": "populations.snps.vcf", - "ontologies": [] - } - } - ] - ], - "genepop": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]" - } - }, - { - "populations.snps.genepop": { - "type": "file", - "description": "Stacks populations genepop output file", - "pattern": "populations.snps.genepop", - "ontologies": [] - } - } - ] - ], - "structure": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]" - } - }, - { - "populations.structure": { - "type": "file", - "description": "Stacks populations structure output file", - "pattern": "populations.structure", - "ontologies": [] - } - } - ] - ], - "versions_stacks_refmap": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "stacks_refmap": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "populations -v 2>&1 | sed 's/^.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "stacks_refmap": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "populations -v 2>&1 | sed 's/^.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@TheGreatJack" - ], - "maintainers": [ - "@TheGreatJack" - ] - } - }, - { - "name": "stadeniolib_scramble", - "path": "modules/nf-core/stadeniolib/scramble/meta.yml", - "type": "module", - "meta": { - "name": "stadeniolib_scramble", - "description": "Advanced sequence file format conversions", - "keywords": [ - "sam", - "bam", - "cram", - "compression" - ], - "tools": [ - { - "scramble": { - "description": "Staden Package 'io_lib' (sometimes referred to as libstaden-read by distributions). This contains code for reading and writing a variety of Bioinformatics / DNA Sequence formats.", - "homepage": "https://github.com/jkbonfield/io_lib", - "documentation": "https://github.com/jkbonfield/io_lib/blob/master/README.md", - "tool_dev_url": "https://github.com/jkbonfield/io_lib", - "licence": [ - "BSD" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } - } - ], - { - "fasta": { - "type": "file", - "description": "Reference genome in FASTA format", - "pattern": "*.{fa,fasta}", - "ontologies": [] - } - }, - { - "fai": { - "type": "file", - "description": "FASTA index file from samtools faidx", - "pattern": "*.{fai}", - "ontologies": [] - } - }, - { - "gzi": { - "type": "file", - "description": "Optional gzip index file for BAM inputs", - "pattern": "*.gzi", - "ontologies": [] - } - } - ], - "output": { - "cram": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.{cram,bam}": { - "type": "file", - "description": "Compressed BAM/CRAM file", - "pattern": "*.{cram,bam}", - "ontologies": [] - } - } - ] - ], - "gzi": [ - { - "*.gzi": { - "type": "file", - "description": "gzip index file for BAM outputs", - "pattern": ".{bam.gzi}", - "ontologies": [] - } - } - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@matthdsm" - ], - "maintainers": [ - "@matthdsm" - ] - } - }, - { - "name": "stainwarpy_extractchannel", - "path": "modules/nf-core/stainwarpy/extractchannel/meta.yml", - "type": "module", - "meta": { - "name": "stainwarpy_extractchannel", - "description": "Extract a single channel image from multiplexed tissue images using stainwarpy", - "keywords": [ - "image registration", - "histology", - "hne", - "multiplexed", - "channel extraction" - ], - "tools": [ - { - "stainwarpy": { - "description": "Register H&E stained and Multiplexed tissue images using feature-based image registration", - "homepage": "https://github.com/tckumarasekara/stainwarpy", - "documentation": "https://github.com/tckumarasekara/stainwarpy", - "tool_dev_url": "https://github.com/tckumarasekara/stainwarpy", - "licence": [ - "MIT License", - "Apache-2.0" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "multiplx_img": { - "type": "file", - "description": "Multiplexed image file", - "pattern": "*.{ome.tif,ome.tiff,tif,tiff}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3727" - }, - { - "edam": "http://edamontology.org/format_3591" - } - ] - } - } - ] - ], - "output": { - "single_ch_image": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*_multiplexed_single_channel_img.ome.tif": { - "type": "file", - "description": "Single channel extracted image file in OME-TIFF format", - "pattern": "*_multiplexed_single_channel_img.ome.tif", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3727" - } - ] - } - } - ] - ], - "versions_stainwarpy": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "stainwarpy": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "stainwarpy --version | sed 's/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "stainwarpy": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "stainwarpy --version | sed 's/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@tckumarasekara" - ], - "maintainers": [ - "@tckumarasekara" - ] - } - }, - { - "name": "stainwarpy_register", - "path": "modules/nf-core/stainwarpy/register/meta.yml", - "type": "module", - "meta": { - "name": "stainwarpy_register", - "description": "Register H&E stained and Multiplexed tissue images using feature-based image registration", - "keywords": [ - "image registration", - "histology", - "hne", - "multiplexed" - ], - "tools": [ - { - "stainwarpy": { - "description": "Register H&E stained and Multiplexed tissue images using feature-based image registration", - "homepage": "https://github.com/tckumarasekara/stainwarpy", - "documentation": "https://github.com/tckumarasekara/stainwarpy", - "tool_dev_url": "https://github.com/tckumarasekara/stainwarpy", - "licence": [ - "MIT License", - "Apache-2.0" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "hne_img": { - "type": "file", - "description": "H&E stained image file", - "pattern": "*.{ome.tif,ome.tiff,tif,tiff}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3727" - }, - { - "edam": "http://edamontology.org/format_3591" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "multiplx_img": { - "type": "file", - "description": "Multiplexed image file", - "pattern": "*.{ome.tif,ome.tiff,tif,tiff}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3727" - }, - { - "edam": "http://edamontology.org/format_3591" - } - ] - } - } - ], - { - "fixed_img": { - "type": "string", - "description": "Which image to use as fixed image for registration. Options - 'hne' or 'multiplexed'", - "ontologies": [] - } - }, - { - "final_sz": { - "type": "string", - "description": "In which pixel size to output the registered image and segmentation mask. Options - 'hne' or 'multiplexed'", - "ontologies": [] - } - } - ], - "output": { - "reg_image": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*_transformed_image.ome.tif": { - "type": "file", - "description": "Registered final channel image in OME-TIFF format", - "pattern": "*_transformed_image.ome.tif", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3727" - } - ] - } - } - ] - ], - "reg_metrics_tform": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*_registration_metrics_tform_map.json": { - "type": "file", - "description": "Registration metrics and transformation map in JSON format", - "pattern": "*_registration_metrics_tform_map.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "tform_map": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*_feature_based_transformation_map.npy": { - "type": "file", - "description": "Feature-based transformation map in NPY format", - "pattern": "*_feature_based_transformation_map.npy", - "ontologies": [] - } - } - ] - ], - "versions_stainwarpy": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "stainwarpy": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "stainwarpy --version | sed 's/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "stainwarpy": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "stainwarpy --version | sed 's/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@tckumarasekara" - ], - "maintainers": [ - "@tckumarasekara" - ] - } - }, - { - "name": "stainwarpy_transformsegmask", - "path": "modules/nf-core/stainwarpy/transformsegmask/meta.yml", - "type": "module", - "meta": { - "name": "stainwarpy_transformsegmask", - "description": "Transform segmentation mask of multiplexed or H&E stained tissue images using stainwarpy", - "keywords": [ - "image registration", - "histology", - "hne", - "multiplexed", - "segmentation mask" - ], - "tools": [ - { - "stainwarpy": { - "description": "Register H&E stained and Multiplexed tissue images using feature-based image registration", - "homepage": "https://github.com/tckumarasekara/stainwarpy", - "documentation": "https://github.com/tckumarasekara/stainwarpy", - "tool_dev_url": "https://github.com/tckumarasekara/stainwarpy", - "licence": [ - "MIT License", - "Apache-2.0" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "hne_img": { - "type": "file", - "description": "H&E stained image file", - "pattern": "*.{ome.tif,ome.tiff,tif,tiff}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3727" - }, - { - "edam": "http://edamontology.org/format_3591" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "multiplx_img": { - "type": "file", - "description": "Multiplexed image file", - "pattern": "*.{ome.tif,ome.tiff,tif,tiff}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3727" - }, - { - "edam": "http://edamontology.org/format_3591" - } - ] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "seg_mask": { - "type": "file", - "description": "Segmentation mask file", - "pattern": "*.{ome.tif,ome.tiff,tif,tiff,npy}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3727" - }, - { - "edam": "http://edamontology.org/format_3591" - } - ] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "tform_map": { - "type": "file", - "description": "Transformation map file", - "pattern": "*.npy", - "ontologies": [] - } - } - ], - { - "fixed_img": { - "type": "string", - "description": "Which image to use as fixed image for registration. Options - 'hne' or 'multiplexed'", - "ontologies": [] - } - }, - { - "final_sz": { - "type": "string", - "description": "In which pixel size to output the registered image and segmentation mask. Options - 'hne' or 'multiplexed'", - "ontologies": [] - } - } - ], - "output": { - "transformed_seg_mask": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*_transformed_segmentation_mask.ome.tif": { - "type": "file", - "description": "Transformed segmentation mask in OME-TIFF format", - "pattern": "*_transformed_segmentation_mask.ome.tif", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3727" - } - ] - } - } - ] - ], - "versions_stainwarpy": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "stainwarpy": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "stainwarpy --version | sed 's/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "stainwarpy": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "stainwarpy --version | sed 's/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@tckumarasekara" - ], - "maintainers": [ - "@tckumarasekara" - ] - } - }, - { - "name": "staphopiasccmec", - "path": "modules/nf-core/staphopiasccmec/meta.yml", - "type": "module", - "meta": { - "name": "staphopiasccmec", - "description": "Predicts Staphylococcus aureus SCCmec type based on primers.", - "keywords": [ - "amr", - "fasta", - "sccmec" - ], - "tools": [ - { - "staphopiasccmec": { - "description": "Predicts Staphylococcus aureus SCCmec type based on primers.", - "homepage": "https://staphopia.emory.edu", - "documentation": "https://github.com/staphopia/staphopia-sccmec", - "tool_dev_url": "https://github.com/staphopia/staphopia-sccmec", - "doi": "10.7717/peerj.5261", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA assembly file", - "pattern": "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}", - "ontologies": [] - } - } - ] - ], - "output": { - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "Tab-delimited results", - "pattern": "*.{tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_staphopiasccmec": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "staphopiasccmec": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "staphopia-sccmec --version 2>&1 | sed \"s/^.*staphopia-sccmec //\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "staphopiasccmec": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "staphopia-sccmec --version 2>&1 | sed \"s/^.*staphopia-sccmec //\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@rpetit3" - ], - "maintainers": [ - "@rpetit3" - ] - } - }, - { - "name": "staphscan", - "path": "modules/nf-core/staphscan/meta.yml", - "type": "module", - "meta": { - "name": "staphscan", - "description": "staphscan is a tool to screen genome assemblies of Staphylococcus aureus", - "keywords": [ - "screen", - "assembly", - "Staphylococcus", - "aureus" - ], - "tools": [ - { - "staphscan": { - "description": "a genomic surveillance framework for Staphylococcus aureus", - "homepage": "https://github.com/riccabolla/StaphSCAN", - "documentation": "https://staphscan.readthedocs.io/en/latest/", - "tool_dev_url": "https://github.com/riccabolla/StaphSCAN", - "doi": "10.5281/zenodo.18458858", - "licence": [ - "MIT" - ], - "identifier": "biotools:staphscan" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fastas": { - "type": "list", - "description": "Staphylococcus aureus genome assemblies to be screened", - "pattern": "*.fasta" - } - } - ] - ], - "output": { - "tsv": [ - [ - { - "meta": { - "type": "string", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "Result file generated after screening", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_staphscan": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "staphscan": { - "type": "string", - "description": "The tool name" - } - }, - { - "staphscan --version | sed 's/staphscan //;'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "staphscan": { - "type": "string", - "description": "The tool name" - } - }, - { - "staphscan --version | sed 's/staphscan //;'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@riccabolla" - ], - "maintainers": [ - "@riccabolla" - ] - } - }, - { - "name": "star_align", - "path": "modules/nf-core/star/align/meta.yml", - "type": "module", - "meta": { - "name": "star_align", - "description": "Align reads to a reference genome using STAR", - "keywords": [ - "align", - "fasta", - "genome", - "reference" - ], - "tools": [ - { - "star": { - "description": "STAR is a software package for mapping DNA sequences against\na large reference genome, such as the human genome.\n", - "homepage": "https://github.com/alexdobin/STAR", - "manual": "https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf", - "doi": "10.1093/bioinformatics/bts635", - "licence": [ - "MIT" - ], - "identifier": "biotools:star" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "index": { - "type": "directory", - "description": "STAR genome index", - "pattern": "star" - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "gtf": { - "type": "file", - "description": "Annotation GTF file", - "pattern": "*.{gtf}", - "ontologies": [] - } - } - ], - { - "star_ignore_sjdbgtf": { - "type": "boolean", - "description": "Ignore annotation GTF file" - } - } - ], - "output": { - "log_final": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*Log.final.out": { - "type": "file", - "description": "STAR final log file", - "pattern": "*Log.final.out", - "ontologies": [] - } - } - ] - ], - "log_out": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*Log.out": { - "type": "file", - "description": "STAR lot out file", - "pattern": "*Log.out", - "ontologies": [] - } - } - ] - ], - "log_progress": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*Log.progress.out": { - "type": "file", - "description": "STAR log progress file", - "pattern": "*Log.progress.out", - "ontologies": [] - } - } - ] - ], - "versions_star": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "star": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "STAR --version | sed \"s/STAR_//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } ] - ], - "versions_samtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools --version | sed -n '1s/samtools //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_gawk": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gawk": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gawk --version | sed -n '1s/GNU Awk \\([0-9.]*\\).*/\\1/p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*d.out.bam": { - "type": "file", - "description": "Output BAM file containing read alignments", - "pattern": "*.{bam}", - "ontologies": [] - } - } - ] - ], - "bam_sorted": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.sortedByCoord.out.bam": { - "type": "file", - "description": "Sorted BAM file of read alignments (optional)", - "pattern": "*sortedByCoord.out.bam", - "ontologies": [] - } - } - ] - ], - "bam_sorted_aligned": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.Aligned.sortedByCoord.out.bam": { - "type": "file", - "description": "Sorted BAM file of read alignments (optional)", - "pattern": "*.Aligned.sortedByCoord.out.bam", - "ontologies": [] - } - } - ] - ], - "bam_transcript": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*toTranscriptome.out.bam": { - "type": "file", - "description": "Output BAM file of transcriptome alignment (optional)", - "pattern": "*toTranscriptome.out.bam", - "ontologies": [] - } - } - ] - ], - "bam_unsorted": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*Aligned.unsort.out.bam": { - "type": "file", - "description": "Unsorted BAM file of read alignments (optional)", - "pattern": "*Aligned.unsort.out.bam", - "ontologies": [] - } - } - ] - ], - "fastq": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*fastq.gz": { - "type": "file", - "description": "Unmapped FastQ files (optional)", - "pattern": "*fastq.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "tab": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tab": { - "type": "file", - "description": "STAR output tab file(s) (optional)", - "pattern": "*.tab", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "spl_junc_tab": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.SJ.out.tab": { - "type": "file", - "description": "STAR output splice junction tab file", - "pattern": "*.SJ.out.tab", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "read_per_gene_tab": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.ReadsPerGene.out.tab": { - "type": "file", - "description": "STAR output read per gene tab file", - "pattern": "*.ReadsPerGene.out.tab", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "junction": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.out.junction": { - "type": "file", - "description": "STAR chimeric junction output file (optional)", - "pattern": "*.out.junction", - "ontologies": [] - } - } - ] - ], - "sam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.out.sam": { - "type": "file", - "description": "STAR output SAM file(s) (optional)", - "pattern": "*.out.sam", - "ontologies": [] - } - } - ] - ], - "wig": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.wig": { - "type": "file", - "description": "STAR output wiggle format file(s) (optional)", - "pattern": "*.wig", - "ontologies": [] - } - } - ] - ], - "bedgraph": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bg": { - "type": "file", - "description": "STAR output bedGraph format file(s) (optional)", - "pattern": "*.bg", - "ontologies": [] - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "star": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "STAR --version | sed \"s/STAR_//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools --version | sed -n '1s/samtools //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gawk": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gawk --version | sed -n '1s/GNU Awk \\([0-9.]*\\).*/\\1/p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@kevinmenden", - "@drpatelh", - "@praveenraj2018" - ], - "maintainers": [ - "@kevinmenden", - "@drpatelh", - "@praveenraj2018" - ] - }, - "pipelines": [ - { - "name": "alleleexpression", - "version": "dev" - }, - { - "name": "circrna", - "version": "dev" - }, - { - "name": "dartseq", - "version": "dev" - }, - { - "name": "evexplorer", - "version": "dev" - }, - { - "name": "lncpipe", - "version": "dev" - }, - { - "name": "marsseq", - "version": "1.0.3" - }, - { - "name": "nascent", - "version": "2.3.0" - }, - { - "name": "panoramaseq", - "version": "dev" }, { - "name": "riboseq", - "version": "1.2.0" - }, - { - "name": "rnadnavar", - "version": "dev" - }, - { - "name": "rnafusion", - "version": "4.1.2" - }, - { - "name": "rnaseq", - "version": "3.26.0" - }, - { - "name": "rnasplice", - "version": "1.0.4" - }, - { - "name": "rnavar", - "version": "1.2.3" - }, - { - "name": "viralintegration", - "version": "0.1.1" - } - ] - }, - { - "name": "star_genomegenerate", - "path": "modules/nf-core/star/genomegenerate/meta.yml", - "type": "module", - "meta": { - "name": "star_genomegenerate", - "description": "Create index for STAR", - "keywords": [ - "index", - "fasta", - "genome", - "reference" - ], - "tools": [ - { - "star": { - "description": "STAR is a software package for mapping DNA sequences against\na large reference genome, such as the human genome.\n", - "homepage": "https://github.com/alexdobin/STAR", - "manual": "https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf", - "doi": "10.1093/bioinformatics/bts635", - "licence": [ - "MIT" - ], - "identifier": "biotools:star" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Fasta file of the reference genome", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "gtf": { - "type": "file", - "description": "GTF file of the reference genome", - "ontologies": [] - } + "name": "multiple_impute_glimpse2", + "path": "subworkflows/nf-core/multiple_impute_glimpse2/meta.yml", + "type": "subworkflow", + "meta": { + "name": "multiple_impute_glimpse2", + "description": "Impute VCF/BCF files, but also CRAM and BAM files with Glimpse2", + "keywords": ["glimpse", "chunk", "phase", "ligate", "split_reference"], + "components": [ + "glimpse2/chunk", + "glimpse2/phase", + "glimpse2/ligate", + "glimpse2/splitreference", + "bcftools/index" + ], + "input": [ + { + "ch_input": { + "type": "file", + "description": "Target dataset in CRAM, BAM or VCF/BCF format.\nIndex file of the input file.\nFile with sample names and ploidy information.\nStructure: [ meta, file, index, txt ]\n" + } + }, + { + "ch_ref": { + "type": "file", + "description": "Reference panel of haplotypes in VCF/BCF format.\nIndex file of the Reference panel file.\nTarget region, usually a full chromosome (e.g. chr20:1000000-2000000 or chr20).\nThe file could possibly be without GT field (for efficiency reasons a file containing only the positions is recommended).\nStructure: [ meta, vcf, csi, region ]\n" + } + }, + { + "ch_map": { + "type": "file", + "description": "File containing the genetic map.\nStructure: [ meta, gmap ]\n" + } + }, + { + "ch_fasta": { + "type": "file", + "description": "Reference genome in fasta format.\nReference genome index in fai format\nStructure: [ meta, fasta, fai ]\n" + } + } + ], + "output": [ + { + "chunk_chr": { + "type": "file", + "description": "Tab delimited output txt file containing buffer and imputation regions.\nStructure: [meta, txt]\n" + } + }, + { + "merged_variants": { + "type": "file", + "description": "Output VCF/BCF file for the merged regions.\nPhased information (HS field) is updated accordingly for the full region.\nStructure: [ val(meta), bcf ]\n" + } + }, + { + "merged_variants_index": { + "type": "file", + "description": "Index file of the ligated phased variants files." + } + }, + { + "versions": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ], + "authors": ["@LouisLeNezet"], + "maintainers": ["@LouisLeNezet"] } - ] - ], - "output": { - "index": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "star": { - "type": "directory", - "description": "Folder containing the star index files", - "pattern": "star" - } - } - ] - ], - "versions_star": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "star": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "STAR --version | sed -e \"s/STAR_//g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_samtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools --version | sed -n '1s/samtools //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_gawk": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gawk": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gawk --version | sed -n '1{s/GNU Awk //;s/,.*//;p}'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "star": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "STAR --version | sed -e \"s/STAR_//g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools --version | sed -n '1s/samtools //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "gawk": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "gawk --version | sed -n '1{s/GNU Awk //;s/,.*//;p}'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@kevinmenden", - "@drpatelh" - ], - "maintainers": [ - "@kevinmenden", - "@drpatelh" - ] - }, - "pipelines": [ - { - "name": "circrna", - "version": "dev" - }, - { - "name": "dartseq", - "version": "dev" - }, - { - "name": "evexplorer", - "version": "dev" - }, - { - "name": "lncpipe", - "version": "dev" - }, - { - "name": "marsseq", - "version": "1.0.3" - }, - { - "name": "nascent", - "version": "2.3.0" - }, - { - "name": "oncoanalyser", - "version": "2.3.0" }, { - "name": "panoramaseq", - "version": "dev" - }, - { - "name": "references", - "version": "0.1" - }, - { - "name": "riboseq", - "version": "1.2.0" - }, - { - "name": "rnadnavar", - "version": "dev" - }, - { - "name": "rnafusion", - "version": "4.1.2" - }, - { - "name": "rnaseq", - "version": "3.26.0" - }, - { - "name": "rnasplice", - "version": "1.0.4" - }, - { - "name": "rnavar", - "version": "1.2.3" - }, - { - "name": "scrnaseq", - "version": "4.1.0" - }, - { - "name": "viralintegration", - "version": "0.1.1" - } - ] - }, - { - "name": "star_indexversion", - "path": "modules/nf-core/star/indexversion/meta.yml", - "type": "module", - "meta": { - "name": "star_indexversion", - "description": "Get the minimal allowed index version from STAR", - "keywords": [ - "index", - "version", - "rna" - ], - "tools": [ - { - "star": { - "description": "STAR is a software package for mapping DNA sequences against\na large reference genome, such as the human genome.\n", - "homepage": "https://github.com/alexdobin/STAR", - "manual": "https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf", - "doi": "10.1093/bioinformatics/bts635", - "licence": [ - "MIT" - ], - "identifier": "biotools:star" - } - } - ], - "output": { - "index_version": [ - { - "*.txt": { - "type": "file", - "description": "File with the minimal index version", - "pattern": "*.txt", - "ontologies": [] - } - } - ], - "versions_star": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "star": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "STAR --version | sed \"s/STAR_//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "star": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "STAR --version | sed \"s/STAR_//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@nvnieuwk" - ], - "maintainers": [ - "@nvnieuwk" - ] - }, - "pipelines": [ - { - "name": "rnavar", - "version": "1.2.3" - } - ] - }, - { - "name": "star_starsolo", - "path": "modules/nf-core/star/starsolo/meta.yml", - "type": "module", - "meta": { - "name": "starsolo", - "description": "Create a counts matrix for single-cell data using STARSolo, handling cell barcodes and UMI information.", - "keywords": [ - "align", - "count", - "genome", - "reference" - ], - "tools": [ - { - "starsolo": { - "description": "Mapping, demultiplexing and quantification for single cell RNA-seq.", - "homepage": "https://github.com/alexdobin/STAR/", - "documentation": "https://github.com/alexdobin/STAR/blob/master/docs/STARsolo.md", - "doi": "10.1101/2021.05.05.442755", - "licence": [ - "MIT" - ], - "identifier": "biotools:star" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information.\nHere, you should add all the specific barcode/umi\ninformation for each sample.\ne.g. `[ id:'test_starsolo', umi_len:'12', cb_start:1 ]`\n" - } - }, - { - "solotype": { - "type": "string", - "description": "Type of single-cell library.\nIt can be CB_UMI_Simple for most common ones such as 10xv2 and 10xv3,\nCB_UMI_Complex for method such as inDrop and SmartSeq for SMART-Seq.\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", - "ontologies": [] - } - } - ], - { - "opt_whitelist": { - "type": "file", - "description": "Optional whitelist file", - "ontologies": [] - } - }, - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing the STAR index information." - } - }, - { - "index": { - "type": "directory", - "description": "STAR genome index", - "pattern": "star" - } - } - ] - ], - "output": { - "counts": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information.\nHere, you should add all the specific barcode/umi\ninformation for each sample.\ne.g. `[ id:'test_starsolo', umi_len:'12', cb_start:1 ]`\n" - } - }, - { - "*.Solo.out": { - "type": "file", - "description": "STARSolo counts matrix", - "pattern": "*.Solo.out", - "ontologies": [] - } - } - ] - ], - "log_final": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information.\nHere, you should add all the specific barcode/umi\ninformation for each sample.\ne.g. `[ id:'test_starsolo', umi_len:'12', cb_start:1 ]`\n" - } - }, - { - "*Log.final.out": { - "type": "file", - "description": "STAR final log file", - "pattern": "*Log.final.out", - "ontologies": [] - } - } - ] - ], - "log_out": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information.\nHere, you should add all the specific barcode/umi\ninformation for each sample.\ne.g. `[ id:'test_starsolo', umi_len:'12', cb_start:1 ]`\n" - } - }, - { - "*Log.out": { - "type": "file", - "description": "STAR lot out file", - "pattern": "*Log.out", - "ontologies": [] - } - } - ] - ], - "log_progress": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information.\nHere, you should add all the specific barcode/umi\ninformation for each sample.\ne.g. `[ id:'test_starsolo', umi_len:'12', cb_start:1 ]`\n" - } - }, - { - "*Log.progress.out": { - "type": "file", - "description": "STAR log progress file", - "pattern": "*Log.progress.out", - "ontologies": [] - } - } - ] - ], - "summary": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information.\nHere, you should add all the specific barcode/umi\ninformation for each sample.\ne.g. `[ id:'test_starsolo', umi_len:'12', cb_start:1 ]`\n" - } - }, - { - "*/Gene/Summary.csv": { - "type": "file", - "description": "STARSolo metrics summary CSV file.", - "pattern": "*/Gene/Summary.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@kevinmenden", - "@ggabernet", - "@grst", - "@fmalmeida", - "@rhreynolds", - "@apeltzer", - "@vivian-chen16", - "@maxulysse", - "@joaodemeirelles" - ], - "maintainers": [ - "@kevinmenden", - "@ggabernet", - "@grst", - "@fmalmeida", - "@rhreynolds", - "@apeltzer", - "@vivian-chen16", - "@maxulysse", - "@joaodemeirelles" - ] - } - }, - { - "name": "staramr_search", - "path": "modules/nf-core/staramr/search/meta.yml", - "type": "module", - "meta": { - "name": "staramr_search", - "description": "Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.", - "keywords": [ - "amr", - "plasmid", - "mlst", - "genomics" - ], - "tools": [ - { - "staramr": { - "description": "Scan genome contigs against the ResFinder and PointFinder databases. In order to use the PointFinder databases, you will have to add --pointfinder-organism ORGANISM to the ext.args options.\n", - "homepage": "https://github.com/phac-nml/staramr", - "documentation": "https://github.com/phac-nml/staramr", - "tool_dev_url": "https://github.com/phac-nml/staramr", - "doi": "10.3390/microorganisms10020292", - "licence": [ - "Apache Software License" - ], - "identifier": "biotools:staramr" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "genome_fasta": { - "type": "file", - "description": "Assembled/complete genome(s) in FASTA format to search for AMR/MLST/Plasmids.\n", - "pattern": "*.{fasta,fna,fsa,fa,fasta.gz,fna.gz,fsa.gz,fa.gz}", - "ontologies": [] - } - } - ] - ], - "output": { - "results_xlsx": [ - [ - { - "meta": { - "type": "file", - "description": "Excel spreadsheet containing summary of StarAMR results.", - "pattern": "*_results/results.xlsx", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3977" - } - ] - } - }, - { - "*_results/results.xlsx": { - "type": "file", - "description": "Excel spreadsheet containing summary of StarAMR results.", - "pattern": "*_results/results.xlsx", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3977" - } - ] - } - } - ] - ], - "summary_tsv": [ - [ - { - "meta": { - "type": "file", - "description": "Excel spreadsheet containing summary of StarAMR results.", - "pattern": "*_results/results.xlsx", - "ontologies": [ + "name": "quant_tximport_summarizedexperiment", + "path": "subworkflows/nf-core/quant_tximport_summarizedexperiment/meta.yml", + "type": "subworkflow", + "meta": { + "name": "quant_tximport_summarizedexperiment", + "description": "Post-process transcript-level quantification results using tximport to produce count matrices and SummarizedExperiment objects", + "keywords": [ + "rnaseq", + "quantification", + "tximport", + "summarizedexperiment", + "salmon", + "kallisto", + "rsem" + ], + "components": ["custom/tx2gene", "tximeta/tximport", "summarizedexperiment/summarizedexperiment"], + "input": [ { - "edam": "http://edamontology.org/format_3977" - } - ] - } - }, - { - "*_results/summary.tsv": { - "type": "file", - "description": "A summary of all detected AMR genes/mutations/plasmids/sequence type in each genome, one genome per line.\nA series of descriptive statistics is also provided for each genome,\nas well as feedback for whether or not the genome passes several quality metrics and if not,\nfeedback on why the genome fails.\n", - "pattern": "*_results/summary.tsv", - "ontologies": [ + "meta": { + "type": "map", + "description": "Groovy Map containing study-level sample sheet information. e.g. [\n id:'SRP1234' ].\n" + } + }, { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "detailed_summary_tsv": [ - [ - { - "meta": { - "type": "file", - "description": "Excel spreadsheet containing summary of StarAMR results.", - "pattern": "*_results/results.xlsx", - "ontologies": [ + "samplesheet": { + "type": "file", + "description": "Sample sheet, to be baked into the `colData` of SummarizedExperiment\nobjects.\n", + "pattern": "*.{csv,tsv}" + } + }, { - "edam": "http://edamontology.org/format_3977" - } - ] - } - }, - { - "*_results/detailed_summary.tsv": { - "type": "file", - "description": "A summary of all detected AMR genes/mutations/plasmids/sequence type in each genome, one genome per line.\nA series of descriptive statistics is also provided for each genome,\nas well as feedback for whether or not the genome passes several quality metrics and if not,\nfeedback on why the genome fails.\n", - "pattern": "*_results/detailed_summary.tsv", - "ontologies": [ + "quant_results": { + "type": "file", + "description": "Per-sample quantification results. For Salmon these are result\ndirectories containing quant.sf, for Kallisto directories containing\nabundance.tsv, and for RSEM the .isoforms.results files. All samples\nmust have been quantified against the same transcriptome, as only a\nsingle sample is used for transcript-to-gene mapping discovery. If\nsupport for mixed transcriptomes is needed in future, tx2gene would\nneed to run independently per sample.\n" + } + }, { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "resfinder_tsv": [ - [ - { - "meta": { - "type": "file", - "description": "Excel spreadsheet containing summary of StarAMR results.", - "pattern": "*_results/results.xlsx", - "ontologies": [ + "gtf": { + "type": "file", + "description": "Channel with features in GTF format, used to generate transcript/gene\nmappings via tx2gene.\n" + } + }, { - "edam": "http://edamontology.org/format_3977" - } - ] - } - }, - { - "*_results/resfinder.tsv": { - "type": "file", - "description": "A tabular file of each AMR gene and additional BLAST information from the ResFinder database, one gene per line.", - "pattern": "*_results/resfinder.tsv", - "ontologies": [ + "gtf_id_attribute": { + "type": "string", + "description": "Attribute in GTF file corresponding to the gene identifier.\n" + } + }, { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "plasmidfinder_tsv": [ - [ - { - "meta": { - "type": "file", - "description": "Excel spreadsheet containing summary of StarAMR results.", - "pattern": "*_results/results.xlsx", - "ontologies": [ + "gtf_extra_attribute": { + "type": "string", + "description": "GTF alternative gene attribute (e.g. gene_name)" + } + }, { - "edam": "http://edamontology.org/format_3977" - } - ] - } - }, - { - "*_results/plasmidfinder.tsv": { - "type": "file", - "description": "A tabular file of each AMR plasmid type and additional BLAST information from the PlasmidFinder database, one plasmid type per line.", - "pattern": "*_results/plasmidfinder.tsv", - "ontologies": [ + "quant_type": { + "type": "string", + "description": "Quantification tool type. One of 'salmon', 'kallisto', or 'rsem'.\n" + } + }, { - "edam": "http://edamontology.org/format_3475" + "skip_merge": { + "type": "boolean", + "description": "Skip cross-sample merging. When true, runs tximport per-sample\ninstead of collecting all samples, and skips SummarizedExperiment\ncreation. Useful for very large cohorts.\n" + } } - ] - } - } - ] - ], - "mlst_tsv": [ - [ - { - "meta": { - "type": "file", - "description": "Excel spreadsheet containing summary of StarAMR results.", - "pattern": "*_results/results.xlsx", - "ontologies": [ + ], + "output": [ { - "edam": "http://edamontology.org/format_3977" - } - ] - } - }, - { - "*_results/mlst.tsv": { - "type": "file", - "description": "A tabular file of each multi-locus sequence type (MLST) and it's corresponding locus/alleles, one genome per line.", - "pattern": "*_results/mlst.tsv", - "ontologies": [ + "tx2gene": { + "type": "file", + "description": "Transcript-to-gene mapping file generated from the GTF.\n", + "pattern": "*.tx2gene.tsv" + } + }, + { + "tpm_gene": { + "type": "file", + "description": "Gene-level matrix of abundance values in TPM.\n", + "pattern": "*.gene_tpm.tsv" + } + }, + { + "counts_gene": { + "type": "file", + "description": "Gene-level matrix of unadjusted estimated counts from tximport\n(`countsFromAbundance = 'no'`).\n", + "pattern": "*.gene_counts.tsv" + } + }, + { + "lengths_gene": { + "type": "file", + "description": "Gene-level matrix of effective length values.\n", + "pattern": "*.gene_lengths.tsv" + } + }, + { + "counts_gene_length_scaled": { + "type": "file", + "description": "Gene-level matrix of estimated counts, generated from abundance (TPM)\nvalues by scaling to library size, additionally scaled using the\naverage transcript length, using tximport\n`countsFromAbundance = 'lengthScaledTPM'`.\n", + "pattern": "*.gene_counts_length_scaled.tsv" + } + }, + { + "counts_gene_scaled": { + "type": "file", + "description": "Gene-level matrix of estimated counts, generated from abundance (TPM)\nvalues by scaling to library size with tximport\n`countsFromAbundance = 'scaledTPM'`.\n", + "pattern": "*.gene_counts_scaled.tsv" + } + }, + { + "tpm_transcript": { + "type": "file", + "description": "Transcript-level matrix of abundance values in TPM.\n", + "pattern": "*.transcript_tpm.tsv" + } + }, + { + "counts_transcript": { + "type": "file", + "description": "Transcript-level matrix of unadjusted estimated counts from tximport\n(`countsFromAbundance = 'no'`).\n", + "pattern": "*.transcript_counts.tsv" + } + }, { - "edam": "http://edamontology.org/format_3475" + "lengths_transcript": { + "type": "file", + "description": "Transcript-level matrix of effective length values.\n", + "pattern": "*.transcript_lengths.tsv" + } + }, + { + "merged_gene_rds": { + "type": "file", + "description": "Serialised SummarizedExperiment object containing gene-level assays\n(counts, length-scaled counts, scaled counts, lengths, TPM).\n", + "pattern": "*.rds" + } + }, + { + "merged_transcript_rds": { + "type": "file", + "description": "Serialised SummarizedExperiment object containing transcript-level\nassays (counts, lengths, TPM).\n", + "pattern": "*.rds" + } } - ] + ], + "authors": ["@pinin4fjords"], + "maintainers": ["@pinin4fjords"] + }, + "pipelines": [ + { + "name": "rnaseq", + "version": "3.26.0" } - } ] - ], - "settings_txt": [ - [ - { - "meta": { - "type": "file", - "description": "Excel spreadsheet containing summary of StarAMR results.", - "pattern": "*_results/results.xlsx", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3977" - } - ] - } - }, - { - "*_results/settings.txt": { - "type": "file", - "description": "The command-line, database versions, and other settings used to run staramr.", - "pattern": "*_results/settings.txt", - "ontologies": [] - } - } - ] - ], - "pointfinder_tsv": [ - [ - { - "meta": { - "type": "file", - "description": "Excel spreadsheet containing summary of StarAMR results.", - "pattern": "*_results/results.xlsx", - "ontologies": [ + }, + { + "name": "quantify_pseudo_alignment", + "path": "subworkflows/nf-core/quantify_pseudo_alignment/meta.yml", + "type": "subworkflow", + "meta": { + "name": "quantify_pseudo_alignment", + "description": "Perform quantification with Salmon or Kallisto to produce count tables and SummarizedExperiment objects", + "keywords": ["rnaseq", "quantification", "kallisto", "salmon"], + "components": ["kallisto/quant", "quant_tximport_summarizedexperiment", "salmon/quant"], + "input": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing study-level sample sheet information. e.g. [\n id:'SRP1234' ].\n" + } + }, + { + "samplesheet": { + "type": "file", + "description": "Sample sheet, to be baked into the `colData` of summarizedexperiment\nobjects.\n", + "pattern": "*.{csv,tsv}" + } + }, + { + "reads": { + "type": "file", + "description": "Channel with input FastQ files of size 1 and 2 for single-end and\npaired-end data, respectively. OR a transcriptome-level BAM file if\nrunning Salmon in alignment mode.\n" + } + }, + { + "index": { + "type": "path", + "description": "Path to Salmon or Kallisto index in the tool-appropriate form.\n" + } + }, + { + "gtf": { + "type": "file", + "description": "Channel with features in GTF format. Passed to pseudoaligners and used\nto generate transcript/ gene mappings.\n" + } + }, + { + "gtf_id_attribute": { + "type": "string", + "description": "Attribute in GTF file corresponding to the gene identifier.\n" + } + }, + { + "gtf_extra_attribute": { + "type": "string", + "description": "GTF alternative gene attribute (e.g. gene_name)" + } + }, + { + "pseudo_aligner": { + "type": "string", + "description": "Pseudoaligner, `kallisto` or `salmon`." + } + }, + { + "alignment_mode": { + "type": "boolean", + "description": "If running Salmon, run in alignment mode (`true` or `false`).\n" + } + }, { - "edam": "http://edamontology.org/format_3977" + "lib_type": { + "type": "string", + "description": "String to override Salmon library type." + } + }, + { + "kallisto_quant_fraglen": { + "type": "integer", + "description": "Estimated fragment length. Required if running Kallisto with\nsingle-ended reads.\n" + } + }, + { + "kallisto_quant_fraglen_sd": { + "type": "integer", + "description": "Estimated standard error for fragment length required by Kallisto in\nsingle-end mode.\n" + } + }, + { + "skip_merge": { + "type": "boolean", + "description": "Skip cross-sample merging. When true, runs tximport per-sample\ninstead of collecting all samples, and skips SummarizedExperiment\ncreation. Useful for very large cohorts.\n" + } } - ] - } - }, - { - "*_results/pointfinder.tsv": { - "type": "file", - "description": "An optional tabular file of each AMR point mutation and additional BLAST information from the PointFinder database, one gene per line.", - "pattern": "*_results/pointfinder.tsv", - "ontologies": [ + ], + "output": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing study-level sample sheet information. e.g. [\n id:'SRP1234' ].\n" + } + }, + { + "results": { + "type": "file", + "description": "Channel containing sample-wise results directories from the\npseudoaligner.\n" + } + }, + { + "multiqc": { + "type": "file", + "description": "Channel containing those pseudoaligner outputs readable by MultiQC for\npassing to workflow-level reporting.\n" + } + }, + { + "tpm_gene": { + "type": "file", + "description": "Gene-level matrix of abundance values in TPM.\n", + "pattern": "*.gene_tpm.tsv" + } + }, + { + "counts_gene": { + "type": "file", + "description": "Gene-level matrix of unadjusted estimated counts from tximport\n(`countsFromAbundance = 'no'`).\n", + "pattern": "*.gene_counts.tsv" + } + }, + { + "lengths_gene": { + "type": "file", + "description": "Gene-level matrix of length values for modelling in downstream\nanalysis.\n", + "pattern": "gene_lengths.tsv" + } + }, + { + "counts_gene_length_scaled": { + "type": "file", + "description": "Gene-level matrix of estimated counts, generated from abundance (TPM)\nvalues by scaling to library size, additionally scaled using the\naverage transcript length, averaged over samples and to library size,\nusing tximport `countsFromAbundance = 'lengthScaledTPM'`.\n", + "pattern": "*.gene_counts_length_scaled.tsv" + } + }, + { + "counts_gene_scaled": { + "type": "file", + "description": "Gene-level matrix of estimated counts, generated from abundance (TPM)\nvalues by scaling to library size with tximport `countsFromAbundance =\n'scaledTPM'`.\n", + "pattern": "*.gene_counts_length_scaled.tsv" + } + }, + { + "tpm_transcript": { + "type": "file", + "description": "Transcript-level matrix of abundance values in TPM.\n", + "pattern": "*.transcript_tpm.tsv" + } + }, + { + "counts_transcript": { + "type": "file", + "description": "Transcript-level matrix of unadjusted estimated counts from tximport\n(`countsFromAbundance = 'no'`).\n", + "pattern": "*.transcript_counts.tsv" + } + }, + { + "lengths_transcript": { + "type": "file", + "description": "Transcript-level matrix of length values for modelling in downstream\nanalysis.\n", + "pattern": "transcript_lengths.tsv" + } + }, + { + "merged_gene_rds_unified": { + "type": "file", + "description": "Serialised SummarizedExperiment object containing gene level\nabundance, count, and length matrices generated from tximport.\n", + "pattern": "*.rds" + } + }, { - "edam": "http://edamontology.org/format_3475" + "merged_transcript_rds_unified": { + "type": "file", + "description": "Serialised SummarizedExperiment object containing transcript level\nabundance, count, and length matrices generated from tximport.\n", + "pattern": "*.rds" + } } - ] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@apetkau" - ], - "maintainers": [ - "@apetkau" - ] - } - }, - { - "name": "stardist", - "path": "modules/nf-core/stardist/meta.yml", - "type": "module", - "meta": { - "name": "stardist", - "description": "Cell and nuclear segmentation with star-convex shapes", - "keywords": [ - "stardist", - "segmentation", - "image", - "gpu", - "spatial-transcriptomics" - ], - "tools": [ - { - "stardist": { - "description": "Stardist is an cell segmentation tool developed in Python by Martin Weigert and Uwe Schmidt", - "homepage": "https://stardist.net/", - "documentation": "https://stardist.net/faq/", - "tool_dev_url": "https://github.com/stardist/stardist", - "doi": "10.1109/ISBIC56247.2022.9854534", - "licence": [ - "BSD 3-Clause" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "image": { - "type": "file", - "description": "Single channel nuclear image", - "pattern": "*.{tiff,tif}", - "ontologies": [] - } - } - ], - [ - { - "model_name": { - "type": "string", - "description": "Name of a pretrained StarDist model (e.g. '2D_versatile_fluo',\n'2D_versatile_he'). Used when model_path is not provided.\nPass '' (empty string) if providing a custom model path or\npassing -m via ext.args.\n" - } + ], + "authors": ["@pinin4fjords", "@adamrtalbot"], + "maintainers": ["@pinin4fjords", "@adamrtalbot"] }, - { - "model_path": { - "type": "file", - "description": "Optional path to a custom StarDist model directory. When provided,\ntakes precedence over model_name. Pass [] (empty list) to use a\npretrained model name instead.\n", - "pattern": "*", - "ontologies": [] - } - } - ] - ], - "output": { - "mask": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.stardist.tif": { - "type": "file", - "description": "labelled mask output from stardist in tif format.", - "pattern": "*.{tiff,tif}", - "ontologies": [] - } - } - ] - ], - "versions_stardist": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "stardist": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pip show stardist | sed -n 's/^Version: //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_python": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "python": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python --version | sed 's/Python //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_tensorflow": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "tensorflow": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pip show tensorflow | sed -n 's/^Version: //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_tifffile": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "tifffile": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pip show tifffile | sed -n 's/^Version: //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "stardist": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pip show stardist | sed -n 's/^Version: //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "python": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python --version | sed 's/Python //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "tensorflow": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pip show tensorflow | sed -n 's/^Version: //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "tifffile": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pip show tifffile | sed -n 's/^Version: //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } + "pipelines": [ + { + "name": "riboseq", + "version": "1.2.0" + }, + { + "name": "rnaseq", + "version": "3.26.0" + } ] - ] - }, - "authors": [ - "@migueLib", - "@dongzehe" - ], - "maintainers": [ - "@migueLib" - ], - "notes": "GPU support: The container (built via Seqera Containers) includes TensorFlow 2.20.0\nwith CUDA support and falls back to CPU automatically when no GPU is available.\nUse the `process_gpu` label to request GPU resources from your executor.\nWhen running with conda/mamba, GPU support depends on having a CUDA-enabled\nTensorFlow installation in your environment.\n\nModel selection via the model input channel [model_name, model_path]:\n - Pretrained model: [ '2D_versatile_fluo', [] ]\n - Custom model directory: [ '', file(\"/path/to/model\") ]\n - Via ext.args only: [ '', [] ] (then set ext.args = '-m ...')\n\nAdditional stardist CLI arguments can be passed via `task.ext.args`:\n ext.args = '--n_tiles 4,4 --prob_thresh 0.5 --nms_thresh 0.3'\n\nModel weights are not bundled in the container. StarDist downloads pretrained\nmodels on first use to ~/.keras/models/.\n" - }, - "pipelines": [ - { - "name": "molkart", - "version": "1.2.0" }, { - "name": "spatialxe", - "version": "dev" - } - ] - }, - { - "name": "stare", - "path": "modules/nf-core/stare/meta.yml", - "type": "module", - "meta": { - "name": "stare", - "description": "Framework that scores enhancer–gene interactions using the Activity-By-Contact model and derives transcription factor affinities on gene level", - "keywords": [ - "enhancer", - "tf_affinity", - "abc_model", - "genomics", - "gene_regulation" - ], - "tools": [ - { - "stare": { - "description": "Score enhancer–gene interactions with ABC and compute TF-gene affinity matrices", - "homepage": "https://github.com/SchulzLab/STARE", - "documentation": "https://stare.readthedocs.io/en/latest/Main.html", - "tool_dev_url": "https://github.com/SchulzLab/STARE", - "doi": "10.1093/bioinformatics/btad062", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "bed_file": { - "type": "file", - "description": "BED file with non-overlapping candidate regions; optional—if omitted runs in promoter-mode around TSS", - "pattern": "*.bed", - "optional": true, - "ontologies": [ - { - "ucsc": "https://genome.ucsc.edu/FAQ/FAQformat#format1" - } - ] - } - }, - { - "contact_folder": { - "type": "directory", - "description": "Directory of gzipped chromatin contact files per chromosome; if not provided use distance-based estimate", - "optional": true - } - }, - { - "existing_abc": { - "type": "file", - "description": "Precomputed ABC‐scoring file (must contain Ensembl ID, PeakID, intergenicScore columns) to reuse interactions", - "pattern": "*.txt.gz", - "optional": true, - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "annotation": { - "type": "file", - "description": "Gene annotation file in GTF format (e.g. Gencode); full annotation recommended for ABC scoring", - "pattern": "*.gtf", - "ontologies": [ - { - "bioontology": "http://edamontology.org/format_2306" - } - ] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "genome": { - "type": "file", - "description": "Genome FASTA file in RefSeq format", - "pattern": "*.{fa,fasta}", - "ontologies": [ - { - "bioontology": "http://edamontology.org/format_1929" - } - ] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "psem": { - "type": "file", - "description": "Position Specific Energy Matrix or Count Matrix in transfac format; converted automatically to PSEM using sequence background from bed_file", - "pattern": "*.transfac", - "ontologies": [] - } - } - ], - [ - { - "meta5": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "exclude_bed": { - "type": "file", - "description": "BED file with regions to exclude; overlapping regions are discarded", - "pattern": "*.bed", - "optional": true, - "ontologies": [ - { - "ucsc": "https://genome.ucsc.edu/FAQ/FAQformat#format1" - } - ] - } - } - ], - [ - { - "meta6": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "genes": { - "type": "file", - "description": "File listing gene IDs or symbols to restrict output; optional", - "pattern": "*.{txt,tsv}", - "optional": true, - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "output": { - "affinities": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n", - "pattern": "${prefix}/Gene_TF_matrices/${prefix}_TF_Gene_Affinities.txt" - } - }, - { - "${meta.id}/Gene_TF_matrices/${meta.id}_TF_Gene_Affinities.txt": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n", - "pattern": "${prefix}/Gene_TF_matrices/${prefix}_TF_Gene_Affinities.txt" - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@LeonHafner" - ], - "maintainers": [ - "@LeonHafner" - ] - }, - "pipelines": [ - { - "name": "tfactivity", - "version": "dev" - } - ] - }, - { - "name": "starfusion_build", - "path": "modules/nf-core/starfusion/build/meta.yml", - "type": "module", - "meta": { - "name": "starfusion_build", - "description": "Download STAR-fusion genome resource required to run STAR-Fusion caller", - "keywords": [ - "download", - "starfusion", - "build" - ], - "tools": [ - { - "star-fusion": { - "description": "Fusion calling algorithm for RNAseq data", - "homepage": "https://github.com/STAR-Fusion/", - "documentation": "https://github.com/STAR-Fusion/STAR-Fusion/wiki/installing-star-fusion", - "tool_dev_url": "https://github.com/STAR-Fusion/STAR-Fusion", - "doi": "10.1186/s13059-019-1842-9", - "licence": [ - "GPL v3" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Metadata map", - "required": true - } - }, - { - "fasta": { - "type": "file", - "description": "Input FASTA file", - "pattern": "*.{fa,fasta}", - "required": true, - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Second metadata map", - "required": true - } + "name": "quantify_rsem", + "path": "subworkflows/nf-core/quantify_rsem/meta.yml", + "type": "subworkflow", + "meta": { + "name": "quantify_rsem", + "description": "Perform quantification with RSEM to produce count tables, legacy merge matrices, and SummarizedExperiment objects", + "keywords": ["rnaseq", "quantification", "rsem", "tximport"], + "components": [ + "rsem/calculateexpression", + "sentieon/rsemcalculateexpression", + "custom/rsemmergecounts", + "quant_tximport_summarizedexperiment" + ], + "input": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing study-level sample sheet information. e.g. [\n id:'SRP1234' ].\n" + } + }, + { + "samplesheet": { + "type": "file", + "description": "Sample sheet, to be baked into the `colData` of summarizedexperiment\nobjects.\n", + "pattern": "*.{csv,tsv}" + } + }, + { + "reads": { + "type": "file", + "description": "Channel with input FastQ files of size 1 and 2 for single-end and\npaired-end data, respectively. OR a transcriptome-level BAM file if\nrunning RSEM in alignment mode.\n" + } + }, + { + "index": { + "type": "path", + "description": "Path to RSEM index directory.\n" + } + }, + { + "gtf": { + "type": "file", + "description": "Channel with features in GTF format. Used to generate transcript/gene\nmappings.\n" + } + }, + { + "gtf_id_attribute": { + "type": "string", + "description": "Attribute in GTF file corresponding to the gene identifier.\n" + } + }, + { + "gtf_extra_attribute": { + "type": "string", + "description": "GTF alternative gene attribute (e.g. gene_name)" + } + }, + { + "use_sentieon_star": { + "type": "boolean", + "description": "Use Sentieon-accelerated STAR for alignment within RSEM. Only\nmeaningful in FASTQ input mode; set to `false` for BAM-mode consumers.\n" + } + }, + { + "skip_merge": { + "type": "boolean", + "description": "Skip cross-sample merging. When true, runs tximport per-sample\ninstead of collecting all samples, skips RSEM merge counts, and\nskips SummarizedExperiment creation. Useful for very large cohorts.\n" + } + } + ], + "output": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information. e.g. [ id:'test' ].\n" + } + }, + { + "raw_counts_gene": { + "type": "file", + "description": "Per-sample RSEM gene-level results files.\n", + "pattern": "*.genes.results" + } + }, + { + "raw_counts_transcript": { + "type": "file", + "description": "Per-sample RSEM transcript-level results files.\n", + "pattern": "*.isoforms.results" + } + }, + { + "stat": { + "type": "file", + "description": "Per-sample RSEM statistics files.\n", + "pattern": "*.stat" + } + }, + { + "logs": { + "type": "file", + "description": "Per-sample RSEM log files (optional, FASTQ mode only).\n", + "pattern": "*.log" + } + }, + { + "merged_counts_gene": { + "type": "file", + "description": "Wide-format gene-level count matrix from RSEM merge.\n", + "pattern": "*.gene_counts.tsv" + } + }, + { + "merged_tpm_gene": { + "type": "file", + "description": "Wide-format gene-level TPM matrix from RSEM merge.\n", + "pattern": "*.gene_tpm.tsv" + } + }, + { + "merged_counts_transcript": { + "type": "file", + "description": "Wide-format transcript-level count matrix from RSEM merge.\n", + "pattern": "*.transcript_counts.tsv" + } + }, + { + "merged_tpm_transcript": { + "type": "file", + "description": "Wide-format transcript-level TPM matrix from RSEM merge.\n", + "pattern": "*.transcript_tpm.tsv" + } + }, + { + "merged_genes_long": { + "type": "file", + "description": "Long-format gene-level results from RSEM merge.\n", + "pattern": "*.genes_long.tsv" + } + }, + { + "merged_isoforms_long": { + "type": "file", + "description": "Long-format isoform-level results from RSEM merge.\n", + "pattern": "*.isoforms_long.tsv" + } + }, + { + "tpm_gene": { + "type": "file", + "description": "Gene-level matrix of abundance values in TPM from tximport.\n", + "pattern": "*.gene_tpm.tsv" + } + }, + { + "counts_gene": { + "type": "file", + "description": "Gene-level matrix of unadjusted estimated counts from tximport\n(`countsFromAbundance = 'no'`).\n", + "pattern": "*.gene_counts.tsv" + } + }, + { + "counts_gene_length_scaled": { + "type": "file", + "description": "Gene-level matrix of estimated counts from tximport using\n`countsFromAbundance = 'lengthScaledTPM'`.\n", + "pattern": "*.gene_counts_length_scaled.tsv" + } + }, + { + "counts_gene_scaled": { + "type": "file", + "description": "Gene-level matrix of estimated counts from tximport using\n`countsFromAbundance = 'scaledTPM'`.\n", + "pattern": "*.gene_counts_scaled.tsv" + } + }, + { + "lengths_gene": { + "type": "file", + "description": "Gene-level matrix of length values from tximport.\n", + "pattern": "*.gene_lengths.tsv" + } + }, + { + "tpm_transcript": { + "type": "file", + "description": "Transcript-level matrix of abundance values in TPM from tximport.\n", + "pattern": "*.transcript_tpm.tsv" + } + }, + { + "counts_transcript": { + "type": "file", + "description": "Transcript-level matrix of unadjusted estimated counts from tximport\n(`countsFromAbundance = 'no'`).\n", + "pattern": "*.transcript_counts.tsv" + } + }, + { + "lengths_transcript": { + "type": "file", + "description": "Transcript-level matrix of length values from tximport.\n", + "pattern": "*.transcript_lengths.tsv" + } + }, + { + "merged_gene_rds_unified": { + "type": "file", + "description": "Serialised SummarizedExperiment object containing gene level\nabundance, count, and length matrices generated from tximport.\n", + "pattern": "*.rds" + } + }, + { + "merged_transcript_rds_unified": { + "type": "file", + "description": "Serialised SummarizedExperiment object containing transcript level\nabundance, count, and length matrices generated from tximport.\n", + "pattern": "*.rds" + } + }, + { + "tx2gene": { + "type": "file", + "description": "Transcript to gene mapping table.\n", + "pattern": "*.tx2gene.tsv" + } + } + ], + "authors": ["@pinin4fjords"], + "maintainers": ["@pinin4fjords"] }, - { - "gtf": { - "type": "file", - "description": "Input GTF (Gene Transfer Format) file", - "pattern": "*.gtf", - "required": true, - "ontologies": [ - { - "edam": "http://edamontology.org/format_2306" - } - ] - } - } - ], - { - "fusion_annot_lib": { - "type": "file", - "description": "Fusion annotation library file containing known fusion genes", - "required": true, - "ontologies": [ + "pipelines": [ { - "edam": "http://edamontology.org/topic_0203" + "name": "rnaseq", + "version": "3.26.0" } - ] - } - }, - { - "dfam_species": { - "type": "string", - "description": "Dfam species name" - } - } - ], - "output": { - "reference": [ - [ - { - "meta": { - "type": "map", - "description": "Metadata map" - } - }, - { - "${prefix}_genome_lib_build_dir": { - "type": "directory", - "description": "Genome library build directory", - "pattern": "*_genome_lib_build_dir" - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@praveenraj2018", - "@martings", - "@alanmmobbs93", - "@delfiterradas", - "@sofiromano" - ], - "maintainers": [ - "@praveenraj2018" - ] - }, - "pipelines": [ - { - "name": "rnafusion", - "version": "4.1.2" - } - ] - }, - { - "name": "starfusion_detect", - "path": "modules/nf-core/starfusion/detect/meta.yml", - "type": "module", - "meta": { - "name": "starfusion_detect", - "description": "Fast and Accurate Fusion Transcript Detection from RNA-Seq", - "keywords": [ - "Fusion", - "starfusion", - "RNA-Seq", - "detect" - ], - "tools": [ - { - "star-fusion": { - "description": "Fast and Accurate Fusion Transcript Detection from RNA-Seq", - "homepage": "https://github.com/STAR-Fusion/STAR-Fusion", - "documentation": "https://github.com/STAR-Fusion/STAR-Fusion/wiki", - "tool_dev_url": "https://github.com/STAR-Fusion/STAR-Fusion/releases", - "doi": "10.1101/120295v1", - "licence": [ - "GPL v3" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "Input fastq files", - "pattern": "*.{fq,fastq,fq.gz,fastq.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - }, - { - "junction": { - "type": "file", - "description": "Chimeric junction output from STAR aligner", - "pattern": "*.{out.junction}", - "ontologies": [] - } - } - ], - { - "reference": { - "type": "directory", - "description": "STAR-fusion reference genome lib folder", - "pattern": "*genome_lib_build_dir" - } - } - ], - "output": { - "fusions": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.fusion_predictions.tsv": { - "type": "file", - "description": "Fusion events from STAR-fusion", - "pattern": "*.{fusion_predictions.tsv}" - } - } - ] - ], - "abridged": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.abridged.tsv": { - "type": "file", - "description": "Abridged version of fusion events from STAR-fusion", - "pattern": "*.{fusion.abridged.tsv}" - } - } - ] - ], - "coding_effect": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.coding_effect.tsv": { - "type": "file", - "description": "Fusion events with their coding effect from STAR-fusion", - "pattern": "*.{coding_effect.tsv}" - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@praveenraj2018" - ] - }, - "pipelines": [ - { - "name": "rnafusion", - "version": "4.1.2" - } - ] - }, - { - "name": "stecfinder", - "path": "modules/nf-core/stecfinder/meta.yml", - "type": "module", - "meta": { - "name": "stecfinder", - "description": "Serotype STEC samples from paired-end reads or assemblies", - "keywords": [ - "serotype", - "Escherichia coli", - "fastq", - "fasta" - ], - "tools": [ - { - "stecfinder": { - "description": "Cluster informed Shigatoxin producing E. coli (STEC) serotyping tool from Illumina reads and assemblies", - "homepage": "https://github.com/LanLab/STECFinder", - "documentation": "https://github.com/LanLab/STECFinder", - "tool_dev_url": "https://github.com/LanLab/STECFinder", - "doi": "10.3389/fcimb.2021.772574", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:stecfinder" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "seqs": { - "type": "file", - "description": "Illumina paired-end reads or an assembly", - "pattern": "*.{fastq.gz,fasta.gz,fna.gz}", - "ontologies": [] - } - } - ] - ], - "output": { - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "A tab-delimited report of results", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@rpetit3" - ], - "maintainers": [ - "@rpetit3" - ] - } - }, - { - "name": "stitch", - "path": "modules/nf-core/stitch/meta.yml", - "type": "module", - "meta": { - "name": "stitch", - "description": "STITCH is an R program for reference panel free, read aware, low coverage sequencing genotype imputation. STITCH runs on a set of samples with sequencing reads in BAM format, as well as a list of positions to genotype, and outputs imputed genotypes in VCF format.", - "keywords": [ - "imputation", - "genomics", - "vcf", - "bgen", - "cram", - "bam", - "sam" - ], - "tools": [ - { - "stitch": { - "description": "STITCH - Sequencing To Imputation Through Constructing Haplotypes", - "homepage": "https://github.com/rwdavies/stitch", - "documentation": "https://github.com/rwdavies/stitch", - "tool_dev_url": "https://github.com/rwdavies/stitch", - "doi": "10.1038/ng.3594", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:stitch-snijderlab" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing information about the set of samples\ne.g. `[ id:'test' ]`\n" - } - }, - { - "collected_crams": { - "type": "file", - "description": "List of sorted BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } - }, - { - "collected_crais": { - "type": "file", - "description": "List of BAM/CRAM/SAM index files", - "pattern": "*.{bai,crai,sai}", - "ontologies": [] - } - }, - { - "cramlist": { - "type": "file", - "description": "Text file with the path to the cram files to use in imputation, one per line. Since the cram files are staged to the working directory for the process, this file should just contain the file names without any pre-pending path.\n", - "pattern": "*.txt", - "ontologies": [] - } - }, - { - "samplename": { - "type": "file", - "description": "(Optional) File with list of samples names in the same order as in bamlist to impute. One file per line.", - "pattern": "*.{txt}", - "ontologies": [] - } - }, - { - "posfile": { - "type": "file", - "description": "Tab-separated file describing the variable positions to be used for imputation. Refer to the documentation for the `--posfile` argument of STITCH for more information.\n", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - }, - { - "input": { - "type": "directory", - "description": "Folder of pre-generated input RData objects used when STITCH is called with the `--regenerateInput FALSE` flag. It is generated by running STITCH with the `--generateInputOnly TRUE` flag.\n", - "pattern": "input" - } - }, - { - "genetic_map": { - "type": "file", - "description": "(Optional) File with genetic map information, a file with 3 white-space delimited entries giving position (1-based), genetic rate map in cM/Mbp, and genetic map in cM. If no file included, rate is based on physical distance and expected rate (expRate).", - "pattern": "*.{txt,map}{,gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - }, - { - "rdata": { - "type": "directory", - "description": "Folder of pre-generated input RData objects used when STITCH is called with the `--regenerateInput FALSE` flag. It is generated by running STITCH with the `--generateInputOnly TRUE` flag.\n", - "pattern": "RData" - } - }, - { - "chromosome_name": { - "type": "string", - "description": "Name of the chromosome to impute. Should match a chromosome name in the reference genome." - } - }, - { - "start": { - "type": "integer", - "description": "Start position of the region to impute." - } - }, - { - "end": { - "type": "integer", - "description": "End position of the region to impute." - } - }, - { - "buffer": { - "type": "integer", - "description": "Buffer, in base pairs, around the region to impute." - } - }, - { - "K": { - "type": "integer", - "description": "Number of ancestral haplotypes to use for imputation. Refer to the documentation for the `--K` argument of STITCH for more information." - } - }, - { - "nGen": { - "type": "integer", - "description": "Number of generations since founding of the population to use for imputation. Refer to the documentation for the `--nGen` argument of STITCH for more information." - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing information about the reference genome used\ne.g. `[ id:'test' ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA reference genome file", - "pattern": "*.{fa,fasta}", - "ontologies": [] - } - }, - { - "fasta_fai": { - "type": "file", - "description": "FASTA index file", - "pattern": "*.{fai}", - "ontologies": [] - } - } - ], - { - "seed": { - "type": "integer", - "description": "Seed for random number generation" - } - } - ], - "output": { - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "input": { - "type": "directory", - "description": "Folder of pre-generated input RData objects used when STITCH is called with the `--regenerateInput FALSE` flag. It is generated by running STITCH with the `--generateInputOnly TRUE` flag.\n", - "pattern": "input" - } - } - ] - ], - "rdata": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "RData": { - "type": "directory", - "description": "Folder of RData objects generated during the imputation process.\n", - "pattern": "RData" - } - } - ] - ], - "plots": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "plots": { - "type": "directory", - "description": "Folder of plots generated during the imputation process.\n", - "pattern": "plots" - } - } - ] - ], - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "*.vcf.gz": { - "type": "file", - "description": "Imputed genotype calls for the positions in `posfile`, in vcf format. This is the default output.\n", - "pattern": ".vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "bgen": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "*.bgen": { - "type": "file", - "description": "Imputed genotype calls for the positions in `posfile`, in vcf format. This is the produced if `--output_format bgen` is specified.\n", - "pattern": ".bgen", - "ontologies": [] - } - } - ] - ], - "versions_r_quilt": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "r-quilt": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "Rscript -e \"cat(as.character(packageVersion('STITCH')))\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_r_base": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "r-base": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "R --version | sed \"1!d; s/.*version //; s/ .*//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_rsync": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "rsync": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "rsync --version | sed '1!d;s/^rsync version //; s/ .*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "r-quilt": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "Rscript -e \"cat(as.character(packageVersion('STITCH')))\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "r-base": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "R --version | sed \"1!d; s/.*version //; s/ .*//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "rsync": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "rsync --version | sed '1!d;s/^rsync version //; s/ .*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@saulpierotti" - ], - "maintainers": [ - "@saulpierotti" - ] - }, - "pipelines": [ - { - "name": "phaseimpute", - "version": "1.1.0" - } - ] - }, - { - "name": "stranger", - "path": "modules/nf-core/stranger/meta.yml", - "type": "module", - "meta": { - "name": "stranger", - "description": "Annotates output files from ExpansionHunter with the pathologic implications of the repeat sizes.", - "keywords": [ - "STR", - "repeat_expansions", - "annotate", - "vcf" - ], - "tools": [ - { - "stranger": { - "description": "Annotate VCF files with str variants", - "homepage": "https://github.com/moonso/stranger", - "documentation": "https://github.com/moonso/stranger", - "tool_dev_url": "https://github.com/moonso/stranger", - "doi": "10.5281/zenodo.4548873", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF with repeat expansions", - "pattern": "*.{vcf.gz,vcf}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "variant_catalog": { - "type": "file", - "description": "json file with repeat expansion sites to genotype", - "pattern": "*.{json}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Annotated VCF file", - "pattern": "*.{vcf.gz}" - } - }, - { - "*.vcf.gz": { - "type": "map", - "description": "Annotated VCF file", - "pattern": "*.{vcf.gz}" - } - } - ] - ], - "tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Annotated VCF file", - "pattern": "*.{vcf.gz}" - } - }, - { - "*.vcf.gz.tbi": { - "type": "map", - "description": "Index of the annotated VCF file", - "pattern": "*.{vcf.gz.tbi}" - } - } - ] - ], - "versions_stranger": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "stranger": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "stranger --version | sed 's/stranger, version //g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_tabix": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "tabix": { - "type": "string", - "description": "The tool name" - } - }, - { - "tabix -h 2>&1 | grep -oP 'Version:\\s*\\K[^\\s]+'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "stranger": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "stranger --version | sed 's/stranger, version //g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "tabix": { - "type": "string", - "description": "The tool name" - } - }, - { - "tabix -h 2>&1 | grep -oP 'Version:\\s*\\K[^\\s]+'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@ljmesi" - ], - "maintainers": [ - "@ljmesi" - ] - }, - "pipelines": [ - { - "name": "raredisease", - "version": "3.0.0" - } - ] - }, - { - "name": "strdrop_build", - "path": "modules/nf-core/strdrop/build/meta.yml", - "type": "module", - "meta": { - "name": "strdrop_build", - "description": "Build reference json from sequencing coverage in STR VCFs", - "keywords": [ - "str", - "vcf", - "lrs" - ], - "tools": [ - { - "strdrop": { - "description": "Flag STR coverage drops in LRS data", - "homepage": "https://github.com/dnil/strdrop", - "documentation": "https://github.com/dnil/strdrop/blob/main/docs/README.md", - "tool_dev_url": "https://github.com/dnil/strdrop", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "training_set": { - "type": "file", - "description": "Input VCF training set files", - "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - }, - { - "edam": "http://edamontology.org/format_3020" - } - ] - } - } - ] - ], - "output": { - "json": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.json": { - "type": "file", - "description": "Output reference json file", - "pattern": "*.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "versions_strdrop": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "strdrop": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "strdrop --version | sed 's/.* //g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "strdrop": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "strdrop --version | sed 's/.* //g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@fellen31" - ], - "maintainers": [ - "@fellen31" - ] - } - }, - { - "name": "strdrop_call", - "path": "modules/nf-core/strdrop/call/meta.yml", - "type": "module", - "meta": { - "name": "strdrop_call", - "description": "Detect drops in STR coverage", - "keywords": [ - "str", - "vcf", - "lrs" - ], - "tools": [ - { - "strdrop": { - "description": "Flag STR coverage drops in LRS data", - "homepage": "https://github.com/dnil/strdrop", - "documentation": "https://github.com/dnil/strdrop/blob/main/docs/README.md", - "tool_dev_url": "https://github.com/dnil/strdrop", - "licence": [ - "MIT" - ] - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "vcf": { - "type": "file", - "description": "Input STR call VCF file", - "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - }, - { - "edam": "http://edamontology.org/format_3020" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing training set information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "training_set_json": { - "type": "file", - "description": "Input training set as json", - "pattern": "*.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing training set information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "training_set_vcfs": { - "type": "file", - "description": "Input training set as VCF files", - "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - }, - { - "edam": "http://edamontology.org/format_3020" - } - ] - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.vcf.gz": { - "type": "file", - "description": "Output annotated VCF file", - "pattern": "*.{vcf.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - } - ] - } - } - ] - ], - "versions_strdrop": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "strdrop": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "strdrop --version | sed 's/.* //g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "strdrop": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "strdrop --version | sed 's/.* //g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@fellen31" - ], - "maintainers": [ - "@fellen31" - ] - } - }, - { - "name": "strdust", - "path": "modules/nf-core/strdust/meta.yml", - "type": "module", - "meta": { - "name": "STRdust", - "description": "Tandem repeat genotyper for long reads", - "keywords": [ - "long read", - "tandem repeats", - "genomics" - ], - "tools": [ - { - "STRdust": { - "description": "Tandem repeat genotyper for long reads.", - "homepage": "https://github.com/wdecoster/STRdust/", - "documentation": "https://github.com/wdecoster/STRdust/blob/main/README.md", - "tool_dev_url": "https://github.com/wdecoster/STRdust", - "doi": "10.1101/gr.279265.124 ", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted (and preferably phased) BAM/CRAM file.\nAdd command line argument `--unphased` if reads are not phased.\n", - "pattern": "*.{bam,cram}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - }, - { - "edam": "http://edamontology.org/format_2573" - }, - { - "edam": "http://edamontology.org/format_3462" - } - ] - } - }, - { - "bai": { - "type": "file", - "description": "Index of BAM/CRAM file", - "pattern": "*.{bai,crai,csi}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3327" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. `[ id: 'GRCh38' ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome", - "pattern": "*.{fa,fasta,fna}?(.gz)", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. `[ id: 'GRCh38' ]`\n" - } - }, - { - "fai": { - "type": "file", - "description": "Index of reference genome", - "pattern": "*.{fai,gzi}", - "ontologies": [] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing interval information\ne.g. `[ id: \"GRCh38_strs\" ] `\n" - } - }, - { - "bed": { - "type": "file", - "description": "BED file containing STR regions to genotype (optional)", - "pattern": "*.bed", - "ontologies": [] - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.vcf.gz": { - "type": "file", - "description": "Called tandem repeats as VCF file.\nSorted if `--sorted` command line argument was specified.\n", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.tbi": { - "type": "file", - "description": "Index of output VCF.\nOutput only if VCF is sorted (i.e. `--sorted` was specified).\n", - "pattern": "*.tbi", - "ontologies": [] - } - } - ] - ], - "versions_strdust": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "strdust": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "STRdust --version |& sed '1!d ; s/STRdust //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_bgzip": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bgzip": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "bgzip --version |& sed '1!d ; s/bgzip (htslib) //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "strdust": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "STRdust --version |& sed '1!d ; s/STRdust //'": { - 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"keywords": [ - "structural variants", - "sv", - "deletions", - "duplications", - "annotations" - ], - "tools": [ - { - "strvctvre": { - "description": "StrVCTVRE, a structural variant classifier for exonic deletions and duplications", - "homepage": "https://github.com/andrewSharo/StrVCTVRE/tree/master", - "documentation": "https://github.com/andrewSharo/StrVCTVRE/tree/master", - "tool_dev_url": "https://github.com/andrewSharo/StrVCTVRE/tree/master", - "licence": [ - "MIT" - ], - "identifier": "biotools:strvctvre" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" - } - }, - { - "sv_file": { - "type": "file", - "description": "Structural variants file in VCF or BED format", - "pattern": "*.{vcf,bed}", - "ontologies": [] - } - }, - { - "sv_file_index": { - "type": "file", - "description": "Index file for the structural variants file VCF file", - "pattern": "*.tbi", - "ontologies": [] - } - }, - { - "assembly": { - "type": "string", - "description": "Genome assembly version, has to be one of 'GRCh38' or 'GRCh37'", - "enum": [ - "GRCh38", - "GRCh37" - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" - } - }, - { - "phylop": { - "type": "file", - "description": "PhyloP bigWig file (fetched from https://hgdownload.cse.ucsc.edu/goldenpath/hg38/phyloP100way/)", - "pattern": "*.bw", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" - } - }, - { - "data_directory": { - "type": "directory", - "description": "Directory containing the StrVCTVRE data files (fetched from https://github.com/andrewSharo/StrVCTVRE/tree/master/data)" - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" - } - }, - { - "*.vcf": { - "type": "file", - "description": "Structural variants file in VCF format", - "pattern": "*.vcf", - "ontologies": [] - } - } - ] - ], - "bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" - } - }, - { - "*.bed": { - "type": "file", - "description": "Structural variants file in BED format", - "pattern": "*.bed", - "ontologies": [] - } - } - ] - ], - "versions_strvctvre": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "strvctvre": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "StrVCTVRE.py --help |& sed -n 's/StrVCTVRE: version *//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "strvctvre": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "StrVCTVRE.py --help |& sed -n 's/StrVCTVRE: version *//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@nvnieuwk" - ], - "maintainers": [ - "@nvnieuwk" - ] - } - }, - { - "name": "subread_featurecounts", - "path": "modules/nf-core/subread/featurecounts/meta.yml", - "type": "module", - "meta": { - "name": "subread_featurecounts", - "description": "Count reads that map to genomic features", - "keywords": [ - "counts", - "fasta", - "genome", - "reference" - ], - "tools": [ - { - "featurecounts": { - "description": "featureCounts is a highly efficient general-purpose read summarization program that counts mapped reads for genomic features such as genes, exons, promoter, gene bodies, genomic bins and chromosomal locations. It can be used to count both RNA-seq and genomic DNA-seq reads.", - "homepage": "http://bioinf.wehi.edu.au/featureCounts/", - "documentation": "http://bioinf.wehi.edu.au/subread-package/SubreadUsersGuide.pdf", - "doi": "10.1093/bioinformatics/btt656", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:subread" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bams": { - "type": "file", - "description": "BAM files containing mapped reads", - "pattern": "*.bam", - "ontologies": [] - } - }, - { - "annotation": { - "type": "file", - "description": "Genomic features annotation in GTF or SAF", - "pattern": "*.{gtf,saf}", - "ontologies": [] - } - } - ] - ], - "output": { - "counts": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*featureCounts.tsv": { - "type": "file", - "description": "Counts of reads mapping to features", - "pattern": "*featureCounts.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "summary": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*featureCounts.tsv.summary": { - "type": "file", - "description": "Summary log file", - "pattern": "*.featureCounts.tsv.summary", - "ontologies": [] - } - } - ] - ], - "versions_subread": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "subread": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "featureCounts -v 2>&1 | sed 's/featureCounts v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "subread": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "featureCounts -v 2>&1 | sed 's/featureCounts v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@ntoda03" - ], - "maintainers": [ - "@ntoda03" - ] - }, - "pipelines": [ - { - "name": "atacseq", - "version": "2.1.2" - }, - { - "name": "callingcards", - "version": "1.0.0" - }, - { - "name": "chipseq", - "version": "2.1.0" }, { - "name": "lncpipe", - "version": "dev" - }, - { - "name": "magmap", - "version": "1.0.0" - }, - { - "name": "metatdenovo", - "version": "1.3.0" - }, - { - "name": "nascent", - "version": "2.3.0" - }, - { - "name": "panoramaseq", - "version": "dev" - }, - { - "name": "rnaseq", - "version": "3.26.0" - }, - { - "name": "rnasplice", - "version": "1.0.4" - } - ] - }, - { - "name": "summarizedexperiment_summarizedexperiment", - "path": "modules/nf-core/summarizedexperiment/summarizedexperiment/meta.yml", - "type": "module", - "meta": { - "name": "summarizedexperiment_summarizedexperiment", - "description": "SummarizedExperiment container\n", - "keywords": [ - "gene", - "transcript", - "sample", - "matrix", - "assay" - ], - "tools": [ - { - "summarizedexperiment": { - "description": "The SummarizedExperiment container contains one or more assays, each represented by a matrix-like object of numeric or other mode. The rows typically represent genomic ranges of interest and the columns represent samples.", - "homepage": "https://bioconductor.org/packages/release/bioc/html/SummarizedExperiment.html", - "documentation": "https://bioconductor.org/packages/release/bioc/vignettes/SummarizedExperiment/inst/doc/SummarizedExperiment.html", - "tool_dev_url": "https://github.com/Bioconductor/SummarizedExperiment", - "doi": "10.18129/B9.bioc.SummarizedExperiment", - "licence": [ - "Artistic-2.0" - ], - "identifier": "biotools:summarizedexperiment" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing information related to the experiment as a whole\ne.g. `[ id:'SRP123456' ]`\n" - } - }, - { - "matrix_files": { - "type": "directory", - "description": "One or more paths to CSV or TSV matrix files. All files must have the\nsame rows and columns.\n", - "pattern": "*.{csv,tsv}" - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information related to the species\nreference from which matrix rows are derived e.g. `[ id:'yeast' ]`\n" - } - }, - { - "rowdata": { - "type": "file", - "description": "Metadata on matrix features. One column must contain all matrix row\nIDs.\n", - "pattern": "*.{csv,tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - }, - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing information related to the experiment as a whole,\nas represented by the matrix columns and the sample sheet e.g.\n`[id:'SRP123456' ]`\n" - } - }, - { - "coldata": { - "type": "file", - "description": "Metadata on matrix columns. One column must contain all matrix column\nIDs.\n", - "pattern": "*.{csv,tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - }, - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "output": { - "rds": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing information related to the experiment as a whole\ne.g. `[ id:'SRP123456' ]`\n" - } - }, - { - "*.rds": { - "type": "file", - "description": "Serialised SummarizedExperiment object", - "pattern": "*.SummarizedExperiment.rds", - "ontologies": [] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing information related to the experiment as a whole\ne.g. `[ id:'SRP123456' ]`\n" - } - }, - { - "*.R_sessionInfo.log": { - "type": "file", - "description": "dump of R SessionInfo", - "pattern": "*.log", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "YAML file containing versions of tools used in the module", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "topics": { - "versions": [ - { - "versions.yml": { - "type": "string", - "description": "The name of the process" - } + "name": "tif_registration_stainwarpy", + "path": "subworkflows/nf-core/tif_registration_stainwarpy/meta.yml", + "type": "subworkflow", + "meta": { + "name": "tif_registration_stainwarpy", + "description": "Register H&E stained and multiplexed tissue images and transform segmentation masks using stainwarpy", + "keywords": ["image registration", "histology", "hne", "multiplexed", "segmentation mask"], + "components": ["stainwarpy/extractchannel", "stainwarpy/register", "stainwarpy/transformsegmask"], + "input": [ + { + "ch_hne": { + "type": "file", + "description": "Channel containing H&E stained tissue image in TIF/OME-TIF format\nStructure: [ val(meta), path(ome.tif) ]\n", + "pattern": "*.{tif,ome.tif,tiff,ome.tiff}" + } + }, + { + "ch_multiplexed": { + "type": "file", + "description": "Channel containing multiplexed tissue image in TIF/OME-TIF format\nStructure: [ val(meta), path(ome.tif) ]\n", + "pattern": "*.{tif,ome.tif,tiff,ome.tiff}" + } + }, + { + "ch_segmask": { + "type": "file", + "description": "Channel containing segmentation mask in TIF/OME-TIF/npy format. (optional input)\nStructure: [ val(meta), path(ome.tif) ]\n", + "pattern": "*.{tif,ome.tif,tiff,ome.tiff,npy}" + } + }, + { + "val_fixed_img": { + "type": "string", + "description": "Fixed image to use for registration (\"multiplexed\" or \"hne\")\n" + } + }, + { + "val_final_img_sz": { + "type": "string", + "description": "Final image size to output registered image and segmentation mask (\"multiplexed\" or \"hne\")\n" + } + } + ], + "output": [ + { + "transformed_image": { + "type": "file", + "description": "Channel containing registered tissue image\nStructure: [ val(meta), path(ome.tif) ]\n", + "pattern": "*_transformed_image.ome.tif" + } + }, + { + "transformed_segmask": { + "type": "file", + "description": "Channel containing transformed segmentation mask (empty if 'ch_segmask' not provided)\nStructure: [ val(meta), path(ome.tif) ]\n", + "pattern": "*_transformed_segmentation_mask.ome.tif" + } + }, + { + "metrics": { + "type": "file", + "description": "Channel containing registration metrics and transformation map file\nStructure: [ val(meta), path(json) ]\n", + "pattern": "*_registration_metrics_tform_map.json" + } + } + ], + "authors": ["@tckumarasekara"], + "maintainers": ["@tckumarasekara"] } - ] }, - "authors": [ - "@pinin4fjords" - ], - "maintainers": [ - "@pinin4fjords" - ] - }, - "pipelines": [ { - "name": "riboseq", - "version": "1.2.0" - }, - { - "name": "rnaseq", - "version": "3.26.0" - } - ] - }, - { - "name": "survivor_bedpetovcf", - "path": "modules/nf-core/survivor/bedpetovcf/meta.yml", - "type": "module", - "meta": { - "name": "survivor_bedpetovcf", - "description": "Converts a bedpe file to a VCF file (beta version)", - "keywords": [ - "bedpe", - "conversion", - "vcf", - "structural variants" - ], - "tools": [ - { - "survivor": { - "description": "Toolset for SV simulation, comparison and filtering", - "homepage": "https://github.com/fritzsedlazeck/SURVIVOR/wiki", - "documentation": "https://github.com/fritzsedlazeck/SURVIVOR/wiki", - "tool_dev_url": "https://github.com/fritzsedlazeck/SURVIVOR", - "doi": "10.1038/NCOMMS14061", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bedpe": { - "type": "file", - "description": "BEDPE file", - "ontologies": [] - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.vcf": { - "type": "file", - "description": "Output VCF file", - "pattern": "*.{vcf}", - "ontologies": [] - } - } - ] - ], - "versions_survivor": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "survivor": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "SURVIVOR 2>&1 | grep 'Version' | sed 's/Version: //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "survivor": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "SURVIVOR 2>&1 | grep 'Version' | sed 's/Version: //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@kubranarci" - ], - "maintainers": [ - "@kubranarci" - ] - } - }, - { - "name": "survivor_filter", - "path": "modules/nf-core/survivor/filter/meta.yml", - "type": "module", - "meta": { - "name": "survivor_filter", - "description": "Filter a vcf file based on size and/or regions to ignore", - "keywords": [ - "survivor", - "filter", - "vcf", - "structural variants" - ], - "tools": [ - { - "survivor": { - "description": "Toolset for SV simulation, comparison and filtering", - "homepage": "https://github.com/fritzsedlazeck/SURVIVOR/wiki", - "documentation": "https://github.com/fritzsedlazeck/SURVIVOR/wiki", - "tool_dev_url": "https://github.com/fritzsedlazeck/SURVIVOR", - "doi": "10.1038/NCOMMS14061", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf_file": { - "type": "file", - "description": "VCF file to filter", - "ontologies": [] - } - }, - { - "bed": { - "type": "file", - "description": "BED file with regions to ignore (NA to disable)", - "ontologies": [] - } - } - ], - { - "minsv": { - "type": "integer", - "description": "Min SV size (-1 to disable)" - } - }, - { - "maxsv": { - "type": "integer", - "description": "Max SV size (-1 to disable)" - } - }, - { - "minallelefreq": { - "type": "float", - "description": "Min allele frequency (0-1)" - } - }, - { - "minnumreads": { - "type": "integer", - "description": "Min number of reads support [RE flag (-1 to disable)]" - } - } - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.vcf": { - 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] - }, - "pipelines": [ - { - "name": "variantbenchmarking", - "version": "1.5.0" - } - ] - }, - { - "name": "survivor_merge", - "path": "modules/nf-core/survivor/merge/meta.yml", - "type": "module", - "meta": { - "name": "survivor_merge", - "description": "Compare or merge VCF files to generate a consensus or multi sample VCF files.", - "keywords": [ - "survivor", - "merge", - "vcf", - "structural variants" - ], - "tools": [ - { - "survivor": { - "description": "Toolset for SV simulation, comparison and filtering", - "homepage": "https://github.com/fritzsedlazeck/SURVIVOR/wiki", - "documentation": "https://github.com/fritzsedlazeck/SURVIVOR/wiki", - "tool_dev_url": "https://github.com/fritzsedlazeck/SURVIVOR", - "doi": "10.1038/NCOMMS14061", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcfs": { - "type": "list", - "description": "The VCF files to be merged\nGzipped VCF files are not supported: https://github.com/fritzsedlazeck/SURVIVOR/issues/158\n", - "pattern": "*.vcf" - } - } - ], - { - "max_distance_breakpoints": { - "type": "integer", - "description": "Max distance between breakpoints (0-1 percent of length, 1- number of bp)" - } - }, - { - "min_supporting_callers": { - "type": "integer", - "description": "Minimum number of supporting caller" - } - }, - { - "account_for_type": { - "type": "integer", - "description": "Take the type into account (1==yes, else no)" - } - }, - { - "account_for_sv_strands": { - "type": "integer", - "description": "Take the strands of SVs into account (1==yes, else no)" - } - }, - { - "estimate_distanced_by_sv_size": { - "type": "integer", - "description": "Estimate distance based on the size of SV (1==yes, else no)" - } - }, - { - "min_sv_size": { - "type": "integer", - "description": "Minimum size of SVs to be taken into account" - } - } - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.vcf": { - "type": "file", - "description": "The merged VCF file", - "pattern": "*.vcf", - "ontologies": [] - } - } - ] - ], - "versions_survivor": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "survivor": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "SURVIVOR 2>&1 | grep 'Version' | sed 's/Version: //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "survivor": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "SURVIVOR 2>&1 | grep 'Version' | sed 's/Version: //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@nvnieuwk" - ], - "maintainers": [ - "@nvnieuwk" - ] - }, - "pipelines": [ - { - "name": "variantbenchmarking", - "version": "1.5.0" - } - ] - }, - { - "name": "survivor_simsv", - "path": "modules/nf-core/survivor/simsv/meta.yml", - "type": "module", - "meta": { - "name": "survivor_simsv", - "description": "Simulate an SV VCF file based on a reference genome", - "keywords": [ - "structural variants", - "simulation", - "sv", - "vcf" - ], - "tools": [ - { - "survivor": { - "description": "Toolset for SV simulation, comparison and filtering", - "homepage": "https://github.com/fritzsedlazeck/SURVIVOR/wiki", - "documentation": "https://github.com/fritzsedlazeck/SURVIVOR/wiki", - "tool_dev_url": "https://github.com/fritzsedlazeck/SURVIVOR", - "doi": "10.1038/NCOMMS14061", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing fasta information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference genome", - "pattern": "*.{fasta,fna,fa}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing fasta index information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "fai": { - "type": "file", - "description": "The index of the reference genome", - "pattern": "*.fai", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing parameters information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "parameters": { - "type": "file", - "description": "A text file containing the parameters to be used for the simulation. Gets automatically generated using defaults when this is not supplied", - "pattern": "*.txt", - "ontologies": [] - } - } - ], - { - "snp_mutation_frequency": { - "type": "float", - "description": "The SNP mutation frequency in the output VCF (0-1)" - } - }, - { - "sim_reads": { - "type": "integer", - "description": "Whether or not to simulate reads (1==yes, else no)" - } - } - ], - "output": { - "parameters": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*.txt": { - "type": "file", - "description": "The created parameters file", - "pattern": "*.txt", - "ontologies": [] - } - } - ] - ], - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*.vcf": { - "type": "file", - "description": "A VCF containing the simulated variants", - "pattern": "*.vcf", - "ontologies": [] - } - } - ] - ], - "bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*.bed": { - "type": "file", - "description": "A BED file of the simulated structural variants", - "pattern": "*.bed", - "ontologies": [] - } - } - ] - ], - "fasta": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*.fasta": { - "type": "file", - "description": "A Fasta file file containing the variants from the output VCF", - "pattern": "*.fasta", - "ontologies": [] - } - } - ] - ], - "insertions": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*.insertions.fa": { - "type": "file", - "description": "A Fasta file file containing insertion sequences", - "pattern": "*.insertions.fa", - "ontologies": [] - } - } - ] - ], - "versions_survivor": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "survivor": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "SURVIVOR 2>&1 | grep 'Version' | sed 's/Version: //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "survivor": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "SURVIVOR 2>&1 | grep 'Version' | sed 's/Version: //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@nvnieuwk" - ], - "maintainers": [ - "@nvnieuwk" - ] - } - }, - { - "name": "survivor_stats", - "path": "modules/nf-core/survivor/stats/meta.yml", - "type": "module", - "meta": { - "name": "survivor_stats", - "description": "Report multiple stats over a VCF file", - "keywords": [ - "survivor", - "statistics", - "vcf", - "structural variants" - ], - "tools": [ - { - "survivor": { - "description": "Toolset for SV simulation, comparison and filtering", - "homepage": "https://github.com/fritzsedlazeck/SURVIVOR/wiki", - "documentation": "https://github.com/fritzsedlazeck/SURVIVOR/wiki", - "tool_dev_url": "https://github.com/fritzsedlazeck/SURVIVOR", - "doi": "10.1038/NCOMMS14061", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF file to filter", - "pattern": "*.{vcf}", - "ontologies": [] - } - } - ], - { - "minsv": { - "type": "integer", - "description": "Min SV size (-1 to disable)" - } - }, - { - "maxsv": { - "type": "integer", - "description": "Max SV size (-1 to disable)" - } - }, - { - "minnumreads": { - "type": "integer", - "description": "Min number of reads support [RE flag (-1 to disable)]" - } - } - ], - "output": { - "stats": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.stats": { - "type": "file", - "description": "File containing statistics given input VCF file", - "pattern": "*.{stats}", - "ontologies": [] - } - } - ] - ], - "versions_survivor": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "survivor": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "SURVIVOR 2>&1 | grep 'Version' | sed 's/Version: //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "survivor": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "SURVIVOR 2>&1 | grep 'Version' | sed 's/Version: //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@kubranarci" - ], - "maintainers": [ - "@kubranarci" - ] - }, - "pipelines": [ - { - "name": "variantbenchmarking", - "version": "1.5.0" - } - ] - }, - { - "name": "sushie", - "path": "modules/nf-core/sushie/meta.yml", - "type": "module", - "meta": { - "name": "sushie", - "description": "Software to perform multi-ancestry SNP fine-mapping on molecular data", - "keywords": [ - "gwas", - "fine mapping", - "ancestry" - ], - "tools": [ - { - "sushie": { - "description": "Software to perform multi-ancestry SNP fine-mapping on molecular data", - "homepage": "https://github.com/mancusolab/sushie/", - "documentation": "https://mancusolab.github.io/sushie/", - "tool_dev_url": "https://github.com/mancusolab/sushie/", - "doi": "10.1038/s41588-025-02262-7", - "licence": [ - "MIT" - ], - "identifier": "biotools:sushie" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "study_locus_files": { - "type": "file", - "description": "Study locus file(s)", - "pattern": "*.gwas", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - { - "ld_files": { - "type": "file", - "description": "LD file(s)", - "pattern": "*.ld", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - }, - { - "sample_sizes": { - "type": "string", - "description": "Sample size(s)" - } - } - ], - "output": { - "corr": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.sushie.corr.tsv.gz": { - "type": "file", - "description": "Effect size correlation", - "pattern": "*.sushie.corr.tsv.gz", - "ontologies": [ + "name": "tiff_segmentation_vpt", + "path": "subworkflows/nf-core/tiff_segmentation_vpt/meta.yml", + "type": "subworkflow", + "meta": { + "name": "tiff_segmentation_vpt", + "description": "Perform segmentation of MERSCOPE TIFF images using the vizgen-postprocessing tool", + "keywords": ["segmentation", "imaging", "merscope", "vizgen", "tiff", "spatial"], + "components": [ + "vizgenpostprocessing/preparesegmentation", + "vizgenpostprocessing/runsegmentationontile", + "vizgenpostprocessing/compiletilesegmentation" + ], + "input": [ { - "edam": "http://edamontology.org/format_3475" + "ch_input": { + "type": "channel", + "description": "The input channel containing image directory and transformation file\nStructure: [ val(meta), path(image_dir), path(micron_to_mosaic_pixel_transform.csv) ]\n", + "pattern": "*" + } }, { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "cs": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.sushie.cs.tsv.gz": { - "type": "file", - "description": "Credible set", - "pattern": "*.sushie.cs.tsv.gz", - "ontologies": [ + "ch_algorithm_json": { + "type": "channel", + "description": "Channel containing algorithm configuration file\nStructure: [ path(algorithm.json) ]\n", + "pattern": "*.json" + } + }, { - "edam": "http://edamontology.org/format_3475" + "ch_images_regex": { + "type": "channel", + "description": "Channel containing regex pattern for image matching\nStructure: [ val(regex) ]\n", + "pattern": "*" + } }, { - "edam": "http://edamontology.org/format_3989" + "ch_custom_weights": { + "type": "channel", + "description": "Channel containing custom weights for segmentation\nStructure: [ path(custom_weights) ]\n", + "pattern": "*" + } } - ] - } - } - ] - ], - "weights": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.sushie.weights.tsv.gz": { - "type": "file", - "description": "Prediction weights", - "pattern": "*.sushie.weights.tsv.gz", - "ontologies": [ + ], + "output": [ { - "edam": "http://edamontology.org/format_3475" + "micron_space_segmentation": { + "type": "file", + "description": "Channel containing micron space segmentation results\nStructure: [ val(meta), path(parquet) ]\n", + "pattern": "*.parquet" + } + }, + { + "mosaic_space_segmentation": { + "type": "file", + "description": "Channel containing mosaic space segmentation results\nStructure: [ val(meta), path(parquet) ]\n", + "pattern": "*.parquet" + } }, { - "edam": "http://edamontology.org/format_3989" + "versions": { + "type": "file", + "description": "File containing software versions\nStructure: [ path(versions.yml) ]\n", + "pattern": "versions.yml" + } } - ] - } - } - ] - ], - "versions_sushie": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "sushie": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "0.19": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.log": { - "type": "file", - "description": "Log file", - "pattern": "*.log", - "ontologies": [] - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "sushie": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "0.19": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@camlloyd" - ], - "maintainers": [ - "@camlloyd" - ] - } - }, - { - "name": "svaba", - "path": "modules/nf-core/svaba/meta.yml", - "type": "module", - "meta": { - "name": "svaba", - "description": "SvABA is an efficient and accurate method for detecting SVs from short-read sequencing data using genome-wide local assembly with low memory and computing requirements", - "keywords": [ - "sv", - "structural variants", - "detecting svs", - "short-read sequencing" - ], - "tools": [ - { - "svaba": { - "description": "Structural variation and indel detection by local assembly", - "homepage": "https://github.com/walaj/svaba", - "documentation": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5880247/", - "tool_dev_url": "https://github.com/walaj/svaba", - "doi": "10.1101/gr.221028.117", - "licence": [ - "GPL v3" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\nid: should be the identification number or sample name. If there is normal file meta should be common\ne.g. [ id:'test' ]\n" - } - }, - { - "tumorbam": { - "type": "file", - "description": "Tumor or metastatic sample, BAM, SAM or CRAM file", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } - }, - { - "tumorbai": { - "type": "file", - "description": "Index of the tumor or metastatic sample", - "pattern": "*.{bai,crai,sai}", - "ontologies": [] - } - }, - { - "normalbam": { - "type": "file", - "description": "Control (or normal) of matching tumor/metastatic sample, BAM, SAM or CRAM file", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } - }, - { - "normalbai": { - "type": "file", - "description": "Index", - "pattern": "*.{bai,crai,sai}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing FASTA information\nid: should be the identification number for alignment file and should be the same used to create BWA index files\ne.g. [ id:'fasta' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA file", - "pattern": "*.{fasta|fa}", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing FASTA information\nid: should be the identification number for alignment file and should be the same used to create BWA index files\ne.g. [ id:'fasta' ]\n" - } - }, - { - "fasta_fai": { - "type": "file", - "description": "Index of FASTA file", - "pattern": "*.{fai}", - "ontologies": [] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing BWA information\nid: should be the identification number same as fasta file\ne.g. [ id:'bwa' ]\n" - } - }, - { - "bwa_index": { - "type": "file", - "description": "BWA genome index files. Note that this tool requires the bwa index files to be of the format `prefix.suffix.amb`, where `prefix.suffix` is the full name of the fasta file, not just the prefix.", - "pattern": "Directory containing BWA index *.{amb,ann,bwt,pac,sa}", - "ontologies": [] - } + ], + "authors": ["@mcmero"], + "maintainers": ["@mcmero"] } - ], - [ - { - "meta5": { - "type": "map", - "description": "Groovy Map containing dbSNP information\nid: should be the identification number for dbSNP files\ne.g. [ id:'test' ]\n" - } - }, - { - "dbsnp": { - "type": "file", - "description": "VCF file including dbSNP variants", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ], - [ - { - "meta6": { - "type": "map", - "description": "Groovy Map containing dbSNP information\nid: should be the identification number for dbSNP files\ne.g. [ id:'test' ]\n" - } - }, - { - "dbsnp_tbi": { - "type": "file", - "description": "Index of VCF file including dbSNP variants", - "pattern": "*.vcf.gz.tbi", - "ontologies": [] - } - } - ], - [ - { - "meta7": { - "type": "map", - "description": "Groovy Map containing regions information\nid: should be the identification number for regions\ne.g. [ id:'test' ]\n" - } - }, - { - "regions": { - "type": "file", - "description": "Targeted intervals. Accepts BED file or Samtools-style string", - "pattern": "*.bed|*.txt|*.tab", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "output": { - "sv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.svaba.sv.vcf.gz": { - "type": "file", - "description": "Filtered SVs for tumor only cases", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "indel": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.svaba.indel.vcf.gz": { - "type": "file", - "description": "Filtered Indels for tumor only cases", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "germ_indel": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.svaba.germline.indel.vcf.gz": { - "type": "file", - "description": "Germline filtered Indels for tumor/normal paired samples", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "germ_sv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.svaba.germline.sv.vcf.gz": { - "type": "file", - "description": "Germline filtered SVs for tumor/normal paired samples", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "som_indel": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.svaba.somatic.indel.vcf.gz": { - "type": "file", - "description": "Somatic filtered Indels for tumor/normal paired samples", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "som_sv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.svaba.somatic.sv.vcf.gz": { - "type": "file", - "description": "Somatic filtered SVs for tumor/normal paired samples", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "unfiltered_sv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.svaba.unfiltered.sv.vcf.gz": { - "type": "file", - "description": "Unfiltered SVs for tumor only cases", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "unfiltered_indel": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.svaba.unfiltered.indel.vcf.gz": { - "type": "file", - "description": "Unfiltered Indels for tumor only cases", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "unfiltered_germ_indel": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.svaba.unfiltered.germline.indel.vcf.gz": { - "type": "file", - "description": "Unfiltered germline Indels for tumor/normal paired samples", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "unfiltered_germ_sv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.svaba.unfiltered.germline.sv.vcf.gz": { - "type": "file", - "description": "Unfiltered germline SVs for tumor/normal paired samples", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "unfiltered_som_indel": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.svaba.unfiltered.somatic.indel.vcf.gz": { - "type": "file", - "description": "Unfiltered somatic Indels for tumor/normal paired samples", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "unfiltered_som_sv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.svaba.unfiltered.somatic.sv.vcf.gz": { - "type": "file", - "description": "Unfiltered somatic SVs for tumor/normal paired samples", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "discordants": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.discordants.txt.gz": { - "type": "file", - "description": "Information on all clusters of discordant reads identified with 2+ reads", - "pattern": "*.txt.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "raw_calls": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.bps.txt.gz": { - "type": "file", - "description": "Raw, unfiltered variants", - "pattern": "*.txt.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.log": { - "type": "file", - "description": "Log file", - "pattern": "*.txt.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "versions_svaba": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "svaba": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "svaba --version 2>&1 | grep -oE '[0-9]+\\.[0-9]+\\.[0-9]+' | head -n 1": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "svaba": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "svaba --version 2>&1 | grep -oE '[0-9]+\\.[0-9]+\\.[0-9]+' | head -n 1": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@kubranarci" - ], - "maintainers": [ - "@kubranarci" - ] - } - }, - { - "name": "svanalyzer_svbenchmark", - "path": "modules/nf-core/svanalyzer/svbenchmark/meta.yml", - "type": "module", - "meta": { - "name": "svanalyzer_svbenchmark", - "description": "SVbenchmark compares a set of “test” structural variants in VCF format to a known truth set (also in VCF format) and outputs estimates of sensitivity and specificity.", - "keywords": [ - "structural variant", - "sv", - "benchmarking" - ], - "tools": [ - { - "svanalyzer": { - "description": "SVanalyzer: tools for the analysis of structural variation in genomes", - "homepage": "https://svanalyzer.readthedocs.io/en/latest/index.html", - "documentation": "https://svanalyzer.readthedocs.io/en/latest/index.html", - "tool_dev_url": "https://github.com/nhansen/SVanalyzer", - "licence": [ - "CC0" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing test sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "test": { - "type": "file", - "description": "A VCF-formatted file of structural variants to test (required)", - "pattern": "*.{vcf,vcf.gz}", - "ontologies": [] - } - }, - { - "test_tbi": { - "type": "file", - "description": "A VCF-formatted file index of structural variants to test only for zipped files", - "pattern": "*.{vcf.gz.tbi}", - "ontologies": [] - } - }, - { - "truth": { - "type": "file", - "description": "A VCF-formatted file of variants to compare against (required)", - "pattern": "*.{vcf,vcf.gz}", - "ontologies": [] - } - }, - { - "truth_tbi": { - "type": "file", - "description": "A VCF-formatted file of variants to compare against only for zipped files", - "pattern": "*.{vcf.gz.tbi}", - "ontologies": [] - } - }, - { - "bed": { - "type": "file", - "description": "BED File of regions from which to include variants. Used to filter both test and truth variants.", - "pattern": "*.{bed}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference genome information for fasta\ne.g. `[ id:'test2' ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference FASTA file for the supplied VCF file or files (required)", - "pattern": "*.{fa,fasta,fa.gz,fasta.gz}", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference genome information for fai\ne.g. `[ id:'test3' ]`\n" - } - }, - { - "fai": { - "type": "file", - "description": "The reference FASTA index file", - "pattern": "*.{fai}", - "ontologies": [] - } - } - ] - ], - "output": { - "fns": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information inherited from test vcf\ne.g. `[ id:'test']`\n" - } - }, - { - "*.falsenegatives.vcf.gz": { - "type": "file", - "description": "VCF file with False Negatives", - "pattern": "*.{vcf.gz}", - "ontologies": [] - } - } - ] - ], - "fps": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information inherited from test vcf\ne.g. `[ id:'test']`\n" - } - }, - { - "*.falsepositives.vcf.gz": { - "type": "file", - "description": "VCF file with False Positives", - "pattern": "*.{vcf.gz}", - "ontologies": [] - } - } - ] - ], - "distances": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information inherited from test vcf\ne.g. `[ id:'test']`\n" - } - }, - { - "*.distances": { - "type": "file", - "description": "TSV file with genomic distances and size differences between structural variants compared", - "pattern": "*.{distances}", - "ontologies": [] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information inherited from test vcf\ne.g. `[ id:'test']`\n" - } - }, - { - "*.log": { - "type": "file", - "description": "LOG file of the run", - "pattern": "*.{log}", - "ontologies": [] - } - } - ] - ], - "report": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information inherited from test vcf\ne.g. `[ id:'test']`\n" - } - }, - { - "*.report": { - "type": "file", - "description": "Text file reporting RECALL, PRECISION and F1.", - "pattern": "*.{report}", - "ontologies": [] - } - } - ] - ], - "versions_svanalyzer": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "svanalyzer": { - "type": "string", - "description": "The tool name" - } - }, - { - "0.36": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "svanalyzer": { - "type": "string", - "description": "The tool name" - } - }, - { - "0.36": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@kubranarci" - ] - }, - "pipelines": [ - { - "name": "variantbenchmarking", - "version": "1.5.0" - } - ] - }, - { - "name": "svdb_build", - "path": "modules/nf-core/svdb/build/meta.yml", - "type": "module", - "meta": { - "name": "svdb_build", - "description": "Build a structural variant database", - "keywords": [ - "structural variants", - "build", - "svdb" - ], - "tools": [ - { - "svdb": { - "description": "structural variant database software", - "homepage": "https://github.com/J35P312/SVDB", - "documentation": "https://github.com/J35P312/SVDB/blob/master/README.md", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "Input VCF file(s) or folder", - "pattern": "*", - "ontologies": [] - } - } - ], - { - "input_type": { - "type": "string", - "description": "input type" - } - } - ], - "output": { - "db": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.db": { - "type": "file", - "description": "SVDB database", - "ontologies": [] - } - } - ] - ], - "versions_svdb": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "svdb": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "svdb | sed -nE 's/.*SVDB-([0-9.]+).*/\\1/p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "svdb": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "svdb | sed -nE 's/.*SVDB-([0-9.]+).*/\\1/p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@fellen31" - ] - } - }, - { - "name": "svdb_merge", - "path": "modules/nf-core/svdb/merge/meta.yml", - "type": "module", - "meta": { - "name": "svdb_merge", - "description": "The merge module merges structural variants within one or more vcf files.", - "keywords": [ - "structural variants", - "vcf", - "merge" - ], - "tools": [ - { - "svdb": { - "description": "structural variant database software", - "homepage": "https://github.com/J35P312/SVDB", - "documentation": "https://github.com/J35P312/SVDB/blob/master/README.md", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "vcfs": { - "type": "list", - "description": "One or more VCF files. The order and number of files should correspond to\nthe order and number of tags in the `priority` input channel.\n", - "pattern": "*.{vcf,vcf.gz}" - } - } - ], - { - "input_priority": { - "type": "list", - "description": "Prioritize the input VCF files according to this list,\ne.g ['tiddit','cnvnator']. The order and number of tags should correspond to\nthe order and number of VCFs in the `vcfs` input channel.\n" - } - }, - { - "sort_inputs": { - "type": "boolean", - "description": "Should the input files be sorted by name. The priority tag will be sorted\ntogether with it's corresponding VCF file.\n" - } - } - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.{vcf,vcf.gz,bcf,bcf.gz}": { - "type": "file", - "description": "VCF output file", - "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}", - "ontologies": [] - } - } - ] - ], - "tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tbi": { - "type": "file", - "description": "Alternative VCF file index", - "pattern": "*.tbi", - "ontologies": [] - } - } - ] - ], - "csi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.csi": { - "type": "file", - "description": "Default VCF file index", - "pattern": "*.csi", - "ontologies": [] - } - } - ] - ], - "versions_svdb": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "svdb": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "svdb | sed -nE 's/.*SVDB-([0-9.]+).*/\\1/p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_bcftools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bcftools": { - "type": "string", - "description": "The tool name" - } - }, - { - "bcftools --version | sed '1!d; s/^.*bcftools //'": { - "type": "eval", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "svdb": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "svdb | sed -nE 's/.*SVDB-([0-9.]+).*/\\1/p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "bcftools": { - "type": "string", - "description": "The tool name" - } - }, - { - "bcftools --version | sed '1!d; s/^.*bcftools //'": { - "type": "eval", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@ramprasadn" - ], - "maintainers": [ - "@ramprasadn", - "@fellen31" - ] - }, - "pipelines": [ - { - "name": "raredisease", - "version": "3.0.0" - }, - { - "name": "sarek", - "version": "3.8.1" - } - ] - }, - { - "name": "svdb_query", - "path": "modules/nf-core/svdb/query/meta.yml", - "type": "module", - "meta": { - "name": "svdb_query", - "description": "Query a structural variant database, using a vcf file as query", - "keywords": [ - "structural variants", - "query", - "svdb" - ], - "tools": [ - { - "svdb": { - "description": "structural variant database software", - "homepage": "https://github.com/J35P312/SVDB", - "documentation": "https://github.com/J35P312/SVDB/blob/master/README.md", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "query vcf file", - "pattern": "*.{vcf,vcf.gz}", - "ontologies": [] - } - } - ], - { - "in_occs": { - "type": "list", - "description": "A list of allele count tags" - } - }, - { - "in_frqs": { - "type": "list", - "description": "A list of allele frequency tags" - } - }, - { - "out_occs": { - "type": "list", - "description": "A list of allele count tags" - } - }, - { - "out_frqs": { - "type": "list", - "description": "A list of allele frequency tags" - } - }, - { - "vcf_dbs": { - "type": "file", - "description": "path to a database vcf, or a comma separated list of vcfs", - "pattern": "*.{vcf,vcf.gz}", - "ontologies": [] - } - }, - { - "bedpe_dbs": { - "type": "file", - "description": "path to a SV database of the following format chrA-posA-chrB-posB-type-count-frequency, or a comma separated list of files", - "pattern": "*.{bedpe}", - "ontologies": [] - } - } - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*_query.vcf": { - "type": "file", - "description": "Annotated output VCF file", - "pattern": "*_query.vcf", - "ontologies": [] - } - } - ] - ], - "versions_svdb": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "svdb": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "svdb | sed -nE 's/.*SVDB-([0-9.]+).*/\\1/p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "svdb": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "svdb | sed -nE 's/.*SVDB-([0-9.]+).*/\\1/p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@ramprasadn" - ] - }, - "pipelines": [ - { - "name": "raredisease", - "version": "3.0.0" - } - ] - }, - { - "name": "svdss_index", - "path": "modules/nf-core/svdss/index/meta.yml", - "type": "module", - "meta": { - "name": "svdss_index", - "description": "Index a reference genome FASTA file using SVDSS (via ropebwt3), producing either an FMD or FMR index for use with SVDSS smooth and search subcommands", - "keywords": [ - "structural variants", - "sv calling", - "indexing", - "reference genome", - "fm-index" - ], - "tools": [ - { - "svdss": { - "description": "SVDSS is a tool for structural variant discovery from short-read sequencing data.\nIt implements an FM-index-based approach to efficiently detect SVs against a reference genome.\n", - "homepage": "https://github.com/Parsoa/SVDSS", - "documentation": "https://github.com/Parsoa/SVDSS", - "tool_dev_url": "https://github.com/Parsoa/SVDSS", - "doi": "10.1038/s41592-022-01674-1", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome in FASTA format", - "pattern": "*.{fasta,fa,fna}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - { - "output_format": { - "type": "string", - "description": "Output index format. Use 'fmd' for the fermi-delta format (adds -d flag)\nor 'fmr' for the ropebwt format (adds -b flag).\n", - "pattern": "fmd|fmr" - } - } - ], - "output": { - "index": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}.${output_format}": { - "type": "file", - "description": "FM-index file produced by SVDSS index, used as input for SVDSS smooth and search", - "pattern": "*.{fmd,fmr}", - "ontologies": [] - } - } - ] - ], - "versions_svdss": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "svdss": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "SVDSS --version 2>&1 | sed 's/SVDSS, v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "svdss": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "SVDSS --version 2>&1 | sed 's/SVDSS, v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@vagkaratzas" - ], - "maintainers": [ - "@vagkaratzas" - ] - } - }, - { - "name": "svim_alignment", - "path": "modules/nf-core/svim/alignment/meta.yml", - "type": "module", - "meta": { - "name": "svim_alignment", - "description": "Structural variant detection from long-read sequencing alignments using SVIM.", - "keywords": [ - "structural variants", - "long reads", - "nanopore", - "pacbio", - "genomics", - "variant calling" - ], - "tools": [ - { - "svim": { - "description": "SVIM is a structural variant caller for long-read sequencing data that detects deletions, insertions, duplications, inversions and translocations from read alignments.", - "homepage": "https://github.com/eldariont/svim", - "documentation": "https://github.com/eldariont/svim/wiki", - "tool_dev_url": "https://github.com/eldariont/svim", - "doi": "10.1093/bioinformatics/btz041", - "licence": [ - "GPL-3.0" - ], - "identifier": "biotools:svim" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "Coordinate-sorted BAM/CRAM/SAM alignment file generated from long-read mapping", - "pattern": "*.{bam,cram,sam}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - }, - { - "edam": "http://edamontology.org/format_2573" - }, - { - "edam": "http://edamontology.org/format_3462" - } - ] - } - }, - { - "bai": { - "type": "file", - "description": "BAM index file", - "pattern": "*.bai", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3327" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome in FASTA format", - "pattern": "*.{fa,fasta,fna}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.vcf": { - "type": "file", - "description": "Structural variant calls in VCF format generated by SVIM", - "pattern": "*.vcf", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - } - ] - } - } - ] - ], - "versions_svim": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "svim": { - "type": "string", - "description": "The tool name" - } - }, - { - "svim --version | sed \"s/^.*svim //; s/ .*//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "svim": { - "type": "string", - "description": "The tool name" - } - }, - { - "svim --version | sed \"s/^.*svim //; s/ .*//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@nourmahfel" - ], - "maintainers": [ - "@nourmahfel" - ] - } - }, - { - "name": "svtk_baftest", - "path": "modules/nf-core/svtk/baftest/meta.yml", - "type": "module", - "meta": { - "name": "svtk_baftest", - "description": "Performs tests on BAF files", - "keywords": [ - "svtk", - "svtk/baftest", - "baftest", - "baf", - "bed", - "structural variants" - ], - "tools": [ - { - "svtk": { - "description": "Utilities for consolidating, filtering, resolving, and annotating structural variants.", - "homepage": "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk", - "documentation": "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk", - "tool_dev_url": "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bed": { - "type": "file", - "description": "A BED file created with `svtk vcf2bed`", - "pattern": "*.bed", - "ontologies": [] - } - }, - { - "baf": { - "type": "file", - "description": "A BAF file created with `gatk PrintSVEvidence`", - "pattern": "*.baf.txt.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - }, - { - "baf_index": { - "type": "file", - "description": "The index of the BAF file", - "pattern": "*.baf.txt.gz.tbi", - "ontologies": [] - } - }, - { - "batch": { - "type": "file", - "description": "A text file containing information about the sample(s)", - "pattern": "*.txt", - "ontologies": [] - } - } - ] - ], - "output": { - "metrics": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.metrics": { - "type": "file", - "description": "The results file from the BAF test", - "pattern": "*.metrics", - "ontologies": [] - } - } - ] - ], - "versions_svtk": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "svtk": { - "type": "string", - "description": "The tool name" - } - }, - { - "0.0.20190615": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "svtk": { - "type": "string", - "description": "The tool name" - } - }, - { - "0.0.20190615": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@nvnieuwk" - ], - "maintainers": [ - "@nvnieuwk" - ] - } - }, - { - "name": "svtk_countsvtypes", - "path": "modules/nf-core/svtk/countsvtypes/meta.yml", - "type": "module", - "meta": { - "name": "svtk_countsvtypes", - "description": "Count the instances of each SVTYPE observed in each sample in a VCF.", - "keywords": [ - "svtk", - "countsvtypes", - "vcf", - "structural variants" - ], - "tools": [ - { - "svtk": { - "description": "Utilities for consolidating, filtering, resolving, and annotating structural variants.", - "homepage": "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk", - "documentation": "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk", - "tool_dev_url": "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk", - "doi": "10.1038/s41586-020-2287-8", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "The VCF file containing structural variants", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "output": { - "counts": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "A tab-delimited file containing the counts of the SV types", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_svtk": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "svtk": { - "type": "string", - "description": "The tool name" - } - }, - { - "0.0.20190615": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "svtk": { - "type": "string", - "description": "The tool name" - } - }, - { - "0.0.20190615": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@nvnieuwk" - ], - "maintainers": [ - "@nvnieuwk" - ] - } - }, - { - "name": "svtk_rdtest2vcf", - "path": "modules/nf-core/svtk/rdtest2vcf/meta.yml", - "type": "module", - "meta": { - "name": "svtk_rdtest2vcf", - "description": "Convert an RdTest-formatted bed to the standard VCF format.", - "keywords": [ - "svtk", - "rdtest2vcf", - "bed", - "rdtest", - "vcf" - ], - "tools": [ - { - "svtk": { - "description": "Utilities for consolidating, filtering, resolving, and annotating structural variants.", - "homepage": "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk", - "documentation": "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk", - "tool_dev_url": "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk", - "doi": "10.1038/s41586-020-2287-8", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bed": { - "type": "file", - "description": "An RdTest-formatted bed", - "pattern": "*.bed", - "ontologies": [] - } - }, - { - "samples": { - "type": "file", - "description": "A text file containing the names of all samples that need to be added to the VCF", - "pattern": "*.txt", - "ontologies": [] - } - } - ], - { - "fasta_fai": { - "type": "file", - "description": "The reference file of a FASTA file containing the contigs", - "pattern": "*.fai", - "ontologies": [] - } - } - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.vcf.gz": { - "type": "file", - "description": "The converted VCF", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.vcf.gz.tbi": { - "type": "file", - "description": "The index of the converted VCF", - "pattern": "*.vcf.gz.tbi", - "ontologies": [] - } - } - ] - ], - "versions_svtk": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "svtk": { - "type": "string", - "description": "The tool name" - } - }, - { - "0.0.20190615": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "svtk": { - "type": "string", - "description": "The tool name" - } - }, - { - "0.0.20190615": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@nvnieuwk" - ], - "maintainers": [ - "@nvnieuwk" - ] - } - }, - { - "name": "svtk_standardize", - "path": "modules/nf-core/svtk/standardize/meta.yml", - "type": "module", - "meta": { - "name": "svtk_standardize", - "description": "Convert SV calls to a standardized format.", - "keywords": [ - "svtk", - "structural variants", - "SV", - "vcf", - "standardization" - ], - "tools": [ - { - "svtk": { - "description": "Utilities for consolidating, filtering, resolving, and annotating structural variants.", - "homepage": "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk", - "documentation": "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk", - "tool_dev_url": "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information. Caller can be one of the tools: delly, manta, melt, wham\ne.g. [ id:'test', caller:\"delly\" ]\n" - } - }, - { - "input": { - "type": "file", - "description": "A gzipped VCF file to be standardized", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test2' ]\n" - } - }, - { - "fai": { - "type": "file", - "description": "Optional fasta index file that specifies the contigs to be used in the VCF header (defaults to all contigs of GRCh37)", - "pattern": "*.fai", - "ontologies": [] - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', caller:\"delly\" ]\n" - } - }, - { - "*.vcf.gz": { - "type": "file", - "description": "A gzipped version of the standardized VCF file", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "versions_svtk": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "svtk": { - "type": "string", - "description": "The tool name" - } - }, - { - "0.0.20190615": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "svtk": { - "type": "string", - "description": "The tool name" - } - }, - { - "0.0.20190615": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@nvnieuwk" - ], - "maintainers": [ - "@nvnieuwk" - ] - }, - "pipelines": [ - { - "name": "variantbenchmarking", - "version": "1.5.0" - } - ] - }, - { - "name": "svtk_vcf2bed", - "path": "modules/nf-core/svtk/vcf2bed/meta.yml", - "type": "module", - "meta": { - "name": "svtk_vcf2bed", - "description": "Converts VCFs containing structural variants to BED format", - "keywords": [ - "vcf", - "bed", - "vcf2bed", - "svtk", - "structural variants" - ], - "tools": [ - { - "svtk": { - "description": "Utilities for consolidating, filtering, resolving, and annotating structural variants.", - "homepage": "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk", - "documentation": "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk", - "tool_dev_url": "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "A VCF file created with a structural variant caller", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - }, - { - "tbi": { - "type": "file", - "description": "The index for the VCF file", - "pattern": "*.vcf.gz.tbi", - "ontologies": [] - } - } - ] - ], - "output": { - "bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bed": { - "type": "file", - "description": "The created BED file", - "pattern": "*.bed", - "ontologies": [] - } - } - ] - ], - "versions_svtk": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "svtk": { - "type": "string", - "description": "The tool name" - } - }, - { - "0.0.20190615": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "svtk": { - "type": "string", - "description": "The tool name" - } - }, - { - "0.0.20190615": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@nvnieuwk" - ], - "maintainers": [ - "@nvnieuwk" - ] - }, - "pipelines": [ - { - "name": "variantbenchmarking", - "version": "1.5.0" - } - ] - }, - { - "name": "svtools_vcftobedpe", - "path": "modules/nf-core/svtools/vcftobedpe/meta.yml", - "type": "module", - "meta": { - "name": "svtools_vcftobedpe", - "description": "Convert a VCF file to a BEDPE file.", - "keywords": [ - "structural", - "bedpe", - "vcf", - "conversion", - "variants" - ], - "tools": [ - { - "svtools": { - "description": "Tools for processing and analyzing structural variants", - "tool_dev_url": "https://github.com/hall-lab/svtools", - "licence": [ - "MIT License" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "vcf": { - "type": "file", - "description": "Input VCF file containing structural variants", - "pattern": "*.{vcf,vcf.gz}", - "ontologies": [] - } - } - ] - ], - "output": { - "bedpe": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.bedpe": { - "type": "file", - "description": "The converted BEDPE file", - "pattern": "*.bedpe", - "ontologies": [] - } - } - ] - ], - "versions_svtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "svtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "svtools --version |& sed 's/svtools //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "svtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "svtools --version |& sed 's/svtools //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@nvnieuwk" - ], - "maintainers": [ - "@nvnieuwk" - ] - } - }, - { - "name": "svtyper_svtyper", - "path": "modules/nf-core/svtyper/svtyper/meta.yml", - "type": "module", - "meta": { - "name": "svtyper_svtyper", - "description": "SVTyper performs breakpoint genotyping of structural variants (SVs) using whole genome sequencing data", - "keywords": [ - "sv", - "structural variants", - "genotyping" - ], - "tools": [ - { - "svtyper": { - "description": "Compute genotype of structural variants based on breakpoint depth", - "homepage": "https://github.com/hall-lab/svtyper", - "documentation": "https://github.com/hall-lab/svtyper", - "tool_dev_url": "https://github.com/hall-lab/svtyper", - "doi": "10.1038/nmeth.3505", - "licence": [ - "MIT" - ], - "identifier": "biotools:svtyper" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } - }, - { - "bam_index": { - "type": "file", - "description": "Index of the BAM/CRAM/SAM file", - "pattern": "*.{bai,crai,sai}", - "ontologies": [] - } - }, - { - "vcf": { - "type": "file", - "description": "Matching VCF of alignments", - "pattern": "*.vcf", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information for FASTA file\ne.g. [ id:'fasta']\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA file used to generate alignments", - "pattern": "*.{fa,fasta}", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information for FASTA file\ne.g. [ id:'fasta']\n" - } - }, - { - "fai": { - "type": "file", - "description": "FAI file used to generate alignments", - "pattern": "*.{fai}", - "ontologies": [] - } - } - ] - ], - "output": { - "json": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.json": { - "type": "file", - "description": "JSON file including Library information", - "pattern": "*.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "gt_vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.vcf": { - "type": "file", - "description": "Genotyped SVs", - "pattern": "*.vcf", - "ontologies": [] - } - } - ] - ], - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "BAM file with", - "pattern": "*.bam", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@kubranarci" - ], - "maintainers": [ - "@kubranarci" - ] - } - }, - { - "name": "svtyper_svtypersso", - "path": "modules/nf-core/svtyper/svtypersso/meta.yml", - "type": "module", - "meta": { - "name": "svtyper_svtypersso", - "description": "SVTyper-sso computes structural variant (SV) genotypes based on breakpoint depth on a SINGLE sample", - "keywords": [ - "sv", - "structural variants", - "genotyping", - "Bayesian" - ], - "tools": [ - { - "svtyper": { - "description": "Bayesian genotyper for structural variants", - "homepage": "https://github.com/hall-lab/svtyper", - "documentation": "https://github.com/hall-lab/svtyper", - "tool_dev_url": "https://github.com/hall-lab/svtyper", - "doi": "10.1038/nmeth.3505", - "licence": [ - "MIT" - ], - "identifier": "biotools:svtyper" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM or CRAM file with alignments", - "pattern": "*.{bam,cram}", - "ontologies": [] - } - }, - { - "bam_index": { - "type": "file", - "description": "BAI file matching the BAM file", - "pattern": "*.{bai}", - "ontologies": [] - } - }, - { - "vcf": { - "type": "file", - "description": "Matching VCF of alignments", - "pattern": "*.vcf", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information for reference FASTA file\ne.g. [ id:'fasta']\n" - } - }, - { - "fasta": { - "type": "file", - "description": "indexed reference FASTA file (recommended for reading CRAM files)", - "pattern": "*.{fa,fasta}", - "ontologies": [] - } - } - ] - ], - "output": { - "gt_vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.vcf": { - "type": "file", - "description": "Genotyped SVs", - "pattern": "*.vcf", - "ontologies": [] - } - } - ] - ], - "json": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.json": { - "type": "file", - "description": "JSON file including library information", - "pattern": "*.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@tstoeriko" - ], - "maintainers": [ - "@tstoeriko" - ] - } - }, - { - "name": "svync", - "path": "modules/nf-core/svync/meta.yml", - "type": "module", - "meta": { - "name": "svync", - "description": "A tool to standardize VCF files from structural variant callers", - "keywords": [ - "structural variants", - "vcf", - "standardization", - "standardize", - "sv" - ], - "tools": [ - { - "svync": { - "description": "A tool to standardize VCF files from structural variant callers", - "homepage": "https://github.com/nvnieuwk/svync", - "documentation": "https://github.com/nvnieuwk/svync", - "tool_dev_url": "https://github.com/nvnieuwk/svync", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "vcf": { - "type": "file", - "description": "The input VCF file containing structural variants", - "pattern": "*.{vcf,vcf.gz}", - "ontologies": [] - } - }, - { - "tbi": { - "type": "file", - "description": "The index of the input VCF file containing structural variants", - "pattern": "*.tbi", - "ontologies": [] - } - }, - { - "config": { - "type": "file", - "description": "The config stating how the standardization should happen", - "pattern": "*.{yml,yaml}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.vcf.gz": { - "type": "file", - "description": "The standardized VCF file", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.tbi": { - "type": "file", - "description": "The index of the standardized VCF file", - "pattern": "*.tbi", - "ontologies": [] - } - } - ] - ], - "versions_svync": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "svync": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "svync --version | sed 's/svync version //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "svync": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "svync --version | sed 's/svync version //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@nvnieuwk" - ], - "maintainers": [ - "@nvnieuwk" - ] - }, - "pipelines": [ - { - "name": "variantbenchmarking", - "version": "1.5.0" - } - ] - }, - { - "name": "sylph_profile", - "path": "modules/nf-core/sylph/profile/meta.yml", - "type": "module", - "meta": { - "name": "sylph_profile", - "description": "Sylph profile command for taxonoming profiling", - "keywords": [ - "profile", - "metagenomics", - "sylph", - "classification" - ], - "tools": [ - { - "sylph": { - "description": "Sylph quickly enables querying of genomes against even low-coverage shotgun metagenomes to find nearest neighbour ANI.", - "homepage": "https://github.com/bluenote-1577/sylph", - "documentation": "https://github.com/bluenote-1577/sylph", - "tool_dev_url": "https://github.com/bluenote-1577/sylph", - "doi": "10.1038/s41587-024-02412-y", - "licence": [ - "MIT" - ], - "identifier": "biotools:sylph" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ/FASTA files of size 1 and 2 for single-end and paired-end data,\nrespectively. They are automatically sketched to .sylsp/.syldb\n", - "pattern": "*.{fasta,fastq,fna,fa,fq,fas,fasta.gz,fastq.gz,fna,fa.gz,fq,fas.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - }, - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ], - { - "database": { - "type": "file", - "description": "Pre-sketched *.syldb/*.sylsp files. Raw single-end fastq/fasta are allowed and will be automatically sketched to .sylsp/.syldb.", - "pattern": "*.{syldb,sylsp}" - } - } - ], - "output": { - "profile_out": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*.tsv": { - "type": "file", - "description": "Output file of species-level taxonomic profiling with abundances and ANIs.", - "pattern": "*tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_sylph": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "sylph": { - "type": "string", - "description": "The tool name" - } - }, - { - "sylph -V | sed \"s/sylph //g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "sylph": { - "type": "string", - "description": "The tool name" - } - }, - { - "sylph -V | sed \"s/sylph //g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@jiahang1234", - "@sofstam" - ], - "maintainers": [ - "@sofstam" - ] - }, - "pipelines": [ - { - "name": "rnaseq", - "version": "3.26.0" - }, - { - "name": "taxprofiler", - "version": "2.0.0" - } - ] - }, - { - "name": "sylph_sketch", - "path": "modules/nf-core/sylph/sketch/meta.yml", - "type": "module", - "meta": { - "name": "sylph_sketch", - "description": "Sketching/indexing sequencing reads", - "keywords": [ - "sketch", - "metagenomics", - "sylph", - "indexing" - ], - "tools": [ - { - "sylph": { - "description": "Sylph quickly enables querying of genomes against even low-coverage shotgun metagenomes to find nearest neighbour ANI.", - "homepage": "https://github.com/bluenote-1577/sylph", - "documentation": "https://github.com/bluenote-1577/sylph", - "tool_dev_url": "https://github.com/bluenote-1577/sylph", - "doi": "10.1038/s41587-024-02412-y", - "licence": [ - "MIT" - ], - "identifier": "biotools:sylph" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "reads": { - "type": "file", - "description": "Input FASTQ files", - "pattern": "*.{fq,fastq,fq.gz,fastq.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ], - { - "reference": { - "type": "file", - "description": "Reference genome file in FASTA format", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - "output": { - "sketch_fastq_genome": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "my_sketches/*.sylsp": { - "type": "map", - "description": "Output sylph sketch files of input reads for profiling\n", - "pattern": "my_sketches/*.sylsp" - } - }, - { - "database.syldb": { - "type": "map", - "description": "Output sylph database files for profiling against database\n", - "pattern": "*.syldb" - } - } - ] - ], - "versions_sylph": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "sylph": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "sylph -V | sed \"s/sylph //g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "sylph": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "sylph -V | sed \"s/sylph //g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@jiahang1234", - "@sofstam" - ], - "maintainers": [ - "@sofstam" - ] - } - }, - { - "name": "sylph_sketchgenomes", - "path": "modules/nf-core/sylph/sketchgenomes/meta.yml", - "type": "module", - "meta": { - "name": "sylph_sketchgenomes", - "description": "Sylph profile command for taxonoming profiling of genomes", - "keywords": [ - "profile", - "metagenomics", - "sylph", - "classification", - "genomes", - "sketch" - ], - "tools": [ - { - "sylph": { - "description": "Sylph quickly enables querying of genomes against even low-coverage shotgun metagenomes to find nearest neighbour ANI.", - "homepage": "https://github.com/bluenote-1577/sylph", - "documentation": "https://github.com/bluenote-1577/sylph", - "tool_dev_url": "https://github.com/bluenote-1577/sylph", - "doi": "10.1038/s41587-024-02412-y", - "licence": [ - "MIT" - ], - "identifier": "biotools:sylph" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "List of reference genome FASTA files to convert to sylph database file", - "pattern": "*.{fasta,fas,fa,fna}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ], - "output": { - "syldb": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*.syldb": { - "type": "file", - "description": "Sylph database sketch file for profiling", - "pattern": "*.syldb" - } - } - ] - ], - "versions_sylph": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "sylph": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "sylph -V | sed \"s/sylph //g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "sylph": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "sylph -V | sed \"s/sylph //g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@jfy133" - ], - "maintainers": [ - "@jfy133" - ] - }, - "pipelines": [ - { - "name": "createtaxdb", - "version": "3.0.0" - } - ] - }, - { - "name": "sylph_sketchsamples", - "path": "modules/nf-core/sylph/sketchsamples/meta.yml", - "type": "module", - "meta": { - "name": "sylph_sketchsamples", - "description": "Sketching/indexing sequencing reads", - "keywords": [ - "sketch", - "metagenomics", - "sylph", - "samples", - "indexing" - ], - "tools": [ - { - "sylph": { - "description": "Sylph quickly enables querying of genomes against even low-coverage shotgun metagenomes to find nearest neighbour ANI.", - "homepage": "https://github.com/bluenote-1577/sylph", - "documentation": "https://github.com/bluenote-1577/sylph", - "tool_dev_url": "https://github.com/bluenote-1577/sylph", - "doi": "10.1038/s41587-024-02412-y", - "licence": [ - "MIT" - ], - "identifier": "biotools:sylph" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "reads": { - "type": "file", - "description": "Input fastq files", - "pattern": "*.{fq,fastq,fq.gz,fastq.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "output": { - "sylsp": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "my_sketches/*.sylsp": { - "type": "map", - "description": "Output sylph sketch files for profiling\n", - "pattern": "my_sketches/*.sylsp" - } - } - ] - ], - "versions_sylph": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "sylph": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "sylph -V | sed \"s/sylph //g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "sylph": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "sylph -V | sed \"s/sylph //g\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@jiahang1234", - "@sofstam" - ], - "maintainers": [ - "@sofstam", - "@jfy133" - ] - } - }, - { - "name": "sylphtax_merge", - "path": "modules/nf-core/sylphtax/merge/meta.yml", - "type": "module", - "meta": { - "name": "sylphtax_merge", - "description": "Merge multiple taxonomic profiles from sylphtaxt/taxprof into a tsv table", - "keywords": [ - "sylph", - "metagenomics", - "merge" - ], - "tools": [ - { - "sylphtax": { - "description": "Integrating taxonomic information into the sylph metagenome profiler.", - "homepage": "https://github.com/bluenote-1577/sylph-tax?tab=readme-ov-file", - "documentation": "https://sylph-docs.github.io/sylph-tax/", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "sylphtax_reports": { - "type": "file", - "description": "Output taxonomic profile from sylph-tax taxprof command.", - "pattern": "*.{sylphmpa}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - { - "data_type": { - "type": "string", - "description": "Can be ANI, relative abundance, or sequence abundance." - } - } - ], - "output": { - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "Output profile with the merged taxonomic profiles in tsv format.", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_sylphtax": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "sylph-tax": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "sylph-tax --version 2>&1 | tail -1": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "sylph-tax": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "sylph-tax --version 2>&1 | tail -1": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@sofstam" - ], - "maintainers": [ - "@sofstam" - ] - }, - "pipelines": [ - { - "name": "taxprofiler", - "version": "2.0.0" - } - ] - }, - { - "name": "sylphtax_taxprof", - "path": "modules/nf-core/sylphtax/taxprof/meta.yml", - "type": "module", - "meta": { - "name": "sylphtax_taxprof", - "description": "Incorporates taxonomy into sylph metagenomic classifier", - "keywords": [ - "taxonomy", - "sylph", - "metagenomics" - ], - "tools": [ - { - "sylphtax": { - "description": "Integrating taxonomic information into the sylph metagenome profiler.", - "homepage": "https://github.com/bluenote-1577/sylph-tax?tab=readme-ov-file", - "documentation": "https://sylph-docs.github.io/sylph-tax/", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "sylph_results": { - "type": "file", - "description": "Output results from sylph classifier. The database file(s) used to create this file with sylph must be the same as those of the taxonomy input channel of this module.", - "pattern": "*.{tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - { - "taxonomy": { - "type": "file", - "description": "A list of sylph-tax identifiers (e.g. GTDB_r220 or IMGVR_4.1). Multiple taxonomy metadata files can be input. Custom taxonomy files are also possible.", - "ontologies": [] - } - } - ], - "output": { - "taxprof_output": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.sylphmpa": { - "type": "file", - "description": "A tab-separated file containing a metagenomic taxonomic profile generated by sylph-tax, including columns for lineage and taxid\n", - "pattern": "*{.sylphmpa}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_sylphtax": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "sylph-tax": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "sylph-tax --version 2>&1 | tail -1": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "sylph-tax": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "sylph-tax --version 2>&1 | tail -1": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@sofstam" - ], - "maintainers": [ - "@sofstam" - ] - }, - "pipelines": [ - { - "name": "rnaseq", - "version": "3.26.0" - }, - { - "name": "taxprofiler", - "version": "2.0.0" - } - ] - }, - { - "name": "syri", - "path": "modules/nf-core/syri/meta.yml", - "type": "module", - "meta": { - "name": "syri", - "description": "Syri compares alignments between two chromosome-level assemblies and identifies synteny and structural rearrangements.", - "keywords": [ - "genomics", - "synteny", - "rearrangements", - "chromosome" - ], - "tools": [ - { - "syri": { - "description": "Synteny and rearrangement identifier between whole-genome assemblies", - "homepage": "https://github.com/schneebergerlab/syri", - "documentation": "https://github.com/schneebergerlab/syri", - "tool_dev_url": "https://github.com/schneebergerlab/syri", - "doi": "10.1186/s13059-019-1911-0", - "licence": [ - "MIT License" - ], - "identifier": "biotools:SyRI" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "infile": { - "type": "file", - "description": "File containing alignment coordinates", - "pattern": "*.{table, sam, bam, paf}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "query_fasta": { - "type": "file", - "description": "Query genome for the alignments", - "pattern": "*.{fasta}", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "reference_fasta": { - "type": "file", - "description": "Reference genome for the alignments", - "pattern": "*.{fasta}", - "ontologies": [] - } - } - ], - { - "file_type": { - "type": "string", - "description": "Input file type which is one of T: Table, S: SAM, B: BAM, P: PAF\n" - } - } - ], - "output": { - "syri": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*syri.out": { - "type": "file", - "description": "Syri output file", - "pattern": "*syri.{out}", - "ontologies": [] - } - } - ] - ], - "error": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.error.log": { - "type": "file", - "description": "Error log if syri fails. This error log enables the pipeline to detect if syri has failed due to one of its\nknown limitations and pass the information to the user in a user-friendly manner such as a HTML report\n", - "pattern": "*.error.{log}", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@GallVp" - ], - "maintainers": [ - "@GallVp" - ] - } - }, - { - "name": "t1k_build", - "path": "modules/nf-core/t1k/build/meta.yml", - "type": "module", - "meta": { - "name": "t1k_build", - "description": "A module to create a reference database and coordinate files for T1K.", - "keywords": [ - "polymorphic", - "genes", - "HLA", - "Kir" - ], - "tools": [ - { - "t1k": { - "description": "T1K is a versatile methods to genotype highly polymorphic genes (e.g. KIR, HLA) with RNA-seq, WGS or WES data.", - "homepage": "https://github.com/mourisl/T1K/blob/v1.0.9/README.md", - "documentation": "https://github.com/mourisl/T1K/blob/v1.0.9/README.md", - "tool_dev_url": "https://github.com/mourisl/T1K", - "doi": "10.1101/gr.277585.122", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "ena": { - "type": "file", - "description": "EMBL-ENA dat file.", - "pattern": "*.dat" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA file containing gene sequences.", - "pattern": "*.fa", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - }, - { - "annotation": { - "type": "file", - "description": "Gene annotation in GTF format.", - "pattern": "*.gtf", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2532" - } - ] - } - } - ] - ], - "output": { - "rna_sequences": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*_rna_seq.fa": { - "type": "file", - "description": "RNA gene sequences file output.", - "pattern": "*_rna_seq.fa", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ], - "dna_sequences": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*_dna_seq.fa": { - "type": "file", - "description": "DNA gene sequences file output.", - "pattern": "*_dna_seq.fa", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ], - "rna_coordinates": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*_rna_coord.fa": { - "type": "file", - "description": "A fasta file with the coordinates of the gene alleles in the header as created form the t1k/build", - "pattern": "*_rna_coord.fa", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ], - "dna_coordinates": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*_dna_coord.fa": { - "type": "file", - "description": "A fasta file with the coordinates of the gene alleles in the header as created form the t1k/build", - "pattern": "*_dna_coord.fa", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ], - "database": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.dat": { - "type": "file", - "description": "EMBL-ENA dat file.", - "pattern": "*.dat" - } - } - ] - ], - "versions_t1k": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "t1k": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "run-t1k 2>&1 | head -n 1 | cut -d '-' -f 1 | cut -d v -f 2": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "t1k": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "run-t1k 2>&1 | head -n 1 | cut -d '-' -f 1 | cut -d v -f 2": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@georgiakes" - ], - "maintainers": [ - "@georgiakes" - ] - } - }, - { - "name": "t1k_run", - "path": "modules/nf-core/t1k/run/meta.yml", - "type": "module", - "meta": { - "name": "t1k_run", - "description": "write your description here", - "keywords": [ - "polymorphic", - "genes", - "HLA", - "Kir" - ], - "tools": [ - { - "t1k": { - "description": "T1K is a versatile methods to genotype highly polymorphic genes (e.g. KIR, HLA) with RNA-seq, WGS or WES data.", - "homepage": "https://github.com/mourisl/T1K/blob/v1.0.8/README.md", - "documentation": "https://github.com/mourisl/T1K/blob/v1.0.8/README.md", - "tool_dev_url": "https://github.com/mourisl/T1K", - "doi": "10.1101/gr.277585.122", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample id and single_end label for fastq input files.\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM or FASTQ file(s).", - "pattern": "*.{bam,fastq}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - }, - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - }, - { - "fasta": { - "type": "file", - "description": "Reference fasta file.", - "pattern": "*.{fa,fasta}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - }, - { - "cordinates": { - "type": "file", - "description": "A fasta file with the coordinates of the gene alleles in the header as created form the t1k/build", - "pattern": "*.fa", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - }, - { - "barcodes": { - "type": "file", - "description": "A file with a list of barcodes.", - "pattern": "*.txt", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2330" - } - ] - } - }, - { - "barcodewhitelist": { - "type": "file", - "description": "A file with a whitelist of barcodes.", - "pattern": "*.txt", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2330" - } - ] - } - } - ] - ], - "output": { - "genotype_tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*_genotype.tsv": { - "type": "file", - "description": "Genotyping file where the allele for each gene has its own line.", - "pattern": "*_genotype.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "allele_tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*_allele.tsv": { - "type": "file", - "description": "File with the representative alleles and their quality scores.", - "pattern": "*_allele.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "allele_vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*_allele.vcf": { - "type": "file", - "description": "A vcf file with the novel SNPs.", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - } - ] - } - } - ] - ], - "candidate_reads": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*_candidate*.fq": { - "type": "file", - "description": "Fastq file containing candidate reads extracted from raw data for genotyping.", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "aligned_reads_single": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*_aligned.fa": { - "type": "file", - "description": "Aligned reads in fasta format from single-end input.", - "pattern": "*_aligned.fa", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ], - "aligned_reads_paired": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*_aligned_{1,2}.fa": { - "type": "file", - "description": "Aligned reads in fasta format from paired-end input.", - "pattern": "*_aligned_{1,2}.fa", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ], - "barcode_tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*_barcode_expr.tsv": { - "type": "file", - "description": "Data matrix where rows are the barcodes and columns are the allele abundances.", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "barcode_candidate": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*_candidate_bc.fa": { - "type": "file", - "description": "Barcodes form candidate reads.", - "pattern": "*_candidate_bc.fa", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ], - "barcode_aligned": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*_aligned_bc.fa": { - "type": "file", - "description": "Barcodes form aligned reads.", - "pattern": "*_aligned_bc.fa", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ], - "versions_t1k": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "t1k": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "run-t1k 2>&1 | head -n 1 | cut -d '-' -f 1 | cut -d v -f 2": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "t1k": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "run-t1k 2>&1 | head -n 1 | cut -d '-' -f 1 | cut -d v -f 2": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@georgiakes" - ], - "maintainers": [ - "@georgiakes" - ] - } - }, - { - "name": "tabix_bgzip", - "path": "modules/nf-core/tabix/bgzip/meta.yml", - "type": "module", - "meta": { - "name": "tabix_bgzip", - "description": "DEPRECATED. Use HTSLIB/BGZIPTABIX instead. Compresses/decompresses files", - "keywords": [ - "compress", - "decompress", - "bgzip", - "tabix" - ], - "tools": [ - { - "bgzip": { - "description": "Bgzip compresses or decompresses files in a similar manner to, and compatible with, gzip.\n", - "homepage": "https://www.htslib.org/doc/tabix.html", - "documentation": "http://www.htslib.org/doc/bgzip.html", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "identifier": "biotools:tabix" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "file to compress or to decompress", - "ontologies": [] - } - } - ] - ], - "output": { - "output": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "output.gz": { - "type": "file", - "description": "Output compressed/decompressed file", - "pattern": "*.", - "ontologies": [] - } - } - ] - ], - "gzi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.gzi": { - "type": "file", - "description": "Optional gzip index file for compressed inputs", - "pattern": "*.gzi", - "ontologies": [] - } - } - ] - ], - "versions_tabix": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "tabix": { - "type": "string", - "description": "The tool name" - } - }, - { - "tabix -h 2>&1 | grep -oP 'Version:\\s*\\K[^\\s]+'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "tabix": { - "type": "string", - "description": "The tool name" - } - }, - { - "tabix -h 2>&1 | grep -oP 'Version:\\s*\\K[^\\s]+'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@joseespinosa", - "@drpatelh", - "@maxulysse", - "@nvnieuwk" - ], - "maintainers": [ - "@joseespinosa", - "@drpatelh", - "@maxulysse", - "@nvnieuwk" - ] - }, - "pipelines": [ - { - "name": "funcscan", - "version": "3.0.0" - }, - { - "name": "nanoseq", - "version": "3.1.0" - }, - { - "name": "pacvar", - "version": "1.0.1" - }, - { - "name": "pangenome", - "version": "1.1.3" - }, - { - "name": "pathogensurveillance", - "version": "1.1.0" - }, - { - "name": "phaseimpute", - "version": "1.1.0" - }, - { - "name": "raredisease", - "version": "3.0.0" - }, - { - "name": "rnadnavar", - "version": "dev" - }, - { - "name": "tbanalyzer", - "version": "dev" - }, - { - "name": "variantbenchmarking", - "version": "1.5.0" - }, - { - "name": "viralrecon", - "version": "3.0.0" - } - ] - }, - { - "name": "tabix_bgziptabix", - "path": "modules/nf-core/tabix/bgziptabix/meta.yml", - "type": "module", - "meta": { - "name": "tabix_bgziptabix", - "description": "DEPRECATED. Use HTSLIB/BGZIPTABIX instead. bgzip a sorted tab-delimited genome file and then create tabix index", - "keywords": [ - "bgzip", - "compress", - "index", - "tabix", - "vcf" - ], - "tools": [ - { - "tabix": { - "description": "Generic indexer for TAB-delimited genome position files.", - "homepage": "https://www.htslib.org/doc/tabix.html", - "documentation": "https://www.htslib.org/doc/tabix.1.html", - "doi": "10.1093/bioinformatics/btq671", - "licence": [ - "MIT" - ], - "identifier": "biotools:tabix" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "Sorted tab-delimited genome file", - "ontologies": [] - } - } - ] - ], - "output": { - "gz_index": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.gz": { - "type": "file", - "description": "bgzipped tab-delimited genome file", - "pattern": "*.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - }, - { - "*.{tbi,csi}": { - "type": "file", - "description": "Tabix index file (either tbi or csi)", - "pattern": "*.{tbi,csi}", - "ontologies": [] - } - } - ] - ], - "versions_tabix": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "tabix": { - "type": "string", - "description": "The tool name" - } - }, - { - "tabix -h 2>&1 | grep -oP 'Version:\\s*\\K[^\\s]+'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_bgzip": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bgzip": { - "type": "string", - "description": "The tool name" - } - }, - { - "bgzip --version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "tabix": { - "type": "string", - "description": "The tool name" - } - }, - { - "tabix -h 2>&1 | grep -oP 'Version:\\s*\\K[^\\s]+'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "bgzip": { - "type": "string", - "description": "The tool name" - } - }, - { - "bgzip --version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@maxulysse", - "@DLBPointon" - ], - "maintainers": [ - "@maxulysse", - "@DLBPointon" - ] - }, - "pipelines": [ - { - "name": "cutandrun", - "version": "3.2.2" - }, - { - "name": "methylong", - "version": "2.0.0" - }, - { - "name": "nanoseq", - "version": "3.1.0" - }, - { - "name": "pacsomatic", - "version": "dev" - }, - { - "name": "raredisease", - "version": "3.0.0" - }, - { - "name": "rnadnavar", - "version": "dev" - }, - { - "name": "rnavar", - "version": "1.2.3" - }, - { - "name": "sarek", - "version": "3.8.1" - }, - { - "name": "variantbenchmarking", - "version": "1.5.0" - }, - { - "name": "variantprioritization", - "version": "1.0.0" - } - ] - }, - { - "name": "tabix_tabix", - "path": "modules/nf-core/tabix/tabix/meta.yml", - "type": "module", - "meta": { - "name": "tabix_tabix", - "description": "DEPRECATED. Use HTSLIB/BGZIPTABIX instead. Create a tabix index from a sorted\nbgzip TAB-delimited genome file, or extract regions from a bgzipped VCF file\nusing an optional regions file.\n", - "keywords": [ - "index", - "tabix", - "vcf", - "extract", - "regions" - ], - "tools": [ - { - "tabix": { - "description": "Generic indexer for TAB-delimited genome position files.", - "homepage": "https://www.htslib.org/doc/tabix.html", - "documentation": "https://www.htslib.org/doc/tabix.1.html", - "doi": "10.1093/bioinformatics/btq671", - "licence": [ - "MIT" - ], - "identifier": "biotools:tabix" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "tab": { - "type": "file", - "description": "TAB-delimited genome position file compressed with bgzip", - "pattern": "*.{bed.gz,gff.gz,sam.gz,vcf.gz}", - "ontologies": [] - } - }, - { - "tai": { - "type": "file", - "description": "Tabix index for the input file. Required when extracting regions.\nPass [] when creating an index instead.\n", - "pattern": "*.{tbi,csi}", - "ontologies": [] - } - }, - { - "regions": { - "type": "file", - "description": "Optional file of regions to extract (BED or chr:start-end format).\nPass [] to create an index instead of extracting regions.\n", - "pattern": "*.{bed,txt,tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "output": { - "index": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.{tbi,csi}": { - "type": "file", - "description": "Tabix index file (tbi or csi). Emitted when no regions file is provided.", - "pattern": "*.{tbi,csi}", - "ontologies": [] - } - } - ] - ], - "extracted": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "output.*gz": { - "type": "file", - "description": "Bgzipped file of extracted regions, preserving the input file extension. Emitted when a regions file is provided.", - "pattern": "*.*gz", - "ontologies": [] - } - } - ] - ], - "versions_tabix": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "tabix": { - "type": "string", - "description": "The tool name" - } - }, - { - "tabix -h 2>&1 | grep -oP 'Version:\\s*\\K[^\\s]+'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "tabix": { - "type": "string", - "description": "The tool name" - } - }, - { - "tabix -h 2>&1 | grep -oP 'Version:\\s*\\K[^\\s]+'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@joseespinosa", - "@drpatelh", - "@maxulysse" - ], - "maintainers": [ - "@joseespinosa", - "@drpatelh", - "@maxulysse" - ] - }, - "pipelines": [ - { - "name": "drop", - "version": "1.0.0" - }, - { - "name": "nanoseq", - "version": "3.1.0" - }, - { - "name": "pathogensurveillance", - "version": "1.1.0" - }, - { - "name": "phaseimpute", - "version": "1.1.0" - }, - { - "name": "radseq", - "version": "dev" - }, - { - "name": "raredisease", - "version": "3.0.0" - }, - { - "name": "references", - "version": "0.1" - }, - { - "name": "rnadnavar", - "version": "dev" - }, - { - "name": "rnavar", - "version": "1.2.3" }, { - "name": "sarek", - "version": "3.8.1" - }, - { - "name": "variantbenchmarking", - "version": "1.5.0" - }, - { - "name": "variantcatalogue", - "version": "dev" - }, - { - "name": "variantprioritization", - "version": "1.0.0" - }, - { - "name": "viralmetagenome", - "version": "1.1.1" - }, - { - "name": "viralrecon", - "version": "3.0.0" - } - ] - }, - { - "name": "tagbam", - "path": "modules/nf-core/tagbam/meta.yml", - "type": "module", - "meta": { - "name": "tagbam", - "description": "A tool for tagging BAM files.", - "keywords": [ - "long-read", - "bam", - "genomics" - ], - "tools": [ - { - "tagbam": { - "description": "A tool for tagging BAM files.", - "homepage": "https://github.com/fellen31/tagbam", - "documentation": "https://github.com/fellen31/tagbam", - "tool_dev_url": "https://github.com/fellen31/tagbam", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:true ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "(u)BAM file", - "pattern": "*.{bam}", - "ontologies": [] - } - } - ] - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "Tagged bam file", - "pattern": "*.{bam}", - "ontologies": [] - } - } - ] - ], - "versions_tagbam": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "tagbam": { - "type": "string", - "description": "The tool name" - } - }, - { - "tagbam --version | sed 's/tagbam //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "tagbam": { - "type": "string", - "description": "The tool name" - } - }, - { - "tagbam --version | sed 's/tagbam //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@fellen31" - ], - "maintainers": [ - "@fellen31" - ] - } - }, - { - "name": "tailfindr", - "path": "modules/nf-core/tailfindr/meta.yml", - "type": "module", - "meta": { - "name": "tailfindr", - "description": "Estimating poly(A)-tail lengths from basecalled fast5 files produced by Nanopore sequencing of RNA and DNA", - "keywords": [ - "polya tail", - "fast5", - "nanopore" - ], - "tools": [ - { - "tailfindr": { - "description": "An R package for estimating poly(A)-tail lengths in Oxford Nanopore RNA and DNA reads.", - "homepage": "https://github.com/adnaniazi/tailfindr", - "documentation": "https://github.com/adnaniazi/tailfindr/blob/master/README.md", - "tool_dev_url": "https://github.com/adnaniazi/tailfindr", - "doi": "10.1261/rna.071332.119", - "licence": [ - "AGPL v3" - ], - "identifier": "biotools:tailfindr" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "fast5": { - "type": "file", - "description": "fast5 file", - "pattern": "*.fast5", - "ontologies": [] - } - } - ] - ], - "output": { - "csv_gz": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.csv.gz": { - "type": "file", - "description": "Compressed csv file", - "pattern": "*.csv.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "versions_tailfindr": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "tailfindr": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "Rscript -e \"cat(paste(packageVersion('tailfindr'), collapse='.'))\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_ont_fast5_api": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "ont-fast5-api": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python -c \"import ont_fast5_api; print(ont_fast5_api.__version__)\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "tailfindr": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "Rscript -e \"cat(paste(packageVersion('tailfindr'), collapse='.'))\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "ont-fast5-api": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python -c \"import ont_fast5_api; print(ont_fast5_api.__version__)\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@lucacozzuto" - ], - "maintainers": [ - "@lucacozzuto" - ] - } - }, - { - "name": "tar", - "path": "modules/nf-core/tar/meta.yml", - "type": "module", - "meta": { - "name": "tar", - "description": "Compress directories into tarballs with various compression options", - "keywords": [ - "untar", - "tar", - "tarball", - "compression", - "archive", - "gzip", - "targz" - ], - "tools": [ - { - "tar": { - "description": "GNU Tar provides the ability to create tar archives, as well as various other kinds of manipulation.", - "homepage": "https://www.gnu.org/software/tar/", - "documentation": "https://www.gnu.org/software/tar/manual/", - "licence": [ - "GPLv3" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "input": { - "type": "directory", - "description": "A file or directory to be archived", - "pattern": "*/", - "ontologies": [ - { - "edam": "http://edamontology.org/data_1049" - } - ] - } - } - ], - { - "compress_type": { - "type": "string", - "description": "A string defining which type of (optional) compression to apply to the archive.\nProvide an empty string in quotes for no compression\n", - "pattern": ".bz2|.xz|.lz|.lzma|.lzo|.zst|.gz" - } - } - ], - "output": { - "archive": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n", - "pattern": "*.tar{.bz2,.xz,.lz,.lzma,.lzo,.zst,.gz,}", - "ontologies": [ + "name": "utils_annotation_cache", + "path": "subworkflows/nf-core/utils_annotation_cache/meta.yml", + "type": "subworkflow", + "meta": { + "name": "utils_annotation_cache", + "description": "Check the path to the annotation cache depending if local or on the cloud, or using annotation-cache itself", + "keywords": ["snpeff", "ensemblvep", "annotation-cache", "annotation", "cache", "verification"], + "components": [], + "input": [ + { + "ensemblvep_cache": { + "description": "Path to root cache\nStructure: [ path(cache) ]\n" + } + }, { - "edam": "http://edamontology.org/format_25722" + "ensemblvep_cache_version": { + "description": "cache_version to use\nStructure: [ val(cache_version) ]\n" + } }, { - "edam": "http://edamontology.org/format_2573" + "ensemblvep_custom_args": { + "description": "custom args, to check if refseq or merged is needed\nStructure: [ val(custom args) ]\n" + } }, { - "edam": "http://edamontology.org/format_3462" - } - ] - } - }, - { - "*.tar${compress_type}": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n", - "pattern": "*.tar{.bz2,.xz,.lz,.lzma,.lzo,.zst,.gz,}", - "ontologies": [ + "ensemblvep_genome": { + "description": "genome to use\nStructure: [ val(genome) ]\n" + } + }, { - "edam": "http://edamontology.org/format_25722" + "ensemblvep_species": { + "description": "species to use\nStructure: [ val(species) ]\n" + } }, { - "edam": "http://edamontology.org/format_2573" + "ensemblvep_enabled": { + "description": "Boolean to enable ensemblvep\nStructure: [ Boolean ]\n" + } }, { - "edam": "http://edamontology.org/format_3462" - } - ] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@jfy133" - ], - "maintainers": [ - "@jfy133" - ] - } - }, - { - "name": "taxonkit_lineage", - "path": "modules/nf-core/taxonkit/lineage/meta.yml", - "type": "module", - "meta": { - "name": "taxonkit_lineage", - "description": "Convert taxonids to taxon lineages", - "keywords": [ - "taxonomy", - "taxids", - "taxon name", - "conversion" - ], - "tools": [ - { - "taxonkit": { - "description": "A Cross-platform and Efficient NCBI Taxonomy Toolkit", - "homepage": "https://bioinf.shenwei.me/taxonkit/", - "documentation": "https://bioinf.shenwei.me/taxonkit/usage/#name2taxid", - "tool_dev_url": "https://github.com/shenwei356/taxonkit", - "doi": "10.1016/j.jgg.2021.03.006", - "licence": [ - "MIT" - ], - "identifier": "biotools:taxonkit" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "taxid": { - "type": "string", - "description": "Taxon id to look up (provide either this or taxidfile, not both)" - } - }, - { - "taxidfile": { - "type": "file", - "description": "File with taxon ids to look up, each on their own line (provide either this or name, not both; the file can contain other information, see the tool's docs)", - "ontologies": [] - } - } - ], - { - "taxdb": { - "type": "file", - "description": "Taxonomy database unpacked from ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz", - "ontologies": [] - } - } - ], - "output": { - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "TSV file with added taxon lineages", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@erikrikarddaniel" - ], - "maintainers": [ - "@erikrikarddaniel" - ] - }, - "pipelines": [ - { - "name": "metatdenovo", - "version": "1.3.0" - } - ] - }, - { - "name": "taxonkit_list", - "path": "modules/nf-core/taxonkit/list/meta.yml", - "type": "module", - "meta": { - "name": "taxonkit_list", - "description": "Generate taxonomic subtrees based on taxonids", - "keywords": [ - "taxonomy", - "taxids", - "lineage" - ], - "tools": [ - { - "taxonkit": { - "description": "A Cross-platform and Efficient NCBI Taxonomy Toolkit", - "homepage": "https://bioinf.shenwei.me/taxonkit/", - "documentation": "https://bioinf.shenwei.me/taxonkit/usage/#name2taxid", - "tool_dev_url": "https://github.com/shenwei356/taxonkit", - "doi": "10.1016/j.jgg.2021.03.006", - "licence": [ - "MIT" - ], - "identifier": "biotools:taxonkit" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - 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val(db) ]\n" + } }, { - "edam": "http://edamontology.org/format_3752" + "snpeff_enabled": { + "description": "Boolean to enable snpeff\nStructure: [ Boolean ]\n" + } }, { - "edam": "http://edamontology.org/format_3977" + "help_message": { + "description": "Extra help message to display when error\nStructure: [ val(species) ]\n" + } + } + ], + "output": [ + { + "ensemblvep_cache": { + "description": "Path to ensemblvep cache\nStructure: [ val(meta), path(cache) ]\n" + } }, { - "edam": "http://edamontology.org/format_3746" + "snpeff_cache": { + "description": "Path to snpeff cache\nStructure: [ val(meta), path(cache) ]\n" + } } - ] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@sofstam", - "@jfy133" - ], - "maintainers": [ - "@sofstam", - "@jfy133" - ] - }, - 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"1.0.1" + }, + { + "name": "pairgenomealign", + "version": "2.2.3" + }, + { + "name": "pangenome", + "version": "1.1.3" + }, + { + "name": "panoramaseq", + "version": "dev" + }, + { + "name": "pathogensurveillance", + "version": "1.1.0" + }, + { + "name": "phaseimpute", + "version": "1.1.0" + }, + { + "name": "phyloplace", + "version": "2.0.0" + }, + { + "name": "pixelator", + "version": "4.0.0" + }, + { + "name": "proteinannotator", + "version": "1.1.0" + }, + { + "name": "proteinfamilies", + "version": "2.3.0" + }, + { + "name": "proteinfold", + "version": "2.0.0" + }, + { + "name": "rangeland", + "version": "1.0.0" + }, + { + "name": "raredisease", + "version": "3.0.0" + }, + { + "name": "rarevariantburden", + "version": "dev" + }, + { + "name": "readsimulator", + "version": "1.0.1" + }, + { + "name": "references", + "version": "0.1" + }, + { + "name": "reportho", + "version": "1.1.0" + }, + { + "name": "ribomsqc", + "version": "1.0.0" + }, + { + "name": "riboseq", + "version": "1.2.0" + }, + { + "name": "rnadnavar", + "version": "dev" + }, + { + "name": "rnafusion", + "version": "4.1.2" + }, + { + "name": "rnaseq", + "version": "3.26.0" + }, + { + "name": "sammyseq", + "version": "dev" + }, + { + "name": "sarek", + "version": "3.8.1" + }, + { + "name": "scdownstream", + "version": "dev" + }, + { + "name": "scnanoseq", + "version": "1.2.2" + }, + { + "name": "scrnaseq", + "version": "4.1.0" + }, + { + "name": "seqinspector", + "version": "1.0.1" + }, + { + "name": "seqsubmit", + "version": "dev" + }, + { + "name": "smrnaseq", + "version": "2.4.1" + }, + { + "name": "sopa", + "version": "dev" + }, + { + "name": "spatialvi", + "version": "dev" + }, + { + "name": "spatialxe", + "version": "dev" + }, + { + "name": "stableexpression", + "version": "dev" + }, + { + "name": "taxprofiler", + "version": "2.0.0" + }, + { + "name": "tbanalyzer", + "version": "dev" + }, + { + "name": "tfactivity", + "version": "dev" + }, + { + "name": "troughgraph", + "version": "dev" + }, + { + "name": "variantbenchmarking", + "version": "1.5.0" + }, + { + "name": "variantprioritization", + "version": "1.0.0" + }, + { + "name": "viralmetagenome", + "version": "1.1.1" + }, + { + "name": "viralrecon", + "version": "3.0.0" + } ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@rpetit3" - ], - "maintainers": [ - "@rpetit3" - ] - }, - "pipelines": [ - { - "name": "tbanalyzer", - "version": "dev" - } - ] - }, - { - "name": "tcoffee_align", - "path": "modules/nf-core/tcoffee/align/meta.yml", - "type": "module", - "meta": { - "name": "tcoffee_align", - "description": "Aligns sequences using T_COFFEE", - "keywords": [ - "alignment", - "MSA", - "genomics" - ], - "tools": [ - { - "tcoffee": { - "description": "A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures.", - "homepage": "http://www.tcoffee.org/Projects/tcoffee/", - "documentation": "https://tcoffee.readthedocs.io/en/latest/tcoffee_main_documentation.html", - "tool_dev_url": "https://github.com/cbcrg/tcoffee", - "doi": "10.1006/jmbi.2000.4042", - "licence": [ - "GPL v3" - ], - "identifier": "" - } - }, - { - "pigz": { - "description": "Parallel implementation of the gzip algorithm.", - "homepage": "https://zlib.net/pigz/", - "documentation": "https://zlib.net/pigz/pigz.pdf", - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input sequences in FASTA format", - "pattern": "*.{fa,fasta}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1919" - }, - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing tree information\ne.g. `[ id:'test_tree']`\n" - } - }, - { - "tree": { - "type": "file", - "description": "Input guide tree in Newick format", - "pattern": "*.{dnd}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2006" - } - ] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing tree information\ne.g. `[ id:'test_infos']`\n" - } - }, - { - "template": { - "type": "file", - "description": "T_coffee template file that maps sequences to the accessory information files to be used.", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1476" - } - ] - } + }, + { + "name": "utils_nfcore_pipeline", + "path": "subworkflows/nf-core/utils_nfcore_pipeline/meta.yml", + "type": "subworkflow", + "meta": { + "name": "UTILS_NFCORE_PIPELINE", + "description": "Subworkflow with utility functions specific to the nf-core pipeline template", + "keywords": ["utility", "pipeline", "initialise", "version"], + "components": [], + "input": [ + { + "nextflow_cli_args": { + "type": "list", + "description": "Nextflow CLI positional arguments\n" + } + } + ], + "output": [ + { + "success": { + "type": "boolean", + "description": "Dummy output to indicate success\n" + } + } + ], + "authors": ["@adamrtalbot"], + "maintainers": ["@adamrtalbot", "@maxulysse"] }, - { - "accessory_information": { - "type": "file", - "description": "Accessory files to be used in the alignment. For example, it could be protein structures or secondary structures.", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1476" - }, - { - "edam": "http://edamontology.org/format_1477" - } - ] - } - } - ], - { - "compress": { - "type": "boolean", - "description": "Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded." - } - } - ], - "output": { - "alignment": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" + "pipelines": [ + { + "name": "abotyper", + "version": "dev" + }, + { + "name": "airrflow", + "version": "5.0.0" + }, + { + "name": "ampliseq", + "version": "2.17.0" + }, + { + "name": "bacass", + "version": "2.6.0" + }, + { + "name": "bamtofastq", + "version": "2.2.1" + }, + { + "name": "cellpainting", + "version": "dev" + }, + { + "name": "chipseq", + "version": "2.1.0" + }, + { + "name": "circrna", + "version": "dev" + }, + { + "name": "coproid", + "version": "2.0.1" + }, + { + "name": "createpanelrefs", + "version": "dev" + }, + { + "name": "createtaxdb", + "version": "3.0.0" + }, + { + "name": "crisprseq", + "version": "2.3.0" + }, + { + "name": "dartseq", + "version": "dev" + }, + { + "name": "datasync", + "version": "dev" + }, + { + "name": "deepmodeloptim", + "version": "dev" + }, + { + "name": "deepmutscan", + "version": "dev" + }, + { + "name": "demo", + "version": "1.1.0" + }, + { + "name": "demultiplex", + "version": "1.7.1" + }, + { + "name": "denovotranscript", + "version": "1.2.1" + }, + { + "name": "detaxizer", + "version": "1.3.0" + }, + { + "name": "differentialabundance", + "version": "1.5.0" + }, + { + "name": "diseasemodulediscovery", + "version": "dev" + }, + { + "name": "drop", + "version": "1.0.0" + }, + { + "name": "drugresponseeval", + "version": "1.2.0" + }, + { + "name": "epigenomesegmentation", + "version": "dev" + }, + { + "name": "epitopeprediction", + "version": "3.1.0" + }, + { + "name": "evexplorer", + "version": "dev" + }, + { + "name": "fastqrepair", + "version": "1.0.0" + }, + { + "name": "fastquorum", + "version": "1.2.0" + }, + { + "name": "fetchngs", + "version": "1.12.0" + }, + { + "name": "funcprofiler", + "version": "dev" + }, + { + "name": "funcscan", + "version": "3.0.0" + }, + { + "name": "genephylomodeler", + "version": "dev" + }, + { + "name": "genomeassembler", + "version": "1.1.0" + }, + { + "name": "genomeqc", + "version": "dev" + }, + { + "name": "genomicrelatedness", + "version": "dev" + }, + { + "name": "gwas", + "version": "dev" + }, + { + "name": "hlatyping", + "version": "2.2.0" + }, + { + "name": "isoseq", + "version": "2.0.0" + }, + { + "name": "lncpipe", + "version": "dev" + }, + { + "name": "lsmquant", + "version": "1.0.0" + }, + { + "name": "mag", + "version": "5.4.2" + }, + { + "name": "magmap", + "version": "1.0.0" + }, + { + "name": "mcmicro", + "version": "dev" + }, + { + "name": "meerpipe", + "version": "dev" + }, + { + "name": "metaboigniter", + "version": "2.0.1" + }, + { + "name": "metapep", + "version": "1.0.0" + }, + { + "name": "metatdenovo", + "version": "1.3.0" + }, + { + "name": "methylarray", + "version": "dev" + }, + { + "name": "methylong", + "version": "2.0.0" + }, + { + "name": "methylseq", + "version": "4.2.0" + }, + { + "name": "mhcquant", + "version": "3.2.0" + }, + { + "name": "mitodetect", + "version": "dev" + }, + { + "name": "molkart", + "version": "1.2.0" + }, + { + "name": "mspepid", + "version": "dev" + }, + { + "name": "multiplesequencealign", + "version": "1.1.1" + }, + { + "name": "nanostring", + "version": "1.3.3" + }, + { + "name": "nascent", + "version": "2.3.0" + }, + { + "name": "ncrnannotator", + "version": "dev" + }, + { + "name": "oncoanalyser", + "version": "2.3.0" + }, + { + "name": "pacsomatic", + "version": "dev" + }, + { + "name": "pacvar", + "version": "1.0.1" + }, + { + "name": "pairgenomealign", + "version": "2.2.3" + }, + { + "name": "pangenome", + "version": "1.1.3" + }, + { + "name": "panoramaseq", + "version": "dev" + }, + { + "name": "pathogensurveillance", + "version": "1.1.0" + }, + { + "name": "phaseimpute", + "version": "1.1.0" + }, + { + "name": "phyloplace", + "version": "2.0.0" + }, + { + "name": "pixelator", + "version": "4.0.0" + }, + { + "name": "proteinannotator", + "version": "1.1.0" + }, + { + "name": "proteinfamilies", + "version": "2.3.0" + }, + { + "name": "proteinfold", + "version": "2.0.0" + }, + { + "name": "rangeland", + "version": "1.0.0" + }, + { + "name": "raredisease", + "version": "3.0.0" + }, + { + "name": "rarevariantburden", + "version": "dev" + }, + { + "name": "readsimulator", + "version": "1.0.1" + }, + { + "name": "references", + "version": "0.1" + }, + { + "name": "reportho", + "version": "1.1.0" + }, + { + "name": "ribomsqc", + "version": "1.0.0" + }, + { + "name": "riboseq", + "version": "1.2.0" + }, + { + "name": "rnadnavar", + "version": "dev" + }, + { + "name": "rnafusion", + "version": "4.1.2" + }, + { + "name": "rnaseq", + "version": "3.26.0" + }, + { + "name": "sammyseq", + "version": "dev" + }, + { + "name": "sarek", + "version": "3.8.1" + }, + { + "name": "scdownstream", + "version": "dev" + }, + { + "name": "scnanoseq", + "version": "1.2.2" + }, + { + "name": "scrnaseq", + "version": "4.1.0" + }, + { + "name": "seqinspector", + "version": "1.0.1" + }, + { + "name": "seqsubmit", + "version": "dev" + }, + { + "name": "smrnaseq", + "version": "2.4.1" + }, + { + "name": "sopa", + "version": "dev" + }, + { + "name": "spatialvi", + "version": "dev" + }, + { + "name": "spatialxe", + "version": "dev" + }, + { + "name": "stableexpression", + "version": "dev" + }, + { + "name": "taxprofiler", + "version": "2.0.0" + }, + { + "name": "tbanalyzer", + "version": "dev" + }, + { + "name": "tfactivity", + "version": "dev" + }, + { + "name": "troughgraph", + "version": "dev" + }, + { + "name": "tumourevo", + "version": "dev" + }, + { + "name": "variantbenchmarking", + "version": "1.5.0" + }, + { + "name": "variantprioritization", + "version": "1.0.0" + }, + { + "name": "viralmetagenome", + "version": "1.1.1" + }, + { + "name": "viralrecon", + "version": "3.0.0" } - }, - { - "*.aln{.gz,}": { - "type": "file", - "description": "Alignment file in FASTA format. May be gzipped.", - "pattern": "*.aln{.gz,}", - "ontologies": [ + ] + }, + { + "name": "utils_nfschema_plugin", + "path": "subworkflows/nf-core/utils_nfschema_plugin/meta.yml", + "type": "subworkflow", + "meta": { + "name": "utils_nfschema_plugin", + "description": "Run nf-schema to validate parameters and create a summary of changed parameters", + "keywords": ["validation", "JSON schema", "plugin", "parameters", "summary"], + "components": [], + "input": [ + { + "input_workflow": { + "type": "object", + "description": "The workflow object of the used pipeline.\nThis object contains meta data used to create the params summary log\n" + } + }, { - "edam": "http://edamontology.org/format_2554" + "validate_params": { + "type": "boolean", + "description": "Validate the parameters and error if invalid." + } + }, + { + "parameters_schema": { + "type": "string", + "description": "Path to the parameters JSON schema.\nThis has to be the same as the schema given to the `validation.parametersSchema` config\noption. When this input is empty it will automatically use the configured schema or\n\"${projectDir}/nextflow_schema.json\" as default. The schema should not be given in this way\nfor meta pipelines.\n" + } + }, + { + "help": { + "type": "boolean, string", + "description": "Show the help message and exit. When a parameter name is given, show the help message for that parameter instead of the general help message.\n" + } + }, + { + "help_full": { + "type": "boolean", + "description": "Show the full help message and exit." + } + }, + { + "show_hidden": { + "type": "boolean", + "description": "Show hidden parameters in the help message." + } + }, + { + "before_text": { + "type": "string", + "description": "Text to show before the parameters summary and help message." + } }, { - "edam": "http://edamontology.org/format_1921" + "after_text": { + "type": "string", + "description": "Text to show after the parameters summary and help message." + } + }, + { + "command": { + "type": "string", + "description": "An example command to run the pipeline, to show in the help message and the summary." + } }, { - "edam": "http://edamontology.org/format_1984" + "cli_typecast": { + "type": "boolean", + "description": "Whether to apply typecasting to the parameters given via the CLI before validation.\nSet this to `null` to use the default behavior.\n" + } } - ] - } - } - ] - ], - "lib": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" - } - }, - { - "*.*lib": { - "type": "file", - "description": "optional output, the library generated from the MSA file.", - "pattern": "*.*lib", - "ontologies": [] - } - } - ] - ], - "versions_tcoffee": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "tcoffee": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "t_coffee -version | awk '{gsub(\"Version_\", \"\"); print \\$3}'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_pigz": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pigz": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pigz --version 2>&1 | sed \"s/^.*pigz[[:space:]]*//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "tcoffee": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "t_coffee -version | awk '{gsub(\"Version_\", \"\"); print \\$3}'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pigz": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pigz --version 2>&1 | sed \"s/^.*pigz[[:space:]]*//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@luisas", - "@JoseEspinosa", - "@alessiovignoli" - ], - "maintainers": [ - "@luisas", - "@JoseEspinosa", - "@lrauschning", - "@alessiovignoli" - ] - }, - "pipelines": [ - { - "name": "multiplesequencealign", - "version": "1.1.1" - } - ] - }, - { - "name": "tcoffee_alncompare", - "path": "modules/nf-core/tcoffee/alncompare/meta.yml", - "type": "module", - "meta": { - "name": "tcoffee_alncompare", - "description": "Compares 2 alternative MSAs to evaluate them.", - "keywords": [ - "alignment", - "MSA", - "evaluation" - ], - "tools": [ - { - "tcoffee": { - "description": "A collection of tools for Multiple Alignments of DNA, RNA, Protein Sequence", - "homepage": "http://www.tcoffee.org/Projects/tcoffee/", - "documentation": "https://tcoffee.readthedocs.io/en/latest/tcoffee_main_documentation.html", - "tool_dev_url": "https://github.com/cbcrg/tcoffee", - "doi": "10.1006/jmbi.2000.4042", - "licence": [ - "GPL v3" - ], - "identifier": "" - } - }, - { - "pigz": { - "description": "Parallel implementation of the gzip algorithm.", - "homepage": "https://zlib.net/pigz/", - "documentation": "https://zlib.net/pigz/pigz.pdf", - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', ... ]\n" - } - }, - { - "msa": { - "type": "file", - "description": "fasta file containing the alignment to be evaluated. Can be gzipped or uncompressed", - "pattern": "*.{aln,fa,fasta,fas}{.gz,}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1919" - }, - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - }, - { - "ref_msa": { - "type": "file", - "description": "fasta file containing the reference alignment used for the evaluation. Can be gzipped or uncompressed", - "pattern": "*.{aln,fa,fasta,fas}{.gz,}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - }, - { - "edam": "http://edamontology.org/format_2554" - }, - { - "edam": "http://edamontology.org/format_1921" - }, - { - "edam": "http://edamontology.org/format_1984" - } - ] - } - } - ] - ], - "output": { - "scores": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.scores": { - "type": "file", - "description": "a file containing the score of the alignment", - "pattern": "*.scores", - "ontologies": [] - } - } - ] - ], - "versions_tcoffee": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "tcoffee": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "t_coffee -version | awk '{gsub(\"Version_\", \"\"); print \\$3}'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_pigz": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pigz": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pigz --version 2>&1 | sed \"s/^.*pigz[[:space:]]*//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "tcoffee": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "t_coffee -version | awk '{gsub(\"Version_\", \"\"); print \\$3}'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pigz": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pigz --version 2>&1 | sed \"s/^.*pigz[[:space:]]*//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@l-mansouri", - "@luisas" - ] - }, - "pipelines": [ - { - "name": "multiplesequencealign", - "version": "1.1.1" - } - ] - }, - { - "name": "tcoffee_consensus", - "path": "modules/nf-core/tcoffee/consensus/meta.yml", - "type": "module", - "meta": { - "name": "tcoffee_consensus", - "description": "Computes a consensus alignment using T_COFFEE", - "keywords": [ - "alignment", - "MSA", - "genomics" - ], - "tools": [ - { - "tcoffee": { - "description": "A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures.", - "homepage": "http://www.tcoffee.org/Projects/tcoffee/", - "documentation": "https://tcoffee.readthedocs.io/en/latest/tcoffee_main_documentation.html", - "tool_dev_url": "https://github.com/cbcrg/tcoffee", - "doi": "10.1006/jmbi.2000.4042", - "licence": [ - "GPL v3" - ], - "identifier": "" - } - }, - { - "pigz": { - "description": "Parallel implementation of the gzip algorithm.", - "homepage": "https://zlib.net/pigz/", - "documentation": "https://zlib.net/pigz/pigz.pdf", - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "aln": { - "type": "file", - "description": "List of multiple sequence alignments in FASTA format to be used to compute the consensus", - "pattern": "*.{fa,fasta}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing tree information\ne.g. `[ id:'test_tree']`\n" - } - }, - { - "tree": { - "type": "file", - "description": "Input guide tree in Newick format", - "pattern": "*.{dnd}", - "ontologies": [] - } - } - ], - { - "compress": { - "type": "boolean", - "description": "Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded." - } - } - ], - "output": { - "alignment": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n", - "pattern": "*.{fa,fasta,aln}" - } - }, - { - "*.{aln,aln.gz}": { - "type": "file", - "description": "Alignment file in FASTA format. May be gzipped.", - "pattern": "*.aln{.gz,}", - "ontologies": [] - } - } - ] - ], - "eval": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n", - "pattern": "*.{fa,fasta,aln}" - } - }, - { - "*.{score_html,sp_ascii}": { - "type": "file", - "description": "Consensus evaluation file.", - "pattern": "*.{score_html, score_ascii}", - "ontologies": [] - } - } - ] - ], - "versions_tcoffee": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "tcoffee": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "t_coffee -version | awk '{gsub(\"Version_\", \"\"); print \\$3}'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_pigz": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pigz": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pigz --version 2>&1 | sed \"s/^.*pigz[[:space:]]*//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "tcoffee": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "t_coffee -version | awk '{gsub(\"Version_\", \"\"); print \\$3}'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pigz": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pigz --version 2>&1 | sed \"s/^.*pigz[[:space:]]*//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@luisas" - ], - "maintainers": [ - "@luisas" - ] - }, - "pipelines": [ - { - "name": "multiplesequencealign", - "version": "1.1.1" - } - ] - }, - { - "name": "tcoffee_extractfrompdb", - "path": "modules/nf-core/tcoffee/extractfrompdb/meta.yml", - "type": "module", - "meta": { - "name": "tcoffee_extractfrompdb", - "description": "Reformats the header of PDB files with t-coffee", - "keywords": [ - "reformatting", - "pdb", - "genomics" - ], - "tools": [ - { - "tcoffee": { - "description": "A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures.", - "homepage": "http://www.tcoffee.org/Projects/tcoffee/", - "documentation": "https://tcoffee.readthedocs.io/en/latest/tcoffee_main_documentation.html", - "tool_dev_url": "https://github.com/cbcrg/tcoffee", - "doi": "10.1006/jmbi.2000.4042", - "licence": [ - "GPL v3" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } + ], + "output": [ + { + "dummy_emit": { + "type": "boolean", + "description": "Dummy emit to make nf-core subworkflows lint happy" + } + } + ], + "authors": ["@nvnieuwk"], + "maintainers": ["@nvnieuwk"] }, - { - "pdb": { - "type": "file", - "description": "Input pdb to be reformatted", - "ontologies": [] - } - } - ] - ], - "output": { - "formatted_pdb": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "${prefix}.pdb": { - "type": "file", - "description": "Formatted pdb file", - "pattern": "*", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@luisas" - ] - }, - "pipelines": [ - { - "name": "multiplesequencealign", - "version": "1.1.1" - } - ] - }, - { - "name": "tcoffee_irmsd", - "path": "modules/nf-core/tcoffee/irmsd/meta.yml", - "type": "module", - "meta": { - "name": "tcoffee_irmsd", - "description": "Computes the irmsd score for a given alignment and the structures.", - "keywords": [ - "alignment", - "MSA", - "evaluation" - ], - "tools": [ - { - "tcoffee": { - "description": "A collection of tools for Multiple Alignments of DNA, RNA, Protein Sequence", - "homepage": "http://www.tcoffee.org/Projects/tcoffee/", - "documentation": "https://tcoffee.readthedocs.io/en/latest/tcoffee_main_documentation.html", - "tool_dev_url": "https://github.com/cbcrg/tcoffee", - "doi": "10.1006/jmbi.2000.4042", - "licence": [ - "GPL v3" - ], - "identifier": "" - } - }, - { - "pigz": { - "description": "Parallel implementation of the gzip algorithm.", - "homepage": "https://zlib.net/pigz/", - "documentation": "https://zlib.net/pigz/pigz.pdf", - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', ... ]\n" - } - }, - { - "msa": { - "type": "file", - "description": "Multiple Sequence Alignment File\n", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - }, - { - "edam": "http://edamontology.org/format_2554" - }, - { - "edam": "http://edamontology.org/format_1921" - }, - { - "edam": "http://edamontology.org/format_1984" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "template": { - "type": "file", - "description": "Template file\n", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1476" - } - ] - } - }, - { - "structures": { - "type": "file", - "description": "Structure file\n", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1476" - } - ] - } - } - ] - ], - "output": { - "irmsd": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.irmsd": { - "type": "file", - "description": "File containing the irmsd of the alignment", - "ontologies": [] - } - } - ] - ], - "versions_tcoffee": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "tcoffee": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "t_coffee -version | awk '{gsub(\"Version_\", \"\"); print \\$3}'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_pigz": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pigz": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pigz --version 2>&1 | sed \"s/^.*pigz[[:space:]]*//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "tcoffee": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "t_coffee -version | awk '{gsub(\"Version_\", \"\"); print \\$3}'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pigz": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pigz --version 2>&1 | sed \"s/^.*pigz[[:space:]]*//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@luisas" - ] - }, - "pipelines": [ - { - "name": "multiplesequencealign", - "version": "1.1.1" - } - ] - }, - { - "name": "tcoffee_regressive", - "path": "modules/nf-core/tcoffee/regressive/meta.yml", - "type": "module", - "meta": { - "name": "tcoffee_regressive", - "description": "Aligns sequences using the regressive algorithm as implemented in the T_COFFEE package", - "keywords": [ - "alignment", - "MSA", - "genomics" - ], - "tools": [ - { - "tcoffee": { - "description": "A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures.", - "homepage": "http://www.tcoffee.org/Projects/tcoffee/", - "documentation": "https://tcoffee.readthedocs.io/en/latest/tcoffee_main_documentation.html", - "tool_dev_url": "https://github.com/cbcrg/tcoffee", - "doi": "10.1038/s41587-019-0333-6", - "licence": [ - "GPL v3" - ], - "identifier": "" - } - }, - { - "pigz": { - "description": "Parallel implementation of the gzip algorithm.", - "homepage": "https://zlib.net/pigz/", - "documentation": "https://zlib.net/pigz/pigz.pdf", - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input sequences in FASTA format", - "pattern": "*.{fa,fasta}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1919" - }, - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing tree information\ne.g. `[ id:'test_tree']`\n" - } - }, - { - "tree": { - "type": "file", - "description": "Input guide tree in Newick format", - "pattern": "*.{dnd}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2006" - } - ] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing tree information\ne.g. `[ id:'test_infos']`\n" - } - }, - { - "template": { - "type": "file", - "description": "T_coffee template file that maps sequences to the accessory information files to be used.", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1476" - } - ] - } - }, - { - "accessory_information": { - "type": "file", - "description": "Accessory files to be used in the alignment. For example, it could be protein structures or secondary structures.", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1476" - } - ] - } - } - ], - { - "compress": { - "type": "boolean", - "description": "Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded." - } - } - ], - "output": { - "alignment": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" - } - }, - { - "*.aln{.gz,}": { - "type": "file", - "description": "Alignment file in FASTA format. May be gzipped.", - "pattern": "*.aln{.gz,}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2554" - }, - { - "edam": "http://edamontology.org/format_1921" - }, - { - "edam": "http://edamontology.org/format_1984" - } - ] - } - } - ] - ], - "versions_tcoffee": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "tcoffee": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "t_coffee -version | awk '{gsub(\"Version_\", \"\"); print \\$3}'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_pigz": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pigz": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pigz --version 2>&1 | sed \"s/^.*pigz[[:space:]]*//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "tcoffee": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "t_coffee -version | awk '{gsub(\"Version_\", \"\"); print \\$3}'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pigz": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pigz --version 2>&1 | sed \"s/^.*pigz[[:space:]]*//\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@luisas" - ], - "maintainers": [ - "@luisas" - ] - }, - "pipelines": [ - { - "name": "multiplesequencealign", - "version": "1.1.1" - } - ] - }, - { - "name": "tcoffee_seqreformat", - "path": "modules/nf-core/tcoffee/seqreformat/meta.yml", - "type": "module", - "meta": { - "name": "tcoffee_seqreformat", - "description": "Reformats files with t-coffee", - "keywords": [ - "reformatting", - "alignment", - "genomics" - ], - "tools": [ - { - "tcoffee": { - "description": "A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures.", - "homepage": "http://www.tcoffee.org/Projects/tcoffee/", - "documentation": "https://tcoffee.readthedocs.io/en/latest/tcoffee_main_documentation.html", - "tool_dev_url": "https://github.com/cbcrg/tcoffee", - "doi": "10.1006/jmbi.2000.4042", - "licence": [ - "GPL v3" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "infile": { - "type": "file", - "description": "Input file to be reformatted", - "ontologies": [] - } - } - ] - ], - "output": { - "formatted_file": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "${prefix}.txt": { - "type": "file", - "description": "Formatted file", - "pattern": "*", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@luisas", - "@JoseEspinosa" - ] - }, - "pipelines": [ - { - "name": "multiplesequencealign", - "version": "1.1.1" - } - ] - }, - { - "name": "tcoffee_tcs", - "path": "modules/nf-core/tcoffee/tcs/meta.yml", - "type": "module", - "meta": { - "name": "tcoffee_tcs", - "description": "Compute the TCS score for a MSA or for a MSA plus a library file. Outputs the tcs as it is and a csv with just the total TCS score.", - "keywords": [ - "alignment", - "MSA", - "evaluation" - ], - "tools": [ - { - "tcoffee": { - "description": "A collection of tools for Multiple Alignments of DNA, RNA, Protein Sequence", - "homepage": "http://www.tcoffee.org/Projects/tcoffee/", - "documentation": "https://tcoffee.readthedocs.io/en/latest/tcoffee_main_documentation.html", - "tool_dev_url": "https://github.com/cbcrg/tcoffee", - "doi": "10.1006/jmbi.2000.4042", - "licence": [ - "GPL v3" - ], - "identifier": "" - } - }, - { - "pigz": { - "description": "Parallel implementation of the gzip algorithm.", - "homepage": "https://zlib.net/pigz/", - "documentation": "https://zlib.net/pigz/pigz.pdf", - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', ... ]\n" - } - }, - { - "msa": { - "type": "file", - "description": "fasta file containing the alignment to be evaluated. May be gzipped or uncompressed.", - "pattern": "*.{aln,fa,fasta,fas}{.gz,}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - }, - { - "edam": "http://edamontology.org/format_2554" - }, - { - "edam": "http://edamontology.org/format_1921" - }, - { - "edam": "http://edamontology.org/format_1984" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "lib": { - "type": "file", - "description": "lib file containing the alignment library of the given msa.", - "pattern": "*{.tc_lib,*_lib}", - "ontologies": [] - } - } - ] - ], - "output": { - "tcs": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.tcs": { - "type": "file", - "description": "The msa represented in tcs format, prepended with TCS scores", - "pattern": "*.tcs", - "ontologies": [] - } - } - ] - ], - "scores": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.scores": { - "type": "file", - "description": "a file containing the score of the alignment in csv format", - "pattern": "*.scores", - "ontologies": [] - } - } - ] - ], - "versions_tcoffee": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "tcoffee": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "t_coffee -version | awk '{gsub(\"Version_\", \"\"); print \\$3}'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_pigz": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "pigz": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pigz --version 2>&1 | sed \"s/^.*pigz[[:space:]]*//\"": { - 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} - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "TD2.LongOrfs": { - "type": "string", - "description": "The tool name" - } - }, - { - "1.0.6": { - "type": "string", - "description": "The tool version" - } - } - ] - ] - }, - "authors": [ - "@khersameesh24" - ], - "maintainers": [ - "@khersameesh24" - ] - } - }, - { - "name": "td2_predict", - "path": "modules/nf-core/td2/predict/meta.yml", - "type": "module", - "meta": { - "name": "td2_predict", - "description": "TD2 identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly", - "keywords": [ - "predict", - "orfs", - "coding regions", - "td2.predict" - ], - "tools": [ - { - "td2": { - "description": "TD2 identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly", - "homepage": "https://github.com/Markusjsommer/TD2", - "documentation": "https://github.com/Markusjsommer/TD2", - "tool_dev_url": "https://github.com/Markusjsommer/TD2", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Transcripts fasta file", - "pattern": "*.fasta", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - }, - { - "orfs_dir": { - "type": "file", - "description": "Directory containing the ORF prediction files generated by the `td2_longorfs` module", - "pattern": "orfs_dir/", - "ontologies": [] - } - } - ] - ], - "output": { - "predictions": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}/*.TD2.{bed,cds,gff3,pep}": { - "type": "file", - "description": "Files containing the TD2 ORF predictions for the input transcript sequences", - 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}, - { - "name": "telescope_assign", - "path": "modules/nf-core/telescope/assign/meta.yml", - "type": "module", - "meta": { - "name": "telescope_assign", - "description": "The telescope assign program finds overlapping reads between an alignment (SAM/BAM) and an annotation (GTF) then reassigns reads using a statistical model.", - "keywords": [ - "EM", - "single-locus", - "transcriptomics" - ], - "tools": [ - { - "telescope": { - "description": "Single locus resolution of Transposable ELEment expression", - "homepage": "https://github.com/mlbendall/telescope", - "documentation": "https://github.com/mlbendall/telescope", - "tool_dev_url": "https://github.com/mlbendall/telescope", - "doi": "10.1371/journal.pcbi.1006453", - "licence": [ - "MIT" - ], - "identifier": "biotools:Telescope-expression" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM/CRAM/SAM file, File must be collated so that all alignments for a read pair appear sequentially in the file", - 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[ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*{updated,other}.sam": { - "type": "file", - "description": "The updated SAM file contains those fragments that has at least 1 initial alignment to a transposable element.", - "pattern": "*{updated,other}.bam", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3462" - } - ] - } - } - ] - ], - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "Statistical report associated with the run", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.log": { - "type": "file", - "description": "Log file for telescope run output.", - "pattern": "*.log" - } - } - ] - ], - "versions_telescope": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "telescope": { - "type": "string", - "description": "The tool name" - } - }, - { - "telescope --version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "telescope": { - "type": "string", - "description": "The tool name" - } - }, - { - "telescope --version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@hanalysis" - ], - "maintainers": [ - "@hanalysis" - ] - } - }, - { - "name": "telogator2", - "path": "modules/nf-core/telogator2/meta.yml", - "type": "module", - "meta": { - "name": "telogator2", - "description": "Allele-specific telomere length estimation and TVR characterization from long reads", - "keywords": [ - "bam", - "cram", - "genomics", - "telomere", - "long-read", - "pacbio", - "nanopore" - ], - "tools": [ - { - "telogator2": { - "description": "A method for measuring allele-specific TL and characterizing telomere variant repeat (TVR) sequences from long reads", - "homepage": "https://github.com/zstephens/telogator2", - "documentation": "https://github.com/zstephens/telogator2", - "tool_dev_url": "https://github.com/zstephens/telogator2", - "doi": "10.1186/s12859-024-05807-5", - "licence": [ - "MIT" - ], - "args_id": "$args", - "identifier": "biotools:telogator2" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "BAM or CRAM file of long reads (PacBio or ONT)", - "pattern": "*.{bam,cram}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - }, - { - "reads_index": { - "type": "file", - "description": "Index file for the input BAM/CRAM", - "pattern": "*.{bai,crai}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Optional reference genome FASTA file", - "pattern": "*.{fa,fasta,fa.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - }, - { - "fai": { - "type": "file", - "description": "Optional FASTA index file", - "pattern": "*.fai", - "ontologies": [] - } - } - ] - ], - "output": { - "tlens": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "${prefix}/tlens_by_allele.tsv": { - "type": "file", - "description": "TSV file with telomere length estimates per allele", - "pattern": "*/tlens_by_allele.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "plots": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "${prefix}/*.png": { - "type": "file", - "description": "PNG plots including allele visualizations and violin plots", - "pattern": "*/*.png", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3603" - } - ] - } - } - ] - ], - "cmd": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "${prefix}/qc/cmd.txt": { - "type": "file", - "description": "Text file recording the telogator2 command that was run", - "pattern": "*/qc/cmd.txt", - "ontologies": [] - } - } - ] - ], - "stats": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "${prefix}/qc/stats.txt": { - "type": "file", - "description": "Text file with QC statistics including read counts and telomere read filtering", - "pattern": "*/qc/stats.txt", - "ontologies": [] - } - } - ] - ], - "qc_readlens": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "${prefix}/qc/qc_readlens.png": { - "type": "file", - "description": "PNG plot of read length distribution", - "pattern": "*/qc/qc_readlens.png", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3603" - } - ] - } - } - ] - ], - "readlens": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "${prefix}/qc/readlens.npz": { - "type": "file", - "description": "Numpy compressed array of read length data", - "pattern": "*/qc/readlens.npz", - "ontologies": [] - } - } - ] - ], - "rng": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "${prefix}/qc/rng.txt": { - "type": "file", - "description": "Text file recording the random seed used", - "pattern": "*/qc/rng.txt", - "ontologies": [] - } - } - ] - ], - "versions_telogator2": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "telogator2": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "telogator2 --version | sed 's/telogator2 //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "telogator2": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "telogator2 --version | sed 's/telogator2 //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@pinin4fjords" - ], - "maintainers": [ - "@pinin4fjords" - ] - } - }, - { - "name": "telomerehunter", - "path": "modules/nf-core/telomerehunter/meta.yml", - "type": "module", - "meta": { - "name": "telomerehunter", - "description": "In silico estimation of telomere content and composition from cancer genomes", - "keywords": [ - "bam", - "genomics", - "telomere", - "telomerehunter", - "cancer" - ], - "tools": [ - { - "telomerehunter": { - "description": "In silico estimation of telomere content and composition from cancer genomes", - "homepage": "https://github.com/linasieverling/TelomereHunter", - "documentation": "https://github.com/linasieverling/TelomereHunter", - "tool_dev_url": "https://github.com/linasieverling/TelomereHunter", - "doi": "10.1186/s12859-019-2851-0", - "licence": [ - "GPL v3" - ], - "args_id": "$args", - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "tumor_bam": { - "type": "file", - "description": "Indexed BAM/CRAM file of the tumor sample. CRAM files are automatically converted to BAM (telomerehunter uses pysam in BAM-only mode).", - "pattern": "*.{bam,cram}", - "ontologies": [] - } - }, - { - "tumor_bai": { - "type": "file", - "description": "BAM/CRAM index file for the tumor sample", - "pattern": "*.{bai,crai}", - "ontologies": [] - } - }, - { - "control_bam": { - "type": "file", - "description": "Optional indexed BAM/CRAM file of the control sample", - "pattern": "*.{bam,cram}", - "ontologies": [] - } - }, - { - "control_bai": { - "type": "file", - "description": "Optional BAM/CRAM index file for the control sample", - "pattern": "*.{bai,crai}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference FASTA file (required when input is CRAM)", - "pattern": "*.{fa,fasta,fna}", - "ontologies": [] - } - }, - { - "fai": { - "type": "file", - "description": "Reference FASTA index", - "pattern": "*.fai", - "ontologies": [] - } - }, - { - "cytoband": { - "type": "file", - "description": "Optional cytoband file for the reference genome.\nWhen not provided ([]), telomerehunter uses its bundled hg19 cytoband.\nMust be supplied for hg38 data to avoid an IndexError caused by\nchromosomes that are longer in hg38 than hg19.\n", - "pattern": "*.txt", - "ontologies": [] - } - } - ] - ], - "output": { - "summary": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "${prefix}/${prefix}_summary.tsv": { - "type": "file", - "description": "Combined summary TSV with telomere content estimates", - "pattern": "*_summary.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "tumor": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "${prefix}/tumor_TelomerCnt_${prefix}/": { - "type": "directory", - "description": "Directory with tumor telomere analysis results", - "ontologies": [] - } - } - ] - ], - "control": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "${prefix}/control_TelomerCnt_${prefix}/": { - "type": "directory", - "description": "Directory with control telomere analysis results", - "ontologies": [] - } - } - ] - ], - "versions_telomerehunter": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "telomerehunter": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pip show telomerehunter | sed -n 's/^Version: //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_samtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools --version |& sed '1!d; s/^.*samtools //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "telomerehunter": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pip show telomerehunter | sed -n 's/^Version: //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools --version |& sed '1!d; s/^.*samtools //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@pinin4fjords" - ], - "maintainers": [ - "@pinin4fjords" - ] - } - }, - { - "name": "telseq", - "path": "modules/nf-core/telseq/meta.yml", - "type": "module", - "meta": { - "name": "telseq", - "description": "Telseq: a software for calculating telomere length", - "keywords": [ - "bam", - "cram", - "genomics", - "samtools", - "telomere", - "telseq" - ], - "tools": [ - { - "telseq": { - "description": "A software for calculating telomere length", - "homepage": "https://github.com/zd1/telseq", - "documentation": "https://github.com/zd1/telseq", - "tool_dev_url": "https://github.com/zd1/telseq", - "doi": "10.1093/nar/gku181", - "licence": [ - "GPL v3" - ], - "args_id": "$args", - "identifier": "" - } - }, - { - "samtools": { - "description": "Tools for dealing with SAM, BAM and CRAM files", - "homepage": "http://www.htslib.org/", - "documentation": "http://www.htslib.org/doc/samtools.html", - "tool_dev_url": "https://github.com/samtools/samtools", - "doi": "10.1093/bioinformatics/btp352", - "licence": [ - "MIT" - ], - "identifier": "biotools:samtools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } - }, - { - "bai": { - "type": "file", - "description": "bam index file", - "pattern": "*.{bai,crai}", - "ontologies": [] - } - }, - { - "bed": { - "type": "file", - "description": "Optional exome regions in BED format. These regions will be excluded", - "pattern": "*.bed", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome file", - "pattern": "*.{fa,fasta}", - "ontologies": [] - } - }, - { - "fai": { - "type": "file", - "description": "Fasta index file", - "pattern": "*.fai", - "ontologies": [] - } - } - ] - ], - "output": { - "output": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.telseq.tsv": { - "type": "file", - "description": "Telseq output", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_telseq": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "telseq": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "echo 0.0.2": { - "type": "eval", - "description": "The expression to obtain the version of telseq" - } - } - ] - ], - "versions_samtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools --version | sed -n '1s/samtools //p'": { - "type": "eval", - "description": "The expression to obtain the version of samtools" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "telseq": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "echo 0.0.2": { - "type": "eval", - "description": "The expression to obtain the version of telseq" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools --version | sed -n '1s/samtools //p'": { - "type": "eval", - "description": "The expression to obtain the version of samtools" - } - } - ] - ] - }, - "authors": [ - "@lindenb" - ], - "maintainers": [ - "@lindenb" - ] - } - }, - { - "name": "tesorter", - "path": "modules/nf-core/tesorter/meta.yml", - "type": "module", - "meta": { - "name": "tesorter", - "description": "An accurate and fast method to classify LTR-retrotransposons in plant genomes", - "keywords": [ - "genomics", - "classify", - "LTR", - "retrotransposons", - "plant" - ], - "tools": [ - { - "tesorter": { - "description": "Lineage-level classification of transposable elements using conserved protein domains.", - "homepage": "https://github.com/zhangrengang/TEsorter", - "documentation": "https://github.com/zhangrengang/TEsorter", - "tool_dev_url": "https://github.com/zhangrengang/TEsorter", - "doi": "10.1093/hr/uhac017", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:TEsorter" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input sequence", - "pattern": "*.{fa,fasta,fsa,faa}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "db_hmm": { - "type": "file", - "optional": true, - "description": "The database HMM file used", - "ontologies": [] - } - } - ] - ], - "output": { - "domtbl": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.domtbl": { - "type": "file", - "description": "HMMScan raw output", - "pattern": "*.{domtbl}", - "ontologies": [] - } - } - ] - ], - "dom_faa": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.dom.faa": { - "type": "file", - "description": "Protein sequences of domain, which can be used for phylogenetic analysis", - "pattern": "*.dom.{faa}", - "ontologies": [] - } - } - ] - ], - "dom_tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.dom.tsv": { - "type": "file", - "description": "Inner domains of TEs/LTR-RTs, which might be used to filter domains based on their scores and coverages", - "pattern": "*.dom.{tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "dom_gff3": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.dom.gff3": { - "type": "file", - "description": "Domain annotations in 'gff3' format", - "pattern": "*.dom.{gff3}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1975" - } - ] - } - } - ] - ], - "cls_tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.cls.tsv": { - "type": "file", - "description": "TEs/LTR-RTs classifications", - "pattern": "*.cls.{tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "cls_lib": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.cls.lib": { - "type": "file", - "description": "Fasta library for RepeatMasker", - "pattern": "*.cls.{lib}", - "ontologies": [] - } - } - ] - ], - "cls_pep": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.cls.pep": { - "type": "file", - "description": "The same sequences as '*.dom.faa', but id is changed with classifications", - "pattern": "*.cls.{pep}", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@GallVp" - ], - "maintainers": [ - "@GallVp" - ] - } - }, - { - "name": "tetranscripts", - "path": "modules/nf-core/tetranscripts/meta.yml", - "type": "module", - "meta": { - "name": "tetranscripts", - "description": "Runs TEtranscripts which summarises transposable element content of a bam file.", - "keywords": [ - "transposable", - "TE", - "transcriptomics" - ], - "tools": [ - { - "tetranscripts": { - "description": "A package for including transposable elements in differential enrichment analysis of sequencing datasets.", - "homepage": "https://github.com/mhammell-laboratory/TEtranscripts", - "documentation": "https://hammelllab.labsites.cshl.edu/software/#TEtranscripts", - "tool_dev_url": "https://github.com/mhammell-laboratory/TEtranscripts", - "doi": "10.1093/bioinformatics/btv422", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:tetranscripts" - } - } - ], - "input": [ - [ - { - "meta_t": { - "type": "map", - "description": "Groovy Map containing treatment sample information. e.g. `[\nid:'sample1' ]`\n" - } - }, - { - "bam_t": { - "type": "file", - "description": "A BAM file for the treatment condition", - "pattern": "*.{bam}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - } - ], - [ - { - "meta_c": { - "type": "map", - "description": "Groovy Map containing control sample information,\ne.g. `[ id:'control1']`\n" - } - }, - { - "bam_c": { - "type": "file", - "description": "A BAM file for the control condition", - "pattern": "*.{bam}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - } - ], - [ - { - "meta_ggtf": { - "type": "map", - "description": "Groovy map containing control sample information\ne.g. `[ id:'control1' ]`\n" - } - }, - { - "g_gtf": { - "type": "file", - "description": "A GTF file for alignment to the genome", - "pattern": "*.{gtf}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2306" - } - ] - } - } - ], - [ - { - "meta_tegtf": { - "type": "map", - "description": "Groovy map containing TE GTF information\ne.g. `[ id:'control1' ]`\n" - } - }, - { - "te_gtf": { - "type": "file", - "description": "A curated GTF file for alignment to transposable elements", - "pattern": "*.{gtf}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2306" - } - ] - } - } - ] - ], - "output": { - "countTable": [ - [ - { - "meta_t": { - "type": "map", - "description": "Groovy Map containing treatment sample information.\ne.g. `id:'sample1' ]`\n" - } - }, - { - "*.cntTable": { - "type": "file", - "description": "Counts table of transposable element families", - "pattern": "*.cntTable", - "ontologies": [] - } - } - ] - ], - "log2fc": [ - [ - { - "meta_t": { - "type": "map", - "description": "Groovy Map containing treatment sample information.\ne.g. `id:'sample1' ]`\n" - } - }, - { - "*.R": { - "type": "file", - "description": "Differential gene expression analysis file", - "pattern": "*.R", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3999" - } - ] - } - } - ] - ], - "analysis": [ - [ - { - "meta_t": { - "type": "map", - "description": "Groovy map containing treatment sample information.\ne.g. `id:'sample1' ]`\n" - } - }, - { - "*_analysis.txt": { - "type": "file", - "description": "DESeq2 analysis file", - "pattern": "*_analysis.txt", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2330" - } - ] - } - } - ] - ], - "sigdiff": [ - [ - { - "meta_t": { - "type": "map", - "description": "Groovy map containing treatment sample information.\ne.g. `id:'sample1' ]`\n" - } - }, - { - "*_gene_TE.txt": { - "type": "file", - "description": "DESeq2 analysis file", - "pattern": "*_gene_TE.txt", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2330" - } - ] - } - } - ] - ], - "versions_tetranscripts": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "tetranscripts": { - "type": "string", - "description": "The tool name" - } - }, - { - "tetranscripts version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "tetranscripts": { - "type": "string", - "description": "The tool name" - } - }, - { - "tetranscripts version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@hanalysis" - ], - "maintainers": [ - "@hanalysis" - ] - } - }, - { - "name": "thermorawfileparser", - "path": "modules/nf-core/thermorawfileparser/meta.yml", - "type": "module", - "meta": { - "name": "thermorawfileparser", - "description": "Parses a Thermo RAW file containing mass spectra to an open file format", - "keywords": [ - "raw", - "mzml", - "mgf", - "parquet", - "parser", - "proteomics" - ], - "tools": [ - { - "thermorawfileparser": { - "description": "Wrapper around the .net (C#) ThermoFisher ThermoRawFileReader library for running on Linux with mono", - "homepage": "https://github.com/compomics/ThermoRawFileParser/blob/master/README.md", - "documentation": "https://github.com/compomics/ThermoRawFileParser/blob/master/README.md", - "tool_dev_url": "https://github.com/compomics/ThermoRawFileParser", - "doi": "10.1021/acs.jproteome.9b00328", - "licence": [ - "Apache Software" - ], - "identifier": "biotools:ThermoRawFileParser" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "raw": { - "type": "file", - "description": "Thermo RAW file", - "pattern": "*.{raw,RAW}", - "ontologies": [] - } - } - ] - ], - "output": { - "spectra": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.{mzML,mzML.gz,mgf,mgf.gz,parquet,parquet.gz}": { - "type": "file", - "description": "Mass spectra in open format", - "pattern": "*.{mzML,mzML.gz,mgf,mgf.gz,parquet,parquet.gz}", - "ontologies": [] - } - } - ] - ], - "versions_thermorawfileparser": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "thermorawfileparser": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "ThermoRawFileParser.sh --version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "thermorawfileparser": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "ThermoRawFileParser.sh --version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@jonasscheid" - ], - "maintainers": [ - "@jonasscheid" - ] - }, - "pipelines": [ - { - "name": "mhcquant", - "version": "3.2.0" - }, - { - "name": "mspepid", - "version": "dev" - }, - { - "name": "ribomsqc", - "version": "1.0.0" - } - ] - }, - { - "name": "tiara_tiara", - "path": "modules/nf-core/tiara/tiara/meta.yml", - "type": "module", - "meta": { - "name": "tiara_tiara", - "description": "Domain-level classification of contigs to bacterial, archaeal, eukaryotic, or organelle", - "keywords": [ - "contigs", - "metagenomics", - "classify" - ], - "tools": [ - { - "tiara": { - "description": "Deep-learning-based approach for identification of eukaryotic sequences in the metagenomic data powered by PyTorch.", - "homepage": "https://ibe-uw.github.io/tiara/", - "documentation": "https://ibe-uw.github.io/tiara/\"", - "tool_dev_url": "https://github.com/ibe-uw/tiara", - "doi": "10.1093/bioinformatics/btab672", - "licence": [ - "MIT" - ], - "identifier": "biotools:tiara-metagenomics" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA file of assembled contigs.", - "pattern": "*.{fa,fa.gz,fasta,fasta.gz,fna,fna.gz}", - "ontologies": [] - } - } - ] - ], - "output": { - "classifications": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.{txt,txt.gz}": { - "type": "file", - "description": "TSV file containing per-contig classification probabilities and overall classifications. Gzipped if flag --gz is set.", - "pattern": "*.{txt,txt.gz}", - "ontologies": [] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "log_*.{txt,txt.gz}": { - "type": "file", - "description": "Log file containing tiara model parameters. Gzipped if flag --gz is set.", - "pattern": "log_*.{txt,txt.gz}", - "ontologies": [] - } - } - ] - ], - "fasta": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.{fasta,fasta.gz}": { - "type": "file", - "description": "(optional) - fasta files for each domain category specified in command flag `-tf`, containing classified contigs\n", - "pattern": "*.{fasta,fasta.gz}", - "ontologies": [] - } - } - ] - ], - "versions_tiara": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "tiara": { - "type": "string", - "description": "The tool name" - } - }, - { - "1.0.3": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "tiara": { - "type": "string", - "description": "The tool name" - } - }, - { - "1.0.3": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@prototaxites" - ], - "maintainers": [ - "@prototaxites" - ] - }, - "pipelines": [ - { - "name": "genomeqc", - "version": "dev" - }, - { - "name": "mag", - "version": "5.4.2" - } - ] - }, - { - "name": "tiddit_cov", - "path": "modules/nf-core/tiddit/cov/meta.yml", - "type": "module", - "meta": { - "name": "tiddit_cov", - "description": "Computes the coverage of different regions from the bam file.", - "keywords": [ - "coverage", - "bam", - "statistics", - "chromosomal rearrangements" - ], - "tools": [ - { - "tiddit": { - "description": "TIDDIT - structural variant calling.", - "homepage": "https://github.com/SciLifeLab/TIDDIT", - "documentation": "https://github.com/SciLifeLab/TIDDIT/blob/master/README.md", - "doi": "10.12688/f1000research.11168.1", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:tiddit" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM file", - "pattern": "*.{bam,cram}", - "ontologies": [] - } - }, - { - "index": { - "type": "file", - "description": "Index of BAM/CRAM file", - "pattern": "*.{bai,crai,csi}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3327" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome file. Only needed when passing in CRAM instead of BAM.\nIf not using CRAM, please pass an empty file instead.\n", - "pattern": "*.fasta", - "ontologies": [] - } - } - ] - ], - "output": { - "cov": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.bed": { - "type": "file", - "description": "The coverage of different regions in bed format. Optional.", - "pattern": "*.bed", - "ontologies": [] - } - } - ] - ], - "wig": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.wig": { - "type": "file", - "description": "The coverage of different regions in WIG format. Optional.", - "pattern": "*.wig", - "ontologies": [] - } - } - ] - ], - "versions_tiddit": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "tiddit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "tiddit | sed -n 's/^usage: tiddit-//; s/ .*//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "tiddit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "tiddit | sed -n 's/^usage: tiddit-//; s/ .*//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@projectoriented", - "@ramprasadn" - ], - "maintainers": [ - "@projectoriented", - "@ramprasadn" - ] - }, - "pipelines": [ - { - "name": "raredisease", - "version": "3.0.0" - } - ] - }, - { - "name": "tiddit_sv", - "path": "modules/nf-core/tiddit/sv/meta.yml", - "type": "module", - "meta": { - "name": "tiddit_sv", - "description": "Identify chromosomal rearrangements.", - "keywords": [ - "structural", - "variants", - "vcf" - ], - "tools": [ - { - "sv": { - "description": "Search for structural variants.", - "homepage": "https://github.com/SciLifeLab/TIDDIT", - "documentation": "https://github.com/SciLifeLab/TIDDIT/blob/master/README.md", - "doi": "10.12688/f1000research.11168.1", - "licence": [ - "GPL-3.0-or-later" - ], - "identifier": "biotools:tiddit" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM file", - "pattern": "*.{bam,cram}", - "ontologies": [] - } - }, - { - "input_index": { - "type": "file", - "description": "BAM/CRAM index file", - "pattern": "*.{bai,crai}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test_fasta']`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input FASTA file", - "pattern": "*.{fasta,fa}", - "ontologies": [] - } - }, - { - "fai": { - "type": "file", - "description": "Input FASTA index file", - "pattern": "*.{fai}", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information from bwa index\ne.g. `[ id:'test_bwa-index' ]`\n" - } - }, - { - "bwa_index": { - "type": "file", - "description": "BWA genome index files", - "pattern": "Directory containing BWA index *.{amb,ann,bwt,pac,sa}", - "ontologies": [] - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.vcf": { - "type": "file", - "description": "vcf", - "pattern": "*.{vcf}", - "ontologies": [] - } - } - ] - ], - "ploidy": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.ploidies.tab": { - "type": "file", - "description": "tab", - "pattern": "*.{ploidies.tab}", - "ontologies": [] - } - } - ] - ], - "versions_tiddit": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "tiddit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "tiddit | sed -n 's/^usage: tiddit-//; s/ .*//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "tiddit": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "tiddit | sed -n 's/^usage: tiddit-//; s/ .*//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@maxulysse" - ], - "maintainers": [ - "@maxulysse" - ] - }, - "pipelines": [ - { - "name": "raredisease", - "version": "3.0.0" - }, - { - "name": "sarek", - "version": "3.8.1" - } - ] - }, - { - "name": "tidk_explore", - "path": "modules/nf-core/tidk/explore/meta.yml", - "type": "module", - "meta": { - "name": "tidk_explore", - "description": "`tidk explore` attempts to find the simple telomeric repeat unit in the genome provided.\nIt will report this repeat in its canonical form (e.g. TTAGG -> AACCT).\n", - "keywords": [ - "genomics", - "telomere", - "search" - ], - "tools": [ - { - "tidk": { - "description": "tidk is a toolkit to identify and visualise telomeric repeats in genomes", - "homepage": "https://github.com/tolkit/telomeric-identifier", - "documentation": "https://github.com/tolkit/telomeric-identifier", - "tool_dev_url": "https://github.com/tolkit/telomeric-identifier", - "doi": "10.5281/zenodo.10091385", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "The input fasta file", - "pattern": "*.{fsa,fa,fasta}", - "ontologies": [] - } - } - ] - ], - "output": { - "explore_tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.tidk.explore.tsv": { - "type": "file", - "description": "Telomeres and their frequencies in TSV format", - "pattern": "*.tidk.explore.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "top_sequence": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.top.sequence.txt": { - "type": "file", - "description": "The most frequent telomere sequence if one or more\nsequences are identified by the toolkit\n", - "pattern": "*.top.sequence.txt", - "ontologies": [] - } - } - ] - ], - "versions_tidk": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "tidk": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "tidk --version | sed 's/tidk //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "tidk": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "tidk --version | sed 's/tidk //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@GallVp" - ], - "maintainers": [ - "@GallVp" - ] - }, - "pipelines": [ - { - "name": "genomeqc", - "version": "dev" - } - ] - }, - { - "name": "tidk_plot", - "path": "modules/nf-core/tidk/plot/meta.yml", - "type": "module", - "meta": { - "name": "tidk_plot", - "description": "Plots telomeric repeat frequency against sliding window location\nusing data produced by `tidk/search`\n", - "keywords": [ - "genomics", - "telomere", - "search", - "plot" - ], - "tools": [ - { - "tidk": { - "description": "tidk is a toolkit to identify and visualise telomeric repeats in genomes", - "homepage": "https://github.com/tolkit/telomeric-identifier", - "documentation": "https://github.com/tolkit/telomeric-identifier", - "tool_dev_url": "https://github.com/tolkit/telomeric-identifier", - "doi": "10.5281/zenodo.10091385", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "tsv": { - "type": "file", - "description": "Search results in TSV format from `tidk search`", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "output": { - "svg": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.svg": { - "type": "file", - "description": "Telomere search plot", - "pattern": "*.svg", - "ontologies": [] - } - } - ] - ], - "versions_tidk": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "tidk": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "tidk --version | sed 's/tidk //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "tidk": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "tidk --version | sed 's/tidk //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@GallVp" - ], - "maintainers": [ - "@GallVp" - ] - }, - "pipelines": [ - { - "name": "genomeqc", - "version": "dev" - } - ] - }, - { - "name": "tidk_search", - "path": "modules/nf-core/tidk/search/meta.yml", - "type": "module", - "meta": { - "name": "tidk_search", - "description": "Searches a genome for a telomere string such as TTAGGG", - "keywords": [ - "genomics", - "telomere", - "search" - ], - "tools": [ - { - "tidk": { - "description": "tidk is a toolkit to identify and visualise telomeric repeats in genomes", - "homepage": "https://github.com/tolkit/telomeric-identifier", - "documentation": "https://github.com/tolkit/telomeric-identifier", - "tool_dev_url": "https://github.com/tolkit/telomeric-identifier", - "doi": "10.5281/zenodo.10091385", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "The input fasta file", - "pattern": "*.{fsa,fa,fasta}", - "ontologies": [] - } - } - ], - { - "string": { - "type": "string", - "description": "Search string such as TTAGGG" - } - } - ], - "output": { - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "Search results in TSV format", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "bedgraph": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.bedgraph": { - "type": "file", - "description": "Search results in BEDGRAPH format", - "pattern": "*.bedgraph", - "ontologies": [] - } - } - ] - ], - "versions_tidk": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "tidk": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "tidk --version | sed 's/tidk //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "tidk": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "tidk --version | sed 's/tidk //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@GallVp" - ], - "maintainers": [ - "@GallVp" - ] - }, - "pipelines": [ - { - "name": "genomeqc", - "version": "dev" - } - ] - }, - { - "name": "tinc", - "path": "modules/nf-core/tinc/meta.yml", - "type": "module", - "meta": { - "name": "tinc", - "description": "TINC is a package to determine the contamination of tumour DNA in a matched normal sample. The approach uses evolutionary theory applied to read counts data from whole-genome sequencing assays.", - "keywords": [ - "genomics", - "tumour contamination", - "normal", - "purity" - ], - "tools": [ - { - "tinc": { - "description": "TINC is a package that implements algorithms to determine the contamination of a bulk sequencing sample in the context of cancer studies (matched tumour/ normal). The contamination estimated by TINC can be either due to normal cells sampled in the tumour biopsy or to tumour cells in the normal biopsy. The former case is traditionally called purity, or cellularity, and a number of tools exist to estimate it. The latter case is less common, and that is the main reason TINC has been developed. For this reason, the package takes name TINC, Tumour-in-Normal contamination. TINC is part of the evoverse, a package that gathers multiple R packages to implement Cancer Evolution analyses.", - "homepage": "https://caravagnalab.github.io/TINC/", - "documentation": "https://caravagnalab.github.io/TINC/", - "tool_dev_url": "https://github.com/caravagnalab/TINC/", - "doi": "10.1038/s41467-023-44158-2", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:r-tinc" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', tumour_sample:'tumour_sample1_name', normal_sample:'normal_sample_name' ]`\n" - } - }, - { - "cna_rds": { - "type": "file", - "description": "RDS file with copy number segments and purity", - "ontologies": [] - } - }, - { - "vcf_rds": { - "type": "file", - "description": "RDS file with vcf calls from tumour and normal sample", - "ontologies": [] - } - } - ] - ], - "output": { - "rds": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', tumour_sample:'tumour_sample1_name', normal_sample:'normal_sample_name' ]`\n" - } - }, - { - "*_fit.rds": { - "type": "file", - "description": "RDS file with the fit results", - "pattern": "*.{rds}", - "ontologies": [] - } - } - ] - ], - "plot_rds": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', tumour_sample:'tumour_sample1_name', normal_sample:'normal_sample_name' ]`\n" - } - }, - { - "*_plot.rds": { - "type": "file", - "description": "RDS file with the plot of the results", - "pattern": "*.{rds}", - "ontologies": [] - } - } - ] - ], - "plot_pdf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', tumour_sample:'tumour_sample1_name', normal_sample:'normal_sample_name' ]`\n" - } - }, - { - "*.pdf": { - "type": "file", - "description": "PDF file with the plot of the results", - "pattern": "*.{pdf}", - "ontologies": [] - } - } - ] - ], - "tinc_csv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', tumour_sample:'tumour_sample1_name', normal_sample:'normal_sample_name' ]`\n" - } - }, - { - "*_qc.csv": { - "type": "file", - "description": "CSV file with the output of TINC qc flag", - "pattern": "*.{csv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@valerianilucrezia" - ], - "maintainers": [ - "@valerianilucrezia" - ] - }, - "pipelines": [ - { - "name": "tumourevo", - "version": "dev" - } - ] - }, - { - "name": "tmb_pytmb", - "path": "modules/nf-core/tmb/pytmb/meta.yml", - "type": "module", - "meta": { - "name": "tmb_pytmb", - "description": "This module calculates Tumor Mutational Burden (TMB) scores from VCF files using the pyTMB tool.", - "keywords": [ - "tumor", - "mutation", - "burden", - "score" - ], - "tools": [ - { - "tmb": { - "description": "This tool was designed to calculate a Tumor Mutational Burden (TMB) score from a VCF file.", - "homepage": "https://github.com/bioinfo-pf-curie/TMB/blob/v1.5.0/README.md", - "documentation": "https://github.com/bioinfo-pf-curie/TMB/blob/v1.5.0/README.md", - "tool_dev_url": "https://github.com/bioinfo-pf-curie/TMB", - "doi": "10.1186/s12915-024-01839-8", - "licence": [ - "CeCILL FREE SOFTWARE LICENSE AGREEMENT" - ], - "identifier": "biotools:TMB" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "vcf": { - "type": "file", - "description": "Annotated VCF file.\n", - "pattern": "*.vcf", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - } - ] - } - }, - { - "bed": { - "type": "file", - "description": "BED file defining the target regions. Required if `eff_genome_size` is not provided.\n", - "pattern": "*.bed", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3003" - } - ] - } - }, - { - "eff_genome_size": { - "type": "string", - "description": "Effective genome size (in bases). Required if `bed` is not provided.\n" - } - }, - { - "var_config": { - "type": "file", - "description": "YAML file defining variant annotation parsing rules. See [example here](modules/nf-core/tmb/pytmb/tests/snpeff.yml).\n", - "pattern": "*.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - }, - { - "db_config": { - "type": "file", - "description": "YAML file defining the database configuration for variant annotations. 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} - }, - { - "*/*.data": { - "type": "file", - "description": "Report data emitted from toulligqc", - "pattern": "*.data", - "ontologies": [] - } - } - ] - ], - "report_html": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*/*.html": { - "type": "file", - "description": "Report data in html format", - "pattern": "*.html", - "ontologies": [] - } - } - ] - ], - "plots_html": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*/images/*.html": { - "type": "file", - "description": "Plots emitted in html format", - "pattern": "*.html", - "ontologies": [] - } - } - ] - ], - "plotly_js": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*/images/plotly.min.js": { - "type": "file", - 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"type": "module", - "meta": { - "name": "transdecoder_longorf", - "description": "TransDecoder identifies candidate coding regions within transcript sequences. it is used to build gff file.", - "keywords": [ - "eucaryotes", - "gff", - "transcript", - "coding" - ], - "tools": [ - { - "transdecoder": { - "description": "TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.", - "homepage": "https://github.com/TransDecoder", - "documentation": "https://github.com/TransDecoder/TransDecoder/wiki", - "tool_dev_url": "https://github.com/TransDecoder/TransDecoder", - "licence": [ - "Broad Institute" - ], - "identifier": "biotools:TransDecoder" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "fasta file", - "pattern": "*.{fasta}", - "ontologies": [] - } - } - ] - ], - "output": { - "pep": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${output_dir_name}/*.pep": { - "type": "file", - "description": "all ORFs meeting the minimum length criteria, regardless of coding potential. file", - "pattern": "*.{pep}", - "ontologies": [] - } - } - ] - ], - "gff3": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${output_dir_name}/*.gff3": { - "type": "file", - "description": "positions of all ORFs as found in the target transcripts. file", - "pattern": "*.{gff3}", - "ontologies": [] - } - } - ] - ], - "cds": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${output_dir_name}/*.cds": { - "type": "file", - "description": "the nucleotide coding sequence for all detected ORFs. file", - "pattern": "*{cds}", - "ontologies": [] - } - } - ] - ], - "dat": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${output_dir_name}/*.dat": { - "type": "file", - "description": "nucleotide frequencies", - "pattern": "*{dat}", - "ontologies": [] - } - } - ] - ], - "folder": [ - { - "${output_dir_name}": { - "type": "directory", - "description": "contains all the files from the run" - } - } - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@Danilo2771" - ], - "maintainers": [ - "@Danilo2771" - ] - } - }, - { - "name": "transdecoder_predict", - "path": "modules/nf-core/transdecoder/predict/meta.yml", - "type": "module", - "meta": { - "name": "transdecoder_predict", - "description": "TransDecoder identifies candidate coding regions within transcript sequences. It is used to build gff file. You can use this module after transdecoder_longorf", - "keywords": [ - "eukaryotes", - "gff", - "cds", - "transcroder" - ], - "tools": [ - { - "transdecoder": { - "description": "TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.", - "homepage": "https://github.com/TransDecoder", - "documentation": "https://github.com/TransDecoder/TransDecoder/wiki", - "tool_dev_url": "https://github.com/TransDecoder/TransDecoder", - "licence": [ - "Broad Institute" - ], - "identifier": "biotools:TransDecoder" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "fasta file", - "pattern": "*.{fasta}", - "ontologies": [] - } - } - ], - { - "fold": { - "type": "directory", - "description": "Output from the module transdecoder_longorf", - "pattern": "*" - } - } - ], - "output": { - "pep": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.transdecoder.pep": { - "type": "file", - "description": "All ORFs meeting the minimum length criteria, regardless of coding potential", - "pattern": "*.{pep}", - "ontologies": [] - } - } - ] - ], - "gff3": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.transdecoder.gff3": { - "type": "file", - "description": "Positions of all ORFs as found in the target transcripts", - "pattern": "*.{gff3}", - "ontologies": [] - } - } - ] - ], - "cds": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.transdecoder.cds": { - "type": "file", - "description": "the nucleotide coding sequence for all detected ORFs", - "pattern": "*{cds}", - "ontologies": [] - } - } - ] - ], - "bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.transdecoder.bed": { - "type": "file", - "description": "bed file", - "pattern": "*{bed}", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@Danilo2771" - ], - "maintainers": [ - "@Danilo2771" - ] - } - }, - { - "name": "trgt_genotype", - "path": "modules/nf-core/trgt/genotype/meta.yml", - "type": "module", - "meta": { - "name": "trgt_genotype", - "description": "Tandem repeat genotyping from PacBio HiFi data", - "keywords": [ - "repeat expansion", - "pacbio", - "genomics" - ], - "tools": [ - { - "trgt": { - "description": "Tandem repeat genotyping and visualization from PacBio HiFi data", - "homepage": "https://github.com/PacificBiosciences/trgt", - "documentation": "https://github.com/PacificBiosciences/trgt/blob/main/docs/tutorial.md", - "tool_dev_url": "https://github.com/PacificBiosciences/trgt", - "doi": "10.1038/s41587-023-02057-3", - "licence": [ - "Pacific Biosciences Software License (https://github.com/PacificBiosciences/trgt/blob/main/LICENSE.md)" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM file", - "pattern": "*.bam", - "ontologies": [] - } - }, - { - "bai": { - "type": "file", - "description": "Index of the BAM file", - "pattern": "*.bam", - "ontologies": [] - } - }, - { - "karyotype": { - "type": "string", - "description": "Karyotype of the sample. Either XX or XY. Defaults to XX if not given", - "enum": [ - "XX", - "XY" - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy map containing reference information\ne.g. `[ id: 'genome' ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA reference file", - "pattern": "*.{fasta,fa,fna}", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy map containing reference information\ne.g. `[ id: 'genome' ]`\n" - } - }, - { - "fai": { - "type": "file", - "description": "Index for FASTA file", - "pattern": "*.fai", - "ontologies": [] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy map containing repeat information\ne.g. `[ id: 'repeats' ]`\n" - } - }, - { - "repeats": { - "type": "file", - "description": "BED file with repeat coordinates", - "pattern": "*.bed", - "ontologies": [] - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.vcf.gz": { - "type": "file", - "description": "VCF file with repeat genotypes", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.spanning.bam": { - "type": "file", - "description": "BAM file with pieces of reads aligning to repeats", - "pattern": "*.spanning.bam", - "ontologies": [] - } - } - ] - ], - "versions_trgt": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "trgt": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "trgt --version | sed 's/.* //g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "trgt": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "trgt --version | sed 's/.* //g'": { - "type": "eval", - "description": "The expression to obtain the version" - } - } - ] - ] - }, - "authors": [ - "@Schmytzi", - "@fellen31" - ], - "maintainers": [ - "@Schmytzi" - ] - }, - "pipelines": [ - { - "name": "pacvar", - "version": "1.0.1" - } - ] - }, - { - "name": "trgt_merge", - "path": "modules/nf-core/trgt/merge/meta.yml", - "type": "module", - "meta": { - "name": "trgt_merge", - "description": "Merge TRGT VCFs from multiple samples", - "keywords": [ - "trgt", - "repeat expansion", - "pacbio", - "genomics" - ], - "tools": [ - { - "trgt": { - "description": "Tandem repeat genotyping and visualization from PacBio HiFi data", - "homepage": "https://github.com/PacificBiosciences/trgt", - "documentation": "https://github.com/PacificBiosciences/trgt/blob/main/docs/tutorial.md", - "tool_dev_url": "https://github.com/PacificBiosciences/trgt", - "doi": "10.1038/s41587-023-02057-3", - "licence": [ - "Pacific Biosciences Software License (https://github.com/PacificBiosciences/trgt/blob/main/LICENSE.md)" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "vcfs": { - "type": "file", - "description": "List containing VCF files from TRGT\nMust contain at least 2 elements unless `--force-single` is given\nSamples in each VCf must be pairwise disjoint\n", - "ontologies": [] - } - }, - { - "tbis": { - "type": "file", - "description": "List containing indexes of VCF files from TRGT\nMust contain at least 2 elements unless `--force-single` is given\n", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy map containing reference information\ne.g. `[ id: 'genome' ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA reference file (optional)\nRequired if VCFs were generated with TRGT pre 1.0\n", - "pattern": "*.{fasta,fa,fna}", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy map containing reference information\ne.g. `[ id: 'genome' ]`\n" - } - }, - { - "fai": { - "type": "file", - "description": "Index for FASTA file (optional)\nRequired if VCFs were generated with TRGT pre 1.0\n", - "pattern": "*.fai", - "ontologies": [] - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.{vcf,vcf.gz,bcf,bcf.gz}": { - "type": "file", - "description": "Merged output file", - "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}", - "ontologies": [] - } - } - ] - ], - "index": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.{tbi,csi}": { - "type": "file", - "description": "Index of merged output file", - "pattern": "*.{tbi,csi}", - "ontologies": [] - } - } - ] - ], - "versions_trgt": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "trgt": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "trgt --version | sed 's/.* //g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "trgt": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "trgt --version | sed 's/.* //g'": { - "type": "eval", - "description": "The expression to obtain the version" - } - } - ] - ] - }, - "authors": [ - "@Schmytzi" - ], - "maintainers": [ - "@Schmytzi" - ] - } - }, - { - "name": "trgt_plot", - "path": "modules/nf-core/trgt/plot/meta.yml", - "type": "module", - "meta": { - "name": "trgt_plot", - "description": "Visualize tandem repeats genotyped by TRGT", - "keywords": [ - "trgt", - "repeat expansion", - "plotting", - "pacbio", - "genomics" - ], - "tools": [ - { - "trgt": { - "description": "Tandem repeat genotyping and visualization from PacBio HiFi data", - "homepage": "https://github.com/PacificBiosciences/trgt", - "documentation": "https://github.com/PacificBiosciences/trgt/blob/main/docs/tutorial.md", - "tool_dev_url": "https://github.com/PacificBiosciences/trgt", - "doi": "10.1038/s41587-023-02057-3", - "licence": [ - "Pacific Biosciences Software License (https://github.com/PacificBiosciences/trgt/blob/main/LICENSE.md)" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted reads spanning tandem repeat from TRGT output", - "pattern": "*.bam", - "ontologies": [] - } - }, - { - "bai": { - "type": "file", - "description": "Index for reads", - "pattern": "*.bai", - "ontologies": [] - } - }, - { - "vcf": { - "type": "file", - "description": "Sorted tandem repeat genotypes called by TRGT", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - }, - { - "tbi": { - "type": "file", - "description": "Index for genotypes", - "pattern": "*.{tbi,csi}", - "ontologies": [] - } - }, - { - "repeat_id": { - "type": "string", - "description": "ID of tandem repeat to plot" - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy map containing reference information\ne.g. `[ id: 'genome' ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA reference file", - "pattern": "*.{fasta,fa,fna}", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy map containing reference information\ne.g. `[ id: 'genome' ]`\n" - } - }, - { - "fai": { - "type": "file", - "description": "Index for FASTA file", - "pattern": "*.fai", - "ontologies": [] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy map containing repeat information\ne.g. `[ id: 'repeats' ]`\n" - } - }, - { - "repeats": { - "type": "file", - "description": "BED file with repeat coordinates and structure", - "pattern": "*.bed", - "ontologies": [] - } - } - ] - ], - "output": { - "plot": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.{png,pdf,svg}": { - "type": "file", - "description": "Plot of region and reads spanning tandem repeat", - "pattern": "*.{png,pdf,svg}", - "ontologies": [] - } - } - ] - ], - "versions_trgt": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "trgt": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "trgt --version | sed 's/.* //g'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "trgt": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "trgt --version | sed 's/.* //g'": { - "type": "eval", - "description": "The expression to obtain the version" - } - } - ] - ] - }, - "authors": [ - "@Schmytzi" - ], - "maintainers": [ - "@Schmytzi" - ] - }, - "pipelines": [ - { - "name": "pacvar", - "version": "1.0.1" - } - ] - }, - { - "name": "trimal", - "path": "modules/nf-core/trimal/meta.yml", - "type": "module", - "meta": { - "name": "trimal", - "description": "trimAl is a tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment.", - "keywords": [ - "alignment", - "trimming", - "phylogeny" - ], - "tools": [ - { - "trimal": { - "description": "A tool for automated alignment trimming in large-scale phylogenetic analyses.", - "homepage": "https://trimal.cgenomics.org/", - "documentation": "https://trimal.readthedocs.io/en/latest/", - "tool_dev_url": "https://github.com/inab/trimal/tree/trimAl", - "doi": "10.1093/bioinformatics/btp348", - "licence": [ - "GPL v3-or-later", - "GPL v3 or later (GPL v3+)" - ], - "identifier": "biotools:trimal" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } - }, - { - "aln": { - "type": "file", - "description": "Input file in several formats (e.g., clustal, fasta, nexus, phylip32, phylip40, pir).", - "pattern": "*", - "ontologies": [ - { - "edam": "http://edamontology.org/data_0863" - } - ] - } - } - ], - { - "out_format": { - "type": "string", - "description": "Output format (e.g., pir, mega, nexus, clustal, fasta, phylip). Default is set to \"trimal\".", - "pattern": "*" - } - } - ], - "output": { - "trimal": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } - }, - { - "${prefix}.${out_extension}": { - "type": "file", - "description": "Trimmed multiple sequence alignment file", - "pattern": "*.*", - "ontologies": [ - { - "edam": "http://edamontology.org/data_1916" - }, - { - "edam": "http://edamontology.org/format_1982" - }, - { - "edam": "http://edamontology.org/format_1997" - }, - { - "edam": "http://edamontology.org/format_1998" - }, - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ], - "summary": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } - }, - { - "${prefix}.html": { - "type": "file", - "description": "HTML summary file, needs -htmlout to be set in ext.args along with a trimming method", - "pattern": "*.html", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2331" - } - ] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@IceGreb" - ], - "maintainers": [ - "@IceGreb" - ] - } - }, - { - "name": "trimgalore", - "path": "modules/nf-core/trimgalore/meta.yml", - "type": "module", - "meta": { - "name": "trimgalore", - "description": "A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files,\nwith extra functionality for RRBS data\n", - "keywords": [ - "trimming", - "adapters", - "sequencing", - "fastq" - ], - "tools": [ - { - "trimgalore": { - "description": "A wrapper tool around Cutadapt and FastQC to consistently apply quality\nand adapter trimming to FastQ files, with some extra functionality for\nMspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.\n", - "homepage": "https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/", - "documentation": "https://github.com/FelixKrueger/TrimGalore/blob/master/Docs/Trim_Galore_User_Guide.md", - "licence": [ - "GPL-3.0-or-later" - ], - "identifier": "biotools:trim_galore" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "output": { - "reads": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*{3prime,5prime,trimmed,val}{,_1,_2}.fq.gz": { - "type": "file", - "description": "The trimmed/modified fastq reads", - "pattern": "*{3prime,5prime,trimmed,val}{,_1,_2}.fq.gz", - 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} - ] - } - } - ] - }, - "authors": [ - "@sguizard", - "@lassefolkersen", - "@ksahlin" - ], - "maintainers": [ - "@sguizard", - "@lassefolkersen", - "@ksahlin" - ] - } - }, - { - "name": "ultraplex", - "path": "modules/nf-core/ultraplex/meta.yml", - "type": "module", - "meta": { - "name": "ultraplex", - "description": "Ultraplex is an all-in-one software package for processing and demultiplexing fastq files.", - "keywords": [ - "demultiplex", - "fastq", - "umi" - ], - "tools": [ - { - "ultraplex": { - "description": "fastq demultiplexer", - "homepage": "https://github.com/ulelab/ultraplex", - "documentation": "https://github.com/ulelab/ultraplex", - "tool_dev_url": "https://github.com/ulelab/ultraplex", - "doi": "10.5281/zenodo.465128", - "licence": [ - "MIT" - ], - "identifier": "biotools:ultraplex" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - 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"genomics" - ], - "tools": [ - { - "umicollapse": { - "description": "UMICollapse contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs).", - "homepage": "https://github.com/Daniel-Liu-c0deb0t/UMICollapse", - "documentation": "https://github.com/Daniel-Liu-c0deb0t/UMICollapse", - "tool_dev_url": "https://github.com/siddharthab/UMICollapse", - "doi": "10.7717/peerj.8275", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\n e.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "Input bam file", - "pattern": "*.bam", - "ontologies": [] - } - }, - { - "bai": { - "type": "file", - "description": "BAM index files corresponding to the input BAM file. 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"log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\n e.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_UMICollapse.log": { - "type": "file", - "description": "A log file with the deduplication statistics.", - "pattern": "*_{UMICollapse.log}", - "ontologies": [] - } - } - ] - ], - "versions_umicollapse": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "umicollapse": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "1.1.0-0": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "umicollapse": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "1.1.0-0": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@CharlotteAnne", - "@chris-cheshire" - ], - "maintainers": [ - "@CharlotteAnne", - "@chris-cheshire", - "@apeltzer", - "@siddharthab", - "@MatthiasZepper" - ] - }, - "pipelines": [ - { - "name": "lncpipe", - "version": "dev" - }, - { - "name": "riboseq", - "version": "1.2.0" - }, - { - "name": "rnaseq", - "version": "3.26.0" - }, - { - "name": "smrnaseq", - "version": "2.4.1" - } - ] - }, - { - "name": "umitools_dedup", - "path": "modules/nf-core/umitools/dedup/meta.yml", - "type": "module", - "meta": { - "name": "umitools_dedup", - "description": "Deduplicate reads based on the mapping co-ordinate and the UMI attached to the read.", - "keywords": [ - "umitools", - "deduplication", - "dedup" - ], - "tools": [ - { - "umi_tools": { - "description": "UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes\n", - "documentation": "https://umi-tools.readthedocs.io/en/latest/", - "license": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file containing reads to be deduplicated via UMIs.\n", - "pattern": "*.{bam}", - "ontologies": [] - } - }, - { - "bai": { - "type": "file", - "description": "BAM index files corresponding to the input BAM file.\n", - "pattern": "*.{bai}", - "ontologies": [] - } - } - ], - { - "get_output_stats": { - "type": "boolean", - "description": "Whether or not to generate output stats.\n" - } - } - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.bam": { - "type": "file", - "description": "BAM file with deduplicated UMIs.", - "pattern": "*.{bam}", - "ontologies": [] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.log": { - "type": "file", - "description": "File with logging information", - "pattern": "*.{log}", - "ontologies": [] - } - } - ] - ], - "tsv_edit_distance": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*edit_distance.tsv": { - "type": "file", - "description": "Reports the (binned) average edit distance between the UMIs at each position.", - "pattern": "*edit_distance.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "tsv_per_umi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*per_umi.tsv": { - "type": "file", - "description": "UMI-level summary statistics.", - "pattern": "*per_umi.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "tsv_umi_per_position": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*per_position.tsv": { - "type": "file", - "description": "Tabulates the counts for unique combinations of UMI and position.", - "pattern": "*per_position.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_umitools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "umitools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "umi_tools --version | sed 's/UMI-tools version: //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "umitools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "umi_tools --version | sed 's/UMI-tools version: //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@drpatelh", - "@grst", - "@klkeys" - ], - "maintainers": [ - "@drpatelh", - "@grst", - "@klkeys" - ] - }, - "pipelines": [ - { - "name": "alleleexpression", - "version": "dev" - }, - { - "name": "lncpipe", - "version": "dev" - }, - { - "name": "nascent", - "version": "2.3.0" - }, - { - "name": "radseq", - "version": "dev" - }, - { - "name": "riboseq", - "version": "1.2.0" - }, - { - "name": "rnaseq", - "version": "3.26.0" - }, - { - "name": "scnanoseq", - "version": "1.2.2" - }, - { - "name": "viralmetagenome", - "version": "1.1.1" - } - ] - }, - { - "name": "umitools_extract", - "path": "modules/nf-core/umitools/extract/meta.yml", - "type": "module", - "meta": { - "name": "umitools_extract", - "description": "Extracts UMI barcode from a read and add it to the read name, leaving any sample barcode in place", - "keywords": [ - "UMI", - "barcode", - "extract", - "umitools" - ], - "tools": [ - { - "umi_tools": { - "description": "UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes\n", - "documentation": "https://umi-tools.readthedocs.io/en/latest/", - "license": "MIT", - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "list", - "description": "List of input FASTQ files whose UMIs will be extracted.\n" - } - } - ] - ], - "output": { - "reads": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.fastq.gz": { - "type": "file", - "description": "Extracted FASTQ files. | For single-end reads, pattern is \\${prefix}.umi_extract.fastq.gz. | For paired-end reads, pattern is \\${prefix}.umi_extract_{1,2}.fastq.gz.\n", - 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"pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@jfy133", - "@pinin4fjords" - ], - "maintainers": [ - "@jfy133", - "@pinin4fjords" - ] - }, - "pipelines": [ - { - "name": "mspepid", - "version": "dev" - }, - { - "name": "pacsomatic", - "version": "dev" - }, - { - "name": "scnanoseq", - "version": "1.2.2" - } - ] - }, - { - "name": "upd", - "path": "modules/nf-core/upd/meta.yml", - "type": "module", - "meta": { - "name": "upd", - "description": "Simple software to call UPD regions from germline exome/wgs trios.", - "keywords": [ - "upd", - "uniparental", - "disomy" - ], - "tools": [ - { - "upd": { - "description": "Simple software to call UPD regions from germline exome/wgs trios.", - "homepage": "https://github.com/bjhall/upd", - "documentation": "https://github.com/bjhall/upd", - "tool_dev_url": "https://github.com/bjhall/upd", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF file", - "pattern": "*.{vcf,vcf.gz}", - "ontologies": [] - } - } - ] - ], - "output": { - "bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bed": { - "type": "file", - "description": "BED file", - "pattern": "*.{bed}", - "ontologies": [] - } - } - ] - ], - "versions_upd": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "upd": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "upd --version 2>&1 | sed 's/upd, version //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "upd": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "upd --version 2>&1 | sed 's/upd, version //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@hrydbeck" - ], - "maintainers": [ - "@hrydbeck" - ] - }, - "pipelines": [ - { - "name": "raredisease", - "version": "3.0.0" - } - ] - }, - { - "name": "upp_align", - "path": "modules/nf-core/upp/align/meta.yml", - "type": "module", - "meta": { - "name": "upp_align", - "description": "Aligns protein structures using UPP", - "keywords": [ - "alignment", - "MSA", - "genomics", - "structure" - ], - "tools": [ - { - "upp": { - "description": "SATe-enabled phylogenetic placement", - "homepage": "https://github.com/smirarab/sepp/tree/master", - "documentation": "https://github.com/smirarab/sepp/blob/master/README.UPP.md", - "tool_dev_url": "https://github.com/smirarab/sepp/tree/master", - "doi": "10.1093/bioinformatics/btad007", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:sepp" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" - } - }, - { - "fasta_unaligned": { - "type": "file", - "description": "Unaligned sequence file. If no backbone tree nor alignment is given, the sequence file will be randomly split into a backbone set and query set", - "pattern": "*.{fa,fna,faa,fasta}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1919" - }, - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - }, - { - "fasta_aligned": { - "type": "file", - "description": "Aligned sequence file. (optional)", - "pattern": "*.{fa,fna,faa,fasta,aln}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1919" - }, - { - "edam": "http://edamontology.org/format_1929" - }, - { - "edam": "http://edamontology.org/format_1984" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing tree information\ne.g. `[ id:'test_tree']`\n" - } - }, - { - "tree": { - "type": "file", - "description": "Input guide tree, in Newick format.", - "pattern": "*.{dnd}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2006" - } - ] - } - } - ], - { - "compress": { - "type": "boolean", - "description": "Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression." - } - } - ], - "output": { - "alignment": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" - } - }, - { - "*.aln{.gz,}": { - "type": "file", - "description": "Alignment file, in FASTA format. May be gzipped or uncompressed, depending on if compress is set to true or false", - "pattern": "*.aln{.gz,}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2554" - }, - { - "edam": "http://edamontology.org/format_1921" - }, - { - "edam": "http://edamontology.org/format_1984" - } - ] - } - } - ] - ], - "versions_sepp": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "sepp": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "run_upp.py -v | grep \"run_upp\" | cut -f2 -d\" \"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "sepp": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "run_upp.py -v | grep \"run_upp\" | cut -f2 -d\" \"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@luisas" - ], - "maintainers": [ - "@luisas" - ] - }, - "pipelines": [ - { - "name": "multiplesequencealign", - "version": "1.1.1" - } - ] - }, - { - "name": "vamb_bin", - "path": "modules/nf-core/vamb/bin/meta.yml", - "type": "module", - "meta": { - "name": "vamb_bin", - "description": "Variational autoencoder for metagenomic binning", - "keywords": [ - "clustering", - "binning", - "metagenomics", - "denovo assembly", - "mag" - ], - "tools": [ - { - "vamb": { - "description": "Variational autoencoder for metagenomic binning.", - "homepage": "https://vamb.readthedocs.io/en/latest", - "documentation": "https://vamb.readthedocs.io/en/latest", - "tool_dev_url": "https://github.com/RasmussenLab/vamb", - "doi": "10.1038/s41587-020-00777-4", - "licence": [ - "MIT" - ], - "identifier": "biotools:vamb" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" - } - }, - { - "assembly": { - "type": "file", - "description": "FASTA file of contigs for binning", - "pattern": "*.{fa,fas,fasta,fna,fa.gz,fas.gz,fasta.gz,fna.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - }, - { - "abundance_tsv": { - "type": "file", - "description": "TSV describing abundance of contigs in the provided assembly with headers\ncontigname\\tsample1\\tsample2...\nctg00001\\t10.0\\t5.0\n\nNot compatible with bam input.\n", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - }, - { - "bams": { - "type": "file", - "description": "List of sorted bam files of reads mapped to the reference assembly. Not compatible with TSV input.\n", - "pattern": "*.bam", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - }, - { - "taxonomy": { - "type": "file", - "description": "TSV describing the taxonomic lineage of each contig, with headers\ncontigs\\tpredictions\nctg00001\\tBacteria;Pseudomonadati;Pseudomonadota;Gammaproteobacteria;Enterobacterales;Enterobacteriacea;Escherichia coli\n", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "output": { - "bins": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" - } - }, - { - "${prefix}/bins/*.fna.gz": { - "type": "file", - "description": "List of FASTA files of binned contigs", - "pattern": "*.fna.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ], - "clusters_metadata": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" - } - }, - { - "${prefix}/vae*_clusters_metadata.tsv": { - "type": "file", - "description": "TSV describing the metadata of the output bin clusters\n", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "clusters_split": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" - } - }, - { - "${prefix}/vae*_clusters_split.tsv": { - "type": "file", - "description": "TSV defining the output bin clusters if binsplitting enabled\n", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "clusters_unsplit": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" - } - }, - { - "${prefix}/vae*_clusters_unsplit.tsv": { - "type": "file", - "description": "TSV defining the output bin clusters without binsplitting\n", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "taxometer_results": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" - } - }, - { - "${prefix}/results_taxometer.tsv": { - "type": "file", - "description": "TSV describing the refined taxonomic lineage of each contig, with headers\ncontigs\\tpredictions\\tscores\n", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "latent_encoding": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" - } - }, - { - "${prefix}/latent.npz": { - "type": "file", - "description": "Numpy array of the latent embedding of the contigs\n", - "pattern": "*.npz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_4003" - } - ] - } - } - ] - ], - "abundance": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" - } - }, - { - "${prefix}/abundance.npz": { - "type": "file", - "description": "Numpy array of the abundance of contigs\n", - "pattern": "*.npz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_4003" - } - ] - } - } - ] - ], - "composition": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" - } - }, - { - "${prefix}/composition.npz": { - "type": "file", - "description": "Numpy array of the kmer composition of the contigs\n", - "pattern": "*.npz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_4003" - } - ] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information. e.g. `[ id:'sample1' ]`" - } - }, - { - "${prefix}/log.txt": { - "type": "file", - "description": "Vamb log file\n", - "pattern": "*.log", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3671" - } - ] - } - } - ] - ], - "versions_vamb": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "vamb": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "vamb --version | sed 's/Vamb //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "vamb": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "vamb --version | sed 's/Vamb //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@prototaxites" - ], - "maintainers": [ - "@prototaxites" - ] - } - }, - { - "name": "vardictjava", - "path": "modules/nf-core/vardictjava/meta.yml", - "type": "module", - "meta": { - "name": "vardictjava", - "description": "The Java port of the VarDict variant caller", - "keywords": [ - "variant calling", - "vcf", - "bam", - "snv", - "sv" - ], - "tools": [ - { - "vardictjava": { - "description": "Java port of the VarDict variant discovery program", - "homepage": "https://github.com/AstraZeneca-NGS/VarDictJava", - "documentation": "https://github.com/AstraZeneca-NGS/VarDictJava", - "tool_dev_url": "https://github.com/AstraZeneca-NGS/VarDictJava", - "doi": "10.1093/nar/gkw227 ", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bams": { - "type": "file", - "description": "One or two BAM files. Supply two BAM files to run Vardict in paired mode.", - "pattern": "*.bam", - "ontologies": [] - } - }, - { - "bais": { - "type": "file", - "description": "Index/indices of the BAM file(s)", - "pattern": "*.bai", - "ontologies": [] - } - }, - { - "bed": { - "type": "file", - "description": "BED with the regions of interest", - "pattern": "*.bed", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing fasta information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA of the reference genome", - "pattern": "*.{fa,fasta}", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing fasta information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta_fai": { - "type": "file", - "description": "The index of the FASTA of the reference genome", - "pattern": "*.fai", - "ontologies": [] - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.vcf.gz": { - "type": "file", - "description": "VCF file output", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "versions_vardictjava": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "vardict-java": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "realpath \\$( command -v vardict-java ) | sed 's/.*java-//;s/-.*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_var2vcfvalid": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "var2vcf_valid.pl": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "var2vcf_valid.pl -h | sed '2!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_htslib": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "htslib": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "tabix -h 2>&1 | sed -n '2s/Version: *//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "vardict-java": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "realpath \\$( command -v vardict-java ) | sed 's/.*java-//;s/-.*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "var2vcf_valid.pl": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "var2vcf_valid.pl -h | sed '2!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "htslib": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "tabix -h 2>&1 | sed -n '2s/Version: *//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@nvnieuwk" - ], - "maintainers": [ - "@nvnieuwk" - ] - } - }, - { - "name": "variancepartition_dream", - "path": "modules/nf-core/variancepartition/dream/meta.yml", - "type": "module", - "meta": { - "name": "variancepartition_dream", - "description": "Runs a differential expression analysis with dream() from variancePartition R package", - "keywords": [ - "rnaseq", - "dream", - "variancepartition" - ], - "tools": [ - { - "dream": { - "description": "Differential expression for repeated measures", - "homepage": "https://www.bioconductor.org/packages/release/bioc/html/variancePartition.html", - "documentation": "https://www.bioconductor.org/packages/release/bioc/manuals/variancePartition/man/variancePartition.pdf", - "tool_dev_url": "https://github.com/DiseaseNeuroGenomics/variancePartition", - "doi": "10.1093/bioinformatics/btaa687", - "licence": [ - "GPL >=2" - ], - "identifier": "biotools:dream_database" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing run and contrast information.\n" - } - }, - { - "contrast_variable": { - "type": "string", - "description": "The column in the sample sheet that should be used to define groups for\ncomparison\n" - } - }, - { - "reference": { - "type": "string", - "description": "The value within the contrast_variable column of the sample sheet that\nshould be used to derive the reference samples\n" - } - }, - { - "target": { - "type": "string", - "description": "The value within the contrast_variable column of the sample sheet that\nshould be used to derive the target samples\n" - } - }, - { - "formula": { - "type": "string", - "description": "(Optional) R formula string used for modeling, e.g. '~ treatment + (1 | sample_number)'." - } - }, - { - "comparison": { - "type": "string", - "description": "(Optional) Literal string passed to `limma::makeContrasts`, e.g. 'treatmenthND6 - treatmentmCherry'." - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy map containing study-wide metadata related to the sample sheet\nand matrix\n" - } - }, - { - "samplesheet": { - "type": "file", - "description": "Sample sheet file containing sample metadata.", - "ontologies": [] - } - }, - { - "counts": { - "type": "file", - "description": "TSV or CSV format expression matrix with genes as rows and samples as columns.\n", - "ontologies": [] - } - } - ] - ], - "output": { - "results": [ - [ - { - "meta": { - "type": "map", - "description": "groovy array with metadata information for the contrast generated\n" - } - }, - { - "*.dream.results.tsv": { - "type": "file", - "description": "TSV-format table of differential expression information as output by Dream\n", - "pattern": "*.dream.results.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "model": [ - [ - { - "meta": { - "type": "map", - "description": "groovy array with metadata information for the contrast generated\n" - } - }, - { - "*.dream.model.txt": { - "type": "file", - "description": "R model description text file.\n", - "pattern": "*.dream.model.txt", - "ontologies": [] - } - } - ] - ], - "normalised_counts": [ - [ - { - "meta": { - "type": "map", - "description": "groovy array with metadata information for the contrast generated\n" - } - }, - { - "*.normalised_counts.tsv": { - "type": "file", - "description": "normalised TSV format expression matrix with genes by row and samples by column", - "pattern": "*.normalised_counts.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "topics": { - "versions": [ - { - "versions.yml": { - "type": "string", - "description": "File containing software versions" - } - } - ] - }, - "authors": [ - "@alanmmobbs03", - "@nschcolnicov", - "@atrigila" - ], - "maintainers": [ - "@alanmmobbs03", - "@nschcolnicov", - "@atrigila" - ] - } - }, - { - "name": "variantbam", - "path": "modules/nf-core/variantbam/meta.yml", - "type": "module", - "meta": { - "name": "variantbam", - "description": "Filtering, downsampling and profiling alignments in BAM/CRAM formats", - "keywords": [ - "filter", - "bam", - "subsample", - "downsample", - "downsample bam", - "subsample bam" - ], - "tools": [ - { - "variantbam": { - "description": "Filtering and profiling of next-generational sequencing data using region-specific rules", - "homepage": "https://github.com/walaj/VariantBam", - "documentation": "https://github.com/walaj/VariantBam#table-of-contents", - "tool_dev_url": "https://github.com/walaj/VariantBam", - "doi": "10.1093/bioinformatics/btw111", - "licence": [ - "Apache-2.0" - ], - "identifier": "biotools:variantbam" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM file", - "pattern": "*.{bam,cram}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - }, - { - "edam": "http://edamontology.org/format_3462" - } - ] - } - } - ] - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "Filtered or downsampled BAM file", - "pattern": "*.{bam}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - } - ] - ], - "versions_variant": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "VariantBam": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "1.4.4a": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "VariantBam": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "1.4.4a": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@bjohnnyd" - ], - "maintainers": [ - "@bjohnnyd" - ] - } - }, - { - "name": "variantextractor", - "path": "modules/nf-core/variantextractor/meta.yml", - "type": "module", - "meta": { - "name": "variantextractor", - "description": "Deterministic and standard extractor of SNVs, indels and structural variants (SVs)\nfrom VCF files. Homogenizes multiallelic variants, MNPs and SVs (including imprecise\npaired breakends and single breakends) to facilitate downstream processing.\n", - "keywords": [ - "vcf", - "variant", - "structural variant", - "normalization", - "homogenization" - ], - "tools": [ - { - "variant-extractor": { - "description": "Deterministic and standard extractor of SNVs, indels and structural variants\nfrom VCF files built under the frame of EUCANCan.\n", - "homepage": "https://github.com/EUCANCan/variant-extractor", - "documentation": "https://eucancan.github.io/variant-extractor/", - "tool_dev_url": "https://github.com/EUCANCan/variant-extractor", - "doi": "10.1016/j.xgen.2024.100639", - "licence": [ - "MIT" - ], - "identifier": "biotools:variant_extractor" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information.\ne.g. [ id:'sample1' ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "Input VCF file containing variants to be extracted and homogenized.", - "pattern": "*.{vcf,vcf.gz}", - "ontologies": [] - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information.\ne.g. [ id:'sample1' ]\n" - } - }, - { - "*.vcf": { - "type": "file", - "description": "VCF file with variants extracted and homogenized (multiallelic split,\nMNPs decomposed, SV breakends deduplicated).\n", - "pattern": "*.vcf", - "ontologies": [] - } - } - ] - ], - "versions_variantextractor": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions.", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "topics": { - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "YAML file containing versions of tools used in the module", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@sbreuch" - ], - "maintainers": [ - "@sbreuch" - ] - }, - "pipelines": [ - { - "name": "variantbenchmarking", - "version": "1.5.0" - } - ] - }, - { - "name": "varlociraptor_callvariants", - "path": "modules/nf-core/varlociraptor/callvariants/meta.yml", - "type": "module", - "meta": { - "name": "varlociraptor_callvariants", - "description": "Call variants for a given scenario specified with the varlociraptor calling grammar, preprocessed by varlociraptor preprocessing", - "keywords": [ - "observations", - "variants", - "calling" - ], - "tools": [ - { - "varlociraptor": { - "description": "Flexible, uncertainty-aware variant calling with parameter free filtration via FDR control.", - "homepage": "https://varlociraptor.github.io/docs/estimating/", - "documentation": "https://varlociraptor.github.io/docs/calling/", - "tool_dev_url": "https://github.com/varlociraptor/varlociraptor", - "doi": "10.1186/s13059-020-01993-6", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:varlociraptor" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcfs": { - "type": "file", - "description": "Sorted VCF/BCF file containing sample observations, Can also be a list of files", - "pattern": "*.{vcf,bcf,vcf.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - }, - { - "edam": "http://edamontology.org/format_3020" - } - ] - } - }, - { - "scenario": { - "type": "file", - "description": "Yaml file containing scenario information (optional)", - "pattern": "*.{yml,yaml}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - }, - { - "scenario_aliases": { - "type": "list", - "description": "List of aliases for the scenario (optional)" - } - } - ] - ], - "output": { - "bcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bcf": { - "type": "file", - "description": "BCF file containing sample observations", - "pattern": "*.bcf", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3020" - } - ] - } - } - ] - ], - "versions_varlociraptor": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "varlociraptor": { - "type": "string", - "description": "The tool name" - } - }, - { - "varlociraptor --version | sed 's/^varlociraptor //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "varlociraptor": { - "type": "string", - "description": "The tool name" - } - }, - { - "varlociraptor --version | sed 's/^varlociraptor //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@FriederikeHanssen" - ], - "maintainers": [ - "@FriederikeHanssen", - "@famosab" - ] - }, - "pipelines": [ - { - "name": "sarek", - "version": "3.8.1" - } - ] - }, - { - "name": "varlociraptor_estimatealignmentproperties", - "path": "modules/nf-core/varlociraptor/estimatealignmentproperties/meta.yml", - "type": "module", - "meta": { - "name": "varlociraptor_estimatealignmentproperties", - "description": "In order to judge about candidate indel and structural variants, Varlociraptor needs to know about certain properties of the underlying sequencing experiment in combination with the used read aligner.", - "keywords": [ - "estimation", - "alignment", - "variants" - ], - "tools": [ - { - "varlociraptor": { - "description": "Flexible, uncertainty-aware variant calling with parameter free filtration via FDR control.", - "homepage": "https://varlociraptor.github.io/docs/estimating/", - "documentation": "https://varlociraptor.github.io/docs/estimating/", - "tool_dev_url": "https://github.com/varlociraptor/varlociraptor", - "doi": "10.1186/s13059-020-01993-6", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:varlociraptor" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - }, - { - "bai": { - "type": "file", - "description": "Index of sorted BAM/CRAM/SAM file", - "pattern": "*.{bai,crai,sai}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3327" - } - ] - } - }, - { - "fasta": { - "type": "file", - "description": "Reference fasta file", - "pattern": "*.{fasta}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - }, - { - "fai": { - "type": "file", - "description": "Index for reference fasta file (must be with samtools index)", - "pattern": "*.{fai}", - "ontologies": [] - } - } - ] - ], - "output": { - "alignment_properties_json": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.alignment-properties.json": { - "type": "file", - "description": "File containing alignment properties", - "pattern": "*.alignment-properties.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "versions_varlociraptor": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "varlociraptor": { - "type": "string", - "description": "The tool name" - } - }, - { - "varlociraptor --version | sed 's/^varlociraptor //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "varlociraptor": { - "type": "string", - "description": "The tool name" - } - }, - { - "varlociraptor --version | sed 's/^varlociraptor //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@FriederikeHanssen" - ], - "maintainers": [ - "@FriederikeHanssen", - "@famosab" - ] - }, - "pipelines": [ - { - "name": "sarek", - "version": "3.8.1" - } - ] - }, - { - "name": "varlociraptor_preprocess", - "path": "modules/nf-core/varlociraptor/preprocess/meta.yml", - "type": "module", - "meta": { - "name": "varlociraptor_preprocess", - "description": "Obtains per-sample observations for the actual calling process with varlociraptor calls", - "keywords": [ - "observations", - "variants", - "preprocessing" - ], - "tools": [ - { - "varlociraptor": { - "description": "Flexible, uncertainty-aware variant calling with parameter free\nfiltration via FDR control.\n", - "homepage": "https://varlociraptor.github.io/docs/estimating/", - "documentation": "https://varlociraptor.github.io/docs/calling/", - "tool_dev_url": "https://github.com/varlociraptor/varlociraptor", - "doi": "10.1186/s13059-020-01993-6", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:varlociraptor" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - }, - { - "bai": { - "type": "file", - "description": "Index of the BAM/CRAM/SAM file", - "pattern": "*.{bai,crai,sai}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3327" - } - ] - } - }, - { - "candidates": { - "type": "file", - "description": "Sorted BCF/VCF file", - "pattern": "*.{bcf,vcf,vcf.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - } - ] - } - }, - { - "alignment_json": { - "type": "file", - "description": "File containing alignment properties obtained with varlociraptor/estimatealignmentproperties", - "pattern": "*.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - }, - { - "fasta": { - "type": "file", - "description": "Reference fasta file", - "pattern": "*.{fasta}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - }, - { - "fai": { - "type": "file", - "description": "Index for reference fasta file (must be with samtools index)", - "pattern": "*.{fai}", - "ontologies": [] - } - } - ] - ], - "output": { - "bcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bcf": { - "type": "file", - "description": "BCF file containing sample observations", - "pattern": "*.bcf", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3020" - } - ] - } - } - ] - ], - "versions_varlociraptor": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "varlociraptor": { - "type": "string", - "description": "The tool name" - } - }, - { - "varlociraptor --version | sed 's/^varlociraptor //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "varlociraptor": { - "type": "string", - "description": "The tool name" - } - }, - { - "varlociraptor --version | sed 's/^varlociraptor //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@FriederikeHanssen" - ], - "maintainers": [ - "@FriederikeHanssen", - "@famosab" - ] - }, - "pipelines": [ - { - "name": "sarek", - "version": "3.8.1" - } - ] - }, - { - "name": "varscan_fpfilter", - "path": "modules/nf-core/varscan/fpfilter/meta.yml", - "type": "module", - "meta": { - "name": "varscan_fpfilter", - "description": "VarScan2 is a tool for variant detection in massively parallel sequencing data. It can detect SNPs, indels, and copy number variations in both somatic and germline samples. It is particularly useful for analyzing tumor/normal sample pairs. Subtool fpfilter is used to filter a set of SNPs/indels based on coverage, reads, p-value, etc.", - "keywords": [ - "variant calling", - "germline", - "somatic", - "vcf", - "variants", - "genomics" - ], - "tools": [ - { - "varscan": { - "description": "variant detection in massively parallel sequencing data", - "homepage": "https://github.com/dkoboldt/varscan", - "documentation": "https://dkoboldt.github.io/varscan/", - "tool_dev_url": "https://github.com/dkoboldt/varscan", - "doi": "10.1101/gr.129684.111", - "licence": [ - "The Non-Profit Open Software License version 3.0 (NPOSL-3.0)" - ], - "identifier": "biotools:varscan" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF file", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - }, - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - }, - { - "rc": { - "type": "file", - "description": "Read counts file from bam-readcount", - "pattern": "*.rc", - "ontologies": [] - } - } - ] - ], - "output": { - "pass_vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.pass.vcf.gz": { - "type": "file", - "description": "VCF file with PASS variants", - "pattern": "*.pass.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - }, - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "fail_vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.fail.vcf.gz": { - "type": "file", - "description": "VCF file with FAIL variants", - "pattern": "*.fail.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - }, - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@vmelichar" - ], - "maintainers": [ - "@vmelichar" - ] - } - }, - { - "name": "varscan_processsomatic", - "path": "modules/nf-core/varscan/processsomatic/meta.yml", - "type": "module", - "meta": { - "name": "varscan_processsomatic", - "description": "VarScan2 is a tool for variant detection in massively parallel sequencing data. It can detect SNPs, indels, and copy number variations in both somatic and germline samples. It is particularly useful for analyzing tumor/normal sample pairs. This subtool divides variants based on status (germline, somatic, loss of heterozygosity) and confidence level (high-confidence or not) and outputs them in separate VCF files.", - "keywords": [ - "variant calling", - "germline", - "somatic", - "vcf", - "variants", - "genomics" - ], - "tools": [ - { - "varscan": { - "description": "variant detection in massively parallel sequencing data", - "homepage": "https://github.com/dkoboldt/varscan", - "documentation": "https://dkoboldt.github.io/varscan/", - "tool_dev_url": "https://github.com/dkoboldt/varscan", - "doi": "10.1101/gr.129684.111", - "licence": [ - "The Non-Profit Open Software License version 3.0 (NPOSL-3.0)" - ], - "identifier": "biotools:varscan" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF file", - "pattern": "*.{snvs,indels}.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - }, - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "output": { - "germline_vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.Germline.vcf.gz": { - "type": "file", - "description": "VCF file with germline variants", - "pattern": "*.Germline.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - }, - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "germline_hc_vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.Germline.hc.vcf.gz": { - "type": "file", - "description": "VCF file with high-confidence germline variants", - "pattern": "*.Germline.hc.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - }, - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "somatic_vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.Somatic.vcf.gz": { - "type": "file", - "description": "VCF file with somatic variants", - "pattern": "*.Somatic.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - }, - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "somatic_hc_vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.Somatic.hc.vcf.gz": { - "type": "file", - "description": "VCF file with high-confidence somatic variants", - "pattern": "*.Somatic.hc.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - }, - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "loh_vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.LOH.vcf.gz": { - "type": "file", - "description": "VCF file with loss of heterozygosity variants", - "pattern": "*.LOH.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - }, - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "loh_hc_vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.LOH.hc.vcf.gz": { - "type": "file", - "description": "VCF file with high-confidence loss of heterozygosity variants", - "pattern": "*.LOH.hc.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - }, - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@vmelichar" - ], - "maintainers": [ - "@vmelichar" - ] - } - }, - { - "name": "varscan_somatic", - "path": "modules/nf-core/varscan/somatic/meta.yml", - "type": "module", - "meta": { - "name": "varscan_somatic", - "description": "VarScan2 is a tool for variant detection in massively parallel sequencing data. It can detect SNPs, indels, and copy number variations in both somatic and germline samples. It is particularly useful for analyzing tumor/normal sample pairs.", - "keywords": [ - "variant calling", - "germline", - "somatic", - "vcf", - "variants", - "genomics" - ], - "tools": [ - { - "varscan": { - "description": "variant detection in massively parallel sequencing data", - "homepage": "https://github.com/dkoboldt/varscan", - "documentation": "https://dkoboldt.github.io/varscan/", - "tool_dev_url": "https://github.com/dkoboldt/varscan", - "doi": "10.1101/gr.129684.111", - "licence": [ - "The Non-Profit Open Software License version 3.0 (NPOSL-3.0)" - ], - "identifier": "biotools:varscan" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "normal_mpileup": { - "type": "file", - "description": "mpileup file from normal sample", - "pattern": "*.mpileup", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3015" - } - ] - } - }, - { - "tumour_mpileup": { - "type": "file", - "description": "mpileup file from tumour sample", - "pattern": "*.mpileup", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3015" - } - ] - } - } - ] - ], - "output": { - "vcf_snvs": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.snvs.vcf.gz": { - "type": "file", - "description": "VCF file with SNVs", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - }, - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "vcf_indels": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.indels.vcf.gz": { - "type": "file", - "description": "VCF file with indels", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - }, - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@vmelichar" - ], - "maintainers": [ - "@vmelichar" - ] - } - }, - { - "name": "vcf2cytosure", - "path": "modules/nf-core/vcf2cytosure/meta.yml", - "type": "module", - "meta": { - "name": "vcf2cytosure", - "description": "Convert VCF with structural variations to CytoSure format", - "keywords": [ - "structural_variants", - "array_cgh", - "vcf", - "cytosure" - ], - "tools": [ - { - "vcf2cytosure": { - "description": "Convert VCF with structural variations to CytoSure format", - "homepage": "https://github.com/NBISweden/vcf2cytosure", - "documentation": "https://github.com/NBISweden/vcf2cytosure", - "tool_dev_url": "https://github.com/NBISweden/vcf2cytosure", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "sv_vcf": { - "type": "file", - "description": "VCF file with structural variants", - "pattern": "*.{vcf,vcf.gz}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "coverage_bed": { - "type": "file", - "description": "Bed file with coverage data", - "pattern": "*.bed", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "cns": { - "type": "file", - "description": "CN file from CNVkit, not compatible with coverage_bed file", - "ontologies": [] - } - } - ], - [ - { - "meta4": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "snv_vcf": { - "type": "file", - "description": "VCF file with SNVs to calculate probe coverage,\nnot compatible with coverage_bed\npattern: \"*.{vcf,vcf.gz}\"\n", - "ontologies": [] - } - } - ], - { - "blacklist_bed": { - "type": "file", - "description": "Bed file with regions to exclude", - "pattern": "*.bed", - "ontologies": [] - } - } - ], - "output": { - "cgh": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*.cgh": { - "type": "file", - "description": "SV:s in CytoSure format", - "pattern": "*.cgh", - "ontologies": [] - } - } - ] - ], - "versions_vcf2cytosure": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "vcf2cytosure": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "vcf2cytosure --version 2>&1 | sed -n 's/.*cytosure //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "vcf2cytosure": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "vcf2cytosure --version 2>&1 | sed -n 's/.*cytosure //p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@jemten" - ] - }, - "pipelines": [ - { - "name": "raredisease", - "version": "3.0.0" - } - ] - }, - { - "name": "vcf2db", - "path": "modules/nf-core/vcf2db/meta.yml", - "type": "module", - "meta": { - "name": "vcf2db", - "description": "A tool to create a Gemini-compatible DB file from an annotated VCF", - "keywords": [ - "vcf2db", - "vcf", - "gemini" - ], - "tools": [ - { - "vcf2db": { - "description": "Create a gemini-compatible database from a VCF", - "homepage": "https://github.com/quinlan-lab/vcf2db", - "documentation": "https://github.com/quinlan-lab/vcf2db", - "tool_dev_url": "https://github.com/quinlan-lab/vcf2db", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF file", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - }, - { - "ped": { - "type": "file", - "description": "PED file", - "pattern": "*.ped", - "ontologies": [] - } - } - ] - ], - "output": { - "db": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.db": { - "type": "file", - "description": "Gemini-compatible database file", - "pattern": "*.db", - "ontologies": [] - } - } - ] - ], - "versions_vcf2db": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "vcf2db": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "2020.02.24": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_python_snappy": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "python-snappy": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "0.5.4": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_snappy": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "snappy": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "1.1.8": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_cyvcf2": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cyvcf2": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python -c 'import cyvcf2; print(cyvcf2.__version__)'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_python": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "python": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python --version 2>&1 | awk '{print \\$2}'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "vcf2db": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "2020.02.24": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "python-snappy": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "0.5.4": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "snappy": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "1.1.8": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "cyvcf2": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python -c 'import cyvcf2; print(cyvcf2.__version__)'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "python": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "python --version 2>&1 | awk '{print \\$2}'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@nvnieuwk" - ], - "maintainers": [ - "@nvnieuwk" - ] - } - }, - { - "name": "vcf2maf", - "path": "modules/nf-core/vcf2maf/meta.yml", - "type": "module", - "meta": { - "name": "vcf2maf", - "description": "vcf2maf", - "keywords": [ - "vcf", - "maf", - "annotation" - ], - "tools": [ - { - "vcf2maf": { - "description": "\"Convert a VCF into a MAF where each variant is annotated to only one of all possible gene isoforms using vcf2maf. vcf2maf is designed to work with VEP, so it is recommended to have VEP and vcf2maf installed when running this module. Running VEP requires a VEP cache to be present. It is recommended to set the --species and --ncbi-build in ext.args (use the module config). If you wish to skip VEP, add `--inhibit-vep` to ext.args. It may also be necessary to set --tumor-id and --normal-id for correct parsing of the VCF.\"\n", - "homepage": "https://github.com/mskcc/vcf2maf", - "documentation": "https://github.com/mskcc/vcf2maf", - "tool_dev_url": "https://github.com/mskcc/vcf2maf", - "doi": "10.5281/zenodo.593251", - "licence": [ - "Apache-2.0" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "vcf to convert to MAF format. Must be uncompressed.\n", - "ontologies": [] - } - } - ], - { - "fasta": { - "type": "file", - "description": "Path to reference genome fasta file.\n", - "ontologies": [] - } - }, - { - "vep_cache": { - "type": "file", - "description": "Path to VEP cache dir. Required for correct running of VEP.\n", - "ontologies": [] - } - } - ], - "output": { - "maf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.maf": { - "type": "file", - "description": "MAF file produced from VCF", - "pattern": "*.maf", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@adamrtalbot" - ], - "maintainers": [ - "@adamrtalbot" - ] - }, - "pipelines": [ - { - "name": "tumourevo", - "version": "dev" - } - ] - }, - { - "name": "vcf2zarr_convert", - "path": "modules/nf-core/vcf2zarr/convert/meta.yml", - "type": "module", - "meta": { - "name": "vcf2zarr_convert", - "description": "Convert VCF data to the VCF Zarr specification reliably, in parallel or distributed over a cluster", - "deprecated": true, - "keywords": [ - "vcf", - "zarr", - "convert" - ], - "tools": [ - { - "vcf2zarr": { - "description": "Convert bioinformatics data to Zarr", - "homepage": "https://sgkit-dev.github.io/bio2zarr/vcf2zarr/overview.html", - "documentation": "https://sgkit-dev.github.io/bio2zarr/", - "tool_dev_url": "https://github.com/sgkit-dev/bio2zarr", - "doi": "10.1101/2024.06.11.598241", - "licence": [ - "Apache-2.0" - ], - "identifier": "biotools:bio2zarr" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "vcf": { - "type": "file", - "description": "Input VCF file", - "pattern": "*.{vcf,vcf.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - } - ] - } - } - ] - ], - "output": { - "vcz": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.vcz": { - "type": "directory", - "description": "Output VCF Zarr store", - "pattern": "*.{vcz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3915" - } - ] - } - } - ] - ], - "versions_vcf2zarr": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "vcf2zarr": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "vcf2zarr --version |& sed -n \"s/.* //p\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "vcf2zarr": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "vcf2zarr --version |& sed -n \"s/.* //p\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@camlloyd" - ], - "maintainers": [ - "@camlloyd" - ] - } - }, - { - "name": "vcf2zarr_explode", - "path": "modules/nf-core/vcf2zarr/explode/meta.yml", - "type": "module", - "meta": { - "name": "vcf2zarr_explode", - "description": "Convert VCF(s) to intermediate columnar format", - "deprecated": true, - "keywords": [ - "vcf", - "icf", - "convert" - ], - "tools": [ - { - "vcf2zarr": { - "description": "Convert bioinformatics data to Zarr", - "homepage": "https://sgkit-dev.github.io/bio2zarr/vcf2zarr/overview.html", - "documentation": "https://sgkit-dev.github.io/bio2zarr/", - "tool_dev_url": "https://github.com/sgkit-dev/bio2zarr", - "doi": "10.1101/2024.06.11.598241", - "licence": [ - "Apache-2.0" - ], - "identifier": "biotools:bio2zarr" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "vcf": { - "type": "file", - "description": "Input VCF file", - "pattern": "*.{vcf,vcf.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - } - ] - } - } - ] - ], - "output": { - "icf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.icf": { - "type": "directory", - "description": "Output intermediate columnar format (ICF)", - "pattern": "*.{icf}", - "ontologies": [] - } - } - ] - ], - "versions_vcf2zarr": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "vcf2zarr": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "vcf2zarr --version |& sed -n \"s/.* //p\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "vcf2zarr": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "vcf2zarr --version |& sed -n \"s/.* //p\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@camlloyd" - ], - "maintainers": [ - "@camlloyd" - ] - } - }, - { - "name": "vcfanno", - "path": "modules/nf-core/vcfanno/meta.yml", - "type": "module", - "meta": { - "name": "vcfanno", - "description": "quickly annotate your VCF with any number of INFO fields from any number of VCFs or BED files", - "keywords": [ - "vcf", - "bed", - "annotate", - "variant", - "lua", - "toml" - ], - "tools": [ - { - "vcfanno": { - "description": "annotate a VCF with other VCFs/BEDs/tabixed files", - "documentation": "https://github.com/brentp/vcfanno#vcfanno", - "tool_dev_url": "https://github.com/brentp/vcfanno", - "doi": "10.1186/s13059-016-0973-5", - "license": [ - "MIT" - ], - "identifier": "biotools:vcfanno" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "query VCF file", - "pattern": "*.{vcf, vcf.gz}", - "ontologies": [] - } - }, - { - "tbi": { - "type": "file", - "description": "tabix index file for the query VCF", - "pattern": "*.tbi", - "ontologies": [] - } - }, - { - "specific_resources": { - "type": "map", - "description": "A list of sample specific reference files defined in toml config, must also include indices if bgzipped." - } - } - ], - { - "toml": { - "type": "file", - "description": "configuration file with reference file basenames", - "pattern": "*.toml", - "ontologies": [] - } - }, - { - "lua": { - "type": "file", - "description": "Lua file for custom annotations", - "pattern": "*.lua", - "ontologies": [] - } - }, - { - "resources": { - "type": "map", - "description": "List of reference files defined in toml config, must also include indices if bgzipped." - } - } - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", - "pattern": "*.vcf.gz" - } - }, - { - "*.vcf.gz": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", - "pattern": "*.vcf.gz" - } - } - ] - ], - "tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", - "pattern": "*.vcf.gz" - } - }, - { - "*.vcf.gz.tbi": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", - "pattern": "*.vcf.gz.tbi" - } - } - ] - ], - "versions_vcfanno": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "vcfanno": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "vcfanno 2>&1 | sed -n 's/.*version \\([0-9.]\\+\\).*/\\1/p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "vcfanno": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "vcfanno 2>&1 | sed -n 's/.*version \\([0-9.]\\+\\).*/\\1/p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@projectoriented", - "@matthdsm", - "@nvnieuwk" - ], - "maintainers": [ - "@projectoriented", - "@matthdsm", - "@nvnieuwk" - ] - }, - "pipelines": [ - { - "name": "raredisease", - "version": "3.0.0" - } - ] - }, - { - "name": "vcfexpress", - "path": "modules/nf-core/vcfexpress/meta.yml", - "type": "module", - "meta": { - "name": "vcfexpress", - "description": "Filter a VCF/BCF and optionally print by template expression. If no template is given the output will be VCF/BCF", - "keywords": [ - "vcf", - "bcf", - "filter", - "lua", - "expressions", - "genomics" - ], - "tools": [ - { - "vcfexpress": { - "description": "expressions on VCFs", - "homepage": "https://github.com/brentp/vcfexpress", - "documentation": "https://github.com/brentp/vcfexpress", - "tool_dev_url": "https://github.com/brentp/vcfexpress", - "doi": "10.5281/zenodo.14898003", - "licence": [ - "MIT" - ], - "identifier": "biotools:vcfexpress" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF file", - "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}" - } - } - ], - { - "prelude": { - "type": "file", - "description": "File(s) containing lua(u) code to run once before any variants are processed. `header` is available here to access or modify the header", - "pattern": "*.lua" - } - } - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.{vcf,vcf.gz,bcf,bcf.gz}": { - "type": "file", - "description": "VCF file", - "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}" - } - } - ] - ], - "versions_vcfexpress": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "vcfexpress": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "vcfexpress --version | sed 's/vcfexpress //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "vcfexpress": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "vcfexpress --version | sed 's/vcfexpress //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@sofiademmou" - ], - "maintainers": [ - "@sofiademmou" - ] - } - }, - { - "name": "vcflib_vcfbreakmulti", - "path": "modules/nf-core/vcflib/vcfbreakmulti/meta.yml", - "type": "module", - "meta": { - "name": "vcflib_vcfbreakmulti", - "description": "If multiple alleles are specified in a single record, break the record into several lines preserving allele-specific INFO fields", - "keywords": [ - "vcflib", - "vcfbreakmulti", - "allele-specific" - ], - "tools": [ - { - "vcflib": { - "description": "Command-line tools for manipulating VCF files", - "homepage": "https://github.com/vcflib/vcflib", - "documentation": "https://github.com/vcflib/vcflib#USAGE", - "doi": "10.1101/2021.05.21.445151", - "licence": [ - "MIT" - ], - "identifier": "biotools:vcflib" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "Compressed VCF file", - "pattern": "*.{.vcf.gz,vcf}", - "ontologies": [] - } - }, - { - "tbi": { - "type": "file", - "description": "Index of VCF file", - "pattern": "*.vcf.gz.tbi", - "ontologies": [] - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.vcf.gz": { - "type": "file", - "description": "Compressed VCF file", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "versions_vcflib": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "vcflib": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "1.0.14": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "vcflib": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "1.0.14": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@lucpen" - ], - "maintainers": [ - "@lucpen" - ] - } - }, - { - "name": "vcflib_vcffilter", - "path": "modules/nf-core/vcflib/vcffilter/meta.yml", - "type": "module", - "meta": { - "name": "vcflib_vcffilter", - "description": "Command line tools for parsing and manipulating VCF files.", - "keywords": [ - "filter", - "variant", - "vcf", - "quality" - ], - "tools": [ - { - "vcflib": { - "description": "Command line tools for parsing and manipulating VCF files.", - "homepage": "https://github.com/vcflib/vcflib", - "documentation": "https://github.com/vcflib/vcflib", - "tool_dev_url": "https://github.com/vcflib/vcflib", - "doi": "10.1371/journal.pcbi.1009123", - "licence": [ - "MIT" - ], - "identifier": "biotools:vcflib" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test_sample_1' ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF file", - "pattern": "*.{vcf,vcf.gz}", - "ontologies": [] - } - }, - { - "tbi": { - "type": "file", - "description": "Index file", - "pattern": "*.{tbi}", - "ontologies": [] - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.vcf.gz": { - "type": "file", - "description": "Filtered VCF file", - "pattern": "*.{vcf.gz}", - "ontologies": [] - } - } - ] - ], - "versions_vcflib": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "vcflib": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "1.0.14": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "vcflib": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "1.0.14": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@zachary-foster" - ], - "maintainers": [ - "@zachary-foster" - ] - }, - "pipelines": [ - { - "name": "pathogensurveillance", - "version": "1.1.0" - }, - { - "name": "sarek", - "version": "3.8.1" - } - ] - }, - { - "name": "vcflib_vcffixup", - "path": "modules/nf-core/vcflib/vcffixup/meta.yml", - "type": "module", - "meta": { - "name": "vcflib_vcffixup", - "description": "Generates a VCF stream where AC and NS have been generated for each record using sample genotypes.", - "keywords": [ - "vcf", - "vcflib", - "vcflib/vcffixup", - "AC/NS/AF" - ], - "tools": [ - { - "vcflib": { - "description": "Command-line tools for manipulating VCF files", - "homepage": "https://github.com/vcflib/vcflib", - "documentation": "https://github.com/vcflib/vcflib#USAGE", - "doi": "10.1101/2021.05.21.445151", - "licence": [ - "MIT" - ], - "identifier": "biotools:vcflib" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "Compressed VCF file", - "pattern": "*.{.vcf.gz,vcf}", - "ontologies": [] - } - }, - { - "tbi": { - "type": "file", - "description": "Index of VCF file", - "pattern": "*.vcf.gz.tbi", - "ontologies": [] - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.vcf.gz": { - "type": "file", - "description": "Compressed VCF file", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "versions_vcflib": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "vcflib": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "1.0.14": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "vcflib": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "1.0.14": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@atrigila" - ], - "maintainers": [ - "@atrigila" - ] - }, - "pipelines": [ - { - "name": "phaseimpute", - "version": "1.1.0" - } - ] - }, - { - "name": "vcflib_vcfuniq", - "path": "modules/nf-core/vcflib/vcfuniq/meta.yml", - "type": "module", - "meta": { - "name": "vcflib_vcfuniq", - "description": "List unique genotypes. Like GNU uniq, but for VCF records. Remove records which have the same position, ref, and alt as the previous record.", - "keywords": [ - "vcf", - "uniq", - "deduplicate" - ], - "tools": [ - { - "vcflib": { - "description": "Command-line tools for manipulating VCF files", - "homepage": "https://github.com/vcflib/vcflib", - "documentation": "https://github.com/vcflib/vcflib#USAGE", - "doi": "10.1101/2021.05.21.445151", - "licence": [ - "MIT" - ], - "identifier": "biotools:vcflib" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "Compressed VCF file", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - }, - { - "tbi": { - "type": "file", - "description": "Index of VCF file", - "pattern": "*.vcf.gz.tbi", - "ontologies": [] - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", - "pattern": "*.vcf.gz" - } - }, - { - "*.vcf.gz": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", - "pattern": "*.vcf.gz" - } - } - ] - ], - "versions_vcflib": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "vcflib": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "1.0.14": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "vcflib": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "1.0.14": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@drpatelh" - ], - "maintainers": [ - "@drpatelh" - ] - }, - "pipelines": [ - { - "name": "viralrecon", - "version": "3.0.0" - } - ] - }, - { - "name": "vcfpgloader_load", - "path": "modules/nf-core/vcfpgloader/load/meta.yml", - "type": "module", - "meta": { - "name": "vcfpgloader_load", - "description": "High-performance VCF to PostgreSQL loader using asyncpg for bulk variant ingestion", - "keywords": [ - "vcf", - "postgresql", - "database", - "variants", - "genomics", - "clinical", - "annotation" - ], - "tools": [ - { - "vcf-pg-loader": { - "description": "High-throughput async PostgreSQL VCF loader using cyvcf2 and asyncpg.\nSupports variant normalization, multi-allelic decomposition, and clinical-grade audit trails.\n", - "homepage": "https://github.com/Zacharyr41/vcf-pg-loader", - "documentation": "https://github.com/Zacharyr41/vcf-pg-loader#readme", - "tool_dev_url": "https://github.com/Zacharyr41/vcf-pg-loader", - "licence": [ - "MIT" - ], - "identifier": "", - "args_id": "$args" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample1', family:'FAM001', affected:true ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "Annotated VCF file containing variants to load", - "pattern": "*.{vcf,vcf.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - } - ] - } - }, - { - "tbi": { - "type": "file", - "description": "Tabix index for the VCF file", - "pattern": "*.tbi", - "ontologies": [] - } - }, - { - "db_host": { - "type": "string", - "description": "PostgreSQL server hostname or IP address" - } - }, - { - "db_port": { - "type": "integer", - "description": "PostgreSQL server port (default 5432)" - } - }, - { - "db_name": { - "type": "string", - "description": "Target database name" - } - }, - { - "db_user": { - "type": "string", - "description": "Database username for authentication" - } - }, - { - "db_schema": { - "type": "string", - "description": "Target schema for variant tables (default public)" - } - } - ] - ], - "output": { - "report": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample1' ]\n" - } - }, - { - "*.load_report.json": { - "type": "file", - "description": "JSON report with loading statistics including variant counts, elapsed time, and throughput metrics", - "pattern": "*.load_report.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample1' ]\n" - } - }, - { - "*.load.log": { - "type": "file", - "description": "Detailed loading log with any warnings or errors", - "pattern": "*.load.log", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2330" - } - ] - } - } - ] - ], - "row_count": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample1' ]\n" - } - }, - { - "ROWS_LOADED": { - "type": "integer", - "description": "Number of variant records successfully loaded" - } - } - ] - ], - "versions_vcfpgloader": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "vcf-pg-loader": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "vcf-pg-loader --version | sed 's/.*version //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "vcf-pg-loader": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "vcf-pg-loader --version | sed 's/.*version //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@Zacharyr41" - ], - "maintainers": [ - "@Zacharyr41" - ] - } - }, - { - "name": "vcftools", - "path": "modules/nf-core/vcftools/meta.yml", - "type": "module", - "meta": { - "name": "vcftools", - "description": "A set of tools written in Perl and C++ for working with VCF files", - "keywords": [ - "VCFtools", - "VCF", - "sort" - ], - "tools": [ - { - "vcftools": { - "description": "A set of tools written in Perl and C++ for working with VCF files. This package only contains the C++ libraries whereas the package perl-vcftools-vcf contains the perl libraries", - "homepage": "http://vcftools.sourceforge.net/", - "documentation": "http://vcftools.sourceforge.net/man_latest.html", - "licence": [ - "LGPL" - ], - "identifier": "biotools:vcftools" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "variant_file": { - "type": "file", - "description": "variant input file which can be vcf, vcf.gz, or bcf format.", - "ontologies": [] - } - } - ], - { - "bed": { - "type": "file", - "description": "bed file which can be used with different arguments in vcftools (optional)", - "ontologies": [] - } - }, - { - "diff_variant_file": { - "type": "file", - "description": "secondary variant file which can be used with the 'diff' suite of tools (optional)", - "ontologies": [] - } - } - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.vcf": { - "type": "file", - "description": "vcf file (optional)", - "pattern": "*.vcf", - "ontologies": [] - } - } - ] - ], - "bcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bcf": { - "type": "file", - "description": "bcf file (optional)", - "pattern": "*.bcf", - "ontologies": [] - } - } - ] - ], - "frq": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.frq": { - "type": "file", - "description": "Allele frequency for each site (optional)", - "pattern": "*.frq", - "ontologies": [] - } - } - ] - ], - "frq_count": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.frq.count": { - "type": "file", - "description": "Allele counts for each site (optional)", - "pattern": "*.frq.count", - "ontologies": [] - } - } - ] - ], - "idepth": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.idepth": { - "type": "file", - "description": "mean depth per individual (optional)", - "pattern": "*.idepth", - "ontologies": [] - } - } - ] - ], - "ldepth": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.ldepth": { - "type": "file", - "description": "depth per site summed across individuals (optional)", - "pattern": "*.ildepth", - "ontologies": [] - } - } - ] - ], - "ldepth_mean": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.ldepth.mean": { - "type": "file", - "description": "mean depth per site calculated across individuals (optional)", - "pattern": "*.ldepth.mean", - "ontologies": [] - } - } - ] - ], - "gdepth": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.gdepth": { - "type": "file", - "description": "depth for each genotype in vcf file (optional)", - "pattern": "*.gdepth", - "ontologies": [] - } - } - ] - ], - "hap_ld": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.hap.ld": { - "type": "file", - "description": "r2, D, and D’ statistics using phased haplotypes (optional)", - "pattern": "*.hap.ld", - "ontologies": [] - } - } - ] - ], - "geno_ld": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.geno.ld": { - "type": "file", - "description": "squared correlation coefficient between genotypes encoded as 0, 1 and 2 to represent the number of non-reference alleles in each individual (optional)", - "pattern": "*.geno.ld", - "ontologies": [] - } - } - ] - ], - "geno_chisq": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.geno.chisq": { - "type": "file", - "description": "test for genotype independence via the chi-squared statistic (optional)", - "pattern": "*.geno.chisq", - "ontologies": [] - } - } - ] - ], - "list_hap_ld": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.list.hap.ld": { - "type": "file", - "description": "r2 statistics of the sites contained in the provided input file verses all other sites (optional)", - "pattern": "*.list.hap.ld", - "ontologies": [] - } - } - ] - ], - "list_geno_ld": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.list.geno.ld": { - "type": "file", - "description": "r2 statistics of the sites contained in the provided input file verses all other sites (optional)", - "pattern": "*.list.geno.ld", - "ontologies": [] - } - } - ] - ], - "interchrom_hap_ld": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.interchrom.hap.ld": { - "type": "file", - "description": "r2 statistics for sites (haplotypes) on different chromosomes (optional)", - "pattern": "*.interchrom.hap.ld", - "ontologies": [] - } - } - ] - ], - "interchrom_geno_ld": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.interchrom.geno.ld": { - "type": "file", - "description": "r2 statistics for sites (genotypes) on different chromosomes (optional)", - "pattern": "*.interchrom.geno.ld", - "ontologies": [] - } - } - ] - ], - "tstv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.TsTv": { - "type": "file", - "description": "Transition / Transversion ratio in bins of size defined in options (optional)", - "pattern": "*.TsTv", - "ontologies": [] - } - } - ] - ], - "tstv_summary": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.TsTv.summary": { - "type": "file", - "description": "Summary of all Transitions and Transversions (optional)", - "pattern": "*.TsTv.summary", - "ontologies": [] - } - } - ] - ], - "tstv_count": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.TsTv.count": { - "type": "file", - "description": "Transition / Transversion ratio as a function of alternative allele count (optional)", - "pattern": "*.TsTv.count", - "ontologies": [] - } - } - ] - ], - "tstv_qual": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.TsTv.qual": { - "type": "file", - "description": "Transition / Transversion ratio as a function of SNP quality threshold (optional)", - "pattern": "*.TsTv.qual", - "ontologies": [] - } - } - ] - ], - "filter_summary": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.FILTER.summary": { - "type": "file", - "description": "Summary of the number of SNPs and Ts/Tv ratio for each FILTER category (optional)", - "pattern": "*.FILTER.summary", - "ontologies": [] - } - } - ] - ], - "sites_pi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.sites.pi": { - "type": "file", - "description": "Nucleotide divergency on a per-site basis (optional)", - "pattern": "*.sites.pi", - "ontologies": [] - } - } - ] - ], - "windowed_pi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.windowed.pi": { - "type": "file", - "description": "Nucleotide diversity in windows, with window size determined by options (optional)", - "pattern": "*windowed.pi", - "ontologies": [] - } - } - ] - ], - "weir_fst": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.weir.fst": { - "type": "file", - "description": "Fst estimate from Weir and Cockerham’s 1984 paper (optional)", - "pattern": "*.weir.fst", - "ontologies": [] - } - } - ] - ], - "heterozygosity": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.het": { - "type": "file", - "description": "Heterozygosity on a per-individual basis (optional)", - "pattern": "*.het", - "ontologies": [] - } - } - ] - ], - "hwe": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.hwe": { - "type": "file", - "description": "Contains the Observed numbers of Homozygotes and Heterozygotes and the corresponding Expected numbers under HWE (optional)", - "pattern": "*.hwe", - "ontologies": [] - } - } - ] - ], - "tajima_d": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.Tajima.D": { - "type": "file", - "description": "Tajima’s D statistic in bins with size of the specified number in options (optional)", - "pattern": "*.Tajima.D", - "ontologies": [] - } - } - ] - ], - "freq_burden": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.ifreqburden": { - "type": "file", - "description": "Number of variants within each individual of a specific frequency in options (optional)", - "pattern": "*.ifreqburden", - "ontologies": [] - } - } - ] - ], - "lroh": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.LROH": { - "type": "file", - "description": "Long Runs of Homozygosity (optional)", - "pattern": "*.LROH", - "ontologies": [] - } - } - ] - ], - "relatedness": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.relatedness": { - "type": "file", - "description": "Relatedness statistic based on the method of Yang et al, Nature Genetics 2010 (doi:10.1038/ng.608) (optional)", - "pattern": "*.relatedness", - "ontologies": [] - } - } - ] - ], - "relatedness2": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.relatedness2": { - "type": "file", - "description": "Relatedness statistic based on the method of Manichaikul et al., BIOINFORMATICS 2010 (doi:10.1093/bioinformatics/btq559) (optional)", - "pattern": "*.relatedness2", - "ontologies": [] - } - } - ] - ], - "lqual": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.lqual": { - "type": "file", - "description": "per-site SNP quality (optional)", - "pattern": "*.lqual", - "ontologies": [] - } - } - ] - ], - "missing_individual": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.imiss": { - "type": "file", - "description": "Missingness on a per-individual basis (optional)", - "pattern": "*.imiss", - "ontologies": [] - } - } - ] - ], - "missing_site": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.lmiss": { - "type": "file", - "description": "Missingness on a per-site basis (optional)", - "pattern": "*.lmiss", - "ontologies": [] - } - } - ] - ], - "snp_density": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.snpden": { - "type": "file", - "description": "Number and density of SNPs in bins of size defined by option (optional)", - "pattern": "*.snpden", - "ontologies": [] - } - } - ] - ], - "kept_sites": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.kept.sites": { - "type": "file", - "description": "All sites that have been kept after filtering (optional)", - "pattern": "*.kept.sites", - "ontologies": [] - } - } - ] - ], - "removed_sites": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.removed.sites": { - "type": "file", - "description": "All sites that have been removed after filtering (optional)", - "pattern": "*.removed.sites", - "ontologies": [] - } - } - ] - ], - "singeltons": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.singletons": { - "type": "file", - "description": "Location of singletons, and the individual they occur in (optional)", - "pattern": "*.singeltons", - "ontologies": [] - } - } - ] - ], - "indel_hist": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.indel.hist": { - "type": "file", - "description": "Histogram file of the length of all indels (including SNPs) (optional)", - "pattern": "*.indel_hist", - "ontologies": [] - } - } - ] - ], - "hapcount": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.hapcount": { - "type": "file", - "description": "Unique haplotypes within user specified bins (optional)", - "pattern": "*.hapcount", - "ontologies": [] - } - } - ] - ], - "mendel": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.mendel": { - "type": "file", - "description": "Mendel errors identified in trios (optional)", - "pattern": "*.mendel", - "ontologies": [] - } - } - ] - ], - "format": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.FORMAT": { - "type": "file", - "description": "Extracted information from the genotype fields in the VCF file relating to a specified FORMAT identifier (optional)", - "pattern": "*.FORMAT", - "ontologies": [] - } - } - ] - ], - "info": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.INFO": { - "type": "file", - "description": "Extracted information from the INFO field in the VCF file (optional)", - "pattern": "*.INFO", - "ontologies": [] - } - } - ] - ], - "genotypes_matrix": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.012": { - "type": "file", - "description": "Genotypes output as large matrix.\nGenotypes of each individual on a separate line.\nGenotypes are represented as 0, 1 and 2, where the number represent that number of non-reference alleles.\nMissing genotypes are represented by -1 (optional)\n", - "pattern": "*.012", - "ontologies": [] - } - } - ] - ], - "genotypes_matrix_individual": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.012.indv": { - "type": "file", - "description": "Details the individuals included in the main genotypes_matrix file (optional)", - "pattern": "*.012.indv", - "ontologies": [] - } - } - ] - ], - "genotypes_matrix_position": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.012.pos": { - "type": "file", - "description": "Details the site locations included in the main genotypes_matrix file (optional)", - "pattern": "*.012.pos", - "ontologies": [] - } - } - ] - ], - "impute_hap": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.impute.hap": { - "type": "file", - "description": "Phased haplotypes in IMPUTE reference-panel format (optional)", - "pattern": "*.impute.hap", - "ontologies": [] - } - } - ] - ], - "impute_hap_legend": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.impute.hap.legend": { - "type": "file", - "description": "Impute haplotype legend file (optional)", - "pattern": "*.impute.hap.legend", - "ontologies": [] - } - } - ] - ], - "impute_hap_indv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.impute.hap.indv": { - "type": "file", - "description": "Impute haplotype individuals file (optional)", - "pattern": "*.impute.hap.indv", - "ontologies": [] - } - } - ] - ], - "ldhat_sites": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.ldhat.sites": { - "type": "file", - "description": "Output data in LDhat format, sites (optional)", - "pattern": "*.ldhat.sites", - "ontologies": [] - } - } - ] - ], - "ldhat_locs": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.ldhat.locs": { - "type": "file", - "description": "output data in LDhat format, locations (optional)", - "pattern": "*.ldhat.locs", - "ontologies": [] - } - } - ] - ], - "beagle_gl": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.BEAGLE.GL": { - "type": "file", - "description": "Genotype likelihoods for biallelic sites (optional)", - "pattern": "*.BEAGLE.GL", - "ontologies": [] - } - } - ] - ], - "beagle_pl": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.BEAGLE.PL": { - "type": "file", - "description": "Genotype likelihoods for biallelic sites (optional)", - "pattern": "*.BEAGLE.PL", - "ontologies": [] - } - } - ] - ], - "ped": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.ped": { - "type": "file", - "description": "output the genotype data in PLINK PED format (optional)", - "pattern": "*.ped", - "ontologies": [] - } - } - ] - ], - "map_": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.map": { - "type": "file", - "description": "output the genotype data in PLINK PED format (optional)", - "pattern": "*.map", - "ontologies": [] - } - } - ] - ], - "tped": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tped": { - "type": "file", - "description": "output the genotype data in PLINK PED format (optional)", - "pattern": "*.tped", - "ontologies": [] - } - } - ] - ], - "tfam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.tfam": { - "type": "file", - "description": "output the genotype data in PLINK PED format (optional)", - "pattern": "*.tfam", - "ontologies": [] - } - } - ] - ], - "diff_sites_in_files": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.diff.sites_in_files": { - "type": "file", - "description": "Sites that are common / unique to each file specified in optional inputs (optional)", - "pattern": "*.diff.sites.in.files", - "ontologies": [] - } - } - ] - ], - "diff_indv_in_files": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.diff.indv_in_files": { - "type": "file", - "description": "Individuals that are common / unique to each file specified in optional inputs (optional)", - "pattern": "*.diff.indv.in.files", - "ontologies": [] - } - } - ] - ], - "diff_sites": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.diff.sites": { - "type": "file", - "description": "Discordance on a site by site basis, specified in optional inputs (optional)", - "pattern": "*.diff.sites", - "ontologies": [] - } - } - ] - ], - "diff_indv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.diff.indv": { - "type": "file", - "description": "Discordance on a individual by individual basis, specified in optional inputs (optional)", - "pattern": "*.diff.indv", - "ontologies": [] - } - } - ] - ], - "diff_discd_matrix": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.diff.discordance.matrix": { - "type": "file", - "description": "Discordance matrix between files specified in optional inputs (optional)", - "pattern": "*.diff.discordance.matrix", - "ontologies": [] - } - } - ] - ], - "diff_switch_error": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.diff.switch": { - "type": "file", - "description": "Switch errors found between sites (optional)", - "pattern": "*.diff.switch", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@Mark-S-Hill" - ], - "maintainers": [ - "@Mark-S-Hill" - ] - }, - "pipelines": [ - { - "name": "genomicrelatedness", - "version": "dev" - }, - { - "name": "rnadnavar", - "version": "dev" - }, - { - "name": "sarek", - "version": "3.8.1" - } - ] - }, - { - "name": "vclust_align", - "path": "modules/nf-core/vclust/align/meta.yml", - "type": "module", - "meta": { - "name": "vclust_align", - "description": "The align command performs pairwise sequence alignments of viral genomes and provides similarity measures like ANI and coverage (alignment fraction)", - "keywords": [ - "cluster", - "virus", - "filter", - "contig", - "scaffold", - "phage" - ], - "tools": [ - { - "vclust": { - "description": "Fast and accurate tool for calculating ANI and clustering virus genomes and metagenomes.", - "homepage": "https://afproject.org/vclust/", - "documentation": "https://github.com/refresh-bio/vclust/wiki", - "tool_dev_url": "https://github.com/refresh-bio/vclust", - "doi": "10.1038/s41592-025-02701-7", - "licence": [ - "GPL v3-or-later" - ], - "identifier": "biotools:vclust" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input fasta file containing sequences needed for filtering", - "pattern": "*.{fasta,fna,fa}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "filter": { - "type": "file", - "description": "Input txt file containing sequences relationships for filtering (generated with vclust prefilter)", - "pattern": "*.txt", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2330" - }, - { - "edam": "http://edamontology.org/format_2082" - } - ] - } - } - ], - { - "save_alignment": { - "type": "boolean", - "default": false, - "description": "Save the pairwise alignments to a blast-like file.\n", - "pattern": "*.aln.tsv" - } - } - ], - "output": { - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}.tsv": { - "type": "file", - "description": "Sorted TSV file", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "ids": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.ids.tsv": { - "type": "file", - "description": "File containing sequence IDs and their number of parts", - "pattern": "*.ids.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "aln": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.aln.tsv": { - "type": "file", - "description": "File similar to the BLASTn tabular output file,\nincludes information on each local alignment between two genomes.\n", - "ontologies": [] - } - } - ] - ], - "versions_vclust": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "vclust": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "vclust --version | sed 's/v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "vclust": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "vclust --version | sed 's/v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@Joon-klaps" - ], - "maintainers": [ - "@Joon-klaps" - ] - } - }, - { - "name": "vclust_cluster", - "path": "modules/nf-core/vclust/cluster/meta.yml", - "type": "module", - "meta": { - "name": "vclust_cluster", - "description": "Vclust cluster performs threshold-based clustering by assigning a genome sequence to a cluster if its similarity (e.g., ANI) to the cluster meets or exceeds a user-defined threshold.", - "keywords": [ - "cluster", - "virus", - "filter", - "contig", - "scaffold", - "phage" - ], - "tools": [ - { - "vclust": { - "description": "\"Fast and accurate tool for calculating ANI and clustering virus\ngenomes and metagenomes.\"\n", - "homepage": "https://afproject.org/vclust/", - "documentation": "https://github.com/refresh-bio/vclust/wiki", - "tool_dev_url": "https://github.com/refresh-bio/vclust", - "doi": "10.1038/s41592-025-02701-7", - "licence": [ - "GPL v3-or-later" - ], - "identifier": "biotools:vclust" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "tsv": { - "type": "file", - "description": "Sorted TSV file, generated by `vclust align`", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "ids": { - "type": "file", - "description": "TSV file containing sequence IDs and their number of parts, generated by `vclust align`", - "pattern": "*.ids.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - { - "metric": { - "type": "string", - "description": "Similarity metric for clustering choices: 'tani','gani' or 'ani'\n", - "pattern": "tani|gani|ani" - } - }, - { - "tani": { - "type": "float", - "description": "Min. total ANI\n" - } - }, - { - "gani": { - "type": "float", - "description": "Min. global ANI\n" - } - }, - { - "ani": { - "type": "float", - "description": "Min. ANI\n" - } - } - ], - "output": { - "clusters": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "A TSV file with genome identifiers followed by 0-based cluster identifiers.\nThe file includes all input genomes, both clustered and singletons, listed in\nthe same order as the IDs file (sorted by decreasing sequence length). The first genome\nin each cluster is the representative.\n", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.log": { - "type": "file", - "description": "Log file containing the stdout", - "pattern": "*.log", - "ontologies": [] - } - } - ] - ], - "versions_vclust": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "vclust": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "vclust --version | sed 's/v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "vclust": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "vclust --version | sed 's/v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@Joon-Klaps" - ], - "maintainers": [ - "@Joon-Klaps" - ] - } - }, - { - "name": "vclust_prefilter", - "path": "modules/nf-core/vclust/prefilter/meta.yml", - "type": "module", - "meta": { - "name": "vclust_prefilter", - "description": "The prefilter command creates a pre-alignment filter that reduces the number of genome pairs to be aligned by filtering out dissimilar sequences before the alignment step.", - "keywords": [ - "cluster", - "virus", - "filter", - "contig", - "scaffold", - "phage" - ], - "tools": [ - { - "vclust": { - "description": "Fast and accurate tool for calculating ANI and clustering virus genomes and metagenomes.", - "homepage": "https://afproject.org/vclust/", - "documentation": "https://github.com/refresh-bio/vclust/wiki", - "tool_dev_url": "https://github.com/refresh-bio/vclust", - "doi": "10.1038/s41592-025-02701-7", - "licence": [ - "GPL v3-or-later" - ], - "identifier": "biotools:vclust" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input fasta file containing sequences needed for filtering", - "pattern": "*.{fasta,fna,fa}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ], - "output": { - "txt": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.txt": { - "type": "file", - "description": "Output text file containing relationships for filtering", - "pattern": "*.txt", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2330" - }, - { - "edam": "http://edamontology.org/format_2082" - } - ] - } - } - ] - ], - "versions_vclust": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "vclust": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "vclust --version | sed 's/v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "vclust": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "vclust --version | sed 's/v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@Joon-Klaps" - ], - "maintainers": [ - "@Joon-Klaps" - ] - } - }, - { - "name": "velocyto", - "path": "modules/nf-core/velocyto/meta.yml", - "type": "module", - "meta": { - "name": "velocyto", - "description": "Velocyto is a library for the analysis of RNA velocity. velocyto.py CLI use\n`Path(resolve_path=True)` and breaks the nextflow logic of symbolic links.\nIf in the work dir velocyto find a file named EXACTLY `cellsorted_[ORIGINAL_BAM_NAME]`\nit will skip the samtools sort step.\nCellsorted bam file should be cell sorted with:\n```bash\n samtools sort -t CB -O BAM -o cellsorted_input.bam input.bam\n```\nSee module test for an example with the SAMTOOLS_SORT nf-core module.\nConfig example to cellsort input bam using SAMTOOLS_SORT:\n```groovy\n withName: SAMTOOLS_SORT {\n ext.prefix = { \"cellsorted_${bam.baseName}\" }\n ext.args = '-t CB -O BAM'\n }\n```\nOptional mask must be passed with `ext.args` and option `--mask`\nThis is why I need to stage in the work dir 2 bam files (cellsorted and original).\nSee also [velocyto tutorial](https://velocyto.org/velocyto.py/tutorial/cli.html#notes-on-first-runtime-and-parallelization)\n", - "keywords": [ - "count", - "rnaseq", - "rna velocity", - "bam" - ], - "tools": [ - { - "velocyto": { - "description": "A library for the analysis of RNA velocity.", - "homepage": "https://github.com/velocyto-team/velocyto.py", - "documentation": "https://velocyto.org/velocyto.py", - "tool_dev_url": "https://github.com/velocyto-team/velocyto.py", - "doi": "10.1038/s41586-018-0414-6", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "barcodes": { - "type": "file", - "description": "Valid barcodes file, to filter the bam", - "pattern": "*.tsv.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } - }, - { - "sorted_bam": { - "type": "file", - "description": "Cell sorted BAM/CRAM/SAM file generated with `samtools sort -t CB -O BAM -o cellsorted_possorted_genome_bam.bam possorted_genome_bam.bam`", - "pattern": "*.bam", - "ontologies": [] - } - } - ], - { - "gtf": { - "type": "file", - "description": "genome annotation file", - "pattern": "*.gtf", - "ontologies": [] - } - } - ], - "output": { - "loom": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.loom": { - "type": "file", - "description": "Loom file with counts divided in spliced/unspliced/ambiguous.", - "pattern": "*.loom", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3913" - } - ] - } - }, - { - "*.velocyto.log": { - "type": "file", - "description": "Loom file with counts divided in spliced/unspliced/ambiguous.", - "pattern": "*.loom", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3913" - } - ] - } - } - ] - ], - "versions_velocyto": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "velocyto": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "velocyto --version | sed 's/^.*version //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "velocyto": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "velocyto --version | sed 's/^.*version //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@tucano" - ], - "maintainers": [ - "@tucano" - ] - } - }, - { - "name": "vembrane_filter", - "path": "modules/nf-core/vembrane/filter/meta.yml", - "type": "module", - "meta": { - "name": "vembrane_filter", - "description": "Filter VCF files with vembrane", - "keywords": [ - "filter", - "vcf", - "bcf", - "genomics", - "variant", - "annotation" - ], - "tools": [ - { - "vembrane": { - "description": "Filter VCF/BCF files with Python expressions.", - "homepage": "https://github.com/vembrane/vembrane/tree/main", - "documentation": "https://github.com/vembrane/vembrane/blob/main/docs/filter.md", - "tool_dev_url": "https://github.com/vembrane/vembrane.git", - "doi": "10.1093/bioinformatics/btac810", - "licence": [ - "MIT" - ], - "identifier": "biotools:vembrane/filter" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "Path to the VCF/BCF file to be filtered.\ne.g. 'file.vcf', 'file.vcf.gz', 'file.bcf', 'file.bcf.gz'\n", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}", - "ontologies": [] - } - } - ], - { - "expression": { - "type": "string", - "description": "The filter expression can be any valid python expression that evaluates to a value of type bool.\ne.g. 'ANN[\"SYMBOL\"] == \"CDH2\"'\n", - "ontologies": [] - } - } - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.{vcf,bcf,bcf.gz}": { - "type": "file", - "description": "Filtered VCF output file", - "pattern": "*.{vcf,bcf,bcf.gz}", - "ontologies": [] - } - } - ] - ], - "versions_vembrane": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "vembrane": { - "type": "string", - "description": "The tool name" - } - }, - { - "vembrane --version | sed '1!d;s/.* //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "vembrane": { - "type": "string", - "description": "The tool name" - } - }, - { - "vembrane --version | sed '1!d;s/.* //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@trangdo-hsc", - "@mkatsanto" - ], - "maintainers": [ - "@trangdo-hsc" - ] - } - }, - { - "name": "vembrane_sort", - "path": "modules/nf-core/vembrane/sort/meta.yml", - "type": "module", - "meta": { - "name": "vembrane_sort", - "description": "Sort VCF/BCF files by custom Python expressions for variant prioritization", - "keywords": [ - "vcf", - "bcf", - "sort", - "genomics", - "variant", - "prioritization" - ], - "tools": [ - { - "vembrane": { - "description": "Filter VCF/BCF files with Python expressions", - "homepage": "https://vembrane.github.io/", - "documentation": "https://github.com/vembrane/vembrane/blob/main/docs/sort.md", - "tool_dev_url": "https://github.com/vembrane/vembrane", - "doi": "10.1093/bioinformatics/btac810", - "licence": [ - "MIT" - ], - "identifier": "biotools:vembrane", - "args_id": "$args" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF/BCF file to sort", - "pattern": "*.{vcf,bcf,bcf.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - } - ] - } - } - ], - { - "expression": { - "type": "string", - "description": "Python expression (or tuple of expressions) returning orderable values to sort by" - } - } - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.{vcf,bcf,bcf.gz}": { - "type": "file", - "description": "Sorted VCF/BCF file", - "pattern": "*.{vcf,bcf,bcf.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - } - ] - } - } - ] - ], - "versions_vembrane": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "vembrane": { - "type": "string", - "description": "The tool name" - } - }, - { - "vembrane --version | sed '1!d;s/.* //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "vembrane": { - "type": "string", - "description": "The tool name" - } - }, - { - "vembrane --version | sed '1!d;s/.* //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@mkatsanto", - "@trangdo-hsc" - ], - "maintainers": [ - "@mkatsanto", - "@trangdo-hsc" - ] - } - }, - { - "name": "vembrane_table", - "path": "modules/nf-core/vembrane/table/meta.yml", - "type": "module", - "meta": { - "name": "vembrane_table", - "description": "Creates tabular (TSV) files from VCF/BCF data with flexible Python expressions", - "keywords": [ - "vcf", - "bcf", - "table", - "genomics", - "variant", - "annotation" - ], - "tools": [ - { - "vembrane": { - "description": "Filter VCF/BCF files with Python expressions", - "homepage": "https://vembrane.github.io/", - "documentation": "https://github.com/vembrane/vembrane/blob/main/docs/table.md", - "tool_dev_url": "https://github.com/vembrane/vembrane", - "doi": "10.1093/bioinformatics/btac810", - "licence": [ - "MIT" - ], - "identifier": "biotools:vembrane", - "args_id": "$args" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF/BCF file to extract tabular data from", - "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - } - ] - } - } - ], - { - "expression": { - "type": "string", - "description": "A comma-separated tuple of expressions that define the table column contents" - } - } - ], - "output": { - "table": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.tsv": { - "type": "file", - "description": "TSV file containing tabular data from VCF/BCF", - "pattern": "*.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_vembrane": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "vembrane": { - "type": "string", - "description": "The tool name" - } - }, - { - "vembrane --version | sed '1!d;s/.* //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "vembrane": { - "type": "string", - "description": "The tool name" - } - }, - { - "vembrane --version | sed '1!d;s/.* //'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@mkatsanto", - "@trangdo-hsc" - ], - "maintainers": [ - "@mkatsanto", - "@trangdo-hsc" - ] - } - }, - { - "name": "verifybamid_verifybamid", - "path": "modules/nf-core/verifybamid/verifybamid/meta.yml", - "type": "module", - "meta": { - "name": "verifybamid_verifybamid", - "description": "Detecting and estimating inter-sample DNA contamination became a crucial quality assessment step to ensure high quality sequence reads and reliable downstream analysis.", - "keywords": [ - "qc", - "contamination", - "bam" - ], - "tools": [ - { - "verifybamid": { - "description": "verifyBamID is a software that verifies whether the reads in particular file match previously known genotypes for an individual (or group of individuals), and checks whether the reads are contaminated as a mixture of two samples.", - "homepage": "https://genome.sph.umich.edu/wiki/VerifyBamID", - "documentation": "http://genome.sph.umich.edu/wiki/VerifyBamID", - "tool_dev_url": "https://github.com/statgen/verifyBamID", - "doi": "10.1016/j.ajhg.2012.09.004", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:verifybamid" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file, a sorted, indexed, base quality recalibrated, and duplication-marked BAM file.\nIt also requires to contain \"@RG\" header lines to annotation different readGroups (sequencing runs and lanes).\nThe SM tag in the \"@RG\" header should match with one of the genotyped sample.\n", - "pattern": "*.bam", - "ontologies": [] - } - }, - { - "bai": { - "type": "file", - "description": "BAM index file BAI", - "pattern": "*.bai", - "ontologies": [] - } - } - ], - { - "refvcf": { - "type": "file", - "description": "The input VCF file contains\n(1) external genotype information and/or\n(2) allele frequency information as AF entry or AC/AN entries in the INFO field.\n", - "pattern": "*.{vcf,vcf.gz}", - "ontologies": [] - } - } - ], - "output": { - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.log": { - "type": "file", - "description": "Detailed summary of the verifyBamID result.", - "pattern": "*.log", - "ontologies": [] - } - } - ] - ], - "selfsm": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.selfSM": { - "type": "file", - "description": "Per-sample statistics describing how well the sample matches to the annotated sample.", - "pattern": "*.selfSM", - "ontologies": [] - } - } - ] - ], - "depthsm": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.depthSM": { - "type": "file", - "description": "The depth distribution of the sequence reads per sample", - "pattern": "*.depthSM", - "ontologies": [] - } - } - ] - ], - "selfrg": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.selfRG": { - "type": "file", - "description": "Per-readGroup statistics describing how well each lane matches to the annotated sample. (available only without --ignoreRG option)", - "pattern": "*.selfRG", - "ontologies": [] - } - } - ] - ], - "depthrg": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.depthRG": { - "type": "file", - "description": "The depth distribution of the sequence reads per readGroup. (available only without --ignoreRG option)", - "pattern": "*.depthRG", - "ontologies": [] - } - } - ] - ], - "bestsm": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bestSM": { - "type": "file", - "description": "Per-sample best-match statistics with best-matching sample among the genotyped sample (available only with --best option)", - "pattern": "*.bestSM", - "ontologies": [] - } - } - ] - ], - "bestrg": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bestRG": { - "type": "file", - "description": "Per-readgroup best-match statistics with best-matching sample among the genotyped sample (available only with --best and without --ignoreRG option)", - "pattern": "*.bestRG", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@manifestoso" - ], - "maintainers": [ - "@manifestoso" - ] - } - }, - { - "name": "verifybamid_verifybamid2", - "path": "modules/nf-core/verifybamid/verifybamid2/meta.yml", - "type": "module", - "meta": { - "name": "VERIFYBAMID_VERIFYBAMID2", - "description": "Detecting and estimating inter-sample DNA contamination became a crucial quality assessment step to ensure high quality sequence reads and reliable downstream analysis.", - "keywords": [ - "contamination", - "bam", - "verifybamid", - "DNA contamination estimation" - ], - "tools": [ - { - "verifybamid2": { - "description": "A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method.", - "homepage": "http://griffan.github.io/VerifyBamID", - "documentation": "http://griffan.github.io/VerifyBamID", - "tool_dev_url": "https://github.com/Griffan/VerifyBamID", - "doi": "10.1101/gr.246934.118", - "licence": [ - "MIT" - ], - "identifier": "biotools:verifybamid" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}", - "ontologies": [] - } - }, - { - "bai": { - "type": "file", - "description": "BAI/CRAI/CSI index file", - "pattern": "*.{bai,crai,csi}", - "ontologies": [] - } - } - ], - [ - { - "svd_ud": { - "type": "file", - "description": ".UD matrix file from SVD result of genotype matrix", - "pattern": "*.UD", - "ontologies": [] - } - }, - { - "svd_mu": { - "type": "file", - "description": ".mu matrix file of genotype matrix", - "pattern": "*.mu", - "ontologies": [] - } - }, - { - "svd_bed": { - "type": "file", - "description": ".Bed file for markers used in this analysis,format(chr\\tpos-1\\tpos\\trefAllele\\taltAllele)[Required]", - "pattern": "*.bed", - "ontologies": [] - } - } - ], - { - "refvcf": { - "type": "file", - "description": "Reference panel VCF with genotype information, for generation of .UD .mu .bed files [Optional]", - "pattern": "*.vcf", - "ontologies": [] - } - }, - { - "references": { - "type": "file", - "description": "reference file [Required]", - "pattern": "*.fasta", - "ontologies": [] - } - } - ], - "output": { - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.log": { - "type": "file", - "description": "Detailed summary of the VerifyBamId2 results", - "pattern": "*.log", - "ontologies": [] - } - } - ] - ], - "ud": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.UD": { - "type": "file", - "description": ".UD matrix file from customized reference vcf input", - "pattern": "*.UD", - "ontologies": [] - } - } - ] - ], - "bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.bed": { - "type": "file", - "description": ".Bed file from customized reference marker vcf input", - "pattern": "*.bed", - "ontologies": [] - } - } - ] - ], - "mu": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.mu": { - "type": "file", - "description": ".mu matrix file of genotype matrix from customized reference vcf input", - "pattern": "*.mu", - "ontologies": [] - } - } - ] - ], - "self_sm": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.selfSM": { - "type": "file", - "description": "Shares the same format as legacy VB1 and the key information FREEMIX indicates the estimated contamination level.", - "pattern": "*.selfSM", - "ontologies": [] - } - } - ] - ], - "ancestry": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.Ancestry": { - "type": "file", - "description": "Ancestry information", - "pattern": "*.Ancestry", - "ontologies": [] - } - } - ] - ], - "versions_verifybamid2": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "verifybamid2": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "verifybamid2 --help 2>&1 | sed -n '3s/.*Version://p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "verifybamid2": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "verifybamid2 --help 2>&1 | sed -n '3s/.*Version://p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@manifestoso" - ], - "maintainers": [ - "@manifestoso" - ] - }, - "pipelines": [ - { - "name": "raredisease", - "version": "3.0.0" - } - ] - }, - { - "name": "vg_construct", - "path": "modules/nf-core/vg/construct/meta.yml", - "type": "module", - "meta": { - "name": "vg_construct", - "description": "Constructs a graph from a reference and variant calls or a multiple sequence alignment file", - "keywords": [ - "vg", - "graph", - "construct", - "fasta", - "vcf", - "structural variants" - ], - "tools": [ - { - "vg": { - "description": "Variation graph data structures, interchange formats, alignment, genotyping,\nand variant calling methods.\n", - "homepage": "https://github.com/vgteam/vg", - "documentation": "https://github.com/vgteam/vg/wiki", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "list", - "description": "Either one or more VCF files containing different contigs or a multiple sequence alignment file\n", - "pattern": "*.{vcf.gz,fa,fasta,fna,clustal}" - } - }, - { - "tbis": { - "type": "list", - "description": "The index files for the VCF files", - "pattern": "*.tbi" - } - }, - { - "insertions_fasta": { - "type": "file", - "description": "A FASTA file containing insertion sequences (referred to in the VCF file(s))", - "pattern": "*.{fa,fasta,fna}", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference FASTA file (cannot be used in combination with `msa`, but is required when using `vcfs`)", - "pattern": "*.{fa,fasta,fna}", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta_fai": { - "type": "file", - "description": "The index of the reference FASTA file", - "pattern": "*.fai", - "ontologies": [] - } - } - ] - ], - "output": { - "graph": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.vg": { - "type": "file", - "description": "The constructed graph", - "pattern": "*.vg", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@nvnieuwk" - ], - "maintainers": [ - "@nvnieuwk" - ] - } - }, - { - "name": "vg_deconstruct", - "path": "modules/nf-core/vg/deconstruct/meta.yml", - "type": "module", - "meta": { - "name": "vg_deconstruct", - "description": "Deconstruct snarls present in a variation graph in GFA format to variants in VCF format", - "keywords": [ - "vcf", - "gfa", - "graph", - "pangenome graph", - "variation graph", - "graph projection to vcf" - ], - "tools": [ - { - "vg": { - "description": "Variation graph data structures, interchange formats, alignment, genotyping,\nand variant calling methods.\n", - "homepage": "https://github.com/vgteam/vg", - "documentation": "https://github.com/vgteam/vg/wiki", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "gfa": { - "type": "file", - "description": "Variation graph in GFA format", - "pattern": "*.{gfa}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3975" - } - ] - } - } - ], - { - "pb": { - "type": "file", - "description": "Optional snarls file (from vg snarls) to avoid recomputing. Usually ends with \"pb\". See \"vg snarls\".", - "pattern": "*.{pb}", - "ontologies": [] - } - }, - { - "gbwt": { - "type": "file", - "description": "Optional GBWT file (from vg gbwt) so to only consider alt traversals that correspond to GBWT threads FILE.", - "pattern": "*.{gbwt}", - "ontologies": [] - } - } - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.vcf": { - "type": "file", - "description": "Variants in VCF format", - "pattern": "*.{vcf}", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@heuermh, @subwaystation" - ], - "maintainers": [ - "@heuermh, @subwaystation" - ] - } - }, - { - "name": "vg_index", - "path": "modules/nf-core/vg/index/meta.yml", - "type": "module", - "meta": { - "name": "vg_index", - "description": "write your description here", - "keywords": [ - "vg", - "index", - "graph", - "structural_variants" - ], - "tools": [ - { - "vg": { - "description": "Variation graph data structures, interchange formats, alignment, genotyping,\nand variant calling methods.\n", - "homepage": "https://github.com/vgteam/vg", - "documentation": "https://github.com/vgteam/vg/wiki", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "list", - "description": "One or more input graph files created with `vg/construct`", - "pattern": "*.vg" - } - } - ] - ], - "output": { - "xg": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.xg": { - "type": "file", - "description": "File containing a succinct, queryable version of the input graph(s) or read for GCSA or distance indexing", - "pattern": "*.xg", - "ontologies": [] - } - } - ] - ], - "vg_index": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.vgi": { - "type": "file", - "description": "An index of the graph(s) created when `--index-sorted-vg` is supplied.", - "pattern": "*.vgi", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@nvnieuwk" - ], - "maintainers": [ - "@nvnieuwk" - ] - } - }, - { - "name": "viber", - "path": "modules/nf-core/viber/meta.yml", - "type": "module", - "meta": { - "name": "viber", - "description": "Multisample subclonal deconvolution of cancer genome sequencing data.", - "keywords": [ - "subclonal deconvolution", - "genomics", - "cancer evolution" - ], - "tools": [ - { - "viber": { - "description": "VIBER is a package that implements a variational Bayesian model to fit multi-variate Binomial mixtures.\nThe statistical model is semi-parametric and fit by a variational mean-field approximation to the model posterior.\nThe components are Binomial distributions which can model count data;\nthese can be used to model sequencing counts in the context of cancer, for instance.\nThe package implements methods to fit and visualize clustering results.\n", - "homepage": "https://caravagnalab.github.io/VIBER/", - "documentation": "https://caravagnalab.github.io/VIBER/", - "tool_dev_url": "https://github.com/caravagnalab/VIBER/", - "doi": "10.1038/s41588-020-0675-5", - "licence": [ - "GPL v3-or-later" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } - }, - { - "rds_join": { - "type": "file", - "description": "Either a .rds object of class mCNAqc or a .csv mutations table", - "pattern": "*.{rds,csv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - }, - { - "tumour_samples": { - "type": "list", - "description": "List of tumour sample identifiers for a specific patient" - } - } - ] - ], - "output": { - "viber_rds": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*_viber_best_fit.rds": { - "type": "file", - "description": "Best viber fit as an .rds object", - "pattern": "*_viber_best_fit.rds", - "ontologies": [] - } - } - ] - ], - "viber_heuristic_rds": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*_viber_best_heuristic_fit.rds": { - "type": "file", - "description": "Cluster-filtering heuristics viber fit as an .rds object", - "pattern": "*_viber_best_heuristic_fit.rds", - "ontologies": [] - } - } - ] - ], - "viber_plots_rds": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*_viber_best_fit_plots.rds": { - "type": "file", - "description": "best fit plot", - "pattern": "_viber_best_fit_plots.rds", - "ontologies": [] - } - } - ] - ], - "viber_heuristic_plots_rds": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*_viber_best_heuristic_fit_plots.rds": { - "type": "file", - "description": "heuristics fit plot", - "pattern": "*_viber_best_heuristic_fit_plots.rds", - "ontologies": [] - } - } - ] - ], - "viber_report_rds": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*_viber_report.rds": { - "type": "file", - "description": "final report plots as a .pdf file", - "pattern": "*_viber_report.rds", - "ontologies": [] - } - } - ] - ], - "viber_report_pdf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*_viber_report.pdf": { - "type": "file", - "description": "final report plots as a .pdf file", - "pattern": "*_viber_report.pdf", - "ontologies": [] - } - } - ] - ], - "viber_report_png": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*_viber_report.png": { - "type": "file", - "description": "final report plots as a .png file", - "pattern": "*_viber_report.png", - "ontologies": [] - } - } - ] - ], - "versions_viber": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "topics": { - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@giorgiagandolfi" - ], - "maintainers": [ - "@giorgiagandolfi" - ] - }, - "pipelines": [ - { - "name": "tumourevo", - "version": "dev" - } - ] - }, - { - "name": "viennarna_rnacofold", - "path": "modules/nf-core/viennarna/rnacofold/meta.yml", - "type": "module", - "meta": { - "name": "viennarna_rnacofold", - "description": "calculate secondary structures of two RNAs with dimerization", - "keywords": [ - "RNA", - "fasta", - "rna_structure" - ], - "tools": [ - { - "viennarna": { - "description": "calculate secondary structures of two RNAs with dimerization\n\nThe program works much like RNAfold, but allows one to specify two RNA\nsequences which are then allowed to form a dimer structure. RNA sequences\nare read from stdin in the usual format, i.e. each line of input\ncorresponds to one sequence, except for lines starting with > which\ncontain the name of the next sequence. To compute the hybrid structure\nof two molecules, the two sequences must be concatenated using the &\ncharacter as separator. RNAcofold can compute minimum free energy (mfe)\nstructures, as well as partition function (pf) and base pairing\nprobability matrix (using the -p switch) Since dimer formation is\nconcentration dependent, RNAcofold can be used to compute equilibrium\nconcentrations for all five monomer and (homo/hetero)-dimer species,\ngiven input concentrations for the monomers. Output consists of the\nmfe structure in bracket notation as well as PostScript structure\nplots and “dot plot” files containing the pair probabilities, see\nthe RNAfold man page for details. In the dot plots a cross marks\nthe chain break between the two concatenated sequences. The program\nwill continue to read new sequences until a line consisting of the\nsingle character @ or an end of file condition is encountered.\n", - "homepage": "https://www.tbi.univie.ac.at/RNA/", - "documentation": "https://viennarna.readthedocs.io/en/latest/", - "doi": "10.1186/1748-7188-6-26", - "licence": [ - "custom" - ], - "identifier": "biotools:viennarna" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "rnacofold_fasta": { - "type": "file", - "description": "A fasta file containing RNA or transcript sequences\n", - "pattern": "*.{fasta,fa}", - "ontologies": [] - } - } - ] - ], - "output": { - "rnacofold_csv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.csv": { - "type": "file", - "description": "The CSV Output of RNAcofold that has the predicted structure and energies", - "pattern": "*.{csv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ] - ], - "rnacofold_ps": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.ps": { - "type": "file", - "description": "The text Output of RNAfold that contains the predicted secondary structure in postscript format", - "pattern": "*.{ps}", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@kokul-atx" - ], - "maintainers": [ - "@kokul-atx" - ] - } - }, - { - "name": "viennarna_rnafold", - "path": "modules/nf-core/viennarna/rnafold/meta.yml", - "type": "module", - "meta": { - "name": "viennarna_rnafold", - "description": "Predict RNA secondary structure using the ViennaRNA RNAfold tools. Calculate minimum free energy secondary structures and partition function of RNAs.", - "keywords": [ - "RNA", - "fasta", - "rna_structure" - ], - "tools": [ - { - "viennarna": { - "description": "Calculate minimum free energy secondary structures and partition function of RNAs\n\nThe program reads RNA sequences, calculates their minimum free energy (mfe) structure and\nprints the mfe structure in bracket notation and its free energy. If not specified differently\nusing commandline arguments, input is accepted from stdin or read from an input file, and\noutput printed to stdout. If the -p option was given it also computes the partition function\n(pf) and base pairing probability matrix, and prints the free energy of the thermodynamic\nensemble, the frequency of the mfe structure in the ensemble, and the ensemble diversity to stdout.\n", - "homepage": "https://www.tbi.univie.ac.at/RNA/", - "documentation": "https://viennarna.readthedocs.io/en/latest/", - "doi": "10.1186/1748-7188-6-26", - "licence": [ - "custom" - ], - "identifier": "biotools:viennarna" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "A fasta file containing RNA or transcript sequences\n", - "pattern": "*.{fasta,fa}", - "ontologies": [] - } - } - ] - ], - "output": { - "rnafold_txt": [ - [ - { - "meta": { - "type": "file", - "description": "The text Output of RNAfold that", - "pattern": "*.{fold}", - "ontologies": [] - } - }, - { - "*.fold": { - "type": "file", - "description": "The text Output of RNAfold that", - "pattern": "*.{fold}", - "ontologies": [] - } - } - ] - ], - "rnafold_ps": [ - [ - { - "meta": { - "type": "file", - "description": "The text Output of RNAfold that", - "pattern": "*.{fold}", - "ontologies": [] - } - }, - { - "*.ps": { - "type": "file", - "description": "The text Output of RNAfold that", - "pattern": "*.ss", - "ontologies": [] - } - } - ] - ], - "versions": [ - [ - { - "meta": { - "type": "file", - "description": "The text Output of RNAfold that", - "pattern": "*.{fold}", - "ontologies": [] - } - }, - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - ] - }, - "authors": [ - "@kokul-atx" - ], - "maintainers": [ - "@kokul-atx" - ] - } - }, - { - "name": "viennarna_rnalfold", - "path": "modules/nf-core/viennarna/rnalfold/meta.yml", - "type": "module", - "meta": { - "name": "viennarna_rnalfold", - "description": "calculate locally stable secondary structures of RNAs", - "keywords": [ - "RNA", - "fasta", - "rna_structure" - ], - "tools": [ - { - "viennarna": { - "description": "calculate locally stable secondary structures of RNAs\n\nCompute locally stable RNA secondary structure with a maximal base pair span.\nFor a sequence of length n and a base pair span of L the algorithm uses only\nO(n+L*L) memory and O(n*L*L) CPU time. Thus it is practical to “scan” very\nlarge genomes for short RNA structures. Output consists of a list of\nsecondary structure components of size <= L, one entry per line. Each\noutput line contains the predicted local structure its energy in\nkcal/mol and the starting position of the local structure.\n", - "homepage": "https://www.tbi.univie.ac.at/RNA/", - "documentation": "https://viennarna.readthedocs.io/en/latest/", - "doi": "10.1186/1748-7188-6-26", - "licence": [ - "custom" - ], - "identifier": "biotools:viennarna" - } - } - ], - "input": [ - { - "fasta": { - "type": "file", - "description": "A fasta file containing RNA or transcript sequences\n", - "pattern": "*.{fasta,fa}", - "ontologies": [] - } - } - ], - "output": { - "rnalfold_txt": [ - { - "*.lfold": { - "type": "file", - "description": "The text Output of RNALfold", - "pattern": "*.{lfold}", - "ontologies": [] - } - } - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@kokul-atx" - ], - "maintainers": [ - "@kokul-atx" - ] - } - }, - { - "name": "viralconsensus", - "path": "modules/nf-core/viralconsensus/meta.yml", - "type": "module", - "meta": { - "name": "viralconsensus", - "description": "Fast and memory-efficient viral consensus genome sequence generation from read alignments", - "keywords": [ - "virus", - "genomics", - "consensus", - "bam", - "fasta" - ], - "tools": [ - { - "viralconsensus": { - "description": "ViralConsensus is a fast and memory-efficient tool for calling viral consensus genome sequences directly from read alignment data.", - "homepage": "https://github.com/niemasd/ViralConsensus", - "documentation": "https://github.com/niemasd/ViralConsensus#usage", - "tool_dev_url": "https://github.com/niemasd/ViralConsensus", - "doi": "10.1093/bioinformatics/btad317", - "licence": [ - "GPL-3.0-or-later" - ], - "identifier": "biotools:viralconsensus" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/SAM/CRAM file containing aligned reads", - "pattern": "*.{bam,sam,cram}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'sarscov2' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome sequence in FASTA format", - "pattern": "*.{fa,fasta,fna}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ], - { - "primer_bed": { - "type": "file", - "description": "Optional BED file with primer coordinates for trimming", - "pattern": "*.bed", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3003" - } - ] - } - }, - { - "save_pos_counts": { - "type": "boolean", - "description": "Save per-position counts to a TSV file\n" - } - }, - { - "save_ins_counts": { - "type": "boolean", - "description": "Save insertion counts to a JSON file\n" - } - } - ], - "output": { - "fasta": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.consensus.fa": { - "type": "file", - "description": "Consensus genome sequence in FASTA format", - "pattern": "*.consensus.fa", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ], - "pos_counts": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.pos_counts.tsv": { - "type": "file", - "description": "Per-position base counts (optional, enabled via save_pos_counts input)", - "pattern": "*.pos_counts.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "ins_counts": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.ins_counts.json": { - "type": "file", - "description": "Insertion counts (optional, enabled via save_ins_counts input)", - "pattern": "*.ins_counts.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "versions_viralconsensus": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "viralconsensus": { - "type": "string", - "description": "The tool name" - } - }, - { - "viral_consensus --version | sed 's/.*v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "viralconsensus": { - "type": "string", - "description": "The tool name" - } - }, - { - "viral_consensus --version | sed 's/.*v//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@niemasd" - ], - "maintainers": [ - "@niemasd", - "@lucaspatel" - ] - } - }, - { - "name": "vireo", - "path": "modules/nf-core/vireo/meta.yml", - "type": "module", - "meta": { - "name": "vireo", - "description": "Use vireo to perform donor deconvolution for multiplexed scRNA-seq data", - "keywords": [ - "genotype-based demultiplexing", - "donor deconvolution", - "cellsnp" - ], - "tools": [ - { - "vireo": { - "description": "vireoSNP - donor deconvolution for multiplexed scRNA-seq data", - "homepage": "https://vireosnp.readthedocs.io/en/latest/", - "documentation": "https://vireosnp.readthedocs.io/en/latest/", - "tool_dev_url": "https://github.com/single-cell-genetics/vireo", - "doi": "10.1186/s13059-019-1865-2", - "licence": [ - "Apache-2.0" - ], - "identifier": "biotools:Vireo" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } - }, - { - "cell_data": { - "type": "file", - "description": "The cell genotype file in VCF format or cellSNP folder with sparse matrices.", - "pattern": "*.vcf|*/", - "ontologies": [] - } - }, - { - "n_donor": { - "type": "integer", - "description": "Number of donors to demultiplex." - } - }, - { - "donor_file": { - "type": "file", - "description": "The optional donor genotype file in VCF format.", - "pattern": "*.vcf", - "ontologies": [] - } - }, - { - "vartrix_data": { - "type": "file", - "description": "The optional cell genotype files in vartrix outputs.", - "ontologies": [] - } - } - ] - ], - "output": { - "summary": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*_summary.tsv": { - "type": "file", - "description": "Summary tsv file of deconvolution result.", - "pattern": "*_summary.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "donor_ids": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*_donor_ids.tsv": { - "type": "file", - "description": "Donor assignment with detailed statistics.", - "pattern": "*_donor_ids.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "prob_singlets": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*_prob_singlet.tsv.gz": { - "type": "file", - "description": "contains probability of classifing singlets", - "pattern": "*_prob_singlet.tsv.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "prob_doublets": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*_prob_doublet.tsv.gz": { - "type": "file", - "description": "contains probability of classifing doublets", - "pattern": "*_prob_doublet.tsv.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "genotype_vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*_GT_donors.vireo.vcf.gz": { - "type": "file", - "description": "contains vireo’s inferred donor genotypes at each SNP (only created if `--forceLearnGT` is set in `ext.args`, see n)", - "pattern": "*_GT_donors.vireo.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - } - ] - } - } - ] - ], - "filtered_variants": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*_filtered_variants.tsv": { - "type": "file", - "description": "contains the minimal set of discriminatory variants created by `GTbarcode` (only created if `--forceLearnGT` is set in `ext.args`, see the hadge pipeline as an example, and only shows consistent results if `--randSeed` is set)", - "pattern": "*_filtered_variants.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@mari-ga", - "@maxozo", - "@wxicu", - "@Zethson" - ], - "maintainers": [ - "@mari-ga", - "@maxozo", - "@wxicu", - "@Zethson" - ] - } - }, - { - "name": "virusrecom", - "path": "modules/nf-core/virusrecom/meta.yml", - "type": "module", - "meta": { - "name": "virusrecom", - "description": "Information-theory-based method for recombination detection of viral lineages using weighted information content (WIC).", - "keywords": [ - "recombination", - "virus", - "genomics", - "phylogenetics" - ], - "tools": [ - { - "virusrecom": { - "description": "An information-theory-based method for recombination detection of viral lineages.", - "homepage": "https://github.com/ZhijianZhou01/virusrecom", - "documentation": "https://github.com/ZhijianZhou01/virusrecom", - "tool_dev_url": "https://github.com/ZhijianZhou01/virusrecom", - "doi": "10.1093/bib/bbac513", - "licence": [ - "GPL v3" - ], - "identifier": "biotools:virusrecom" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "alignment": { - "type": "file", - "description": "Aligned FASTA file containing viral sequences. Use [] when providing iwic input.", - "pattern": "*.{fasta,fa,fna,fas}", - "ontologies": [] - } - }, - { - "mapping": { - "type": "file", - "description": "Tab-separated file mapping sequence names to lineages", - "pattern": "*.{txt,tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - }, - { - "iwic": { - "type": "file", - "description": "Optional CSV file containing pre-computed WIC values. Use [] to skip.", - "pattern": "*.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ], - { - "query": { - "type": "string", - "description": "Name of the query lineage to test for recombination (e.g. query_recombinant). Use auto to scan all lineages." - } - } - ], - "output": { - "results": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}/": { - "type": "directory", - "description": "Directory containing virusrecom output files including WIC plots and recombination tables" - } - } - ] - ], - "versions_virusrecom": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "virusrecom": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "virusrecom -h 2>&1 | sed -n 's/.*Version: \\([^ ]*\\).*/\\1/p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "virusrecom": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "virusrecom -h 2>&1 | sed -n 's/.*Version: \\([^ ]*\\).*/\\1/p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@haggaikelisha-ai" - ], - "maintainers": [ - "@haggaikelisha-ai" - ] - } - }, - { - "name": "vizgenpostprocessing_compiletilesegmentation", - "path": "modules/nf-core/vizgenpostprocessing/compiletilesegmentation/meta.yml", - "type": "module", - "meta": { - "name": "vizgenpostprocessing_compiletilesegmentation", - "description": "The module compiles segmentation tiles using Vizgen's post-processing tool.", - "keywords": [ - "vpt", - "vizgen", - "segmentation", - "microscopy", - "spatial transcriptomics" - ], - "tools": [ - { - "vizgenpostprocessing": { - "description": "Vizgen's post-processing tool", - "homepage": "https://github.com/Vizgen/vizgen-postprocessing", - "documentation": "https://vizgen.github.io/vizgen-postprocessing", - "tool_dev_url": "https://github.com/Vizgen/vizgen-postprocessing", - "licence": [ - "Apache-2.0" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample1', single_end:false ]\n" - } - }, - { - "input_images": { - "type": "directory", - "description": "Path to the input images directory to be used for segmentation.\n", - "ontologies": [ - { - "edam": "http://edamontology.org/data_1049" - } - ] - } - }, - { - "segmentation_params": { - "type": "file", - "description": "Path to the segmentation parameters (algorithm specification) JSON\nfile generated by the preparesegmentation module.\n", - "pattern": "*.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ], - { - "algorithm_json": { - "type": "file", - "description": "JSON file containing the algorithm parameters.", - "pattern": "*.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - }, - { - "segmentation_tiles": { - "type": "file", - "description": "Parquet files containing the segmentation results for tiles to compile.\n", - "pattern": "*.parquet", - "ontologies": [] - } - } - ], - "output": { - "mosaic_space": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "${prefix}/*_mosaic_space.parquet": { - "type": "file", - "description": "Parquet file containing the compiled segmentation results in mosaic space.\n", - "ontologies": [] - } - } - ] - ], - "micron_space": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "${prefix}/*_micron_space.parquet": { - "type": "file", - "description": "Parquet file containing the compiled segmentation results in micron space.\n", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@mcmero" - ], - "maintainers": [ - "@mcmero" - ] - } - }, - { - "name": "vizgenpostprocessing_preparesegmentation", - "path": "modules/nf-core/vizgenpostprocessing/preparesegmentation/meta.yml", - "type": "module", - "meta": { - "name": "vizgenpostprocessing_preparesegmentation", - "description": "The module prepares the specification JSON file for Vizgen's post-processing tool\ncell segmentation workflow.\n", - "keywords": [ - "vpt", - "vizgen", - "segmentation", - "microscopy", - "spatial transcriptomics" - ], - "tools": [ - { - "vizgenpostprocessing": { - "description": "Vizgen's post-processing tool", - "homepage": "https://github.com/Vizgen/vizgen-postprocessing", - "documentation": "https://vizgen.github.io/vizgen-postprocessing", - "tool_dev_url": "https://github.com/Vizgen/vizgen-postprocessing", - "licence": [ - "Apache-2.0" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample1', single_end:false ]\n" - } - }, - { - "input_images": { - "type": "directory", - "description": "Path to the input images directory to be used for segmentation.\n", - "ontologies": [ - { - "edam": "http://edamontology.org/data_1049" - } - ] - } - }, - { - "um_to_mosaic_file": { - "type": "file", - "description": "Path to the micron-to-mosaic pixel transform matrix file.\n", - "pattern": "*.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - } - ], - { - "algorithm_json": { - "type": "file", - "description": "JSON file containing the algorithm specification", - "pattern": "*.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - }, - { - "images_regex": { - "type": "string", - "description": "Can either be blank to match files by MERSCOPE convention, or a\npython formatting string specifying the file name (e.g.,\nimage_{stain}_z{z}.tif), or a regular expression matching the tiff\nfiles to be used (e.g., mosaic_(?P[\\w|-]+)_z(?P[0-9]+).tif)\n", - "ontologies": [ - { - "edam": "http://edamontology.org/data_1352" - } - ] - } - } - ], - "output": { - "segmentation_files": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "${prefix}/*.json": { - "type": "file", - "description": "Segmentation specification JSON file", - "pattern": "*.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@mcmero" - ], - "maintainers": [ - "@mcmero" - ] - } - }, - { - "name": "vizgenpostprocessing_runsegmentationontile", - "path": "modules/nf-core/vizgenpostprocessing/runsegmentationontile/meta.yml", - "type": "module", - "meta": { - "name": "vizgenpostprocessing_runsegmentationontile", - "description": "The module runs the segmentation algorithm on a specific tile using Vizgen's\npost-processing tool.\n", - "keywords": [ - "vpt", - "vizgen", - "segmentation", - "microscopy", - "spatial transcriptomics" - ], - "tools": [ - { - "vizgenpostprocessing": { - "description": "Vizgen's post-processing tool", - "homepage": "https://github.com/Vizgen/vizgen-postprocessing", - "documentation": "https://vizgen.github.io/vizgen-postprocessing", - "tool_dev_url": "https://github.com/Vizgen/vizgen-postprocessing", - "licence": [ - "Apache-2.0" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample1', single_end:false ]\n" - } - }, - { - "input_images": { - "type": "directory", - "description": "Path to the input images directory to be used for segmentation.\n", - "ontologies": [ - { - "edam": "http://edamontology.org/data_1049" - } - ] - } - }, - { - "segmentation_params": { - "type": "file", - "description": "Path to the segmentation parameters (algorithm specification) JSON\nfile generated by the preparesegmentation module.\n", - "pattern": "*.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - }, - { - "tile_index": { - "type": "integer", - "description": "The index of the tile to run the segmentation algorithm on.\n" - } - } - ], - { - "algorithm_json": { - "type": "file", - "description": "JSON file containing the algorithm parameters.", - "pattern": "*.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - }, - { - "custom_weights": { - "type": "directory", - "description": "Directory containing custom weights for the segmentation algorithm.\nMust be defined in the algorithm JSON file under \"custom_weights\"\nas directory name only (not full path).\n" - } - } - ], - "output": { - "segmented_tile": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "${prefix}/result_tiles/*.parquet": { - "type": "file", - "description": "Parquet file containing the segmentation results for the specified tile.\n", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@mcmero" - ], - "maintainers": [ - "@mcmero" - ] - } - }, - { - "name": "vrhyme_extractunbinned", - "path": "modules/nf-core/vrhyme/extractunbinned/meta.yml", - "type": "module", - "meta": { - "name": "vrhyme_extractunbinned", - "description": "Extracting sequences that were unbinnned by vRhyme into a FASTA file", - "keywords": [ - "bin", - "binning", - "link", - "vrhyme", - "extractunbinned" - ], - "tools": [ - { - "vrhyme": { - "description": "vRhyme functions by utilizing coverage variance comparisons and supervised machine learning classification of sequence features to construct viral metagenome-assembled genomes (vMAGs).", - "homepage": "https://github.com/AnantharamanLab/vRhyme", - "documentation": "https://github.com/AnantharamanLab/vRhyme", - "tool_dev_url": "https://github.com/AnantharamanLab/vRhyme", - "doi": "10.1093/nar/gkac341", - "licence": [ - "GPL v3 license", - "GPL v3" - ], - "identifier": "biotools:vrhyme" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "membership": { - "type": "file", - "description": "TSV file containing information regarding which bins input sequences were placed information", - "pattern": "*.{tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing information related to the fasta\ne.g. [ id:'test' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA file containing contigs/scaffolds input into vRhyme", - "pattern": "*.{fasta,fna,fa,fasta.gz,fna.gz,fa.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ], - "output": { - "unbinned_sequences": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.fasta": { - "type": "file", - "description": "FASTA file containing unbinned sequences", - "pattern": "*_unbinned_sequences.fasta", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@CarsonJM" - ], - "maintainers": [ - "@CarsonJM" - ] - } - }, - { - "name": "vrhyme_linkbins", - "path": "modules/nf-core/vrhyme/linkbins/meta.yml", - "type": "module", - "meta": { - "name": "vrhyme_linkbins", - "description": "Linking bins output by vRhyme to create one sequences per bin", - "keywords": [ - "bin", - "binning", - "link", - "vrhyme", - "linkbins" - ], - "tools": [ - { - "vrhyme": { - "description": "vRhyme functions by utilizing coverage variance comparisons and supervised machine learning classification of sequence features to construct viral metagenome-assembled genomes (vMAGs).", - "homepage": "https://github.com/AnantharamanLab/vRhyme", - "documentation": "https://github.com/AnantharamanLab/vRhyme", - "tool_dev_url": "https://github.com/AnantharamanLab/vRhyme", - "doi": "10.1093/nar/gkac341", - "licence": [ - "GPL v3 license", - "GPL v3" - ], - "identifier": "biotools:vrhyme" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "bins": { - "type": "directory", - "description": "Directory file containing bin FASTA files output by vRhyme (each bin having multiple sequences)" - } - } - ] - ], - "output": { - "linked_bins": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*_linked_bins.fasta": { - "type": "file", - "description": "FASTA file containing all bins that have been linked by N's", - "pattern": "*_linked_bins.fasta", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@CarsonJM" - ], - "maintainers": [ - "@CarsonJM" - ] - } - }, - { - "name": "vrhyme_vrhyme", - "path": "modules/nf-core/vrhyme/vrhyme/meta.yml", - "type": "module", - "meta": { - "name": "vrhyme_vrhyme", - "description": "Binning virus genomes from metagenomes", - "keywords": [ - "binning", - "bin", - "phage", - "virus", - "vrhyme" - ], - "tools": [ - { - "vrhyme": { - "description": "vRhyme functions by utilizing coverage variance comparisons and supervised machine learning classification of sequence features to construct viral metagenome-assembled genomes (vMAGs).", - "homepage": "https://github.com/AnantharamanLab/vRhyme", - "documentation": "https://github.com/AnantharamanLab/vRhyme", - "tool_dev_url": "https://github.com/AnantharamanLab/vRhyme", - "doi": "10.1093/nar/gkac341", - "licence": [ - "GPL v3", - "GPL v3 license" - ], - "identifier": "biotools:vrhyme" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "reads": { - "type": "file", - "description": "Preprocessed FASTQ file containing sample reads", - "pattern": "*.{fastq}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing fasta information\ne.g. [ id:'test']\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Contigs/scaffolds identified as viral", - "pattern": "*.{fna,fasta,fa,fasta.gz,fa.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ], - "output": { - "bins": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "vRhyme_best_bins_fasta/": { - "type": "directory", - "description": "Directory containing bin FASTA files", - "pattern": "**/vRhyme_best_bins_fasta/" - } - } - ] - ], - "membership": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "**/vRhyme_best_bins.*.membership.tsv": { - "type": "file", - "description": "TSV file describing the contig/scaffold membership of each bin", - "pattern": "vRhyme_best_bins.*.membership.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "summary": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "**/vRhyme_best_bins.*.summary.tsv": { - "type": "file", - "description": "TSV file summarizing the attributes of each bin", - "pattern": "vRhyme_best_bins.*.summary.tsv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@CarsonJM" - ], - "maintainers": [ - "@CarsonJM" - ] - }, - "pipelines": [ - { - "name": "viralmetagenome", - "version": "1.1.1" - } - ] - }, - { - "name": "vsearch_cluster", - "path": "modules/nf-core/vsearch/cluster/meta.yml", - "type": "module", - "meta": { - "name": "vsearch_cluster", - "description": "Cluster sequences using a single-pass, greedy centroid-based clustering algorithm.", - "keywords": [ - "vsearch", - "clustering", - "microbiome" - ], - "tools": [ - { - "vsearch": { - "description": "VSEARCH is a versatile open-source tool for microbiome analysis, including chimera detection, clustering, dereplication and rereplication, extraction, FASTA/FASTQ/SFF file processing, masking, orienting, pair-wise alignment, restriction site cutting, searching, shuffling, sorting, subsampling, and taxonomic classification of amplicon sequences for metagenomics, genomics, and population genetics. (USEARCH alternative)", - "homepage": "https://github.com/torognes/vsearch", - "documentation": "https://github.com/torognes/vsearch/releases/download/v2.31.0/vsearch_manual.pdf", - "tool_dev_url": "https://github.com/torognes/vsearch", - "doi": "10.7717/peerj.2584", - "licence": [ - "GPL v3-or-later OR BSD-2-clause" - ], - "identifier": "biotools:vsearch" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test' ]" - } - }, - { - "fasta": { - "type": "file", - "description": "Sequences to cluster in FASTA format", - "pattern": "*.{fasta,fa,fasta.gz,fa.gz}", - "ontologies": [] - } - } - ] - ], - "output": { - "aln": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.aln.gz": { - "type": "file", - "description": "Results in pairwise alignment format", - "pattern": "*.aln.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "biom": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.biom.gz": { - "type": "file", - "description": "Results in an OTU table in the biom version 1.0 file format", - "pattern": "*.biom.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "mothur": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.mothur.tsv.gz": { - "type": "file", - "description": "Results in an OTU table in the mothur ’shared’ tab-separated plain text file format", - "pattern": "*.mothur.tsv.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "otu": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.otu.tsv.gz": { - "type": "file", - "description": "Results in an OTU table in the classic tab-separated plain text format", - "pattern": "*.otu.tsv.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "Results written in bam format", - "pattern": "*.bam", - "ontologies": [] - } - } - ] - ], - "out": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.out.tsv.gz": { - "type": "file", - "description": "Results in tab-separated output, columns defined by user", - "pattern": "*.out.tsv.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "blast": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.blast.tsv.gz": { - "type": "file", - "description": "Tab delimited results in blast-like tabular format", - "pattern": "*.blast.tsv.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "uc": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.uc.tsv.gz": { - "type": "file", - "description": "Tab delimited results in a uclust-like format with 10 columns", - "pattern": "*.uc.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "centroids": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.centroids.fasta.gz": { - "type": "file", - "description": "Centroid sequences in FASTA format", - "pattern": "*.centroids.fasta.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "clusters": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.clusters.fasta*.gz": { - "type": "file", - "description": "Clustered sequences in FASTA format", - "pattern": "*.clusters.fasta*.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "profile": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.profile.txt.gz": { - "type": "file", - "description": "Profile of the clustering results", - "pattern": "*.profile.txt.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "msa": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "*.msa.fasta.gz": { - "type": "file", - "description": "Multiple sequence alignment of the centroids", - "pattern": "*.msa.fasta.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "versions_vsearch": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "vsearch": { - "type": "string", - "description": "The tool name" - } - }, - { - "vsearch --version 2>&1 | sed -n \"1s/.*v\\([0-9.]*\\).*/\\\\1/p\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ], - "versions_samtools": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "vsearch": { - "type": "string", - "description": "The tool name" - } - }, - { - "vsearch --version 2>&1 | sed -n \"1s/.*v\\([0-9.]*\\).*/\\\\1/p\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ], - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "samtools": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "samtools version | sed '1!d;s/.* //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@mirpedrol" - ], - "maintainers": [ - "@mirpedrol" - ] - }, - "pipelines": [ - { - "name": "ampliseq", - "version": "2.17.0" - }, - { - "name": "crisprseq", - "version": "2.3.0" - }, - { - "name": "viralmetagenome", - "version": "1.1.1" - } - ] - }, - { - "name": "vsearch_dereplicate", - "path": "modules/nf-core/vsearch/dereplicate/meta.yml", - "type": "module", - "meta": { - "name": "vsearch_dereplicate", - "description": "Merge strictly identical sequences contained in filename. Identical sequences are defined as having the same length and the same string of nucleotides (case insensitive, T and U are considered the same).", - "keywords": [ - "vsearch/dereplicate", - "vsearch", - "dereplicate", - "amplicon sequences", - "metagenomics", - "genomics", - "population genetics" - ], - "tools": [ - { - "vsearch": { - "description": "A versatile open source tool for metagenomics (USEARCH alternative)", - "homepage": "https://github.com/torognes/vsearch", - "documentation": "https://github.com/torognes/vsearch/releases/download/v2.31.0/vsearch_manual.pdf", - "tool_dev_url": "https://github.com/torognes/vsearch", - "doi": "10.7717/peerj.2584", - "licence": [ - "GPL v3-or-later OR BSD-2-clause" - ], - "identifier": "biotools:vsearch" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test' ]" - } - }, - { - "fasta": { - "type": "file", - "description": "Sequences to be sorted in FASTA format", - "pattern": "*.{fasta,fa,fasta.gz,fa.gz,.fna,.fna.gz}", - "ontologies": [] - } - } - ] - ], - "output": { - "fasta": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test']" - } - }, - { - "${prefix}.fasta": { - "type": "file", - "description": "dereplicated fasta", - "pattern": "${prefix}.fasta", - "ontologies": [] - } - } - ] - ], - "clustering": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test']" - } - }, - { - "${prefix}.uc": { - "type": "file", - "description": "dereplicated derep.uc file", - "pattern": "${prefix}.uc", - "ontologies": [] - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test']" - } - }, - { - "${prefix}.log": { - "type": "file", - "description": "a log file of the run", - "pattern": "${prefix}.log", - "ontologies": [] - } - } - ] - ], - "versions_vsearch": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "vsearch": { - "type": "string", - "description": "The tool name" - } - }, - { - "vsearch --version 2>&1 | sed -n \"1s/.*v\\([0-9.]*\\).*/\\\\1/p\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "vsearch": { - "type": "string", - "description": "The tool name" - } - }, - { - "vsearch --version 2>&1 | sed -n \"1s/.*v\\([0-9.]*\\).*/\\\\1/p\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@chriswyatt1" - ], - "maintainers": [ - "@chriswyatt1" - ] - } - }, - { - "name": "vsearch_fastqfilter", - "path": "modules/nf-core/vsearch/fastqfilter/meta.yml", - "type": "module", - "meta": { - "name": "vsearch_fastqfilter", - "description": "Performs quality filtering and / or conversion of a FASTQ file to FASTA format.", - "keywords": [ - "vsearch/fastqfilter", - "vsearch", - "fastqfilter", - "amplicon sequences", - "metagenomics", - "genomics", - "population genetics" - ], - "tools": [ - { - "vsearch": { - "description": "VSEARCH is a versatile open-source tool for microbiome analysis, including chimera detection, clustering, dereplication and rereplication, extraction, FASTA/FASTQ/SFF file processing, masking, orienting, pair-wise alignment, restriction site cutting, searching, shuffling, sorting, subsampling, and taxonomic classification of amplicon sequences for metagenomics, genomics, and population genetics. (USEARCH alternative)", - "homepage": "https://github.com/torognes/vsearch", - "documentation": "https://github.com/torognes/vsearch/releases/download/v2.31.0/vsearch_manual.pdf", - "tool_dev_url": "https://github.com/torognes/vsearch", - "doi": "10.7717/peerj.2584", - "licence": [ - "GPL v3-or-later OR BSD-2-clause" - ], - "identifier": "biotools:vsearch" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'sample1']" - } - }, - { - "fastq": { - "type": "file", - "description": "FASTQ file to filter", - "pattern": "*.{fastq,fq,fastq.gz,fq.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "output": { - "fasta": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'sample1']" - } - }, - { - "*.fasta": { - "type": "file", - "description": "Filtered FASTA file", - "pattern": "*.fasta", - "ontologies": [] - } - } - ] - ], - "log": [ - { - "*.log": { - "type": "file", - "description": "Log file of the run", - "pattern": "*.log", - "ontologies": [] - } - } - ], - "versions_vsearch": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "vsearch": { - "type": "string", - "description": "The tool name" - } - }, - { - "vsearch --version 2>&1 | sed -n \"1s/.*v\\([0-9.]*\\).*/\\\\1/p\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "vsearch": { - "type": "string", - "description": "The tool name" - } - }, - { - "vsearch --version 2>&1 | sed -n \"1s/.*v\\([0-9.]*\\).*/\\\\1/p\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@FernandoDuarteF" - ], - "maintainers": [ - "@FernandoDuarteF" - ] - } - }, - { - "name": "vsearch_sintax", - "path": "modules/nf-core/vsearch/sintax/meta.yml", - "type": "module", - "meta": { - "name": "vsearch_sintax", - "description": "Taxonomic classification using the sintax algorithm.", - "keywords": [ - "vsearch", - "sintax", - "taxonomy" - ], - "tools": [ - { - "vsearch": { - "description": "VSEARCH is a versatile open-source tool for microbiome analysis, including chimera detection, clustering, dereplication and rereplication, extraction, FASTA/FASTQ/SFF file processing, masking, orienting, pair-wise alignment, restriction site cutting, searching, shuffling, sorting, subsampling, and taxonomic classification of amplicon sequences for metagenomics, genomics, and population genetics. (USEARCH alternative)", - "homepage": "https://github.com/torognes/vsearch", - "documentation": "https://github.com/torognes/vsearch/releases/download/v2.31.0/vsearch_manual.pdf", - "tool_dev_url": "https://github.com/torognes/vsearch", - "doi": "10.7717/peerj.2584", - "licence": [ - "GPL v3-or-later OR BSD-2-clause" - ], - "identifier": "biotools:vsearch" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing query file information e.g. [ id:'test']" - } - }, - { - "queryfasta": { - "type": "file", - "description": "Query sequences in FASTA or FASTQ format", - "pattern": "*.{fasta,fa,fna,faa,fastq,fq}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ], - { - "db": { - "type": "file", - "description": "Reference database file in FASTA or UDB format", - "pattern": "*", - "ontologies": [] - } - } - ], - "output": { - "tsv": [ - [ - { - "meta": { - "type": "file", - "description": "Results written to tab-delimited file", - "pattern": "*.{tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - }, - { - "*.tsv": { - "type": "file", - "description": "Results written to tab-delimited file", - "pattern": "*.{tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_vsearch": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "vsearch": { - "type": "string", - "description": "The tool name" - } - }, - { - "vsearch --version 2>&1 | sed -n \"1s/.*v\\([0-9.]*\\).*/\\\\1/p\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "vsearch": { - "type": "string", - "description": "The tool name" - } - }, - { - "vsearch --version 2>&1 | sed -n \"1s/.*v\\([0-9.]*\\).*/\\\\1/p\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@jtangrot" - ], - "maintainers": [ - "@jtangrot" - ] - }, - "pipelines": [ - { - "name": "ampliseq", - "version": "2.17.0" - } - ] - }, - { - "name": "vsearch_sort", - "path": "modules/nf-core/vsearch/sort/meta.yml", - "type": "module", - "meta": { - "name": "vsearch_sort", - "description": "Sort fasta entries by decreasing abundance (--sortbysize) or sequence length (--sortbylength).", - "keywords": [ - "vsearch/sort", - "vsearch", - "sort", - "amplicon sequences", - "metagenomics", - "genomics", - "population genetics" - ], - "tools": [ - { - "vsearch": { - "description": "VSEARCH is a versatile open-source tool for microbiome analysis, including chimera detection, clustering, dereplication and rereplication, extraction, FASTA/FASTQ/SFF file processing, masking, orienting, pair-wise alignment, restriction site cutting, searching, shuffling, sorting, subsampling, and taxonomic classification of amplicon sequences for metagenomics, genomics, and population genetics. (USEARCH alternative)", - "homepage": "https://github.com/torognes/vsearch", - "documentation": "https://github.com/torognes/vsearch/releases/download/v2.31.0/vsearch_manual.pdf", - "tool_dev_url": "https://github.com/torognes/vsearch", - "doi": "10.7717/peerj.2584", - "licence": [ - "GPL v3-or-later OR BSD-2-clause" - ], - "identifier": "biotools:vsearch" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test' ]" - } - }, - { - "fasta": { - "type": "file", - "description": "Sequences to be sorted in FASTA format", - "pattern": "*.{fasta,fa,fasta.gz,fa.gz}", - "ontologies": [] - } - } - ], - { - "sort_arg": { - "type": "string", - "description": "Argument to provide to sort algorithm. Sort by abundance with --sortbysize or by sequence length with --sortbylength.", - "enum": [ - "--sortbysize", - "--sortbylength" - ] - } - } - ], - "output": { - "fasta": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.fasta": { - "type": "file", - "description": "Sorted FASTA file", - "pattern": "*.{fasta}", - "ontologies": [] - } - } - ] - ], - "versions_vsearch": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "vsearch": { - "type": "string", - "description": "The tool name" - } - }, - { - "vsearch --version 2>&1 | sed -n \"1s/.*v\\([0-9.]*\\).*/\\\\1/p\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "vsearch": { - "type": "string", - "description": "The tool name" - } - }, - { - "vsearch --version 2>&1 | sed -n \"1s/.*v\\([0-9.]*\\).*/\\\\1/p\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@mirpedrol" - ], - "maintainers": [ - "@mirpedrol" - ] - }, - "pipelines": [ - { - "name": "crisprseq", - "version": "2.3.0" - } - ] - }, - { - "name": "vsearch_usearchglobal", - "path": "modules/nf-core/vsearch/usearchglobal/meta.yml", - "type": "module", - "meta": { - "name": "vsearch_usearchglobal", - "description": "Compare target sequences to fasta-formatted query sequences using global pairwise alignment.", - "keywords": [ - "vsearch", - "usearch", - "alignment", - "fasta" - ], - "tools": [ - { - "vsearch": { - "description": "VSEARCH is a versatile open-source tool for microbiome analysis, including chimera detection, clustering, dereplication and rereplication, extraction, FASTA/FASTQ/SFF file processing, masking, orienting, pair-wise alignment, restriction site cutting, searching, shuffling, sorting, subsampling, and taxonomic classification of amplicon sequences for metagenomics, genomics, and population genetics. (USEARCH alternative)", - "homepage": "https://github.com/torognes/vsearch", - "documentation": "https://github.com/torognes/vsearch/releases/download/v2.31.0/vsearch_manual.pdf", - "tool_dev_url": "https://github.com/torognes/vsearch", - "doi": "10.7717/peerj.2584", - "licence": [ - "GPL v3-or-later OR BSD-2-clause" - ], - "identifier": "biotools:vsearch" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test' ]" - } - }, - { - "queryfasta": { - "type": "file", - "description": "Query sequences in FASTA format", - "pattern": "*.{fasta,fa,fna,faa}", - "ontologies": [] - } - } - ], - { - "db": { - "type": "file", - "description": "Reference database file in FASTA or UDB format", - "pattern": "*", - "ontologies": [] - } - }, - { - "idcutoff": { - "type": "float", - "description": "Reject the sequence match if the pairwise identity is lower than the given id cutoff value (value ranging from 0.0 to 1.0 included)" - } - }, - { - "outoption": { - "type": "string", - "description": "Specify the type of output file to be generated by selecting one of the vsearch output file options", - "pattern": "alnout|biomout|blast6out|mothur_shared_out|otutabout|samout|uc|userout|lcaout" - } - }, - { - "user_columns": { - "type": "string", - "description": "If using the `userout` option, specify which columns to include in output, with fields separated with `+` (e.g. query+target+id). See USEARCH manual for valid options. For other output options, use an empty string." - } - } - ], - "output": { - "aln": [ - [ - { - "meta": { - "type": "file", - "description": "Results in pairwise alignment format", - "pattern": "*.{aln}", - "ontologies": [] - } - }, - { - "*.aln": { - "type": "file", - "description": "Results in pairwise alignment format", - "pattern": "*.{aln}", - "ontologies": [] - } - } - ] - ], - "biom": [ - [ - { - "meta": { - "type": "file", - "description": "Results in pairwise alignment format", - "pattern": "*.{aln}", - "ontologies": [] - } - }, - { - "*.biom": { - "type": "file", - "description": "Results in an OTU table in the biom version 1.0 file format", - "pattern": "*.{biom}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3746" - } - ] - } - } - ] - ], - "lca": [ - [ - { - "meta": { - "type": "file", - "description": "Results in pairwise alignment format", - "pattern": "*.{aln}", - "ontologies": [] - } - }, - { - "*.lca": { - "type": "file", - "description": "Last common ancestor (LCA) information about the hits of each query in tab-separated format", - "pattern": "*.{lca}", - "ontologies": [] - } - } - ] - ], - "mothur": [ - [ - { - "meta": { - "type": "file", - "description": "Results in pairwise alignment format", - "pattern": "*.{aln}", - "ontologies": [] - } - }, - { - "*.mothur": { - "type": "file", - "description": "Results in an OTU table in the mothur ’shared’ tab-separated plain text file format", - "pattern": "*.{mothur}", - "ontologies": [] - } - } - ] - ], - "otu": [ - [ - { - "meta": { - "type": "file", - "description": "Results in pairwise alignment format", - "pattern": "*.{aln}", - "ontologies": [] - } - }, - { - "*.otu": { - "type": "file", - "description": "Results in an OTU table in the classic tab-separated plain text format", - "pattern": "*.{otu}", - "ontologies": [] - } - } - ] - ], - "sam": [ - [ - { - "meta": { - "type": "file", - "description": "Results in pairwise alignment format", - "pattern": "*.{aln}", - "ontologies": [] - } - }, - { - "*.sam": { - "type": "file", - "description": "Results written in sam format", - "pattern": "*.{sam}", - "ontologies": [] - } - } - ] - ], - "tsv": [ - [ - { - "meta": { - "type": "file", - "description": "Results in pairwise alignment format", - "pattern": "*.{aln}", - "ontologies": [] - } - }, - { - "*.tsv": { - "type": "file", - "description": "Results in tab-separated output, columns defined by user", - "pattern": "*.{tsv}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "txt": [ - [ - { - "meta": { - "type": "file", - "description": "Results in pairwise alignment format", - "pattern": "*.{aln}", - "ontologies": [] - } - }, - { - "*.txt": { - "type": "file", - "description": "Tab delimited results in blast-like tabular format", - "pattern": "*.{txt}", - "ontologies": [] - } - } - ] - ], - "uc": [ - [ - { - "meta": { - "type": "file", - "description": "Results in pairwise alignment format", - "pattern": "*.{aln}", - "ontologies": [] - } - }, - { - "*.uc": { - "type": "file", - "description": "Tab delimited results in a uclust-like format with 10 columns", - "pattern": "*.{uc}", - "ontologies": [] - } - } - ] - ], - "versions_vsearch": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "vsearch": { - "type": "string", - "description": "The tool name" - } - }, - { - "vsearch --version 2>&1 | sed -n \"1s/.*v\\([0-9.]*\\).*/\\\\1/p\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "vsearch": { - "type": "string", - "description": "The tool name" - } - }, - { - "vsearch --version 2>&1 | sed -n \"1s/.*v\\([0-9.]*\\).*/\\\\1/p\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@jtangrot" - ], - "maintainers": [ - "@jtangrot" - ] - }, - "pipelines": [ - { - "name": "ampliseq", - "version": "2.17.0" - } - ] - }, - { - "name": "vt_decompose", - "path": "modules/nf-core/vt/decompose/meta.yml", - "type": "module", - "meta": { - "name": "vt_decompose", - "description": "decomposes multiallelic variants into biallelic in a VCF file.", - "keywords": [ - "decompose", - "multiallelic", - "small variants", - "snps", - "indels" - ], - "tools": [ - { - "vt": { - "description": "A tool set for short variant discovery in genetic sequence data", - "homepage": "https://genome.sph.umich.edu/wiki/Vt", - "documentation": "https://genome.sph.umich.edu/wiki/Vt", - "tool_dev_url": "https://github.com/atks/vt", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "vcf": { - "type": "file", - "description": "The VCF file to decompose", - "pattern": "*.vcf(.gz)?", - "ontologies": [] - } - }, - { - "intervals": { - "type": "file", - "description": "The intervals of the variants of decompose", - "pattern": "*.bed", - "ontologies": [] - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*.vcf.gz": { - "type": "file", - "description": "The decomposed VCF file", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@nvnieuwk" - ], - "maintainers": [ - "@nvnieuwk" - ] - }, - "pipelines": [ - { - "name": "rnadnavar", - "version": "dev" - } - ] - }, - { - "name": "vt_decomposeblocksub", - "path": "modules/nf-core/vt/decomposeblocksub/meta.yml", - "type": "module", - "meta": { - "name": "vt_decomposeblocksub", - "description": "Decomposes biallelic block substitutions into its constituent SNPs.", - "keywords": [ - "decomposeblocksub", - "multiallelic", - "small variants", - "snps", - "indels", - "block substitutions" - ], - "tools": [ - { - "vt": { - "description": "A tool set for short variant discovery in genetic sequence data", - "homepage": "https://genome.sph.umich.edu/wiki/Vt", - "documentation": "https://genome.sph.umich.edu/wiki/Vt", - "tool_dev_url": "https://github.com/atks/vt", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "vcf": { - "type": "file", - "description": "The VCF file to decompose", - "pattern": "*.vcf(.gz)?", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - } - ] - } - }, - { - "index": { - "type": "file", - "description": "The VCF file to decompose", - "pattern": "*.tbi", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3616" - } - ] - } - }, - { - "intervals": { - "type": "file", - "description": "The intervals of the variants of decompose", - "pattern": "*.bed", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3003" - } - ] - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*.vcf.gz": { - "type": "file", - "description": "The decomposed VCF file", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - }, - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@kubranarci" - ], - "maintainers": [ - "@kubranarci" - ] - } - }, - { - "name": "vt_normalize", - "path": "modules/nf-core/vt/normalize/meta.yml", - "type": "module", - "meta": { - "name": "vt_normalize", - "description": "normalizes variants in a VCF file", - "keywords": [ - "normalization", - "vcf", - "snps", - "indels" - ], - "tools": [ - { - "vt": { - "description": "A tool set for short variant discovery in genetic sequence data", - "homepage": "https://genome.sph.umich.edu/wiki/Vt", - "documentation": "https://genome.sph.umich.edu/wiki/Vt", - "tool_dev_url": "https://github.com/atks/vt", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "vcf": { - "type": "file", - "description": "The VCF file to normalize", - "pattern": "*.vcf(.gz)?", - "ontologies": [] - } - }, - { - "tbi": { - "type": "file", - "description": "The tabix index of the VCF file when bgzipped", - "pattern": "*.tbi", - "ontologies": [] - } - }, - { - "intervals": { - "type": "file", - "description": "The intervals of the variants of normalize", - "pattern": "*.bed", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference fasta file", - "pattern": "*.{fasta,fn,fna,fa}", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference index information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "fai": { - "type": "file", - "description": "The index of the reference fasta file (OPTIONAL)", - "pattern": "*.fai", - "ontologies": [] - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "*.vcf.gz": { - "type": "file", - "description": "The normalized VCF file", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "fai": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "${fasta}.fai": { - "type": "file", - "description": "The created index of the reference fasta file (only when the fai wasn't supplied)", - "pattern": "*.fai", - "ontologies": [] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@nvnieuwk" - ], - "maintainers": [ - "@nvnieuwk" - ] - }, - "pipelines": [ - { - "name": "rnadnavar", - "version": "dev" - } - ] - }, - { - "name": "vuegen", - "path": "modules/nf-core/vuegen/meta.yml", - "type": "module", - "meta": { - "name": "vuegen", - "description": "The VueGen nf-core module is designed to automate report generation from outputs produced by other modules, subworkflows, or pipelines. The module integrates the VueGen Python library and customizes it for compatibility with the Nextflow environment. VueGen automates the creation of reports from bioinformatics outputs, supporting formats like PDF, HTML, DOCX, ODT, PPTX, Reveal.js, Jupyter notebooks, and Streamlit web applications.\n", - "keywords": [ - "reports", - "data-visualization", - "streamlit", - "quarto" - ], - "tools": [ - { - "vuegen": { - "description": "The VueGen nf-core module is designed to automate report generation from outputs produced by other modules, subworkflows, or pipelines. The module integrates the VueGen Python library and customizes it for compatibility with the Nextflow environment. VueGen automates the creation of reports from bioinformatics outputs, supporting formats like PDF, HTML, DOCX, ODT, PPTX, Reveal.js, Jupyter notebooks, and Streamlit web applications.\n", - "homepage": "https://github.com/Multiomics-Analytics-Group/vuegen", - "documentation": "https://vuegen.readthedocs.io/", - "tool_dev_url": "https://github.com/Multiomics-Analytics-Group/vuegen", - "doi": "10.1101/2025.03.05.641152", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - { - "input_type": { - "type": "string", - "pattern": "^(config|directory)$", - "description": "Specifies whether the input is a configuration file ('config') or a directory ('directory')." - } - }, - { - "input_path": { - "type": "file", - "description": "Path to the input directory or configuration file used by VueGen.", - "ontologies": [] - } - }, - { - "report_type": { - "type": "string", - "pattern": "^(streamlit|html|pdf|docx|odt|revealjs|pptx|jupyter)$", - "description": "The type of report to generate. Options include 'streamlit', 'html', 'pdf', 'docx', 'odt', 'revealjs', 'pptx', and 'jupyter'." - } - } - ], - "output": { - "output_folder": [ - { - "*report": { - "type": "directory", - "description": "The output directory containing the generated report files.\n- If `report_type` is 'streamlit', a 'streamlit_report' directory is created, containing subfolders for each section with Python scripts corresponding to the web application's pages.\n- For other report types, a 'quarto_report' directory is generated, containing a Quarto Markdown (qmd) file that structures the entire report.\n", - "pattern": "*report" - } - } - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@sayalaruano", - "@enryH", - "@albsantosdel" - ], - "maintainers": [ - "@sayalaruano", - "@enryH", - "@albsantosdel" - ] - } - }, - { - "name": "wfmash", - "path": "modules/nf-core/wfmash/meta.yml", - "type": "module", - "meta": { - "name": "wfmash", - "description": "a pangenome-scale aligner", - "keywords": [ - "long read alignment", - "pangenome-scale", - "all versus all", - "mashmap", - "wavefront" - ], - "tools": [ - { - "wfmash": { - "description": "a pangenome-scale aligner", - "homepage": "https://github.com/waveygang/wfmash", - "documentation": "https://github.com/waveygang/wfmash", - "tool_dev_url": "https://github.com/waveygang/wfmash", - "doi": "10.5281/zenodo.6949373", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta_gz": { - "type": "file", - "description": "BGZIPPED FASTA target file to create the mappings from.", - "pattern": "{fa.gz,fna.gz,fasta.gz}", - "ontologies": [] - } - }, - { - "paf": { - "type": "file", - "description": "Optional inpute file in PAF format to derive the precise alignments for.", - "pattern": "*.{paf}", - "ontologies": [] - } - }, - { - "gzi": { - "type": "file", - "description": "The GZI index of the input FASTA file.", - "pattern": "*.{gzi}", - "ontologies": [] - } - }, - { - "fai": { - "type": "file", - "description": "The FASTA index of the input FASTA file.", - "pattern": "*.{fai}", - "ontologies": [] - } - } - ], - { - "query_self": { - "type": "boolean", - "description": "If set to true, the input FASTA will also be used as the query FASTA." - } - }, - { - "fasta_query_list": { - "type": "file", - "description": "Optional inpute file in FASTA format specifying the query sequences as a list.", - "pattern": "*.{fa,fna,fasta}", - "ontologies": [] - } - } - ], - "output": { - "paf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.paf": { - "type": "file", - "description": "Alignments in PAF format", - "pattern": "*.{paf}", - "ontologies": [] - } - } - ] - ], - "versions_wfmash": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "wfmash": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "wfmash --version 2>&1 | cut -f 1 -d \"-\" | cut -f 2 -d \"v\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "wfmash": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "wfmash --version 2>&1 | cut -f 1 -d \"-\" | cut -f 2 -d \"v\"": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@subwaystation" - ], - "maintainers": [ - "@subwaystation" - ] - }, - "pipelines": [ - { - "name": "pangenome", - "version": "1.1.3" - } - ] - }, - { - "name": "wget", - "path": "modules/nf-core/wget/meta.yml", - "type": "module", - "meta": { - "name": "wget", - "description": "The non-interactive network downloader", - "keywords": [ - "wget", - "download", - "network" - ], - "tools": [ - { - "wget": { - "description": "wget is a free utility for non-interactive download of files from the Web.", - "homepage": "https://www.gnu.org/software/wget/", - "documentation": "https://www.gnu.org/software/wget/manual/wget.html", - "licence": [ - "GPL" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "url": { - "type": "string", - "description": "URL to download", - "pattern": "^https?://*.*" - } - }, - { - "suffix": { - "type": "string", - "description": "Output suffix" - } - } - ] - ], - "output": { - "outfile": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "${prefix}.${suffix}": { - "type": "file", - "description": "Downloaded file", - "pattern": "*.*", - "ontologies": [] - } - } - ] - ], - "versions_wget": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "wget": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "wget --version | head -1 | cut -d \" \" -f 3": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "wget": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "wget --version | head -1 | cut -d \" \" -f 3": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@itrujnara" - ], - "maintainers": [ - "@itrujnara" - ] - }, - "pipelines": [ - { - "name": "magmap", - "version": "1.0.0" - } - ] - }, - { - "name": "wgsim", - "path": "modules/nf-core/wgsim/meta.yml", - "type": "module", - "meta": { - "name": "wgsim", - "description": "simulating sequence reads from a reference genome", - "keywords": [ - "simulate", - "fasta", - "reads" - ], - "tools": [ - { - "wgsim": { - "description": "simulating sequence reads from a reference genome", - "homepage": "https://github.com/lh3/wgsim", - "documentation": "https://github.com/lh3/wgsim", - "tool_dev_url": "https://github.com/lh3/wgsim", - "licence": [ - "MIT" - ], - "identifier": "biotools:wgsim" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Genome fasta file", - "pattern": "*.{fa,fasta}", - "ontologies": [] - } - } - ] - ], - "output": { - "fastq": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.fastq": { - "type": "file", - "description": "Simulated FASTQ read files", - "pattern": "*.{fastq}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1930" - } - ] - } - } - ] - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@priyanka-surana" - ], - "maintainers": [ - "@priyanka-surana" - ] - } - }, - { - "name": "whamg", - "path": "modules/nf-core/whamg/meta.yml", - "type": "module", - "meta": { - "name": "whamg", - "description": "The wham suite consists of two programs, wham and whamg. wham, the original tool, is a very sensitive method with a high false discovery rate. The second program, whamg, is more accurate and better suited for general structural variant (SV) discovery.", - "keywords": [ - "whamg", - "wham", - "vcf", - "bam", - "variant calling" - ], - "tools": [ - { - "whamg": { - "description": "Structural variant detection and association testing", - "homepage": "https://github.com/zeeev/wham", - "documentation": "https://github.com/zeeev/wham", - "tool_dev_url": "https://github.com/zeeev/wham", - "doi": "10.1371/journal.pcbi.1004572", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/SAM file", - "pattern": "*.{bam,sam}", - "ontologies": [] - } - }, - { - "bai": { - "type": "file", - "description": "BAM index file", - "pattern": "*.bai", - "ontologies": [] - } - } - ], - { - "fasta": { - "type": "file", - "description": "Reference Fasta file", - "pattern": "*.{fasta,fa}", - "ontologies": [] - } - }, - { - "fasta_fai": { - "type": "file", - "description": "Index of the reference Fasta", - "pattern": "*.fai", - "ontologies": [] - } - } - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.vcf.gz": { - "type": "file", - "description": "Compressed VCF file", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.vcf.gz.tbi": { - "type": "file", - "description": "Index of the VCF file", - "pattern": "*.vcf.gz.tbi", - "ontologies": [] - } - } - ] - ], - "graph": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.txt": { - "type": "file", - "description": "Graph file", - "pattern": "*.txt", - "ontologies": [] - } - } - ] - ], - "versions_whamg": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "whamg": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "whamg 2>&1 | sed -n 's/^Version: v\\([^-]*\\).*/\\1/p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "whamg": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "whamg 2>&1 | sed -n 's/^Version: v\\([^-]*\\).*/\\1/p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@nvnieuwk" - ], - "maintainers": [ - "@nvnieuwk" - ] - } - }, - { - "name": "whatshap_haplotag", - "path": "modules/nf-core/whatshap/haplotag/meta.yml", - "type": "module", - "meta": { - "name": "whatshap_haplotag", - "description": "Tag reads by haplotype", - "keywords": [ - "haplotypes", - "tagging", - "long-reads", - "nanopore", - "pacbio" - ], - "tools": [ - { - "whatshap": { - "description": "WhatsHap is a software for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly.", - "homepage": "https://whatshap.readthedocs.io", - "documentation": "https://whatshap.readthedocs.io", - "tool_dev_url": "https://github.com/whatshap/whatshap", - "doi": "10.1101/085050", - "licence": [ - "MIT" - ], - "identifier": "biotools:whatshap" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF file with phased variants (must be gzip-compressed and indexed)", - "pattern": "*.{vcf.gz}", - "ontologies": [] - } - }, - { - "tbi": { - "type": "file", - "description": "VCF index file", - "pattern": "*.{tbi,csi}", - "ontologies": [] - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM file with alignments to be tagged by haplotype", - "pattern": "*.{bam,cram}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - }, - { - "edam": "http://edamontology.org/format_2573" - } - ] - } - }, - { - "bai": { - "type": "file", - "description": "BAM index file", - "pattern": "*.bai", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference file. Must be accompanied by .fai index", - "pattern": "*.{fasta,fa}", - "ontologies": [] - } - } - ], - [ - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "fai": { - "type": "file", - "description": "Index for reference file.", - "pattern": "*.fai", - "ontologies": [] - } - } - ], - { - "include_tsv_output": { - "type": "boolean", - "description": "Whether to include TSV output file", - "default": false - } - } - ], - "output": { - "bam": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.bam": { - "type": "file", - "description": "BAM/CRAM/SAM file with tagged reads", - "pattern": "*.{bam,cram,sam}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_2572" - }, - { - "edam": "http://edamontology.org/format_2573" - }, - { - "edam": "http://edamontology.org/format_3462" - } - ] - } - } - ] - ], - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "*.{tsv,tsv.gz}": { - "type": "file", - "description": "Write assignments of read names to haplotypes (tab separated) to given output file. If filename ends in .gz, then output is gzipped.", - "pattern": "*.{tsv,tsv.gz}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - } - ] - ], - "versions_whatshap": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "whatshap": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "whatshap --version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "whatshap": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "whatshap --version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@sofiademmou" - ], - "maintainers": [ - "@sofiademmou" - ] - } - }, - { - "name": "whatshap_phase", - "path": "modules/nf-core/whatshap/phase/meta.yml", - "type": "module", - "meta": { - "name": "whatshap_phase", - "description": "Phase variants in a VCF file using long-read sequencing data", - "keywords": [ - "phasing", - "haplotypes", - "vcf", - "long-reads", - "nanopore", - "pacbio" - ], - "tools": [ - { - "whatshap": { - "description": "WhatsHap is a software for phasing genomic variants using DNA sequencing\nreads, also called read-based phasing or haplotype assembly.\n", - "homepage": "https://whatshap.readthedocs.io/", - "documentation": "https://whatshap.readthedocs.io/", - "tool_dev_url": "https://github.com/whatshap/whatshap", - "doi": "10.1101/085050", - "licence": [ - "MIT" - ] - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF file with unphased variants (can be gzipped)", - "pattern": "*.{vcf,vcf.gz}" - } - }, - { - "tbi": { - "type": "file", - "description": "VCF index file (optional but recommended)", - "pattern": "*.{tbi,csi}" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file with aligned reads", - "pattern": "*.bam" - } - }, - { - "bai": { - "type": "file", - "description": "BAM index file (optional but recommended)", - "pattern": "*.bai" - } - }, - { - "pedigree": { - "type": "file", - "description": "Pedigree file to improve phasing of multiple related individuals (optional)", - "pattern": "*.ped" - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome in FASTA format", - "pattern": "*.{fa,fasta}" - } - }, - { - "fai": { - "type": "file", - "description": "Reference genome index", - "pattern": "*.fai" - } - } - ] - ], - "output": { - "vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.vcf.gz": { - "type": "file", - "description": "Bgzipped phased VCF file", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.vcf.gz.tbi": { - "type": "file", - "description": "Phased VCF index file", - "pattern": "*.vcf.gz.tbi", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3616" - } - ] - } - } - ] - ], - "versions_whatshap": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "whatshap": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "whatshap --version": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "whatshap": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "whatshap --version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@haidyi" - ], - "maintainers": [ - "@haidyi" - ] - } - }, - { - "name": "whatshap_stats", - "path": "modules/nf-core/whatshap/stats/meta.yml", - "type": "module", - "meta": { - "name": "whatshap_stats", - "description": "Compute statistics from phased variant file using Whatshap", - "keywords": [ - "vcf", - "whatshap", - "stats", - "phasing", - "phase" - ], - "tools": [ - { - "whatshap": { - "description": "Phase genomic variants using DNA sequencing reads (haplotype assembly).", - "args_id": "$args", - "homepage": "https://whatshap.readthedocs.io", - "documentation": "https://whatshap.readthedocs.io", - "tool_dev_url": "https://github.com/whatshap/whatshap", - "doi": "10.1101/085050", - "licence": [ - "MIT" - ], - "identifier": "biotools:whatshap" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample1' ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "Phased variant vcf file", - "pattern": "*.vcf", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3016" - } - ] - } - } - ], - { - "include_tsv_output": { - "type": "boolean", - "description": "Whether to include TSV output file", - "default": false - } - }, - { - "include_gtf_output": { - "type": "boolean", - "description": "Whether to include GTF output file", - "default": false - } - }, - { - "inlude_block_output": { - "type": "boolean", - "description": "Whether to include block list output file", - "default": false - } - } - ], - "output": { - "tsv": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample1' ]\n" - } - }, - { - "${prefix}.tsv": { - "type": "file", - "description": "Whatshap stats output in TSV format", - "pattern": "*.tsv" - } - } - ] - ], - "gtf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample1' ]\n" - } - }, - { - "${prefix}.gtf": { - "type": "file", - "description": "Whatshap stats output in GTF format", - "pattern": "*.gtf" - } - } - ] - ], - "block": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample1' ]\n" - } - }, - { - "${prefix}.txt": { - "type": "file", - "description": "Whatshap stats block list output", - "pattern": "*.txt" - } - } - ] - ], - "log": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample1' ]\n" - } - }, - { - "${prefix}.log": { - "type": "file", - "description": "Whatshap stats output in TXT format", - "pattern": "*.log" - } - } - ] - ], - "versions_whatshap": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "whatshap": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "whatshap --version": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "whatshap": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "whatshap --version": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@eliottBo" - ], - "maintainers": [ - "@eliottBo" - ] - } - }, - { - "name": "windowmasker_convert", - "path": "modules/nf-core/windowmasker/convert/meta.yml", - "type": "module", - "meta": { - "name": "windowmasker_convert", - "description": "Masks out highly repetitive DNA sequences with low complexity in a genome", - "keywords": [ - "fasta", - "blast", - "windowmasker" - ], - "tools": [ - { - "windowmasker": { - "description": "A program to mask highly repetitive and low complexity DNA sequences within a genome.", - "homepage": "https://blast.ncbi.nlm.nih.gov/Blast.cgi", - "documentation": "ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/windowmasker/README.windowmasker", - "doi": "10.1016/S0022-2836(05)80360-2", - "licence": [ - "US-Government-Work" - ], - "identifier": "biotools:windowmasker" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "counts": { - "type": "file", - "description": "valid unit counts file", - "pattern": "*.{ascii,binary,oascii,obinary,txt}", - "ontologies": [] - } - } - ] - ], - "output": { - "converted": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${output}": { - "type": "file", - "description": "converted file", - "ontologies": [] - } - } - ] - ], - "versions_windowmasker": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "windowmasker": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "windowmasker -version-full | head -n 1 | sed 's/^.*windowmasker. //; s/ .*\\$//'": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "windowmasker": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "windowmasker -version-full | head -n 1 | sed 's/^.*windowmasker. //; s/ .*\\$//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@alxndrdiaz" - ], - "maintainers": [ - "@alxndrdiaz" - ] - } - }, - { - "name": "windowmasker_mkcounts", - "path": "modules/nf-core/windowmasker/mkcounts/meta.yml", - "type": "module", - "meta": { - "name": "windowmasker_mkcounts", - "description": "A program to generate frequency counts of repetitive units.", - "keywords": [ - "fasta", - "interval", - "windowmasker" - ], - "tools": [ - { - "windowmasker": { - "description": "A program to mask highly repetitive and low complexity DNA sequences within a genome.\n", - "homepage": "https://github.com/ncbi/ncbi-cxx-toolkit-public", - "documentation": "https://ncbi.github.io/cxx-toolkit/", - "licence": [ - "MIT" - ], - "identifier": "biotools:windowmasker" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "ref": { - "type": "file", - "description": "An input nucleotide fasta file.", - "ontologies": [] - } - } - ] - ], - "output": { - "counts": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "*.txt": { - "type": "file", - "description": "A file containing frequency counts of repetitive units.", - "pattern": "*.txt", - "ontologies": [] - } - } - ] - ], - "versions_windowmasker": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "windowmasker": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "windowmasker -version-full | head -n 1 | sed 's/^.*windowmasker. //; s/ .*\\$//'": { - "type": "string", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "windowmasker": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "windowmasker -version-full | head -n 1 | sed 's/^.*windowmasker. //; s/ .*\\$//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@DLBPointon" - ], - "maintainers": [ - "@DLBPointon" - ] - } - }, - { - "name": "windowmasker_ustat", - "path": "modules/nf-core/windowmasker/ustat/meta.yml", - "type": "module", - "meta": { - "name": "windowmasker_ustat", - "description": "A program to take a counts file and creates a file of genomic co-ordinates to be masked.", - "keywords": [ - "fasta", - "interval", - "windowmasker" - ], - "tools": [ - { - "windowmasker": { - "description": "A program to mask highly repetitive and low complexity DNA sequences within a genome.\n", - "homepage": "https://github.com/ncbi/ncbi-cxx-toolkit-public", - "documentation": "https://ncbi.github.io/cxx-toolkit/", - "licence": [ - "MIT" - ], - "identifier": "biotools:windowmasker" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "counts": { - "type": "file", - "description": "Contains count data of repetitive regions.", - "ontologies": [] - } - } - ], - [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "ref": { - "type": "file", - "description": "An input nucleotide fasta file.", - "ontologies": [] - } - } - ] - ], - "output": { - "intervals": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${output}": { - "type": "file", - "description": "intervals", - "ontologies": [] - } - } - ] - ], - "versions_windowmasker": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "windowmasker": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "windowmasker -version-full | head -n 1 | sed 's/^.*windowmasker. //; s/ .*\\$//'": { - 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} - }, - { - "blacklist": { - "type": "file", - "description": "OPTIONAL - A BED file containing blacklist regions (used mainly when the reference is small)", - "pattern": "*.bed", - "ontologies": [] - } - } - ] - ], - "output": { - "aberrations_bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", - "pattern": "*_aberrations.bed" - } - }, - { - "*_aberrations.bed": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", - "pattern": "*_aberrations.bed" - } - } - ] - ], - "bins_bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", - "pattern": "*_aberrations.bed" - } - }, - { - "*_bins.bed": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", - "pattern": "*_bins.bed" - } - } - ] - ], - "segments_bed": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", - "pattern": "*_aberrations.bed" - } - }, - { - "*_segments.bed": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", - "pattern": "*_segments.bed" - } - } - ] - ], - "chr_statistics": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", - "pattern": "*_aberrations.bed" - } - }, - { - "*_statistics.txt": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", - "pattern": "*_chr_statistics.txt" - } - } - ] - ], - "chr_plots": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", - "pattern": "*_aberrations.bed" - } - }, - { - "[!genome_wide]*.png": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", - "pattern": "[!genome_wide]*.png" - } - } - ] - ], - "genome_plot": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", - "pattern": "*_aberrations.bed" - } - }, - { - "genome_wide.png": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", - "pattern": "genome_wide.png" - } - } - ] - ], - "versions_wisecondorx": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "wisecondorx": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pip list |& sed -n 's/wisecondorx *//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "wisecondorx": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "pip list |& sed -n 's/wisecondorx *//p'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@nvnieuwk" - ], - "maintainers": [ - "@nvnieuwk" - ] - } - }, - { - "name": "wittyer", - "path": "modules/nf-core/wittyer/meta.yml", - "type": "module", - "meta": { - "name": "wittyer", - "description": "A large variant benchmarking tool analogous to hap.py for small variants.", - "keywords": [ - "structural-variants", - "benchmarking", - "vcf" - ], - "tools": [ - { - "wittyer": { - "description": "Illumina tool for large variant benchmarking", - "homepage": "https://github.com/Illumina/witty.er", - "documentation": "https://github.com/Illumina/witty.er", - "tool_dev_url": "https://github.com/Illumina/witty.er", - "licence": [ - "BSD-2" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "query_vcf": { - "type": "file", - "description": "A VCF with called variants to benchmark against the standard", - "pattern": "*.{vcf}", - "ontologies": [] - } - }, - { - "truth_vcf": { - "type": "file", - "description": "A standard VCF to compare against", - "pattern": "*.{vcf}", - "ontologies": [] - } - }, - { - "bed": { - "type": "file", - "description": "A BED file specifying regions to be included in the analysis (optional)", - "pattern": "*.bed", - "ontologies": [] - } - }, - { - "wittyer_config": { - "type": "file", - "description": "Config file in json format used to specify per variant type settings.\nUsed in place of include bed arguments. (optional)\n", - "pattern": "*.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "output": { - "report": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.json": { - "type": "file", - "description": "Detailed per-sample-pair, per-svtype, per-bin stats", - "pattern": "*.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "bench_vcf": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.vcf.gz": { - "type": "file", - "description": "Updated query and truth entries merged into one file", - "pattern": "*.vcf.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3989" - } - ] - } - } - ] - ], - "bench_vcf_tbi": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "*.vcf.gz.tbi": { - "type": "file", - "description": "Index of merged query and truth entries VCF file", - "pattern": "*.vcf.gz.tbi", - "ontologies": [] - } - } - ] - ], - "versions_wittyer": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "wittyer": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "dotnet /opt/Wittyer/Wittyer.dll --version | sed '1!d ; s/witty.er //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "wittyer": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "dotnet /opt/Wittyer/Wittyer.dll --version | sed '1!d ; s/witty.er //'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@famosab" - ], - "maintainers": [ - "@famosab" - ] - }, - "pipelines": [ - { - "name": "variantbenchmarking", - "version": "1.5.0" - } - ] - }, - { - "name": "xengsort_index", - "path": "modules/nf-core/xengsort/index/meta.yml", - "type": "module", - "meta": { - "name": "xengsort_index", - "description": "Fast lightweight accurate xenograft sorting", - "keywords": [ - "index", - "QC", - "reference", - "fasta", - "xenograft", - "sort", - "k-mer" - ], - "tools": [ - { - "xengsort": { - "description": "A fast xenograft read sorter based on space-efficient k-mer hashing", - "homepage": "https://gitlab.com/genomeinformatics/xengsort", - "documentation": "https://gitlab.com/genomeinformatics/xengsort", - "tool_dev_url": "https://gitlab.com/genomeinformatics/xengsort", - "doi": "10.4230/LIPIcs.WABI.2020.4", - "licence": [ - "MIT" - ], - "identifier": "" - } - } - ], - "input": [ - { - "host_fasta": { - "type": "file", - "description": "Reference genome fasta file from host, compressed or uncompressed.\n", - "ontologies": [] - } - }, - { - "graft_fasta": { - "type": "file", - "description": "Reference genome fasta file from graft, compressed or uncompressed.\n", - "ontologies": [] - } - }, - { - "index": { - "type": "string", - "description": "File name prefix to store index files.\n" - } - }, - { - "nobjects": { - "type": "string", - "description": "Number of k-mers that will be stored in the hash table. Underscore should be used, i.e for 1000000, it should be typed 1_000_000.\n" - } - }, - { - "mask": { - "type": "string", - "description": "Gapped k-mer mask (quoted string like '#__##_##__#').\n" - } - } - ], - "output": { - "hash": [ - { - "${index}.hash": { - "type": "file", - "description": "File with index hash file.", - "pattern": "*hash", - "ontologies": [] - } - } - ], - "info": [ - { - "${index}.info": { - "type": "file", - "description": "File with index info file.", - "pattern": "*info", - "ontologies": [] - } - } - ], - "versions": [ - { - "versions.yml": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - }, - "authors": [ - "@diegomscoelho" - ], - "maintainers": [ - "@diegomscoelho" - ] - } - }, - { - "name": "xeniumranger_import-segmentation", - "path": "modules/nf-core/xeniumranger/import-segmentation/meta.yml", - "type": "module", - "meta": { - "name": "xeniumranger_import_segmentation", - "description": "The xeniumranger import-segmentation module runs `xeniumranger import-segmentation`\nto recompute Xenium Onboard Analysis outputs using external segmentation results.\nIt supports two execution modes mirroring the Xenium Ranger CLI: an image-based\nmode that accepts nuclei and/or cell masks (TIFF/NPY) or GeoJSON polygons together\nwith optional coordinate transforms and unit definitions, and a transcript-based\nmode that ingests Baysor-style transcript assignment CSV files plus visualization\npolygons. Use the image-based inputs when providing label masks or polygons, or\nswitch to the transcript-based inputs when supplying transcript-level assignments\nso the appropriate command-line arguments are passed to Xenium Ranger.\n", - "keywords": [ - "spatial", - "segmentation", - "import segmentation", - "nuclear segmentation", - "cell segmentation", - "xeniumranger", - "imaging" - ], - "tools": [ - { - "xeniumranger": { - "description": "Xenium Ranger is a set of analysis pipelines that process Xenium In Situ Gene Expression data to relabel, resegment, or import new segmentation results from community-developed tools. Xenium Ranger provides flexible off-instrument reanalysis of Xenium In Situ data. Relabel transcripts, resegment cells with the latest 10x segmentation algorithms, or import your own segmentation data to assign transcripts to cells.\n", - "homepage": "https://www.10xgenomics.com/support/software/xenium-ranger/latest", - "documentation": "https://www.10xgenomics.com/support/software/xenium-ranger/latest/getting-started", - "tool_dev_url": "https://www.10xgenomics.com/support/software/xenium-ranger/latest/analysis", - "licence": [ - "10x Genomics EULA" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing run information\ne.g. [ id:'xenium_sample' ]\n" - } - }, - { - "xenium_bundle": { - "type": "directory", - "description": "Path to the Xenium output bundle generated by the Xenium Onboard Analysis pipeline" - } - }, - { - "transcript_assignment": { - "type": "file", - "optional": true, - "description": "Transcript assignment CSV with cell assignment, such as from Baysor v0.6, (transcript-based mode).\nMutually exclusive with image-based inputs (`nuclei`, `cells`). Required when using\ntranscript-based mode. Passed to `--transcript-assignment`.\n", - "pattern": "*.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - }, - { - "viz_polygons": { - "type": "file", - "optional": true, - "description": "Cell boundary polygons (GeoJSON) for visualization, such as from Baysor v0.6 (transcript-based mode).\nMutually exclusive with image-based inputs (`nuclei`, `cells`). Required when using\n`transcript_assignment`. Passed to `--viz-polygons`.\n", - "pattern": "*.{json,geojson}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - }, - { - "nuclei": { - "type": "file", - "optional": true, - "description": "Nucleus segmentation input as label mask (TIFF/NPY), polygons (GeoJSON), or Xenium Onboard\nAnalysis cells.zarr.zip (image-based mode).\nMutually exclusive with transcript-based inputs\n(`transcript_assignment`, `viz_polygons`). Passed to `--nuclei`.\n", - "pattern": "*.{tif,tiff,npy,json,geojson,zarr.zip}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_4003" - }, - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - }, - { - "cells": { - "type": "file", - "optional": true, - "description": "Cell segmentation input as label mask (TIFF/NPY), polygons (GeoJSON), or Xenium Onboard\nAnalysis cells.zarr.zip (image-based mode).\nMutually exclusive with transcript-based inputs\n(`transcript_assignment`, `viz_polygons`). Passed to `--cells`.\n", - "pattern": "*.{tif,tiff,npy,json,geojson,zarr.zip}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_4003" - }, - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - }, - { - "coordinate_transform": { - "type": "file", - "optional": true, - "description": "Image alignment file containing similarity transform matrix (e.g., `_imagealignment.csv` from\nXenium Explorer). Only used with image-based mode inputs (`nuclei`, `cells`). `units` will be automatically set to \"microns\". Passed to `--coordinate-transform`.\n", - "pattern": "*.csv", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3752" - } - ] - } - }, - { - "units": { - "type": "string", - "optional": true, - "description": "Units for segmentation results. Must be one of two options: \"microns\" (physical space) or\n\"pixels\" (pixel space). Can be used with both image-based and transcript-based modes.\nDefault: \"pixels\". Must be \"microns\" if `coordinate_transform` is used. For Baysor v0.6\ninputs, must be \"microns\". Passed to `--units`.\n", - "enum": [ - "microns", - "pixels" - ] - } - } - ] - ], - "output": { - "outs": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test' ]" - } - }, - { - "${prefix}": { - "type": "directory", - "description": "Directory containing the output xenium bundle of Xenium Ranger", - "pattern": "${prefix}" - } - } - ] - ], - "versions_xeniumranger": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "xeniumranger": { - "type": "string", - "description": "The tool name" - } - }, - { - "xeniumranger -V | sed -e 's/.*xenium-//'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "xeniumranger": { - "type": "string", - "description": "The tool name" - } - }, - { - "xeniumranger -V | sed -e 's/.*xenium-//'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@khersameesh24", - "@dongzehe" - ], - "maintainers": [ - "@khersameesh24", - "@dongzehe" - ] - }, - "pipelines": [ - { - "name": "spatialxe", - "version": "dev" - } - ] - }, - { - "name": "xeniumranger_relabel", - "path": "modules/nf-core/xeniumranger/relabel/meta.yml", - "type": "module", - "meta": { - "name": "xeniumranger_relabel", - "description": "The xeniumranger relabel module allows you to change the gene labels applied to decoded transcripts.", - "keywords": [ - "spatial", - "relabel", - "gene labels", - "transcripts", - "xeniumranger" - ], - "tools": [ - { - "xeniumranger": { - "description": "Xenium Ranger is a set of analysis pipelines that process Xenium In Situ Gene Expression data to relabel, resegment, or import new segmentation results from community-developed tools. Xenium Ranger provides flexible off-instrument reanalysis of Xenium In Situ data. Relabel transcripts, resegment cells with the latest 10x segmentation algorithms, or import your own segmentation data to assign transcripts to cells.\n", - "homepage": "https://www.10xgenomics.com/support/software/xenium-ranger/latest", - "documentation": "https://www.10xgenomics.com/support/software/xenium-ranger/latest/getting-started", - "tool_dev_url": "https://www.10xgenomics.com/support/software/xenium-ranger/latest/analysis", - "licence": [ - "10x Genomics EULA" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing run information\ne.g. [ id:'xenium_bundle_path' ]\n" - } - }, - { - "xenium_bundle": { - "type": "directory", - "description": "Path to the xenium output bundle generated by the Xenium Onboard Analysis pipeline" - } - }, - { - "panel": { - "type": "file", - "description": "Path to the gene panel file", - "pattern": "*.json", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3464" - } - ] - } - } - ] - ], - "output": { - "outs": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test' ]" - } - }, - { - "${prefix}": { - "type": "directory", - "description": "Directory containing the output xenium bundle of Xenium Ranger", - "pattern": "${prefix}" - } - } - ] - ], - "versions_xeniumranger": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "xeniumranger": { - "type": "string", - "description": "The tool name" - } - }, - { - "xeniumranger -V | sed -e 's/.*xenium-//'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "xeniumranger": { - "type": "string", - "description": "The tool name" - } - }, - { - "xeniumranger -V | sed -e 's/.*xenium-//'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@khersameesh24", - "@dongzehe" - ], - "maintainers": [ - "@khersameesh24", - "@dongzehe" - ] - }, - "pipelines": [ - { - "name": "spatialxe", - "version": "dev" - } - ] - }, - { - "name": "xeniumranger_rename", - "path": "modules/nf-core/xeniumranger/rename/meta.yml", - "type": "module", - "meta": { - "name": "xeniumranger_rename", - "description": "The xeniumranger rename module allows you to change the sample region_name and cassette_name throughout all the Xenium Onboard Analysis output files that contain this information.", - "keywords": [ - "spatial", - "rename", - "gene labels", - "transcripts", - "xeniumranger" - ], - "tools": [ - { - "xeniumranger": { - "description": "Xenium Ranger is a set of analysis pipelines that process Xenium In Situ Gene Expression data to relabel, resegment, or import new segmentation results from community-developed tools. Xenium Ranger provides flexible off-instrument reanalysis of Xenium In Situ data. Relabel transcripts, resegment cells with the latest 10x segmentation algorithms, or import your own segmentation data to assign transcripts to cells.\n", - "homepage": "https://www.10xgenomics.com/support/software/xenium-ranger/latest", - "documentation": "https://www.10xgenomics.com/support/software/xenium-ranger/latest/getting-started", - "tool_dev_url": "https://www.10xgenomics.com/support/software/xenium-ranger/latest/analysis", - "licence": [ - "10x Genomics EULA" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test' ]" - } - }, - { - "xenium_bundle": { - "type": "directory", - "description": "Path to the xenium output bundle generated by the Xenium Onboard Analysis pipeline" - } - }, - { - "region_name": { - "type": "string", - "description": "New region name" - } - }, - { - "cassette_name": { - "type": "string", - "description": "New cassette name" - } - } - ] - ], - "output": { - "outs": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test' ]" - } - }, - { - "${prefix}": { - "type": "directory", - "description": "Directory containing the output xenium bundle of Xenium Ranger", - "pattern": "${prefix}" - } - } - ] - ], - "versions_xeniumranger": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "xeniumranger": { - "type": "string", - "description": "The tool name" - } - }, - { - "xeniumranger -V | sed -e 's/.*xenium-//'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "xeniumranger": { - "type": "string", - "description": "The tool name" - } - }, - { - "xeniumranger -V | sed -e 's/.*xenium-//'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@khersameesh24", - "@dongzehe" - ], - "maintainers": [ - "@khersameesh24", - "@dongzehe" - ] - } - }, - { - "name": "xeniumranger_resegment", - "path": "modules/nf-core/xeniumranger/resegment/meta.yml", - "type": "module", - "meta": { - "name": "xeniumranger_resegment", - "description": "The xeniumranger resegment module allows you to generate a new segmentation of the morphology image space by rerunning the Xenium Onboard Analysis (XOA) segmentation algorithms with modified parameters.", - "keywords": [ - "spatial", - "resegment", - "morphology", - "segmentation", - "xeniumranger" - ], - "tools": [ - { - "xeniumranger": { - "description": "Xenium Ranger is a set of analysis pipelines that process Xenium In Situ Gene Expression data to relabel, resegment, or import new segmentation results from community-developed tools. Xenium Ranger provides flexible off-instrument reanalysis of Xenium In Situ data. Relabel transcripts, resegment cells with the latest 10x segmentation algorithms, or import your own segmentation data to assign transcripts to cells.\n", - "homepage": "https://www.10xgenomics.com/support/software/xenium-ranger/latest", - "documentation": "https://www.10xgenomics.com/support/software/xenium-ranger/latest/getting-started", - "tool_dev_url": "https://www.10xgenomics.com/support/software/xenium-ranger/latest/analysis", - "licence": [ - "10x Genomics EULA" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing run information\ne.g. [ id:'xenium_experiment' ]\n" - } - }, - { - "xenium_bundle": { - "type": "directory", - "description": "Path to the xenium output bundle generated by the Xenium Onboard Analysis pipeline" - } - } - ] - ], - "output": { - "outs": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "${prefix}": { - "type": "directory", - "description": "Directory containing the output xenium bundle of Xenium Ranger", - "pattern": "${prefix}" - } - } - ] - ], - "versions_xeniumranger": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "xeniumranger": { - "type": "string", - "description": "The tool name" - } - }, - { - "xeniumranger -V | sed -e 's/.*xenium-//'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "xeniumranger": { - "type": "string", - "description": "The tool name" - } - }, - { - "xeniumranger -V | sed -e 's/.*xenium-//'": { - "type": "string", - "description": "The command used to generate the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@khersameesh24", - "@dongzehe" - 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} - } - ] - ], - "output": { - "rendered": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "*.yaml": { - "type": "file", - "description": "Rendered YAML file", - "pattern": "*.yaml", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3750" - } - ] - } - } - ] - ], - "versions_yte": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "yte": { - "type": "string", - "description": "The tool name" - } - }, - { - "1.9.4": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The process the versions were collected from" - } - }, - { - "yte": { - "type": "string", - "description": "The tool name" - } - }, - { - "1.9.4": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@famosab" - ], - "maintainers": [ - "@famosab" - ] - }, - "pipelines": [ - { - "name": "sarek", - "version": "3.8.1" - } - ] - }, - { - "name": "zip", - "path": "modules/nf-core/zip/meta.yml", - "type": "module", - "meta": { - "name": "zip", - "description": "Compress file lists to produce ZIP archive files", - "keywords": [ - "unzip", - "decompression", - "zip", - "archiving" - ], - "tools": [ - { - "unzip": { - "description": "p7zip is a quick port of 7z.exe and 7za.exe (command line version of 7zip, see www.7-zip.org) for Unix.", - "homepage": "https://sourceforge.net/projects/p7zip/", - "documentation": "https://sourceforge.net/projects/p7zip/", - "tool_dev_url": "https://sourceforge.net/projects/p7zip\"", - "licence": [ - "LGPL-2.1-or-later" - ], - "identifier": "" - } - } - ], - "input": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "files": { - "type": "file", - "description": "File or list of files to be zipped", - "ontologies": [] - } - } - ] - ], - "output": { - "zipped_archive": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "${prefix}.zip": { - "type": "file", - "description": "ZIP file", - "pattern": "*.zip", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3987" - } - ] - } - } - ] - ], - "versions_zip": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "zip": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "7za i 2>&1 | grep 'p7zip Version' | sed 's/.*p7zip Version //; s/(.*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "topics": { - "versions": [ - [ - { - "${task.process}": { - "type": "string", - "description": "The name of the process" - } - }, - { - "zip": { - "type": "string", - "description": "The name of the tool" - } - }, - { - "7za i 2>&1 | grep 'p7zip Version' | sed 's/.*p7zip Version //; s/(.*//'": { - "type": "eval", - "description": "The expression to obtain the version of the tool" - } - } - ] - ] - }, - "authors": [ - "@jfy133", - "@pinin4fjords" - ], - "maintainers": [ - "@jfy133", - "@pinin4fjords", - "@JoseEspinosa" - ] - }, - "pipelines": [ - { - "name": "differentialabundance", - "version": "1.5.0" - }, - { - "name": "tfactivity", - "version": "dev" - } - ] - } - ], - "subworkflows": [ - { - "name": "abundance_differential_filter", - "path": "subworkflows/nf-core/abundance_differential_filter/meta.yml", - "type": "subworkflow", - "meta": { - "name": "abundance_differential_filter", - "description": "A subworkflow for filtering differential abundance results", - "keywords": [ - "differential", - "abundance", - "expression", - "count matrix", - "fold-change" - ], - "components": [ - "limma/differential", - "deseq2/differential", - "propr/propd", - "custom/filterdifferentialtable", - "variancepartition/dream" - ], - "input": [ - { - "ch_input": { - "description": "Channel with input data for differential analysis", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata map" - } - }, - { - "counts": { - "type": "file", - "description": "Count matrix file" - } - }, - { - "analysis_method": { - "type": "value", - "description": "Analysis method (deseq2, limma, or propd)" - } - }, - { - "fc_threshold": { - "type": "value", - "description": "Fold change threshold for filtering" - } - }, - { - "stat_threshold": { - "type": "value", - "description": "Threshold for filtering the significance statistics\n(eg. adjusted p-values in the case of deseq2 or limma,\nweighted connectivity in the case of propd)\n" - } - } - ] - } - }, - { - "ch_samplesheet": { - "description": "Channel with sample information", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata map" - } - }, - { - "samplesheet": { - "type": "file", - "description": "Sample information file" - } - } - ] - } - }, - { - "ch_transcript_lengths": { - "description": "Channel with transcript length information", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata map" - } - }, - { - "transcript_lengths": { - "type": "file", - "description": "Transcript length information file" - } - } - ] - } - }, - { - "ch_control_features": { - "description": "Channel with control features information", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata map" - } - }, - { - "control_features": { - "type": "file", - "description": "Control features information file" - } - } - ] - } - }, - { - "ch_contrasts": { - "description": "Channel with contrast information", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata map" - } - }, - { - "meta_contrast": { - "type": "map", - "description": "Map with all the contrast info, such as contrast\nid, variable, reference, target, etc.\n" - } - }, - { - "variable": { - "type": "list", - "description": "List of contrast variable" - } - }, - { - "reference": { - "type": "list", - "description": "List of reference level" - } - }, - { - "target": { - "type": "list", - "description": "List of target level" - } - }, - { - "formula": { - "type": "list", - "description": "List of contrast formula" - } - }, - { - "comparison": { - "type list": null, - "description": "List of contrast comparison" - } - } - ] - } - } - ], - "output": [ - { - "versions": { - "description": "Channel containing software versions file", - "structure": [ - { - "versions.yml": { - "type": "file", - "description": "File containing versions of the software used" - } - } - ] - } - }, - { - "results_genewise": { - "description": "Channel containing unfiltered differential analysis results", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata map" - } - }, - { - "results": { - "type": "file", - "description": "Unfiltered differential analysis results file", - "pattern": "*.{csv,tsv}" - } - } - ] - } - }, - { - "results_genewise_filtered": { - "description": "Channel containing filtered differential analysis results", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata map" - } - }, - { - "filtered_results": { - "type": "file", - "description": "Filtered differential analysis results file", - "pattern": "*.{csv,tsv}" - } - } - ] - } - }, - { - "adjacency": { - "description": "Channel containing the adjacency matrix suited for downstream graph-based functional analysis", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata map" - } - }, - { - "adjacency_matrix": { - "type": "file", - "description": "Adjacency matrix file", - "pattern": "*.{csv,tsv}" - } - } - ] - } - }, - { - "normalised_matrix": { - "description": "Channel containing normalised count matrix", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata map" - } - }, - { - "matrix": { - "type": "file", - "description": "Normalised count matrix file", - "pattern": "*.{csv,tsv}" - } - } - ] - } - }, - { - "variance_stabilised_matrix": { - "description": "Channel containing variance stabilised count matrix (DESeq2 only)", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata map" - } - }, - { - "matrices": { - "type": "list", - "description": "A list of variance stabilised count matrix files", - "pattern": "*.{csv,tsv}" - } - } - ] - } - }, - { - "model": { - "description": "Channel containing statistical model object from differential analysis", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata map" - } - }, - { - "model": { - "type": "file", - "description": "Statistical model object file", - "pattern": "*.rds" - } - } - ] - } - }, - { - "plots": { - "description": "Channel containing plots from differential analysis", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata map" - } - }, - { - "plots": { - "type": "file", - "description": "Plot file", - "pattern": "*.{png,pdf}" - } - } - ] - } - }, - { - "other": { - "description": "Channel containing other outputs from differential analysis", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata map" - } - }, - { - "other_files": { - "type": "file", - "description": "Other output file from differential analysis", - "pattern": "*.{rds,tsv,log}" - } - } - ] - } - } - ], - "authors": [ - "@pinin4fjords", - "@bjlang", - "@caraiz2001", - "@suzannejin", - "@delfiterradas", - "@sofiromano" - ], - "maintainers": [ - "@pinin4fjords", - "@suzannejin" - ] - } - }, - { - "name": "archive_extract", - "path": "subworkflows/nf-core/archive_extract/meta.yml", - "type": "subworkflow", - "meta": { - "name": "archive_extract", - "description": "Extract archive(s) from any format\nCurrently supported format are .gz, .tar.gz, .zip\n", - "keywords": [ - "archive", - "gzip", - "tar", - "zip" - ], - "components": [ - "gunzip", - "untar", - "unzip" - ], - "input": [ - { - "archive": { - "description": "Channel with archive to extract", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata map" - } - }, - { - "archive": { - "type": "file", - "description": "Structure: [path(archive)]\nFile containing the archive to extract\n", - "pattern": "*{.tar.gz, .gz, .zip}" - } - } - ] - } - } - ], - "output": [ - { - "extracted": { - "description": "Channel with extracted archive", - "structure": [ - { - "meta": null, - "type": "map", - "description": "Metadata map" - }, - { - "*": null, - "type": "file", - "description": "Structure: [path]\nFolder or file(s) extracted\n" - } - ] - } - }, - { - "not_extracted": { - "description": "Channel with any not extracted (ie not recognized) archive", - "structure": [ - { - "meta": null, - "type": "map", - "description": "Metadata map" - }, - { - "*": null, - "type": "file", - "description": "Structure: [path]\nFile(s) not extracted\n" - } - ] - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@maxulysse" - ], - "maintainers": [ - "@maxulysse" - ] - } - }, - { - "name": "bam_cnv_wisecondorx", - "path": "subworkflows/nf-core/bam_cnv_wisecondorx/meta.yml", - "type": "subworkflow", - "meta": { - "name": "bam_cnv_wisecondorx", - "description": "A subworkflow for calling CNVs using WisecondorX", - "keywords": [ - "cnv", - "bam", - "bed", - "cram", - "plots", - "genomics" - ], - "components": [ - "wisecondorx/convert", - "wisecondorx/predict" - ], - "input": [ - { - "ch_bam": { - "description": "An input channel containing BAM/CRAM files and their indices\nStructure: [ val(meta), path(bam), path(bai) ]\n" - } - }, - { - "ch_fasta": { - "description": "A channel containing the reference FASTA file\nStructure: [ val(meta2), path(fasta) ]\n" - } - }, - { - "ch_fai": { - "description": "A channel containing the index of the reference FASTA file\nStructure: [ val(meta3), path(fai) ]\n" - } - }, - { - "ch_ref": { - "description": "A channel containing WisecondorX reference created with `WisecondorX newref`\nStructure: [ val(meta4), path(reference) ]\n" - } - }, - { - "ch_blacklist": { - "description": "An optional channel containing a BED file with regions to mask from the analysis\nStructure: [ val(meta5), path(blacklist) ]\n" - } - } - ], - "output": [ - { - "aberrations_bed": { - "description": "A channel containing the BED files with CNV aberrations\nStructure: [ val(meta), path(bed) ]\n" - } - }, - { - "bins_bed": { - "description": "A channel containing the BED files with the used bins\nStructure: [ val(meta), path(bed) ]\n" - } - }, - { - "segments_bed": { - "description": "A channel containing the segment BED files\nStructure: [ val(meta), path(bed) ]\n" - } - }, - { - "chr_statistics": { - "description": "A channel containing TXT files with chromosome statistics\nStructure: [ val(meta), path(txt) ]\n" - } - }, - { - "chr_plots": { - "description": "A channel containing lists of chromosome plots\nStructure: [ val(meta), [ path(png), path(png), ... ] ]\n" - } - }, - { - "genome_plot": { - "description": "A channel containing the plots of the whole genomes\nStructure: [ val(meta), path(png) ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@nvnieuwk" - ], - "maintainers": [ - "@nvnieuwk" - ] - } - }, - { - "name": "bam_create_som_pon_gatk", - "path": "subworkflows/nf-core/bam_create_som_pon_gatk/meta.yml", - "type": "subworkflow", - "meta": { - "name": "bam_create_som_pon_gatk", - "description": "Perform variant calling on a set of normal samples using mutect2 panel of normals mode. Group them into a genomicsdbworkspace using genomicsdbimport, then use this to create a panel of normals using createsomaticpanelofnormals.", - "keywords": [ - "gatk4", - "mutect2", - "genomicsdbimport", - "createsomaticpanelofnormals", - "variant_calling", - "genomicsdb_workspace", - "panel_of_normals" - ], - "components": [ - "gatk4/mutect2", - "gatk4/genomicsdbimport", - "gatk4/createsomaticpanelofnormals", - "gatk4/mergevcfs", - "gatk4/mergemutectstats" - ], - "input": [ - { - "ch_input": { - "type": "list", - "description": "An input channel containing the following files:\n- input: One or more BAM/CRAM files\n- input_index: The index/indices from the BAM/CRAM file(s)\nStructure: [ meta, path(input), path(input_index) ]\n" - } - }, - { - "ch_fasta": { - "type": "list", - "description": "Reference fasta file\nStructure: [ meta, path(fasta) ]\n" - } - }, - { - "ch_fai": { - "type": "list", - "description": "Reference fasta file index\nStructure: [ meta, path(fai) ]\n" - } - }, - { - "ch_dict": { - "type": "list", - "description": "GATK sequence dictionary\nStructure: [ meta, path(dict) ]\n" - } - }, - { - "ch_intervals_gendb": { - "type": "file", - "description": "Interval file used for GenomicsDBImport", - "pattern": "*.{bed,interval_list}" - } - }, - { - "ch_intervals_num": { - "type": "list", - "description": "Intervals channel for scatter and gather strategy. Each item is a tuple of\nan interval file and the total number of intervals. Use [ [], 0 ] if no intervals.\nStructure: [ path(intervals), val(num_intervals) ]\n" - } - } - ], - "output": [ - { - "mutect2_vcf": { - "type": "list", - "description": "List of compressed vcf files to be used to make the gendb workspace", - "pattern": "[ *.vcf.gz ]" - } - }, - { - "mutect2_index": { - "type": "list", - "description": "List of indexes of mutect2_vcf files", - "pattern": "[ *vcf.gz.tbi ]" - } - }, - { - "mutect2_stats": { - "type": "list", - "description": "List of stats files that pair with mutect2_vcf files", - "pattern": "[ *vcf.gz.stats ]" - } - }, - { - "genomicsdb": { - "type": "directory", - "description": "Directory containing the files that compose the genomicsdb workspace.", - "pattern": "path/name_of_workspace" - } - }, - { - "pon_vcf": { - "type": "file", - "description": "Panel of normal as compressed vcf file", - "pattern": "*.vcf.gz" - } - }, - { - "pon_index": { - "type": "file", - "description": "Index of pon_vcf file", - "pattern": "*vcf.gz.tbi" - } - } - ], - "authors": [ - "@GCJMackenzie" - ], - "maintainers": [ - "@GCJMackenzie", - "@maxulysse" - ] - }, - "pipelines": [ - { - "name": "createpanelrefs", - "version": "dev" - } - ] - }, - { - "name": "bam_dedup_stats_samtools_umicollapse", - "path": "subworkflows/nf-core/bam_dedup_stats_samtools_umicollapse/meta.yml", - "type": "subworkflow", - "meta": { - "name": "bam_dedup_stats_samtools_umicollapse", - "description": "umicollapse, index BAM file and run samtools stats, flagstat and idxstats", - "keywords": [ - "umi", - "dedup", - "index", - "bam", - "sam", - "cram" - ], - "components": [ - "umicollapse", - "samtools/index", - "samtools/stats", - "samtools/idxstats", - "samtools/flagstat", - "bam_stats_samtools" - ], - "input": [ - { - "ch_bam_bai": { - "description": "input BAM file\nStructure: [ val(meta), path(bam), path(bai) ]\n" - } - } - ], - "output": [ - { - "bam": { - "description": "Umi deduplicated BAM/SAM file\nStructure: [ val(meta), path(bam) ]\n" - } - }, - { - "bai": { - "description": "Umi deduplicated BAM/SAM samtools index\nStructure: [ val(meta), path(bai) ]\n" - } - }, - { - "csi": { - "description": "CSI samtools index\nStructure: [ val(meta), path(csi) ]\n" - } - }, - { - "dedupstats": { - "description": "File containing umicollapse deduplication stats\nStructure: [ val(meta), path(stats) ]\n" - } - }, - { - "stats": { - "description": "File containing samtools stats output\nStructure: [ val(meta), path(stats) ]\n" - } - }, - { - "flagstat": { - "description": "File containing samtools flagstat output\nStructure: [ val(meta), path(flagstat) ]\n" - } - }, - { - "idxstats": { - "description": "File containing samtools idxstats output\nStructure: [ val(meta), path(idxstats) ]\n" - } - }, - { - "versions": { - "description": "Files containing software versions\nStructure: [ path(versions.yml) ]\n" - } - } - ], - "authors": [ - "@MatthiasZepper" - ], - "maintainers": [ - "@MatthiasZepper" - ] - }, - "pipelines": [ - { - "name": "lncpipe", - "version": "dev" - }, - { - "name": "riboseq", - "version": "1.2.0" - }, - { - "name": "rnaseq", - "version": "3.26.0" - } - ] - }, - { - "name": "bam_dedup_stats_samtools_umitools", - "path": "subworkflows/nf-core/bam_dedup_stats_samtools_umitools/meta.yml", - "type": "subworkflow", - "meta": { - "name": "bam_dedup_stats_samtools_umitools", - "description": "UMI-tools dedup, index BAM file and run samtools stats, flagstat and idxstats", - "keywords": [ - "umi", - "dedup", - "index", - "bam", - "sam", - "cram" - ], - "components": [ - "umitools/dedup", - "samtools/index", - "samtools/view", - "samtools/stats", - "samtools/idxstats", - "samtools/flagstat", - "bam_stats_samtools" - ], - "input": [ - { - "ch_bam_bai": { - "description": "input BAM file\nStructure: [ val(meta), path(bam), path(bai) ]\n" - } - }, - { - "val_get_dedup_stats": { - "type": "boolean", - "description": "Generate output stats when running \"umi_tools dedup\"\n" - } - }, - { - "val_primary_only": { - "type": "boolean", - "description": "Filter to primary alignments (SAM flag 0x900) before running UMI-tools dedup.\nWhen true, secondary and supplementary alignments are removed so that dedup\nstatistics reflect only primary alignments.\n" - } - } - ], - "output": [ - { - "bam": { - "description": "Umi deduplicated BAM/SAM file\nStructure: [ val(meta), path(bam) ]\n" - } - }, - { - "bai": { - "description": "Umi deduplicated BAM/SAM samtools index\nStructure: [ val(meta), path(bai) ]\n" - } - }, - { - "csi": { - "description": "CSI samtools index\nStructure: [ val(meta), path(csi) ]\n" - } - }, - { - "deduplog": { - "description": "UMI-tools deduplication log\nStructure: [ val(meta), path(log) ]\n" - } - }, - { - "stats": { - "description": "File containing samtools stats output\nStructure: [ val(meta), path(stats) ]\n" - } - }, - { - "flagstat": { - "description": "File containing samtools flagstat output\nStructure: [ val(meta), path(flagstat) ]\n" - } - }, - { - "idxstats": { - "description": "File containing samtools idxstats output\nStructure: [ val(meta), path(idxstats) ]\n" - } - }, - { - "versions": { - "description": "Files containing software versions\nStructure: [ path(versions.yml) ]\n" - } - } - ], - "authors": [ - "@drpatelh", - "@KamilMaliszArdigen" - ], - "maintainers": [ - "@drpatelh", - "@KamilMaliszArdigen" - ] - }, - "pipelines": [ - { - "name": "lncpipe", - "version": "dev" - }, - { - "name": "nascent", - "version": "2.3.0" - }, - { - "name": "riboseq", - "version": "1.2.0" - }, - { - "name": "rnaseq", - "version": "3.26.0" - } - ] - }, - { - "name": "bam_dedup_umi", - "path": "subworkflows/nf-core/bam_dedup_umi/meta.yml", - "type": "subworkflow", - "meta": { - "name": "bam_dedup_umi", - "description": "BAM deduplication with UMI processing for both genome and transcriptome alignments", - "keywords": [ - "deduplication", - "UMI", - "BAM", - "genome", - "transcriptome", - "umicollapse", - "umitools" - ], - "components": [ - "umitools/prepareforrsem", - "samtools/sort", - "bam_dedup_stats_samtools_umicollapse", - "bam_dedup_stats_samtools_umitools", - "bam_sort_stats_samtools" - ], - "input": [ - { - "ch_genome_bam": { - "description": "Channel with genome BAM files", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata map" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file", - "pattern": "*.bam" - } - }, - { - "bai": { - "type": "file", - "description": "BAM index file", - "pattern": "*.bai" - } - } - ] - } - }, - { - "ch_fasta_fai": { - "description": "Channel with genome FASTA file and index", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata map" - } - }, - { - "fasta": { - "type": "file", - "description": "Genome FASTA file", - "pattern": "*.{fa,fna,fasta}" - } - }, - { - "fai": { - "type": "file", - "description": "Genome FASTA index file", - "pattern": "*.fai" - } - } - ] - } - }, - { - "umi_dedup_tool": { - "description": "UMI deduplication tool to use", - "structure": [ - { - "value": { - "type": "string", - "description": "Either 'umicollapse' or 'umitools'" - } - } - ] - } - }, - { - "umitools_dedup_stats": { - "description": "Whether to generate UMI-tools deduplication stats", - "structure": [ - { - "value": { - "type": "boolean", - "description": "True or False" - } - } - ] - } - }, - { - "bam_csi_index": { - "description": "Whether to generate CSI index", - "structure": [ - { - "value": { - "type": "boolean", - "description": "True or False" - } - } - ] - } - }, - { - "ch_transcriptome_bam": { - "description": "Channel with transcriptome BAM files", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata map" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file", - "pattern": "*.bam" - } - } - ] - } - }, - { - "ch_transcript_fasta_fai": { - "description": "Channel with transcript FASTA file and index", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata map" - } - }, - { - "fasta": { - "type": "file", - "description": "Transcript FASTA file", - "pattern": "*.{fa,fasta}" - } - }, - { - "fai": { - "type": "file", - "description": "Transcript FASTA index file", - "pattern": "*.fai" - } - } - ] - } - }, - { - "umitools_dedup_primary_only": { - "description": "Whether to filter to primary alignments before UMI-tools dedup", - "structure": [ - { - "value": { - "type": "boolean", - "description": "When true, secondary and supplementary alignments (SAM flag 0x900) are\nremoved before running UMI-tools dedup so that dedup statistics reflect\nonly primary alignments.\n" - } - } - ] - } - } - ], - "output": [ - { - "bam": { - "description": "Channel containing deduplicated genome BAM files", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata map" - } - }, - { - "bam": { - "type": "file", - "description": "Deduplicated BAM file", - "pattern": "*.bam" - } - } - ] - } - }, - { - "bai": { - "description": "Channel containing indexed BAM (BAI) files", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata map" - } - }, - { - "bai": { - "type": "file", - "description": "BAM index file", - "pattern": "*.bai" - } - } - ] - } - }, - { - "csi": { - "description": "Channel containing CSI files (if bam_csi_index is true)", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata map" - } - }, - { - "csi": { - "type": "file", - "description": "CSI index file", - "pattern": "*.csi" - } - } - ] - } - }, - { - "dedup_log": { - "description": "Channel containing deduplication log files", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata map" - } - }, - { - "log": { - "type": "file", - "description": "Deduplication log file", - "pattern": "*.log" - } - } - ] - } - }, - { - "stats": { - "description": "Channel containing BAM statistics files", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata map" - } - }, - { - "stats": { - "type": "file", - "description": "BAM statistics file", - "pattern": "*.stats" - } - } - ] - } - }, - { - "flagstat": { - "description": "Channel containing flagstat files", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata map" - } - }, - { - "flagstat": { - "type": "file", - "description": "Flagstat file", - "pattern": "*.flagstat" - } - } - ] - } - }, - { - "idxstats": { - "description": "Channel containing idxstats files", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata map" - } - }, - { - "idxstats": { - "type": "file", - "description": "Idxstats file", - "pattern": "*.idxstats" - } - } - ] - } - }, - { - "genome_stats": { - "description": "Channel containing BAM statistics for the genome-aligned BAM only (transcriptome excluded)", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata map" - } - }, - { - "stats": { - "type": "file", - "description": "BAM statistics file", - "pattern": "*.stats" - } - } - ] - } - }, - { - "genome_flagstat": { - "description": "Channel containing flagstat for the genome-aligned BAM only", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata map" - } - }, - { - "flagstat": { - "type": "file", - "description": "Flagstat file", - "pattern": "*.flagstat" - } - } - ] - } - }, - { - "genome_idxstats": { - "description": "Channel containing idxstats for the genome-aligned BAM only", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata map" - } - }, - { - "idxstats": { - "type": "file", - "description": "Idxstats file", - "pattern": "*.idxstats" - } - } - ] - } - }, - { - "per_sample_mqc_bundle": { - "description": "Per-sample MultiQC-feeding outputs (genome-side only: genomic dedup log,\ngenome stats, flagstat, idxstats) joined on meta. Transcriptome stats\nexcluded (MultiQC can't disambiguate them from genome stats).\n", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata map" - } - }, - { - "files": { - "type": "file", - "description": "List of MultiQC-relevant files for the sample" - } - } - ] - } - }, - { - "multiqc_files": { - "description": "Channel containing files for MultiQC", - "structure": [ - { - "file": { - "type": "file", - "description": "File for MultiQC" - } - } - ] - } - }, - { - "transcriptome_bam": { - "description": "Channel containing deduplicated transcriptome BAM files", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata map" - } - }, - { - "bam": { - "type": "file", - "description": "Deduplicated transcriptome BAM file", - "pattern": "*.bam" - } - } - ] - } - }, - { - "versions": { - "description": "Channel containing software versions file", - "structure": [ - { - "versions": { - "type": "file", - "description": "File containing versions of the software used", - "pattern": "versions.yml" - } - } - ] - } - } - ], - "authors": [ - "@pinin4fjords" - ], - "maintainers": [ - "@pinin4fjords" - ] - }, - "pipelines": [ - { - "name": "lncpipe", - "version": "dev" - }, - { - "name": "riboseq", - "version": "1.2.0" - }, - { - "name": "rnaseq", - "version": "3.26.0" - } - ] - }, - { - "name": "bam_docounts_contamination_angsd", - "path": "subworkflows/nf-core/bam_docounts_contamination_angsd/meta.yml", - "type": "subworkflow", - "meta": { - "name": "bam_docounts_contamination_angsd", - "description": "Calculate contamination of the X-chromosome with ANGSD", - "keywords": [ - "angsd", - "bam", - "contamination", - "docounts" - ], - "components": [ - "angsd/docounts", - "angsd/contamination" - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM or CRAM file", - "pattern": "*.{bam,cram}" - } - }, - { - "bai": { - "type": "file", - "description": "BAM/SAM samtools index", - "pattern": "*.{bai,csi}" - } - }, - { - "hapmap_file": { - "type": "file", - "description": "Hapmap file" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\n" - } - }, - { - "txt": { - "type": "file", - "description": "Contamination estimation file", - "pattern": "*.txt" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@scarlhoff" - ], - "maintainers": [ - "@scarlhoff" - ] - } - }, - { - "name": "bam_impute_quilt", - "path": "subworkflows/nf-core/bam_impute_quilt/meta.yml", - "type": "subworkflow", - "meta": { - "name": "BAM_IMPUTE_QUILT", - "description": "Subworkflow to impute BAM files using QUILT software.\nVariants location to impute are obtain through the tsv file given\n", - "keywords": [ - "BAM", - "imputation", - "quilt" - ], - "components": [ - "gawk", - "quilt/quilt", - "bcftools/index", - "glimpse2/ligate" - ], - "input": [ - { - "ch_input": { - "description": "Channel with input data", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata map" - } - }, - { - "file": { - "type": "file", - "description": "List of input BAM files", - "pattern": "*.bam" - } - }, - { - "index": { - "type": "file", - "description": "List of input index file", - "pattern": "*.{bai,csi}" - } - }, - { - "bampaths": { - "type": "file", - "description": "File containing the list of BAM/CRAM files to be phased.\nOne file per line.\n", - "pattern": "*.{txt,tsv}" - } - }, - { - "bamnames": { - "type": "file", - "description": "File containing the sample names of each BAM files listed in bampaths.\nOne file per line.\n", - "pattern": "*.{txt,tsv}" - } - } - ] - } - }, - { - "ch_hap_legend": { - "description": "Channel with reference panel variants data", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata map that will be combined with the input data map\nNeed to have the \"chr\" as chromosome name and \"id\" as panel name\n" - } - }, - { - "hap": { - "type": "file", - "description": "Panel VCF haplotypes files by chromosomes", - "pattern": "*.hap[.gz]+" - } - }, - { - "legend": { - "type": "file", - "description": "Panel VCF legend files by chromosomes", - "pattern": "*.legend[.gz]+" - } - }, - { - "posfile": { - "type": "file", - "description": "Position to impute variants file in TSV format (chromosome, position, ref, alt)" - } - } - ] - } - }, - { - "ch_chunks": { - "description": "Channel with chromosome chunks data", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata map with chromosome information" - } - }, - { - "chr": { - "type": "string", - "description": "Chromosome name" - } - }, - { - "start": { - "type": "integer", - "description": "Start position of the chunk" - } - }, - { - "end": { - "type": "integer", - "description": "End position of the chunk" - } - } - ] - } - }, - { - "ch_map": { - "description": "Channel with genetic map data", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata map with chromosome information\n" - } - }, - { - "map": { - "type": "file", - "description": "Stitch format genetic map files", - "pattern": "*.map" - } - } - ] - } - }, - { - "ch_fasta": { - "description": "Channel with reference genome data", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata map" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA file of the reference genome", - "pattern": "*.fa[sta]+" - } - }, - { - "fai": { - "type": "file", - "description": "FASTA index file of the reference genome", - "pattern": "*.fai" - } - } - ] - } - }, - { - "n_gen": { - "type": "integer", - "description": "Number of generations since founding or mixing" - } - }, - { - "buffer": { - "type": "integer", - "description": "Buffer of region to perform imputation over" - } - } - ], - "output": [ - { - "vcf_index": { - "description": "Channel with imputed VCF files", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata map combined with the posfile, chunks and map data map.\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF imputed file", - "pattern": "*.{vcf,bcf,vcf.gz}" - } - }, - { - "index": { - "type": "file", - "description": "VCF index file", - "pattern": "*.{tbi,csi}" - } - } - ] - } - } - ], - "authors": [ - "@louislenezet" - ], - "maintainers": [ - "@louislenezet" - ] - } - }, - { - "name": "bam_impute_quilt2", - "path": "subworkflows/nf-core/bam_impute_quilt2/meta.yml", - "type": "subworkflow", - "meta": { - "name": "bam_impute_quilt2", - "description": "Impute low-coverage BAM or CRAM inputs with QUILT2 and ligate chunked outputs per chromosome. 'regionout' key will be used to store temporarily the region and therefore shouldn't be used in the meta maps.\n", - "keywords": [ - "bam", - "cram", - "imputation", - "quilt", - "quilt2", - "vcf" - ], - "components": [ - "quilt/quilt2", - "glimpse2/ligate", - "bcftools/index" - ], - "input": [ - { - "ch_input": { - "description": "Channel with target sequencing data and optional rename files.\n", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata map for the input batch." - } - }, - { - "bam_or_cram": { - "type": "file", - "description": "Input BAM or CRAM file, or a list of BAM or CRAM files.", - "pattern": "*.{bam,cram}" - } - }, - { - "index": { - "type": "file", - "description": "Index for the BAM or CRAM input.", - "pattern": "*.{bai,crai}" - } - }, - { - "bampaths": { - "type": "file", - "description": "Optional text file listing BAM or CRAM paths to impute.\nOne file per line.\n", - "pattern": "*.{txt,tsv}" - } - }, - { - "bamnames": { - "type": "file", - "description": "Optional text file listing sample names in the same order as `bampaths`.\nOne file per line.\n", - "pattern": "*.{txt,tsv}" - } - } - ] - } - }, - { - "ch_reference_panel": { - "description": "Channel with phased reference panel VCFs per chromosome.\n", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata map that will be combined with the input metadata.\nMust include `id` for the panel name and `chr` for the chromosome.\n" - } - }, - { - "vcf": { - "type": "file", - "description": "Reference panel VCF or BCF.", - "pattern": "*.{vcf,vcf.gz,bcf}" - } - }, - { - "index": { - "type": "file", - "description": "Index for the reference panel VCF or BCF.", - "pattern": "*.{tbi,csi}" - } - } - ] - } - }, - { - "ch_chunks": { - "description": "Channel with optional imputation chunks per chromosome.\n", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata map with the panel id and chromosome." - } - }, - { - "chr": { - "type": "string", - "description": "Chromosome name." - } - }, - { - "start": { - "type": "integer", - "description": "Start position of the chunk." - } - }, - { - "end": { - "type": "integer", - "description": "End position of the chunk." - } - } - ] - } - }, - { - "ch_map": { - "description": "Channel with optional genetic maps per chromosome.\n", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata map with the panel id and chromosome." - } - }, - { - "map": { - "type": "file", - "description": "Genetic map used by QUILT2.", - "pattern": "*.{txt,map}{,gz}" - } - } - ] - } - }, - { - "ch_fasta": { - "description": "Channel with optional reference FASTA data, required for CRAM inputs.\n", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata map for the reference genome." - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome FASTA.", - "pattern": "*.{fa,fasta}" - } - }, - { - "fai": { - "type": "file", - "description": "FASTA index file.", - "pattern": "*.fai" - } - } - ] - } - }, - { - "n_gen": { - "type": "integer", - "description": "Number of generations since founding or mixing." - } - }, - { - "buffer": { - "type": "integer", - "description": "Buffer of region to perform imputation over." - } - } - ], - "output": [ - { - "vcf_index": { - "description": "Imputed and indexed VCFs after ligating chunked outputs per chromosome.\n", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata map combined from the input batch and panel metadata." - } - }, - { - "vcf": { - "type": "file", - "description": "Imputed VCF file.", - "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}" - } - }, - { - "index": { - "type": "file", - "description": "Index for the imputed VCF or BCF file.", - "pattern": "*.{tbi,csi}" - } - } - ] - } - } - ], - "authors": [ - "@atrigila" - ], - "maintainers": [ - "@atrigila" - ] - } - }, - { - "name": "bam_impute_stitch", - "path": "subworkflows/nf-core/bam_impute_stitch/meta.yml", - "type": "subworkflow", - "meta": { - "name": "BAM_IMPUTE_STITCH", - "description": "Subworkflow to impute BAM files using STITCH software.\nVariants location to impute are obtain through the legend file given\n", - "keywords": [ - "BAM", - "imputation", - "stitch" - ], - "components": [ - "stitch", - "bcftools/index", - "glimpse2/ligate" - ], - "input": [ - { - "ch_input": { - "description": "Channel with input data", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata map" - } - }, - { - "file": { - "type": "file", - "description": "List of input BAM files", - "pattern": "*.bam" - } - }, - { - "index": { - "type": "file", - "description": "List of input index file", - "pattern": "*.{bai,csi}" - } - }, - { - "bampaths": { - "type": "file", - "description": "File containing the list of BAM/CRAM files to be phased.\nOne file per line.\n", - "pattern": "*.{txt,tsv}" - } - }, - { - "bamnames": { - "type": "file", - "description": "File containing the sample names of each BAM files listed in bampaths.\nOne file per line.\n", - "pattern": "*.{txt,tsv}" - } - } - ] - } - }, - { - "ch_posfile": { - "description": "Channel with position to call variants by chromosomes", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata map with chromosome information\n" - } - }, - { - "tsv": { - "type": "file", - "description": "Position to impute variants file in TSV format (chromosome, position, ref, alt)" - } - } - ] - } - }, - { - "ch_chunks": { - "description": "Channel with chromosome chunks data", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata map with chromosome information" - } - }, - { - "chr": { - "type": "string", - "description": "Chromosome name" - } - }, - { - "start": { - "type": "integer", - "description": "Start position of the chunk" - } - }, - { - "end": { - "type": "integer", - "description": "End position of the chunk" - } - } - ] - } - }, - { - "ch_map": { - "description": "Channel with genetic map data", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata map with chromosome information\n" - } - }, - { - "map": { - "type": "file", - "description": "Stitch format genetic map files", - "pattern": "*.map" - } - } - ] - } - }, - { - "ch_fasta": { - "description": "Channel with reference genome data", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata map" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA file of the reference genome", - "pattern": "*.fa[sta]+" - } - }, - { - "fai": { - "type": "file", - "description": "FASTA index file of the reference genome", - "pattern": "*.fai" - } - } - ] - } - }, - { - "k_val": { - "type": "integer", - "description": "K value for STITCH imputation" - } - }, - { - "n_gen": { - "type": "integer", - "description": "Number of generations for STITCH imputation" - } - }, - { - "buffer": { - "type": "integer", - "description": "Buffer size around each chunk for STITCH imputation" - } - }, - { - "seed": { - "type": "integer", - "description": "Random seed for STITCH imputation" - } - } - ], - "output": [ - { - "vcf_index": { - "description": "Channel with imputed VCF files", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata map combined with the posfile, chunks and map data map.\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF imputed file", - "pattern": "*.{vcf,bcf,vcf.gz}" - } - }, - { - "index": { - "type": "file", - "description": "VCF index file", - "pattern": "*.{tbi,csi}" - } - } - ] - } - }, - { - "versions": { - "description": "Channel containing software versions file", - "structure": [ - { - "versions.yml": { - "type": "file", - "description": "File containing versions of the software used" - } - } - ] - } - } - ], - "authors": [ - "@louislenezet" - ], - "maintainers": [ - "@louislenezet" - ] - } - }, - { - "name": "bam_markduplicates_picard", - "path": "subworkflows/nf-core/bam_markduplicates_picard/meta.yml", - "type": "subworkflow", - "meta": { - "name": "bam_markduplicates_picard", - "description": "Picard MarkDuplicates, index BAM file and run samtools stats, flagstat and idxstats", - "keywords": [ - "markduplicates", - "bam", - "sam", - "cram" - ], - "components": [ - "picard/markduplicates", - "samtools/index", - "samtools/stats", - "samtools/idxstats", - "samtools/flagstat", - "bam_stats_samtools" - ], - "input": [ - { - "ch_reads": { - "description": "Sequence reads in BAM/CRAM/SAM format\nStructure: [ val(meta), path(reads) ]\n" - } - }, - { - "ch_fasta_fai": { - "description": "Reference genome fasta file required for CRAM input\nStructure: [ path(fasta), path(fai) ]\n" - } - } - ], - "output": [ - { - "bam": { - "description": "processed BAM/SAM file\nStructure: [ val(meta), path(bam) ]\n" - } - }, - { - "bai": { - "description": "BAM/SAM samtools index\nStructure: [ val(meta), path(bai) ]\n" - } - }, - { - "cram": { - "description": "processed CRAM file\nStructure: [ val(meta), path(cram) ]\n" - } - }, - { - "crai": { - "description": "CRAM samtools index\nStructure: [ val(meta), path(crai) ]\n" - } - }, - { - "csi": { - "description": "CSI samtools index\nStructure: [ val(meta), path(csi) ]\n" - } - }, - { - "stats": { - "description": "File containing samtools stats output\nStructure: [ val(meta), path(stats) ]\n" - } - }, - { - "flagstat": { - "description": "File containing samtools flagstat output\nStructure: [ val(meta), path(flagstat) ]\n" - } - }, - { - "idxstats": { - "description": "File containing samtools idxstats output\nStructure: [ val(meta), path(idxstats) ]\n" - } - }, - { - "per_sample_mqc_bundle": { - "description": "Per-sample MultiQC-feeding outputs (stats, flagstat, idxstats, metrics) joined on meta.\nStructure: [ val(meta), list(files) ]\n" - } - }, - { - "versions": { - "description": "Files containing software versions\nStructure: [ path(versions.yml) ]\n" - } - } - ], - "authors": [ - "@dmarron", - "@drpatelh" - ], - "maintainers": [ - "@dmarron", - "@drpatelh" - ] - }, - "pipelines": [ - { - "name": "atacseq", - "version": "2.1.2" - }, - { - "name": "chipseq", - "version": "2.1.0" - }, - { - "name": "circdna", - "version": "1.1.0" - }, - { - "name": "rnaseq", - "version": "3.26.0" - }, - { - "name": "rnavar", - "version": "1.2.3" - }, - { - "name": "sammyseq", - "version": "dev" - }, - { - "name": "viralrecon", - "version": "3.0.0" - } - ] - }, - { - "name": "bam_markduplicates_samtools", - "path": "subworkflows/nf-core/bam_markduplicates_samtools/meta.yml", - "type": "subworkflow", - "meta": { - "name": "bam_markduplicates_samtools", - "description": "Samtools markduplicate SAM/BAM/CRAM file", - "keywords": [ - "markdup", - "bam", - "sam", - "cram" - ], - "components": [ - "samtools/collate", - "samtools/fixmate", - "samtools/sort", - "samtools/markdup" - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "fasta_fai": { - "type": "file", - "description": "FASTA file and index", - "pattern": "*.{fasta,fa,fai}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted and markduplicate BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - } - ], - "authors": [ - "@priyanka-surana" - ], - "maintainers": [ - "@priyanka-surana" - ] - } - }, - { - "name": "bam_methyldackel", - "path": "subworkflows/nf-core/bam_methyldackel/meta.yml", - "type": "subworkflow", - "meta": { - "name": "bam_methyldackel", - "description": "Performs methylation quantification based on negative readout of C to T conversion of 3-letter genome alignments using Methyldackel.", - "keywords": [ - "3-letter genome", - "methylation", - "5mC", - "methylseq", - "bisulphite", - "bisulfite", - "bam" - ], - "components": [ - "methyldackel/extract", - "methyldackel/mbias" - ], - "input": [ - { - "ch_bam": { - "type": "file", - "description": "BAM alignment files\nStructure: [ val(meta), path(bam) ]\n", - "pattern": "*.bam" - } - }, - { - "ch_bai": { - "type": "file", - "description": "BAM index files\nStructure: [ val(meta), path(bai) ]\n", - "pattern": "*.bai" - } - }, - { - "ch_fasta": { - "type": "file", - "description": "Structure: [ val(meta), path(fasta) ]\n", - "pattern": "*.{fa,fa.gz}" - } - }, - { - "ch_fasta_index": { - "type": "file", - "description": "Structure: [ val(meta), path(fasta index) ]\n" - } - } - ], - "output": [ - { - "methydackel_extract_bedgraph": { - "type": "file", - "description": "bedGraph file, containing per-base methylation metrics\nStructure: [ val(meta), path(bedgraph) ]\n", - "pattern": "*.bedGraph" - } - }, - { - "methydackel_extract_methylkit": { - "type": "file", - "description": "methylKit file, containing per-base methylation metrics\nStructure: [ val(meta), path(methylKit) ]\n", - "pattern": "*.methylKit" - } - }, - { - "methydackel_mbias": { - "type": "file", - "description": "Text file containing methylation bias\nStructure: [ val(meta), path(mbias) ]\n", - "pattern": "*.{txt}" - } - } - ], - "authors": [ - "@eduard-watchmaker" - ], - "maintainers": [ - "@eduard-watchmaker" - ] - }, - "pipelines": [ - { - "name": "methylseq", - "version": "4.2.0" - } - ] - }, - { - "name": "bam_ngscheckmate", - "path": "subworkflows/nf-core/bam_ngscheckmate/meta.yml", - "type": "subworkflow", - "meta": { - "name": "bam_ngscheckmate", - "description": "Take a set of bam files and run NGSCheckMate to determine whether samples match with each other, using a set of SNPs.", - "keywords": [ - "ngscheckmate", - "qc", - "bam", - "snp" - ], - "components": [ - "bcftools/mpileup", - "ngscheckmate/ncm" - ], - "input": [ - { - "meta1": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM files for each sample", - "pattern": "*.{bam}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing bed file information\ne.g. [ id:'sarscov2' ]\n" - } - }, - { - "snp_bed": { - "type": "file", - "description": "BED file containing the SNPs to analyse. NGSCheckMate provides some default ones for hg19/hg38.", - "pattern": "*.{bed}" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference genome meta information\ne.g. [ id:'sarscov2' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "fasta file for the genome", - "pattern": "*.{fasta}" - } - }, - { - "fai": { - "type": "file", - "description": "fasta file index for the genome", - "pattern": "*.{fai}" - } - } - ], - "output": [ - { - "pdf": { - "type": "file", - "description": "A pdf containing a dendrogram showing how the samples match up", - "pattern": "*.{pdf}" - } - }, - { - "corr_matrix": { - "type": "file", - "description": "A text file containing the correlation matrix between each sample", - "pattern": "*corr_matrix.txt" - } - }, - { - "matched": { - "type": "file", - "description": "A txt file containing only the samples that match with each other", - "pattern": "*matched.txt" - } - }, - { - "all": { - "type": "file", - "description": "A txt file containing all the sample comparisons, whether they match or not", - "pattern": "*all.txt" - } - }, - { - "vcf": { - "type": "file", - "description": "vcf files for each sample giving the SNP calls", - "pattern": "*.vcf" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@SPPearce" - ], - "maintainers": [ - "@SPPearce" - ] - }, - "pipelines": [ - { - "name": "sarek", - "version": "3.8.1" - } - ] - }, - { - "name": "bam_qc_picard", - "path": "subworkflows/nf-core/bam_qc_picard/meta.yml", - "type": "subworkflow", - "meta": { - "name": "bam_qc_picard", - "description": "Produces comprehensive statistics from BAM file", - "keywords": [ - "statistics", - "counts", - "hs_metrics", - "wgs_metrics", - "bam", - "sam", - "cram" - ], - "components": [ - "picard/collectmultiplemetrics", - "picard/collectwgsmetrics", - "picard/collecthsmetrics" - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "bai": { - "type": "file", - "description": "BAM/CRAM/SAM file index", - "pattern": "*.{bai,crai,sai}" - } - }, - { - "bait_intervals": { - "type": "optional file", - "description": "An interval list or bed file that contains the locations of the baits used.", - "pattern": "baits.{interval_list,bed,bed.gz}" - } - }, - { - "target_intervals": { - "type": "optional file", - "description": "An interval list or bed file that contains the locations of the targets.", - "pattern": "targets.{interval_list,bed,bed.gz}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "optional file", - "description": "Reference fasta file", - "pattern": "*.{fasta,fa,fna}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta_fai": { - "type": "optional file", - "description": "Reference fasta file index", - "pattern": "*.{fasta,fa,fna}.fai" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta_dict": { - "type": "optional file", - "description": "Reference fasta sequence dictionary", - "pattern": "*.{dict}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "coverage_metrics": { - "type": "file", - "description": "Alignment metrics files generated by picard CollectHsMetrics or CollectWgsMetrics", - "pattern": "*_metrics.txt" - } - }, - { - "multiple_metrics": { - "type": "file", - "description": "Alignment metrics files generated by picard CollectMultipleMetrics", - "pattern": "*_{metrics}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@matthdsm" - ], - "maintainers": [ - "@matthdsm" - ] - } - }, - { - "name": "bam_qc_rnaseq", - "path": "subworkflows/nf-core/bam_qc_rnaseq/meta.yml", - "type": "subworkflow", - "meta": { - "name": "bam_qc_rnaseq", - "description": "Run post-alignment QC tools on RNA-seq BAM files including library complexity\nestimation (Preseq), biotype QC (featureCounts), RNA-seq-specific QC metrics\n(Qualimap), duplicate rate analysis (dupRadar), and comprehensive RSeQC analysis.\n", - "keywords": [ - "rnaseq", - "bam", - "qc", - "quality_control", - "preseq", - "qualimap", - "dupradar", - "rseqc", - "featurecounts", - "biotype" - ], - "components": [ - "preseq/lcextrap", - "qualimap/rnaseq", - "dupradar", - "subread/featurecounts", - "custom/multiqccustombiotype", - "samtools/sort", - "bam_rseqc" - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false, strandedness:'reverse' ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "Coordinate-sorted BAM file aligned to the genome", - "pattern": "*.{bam}" - } - }, - { - "bai": { - "type": "file", - "description": "Index for the genome-aligned BAM file", - "pattern": "*.{bai}" - } - }, - { - "gtf": { - "type": "file", - "description": "GTF annotation file", - "pattern": "*.{gtf}" - } - }, - { - "gene_bed": { - "type": "file", - "description": "BED12 file for the reference gene model", - "pattern": "*.{bed}" - } - }, - { - "fasta_fai": { - "type": "file", - "description": "Tuple of FASTA and FAI files for samtools sort\n[ val(meta), path(fasta), path(fai) ]\n" - } - }, - { - "biotypes_header": { - "type": "file", - "description": "Header file for biotype counts MultiQC section", - "pattern": "*.{txt}" - } - }, - { - "tools": { - "type": "list", - "description": "List of QC tools to run. Top-level tools: 'preseq', 'biotype_qc', 'qualimap',\n'dupradar'. RSeQC modules use an 'rseqc_' prefix: 'rseqc_bam_stat',\n'rseqc_inner_distance', 'rseqc_infer_experiment', 'rseqc_junction_annotation',\n'rseqc_junction_saturation', 'rseqc_read_distribution', 'rseqc_read_duplication',\n'rseqc_tin'. Pass an empty list to skip all.\n" - } - }, - { - "biotype": { - "type": "string", - "description": "GTF attribute for biotype grouping (e.g. \"gene_type\" or \"gene_biotype\").\nOnly used when 'biotype_qc' is in tools. Set to empty string to skip biotype QC.\n" - } - } - ], - "output": [ - { - "multiqc_files": { - "type": "file", - "description": "Collected MultiQC-compatible output files from all enabled tools" - } - }, - { - "preseq_lc_extrap": { - "type": "file", - "description": "Preseq library complexity extrapolation curve", - "pattern": "*.lc_extrap.txt" - } - }, - { - "preseq_log": { - "type": "file", - "description": "Preseq log file", - "pattern": "*.log" - } - }, - { - "featurecounts_counts": { - "type": "file", - "description": "featureCounts count matrix", - "pattern": "*.featureCounts.txt" - } - }, - { - "featurecounts_summary": { - "type": "file", - "description": "featureCounts summary statistics", - "pattern": "*.featureCounts.txt.summary" - } - }, - { - "biotype_tsv": { - "type": "file", - "description": "Biotype counts formatted for MultiQC bargraph", - "pattern": "*biotype_counts_mqc.tsv" - } - }, - { - "biotype_rrna": { - "type": "file", - "description": "rRNA percentage for MultiQC general stats", - "pattern": "*biotype_counts_rrna_mqc.tsv" - } - }, - { - "qualimap_results": { - "type": "directory", - "description": "Qualimap RNA-seq QC results directory" - } - }, - { - "dupradar_multiqc": { - "type": "file", - "description": "dupRadar MultiQC-compatible output", - "pattern": "*_mqc.txt" - } - }, - { - "inferexperiment_txt": { - "type": "file", - "description": "RSeQC infer_experiment results (for strandedness detection)", - "pattern": "*.infer_experiment.txt" - } - }, - { - "bamstat_txt": { - "type": "file", - "description": "RSeQC bam_stat report", - "pattern": "*.bam_stat.txt" - } - }, - { - "readdistribution_txt": { - "type": "file", - "description": "RSeQC read_distribution report", - "pattern": "*.read_distribution.txt" - } - }, - { - "tin_txt": { - "type": "file", - "description": "RSeQC TIN results summary", - "pattern": "*.txt" - } - }, - { - "per_sample_mqc_bundle": { - "type": "tuple", - "description": "Per-sample MultiQC-feeding outputs (Preseq, biotype TSV, Qualimap,\ndupRadar, and RSeQC bamstat/inferexperiment/innerdistance_freq/\njunctionannotation_log/junctionsaturation_rscript/readdistribution/\nreadduplication_pos/tin) joined on meta.\nStructure: [ val(meta), list(files) ]\n" - } - } - ], - "authors": [ - "@pinin4fjords" - ], - "maintainers": [ - "@pinin4fjords" - ] - }, - "pipelines": [ - { - "name": "rnaseq", - "version": "3.26.0" - } - ] - }, - { - "name": "bam_rseqc", - "path": "subworkflows/nf-core/bam_rseqc/meta.yml", - "type": "subworkflow", - "meta": { - "name": "bam_rseqc", - "description": "Subworkflow to run multiple commands in the RSeqC package", - "keywords": [ - "rnaseq", - "experiment", - "inferexperiment", - "bamstat", - "innerdistance", - "junctionannotation", - "junctionsaturation", - "readdistribution", - "readduplication", - "tin" - ], - "components": [ - "rseqc", - "rseqc/tin", - "rseqc/readduplication", - "rseqc/readdistribution", - "rseqc/junctionsaturation", - "rseqc/junctionannotation", - "rseqc/innerdistance", - "rseqc/inferexperiment", - "rseqc/bamstat" - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file to calculate statistics", - "pattern": "*.{bam}" - } - }, - { - "bai": { - "type": "file", - "description": "Index for input BAM file", - "pattern": "*.{bai}" - } - }, - { - "bed": { - "type": "file", - "description": "BED file for the reference gene model", - "pattern": "*.{bed}" - } - }, - { - "rseqc_modules": { - "type": "list", - "description": "List of rseqc modules to run\ne.g. [ 'bam_stat', 'infer_experiment' ]\n" - } - } - ], - "output": [ - { - "bamstat_txt": { - "type": "file", - "description": "bam statistics report", - "pattern": "*.bam_stat.txt" - } - }, - { - "innerdistance_all": { - "type": "file", - "description": "All the output files from RSEQC_INNERDISTANCE", - "pattern": "*.{txt,pdf,R}" - } - }, - { - "innerdistance_distance": { - "type": "file", - "description": "the inner distances", - "pattern": "*.inner_distance.txt" - } - }, - { - "innerdistance_freq": { - "type": "file", - "description": "frequencies of different insert sizes", - "pattern": "*.inner_distance_freq.txt" - } - }, - { - "innerdistance_mean": { - "type": "file", - "description": "mean/median values of inner distances", - "pattern": "*.inner_distance_mean.txt" - } - }, - { - "innerdistance_pdf": { - "type": "file", - "description": "distribution plot of inner distances", - "pattern": "*.inner_distance_plot.pdf" - } - }, - { - "innerdistance_rscript": { - "type": "file", - "description": "script to reproduce the plot", - "pattern": "*.inner_distance_plot.R" - } - }, - { - "inferexperiment_txt": { - "type": "file", - "description": "infer_experiment results report", - "pattern": "*.infer_experiment.txt" - } - }, - { - "junctionannotation_all": { - "type": "file", - "description": "All the output files from RSEQC_JUNCTIONANNOTATION", - "pattern": "*.{bed,xls,pdf,R,log}" - } - }, - { - "junctionannotation_bed": { - "type": "file", - "description": "bed file of annotated junctions", - "pattern": "*.junction.bed" - } - }, - { - "junctionannotation_interact_bed": { - "type": "file", - "description": "Interact bed file", - "pattern": "*.Interact.bed" - } - }, - { - "junctionannotation_xls": { - "type": "file", - "description": "xls file with junction information", - "pattern": "*.xls" - } - }, - { - "junctionannotation_pdf": { - "type": "file", - "description": "junction plot", - "pattern": "*.junction.pdf" - } - }, - { - "junctionannotation_events_pdf": { - "type": "file", - "description": "events plot", - "pattern": "*.events.pdf" - } - }, - { - "junctionannotation_rscript": { - "type": "file", - "description": "Rscript to reproduce the plots", - "pattern": "*.r" - } - }, - { - "junctionannotation_log": { - "type": "file", - "description": "Log file generated by tool", - "pattern": "*.log" - } - }, - { - "junctionsaturation_all": { - "type": "file", - "description": "All the output files from RSEQC_JUNCTIONSATURATION", - "pattern": "*.{pdf,R}" - } - }, - { - "junctionsaturation_pdf": { - "type": "file", - "description": "Junction saturation report", - "pattern": "*.pdf" - } - }, - { - "junctionsaturation_rscript": { - "type": "file", - "description": "Junction saturation R-script", - "pattern": "*.r" - } - }, - { - "readdistribution_txt": { - "type": "file", - "description": "the read distribution report", - "pattern": "*.read_distribution.txt" - } - }, - { - "readduplication_all": { - "type": "file", - "description": "All the output files from RSEQC_READDUPLICATION", - "pattern": "*.{xls,pdf,R}" - } - }, - { - "readduplication_seq_xls": { - "type": "file", - "description": "Read duplication rate determined from mapping position of read", - "pattern": "*seq.DupRate.xls" - } - }, - { - "readduplication_pos_xls": { - "type": "file", - "description": "Read duplication rate determined from sequence of read", - "pattern": "*pos.DupRate.xls" - } - }, - { - "readduplication_pdf": { - "type": "file", - "description": "plot of duplication rate", - "pattern": "*.pdf" - } - }, - { - "readduplication_rscript": { - "type": "file", - "description": "script to reproduce the plot", - "pattern": "*.R" - } - }, - { - "tin_txt": { - "type": "file", - "description": "TXT file containing tin.py results summary", - "pattern": "*.txt" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@drpatelh", - "@kevinmenden" - ], - "maintainers": [ - "@drpatelh", - "@kevinmenden" - ] - }, - "pipelines": [ - { - "name": "callingcards", - "version": "1.0.0" - }, - { - "name": "nascent", - "version": "2.3.0" - }, - { - "name": "rnaseq", - "version": "3.26.0" - } - ] - }, - { - "name": "bam_sort_stats_samtools", - "path": "subworkflows/nf-core/bam_sort_stats_samtools/meta.yml", - "type": "subworkflow", - "meta": { - "name": "bam_sort_stats_samtools", - "description": "Sort SAM/BAM/CRAM file", - "keywords": [ - "sort", - "bam", - "sam", - "cram" - ], - "components": [ - "samtools/sort", - "samtools/index", - "samtools/stats", - "samtools/idxstats", - "samtools/flagstat", - "bam_stats_samtools" - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome fasta file", - "pattern": "*.{fasta,fa}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "bai": { - "type": "file", - "description": "BAM/CRAM/SAM index file", - "pattern": "*.{bai,crai,sai}" - } - }, - { - "crai": { - "type": "file", - "description": "BAM/CRAM/SAM index file", - "pattern": "*.{bai,crai,sai}" - } - }, - { - "stats": { - "type": "file", - "description": "File containing samtools stats output", - "pattern": "*.{stats}" - } - }, - { - "flagstat": { - "type": "file", - "description": "File containing samtools flagstat output", - "pattern": "*.{flagstat}" - } - }, - { - "idxstats": { - "type": "file", - "description": "File containing samtools idxstats output", - "pattern": "*.{idxstats}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@drpatelh", - "@ewels" - ], - "maintainers": [ - "@drpatelh", - "@ewels" - ] - }, - "pipelines": [ - { - "name": "atacseq", - "version": "2.1.2" - }, - { - "name": "chipseq", - "version": "2.1.0" - }, - { - "name": "circrna", - "version": "dev" - }, - { - "name": "cutandrun", - "version": "3.2.2" - }, - { - "name": "genomeassembler", - "version": "1.1.0" - }, - { - "name": "lncpipe", - "version": "dev" - }, - { - "name": "magmap", - "version": "1.0.0" - }, - { - "name": "metatdenovo", - "version": "1.3.0" - }, - { - "name": "methylseq", - "version": "4.2.0" - }, - { - "name": "nascent", - "version": "2.3.0" - }, - { - "name": "pacsomatic", - "version": "dev" - }, - { - "name": "phageannotator", - "version": "dev" - }, - { - "name": "riboseq", - "version": "1.2.0" - }, - { - "name": "rnadnavar", - "version": "dev" - }, - { - "name": "rnafusion", - "version": "4.1.2" - }, - { - "name": "rnaseq", - "version": "3.26.0" - }, - { - "name": "rnasplice", - "version": "1.0.4" - }, - { - "name": "rnavar", - "version": "1.2.3" - }, - { - "name": "sammyseq", - "version": "dev" - }, - { - "name": "scnanoseq", - "version": "1.2.2" - }, - { - "name": "smrnaseq", - "version": "2.4.1" - }, - { - "name": "viralrecon", - "version": "3.0.0" - } - ] - }, - { - "name": "bam_split_by_region", - "path": "subworkflows/nf-core/bam_split_by_region/meta.yml", - "type": "subworkflow", - "meta": { - "name": "bam_split_by_region", - "description": "Split the reads in the input bam by specified genomic region.", - "keywords": [ - "split", - "bam", - "sam", - "cram", - "index" - ], - "components": [ - "samtools/view", - "samtools/index" - ], - "input": [ - { - "ch_bam": { - "description": "The input channel of this subworkflow containing:\n- meta: Groovy Map containing sample information => doesn't have a field called 'genomic_region'\n- bam: BAM/CRAM/SAM file\n- bai: Index for BAM/CRAM/SAM file\n- regions_file: A file containing the genomic regions used to separate the reads in the\n input bam. This should be a BED or TSV file containing either a single\n column of chromosome names, two columns (chromosome name and position),\n or three columns (chromosome name, start position, and end position).\nStructure: [ val(meta), path(bam), path(bai), path(regions_file) ]\n" - } - } - ], - "output": [ - { - "bam_bai": { - "description": "BAM/CRAM/SAM file, the meta contains a new 'genomic_region' field with the included regions\nStructure: [ val(meta), path(bam), path(bai) ]\n" - } - }, - { - "versions": { - "description": "Files containing software versions\nStructure: [ path(versions.yml) ]\n" - } - } - ], - "authors": [ - "@TCLamnidis" - ], - "maintainers": [ - "@TCLamnidis" - ] - } - }, - { - "name": "bam_stats_mirna_mirtop", - "path": "subworkflows/nf-core/bam_stats_mirna_mirtop/meta.yml", - "type": "subworkflow", - "meta": { - "name": "bam_stats_mirna_mirtop", - "description": "mirtop is a command line tool to annotate miRNAs and isomiRs and compute general statistics using the mirGFF3 format.", - "keywords": [ - "miRNA", - "isomirs", - "bam", - "stats" - ], - "components": [ - "mirtop/gff", - "mirtop/counts", - "mirtop/export", - "mirtop/stats" - ], - "input": [ - { - "ch_bam": { - "type": "file", - "description": "The input channel containing the BAM/CRAM/SAM files\nStructure: [ val(meta), path(bam) ]\n", - "pattern": "*.{bam/cram/sam}" - } - }, - { - "ch_hairpin": { - "type": "file", - "description": "Input channel containing the hairpin fasta file\nStructure: [ val(meta), path(fasta) ]\n", - "pattern": "*.{fasta,fa}" - } - }, - { - "ch_gtf_species": { - "type": "file", - "description": "Input channel containing the species gtf and the name of species in miRbase format\nStructure: [ val(meta), path(gtf), val(species)]\n", - "pattern": "*.{gtf}" - } - } - ], - "output": [ - { - "rawdata_tsv": { - "type": "file", - "description": "Channel containing isomiRs compatible files\nStructure: [ val(meta), path(tsv) ]\n", - "pattern": "*.tsv" - } - }, - { - "stats_txt": { - "type": "file", - "description": "Channel containing TXT file with a table with different statistics for each type of isomiRs: total counts, average counts, total sequences.\nStructure: [ val(meta), path(txt) ]\n", - "pattern": "*.txt" - } - }, - { - "stats_log": { - "type": "file", - "description": "Channel containing log files in JSON format with the same information as stats_txt\nStructure: [ val(meta), path(log) ]\n", - "pattern": "*.log" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions\nStructure: [ path(versions.yml) ]\n", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@atrigila" - ], - "maintainers": [ - "@atrigila" - ] - }, - "pipelines": [ - { - "name": "smrnaseq", - "version": "2.4.1" - } - ] - }, - { - "name": "bam_stats_samtools", - "path": "subworkflows/nf-core/bam_stats_samtools/meta.yml", - "type": "subworkflow", - "meta": { - "name": "bam_stats_samtools", - "description": "Produces comprehensive statistics from SAM/BAM/CRAM file", - "keywords": [ - "statistics", - "counts", - "bam", - "sam", - "cram" - ], - "components": [ - "samtools/stats", - "samtools/idxstats", - "samtools/flagstat" - ], - "input": [ - { - "ch_bam_bai": { - "description": "The input channel containing the BAM/CRAM and it's index\nStructure: [ val(meta), path(bam), path(bai) ]\n" - } - }, - { - "ch_fasta": { - "description": "Reference genome fasta file\nStructure: [ path(fasta) ]\n" - } - } - ], - "output": [ - { - "stats": { - "description": "File containing samtools stats output\nStructure: [ val(meta), path(stats) ]\n" - } - }, - { - "flagstat": { - "description": "File containing samtools flagstat output\nStructure: [ val(meta), path(flagstat) ]\n" - } - }, - { - "idxstats": { - "description": "File containing samtools idxstats output\nStructure: [ val(meta), path(idxstats)]\n" - } - }, - { - "versions": { - "description": "Files containing software versions\nStructure: [ path(versions.yml) ]\n" - } - } - ], - "authors": [ - "@drpatelh" - ], - "maintainers": [ - "@drpatelh" - ] - }, - "pipelines": [ - { - "name": "atacseq", - "version": "2.1.2" - }, - { - "name": "callingcards", - "version": "1.0.0" - }, - { - "name": "chipseq", - "version": "2.1.0" - }, - { - "name": "circdna", - "version": "1.1.0" - }, - { - "name": "circrna", - "version": "dev" - }, - { - "name": "cutandrun", - "version": "3.2.2" - }, - { - "name": "genomeassembler", - "version": "1.1.0" - }, - { - "name": "lncpipe", - "version": "dev" - }, - { - "name": "magmap", - "version": "1.0.0" - }, - { - "name": "metatdenovo", - "version": "1.3.0" - }, - { - "name": "methylseq", - "version": "4.2.0" - }, - { - "name": "nascent", - "version": "2.3.0" - }, - { - "name": "pacsomatic", - "version": "dev" - }, - { - "name": "phageannotator", - "version": "dev" - }, - { - "name": "riboseq", - "version": "1.2.0" - }, - { - "name": "rnadnavar", - "version": "dev" - }, - { - "name": "rnafusion", - "version": "4.1.2" - }, - { - "name": "rnaseq", - "version": "3.26.0" - }, - { - "name": "rnasplice", - "version": "1.0.4" - }, - { - "name": "rnavar", - "version": "1.2.3" - }, - { - "name": "sammyseq", - "version": "dev" - }, - { - "name": "scnanoseq", - "version": "1.2.2" - }, - { - "name": "smrnaseq", - "version": "2.4.1" - }, - { - "name": "viralmetagenome", - "version": "1.1.1" - }, - { - "name": "viralrecon", - "version": "3.0.0" - } - ] - }, - { - "name": "bam_stringtie_merge", - "path": "subworkflows/nf-core/bam_stringtie_merge/meta.yml", - "type": "subworkflow", - "meta": { - "name": "bam_stringtie_merge", - "description": "Assemble transcripts from sorted BAM alignments using StringTie, then merge per-sample transcript GTFs into a unified annotation.\n", - "keywords": [ - "rna-seq", - "transcript-assembly", - "transcript-merge", - "stringtie", - "gtf" - ], - "components": [ - "stringtie/stringtie", - "stringtie/merge" - ], - "input": [ - { - "bam_sorted": { - "type": "file", - "description": "Sorted alignment files.\nStructure: [ val(meta), path(bam) ]\n", - "pattern": "*.bam" - } - }, - { - "ch_chrgtf": { - "type": "file", - "description": "Reference gene annotation (GTF) for guided assembly and merge.\nStructure: [ val(meta), path(gtf) ]\n", - "pattern": "*.gtf" - } - } - ], - "output": [ - { - "stringtie_gtf": { - "type": "file", - "description": "Merged transcript annotation produced by StringTie --merge.\nStructure: [ val(meta), path(gtf) ]\n", - "pattern": "*.gtf" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions for the subworkflow components.\nStructure: [ path(versions.yml) ]\n", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@atrigila", - "@rannick", - "@nvnieuwk" - ], - "maintainers": [ - "@atrigila", - "@rannick", - "@nvnieuwk" - ] - }, - "pipelines": [ - { - "name": "rnafusion", - "version": "4.1.2" - }, - { - "name": "rnaseq", - "version": "3.26.0" - } - ] - }, - { - "name": "bam_subsampledepth_samtools", - "path": "subworkflows/nf-core/bam_subsampledepth_samtools/meta.yml", - "type": "subworkflow", - "meta": { - "name": "bam_subsampledepth_samtools", - "description": "Subsample a BAM/CRAM/SAM file using samtools to a given mean depth", - "keywords": [ - "subsample", - "bam", - "sam", - "cram" - ], - "components": [ - "samtools/depth", - "samtools/view", - "gawk" - ], - "input": [ - { - "ch_bam": { - "type": "file", - "description": "The input channel containing the BAM/CRAM/SAM files and their indexes.\nStructure: [ val(meta), path(bam), path(bai) ]\n", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "ch_depth": { - "type": "float", - "description": "Target depth to downsample each input of ch_bam to.\nStructure: [ val(meta), val(depth) ]\nThe meta map will be combined to the meta map of the ch_bam channel.\n" - } - }, - { - "ch_fasta": { - "type": "file", - "description": "The reference genome channel containing the fasta files and its index\nStructure: [ val(meta), path(fasta), path(fai) ]\n", - "pattern": "*.{fa(sta)?}" - } - } - ], - "output": [ - { - "bam_subsampled": { - "type": "file", - "description": "Channel containing subsampled BAM/CRAM/SAM files and their indexes.\ndepth and subsample_fraction parameter will be added to the meta map.\nThe later will be used to set the `--subsample` parameter in SAMTOOLS/VIEW command.\nStructure: [ val(meta), path(bam), path(csi) ]\n", - "pattern": "*.{bam,cram,sam}" - } - } - ], - "authors": [ - "@louislenezet" - ], - "maintainers": [ - "@louislenezet" - ] - } - }, - { - "name": "bam_taps_conversion", - "path": "subworkflows/nf-core/bam_taps_conversion/meta.yml", - "type": "subworkflow", - "meta": { - "name": "bam_taps_conversion", - "description": "Uses rastair to assess C->T conversion as a readout for methylation in a genome-wide basis", - "keywords": [ - "TAPS conversion", - "Methylation analysis", - "Molecular bias (MBIAS)", - "mCtoT", - "rastair", - "4-letter genome" - ], - "components": [ - "rastair/mbias", - "rastair/call", - "rastair/methylkit", - "rastair/mbiasparser" - ], - "input": [ - { - "ch_fasta": { - "type": "file", - "description": "Reference genome fasta file\nStructure: [ [:], path(fasta) ]\n", - "pattern": "*.{fa,fasta}" - } - }, - { - "ch_fasta_index": { - "type": "file", - "description": "Reference genome index file\nStructure: [ val(meta), path(fai) ]\n", - "pattern": "*.fai" - } - }, - { - "ch_bam": { - "type": "file", - "description": "BAM alignment files\nStructure: [ val(meta), path(bam) ]\n", - "pattern": "*.bam" - } - }, - { - "ch_bai": { - "type": "file", - "description": "BAM index files\nStructure: [ val(meta), path(bai) ]\n", - "pattern": "*.bai" - } - } - ], - "output": [ - { - "mbias": { - "type": "file", - "description": "File describing the molecular bias (MBIAS) of the TAPS conversion\nStructure: [ val(meta), path(mbias) ]\n", - "pattern": "*.txt" - } - }, - { - "call": { - "type": "file", - "description": "Rastair call output files (similar to bed format, genome-wide)\nStructure: [ val(meta), path(call) ]\n", - "pattern": "*.txt" - } - }, - { - "methylkit": { - "type": "file", - "description": "Rastair call output files in MethylKit format (similar to bed format, genome-wide)\nStructure: [ val(meta), path(methylkit) ]\n", - "pattern": "*.gz" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions\nStructure: [ path(versions.yml) ]\n", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@eduard-watchmaker" - ], - "maintainers": [ - "@eduard-watchmaker" - ] - }, - "pipelines": [ - { - "name": "methylseq", - "version": "4.2.0" - } - ] - }, - { - "name": "bam_telomere_estimation", - "path": "subworkflows/nf-core/bam_telomere_estimation/meta.yml", - "type": "subworkflow", - "meta": { - "name": "bam_telomere_estimation", - "description": "Estimate telomere length and content from aligned reads using telseq, telogator2, and telomerehunter", - "keywords": [ - "telomere", - "telseq", - "telogator2", - "telomerehunter", - "bam", - "cram" - ], - "components": [ - "telseq", - "telogator2", - "telomerehunter", - "custom/summarisetelomereestimation" - ], - "input": [ - { - "ch_reads": { - "type": "file", - "description": "Channel of aligned reads with data type and optional index.\nStructure: [ val(meta), val(data_type), path(reads), path(reads_index) ]\ndata_type: 'short' routes to telseq, 'long' routes to telogator2.\nThe calling pipeline is responsible for determining the sequencing type.\nReads must be indexed. bed is an optional exome BED for telseq ([] if not needed).\n" - } - }, - { - "ch_control": { - "type": "file", - "description": "Channel of control/normal BAM files for telomerehunter.\nStructure: [ val(meta), path(control_bam), path(control_bai) ]\nPass Channel.empty() if not needed.\n" - } - }, - { - "ch_fasta": { - "type": "file", - "description": "Reference genome FASTA with index.\nStructure: [ val(meta2), path(fasta), path(fai) ]\n" - } - }, - { - "ch_cytoband": { - "type": "file", - "description": "Optional cytoband file for telomerehunter.\nStructure: [ path(cytoband) ]\nWhen not provided ([[]] / empty), telomerehunter uses its bundled hg19 cytoband.\nMust be supplied for hg38 data to avoid an IndexError caused by\nchromosomes that are longer in hg38 than hg19.\n" - } - }, - { - "run_telomerehunter": { - "type": "boolean", - "description": "Enable telomerehunter content profiling" - } - }, - { - "length_estimator": { - "type": "string", - "description": "Global override for length estimation tool. If set, all samples\nuse this tool regardless of per-sample data_type.\nValues: 'short', 'long', or null.\n" - } - } - ], - "output": [ - { - "length_tsv": { - "type": "file", - "description": "Raw telomere length TSV from telseq or telogator2.\nStructure: [ val(meta), path(tsv) ]\n" - } - }, - { - "content_tsv": { - "type": "file", - "description": "Raw telomere content TSV from telomerehunter (empty if not run).\nStructure: [ val(meta), path(tsv) ]\n" - } - }, - { - "summary": { - "type": "file", - "description": "Normalised summary combining length and content per sample.\nStructure: [ val(meta), path(tsv) ]\n" - } - }, - { - "telomerehunter_tumor": { - "type": "directory", - "description": "Telomerehunter tumor analysis directory (empty if not run).\nStructure: [ val(meta), path(dir) ]\n" - } - }, - { - "telomerehunter_control": { - "type": "directory", - "description": "Telomerehunter control analysis directory (empty if not run).\nStructure: [ val(meta), path(dir) ]\n" - } - }, - { - "telogator2_plots": { - "type": "file", - "description": "Telogator2 allele and violin plots.\nStructure: [ val(meta), path(*.png) ]\n" - } - }, - { - "telogator2_stats": { - "type": "file", - "description": "Telogator2 QC statistics.\nStructure: [ val(meta), path(stats.txt) ]\n" - } - } - ], - "authors": [ - "@pinin4fjords" - ], - "maintainers": [ - "@pinin4fjords" - ] - } - }, - { - "name": "bam_tumor_normal_somatic_variant_calling_gatk", - "path": "subworkflows/nf-core/bam_tumor_normal_somatic_variant_calling_gatk/meta.yml", - "type": "subworkflow", - "meta": { - "name": "bam_tumor_normal_somatic_variant_calling_gatk", - "description": "Perform variant calling on a paired tumor normal set of samples using mutect2 tumor normal mode.\nf1r2 output of mutect2 is run through learnreadorientationmodel to get the artifact priors.\nRun the input bam files through getpileupsummarries and then calculatecontamination to get the contamination and segmentation tables.\nFilter the mutect2 output vcf using filtermutectcalls, artifact priors and the contamination & segmentation tables for additional filtering.\n", - "keywords": [ - "gatk4", - "mutect2", - "learnreadorientationmodel", - "getpileupsummaries", - "calculatecontamination", - "filtermutectcalls", - "variant_calling", - "tumor_only", - "filtered_vcf" - ], - "components": [ - "gatk4/mutect2", - "gatk4/learnreadorientationmodel", - "gatk4/getpileupsummaries", - "gatk4/calculatecontamination", - "gatk4/filtermutectcalls" - ], - "input": [ - { - "ch_input": { - "description": "The tumor and normal BAM files, in that order, also able to take CRAM as an input\nCan contain an optional list of sample headers contained in the normal sample input file.\nStructure: [ val(meta), path(input), path(input_index), val(which_norm) ]\n" - } - }, - { - "ch_fasta": { - "description": "The reference fasta file\nStructure: [ path(fasta) ]\n" - } - }, - { - "ch_fai": { - "description": "Index of reference fasta file\nStructure: [ path(fai) ]\n" - } - }, - { - "ch_dict": { - "description": "GATK sequence dictionary\nStructure: [ path(dict) ]\n" - } - }, - { - "ch_alleles": { - "description": "VCF file to be used for force calling of alleles.\nStructure: [ path(alleles) ]\n" - } - }, - { - "ch_alleles_tbi": { - "description": "Index of VCF file of alleles for force calling.\nStructure: [ path(alleles_tbi) ]\n" - } - }, - { - "ch_germline_resource": { - "description": "Population vcf of germline sequencing, containing allele fractions.\nStructure: [ path(germline_resources) ]\n" - } - }, - { - "ch_germline_resource_tbi": { - "description": "Index file for the germline resource.\nStructure: [ path(germline_resources_tbi) ]\n" - } - }, - { - "ch_panel_of_normals": { - "description": "Vcf file to be used as a panel of normals.\nStructure: [ path(panel_of_normals) ]\n" - } - }, - { - "ch_panel_of_normals_tbi": { - "description": "Index for the panel of normals.\nStructure: [ path(panel_of_normals_tbi) ]\n" - } - }, - { - "ch_interval_file": { - "description": "File containing intervals.\nStructure: [ path(interval_files) ]\n" - } - } - ], - "output": [ - { - "mutect2_vcf": { - "description": "Compressed vcf file to be used for variant_calling.\nStructure: [ val(meta), path(vcf) ]\n" - } - }, - { - "mutect2_tbi": { - "description": "Indexes of the mutect2_vcf file\nStructure: [ val(meta), path(tbi) ]\n" - } - }, - { - "mutect2_stats": { - "description": "Stats files for the mutect2 vcf\nStructure: [ val(meta), path(stats) ]\n" - } - }, - { - "mutect2_f1r2": { - "description": "File containing information to be passed to LearnReadOrientationModel.\nStructure: [ val(meta), path(f1r2) ]\n" - } - }, - { - "artifact_priors": { - "description": "File containing artifact-priors to be used by filtermutectcalls.\nStructure: [ val(meta), path(artifact_priors) ]\n" - } - }, - { - "pileup_table_tumor": { - "description": "File containing the tumor pileup summary table, kept separate as calculatecontamination needs them individually specified.\nStructure: [ val(meta), path(table) ]\n" - } - }, - { - "pileup_table_normal": { - "description": "File containing the normal pileup summary table, kept separate as calculatecontamination needs them individually specified.\nStructure: [ val(meta), path(table) ]\n" - } - }, - { - "contamination_table": { - "description": "File containing the contamination table.\nStructure: [ val(meta), path(table) ]\n" - } - }, - { - "segmentation_table": { - "description": "Output table containing segmentation of tumor minor allele fractions.\nStructure: [ val(meta), path(table) ]\n" - } - }, - { - "filtered_vcf": { - "description": "File containing filtered mutect2 calls.\nStructure: [ val(meta), path(vcf) ]\n" - } - }, - { - "filtered_tbi": { - "description": "Tbi file that pairs with filtered vcf.\nStructure: [ val(meta), path(tbi) ]\n" - } - }, - { - "filtered_stats": { - "description": "File containing statistics of the filtermutectcalls run.\nStructure: [ val(meta), path(stats) ]\n" - } - } - ], - "authors": [ - "@GCJMackenzie" - ], - "maintainers": [ - "@GCJMackenzie" - ] - } - }, - { - "name": "bam_tumor_normal_somatic_variant_calling_strelka", - "path": "subworkflows/nf-core/bam_tumor_normal_somatic_variant_calling_strelka/meta.yml", - "type": "subworkflow", - "meta": { - "name": "bam_tumor_normal_somatic_variant_calling_strelka", - "description": "Perform variant calling on a paired tumor normal set of samples using strelka somatic mode.\nf1r2 output of mutect2 is run through learnreadorientationmodel to get the artifact priors.\nRun the input bam files through getpileupsummarries and then calculatecontamination to get the contamination and segmentation tables.\nFilter the mutect2 output vcf using filtermutectcalls, artifact priors and the contamination & segmentation tables for additional filtering.\n", - "keywords": [ - "strelka", - "variant_calling", - "filtered_vcf" - ], - "components": [ - "gatk4/mergevcfs", - "strelka/somatic" - ], - "input": [ - { - "ch_cram": { - "description": "The normal and tumor CRAM files, in that order.\nStructure: [ meta, normal_cram, normal_crai, tumor_cram, tumor_crai, manta_vcf, manta_tbi ] manta* are optional\n" - } - }, - { - "ch_dict": { - "description": "GATK sequence dictionary, optional\nStructure: [ meta, dict ]\n" - } - }, - { - "ch_fasta": { - "type": "file", - "description": "reference fasta file", - "pattern": ".{fa,fa.gz,fasta,fasta.gz}" - } - }, - { - "ch_fasta_fai": { - "type": "file", - "description": "reference fasta file index", - "pattern": "*.{fa,fasta}.fai" - } - }, - { - "ch_intervals": { - "description": "Intervals to be used for variant calling.\nStructure: [ interval.bed.gz, interval.bed.gz.tbi, num_intervals ] or [ [], [], 0 ] if no intervals\n" - } - } - ], - "output": [ - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "vcf": { - "type": "file", - "description": "Compressed vcf files for indels and snvs, in that order.\nStructure: [ val(meta), path(vcf), path(vcf) ]\n", - "pattern": "*.{vcf.gz}" - } - } - ], - "authors": [ - "@famosab" - ], - "maintainers": [ - "@famosab" - ] - } - }, - { - "name": "bam_tumor_only_somatic_variant_calling_gatk", - "path": "subworkflows/nf-core/bam_tumor_only_somatic_variant_calling_gatk/meta.yml", - "type": "subworkflow", - "meta": { - "name": "bam_tumor_only_somatic_variant_calling_gatk", - "description": "Perform variant calling on a single tumor sample using mutect2 tumor only mode.\nRun the input bam file through getpileupsummarries and then calculatecontaminationto get the contamination and segmentation tables.\nFilter the mutect2 output vcf using filtermutectcalls and the contamination & segmentation tables for additional filtering.\n", - "keywords": [ - "gatk4", - "mutect2", - "getpileupsummaries", - "calculatecontamination", - "filtermutectcalls", - "variant_calling", - "tumor_only", - "filtered_vcf" - ], - "components": [ - "gatk4/mutect2", - "gatk4/getpileupsummaries", - "gatk4/calculatecontamination", - "gatk4/filtermutectcalls" - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "input": { - "type": "list", - "description": "list containing one BAM file, also able to take CRAM as an input", - "pattern": "[ *.{bam/cram} ]" - } - }, - { - "input_index": { - "type": "list", - "description": "list containing one BAM file indexe, also able to take CRAM index as an input", - "pattern": "[ *.{bam.bai/cram.crai} ]" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference fasta file", - "pattern": "*.fasta" - } - }, - { - "fai": { - "type": "file", - "description": "Index of reference fasta file", - "pattern": "*.fasta.fai" - } - }, - { - "dict": { - "type": "file", - "description": "GATK sequence dictionary", - "pattern": "*.dict" - } - }, - { - "alleles": { - "type": "file", - "description": "vcf file to be used to force-call alleles.", - "pattern": "*.vcf.gz" - } - }, - { - "alleles_tbi": { - "type": "file", - "description": "Index file for alleles to be force-called.", - "pattern": "*.vcf.gz.tbi" - } - }, - { - "germline_resource": { - "type": "file", - "description": "Population vcf of germline sequencing, containing allele fractions.", - "pattern": "*.vcf.gz" - } - }, - { - "germline_resource_tbi": { - "type": "file", - "description": "Index file for the germline resource.", - "pattern": "*.vcf.gz.tbi" - } - }, - { - "panel_of_normals": { - "type": "file", - "description": "vcf file to be used as a panel of normals.", - "pattern": "*.vcf.gz" - } - }, - { - "panel_of_normals_tbi": { - "type": "file", - "description": "Index for the panel of normals.", - "pattern": "*.vcf.gz.tbi" - } - }, - { - "interval_file": { - "type": "file", - "description": "File containing intervals.", - "pattern": "*.interval_list" - } - } - ], - "output": [ - { - "mutect2_vcf": { - "type": "file", - "description": "Compressed vcf file to be used for variant_calling.", - "pattern": "[ *.vcf.gz ]" - } - }, - { - "mutect2_tbi": { - "type": "file", - "description": "Indexes of the mutect2_vcf file", - "pattern": "[ *vcf.gz.tbi ]" - } - }, - { - "mutect2_stats": { - "type": "file", - "description": "Stats files for the mutect2 vcf", - "pattern": "[ *vcf.gz.stats ]" - } - }, - { - "pileup_table": { - "type": "file", - "description": "File containing the pileup summary table.", - "pattern": "*.pileups.table" - } - }, - { - "contamination_table": { - "type": "file", - "description": "File containing the contamination table.", - "pattern": "*.contamination.table" - } - }, - { - "segmentation_table": { - "type": "file", - "description": "Output table containing segmentation of tumor minor allele fractions.", - "pattern": "*.segmentation.table" - } - }, - { - "filtered_vcf": { - "type": "file", - "description": "file containing filtered mutect2 calls.", - "pattern": "*.vcf.gz" - } - }, - { - "filtered_tbi": { - "type": "file", - "description": "tbi file that pairs with filtered vcf.", - "pattern": "*.vcf.gz.tbi" - } - }, - { - "filtered_stats": { - "type": "file", - "description": "file containing statistics of the filtermutectcalls run.", - "pattern": "*.filteringStats.tsv" - } - } - ], - "authors": [ - "@GCJMackenzie" - ], - "maintainers": [ - "@GCJMackenzie" - ] - } - }, - { - "name": "bam_variant_calling_mpileup_bcftools", - "path": "subworkflows/nf-core/bam_variant_calling_mpileup_bcftools/meta.yml", - "type": "subworkflow", - "meta": { - "name": "BAM_VARIANT_CALLING_MPILEUP_BCFTOOLS", - "description": "Subworkflow to compute genotype likelihoods from BAM files using\nbcftools/mpileup and bcftools/call variants by chromosomes.\nThe resulting VCF files are then merged by chromosomes and\nannotated with bcftools/annotate to give an ID for each variants.\nDuring samples merging and region concatenation, all metadata will\nbe preserved and stored in the key `metas` at each step.\n", - "keywords": [ - "BAM", - "genotype likelihoods", - "bcftools" - ], - "components": [ - "gawk", - "tabix/bgzip", - "bcftools/mpileup", - "bcftools/merge", - "bcftools/annotate", - "bcftools/concat", - "vcf_gather_bcftools" - ], - "input": [ - { - "ch_bam": { - "description": "Channel with input data", - "structure": [ - { - "meta": null, - "type": "map", - "description": "Metadata map" - }, - { - "bam": null, - "type": "file", - "description": "Input BAM file", - "pattern": "*.bam" - }, - { - "index": null, - "type": "file", - "description": "Input BAM index file", - "pattern": "*.{bai,csi}" - } - ] - } - }, - { - "ch_posfile": { - "description": "Channel with position to call variants by chromosomes", - "structure": [ - { - "meta": null, - "type": "map", - "description": "Metadata map that will be combined with the input data map\n" - }, - { - "posfile": null, - "type": "file", - "description": "Region to extract from the BAM file in the format \"CHR\\tPOS\\tREF,ALT\"" - } - ] - } - }, - { - "ch_fasta": { - "description": "Channel with reference genome data", - "structure": [ - { - "meta": null, - "type": "map", - "description": "Metadata map" - }, - { - "fasta": null, - "type": "file", - "description": "FASTA file of the reference genome", - "pattern": "*.fa[sta]+" - }, - { - "fai": null, - "type": "file", - "description": "FASTA index file of the reference genome", - "pattern": "*.fai" - } - ] - } - }, - { - "meta_sample_merge_key": { - "type": "list", - "description": "List of keys that define the sample.\nAll file sharing the same values for these keys will be merged together.\ne.g. [ \"id\" ]\n" - } - }, - { - "meta_sample_merge_value": { - "description": "Shared value that will be set to `meta_sample_merge_key` for all samples to be merged together.\ne.g. \"all_samples\"\n" - } - }, - { - "meta_region_gather_keys": { - "type": "list", - "description": "List of keys to be used to gather the VCF files by region with vcf_gather_bcftools.\nAll file sharing the same values for these keys will be gathered together.\ne.g. [ \"id\", \"panel_id\" ]\n" - } - }, - { - "sort_region_gather": { - "type": "boolean", - "description": "Whether to sort the VCF files by region after concatenation with\nvcf_gather_bcftools.\n" - } - }, - { - "annotate": { - "type": "boolean", - "description": "Whether to annotate the merged VCF file with bcftools/annotate to give\nan ID for each variants\n" - } - } - ], - "output": [ - { - "multiqc_files": { - "description": "Channel containing stat files of bcftools mpileup and call", - "type": "file" - } - }, - { - "vcf_index": { - "description": "Channel with one VCF files by chromosomes", - "structure": [ - { - "meta": null, - "type": "map", - "description": "Metadata map combined with the ch_posfile data map.\n" - }, - { - "vcf": null, - "type": "file", - "description": "VCF file with all individuals merged by chromosomes", - "pattern": "*.{vcf,bcf,vcf.gz}" - }, - { - "index": null, - "type": "file", - "description": "VCF index file", - "pattern": "*.{tbi,csi}" - } - ] - } - } - ], - "authors": [ - "@louislenezet" - ], - "maintainers": [ - "@louislenezet" - ] - } - }, - { - "name": "bam_variant_calling_sort_freebayes_bcftools", - "path": "subworkflows/nf-core/bam_variant_calling_sort_freebayes_bcftools/meta.yml", - "type": "subworkflow", - "meta": { - "name": "bam_variant_calling_sort_freebayes_bcftools", - "description": "Call variants using freebayes, then sort and index", - "keywords": [ - "variant", - "sort", - "index", - "bam", - "cram", - "vcf" - ], - "components": [ - "freebayes", - "bcftools/sort", - "bcftools/index" - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "input1": { - "type": "file", - "description": "BAM/CRAM/SAM file;", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "index1": { - "type": "file", - "description": "Index BAI/CRAI/CSI file", - "pattern": "*.{bai,crai,csi}" - } - }, - { - "input2": { - "type": "file", - "description": "BAM/CRAM/SAM file; used to run variant calling with pair (normal vs tumor)", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "index2": { - "type": "file", - "description": "Index BAI/CRAI/CSI file", - "pattern": "*.{bai,crai,csi}" - } - }, - { - "bed": { - "type": "file", - "description": "Optional - Limit analysis to targets listed in this BED-format FILE.", - "pattern": "*.bed" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "reference fasta file", - "pattern": ".{fa,fa.gz,fasta,fasta.gz}" - } - }, - { - "fai": { - "type": "file", - "description": "reference fasta file index", - "pattern": "*.{fa,fasta}.fai" - } - }, - { - "samples": { - "type": "file", - "description": "Optional - Limit analysis to samples listed (one per line) in the FILE.", - "pattern": "*.txt" - } - }, - { - "populations": { - "type": "file", - "description": "Optional - Each line of FILE should list a sample and a population which it is part of.", - "pattern": "*.txt" - } - }, - { - "cnv": { - "type": "file", - "description": "A copy number map BED file, which has either a sample-level ploidy:\nsample_name copy_number\nor a region-specific format:\nseq_name start end sample_name copy_number\n", - "pattern": "*.bed" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "Sorted VCF file", - "pattern": "*.{vcf.gz}" - } - }, - { - "csi": { - "type": "file", - "description": "Default VCF file index file", - "pattern": "*.csi" - } - }, - { - "tbi": { - "type": "file", - "description": "Alternative VCF file index file (activated with -t parameter)", - "pattern": "*.tbi" - } - } - ], - "authors": [ - "@priyanka-surana", - "@FriederikeHanssen", - "@ramprasadn" - ], - "maintainers": [ - "@priyanka-surana", - "@FriederikeHanssen", - "@ramprasadn" - ] - } - }, - { - "name": "bam_variant_demix_boot_freyja", - "path": "subworkflows/nf-core/bam_variant_demix_boot_freyja/meta.yml", - "type": "subworkflow", - "meta": { - "name": "bam_variant_demix_boot_freyja", - "description": "Recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset (BAM aligned to the Hu-1 reference)", - "keywords": [ - "bam", - "variants", - "cram" - ], - "components": [ - "freyja/variants", - "freyja/demix", - "freyja/update", - "freyja/boot" - ], - "input": [ - { - "ch_bam": { - "type": "file", - "description": "Structure: [ val(meta), path(bam) ]\nGroovy Map containing sample information e.g. [ id:'test', single_end:false ] and sorted BAM file\n" - } - }, - { - "ch_fasta": { - "type": "file", - "description": "Structure: [ val(meta), path(fasta) ]\nGroovy Map containing sample information e.g. [ id:'test', single_end:false ] and the fasta reference used for the sorted BAM file\n" - } - }, - { - "val_repeats": { - "type": "integer", - "description": "Number of bootstrap repeats to perform" - } - }, - { - "val_db_name": { - "type": "string", - "description": "Name of the dir where UShER's files will be stored" - } - }, - { - "ch_barcodes": { - "type": "file", - "description": "Structure: path(barcodes)\nFile containing lineage defining barcodes\n" - } - }, - { - "ch_lineages_meta": { - "type": "file", - "description": "Structure: path(lineages_meta)\nFile containing lineage metadata that correspond to barcodes\n" - } - }, - { - "ch_lineages_topology": { - "type": "file", - "description": "Structure: path(lineages_topology)\nFile containing lineage topology information that correspond to barcodes\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "variants": { - "type": "file", - "description": "Structure: [ val(meta), path(variants) ]\nFile containing identified variants in a gff-like format\n" - } - }, - { - "depths": { - "type": "file", - "description": "Structure: [ val(meta), path(variants) ]\nFile containing depth of the variants\n" - } - }, - { - "demix": { - "type": "file", - "description": "Structure: [ val(meta), path(demix) ]\na tsv file that includes the lineages present, their corresponding abundances, and summarization by constellation\n" - } - }, - { - "lineages": { - "type": "file", - "description": "Structure: [ val(meta), path(lineages) ]\na csv file that includes the lineages present and their corresponding abundances\n" - } - }, - { - "summarized": { - "type": "file", - "description": "Structure: [ val(meta), path(lineages) ]\na csv file that includes the lineages present but summarized by constellation and their corresponding abundances\n" - } - }, - { - "barcodes": { - "type": "file", - "description": "File containing lineage defining barcodes" - } - }, - { - "lineages_meta": { - "type": "file", - "description": "File containing lineage topology information that correspond to barcodes" - } - }, - { - "lineages_topology": { - "type": "file", - "description": "File containing lineage metadata that correspond to barcodes" - } - } - ], - "authors": [ - "@Joon-Klaps" - ], - "maintainers": [ - "@Joon-Klaps" - ] - }, - "pipelines": [ - { - "name": "viralrecon", - "version": "3.0.0" - } - ] - }, - { - "name": "bam_vcf_impute_glimpse2", - "path": "subworkflows/nf-core/bam_vcf_impute_glimpse2/meta.yml", - "type": "subworkflow", - "meta": { - "name": "bam_vcf_impute_glimpse2", - "description": "Impute VCF/BCF files, but also CRAM and BAM files with Glimpse2", - "keywords": [ - "glimpse", - "chunk", - "phase", - "ligate", - "split_reference" - ], - "components": [ - "glimpse2/chunk", - "glimpse2/phase", - "glimpse2/ligate", - "glimpse2/splitreference", - "bcftools/index" - ], - "input": [ - { - "ch_input": { - "type": "file", - "description": "Target dataset in CRAM, BAM or VCF/BCF format.\nIndex file of the input file.\nFile containing the list of files to be imputed and their sample names (for CRAM/BAM input).\nFile with sample names and ploidy information.\nStructure: [ meta, file, index, bamlist, ploidy ]\n" - } - }, - { - "ch_ref": { - "type": "file", - "description": "Reference panel of haplotypes in VCF/BCF format.\nIndex file of the Reference panel file.\nTarget region, usually a full chromosome (e.g. chr20:1000000-2000000 or chr20).\nThe file could possibly be without GT field (for efficiency reasons a file containing only the positions is recommended).\nStructure: [ meta, vcf, csi, region ]\n" - } - }, - { - "ch_chunks": { - "type": "string", - "description": "Channel containing the chunking regions for each chromosome.\nStructure: [ meta, region with buffer, region without buffer ]\n" - } - }, - { - "ch_map": { - "type": "file", - "description": "Genetic map file for each chromosome.\nStructure: [ meta, gmap ]\n" - } - }, - { - "ch_fasta": { - "type": "file", - "description": "Reference genome in fasta format.\nReference genome index in fai format\nStructure: [ meta, fasta, fai ]\n" - } - }, - { - "chunk": { - "type": "boolean", - "description": "Whether to perform chunking of the input data before imputation." - } - }, - { - "chunk_model": { - "type": "string", - "description": "Chunking model to use.\nOptions: \"sequential\", \"recursive\"\n" - } - }, - { - "splitreference": { - "type": "boolean", - "description": "Whether to split the reference panel and convert it to binary files before imputation." - } - } - ], - "output": [ - { - "ch_chunks": { - "type": "string", - "description": "Channel containing the chunking regions for each chromosome.\nStructure: [ meta, region with buffer, region without buffer ]\n" - } - }, - { - "ch_vcf_index": { - "type": "file", - "description": "Output VCF/BCF file for the merged regions.\nIndex file of the output VCF/BCF file.\nStructure: [ val(meta), variants, index ]\n" - } - } - ], - "authors": [ - "@LouisLeNezet" - ], - "maintainers": [ - "@LouisLeNezet" - ] - } - }, - { - "name": "bcl_demultiplex", - "path": "subworkflows/nf-core/bcl_demultiplex/meta.yml", - "type": "subworkflow", - "meta": { - "name": "bcl_demultiplex", - "description": "Demultiplex Illumina BCL data using bcl-convert or bcl2fastq", - "keywords": [ - "bcl", - "bclconvert", - "bcl2fastq", - "demultiplex", - "fastq" - ], - "components": [ - "bcl2fastq", - "bclconvert", - "multiqcsav" - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'string', lane: int ]\n" - } - }, - { - "samplesheet": { - "type": "file", - "description": "CSV file containing information about samples to be demultiplexed in Illumina SampleSheet format\n" - } - }, - { - "flowcell": { - "type": "file", - "description": "Directory or tar archive containing Illumina BCL data, sequencer output directory" - } - }, - { - "demultiplexer": { - "type": "string", - "description": "Which demultiplexer to use, bcl2fastq or bclconvert" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "fastq": { - "type": "file", - "description": "Demultiplexed fastq files", - "pattern": "*.fastq.gz" - } - }, - { - "reports": { - "type": "file", - "description": "Demultiplexing reports", - "pattern": "Reports/*" - } - }, - { - "interop": { - "type": "file", - "description": "InterOp files", - "pattern": "InterOp/*" - } - }, - { - "stats": { - "type": "file", - "description": "Demultiplexing statistics (bcl2fastq only)", - "pattern": "Stats/*" - } - }, - { - "logs": { - "type": "file", - "description": "Demultiplexing logs (bclconvert only)", - "pattern": "Logs/*" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@matthdsm" - ], - "maintainers": [ - "@matthdsm" - ] - }, - "pipelines": [ - { - "name": "demultiplex", - "version": "1.7.1" - } - ] - }, - { - "name": "bed_scatter_bedtools", - "path": "subworkflows/nf-core/bed_scatter_bedtools/meta.yml", - "type": "subworkflow", - "meta": { - "name": "bed_scatter_bedtools", - "description": "Scatters inputted BED files by the amount specified.\nThe configuration in nextflow.config should be added to your modules.config for the subworkflow to work.\n", - "keywords": [ - "bed", - "scatter", - "bedtools" - ], - "components": [ - "bedtools/split" - ], - "input": [ - { - "ch_bed": { - "description": "The input channel containing the BED file and an integer stating the amount of files it should be split into\nStructure: [ val(meta), path(bed), val(scatter_count) ]\n" - } - } - ], - "output": [ - { - "scattered_beds": { - "description": "One channel entry per scattered BED file (all BED files from the same source are transposed but contain the same meta)\nStructure: [ val(meta), path(bed), val(scatter_count) ]\n" - } - } - ], - "authors": [ - "@nvnieuwk" - ], - "maintainers": [ - "@nvnieuwk" - ] - } - }, - { - "name": "bedgraph_bedclip_bedgraphtobigwig", - "path": "subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/meta.yml", - "type": "subworkflow", - "meta": { - "name": "bedgraph_bedclip_bedgraphtobigwig", - "description": "Convert bedgraph to bigwig with clip", - "keywords": [ - "bedgraph", - "bigwig", - "clip", - "conversion" - ], - "components": [ - "ucsc/bedclip", - "ucsc/bedgraphtobigwig" - ], - "input": [ - { - "bedgraph": { - "type": "file", - "description": "bedGraph file which should be converted", - "pattern": "*.bedGraph" - } - }, - { - "sizes": { - "type": "file", - "description": "File with chromosome sizes", - "pattern": "*.sizes" - } - } - ], - "output": [ - { - "bigwig": { - "type": "file", - "description": "bigWig coverage file relative to genes on the input file", - "pattern": ".bigWig" - } - }, - { - "bedgraph": { - "type": "file", - "description": "bedGraph file after clipping", - "pattern": "*.bedGraph" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@drpatelh", - "@KamilMaliszArdigen" - ], - "maintainers": [ - "@drpatelh", - "@KamilMaliszArdigen" - ] - }, - "pipelines": [ - { - "name": "rnaseq", - "version": "3.26.0" - }, - { - "name": "rnasplice", - "version": "1.0.4" - } - ] - }, - { - "name": "cache_download_ensemblvep_snpeff", - "path": "subworkflows/nf-core/cache_download_ensemblvep_snpeff/meta.yml", - "type": "subworkflow", - "meta": { - "name": "cache_download_ensemblvep_snpeff", - "description": "downlad annotation cache for snpeff and ensemblvep", - "keywords": [ - "ensemblvep", - "snpeff", - "download", - "annotation", - "cache" - ], - "components": [ - "ensemblvep/download", - "snpeff/download" - ], - "input": [ - { - "ensemblvep_info": { - "description": "All information necessary to download the cache\nStructure: [ val(meta), val(ensemblvep_genome), val(ensemblvep_species), val(ensemblvep_cache_version) ]\n" - } - }, - { - "snpeff_info": { - "description": "All information necessary to download the cache\nStructure: [ val(meta), val(snpeff_db) ]\n" - } - }, - { - "ensemblvep_preflight_check": { - "description": "Whether to check that the expected cache file is listed in the Ensembl CHECKSUMS file before downloading\nStructure: val(true/false)\n" - } - } - ], - "output": [ - { - "ensemblvep_cache": { - "description": "Path to ensemblvep cache\nStructure: [ val(meta), path(cache) ]\n" - } - }, - { - "snpeff_cache": { - "description": "Path to snpeff cache\nStructure: [ val(meta), path(cache) ]\n" - } - } - ], - "authors": [ - "@maxulysse" - ], - "maintainers": [ - "@maxulysse" - ] - } - }, - { - "name": "deepvariant", - "path": "subworkflows/nf-core/deepvariant/meta.yml", - "type": "subworkflow", - "meta": { - "name": "deepvariant", - "description": "DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data", - "keywords": [ - "variant calling", - "machine learning", - "neural network" - ], - "components": [ - "deepvariant/makeexamples", - "deepvariant/callvariants", - "deepvariant/postprocessvariants" - ], - "input": [ - { - "ch_input": { - "type": "list", - "description": "Input aligned reads in bam or cram format, with index, and optional intervals BED file\nStructure: [ val(meta), path(bam_or_cram), path(bai_or_crai), path(intervals_bed) ]\n" - } - }, - { - "ch_fasta": { - "type": "file", - "description": "Reference genome\nStructure: [ val(meta2), path(fasta) ]\n" - } - }, - { - "ch_fai": { - "type": "string", - "description": "Reference genome index in fai format\nStructure: [ val(meta3), path(fai) ]\n" - } - }, - { - "ch_gzi": { - "type": "string", - "description": "Reference genome index in gzi format (either gzi or fai should be used)\nStructure: [ val(meta4), val(gzi) ]\n" - } - }, - { - "ch_par_bed": { - "type": "string", - "description": "bed file of pseudoautosomal regions (optional)\nStructure: [ val(meta5), val(par_bed) ]\n", - "pattern": "*.bed" - } - } - ], - "output": [ - { - "vcf": { - "type": "file", - "description": "Variant calls\nStructure: [ val(meta), path(vcf) ]\n", - "pattern": "*.vcf.gz" - } - }, - { - "vcf_tbi": { - "type": "file", - "description": "Index for variant call file\nStructure: [ val(meta), path(vcf_tbi) ]\n", - "pattern": "*.tbi" - } - }, - { - "gvcf": { - "type": "file", - "description": "Variant call file with genomic coverage information\nStructure: [ val(meta), path(gvcf) ]\n", - "pattern": "*.g.vcf.gz" - } - }, - { - "gvcf_tbi": { - "type": "file", - "description": "Index for the GVCF.\nStructure: [ val(meta), path(gvcf_tbi) ]\n", - "pattern": "*.tbi" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions\nStructure: path(versions.yml)\n", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@abhi18av", - "@ramprasadn", - "@fa2k" - ], - "maintainers": [ - "@abhi18av", - "@ramprasadn", - "@fa2k" - ] - } - }, - { - "name": "dia_proteomics_analysis", - "path": "subworkflows/nf-core/dia_proteomics_analysis/meta.yml", - "type": "subworkflow", - "meta": { - "name": "dia_proteomics_analysis", - "description": "Complete DIA-NN proteomics analysis pipeline including in-silico library generation,\npreliminary analysis, empirical library assembly, individual analysis, and final quantification.\nThis subworkflow combines DIA-NN modules with quantms-utils for comprehensive\ndata-independent acquisition (DIA) proteomics data processing.\n", - "keywords": [ - "diann", - "proteomics", - "dia", - "quantification", - "spectral library", - "quantms-utils" - ], - "tools": [ - { - "diann": { - "description": "DIA-NN is a universal software for data-independent acquisition (DIA) proteomics data processing.\nIt uses deep learning to predict spectral libraries and perform peptide identification and quantification.\n", - "homepage": "https://github.com/vdemichev/DiaNN", - "documentation": "https://github.com/vdemichev/DiaNN", - "tool_dev_url": "https://github.com/vdemichev/DiaNN", - "doi": "10.1038/s41592-020-01009-0", - "licence": [ - "https://github.com/vdemichev/DiaNN/blob/1.8.1/LICENSE.txt" - ], - "identifier": "biotools:diann" - } - }, - { - "quantms-utils": { - "description": "quantms-utils is a Python package with scripts and functions for quantitative proteomics data analysis.\nProvides utilities for DIA-NN configuration, mzML statistics, and format conversion to mzTab.\n", - "homepage": "https://github.com/bigbio/quantms-utils", - "documentation": "https://github.com/bigbio/quantms-utils", - "tool_dev_url": "https://github.com/bigbio/quantms-utils", - "licence": [ - "MIT" - ], - "identifier": "biotools:quantms-utils" - } - } - ], - "components": [ - "diann", - "quantmsutils/dianncfg", - "quantmsutils/mzmlstatistics", - "quantmsutils/diann2mztab" - ], - "input": [ - { - "ch_input": { - "type": "channel", - "description": "Channel containing tuples of meta maps, mass spectrometry files, and search parameters.\nStructure: [meta, ms_file, enzyme, fixed_mods, variable_mods, precursor_tolerance,\nfragment_tolerance, precursor_tolerance_unit, fragment_tolerance_unit]\ne.g. `[[id:'sample1'], file('sample1.mzML'), 'Trypsin', 'Carbamidomethyl (C)',\n'Oxidation (M)', 10, 20, 'ppm', 'ppm']`\nNote: For Thermo RAW file conversion to mzML, the ThermoRawFileParser module is available\nin nf-core/modules and can be used upstream of this subworkflow.\n", - "pattern": "*.{mzML,mzml}" - } - }, - { - "ch_searchdb": { - "type": "channel", - "description": "Channel containing tuples of meta maps and protein sequence database in FASTA format.\nStructure: [meta, fasta]\ne.g. `[[id:'uniprot_human'], file('uniprot_human.fasta')]`\n", - "pattern": "*.{fasta,fa}" - } - }, - { - "ch_expdesign": { - "type": "channel", - "description": "Channel containing tuples of meta maps and experimental design files.\nStructure: [meta, expdesign]\ne.g. `[[id:'experiment1'], file('design.tsv')]`\n", - "pattern": "*.tsv" - } - }, - { - "random_preanalysis": { - "type": "tuple", - "description": "Tuple controlling random sampling for preliminary analysis.\nStructure: [boolean, integer, integer] for [enable_random, n_samples, seed]\ne.g. `[true, 5, 42]` to randomly sample 5 files with seed 42\nSet to null or [false, null, null] to use all files\n" - } - }, - { - "wf_scan_window": { - "type": "integer", - "description": "Scan window parameter for DIA-NN individual analysis.\nOnly used if wf_scan_window_automatic is false.\n" - } - }, - { - "wf_mass_acc_automatic": { - "type": "boolean", - "description": "If true, use automatic mass accuracy settings extracted from DIA-NN preliminary analysis log.\nIf false, use user-provided precursor_tolerance and fragment_tolerance from ch_input.\n" - } - }, - { - "wf_scan_window_automatic": { - "type": "boolean", - "description": "If true, use automatic scan window settings extracted from DIA-NN preliminary analysis log.\nIf false, use user-provided wf_scan_window parameter.\n" - } - }, - { - "wf_diann_debug": { - "type": "boolean", - "description": "Enable DIA-NN debug output mode for troubleshooting.\n" - } - }, - { - "wf_pg_level": { - "type": "string", - "description": "Protein group level for DIA-NN analysis.\nOptions: 'genes', 'proteins', etc.\n" - } - }, - { - "ch_speclib_in": { - "type": "channel", - "description": "Optional channel containing pre-generated spectral library file.\nIf provided, skips in-silico library generation.\nApplied to all samples in the workflow.\nStructure: path(speclib)\ne.g. `file('pregenerated.speclib')`\n", - "pattern": "*.{speclib,tsv}" - } - }, - { - "ch_empirical_library_in": { - "type": "channel", - "description": "Optional channel containing pre-generated empirical library file.\nIf provided, skips preliminary analysis and empirical library assembly.\nApplied to all samples in the workflow.\nStructure: path(empirical_library)\ne.g. `file('empirical_library.speclib')`\n", - "pattern": "*.speclib" - } - }, - { - "ch_empirical_log_in": { - "type": "channel", - "description": "Optional channel containing assembly log from pre-generated empirical library.\nRequired if ch_empirical_library_in is provided (for extracting mass accuracy settings).\nStructure: path(assembly_log)\ne.g. `file('assembly.log')`\n", - "pattern": "*.log" - } - } - ], - "output": [ - { - "versions": { - "description": "File containing software versions", - "structure": [ - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - } - ] - } - }, - { - "diann_report": { - "description": "Main DIA-NN report in TSV format containing quantification results", - "structure": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing experiment and search database information" - } - }, - { - "report": { - "type": "file", - "description": "Main DIA-NN report in TSV format", - "pattern": "*.tsv" - } - } - ] - } - }, - { - "diann_report_parquet": { - "description": "Main DIA-NN report in Parquet format containing quantification results", - "structure": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing experiment and search database information" - } - }, - { - "report": { - "type": "file", - "description": "Main DIA-NN report in Parquet format", - "pattern": "*.parquet" - } - } - ] - } - }, - { - "mzml_statistics": { - "description": "Statistics extracted from mzML files", - "structure": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "statistics": { - "type": "file", - "description": "mzML statistics in parquet format", - "pattern": "*_ms_info.parquet" - } - } - ] - } - }, - { - "msstats_in": { - "description": "MSstats-compatible input file for statistical analysis", - "structure": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing experiment and search database information" - } - }, - { - "msstats": { - "type": "file", - "description": "MSstats input file", - "pattern": "*_msstats_in.csv" - } - } - ] - } - }, - { - "out_triqler": { - "description": "Triqler-compatible input file for protein quantification with uncertainty", - "structure": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing experiment and search database information" - } - }, - { - "triqler": { - "type": "file", - "description": "Triqler input file", - "pattern": "*_triqler_in.tsv" - } - } - ] - } - }, - { - "final_result": { - "description": "Final quantification results in mzTab format", - "structure": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing experiment and search database information" - } - }, - { - "mztab": { - "type": "file", - "description": "Final results in mzTab format (standard proteomics exchange format)", - "pattern": "*.mzTab" - } - } - ] - } - } - ], - "authors": [ - "@daichengxin", - "@wanghong", - "@pinin4fjords", - "@DongzeHE" - ], - "maintainers": [ - "@daichengxin", - "@pinin4fjords", - "@DongzeHE" - ] - } - }, - { - "name": "differential_functional_enrichment", - "path": "subworkflows/nf-core/differential_functional_enrichment/meta.yml", - "type": "subworkflow", - "meta": { - "name": "differential_functional_enrichment", - "description": "Run functional analysis on differential abundance analysis output", - "keywords": [ - "functional analysis", - "functional enrichment", - "differential", - "over-representation analysis" - ], - "components": [ - "gprofiler2/gost", - "gsea/gsea", - "decoupler/decoupler", - "propr/grea", - "custom/tabulartogseagct", - "custom/tabulartogseacls", - "custom/tabulartogseachip" - ], - "input": [ - { - "ch_input": { - "description": "Channel with the input data for functional analysis.", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata map" - } - }, - { - "input": { - "type": "file", - "description": "Input file. This should be the DE statistics obtained from the DE modules,\nor the normalized abundance matrix (in the case of running GSEA).\n" - } - }, - { - "genesets": { - "type": "file", - "description": "Gene sets database. Currently all methods support GMT format.\n" - } - }, - { - "background": { - "type": "file", - "description": "Background features for functional analysis.\nFor the moment, it is only required for gprofiler2.\n" - } - }, - { - "analysis_method": { - "type": "value", - "description": "Analysis method (gprofiler2, gsea, decoupler or grea)" - } - } - ] - } - }, - { - "ch_contrasts": { - "description": "Channel with contrast information", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata map" - } - }, - { - "meta_contrast": { - "type": "map", - "description": "Map with all the contrast info, such as contrast\nid, variable, reference, target, etc.\n" - } - }, - { - "variable": { - "type": "list", - "description": "List of contrast variable" - } - }, - { - "reference": { - "type": "list", - "description": "List of reference level" - } - }, - { - "target": { - "type": "list", - "description": "List of target level" - } - }, - { - "formula": { - "type": "list", - "description": "List of contrast formula" - } - }, - { - "comparison": { - "type": "list", - "description": "List of contrast comparison" - } - } - ] - } - }, - { - "ch_samplesheet": { - "description": "Channel with sample information", - "structure": [ - { - "meta_exp": { - "type": "map", - "description": "Experiment metadata map" - } - }, - { - "samplesheet": { - "type": "file", - "description": "Sample information file", - "pattern": "*.{csv,tsv}" - } - } - ] - } - }, - { - "ch_featuresheet": { - "description": "Channel with features information", - "structure": [ - { - "meta_exp": { - "type": "map", - "description": "Experiment metadata map" - } - }, - { - "features": { - "type": "file", - "description": "Features information file", - "pattern": "*.{csv,tsv}" - } - }, - { - "features_id": { - "type": "value", - "description": "Features id column" - } - }, - { - "features_symbol": { - "type": "value", - "description": "Features symbol column" - } - } - ] - } - } - ], - "output": [ - { - "versions": { - "type": "file", - "description": "File containing software versions\nStructure: [ path(versions.yml) ]\n", - "pattern": "versions.yml" - } - }, - { - "gprofiler2_all_enrich": { - "description": "Channel containing the main enrichment table output from gprofiler2", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata map" - } - }, - { - "all_enrich": { - "type": "file", - "description": "Table listing all enriched pathways that were found by gprofiler2.\nIt can be empty, if none is found.\n", - "pattern": "*.gprofiler2.all_enriched_pathways.tsv" - } - } - ] - } - }, - { - "gprofiler2_sub_enrich": { - "description": "Channel containing the secondary enrichment table output from gprofiler2.", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata map" - } - }, - { - "sub_enrich": { - "type": "file", - "description": "Table listing enriched pathways that were found from one particular source.\nNote that it will only be created if any were found.\n", - "pattern": "*.gprofiler2.*.sub_enriched_pathways.tsv" - } - } - ] - } - }, - { - "gprofiler2_plot_html": { - "description": "Channel containing the html report generated from gprofiler2.", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata map" - } - }, - { - "plot_html": { - "type": "file", - "description": "HTML file; interactive Manhattan plot of all enriched pathways.\nNote that this file will only be generated if enriched pathways were found.\n", - "pattern": "*.gprofiler2.gostplot.html" - } - } - ] - } - }, - { - "gprofiler2_artifacts": { - "description": "Channel containing additional gprofiler2 artifacts.", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata map" - } - }, - { - "artifact": { - "type": "file", - "description": "Additional outputs from gprofiler2, including gost results (RDS),\nfiltered GMT files, R session logs, and PNG plot files.\n", - "pattern": "*.{rds,gmt,log,png}" - } - } - ] - } - }, - { - "gsea_report": { - "description": "Channel containing all the output from GSEA needed for further reporting.", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata map" - } - }, - { - "reports_ref": { - "type": "file", - "description": "Main TSV results report file for the reference group.", - "pattern": "*gsea_report_for_${reference}.tsv" - } - }, - { - "reports_target": { - "type": "file", - "description": "Main TSV results report file for the target group.", - "pattern": "*gsea_report_for_${target}.tsv" - } - } - ] - } - }, - { - "gsea_artifacts": { - "description": "Channel containing additional GSEA output artifacts.", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata map" - } - }, - { - "artifact": { - "type": "file", - "description": "Additional files generated by GSEA, including reports, plots, archives,\nand supporting HTML/TSV outputs.\n", - "pattern": "*.{rpt,html,tsv,png,zip}" - } - } - ] - } - }, - { - "decoupler_dc_estimate": { - "description": "Channel containing decoupler estimate results.", - "structure": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end ]\n" - } - }, - { - "estimate_files": { - "type": "file", - "description": "Files containing the estimation results of the enrichment(s)\n", - "pattern": "*estimate_decoupler.tsv" - } - } - ] - } - }, - { - "decoupler_dc_pvals": { - "description": "Channel containing decoupler pvals results.", - "structure": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end ]\n" - } - }, - { - "pvals_files": { - "type": "file", - "description": "Files containing the p-values associated to the estimation\nresults of the enrichment(s)\n", - "pattern": "*pvals_decoupler.tsv" - } - } - ] - } - }, - { - "decoupler_png": { - "description": "Channel containing decoupler png results.", - "structure": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end ]\n" - } - }, - { - "plot_files": { - "type": "file", - "description": "Files containing the plots associated to the estimation\nresults of the enrichment(s)\n", - "pattern": "*estimate_decoupler_plot.png" - } - } - ] - } - }, - { - "grea_results": { - "description": "Channel containing the output from GREA.", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata map" - } - }, - { - "results": { - "type": "file", - "description": "Main TSV results file.", - "pattern": "*.grea.tsv" - } - } - ] - } - } - ], - "authors": [ - "@suzannejin", - "@bjlang", - "@caraiz2001" - ], - "maintainers": [ - "@suzannejin", - "@pinin4fjords" - ] - } - }, - { - "name": "faa_seqfu_seqkit", - "path": "subworkflows/nf-core/faa_seqfu_seqkit/meta.yml", - "type": "subworkflow", - "meta": { - "name": "faa_seqfu_seqkit", - "description": "Subworkflow that optionally preprocesses amino acid FASTA sequences\n(seqkit seq/replace/rmdup), computes sequence statistics before and\nafter preprocessing using seqfu stats, and exports MultiQC-compatible\nstatistics and software versions.\n", - "keywords": [ - "fasta", - "protein", - "preprocessing", - "statistics", - "quality check" - ], - "components": [ - "seqfu/stats", - "seqkit/seq", - "seqkit/rmdup", - "seqkit/replace" - ], - "input": [ - { - "ch_fasta": { - "type": "file", - "description": "Amino acid sequences fasta file.\nStructure: [ val(meta), [ path(fasta) ] ]\n" - } - }, - { - "skip_preprocessing": { - "type": "boolean", - "description": "If true, skip seqkit-based preprocessing steps and only compute\ninitial sequence statistics.\n" - } - } - ], - "output": [ - { - "fasta": { - "type": "file", - "description": "Contains the final amino acid FASTA file\n(either preprocessed or original if preprocessing is skipped).\n" - } - }, - { - "multiqc_files": { - "type": "file", - "description": "Statistics file for MultiQC.\n" - } - }, - { - "versions": { - "type": "file", - "description": "Versions file containing the software versions used in the workflow.\n" - } - } - ], - "authors": [ - "@vagkaratzas" - ], - "maintainers": [ - "@vagkaratzas" - ] - }, - "pipelines": [ - { - "name": "proteinannotator", - "version": "1.1.0" - }, - { - "name": "proteinfamilies", - "version": "2.3.0" - } - ] - }, - { - "name": "fasta_binning_concoct", - "path": "subworkflows/nf-core/fasta_binning_concoct/meta.yml", - "type": "subworkflow", - "meta": { - "name": "fasta_binning_concoct", - "description": "Runs the CONCOCT workflow of contig binning", - "keywords": [ - "concoct", - "binning", - "metagenomics", - "contigs" - ], - "components": [ - "concoct/cutupfasta", - "concoct/concoctcoveragetable", - "concoct/concoct", - "concoct/mergecutupclustering", - "concoct/extractfastabins" - ], - "input": [ - { - "ch_fasta": { - "type": "file", - "description": "Structure: [ val(meta), path(fasta)]\nFile containing raw assembled contigs in FASTA format.\n" - } - }, - { - "ch_bam": { - "type": "file", - "description": "Structure: [ val(meta), path(bam), path(bai)]\nBAM and associated index files file representing reads mapped against each\ncontig in ch_fasta. Meta must be identical between ch_fasta and ch_bam entries.\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "coverage_table": { - "type": "file", - "description": "Structure: [ val(meta), path(tsv)]\n(Sub)contig coverage table\n" - } - }, - { - "original_csv": { - "type": "file", - "description": "Structure: [ val(meta), path(csv) ]\nOriginal CONCOCT GT1000 output\n" - } - }, - { - "raw_clustering_csv": { - "type": "file", - "description": "Structure: [ val(meta), path(csv) ]\nCSV containing information which subcontig is assigned to which cluster\n" - } - }, - { - "pca_original": { - "type": "file", - "description": "Structure: [ val(meta), path(csv) ]\nCSV file containing untransformed PCA component values\n" - } - }, - { - "pca_transformed": { - "type": "file", - "description": "Structure: [ val(meta), path(csv) ]\nCSV file transformed PCA component values\n" - } - }, - { - "cluster_table": { - "type": "file", - "description": "Structure: [ val(meta), path(csv) ]\nCSV file containing final cluster assignments of original input contigs\n" - } - }, - { - "bin": { - "type": "file", - "description": "Structure: [ val(meta), path(fasta) ]\nFASTA files containing CONCOCT predicted bin clusters, named numerically\nby CONCOCT cluster ID\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@jfy133" - ], - "maintainers": [ - "@jfy133" - ] - }, - "pipelines": [ - { - "name": "mag", - "version": "5.4.2" - } - ] - }, - { - "name": "fasta_build_add_kraken2", - "path": "subworkflows/nf-core/fasta_build_add_kraken2/meta.yml", - "type": "subworkflow", - "meta": { - "name": "fasta_build_add_kraken2", - "description": "KRAKEN2 build custom database subworkflow", - "keywords": [ - "metagenomics", - "kraken2", - "database", - "build", - "custom" - ], - "components": [ - "kraken2/add", - "kraken2/build" - ], - "input": [ - { - "ch_fasta": { - "type": "file", - "description": "Channel containing a meta with a list of FASTAs to be built\nStructure: [ val(meta), [ fasta1, fasta2, fasta3 ] ]\n", - "pattern": "*.{fasta,fa,fna}" - } - }, - { - "ch_taxonomy_names": { - "type": "file", - "description": "Channel containing a NCBI-style taxdump names file\nStructure: [ names.dmp ]\n", - "pattern": "names.dmp" - } - }, - { - "ch_taxonomy_nodes": { - "type": "file", - "description": "Channel containing a NCBI-style taxdump nodes file\nStructure: [ nodes.dmp ]\n", - "pattern": "nodes.dmp" - } - }, - { - "ch_accession2taxid": { - "type": "file", - "description": "Channel containing a NCBI-style taxdump accession2taxid (acc2tax) file\nStructure: [ accession2taxid_file ]\n", - "pattern": "*.accession2taxid" - } - }, - { - "val_cleanintermediate": { - "type": "boolean", - "description": "Boolean flag whether to clean up intermediate files after build or not\nStructure: [ val_cleanintermediate ]\n", - "pattern": "true|false" - } - }, - { - "ch_custom_seqid2taxid": { - "type": "file", - "description": "Optional custom or prebuilt seqid2taxid text file. If not provided, it will be generated by kraken2-build.\n", - "pattern": "seqid2taxid.map" - } - } - ], - "output": [ - { - "db": { - "type": "directory", - "description": "Channel containing KRAKEN2 database directory.\nUse publishDir in a modules.conf file to change default name for user\nStructure: [ val(meta), path(db) ]\n", - "pattern": "kraken2-database/" - } - }, - { - "db_separated": { - "type": "file", - "description": "Channel containing a list of KRAKEN2 database directory files as separate elements of a tuple.\nUse publishDir in a modules.conf file to change default name for user\nStructure: [ val(meta), path(k2d_files), path(map_files), path(added_files), path(taxonomy_files) ]\n", - "pattern": "kraken2-database/" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions\nStructure: [ path(versions.yml) ]\n", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@jfy133" - ], - "maintainers": [ - "@jfy133" - ] - } - }, - { - "name": "fasta_build_add_kraken2_bracken", - "path": "subworkflows/nf-core/fasta_build_add_kraken2_bracken/meta.yml", - "type": "subworkflow", - "meta": { - "name": "fasta_build_add_kraken2_bracken", - "description": "KRAKEN2 and BRACKEN build custom database subworkflow", - "keywords": [ - "metagenomics", - "kraken2", - "database", - "build", - "custom", - "bracken" - ], - "components": [ - "kraken2/add", - "kraken2/build", - "bracken/build" - ], - "input": [ - { - "ch_fasta": { - "type": "file", - "description": "Channel containing a meta with a list of FASTAs to be built\nStructure: [ val(meta), [ fasta1, fasta2, fasta3 ] ]\n", - "pattern": "*.{fasta,fa,fna}" - } - }, - { - "ch_taxonomy_names": { - "type": "file", - "description": "Channel containing a NCBI-style taxdump names file\nStructure: [ names.dmp ]\n", - "pattern": "names.dmp" - } - }, - { - "ch_taxonomy_nodes": { - "type": "file", - "description": "Channel containing a NCBI-style taxdump nodes file\nStructure: [ nodes.dmp ]\n", - "pattern": "nodes.dmp" - } - }, - { - "ch_accession2taxid": { - "type": "file", - "description": "Channel containing a NCBI-style taxdump accession2taxid (acc2tax) file\nStructure: [ accession2taxid_file ]\n", - "pattern": "*.accession2taxid" - } - }, - { - "val_cleanintermediates": { - "type": "boolean", - "description": "Boolean flag whether to clean up intermediate files after build or not.\nIf val_runbrackenbuild set, will be ignored as BRACKEN requires intermediate files.\nStructure: [ val_cleanintermediate ]\n", - "pattern": "true|false" - } - }, - { - "ch_custom_seqid2taxid": { - "type": "file", - "description": "Optional custom or prebuilt seqid2taxid text file. If not provided, it will be generated by kraken2-build.\n", - "pattern": "seqid2taxid.map" - } - }, - { - "val_runbrackenbuild": { - "type": "boolean", - "description": "Boolean flag whether to additionally insert required BRACKEN database files into KRAKEN2 directory.\nNote any changes for k-mer or read lengths must come via Nextflow config `ext.args`.\nStructure: [ val_runbrackenbuild ]\n", - "pattern": "true|false" - } - } - ], - "output": [ - { - "db": { - "type": "directory", - "description": "Channel containing KRAKEN2 (and BRACKEN) database directory files.\nUse publishDir in a modules.conf file to change default name for user\nStructure: [ val(meta), path(db) ]\n", - "pattern": "bracken-database/" - } - }, - { - "db_separated": { - "type": "file", - "description": "Channel containing a list of KRAKEN2 (and BRACKEN) database directory files as separate elements of a tuple.\nUse publishDir in a modules.conf file to change default name for user\nStructure: [ val(meta), path(k2d_files), path(map_files), path(added_files), path(taxonomy_files) ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions\nStructure: [ path(versions.yml) ]\n", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@jfy133" - ], - "maintainers": [ - "@jfy133" - ] - }, - "pipelines": [ - { - "name": "createtaxdb", - "version": "3.0.0" - } - ] - }, - { - "name": "fasta_classify_catpack", - "path": "subworkflows/nf-core/fasta_classify_catpack/meta.yml", - "type": "subworkflow", - "meta": { - "name": "fasta_classify_catpack", - "description": "Taxonomic classification of binned MAGs and contigs using CAT/BAT (CAT_pack).", - "keywords": [ - "metagenomics", - "taxonomy", - "classification", - "bins", - "MAGs", - "contigs", - "CAT", - "BAT" - ], - "components": [ - "catpack/addnames", - "catpack/bins", - "catpack/contigs", - "catpack/download", - "catpack/prepare", - "catpack/summarise", - "untar" - ], - "input": [ - { - "ch_bins": { - "type": "file", - "description": "Channel containing binned MAG FASTA files.\nStructure: [ val(meta), path(fasta) ]\n", - "pattern": "*.{fa,fasta,fna}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - }, - { - "ch_contigs": { - "type": "file", - "description": "Channel containing contig FASTA files. Provide channel.empty() to skip\ncontig classification.\nStructure: [ val(meta), path(fasta) ]\n", - "pattern": "*.{fa,fasta,fna}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - }, - { - "ch_cat_db": { - "type": "directory", - "description": "Channel containing a pre-built CAT/BAT database. Can be a directory with db/ and tax/\nsubdirectories, or a .tar.gz archive of such a directory. Provide channel.empty() to\ntrigger automatic database download using ch_cat_db_download_id. Supplying both\nch_cat_db and ch_cat_db_download_id will cause a runtime error.\nStructure: [ val(meta), path(db) ]\n", - "ontologies": [ - { - "edam": "http://edamontology.org/data_1049" - } - ] - } - }, - { - "ch_cat_db_download_id": { - "type": "string", - "description": "Channel containing the database identifier to download via CATPACK_DOWNLOAD (e.g. 'nr').\nOnly used when ch_cat_db is channel.empty(). Provide channel.empty() when supplying a\npre-built database via ch_cat_db. Supplying both inputs will cause a runtime error.\nStructure: [ val(meta), val(db_id) ]\n" - } - }, - { - "run_summarise": { - "type": "boolean", - "description": "Whether to run CATPACK_SUMMARISE on the classification outputs. Requires\next.args = \"--only_official\" to be set on CATPACK_ADDNAMES_BINS and\nCATPACK_ADDNAMES_CONTIGS in the pipeline configuration, as CATPACK_SUMMARISE\nrequires official-rank headers in its input.\n" - } - }, - { - "bin_suffix": { - "type": "string", - "description": "File extension of the bin FASTA files passed to CATPACK_BINS (e.g. '.fa').\n" - } - } - ], - "output": [ - { - "bin2classification": { - "type": "file", - "description": "Raw per-bin taxonomic classification file produced by CATPACK_BINS, before human-readable\nnames are added by CATPACK_ADDNAMES. Useful for downstream tools that consume the raw\nCAT_pack output directly.\nStructure: [ val(meta), path(txt) ]\n", - "pattern": "*.bin2classification.txt", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - }, - { - "bat_classification": { - "type": "file", - "description": "Per-bin taxonomic classification with human-readable names added by CATPACK_ADDNAMES.\nStructure: [ val(meta), path(txt) ]\n", - "pattern": "*.txt", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - }, - { - "bat_summary": { - "type": "file", - "description": "Summary of bin classifications produced by CATPACK_SUMMARISE. Empty channel when\nrun_summarise is false.\nStructure: [ val(meta), path(txt) ]\n", - "pattern": "*.txt", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - }, - { - "contig2classification": { - "type": "file", - "description": "Raw per-contig taxonomic classification file produced by CATPACK_CONTIGS, before\nhuman-readable names are added by CATPACK_ADDNAMES. Empty channel when ch_contigs\nis channel.empty(). Useful for downstream tools that consume the raw CAT_pack output directly.\nStructure: [ val(meta), path(txt) ]\n", - "pattern": "*.contig2classification.txt", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - }, - { - "contigs_classification": { - "type": "file", - "description": "Per-contig taxonomic classification with human-readable names added by CATPACK_ADDNAMES.\nEmpty channel when ch_contigs is channel.empty().\nStructure: [ val(meta), path(txt) ]\n", - "pattern": "*.txt", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - }, - { - "contigs_summary": { - "type": "file", - "description": "Summary of contig classifications produced by CATPACK_SUMMARISE. Empty channel when\nch_contigs is channel.empty() or run_summarise is false.\nStructure: [ val(meta), path(txt) ]\n", - "pattern": "*.txt", - "ontologies": [ - { - "edam": "http://edamontology.org/format_3475" - } - ] - } - }, - { - "versions": { - "type": "file", - "description": "Channel containing software versions.\nStructure: versions\n" - } - } - ], - "authors": [ - "@mberacochea", - "@dialvarezs" - ], - "maintainers": [ - "@mberacochea", - "@dialvarezs", - "@jfy133", - "@prototaxites", - "@dialvarezs", - "@d4straub", - "@muabnezor" - ] - }, - "pipelines": [ - { - "name": "seqsubmit", - "version": "dev" - } - ] - }, - { - "name": "fasta_clean_fcs", - "path": "subworkflows/nf-core/fasta_clean_fcs/meta.yml", - "type": "subworkflow", - "meta": { - "name": "fasta_clean_fcs", - "description": "Foreign Contamination Screen (FCS) is a tool suite for identifying and removing contaminant sequences in genome assemblies", - "keywords": [ - "contamination screening", - "cleaning", - "assemblies", - "fasta" - ], - "components": [ - "fcs/fcsadaptor", - "fcsgx/rungx" - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\nwith taxonomy ID of the expected organism\ne.g. [ id:'test', taxid:'id' ]\n" - } - }, - { - "assembly": { - "type": "file", - "description": "assembly fasta file", - "pattern": "*.{fasta,fa}" - } - }, - { - "database": { - "type": "directory", - "description": "Directory containing the FCS-GX database" - } - }, - { - "ramdisk_path": { - "type": "string", - "description": "Path to RAM disk for improved performance (optional)" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "fcsadaptor_cleaned_assembly": { - "type": "file", - "description": "Cleaned assembly in fasta format", - "pattern": "*.{cleaned_sequences.fa.gz}" - } - }, - { - "fcsadaptor_report": { - "type": "file", - "description": "Report of identified adaptors", - "pattern": "*.{fcs_adaptor_report.txt}" - } - }, - { - "fcsadaptor_log": { - "type": "file", - "description": "Log file", - "pattern": "*.{fcs_adaptor.log}" - } - }, - { - "fcsadaptor_pipeline_args": { - "type": "file", - "description": "Run arguments", - "pattern": "*.{pipeline_args.yaml}" - } - }, - { - "fcsadaptor_skipped_trims": { - "type": "file", - "description": "Skipped trim information", - "pattern": "*.{skipped_trims.jsonl}" - } - }, - { - "fcs_gx_report": { - "type": "file", - "description": "Report containing the contig identifier and recommended action (EXCLUDE, TRIM, FIX, REVIEW)", - "pattern": "*.fcs_gx_report.txt" - } - }, - { - "fcsgx_taxonomy_report": { - "type": "file", - "description": "Report containing the contig identifier and mapped contaminant species", - "pattern": "*.taxonomy.rpt" - } - } - ], - "authors": [ - "@scorreard" - ], - "maintainers": [ - "@scorreard" - ] - } - }, - { - "name": "fasta_consensus_autocycler", - "path": "subworkflows/nf-core/fasta_consensus_autocycler/meta.yml", - "type": "subworkflow", - "meta": { - "name": "fasta_consensus_autocycler", - "description": "Generate consensus assemblies and assembly graphs from grouped contig FASTA files using autocycler", - "keywords": [ - "autocycler", - "consensus", - "assembly", - "fasta" - ], - "components": [ - "autocycler/compress", - "autocycler/cluster", - "autocycler/trim", - "autocycler/resolve", - "autocycler/combine" - ], - "input": [ - { - "ch_grouped_contigs": { - "type": "file", - "description": "The input channel containing grouped contig FASTA files\nStructure: [ val(meta), [ fasta, fasta, ... ] ]\n", - "pattern": "*.{fasta,fa,fna}" - } - } - ], - "output": [ - { - "consensus_assembly": { - "type": "file", - "description": "Channel containing consensus assembly FASTA files\nStructure: [ val(meta), path(fasta) ]\n", - "pattern": "*/consensus_assembly.fasta" - } - }, - { - "consensus_assembly_graph": { - "type": "file", - "description": "Channel containing consensus assembly graphs\nStructure: [ val(meta), path(gfa) ]\n", - "pattern": "*/consensus_assembly.gfa" - } - } - ], - "authors": [ - "@dwells-eit" - ], - "maintainers": [ - "@dwells-eit" - ] - }, - "pipelines": [ - { - "name": "bacass", - "version": "2.6.0" - } - ] - }, - { - "name": "fasta_explore_search_plot_tidk", - "path": "subworkflows/nf-core/fasta_explore_search_plot_tidk/meta.yml", - "type": "subworkflow", - "meta": { - "name": "fasta_explore_search_plot_tidk", - "description": "Uses Telomere Identification toolKit (TIDK) to identify the frequency of telomeric repeats\nalong a sliding window for each sequence in the input fasta file. Results are presented in\nTSV and SVG formats. The user can specify an a priori sequence for identification.\nPossible a posteriori sequences are also explored and the most frequent sequence is\nused for identification similar to the a priori sequence. seqkit/seq and seqkit/sort modules are\nalso included to filter out small sequences and sort sequences by length.\n", - "keywords": [ - "genomics", - "telomere", - "repeat", - "search", - "plot" - ], - "components": [ - "seqkit/seq", - "seqkit/sort", - "tidk/explore", - "tidk/plot", - "tidk/search" - ], - "input": [ - { - "ch_fasta": { - "type": "file", - "description": "Input assembly\nStructure: [ val(meta), path(fasta) ]\n", - "pattern": "*.{fsa/fa/fasta}" - } - }, - { - "ch_apriori_sequence": { - "type": "string", - "description": "A priori sequence\nStructure: [ val(meta), val(sequence) ]\n" - } - } - ], - "output": [ - { - "apriori_tsv": { - "type": "file", - "description": "Frequency table for the identification of the a priori sequence\nStructure: [ val(meta), path(tsv) ]\n", - "pattern": "*.tsv" - } - }, - { - "apriori_svg": { - "type": "file", - "description": "Frequency graph for the identification of the a priori sequence\nStructure: [ val(meta), path(svg) ]\n", - "pattern": "*.svg" - } - }, - { - "aposteriori_sequence": { - "type": "file", - "description": "The most frequent a posteriori sequence\nStructure: [ val(meta), path(txt) ]\n", - "pattern": "*.txt" - } - }, - { - "aposteriori_tsv": { - "type": "file", - "description": "Frequency table for the identification of the a aposteriori sequence\nStructure: [ val(meta), path(tsv) ]\n", - "pattern": "*.tsv" - } - }, - { - "aposteriori_svg": { - "type": "file", - "description": "Frequency graph for the identification of the a aposteriori sequence\nStructure: [ val(meta), path(svg) ]\n", - "pattern": "*.svg" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions\nStructure: [ path(versions.yml) ]\n", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@GallVp" - ], - "maintainers": [ - "@GallVp" - ] - }, - "pipelines": [ - { - "name": "genomeqc", - "version": "dev" - } - ] - }, - { - "name": "fasta_gxf_busco_plot", - "path": "subworkflows/nf-core/fasta_gxf_busco_plot/meta.yml", - "type": "subworkflow", - "meta": { - "name": "fasta_gxf_busco_plot", - "description": "Runs BUSCO for input assemblies and their annotations in GFF/GFF3/GTF format, and creates summary plots using `BUSCO/generate_plot.py` script\n", - "keywords": [ - "genome", - "annotation", - "busco", - "plot" - ], - "components": [ - "busco/busco", - "busco/generateplot", - "gffread" - ], - "input": [ - { - "ch_fasta": { - "type": "file", - "description": "Channel containing FASTA files\nStructure:[ val(meta), fasta ]\n", - "pattern": "*.{fa,faa,fsa,fas,fasta}(.gz)?" - } - }, - { - "ch_gxf": { - "type": "file", - "description": "Channel containing GFF/GFF3/GTF files\nStructure:[ val(meta2), gxf ]\n", - "pattern": "*.{gff,gff3,gtf}" - } - }, - { - "val_mode": { - "type": "string", - "description": "String containing BUSCO mode to apply to ch_fasta files\nStructure:val(mode)\n" - } - }, - { - "val_lineages": { - "type": "array", - "description": "Array of strings representing BUSCO lineage datasets\nStructure:[ val(lineage) ]\n" - } - }, - { - "val_busco_lineages_path": { - "type": "path", - "description": "Path where BUSCO lineages are located or downloaded if not already there. If this input is `[]`,\nBUSCO will download the datasets in the task work directory\nStructure:val(busco_lineages_path)\n" - } - }, - { - "val_busco_config": { - "type": "path", - "description": "Path to BUSCO config. It is optional and can be set to `[]`\nStructure:val(busco_config)\n" - } - }, - { - "val_busco_cleanup": { - "type": "boolean", - "description": "Flag to indicate if intermediate BUSCO files should be removed\nStructure:val(busco_cleanup)\n" - } - } - ], - "output": [ - { - "assembly_batch_summary": { - "type": "file", - "description": "Channel containing BUSCO batch summaries corresponding to fasta files\nStructure: [ val(meta), txt ]\n", - "pattern": "*.txt" - } - }, - { - "assembly_short_summaries_txt": { - "type": "file", - "description": "Channel containing BUSCO short summaries corresponding to fasta files\nStructure: [ val(meta), txt ]\n", - "pattern": "*.txt" - } - }, - { - "assembly_short_summaries_json": { - "type": "file", - "description": "Channel containing BUSCO short summaries corresponding to fasta files\nStructure: [ val(meta), json ]\n", - "pattern": "*.json" - } - }, - { - "assembly_full_table": { - "description": "Channel containing complete results in a tabular format with scores and lengths of BUSCO matches,\nand coordinates (for genome mode) or gene/protein IDs (for transcriptome or protein modes)\nStructure: [ val(meta), tsv ]\n", - "pattern": "*.tsv" - } - }, - { - "assembly_plot_summary_txt": { - "type": "file", - "description": "Channel containing BUSCO short summaries corresponding to fasta files renamed to include lineage in sample id\nStructure: [ txt ]\n", - "pattern": "*.txt" - } - }, - { - "assembly_png": { - "type": "file", - "description": "Channel containing summary plot for assemblies\nStructure: png\n", - "pattern": "*.png" - } - }, - { - "annotation_batch_summary": { - "type": "file", - "description": "Channel containing BUSCO batch summaries corresponding to annotation files\nStructure: [ val(meta), txt ]\n", - "pattern": "*.txt" - } - }, - { - "annotation_short_summaries_txt": { - "type": "file", - "description": "Channel containing BUSCO short summaries corresponding to annotation files\nStructure: [ val(meta), txt ]\n", - "pattern": "*.txt" - } - }, - { - "annotation_short_summaries_json": { - "type": "file", - "description": "Channel containing BUSCO short summaries corresponding to annotation files\nStructure: [ val(meta), json ]\n", - "pattern": "*.json" - } - }, - { - "annotation_full_table": { - "description": "Channel containing complete results in a tabular format with scores and lengths of BUSCO matches,\nprotein IDs in protein mode\nStructure: [ val(meta), tsv ]\n", - "pattern": "*.tsv" - } - }, - { - "annotation_plot_summary_txt": { - "type": "file", - "description": "Channel containing BUSCO short summaries corresponding to annotation files renamed to include lineage in sample id\nStructure: [ txt ]\n", - "pattern": "*.txt" - } - }, - { - "annotation_png": { - "type": "file", - "description": "Channel containing summary plot for annotations\nStructure: png\n", - "pattern": "*.png" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions\nStructure: [ path(versions.yml) ]\n", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@GallVp" - ], - "maintainers": [ - "@GallVp", - "@FernandoDuarteF" - ] - } - }, - { - "name": "fasta_hmmsearch_rank_fastas", - "path": "subworkflows/nf-core/fasta_hmmsearch_rank_fastas/meta.yml", - "type": "subworkflow", - "meta": { - "name": "fasta_hmmsearch_rank_fastas", - "description": "Run hmmsearch and output separate fasta files for top scoring hits to each profile", - "keywords": [ - "hmmer", - "search", - "rank", - "fasta" - ], - "components": [ - "hmmer/hmmsearch", - "hmmer/hmmrank", - "seqtk/subseq" - ], - "input": [ - { - "ch_hmms": { - "type": "file", - "description": "The input channel containing hmm profiles\nStructure: [ val(meta), path(hmm) ]\n", - "pattern": "*.{hmm}" - } - }, - { - "ch_fasta": { - "type": "file", - "description": "The input channel containing sequences to be searched and ranked\n" - } - } - ], - "output": [ - { - "hmmrank": { - "type": "file", - "description": "Channel containing the TSV file from ranking hmmsearch hits\nStructure: [ val(meta), path(hmmrank) ]\n", - "pattern": "*.hmmrank.tsv.gz" - } - }, - { - "bai": { - "type": "file", - "description": "Channel containing subsets of sequences\nStructure: [ val(meta), path(fasta) ]\n", - "pattern": "*.fa.gz" - } - } - ], - "authors": [ - "@erikrikarddaniel" - ], - "maintainers": [ - "@erikrikarddaniel" - ] - }, - "pipelines": [ - { - "name": "ampliseq", - "version": "2.17.0" - }, - { - "name": "phyloplace", - "version": "2.0.0" - } - ] - }, - { - "name": "fasta_index_bismark_bwameth", - "path": "subworkflows/nf-core/fasta_index_bismark_bwameth/meta.yml", - "type": "subworkflow", - "meta": { - "name": "fasta_index_bismark_bwameth", - "description": "Generate index files from reference fasta for bismark and bwameth", - "keywords": [ - "bismark", - "bwameth", - "prepare genome", - "index" - ], - "components": [ - "untar", - "gunzip", - "bismark/genomepreparation", - "bwameth/index", - "samtools/faidx" - ], - "input": [ - { - "fasta_fai": { - "type": "file", - "description": "Reference genome\nStructure: [ val(meta), path(fasta), path(fai) ]\n", - "pattern": "*.{fa/fa.gz,fai}" - } - }, - { - "bismark_index": { - "type": "file", - "description": "Bismark genome index files\nStructure: [ val(meta), path(bismark_index) ]\n" - } - }, - { - "bwameth_index": { - "type": "file", - "description": "Bwameth genome index files\nStructure: [ val(meta), path(bwameth_index) ]\n" - } - }, - { - "aligner": { - "type": "string", - "description": "Aligner name (bismark, bismark_hisat, or bwameth)\n" - } - }, - { - "use_mem2": { - "type": "boolean", - "description": "Build a mem2 index when bwameth is chosen as an aligner, and an index path is not supplied\n" - } - } - ], - "output": [ - { - "fasta_fai": { - "type": "file", - "description": "Reference genome\nStructure: [ val(meta), path(fasta), path(fai) ]\n", - "pattern": "*.{fa/fa.gz,fai}" - } - }, - { - "bismark_index": { - "type": "file", - "description": "Bismark genome index files\nStructure: [ val(meta), path(bismark_index) ]\npattern: \"BismarkIndex\"\n" - } - }, - { - "bwameth_index": { - "type": "file", - "description": "Bwameth genome index files\nStructure: [ val(meta), path(bwameth_index) ]\npattern: \"index\"\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions\nStructure: [ path(versions.yml) ]\n", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@sateeshperi", - "dcarrillox" - ], - "maintainers": [ - "@sateeshperi", - "@dcarrillox" - ] - }, - "pipelines": [ - { - "name": "methylseq", - "version": "4.2.0" - } - ] - }, - { - "name": "fasta_index_dna", - "path": "subworkflows/nf-core/fasta_index_dna/meta.yml", - "type": "subworkflow", - "meta": { - "name": "fasta_index_dna", - "description": "Generate aligner index for a reference genome.\nPlease note, this workflow requires input CHANNELS. Input values will cause errors\n", - "keywords": [ - "fasta", - "index", - "bowtie2", - "bwamem", - "bwamem2", - "dragmap", - "snapaligner" - ], - "components": [ - "bowtie2/build", - "bwa/index", - "bwamem2/index", - "dragmap/hashtable", - "snapaligner/index" - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome fasta file" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing altliftover information\ne.g. [ id:'test' ]\n" - } - }, - { - "altliftover": { - "type": "file", - "description": "Sam formatted liftover file for the reference genome alt contigs\nSee: https://github.com/lh3/bwa/blob/master/README-alt.md\nDownload from: https://sourceforge.net/projects/bio-bwa/files/bwakit\n" - } - }, - { - "val_aligner": { - "type": "string", - "description": "Aligner to use for alignment", - "enum": [ - "bowtie2", - "bwa", - "bwamem2", - "dragmap", - "snap" - ] - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "index": { - "type": "file", - "description": "aligner index" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@matthdsm", - "@ramprasadn" - ], - "maintainers": [ - "@matthdsm", - "@ramprasadn" - ] - } - }, - { - "name": "fasta_index_methylseq", - "path": "subworkflows/nf-core/fasta_index_methylseq/meta.yml", - "type": "subworkflow", - "meta": { - "name": "fasta_index_methylseq", - "description": "Generate index files from reference fasta for bismark, bwameth and bwamem aligners", - "keywords": [ - "bismark", - "bwameth", - "bwamem", - "prepare genome", - "index" - ], - "components": [ - "untar", - "gunzip", - "bismark/genomepreparation", - "bwameth/index", - "bwa/index", - "samtools/faidx" - ], - "input": [ - { - "fasta": { - "type": "file", - "description": "Reference genome\nStructure: [ val(meta), path(fasta) ]\n", - "pattern": "*.{fa/fa.gz}" - } - }, - { - "fasta_index": { - "type": "file", - "description": "Reference genome index file\nStructure: [ val(meta), path(fasta) ]\n", - "pattern": "*.fai" - } - }, - { - "bismark_index": { - "type": "file", - "description": "Bismark genome index files\nStructure: [ val(meta), path(bismark_index) ]\n" - } - }, - { - "bwameth_index": { - "type": "file", - "description": "Bwameth genome index files\nStructure: [ val(meta), path(bwameth_index) ]\n" - } - }, - { - "bwamem_index": { - "type": "file", - "description": "Bwamem genome index files\nStructure: [ val(meta), path(bwamem_index) ]\n" - } - }, - { - "aligner": { - "type": "string", - "description": "Aligner name (bismark, bismark_hisat, bwameth, or bwamem)\n" - } - }, - { - "collecthsmetrics": { - "type": "boolean", - "description": "Whether to run picard collecthsmetrics tool\n" - } - }, - { - "use_mem2": { - "type": "boolean", - "description": "Build a mem2 index when bwameth is chosen as an aligner, and an index path is not supplied\n" - } - } - ], - "output": [ - { - "fasta": { - "type": "file", - "description": "Reference genome\nStructure: [ val(meta), path(fasta) ]\n", - "pattern": "*.fa" - } - }, - { - "fasta_index": { - "type": "file", - "description": "Reference genome index file\nStructure: [ val(meta), path(fasta) ]\n", - "pattern": "*.fai" - } - }, - { - "bismark_index": { - "type": "file", - "description": "Bismark genome index files\nStructure: [ val(meta), path(bismark_index) ]\npattern: \"BismarkIndex\"\n" - } - }, - { - "bwameth_index": { - "type": "file", - "description": "Bwameth genome index files\nStructure: [ val(meta), path(bwameth_index) ]\npattern: \"index\"\n" - } - }, - { - "bwamem_index": { - "type": "file", - "description": "Bwamem genome index files\nStructure: [ val(meta), path(bwamem_index) ]\npattern: \"index\"\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions\nStructure: [ path(versions.yml) ]\n", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@sateeshperi", - "@dcarrillox", - "@eduard.watchmaker" - ], - "maintainers": [ - "@sateeshperi", - "@dcarrillox", - "@eduard.watchmaker" - ] - }, - "pipelines": [ - { - "name": "methylseq", - "version": "4.2.0" - } - ] - }, - { - "name": "fasta_newick_epang_gappa", - "path": "subworkflows/nf-core/fasta_newick_epang_gappa/meta.yml", - "type": "subworkflow", - "meta": { - "name": "fasta_newick_epang_gappa", - "description": "Run phylogenetic placement with a number of query sequences plus a reference alignment and phylogeny. Used in nf-core/phyloplace.", - "keywords": [ - "phylogenetic placement", - "phylogenetics", - "alignment", - "fasta", - "newick" - ], - "components": [ - "hmmer/hmmbuild", - "hmmer/hmmalign", - "hmmer/eslalimask", - "hmmer/eslreformat", - "clustalo/align", - "mafft/align", - "epang/place", - "epang/split", - "gappa/examinegraft", - "gappa/examineassign", - "gappa/examineheattree" - ], - "input": [ - { - "ch_pp_data": { - "type": "map", - "description": "Structure: [\n meta: val(meta),\n data: [\n alignmethod: 'hmmer',\n queryseqfile: path(\"*.faa\"),\n refseqfile: path(\"*.alnfaa\"),\n refphylogeny: path(\"*.newick\"),\n model: \"LG\",\n taxonomy: path(\"*.tsv\")\n ]\n]\n" - } - }, - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "queryseqfile": { - "type": "file", - "description": "Fasta file with query sequences", - "pattern": "*.{faa,fna,fa,fasta,fa,faa.gz,fna.gz,fa.gz,fasta.gz,fa.gz}" - } - }, - { - "refseqfile": { - "type": "file", - "description": "File with reference sequences; aligned unless an hmmfile is provided", - "pattern": "*.{faa,fna,fa,fasta,fa,phy,aln,alnfaa,alnfna,alnfa,mfa,faa.gz,fna.gz,fa.gz,fasta.gz,fa.gz,phy.gz,aln.gz,alnfaa.gz,alnfna.gz,alnfa.gz,mfa.gz}" - } - }, - { - "refphylogeny": { - "type": "file", - "description": "Newick file with reference phylogenetic tree", - "pattern": "*.{newick,tree}" - } - }, - { - "hmmfile": { - "type": "file", - "description": "HMM file to use for alignment; implies that refseqfile is not aligned. Optional.", - "pattern": "*.{hmm,HMM,hmm.gz,HMM.gz}" - } - }, - { - "model": { - "type": "string", - "description": "Phylogenetic model to use in placement, e.g. 'LG+F' or 'GTR+I+F'" - } - }, - { - "alignmethod": { - "type": "string", - "description": "Method used for alignment, 'hmmer', 'clustalo' or 'mafft'" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "epang": { - "type": "directory", - "description": "All output from EPA-NG", - "pattern": "*" - } - }, - { - "jplace": { - "type": "file", - "description": "jplace file from EPA-NG", - "pattern": "*.jplace" - } - }, - { - "grafted_phylogeny": { - "type": "file", - "description": "Newick file with query sequences placed in reference tree", - "pattern": "*.newick" - } - }, - { - "taxonomy_profile": { - "type": "file", - "description": "Tab separated file with taxonomy information from classification", - "pattern": "*.tsv" - } - }, - { - "taxonomy_per_query": { - "type": "file", - "description": "Tab separated file with taxonomy information per query from classification", - "pattern": "*.tsv" - } - }, - { - "heattree": { - "type": "file", - "description": "Heattree in SVG format", - "pattern": "*.svg" - } - } - ], - "authors": [ - "@erikrikarddaniel" - ], - "maintainers": [ - "@erikrikarddaniel" - ] - }, - "pipelines": [ - { - "name": "ampliseq", - "version": "2.17.0" - }, - { - "name": "phyloplace", - "version": "2.0.0" - } - ] - }, - { - "name": "fasta_vclust_prefilter_align_cluster", - "path": "subworkflows/nf-core/fasta_vclust_prefilter_align_cluster/meta.yml", - "type": "subworkflow", - "meta": { - "name": "fasta_vclust_prefilter_align_cluster", - "description": "Subworkflow that runs a three-stage VCLUST pipeline: 1) create a prefilter\nof candidate sequence pairs with `vclust prefilter`, 2) compute pairwise\nalignments and similarity metrics with `vclust align`, and 3) generate\nthreshold-based clusters with `vclust cluster`.\n", - "keywords": [ - "fasta", - "vclust", - "cluster", - "prefilter", - "align" - ], - "components": [ - "vclust/prefilter", - "vclust/align", - "vclust/cluster" - ], - "input": [ - { - "ch_fasta": { - "type": "file", - "description": "Input channel containing FASTA files to cluster. Each entry is a two-item\ntuple: [ val(meta), path(fasta) ] where `meta` is a Groovy map (e.g.\n[ id:'sample1' ]) and `fasta` is the path to the FASTA file.\n", - "pattern": "*.{fasta,fna,fa}" - } - }, - { - "save_alignment": { - "type": "boolean", - "description": "Whether to save pairwise alignments produced by `vclust align`.\n", - "default": false - } - }, - { - "metric": { - "type": "string", - "description": "Similarity metric to use for clustering. Allowed values: 'tani', 'gani',\nor 'ani'.\n", - "enum": [ - "tani", - "gani", - "ani" - ] - } - }, - { - "tani": { - "type": "float", - "description": "Minimum total ANI threshold.\n" - } - }, - { - "gani": { - "type": "float", - "description": "Minimum global ANI threshold.\n" - } - }, - { - "ani": { - "type": "float", - "description": "Minimum ANI threshold.\n" - } - } - ], - "output": [ - { - "versions": { - "type": "file", - "description": "File containing software versions used by the subworkflow", - "pattern": "versions.yml" - } - }, - { - "fasta": { - "type": "file", - "description": "Input FASTA file forwarded from the workflow. Each output is associated\nwith its input sample/meta tuple.\n", - "pattern": "*.{fasta,fna,fa}" - } - }, - { - "clusters": { - "type": "file", - "description": "TSV file containing clustering assignments produced by `vclust cluster`.\nFormat: genome identifier followed by 0-based cluster identifier.\n", - "pattern": "*.tsv" - } - }, - { - "alignment": { - "type": "file", - "description": "Optional pairwise alignment file(s) produced by `vclust align`.", - "pattern": "*.aln.tsv" - } - }, - { - "ids": { - "type": "file", - "description": "IDs file produced by `vclust align` mapping sequence IDs and part counts.", - "pattern": "*.ids.tsv" - } - } - ], - "authors": [ - "@Joon-Klaps" - ], - "maintainers": [ - "@Joon-Klaps" - ] - } - }, - { - "name": "fastq_align_bamcmp_bwa", - "path": "subworkflows/nf-core/fastq_align_bamcmp_bwa/meta.yml", - "type": "subworkflow", - "meta": { - "name": "fastq_align_bamcmp_bwa", - "description": "Align reads to two different reference genomes using bwa, then use bamcmp to keep only reads that align better to the first genome, then sort with samtools", - "keywords": [ - "bam", - "cram", - "bamcmp", - "contamination", - "align" - ], - "components": [ - "bamcmp", - "bwa/mem", - "bwa/align", - "samtools/sort", - "samtools/index", - "samtools/stats", - "samtools/idxstats", - "samtools/flagstat", - "bam_sort_stats_samtools" - ], - "input": [ - { - "ch_reads": { - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\nStructure: [ val(meta), [ path(reads) ] ]\n" - } - }, - { - "ch_primary_index": { - "description": "BWA genome index files for the primary species.\nStructure: [ val(meta2), path(primary_index) ]\n" - } - }, - { - "ch_contaminant_index": { - "description": "BWA genome index files for the contamination species.\nStructure: [ val(meta3), path(contaminant_index) ]\n" - } - }, - { - "val_sort_bam": { - "type": "boolean", - "description": "If true sort resulting primary bam files.", - "pattern": "true|false" - } - }, - { - "ch_primary_fasta_fai": { - "type": "file", - "description": "Optional reference fasta file for the primary genome. This only needs to be given if val_sort_bam = true\nStructure: [ path(fasta), path(fai) ]\n" - } - } - ], - "output": [ - { - "bam": { - "description": "BAM file, sorted by samtools if requested\nStructure: [ val(meta), path(bam) ]\n" - } - }, - { - "contaminant_bam": { - "description": "BAM file of the reads that map better to the contamination genome. Sorted by queryname.\nStructure: [ val(meta), path(bam) ]\n" - } - }, - { - "bai": { - "description": "BAI index of the ordered BAM file\nStructure: [ val(meta), path(bai) ]\n" - } - }, - { - "csi": { - "description": "CSI index of the ordered BAM file\nStructure: [ val(meta), path(csi) ]\n" - } - }, - { - "stats": { - "description": "File containing samtools stats output\nStructure: [ val(meta), path(stats) ]\n" - } - }, - { - "flagstat": { - "description": "File containing samtools flagstat output\nStructure: [ val(meta), path(flagstat) ]\n" - } - }, - { - "idxstats": { - "description": "File containing samtools idxstats output\nStructure: [ val(meta), path(idxstats) ]\n" - } - }, - { - "unfiltered_stats": { - "description": "File containing samtools stats output for primary unfiltered alignment.\nStructure: [ val(meta), path(stats) ]\n" - } - }, - { - "unfiltered_flagstat": { - "description": "File containing samtools flagstat output for primary unfiltered alignment.\nStructure: [ val(meta), path(flagstat) ]\n" - } - }, - { - "unfiltered_idxstats": { - "description": "File containing samtools idxstats output for primary unfiltered alignment.\nStructure: [ val(meta), path(idxstats) ]\n" - } - }, - { - "versions": { - "description": "Files containing software versions\nStructure: [ path(versions.yml) ]\n" - } - } - ], - "authors": [ - "@sppearce" - ], - "maintainers": [ - "@sppearce" - ] - } - }, - { - "name": "fastq_align_bowtie2", - "path": "subworkflows/nf-core/fastq_align_bowtie2/meta.yml", - "type": "subworkflow", - "meta": { - "name": "fastq_align_bowtie2", - "description": "Align reads to a reference genome using bowtie2 then sort with samtools", - "keywords": [ - "align", - "fasta", - "genome", - "reference" - ], - "components": [ - "bowtie2/align", - "samtools/sort", - "samtools/index", - "samtools/stats", - "samtools/idxstats", - "samtools/flagstat", - "bam_sort_stats_samtools" - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "ch_reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" - } - }, - { - "ch_index": { - "type": "file", - "description": "Bowtie2 genome index files", - "pattern": "*.ebwt" - } - }, - { - "save_unaligned": { - "type": "boolean", - "description": "Save reads that do not map to the reference (true) or discard them (false)\n(default: false)\n" - } - }, - { - "sort_bam": { - "type": "boolean", - "description": "Use samtools sort (true) or samtools view (false)\n", - "default": false - } - }, - { - "ch_fasta_fai": { - "type": "file", - "description": "Reference fasta file and index", - "pattern": "*.{fasta,fa},*.{fai,fai}" - } - } - ], - "output": [ - { - "bam": { - "type": "file", - "description": "Output BAM file containing read alignments", - "pattern": "*.{bam}" - } - }, - { - "fastq": { - "type": "file", - "description": "Unaligned FastQ files", - "pattern": "*.fastq.gz" - } - }, - { - "log": { - "type": "file", - "description": "Alignment log", - "pattern": "*.log" - } - } - ], - "authors": [ - "@drpatelh" - ], - "maintainers": [ - "@drpatelh" - ] - }, - "pipelines": [ - { - "name": "atacseq", - "version": "2.1.2" - }, - { - "name": "chipseq", - "version": "2.1.0" - }, - { - "name": "nascent", - "version": "2.3.0" - }, - { - "name": "phageannotator", - "version": "dev" - }, - { - "name": "viralrecon", - "version": "3.0.0" - } - ] - }, - { - "name": "fastq_align_bwa", - "path": "subworkflows/nf-core/fastq_align_bwa/meta.yml", - "type": "subworkflow", - "meta": { - "name": "fastq_align_bwa", - "description": "Align reads to a reference genome using bwa then sort with samtools", - "keywords": [ - "align", - "fasta", - "genome", - "reference" - ], - "components": [ - "bwa/mem", - "bwa/align", - "samtools/sort", - "samtools/index", - "samtools/stats", - "samtools/idxstats", - "samtools/flagstat", - "bam_sort_stats_samtools" - ], - "input": [ - { - "ch_reads": { - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\nStructure: [ val(meta), [ path(reads) ] ]\n" - } - }, - { - "ch_index": { - "description": "BWA genome index files\nStructure: [ val(meta), path(index) ]\n" - } - }, - { - "val_sort_bam": { - "type": "boolean", - "description": "If true bwa modules sort resulting bam files", - "pattern": "true|false" - } - }, - { - "ch_fasta_fai": { - "type": "file", - "description": "Optional reference fasta file and index. This only needs to be given if val_sort_bam = true.\nStructure: [ val(meta), path(fasta), path(fai) ]\n" - } - } - ], - "output": [ - { - "bam_orig": { - "description": "BAM file produced by bwa\nStructure: [ val(meta), path(bam) ]\n" - } - }, - { - "bam": { - "description": "BAM file ordered by samtools\nStructure: [ val(meta), path(bam) ]\n" - } - }, - { - "bai": { - "description": "BAI index of the ordered BAM file\nStructure: [ val(meta), path(bai) ]\n" - } - }, - { - "csi": { - "description": "CSI index of the ordered BAM file\nStructure: [ val(meta), path(csi) ]\n" - } - }, - { - "stats": { - "description": "File containing samtools stats output\nStructure: [ val(meta), path(stats) ]\n" - } - }, - { - "flagstat": { - "description": "File containing samtools flagstat output\nStructure: [ val(meta), path(flagstat) ]\n" - } - }, - { - "idxstats": { - "description": "File containing samtools idxstats output\nStructure: [ val(meta), path(idxstats) ]\n" - } - } - ], - "authors": [ - "@JoseEspinosa" - ], - "maintainers": [ - "@JoseEspinosa" - ] - }, - "pipelines": [ - { - "name": "atacseq", - "version": "2.1.2" - }, - { - "name": "chipseq", - "version": "2.1.0" - }, - { - "name": "methylseq", - "version": "4.2.0" - }, - { - "name": "nascent", - "version": "2.3.0" - } - ] - }, - { - "name": "fastq_align_bwaaln", - "path": "subworkflows/nf-core/fastq_align_bwaaln/meta.yml", - "type": "subworkflow", - "meta": { - "name": "fastq_align_bwaaln", - "description": "Align FASTQ files against reference genome with the bwa aln short-read aligner producing a sorted and indexed BAM files", - "keywords": [ - "bwa", - "aln", - "fasta", - "bwa", - "align", - "map" - ], - "components": [ - "bwa/aln", - "bwa/sampe", - "bwa/samse", - "samtools/index" - ], - "input": [ - { - "ch_reads": { - "description": "Structure: [ val(meta), path(fastq) ]\nOne or two FASTQ files for single or paired end data respectively.\nNote: the subworkflow adds a new meta ID `meta.id_index` that _must_\nbe used in `prefix` to ensure unique file names. See the associated\nnextflow.config file.\n" - } - }, - { - "ch_index": { - "description": "Structure: [ val(meta), path(index) ]\nA directory containing bwa aln reference indices as from `bwa index`\nContains files ending in extensions such as .amb, .ann, .bwt etc.\n" - } - } - ], - "output": [ - { - "bam": { - "description": "Structure: [ val(meta), path(bam) ]\nSorted BAM/CRAM/SAM file\nNote: the subworkflow adds a new meta ID `meta.id_index` that _must_\nbe used in `prefix` to ensure unique file names. See the associated\nnextflow.config file.\n" - } - }, - { - "bai": { - "description": "Structure: [ val(meta), path(bai) ]\nBAM/CRAM/SAM samtools index file\n" - } - }, - { - "csi": { - "description": "Structure: [ val(meta), path(csi) ]\nBAM/CRAM/SAM samtools index file for larger references\n" - } - }, - { - "versions": { - "description": "Files containing software versions\nStructure: [ path(versions.yml) ]\n" - } - } - ], - "authors": [ - "@jfy133" - ], - "maintainers": [ - "@jfy133" - ] - }, - "pipelines": [ - { - "name": "callingcards", - "version": "1.0.0" - }, - { - "name": "sammyseq", - "version": "dev" - } - ] - }, - { - "name": "fastq_align_chromap", - "path": "subworkflows/nf-core/fastq_align_chromap/meta.yml", - "type": "subworkflow", - "meta": { - "name": "fastq_align_chromap", - "description": "Align high throughput chromatin profiles using Chromap then sort with samtools", - "keywords": [ - "align", - "fasta", - "genome", - "reference", - "chromatin profiles", - "chip-seq", - "atac-seq", - "hic" - ], - "components": [ - "chromap/chromap", - "samtools/sort", - "samtools/index", - "samtools/stats", - "samtools/idxstats", - "samtools/flagstat", - "bam_sort_stats_samtools" - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "ch_reads": { - "type": "file", - "description": "Structure: [val(meta), path(reads)]\nList of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "ch_index": { - "type": "file", - "description": "Structure: [val(meta2), path(index)]\nChromap genome index files\n", - "pattern": "*.index" - } - }, - { - "ch_fasta_fai": { - "type": "file", - "description": "Structure: [val(meta2), path(fasta), path(fai)]\nReference fasta file and index\n", - "pattern": "*.{fasta,fa},*.fai" - } - }, - { - "ch_barcodes": { - "type": "file", - "description": "Structure: [path(barcodes)]\nCell barcode files\n" - } - }, - { - "ch_whitelist": { - "type": "file", - "description": "Structure: [path(whitelist)]\nCell barcode whitelist file\n" - } - }, - { - "ch_chr_order": { - "type": "file", - "description": "Structure: [path(chr_order)]\nCustom chromosome order\n" - } - }, - { - "ch_pairs_chr_order": { - "type": "file", - "description": "Structure: [path(pairs_chr_order)]\nNatural chromosome order for pairs flipping\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file", - "pattern": "*.bam" - } - }, - { - "bai": { - "type": "file", - "description": "BAM index (currently only for snapaligner)", - "pattern": "*.bai" - } - }, - { - "stats": { - "type": "file", - "description": "File containing samtools stats output", - "pattern": "*.{stats}" - } - }, - { - "flagstat": { - "type": "file", - "description": "File containing samtools flagstat output", - "pattern": "*.{flagstat}" - } - }, - { - "idxstats": { - "type": "file", - "description": "File containing samtools idxstats output", - "pattern": "*.{idxstats}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@JoseEspinosa" - ], - "maintainers": [ - "@JoseEspinosa" - ] - }, - "pipelines": [ - { - "name": "atacseq", - "version": "2.1.2" - }, - { - "name": "chipseq", - "version": "2.1.0" - } - ] - }, - { - "name": "fastq_align_dedup_bismark", - "path": "subworkflows/nf-core/fastq_align_dedup_bismark/meta.yml", - "type": "subworkflow", - "meta": { - "name": "fastq_align_dedup_bismark", - "description": "Align BS-Seq reads to a reference genome using bismark, deduplicate and sort", - "keywords": [ - "bismark", - "3-letter genome", - "map", - "methylation", - "5mC", - "methylseq", - "bisulphite", - "bisulfite", - "bam" - ], - "components": [ - "bismark/align", - "samtools/sort", - "samtools/index", - "bismark/deduplicate", - "bismark/methylationextractor", - "bismark/coverage2cytosine", - "bismark/report", - "bismark/summary" - ], - "input": [ - { - "ch_reads": { - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\nStructure: [ val(meta), [ path(reads) ] ]\n", - "pattern": "*.{fastq,fastq.gz}" - } - }, - { - "ch_fasta_fai": { - "type": "file", - "description": "Structure: [ val(meta), path(fasta), path(fai) ]\n", - "pattern": "*.{fa,fa.gz}" - } - }, - { - "ch_bismark_index": { - "description": "Bismark genome index files\nStructure: [ val(meta), path(index) ]\n", - "pattern": "BismarkIndex" - } - }, - { - "skip_deduplication": { - "type": "boolean", - "description": "Skip deduplication of aligned reads\n" - } - }, - { - "cytosine_report": { - "type": "boolean", - "description": "Produce coverage2cytosine reports that relates methylation calls back to genomic cytosine contexts\n" - } - } - ], - "output": [ - { - "bam": { - "type": "file", - "description": "Channel containing aligned or deduplicated BAM files.\nStructure: [ val(meta), path(bam) ]\n", - "pattern": "*.bam" - } - }, - { - "bai": { - "type": "file", - "description": "Channel containing aligned or deduplicated BAM index files.\nStructure: [ val(meta), path(bam.bai) ]\n", - "pattern": "*.bai" - } - }, - { - "coverage2cytosine_coverage": { - "type": "file", - "description": "Channel containing coverage information from coverage2cytosine.\nStructure: [ val(meta), path(coverage.txt) ]\n", - "pattern": "*.cov.gz" - } - }, - { - "coverage2cytosine_report": { - "type": "file", - "description": "Channel containing report from coverage2cytosine summarizing cytosine methylation coverage.\nStructure: [ val(meta), path(report.txt) ]\n", - "pattern": "*report.txt.gz" - } - }, - { - "coverage2cytosine_summary": { - "type": "file", - "description": "Channel containing summary information from coverage2cytosine.\nStructure: [ val(meta), path(summary.txt) ]\n", - "pattern": "*cytosine_context_summary.txt" - } - }, - { - "methylation_bedgraph": { - "type": "file", - "description": "Channel containing methylation data in bedGraph format.\nStructure: [ val(meta), path(methylation.bedgraph) ]\n", - "pattern": "*.bedGraph.gz" - } - }, - { - "methylation_calls": { - "type": "file", - "description": "Channel containing methylation call data.\nStructure: [ val(meta), path(calls.txt) ]\n", - "pattern": "*.txt.gz" - } - }, - { - "methylation_coverage": { - "type": "file", - "description": "Channel containing methylation coverage data.\nStructure: [ val(meta), path(coverage.txt) ]\n", - "pattern": "*.cov.gz" - } - }, - { - "methylation_report": { - "type": "file", - "description": "Channel containing methylation report detailing methylation patterns.\nStructure: [ val(meta), path(report.txt) ]\n", - "pattern": "*_splitting_report.txt" - } - }, - { - "methylation_mbias": { - "type": "file", - "description": "Channel containing M-bias report showing methylation bias across read positions.\nStructure: [ val(meta), path(mbias.txt) ]\n", - "pattern": "*.M-bias.txt" - } - }, - { - "bismark_report": { - "type": "file", - "description": "Channel containing Bismark report with mapping and methylation statistics.\nStructure: [ val(meta), path(bismark_report.txt) ]\n", - "pattern": "*report.{html,txt}" - } - }, - { - "bismark_summary": { - "type": "file", - "description": "Channel containing Bismark summary report.\nStructure: [ val(meta), path(bismark_summary.txt) ]\n", - "pattern": "*report.{html,txt}" - } - }, - { - "multiqc": { - "type": "file", - "description": "Channel containing files for MultiQC input (reports, alignment reports, methylation reports).\nStructure: [ path(files) ]\n", - "pattern": "*.{html,txt}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions.\nStructure: [ path(versions.yml) ]\n", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@sateeshperi" - ], - "maintainers": [ - "@sateeshperi" - ] - }, - "pipelines": [ - { - "name": "methylseq", - "version": "4.2.0" - } - ] - }, - { - "name": "fastq_align_dedup_bwamem", - "path": "subworkflows/nf-core/fastq_align_dedup_bwamem/meta.yml", - "type": "subworkflow", - "meta": { - "name": "fastq_align_dedup_bwamem", - "description": "Performs alignment of DNA or TAPS-treated reads using bwamem or parabricks/fq2bam, sort and deduplicate", - "keywords": [ - "bwamem", - "alignment", - "map", - "5mC", - "methylseq", - "DNA", - "fastq", - "bam" - ], - "components": [ - "parabricks/fq2bam", - "samtools/index", - "picard/addorreplacereadgroups", - "picard/markduplicates", - "bam_sort_stats_samtools", - "fastq_align_bwa" - ], - "input": [ - { - "ch_reads": { - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\nStructure: [ val(meta), [ path(reads) ] ]\n", - "pattern": "*.{fastq,fastq.gz}" - } - }, - { - "ch_fasta": { - "type": "file", - "description": "Structure: [ val(meta), path(fasta) ]\n", - "pattern": "*.{fa,fa.gz}" - } - }, - { - "ch_fasta_index": { - "type": "file", - "description": "Structure: [ val(meta), path(fasta index) ]\n" - } - }, - { - "ch_bwamem_index": { - "type": "directory", - "description": "Bwa-mem genome index files\nStructure: [ val(meta), path(index) ]\n", - "pattern": "Bwa-memIndex" - } - }, - { - "skip_deduplication": { - "type": "boolean", - "description": "Skip deduplication of aligned reads\n" - } - }, - { - "use_gpu": { - "type": "boolean", - "description": "Use GPU for alignment\n" - } - }, - { - "output_fmt": { - "type": "string", - "description": "Output format for the alignment. Options are 'bam' or 'cram'", - "pattern": "{bam,cram}" - } - }, - { - "interval_file": { - "type": "file", - "description": "Structure: [ val(meta), path(interval file) ]\n", - "pattern": "*.{bed,intervals}" - } - }, - { - "known_sites": { - "type": "file", - "description": "Structure: [ val(meta), path(known sites) ]\n", - "pattern": "*.{vcf,vcf.gz}" - } - } - ], - "output": [ - { - "bam": { - "type": "file", - "description": "Channel containing BAM files\nStructure: [ val(meta), path(bam) ]\n", - "pattern": "*.bam" - } - }, - { - "bai": { - "type": "file", - "description": "Channel containing indexed BAM (BAI) files\nStructure: [ val(meta), path(bai) ]\n", - "pattern": "*.bai" - } - }, - { - "samtools_flagstat": { - "type": "file", - "description": "File containing samtools flagstat output\nStructure: [ val(meta), path(flagstat) ]\n", - "pattern": "*.flagstat" - } - }, - { - "samtools_idxstats": { - "type": "file", - "description": "File containing samtools idxstats output\nStructure: [ val(meta), path(idxstats) ]\n", - "pattern": "*.idxstats" - } - }, - { - "samtools_stats": { - "type": "file", - "description": "File containing samtools stats output\nStructure: [ val(meta), path(stats) ]\n", - "pattern": "*.{stats}" - } - }, - { - "picard_metrics": { - "type": "file", - "description": "Duplicate metrics file generated by picard\nStructure: [ val(meta), path(metrics) ]\n", - "pattern": "*.{metrics.txt}" - } - }, - { - "multiqc": { - "type": "file", - "description": "Channel containing files for MultiQC input (metrics, stats, flagstat, idxstats).\nStructure: [ path(file) ]\n", - "pattern": "*{.txt,.stats,.flagstat,.idxstats}" - } - } - ], - "authors": [ - "@eduard-watchmaker" - ], - "maintainers": [ - "@eduard-watchmaker" - ] - }, - "pipelines": [ - { - "name": "methylseq", - "version": "4.2.0" - } - ] - }, - { - "name": "fastq_align_dedup_bwameth", - "path": "subworkflows/nf-core/fastq_align_dedup_bwameth/meta.yml", - "type": "subworkflow", - "meta": { - "name": "fastq_align_dedup_bwameth", - "description": "Performs alignment of BS-Seq reads using bwameth or parabricks/fq2bammeth, sort and deduplicate", - "keywords": [ - "bwameth", - "alignment", - "3-letter genome", - "map", - "methylation", - "5mC", - "methylseq", - "bisulphite", - "bisulfite", - "fastq", - "bam" - ], - "components": [ - "bwameth/align", - "parabricks/fq2bammeth", - "samtools/sort", - "samtools/index", - "samtools/flagstat", - "samtools/stats", - "picard/markduplicates" - ], - "input": [ - { - "ch_reads": { - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\nStructure: [ val(meta), [ path(reads) ] ]\n", - "pattern": "*.{fastq,fastq.gz}" - } - }, - { - "ch_fasta_fai": { - "type": "file", - "description": "Structure: [ val(meta), path(fasta), path(fai) ]\n", - "pattern": "*.{fa,fa.gz}" - } - }, - { - "ch_bwameth_index": { - "description": "Bwa-meth genome index files\nStructure: [ val(meta), path(index) ]\n", - "pattern": "Bwa-methIndex" - } - }, - { - "skip_deduplication": { - "type": "boolean", - "description": "Skip deduplication of aligned reads\n" - } - }, - { - "use_gpu": { - "type": "boolean", - "description": "Use GPU for alignment\n" - } - } - ], - "output": [ - { - "bam": { - "type": "file", - "description": "Channel containing BAM files\nStructure: [ val(meta), path(bam) ]\n", - "pattern": "*.bam" - } - }, - { - "bai": { - "type": "file", - "description": "Channel containing indexed BAM (BAI) files\nStructure: [ val(meta), path(bai) ]\n", - "pattern": "*.bai" - } - }, - { - "samtools_flagstat": { - "type": "file", - "description": "File containing samtools flagstat output\nStructure: [ val(meta), path(flagstat) ]\n", - "pattern": "*.flagstat" - } - }, - { - "samtools_stats": { - "type": "file", - "description": "File containing samtools stats output\nStructure: [ val(meta), path(stats) ]\n", - "pattern": "*.{stats}" - } - }, - { - "picard_metrics": { - "type": "file", - "description": "Duplicate metrics file generated by picard\nStructure: [ val(meta), path(metrics) ]\n", - "pattern": "*.{metrics.txt}" - } - }, - { - "multiqc": { - "type": "file", - "description": "Channel containing files for MultiQC input (metrics, stats, flagstat).\nStructure: [ path(files) ]\n", - "pattern": "*.{txt,stats,flagstat}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions\nStructure: [ path(versions.yml) ]\n", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@sateeshperi" - ], - "maintainers": [ - "@sateeshperi", - "@gallvp", - "@eduard-watchmaker" - ] - }, - "pipelines": [ - { - "name": "methylseq", - "version": "4.2.0" - } - ] - }, - { - "name": "fastq_align_dna", - "path": "subworkflows/nf-core/fastq_align_dna/meta.yml", - "type": "subworkflow", - "meta": { - "name": "fastq_align_dna", - "description": "Align fastq files to a reference genome", - "keywords": [ - "fastq", - "bam", - "sort", - "bwamem", - "bwamem2", - "dragmap", - "snapaligner", - "strobealign" - ], - "components": [ - "bowtie2/align", - "bwa/mem", - "bwamem2/mem", - "dragmap/align", - "snapaligner/align", - "strobealign" - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "index": { - "type": "file", - "description": "Aligner genome index files", - "pattern": "Directory containing aligner index" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome in fasta format", - "pattern": "*.{fa, fasta, fna}" - } - }, - { - "aligner": { - "type": "string", - "description": "Aligner to use for alignment", - "enum": [ - "bowtie2", - "bwa", - "bwamem2", - "dragmap", - "snap", - "strobealign" - ] - } - }, - { - "sort_bam": { - "type": "boolean", - "description": "sort output" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file", - "pattern": "*.bam" - } - }, - { - "bam_index": { - "type": "file", - "description": "BAM index (currently only for snapaligner)", - "pattern": "*.{bai, csi}" - } - }, - { - "report": { - "type": "file", - "description": "Alignment report (currently only for dragmap)", - "pattern": "*.txt" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@matthdsm" - ], - "maintainers": [ - "@matthdsm" - ] - }, - "pipelines": [ - { - "name": "sammyseq", - "version": "dev" - } - ] - }, - { - "name": "fastq_align_hisat2", - "path": "subworkflows/nf-core/fastq_align_hisat2/meta.yml", - "type": "subworkflow", - "meta": { - "name": "fastq_align_hisat2", - "description": "Align reads to a reference genome using hisat2 then sort with samtools", - "keywords": [ - "align", - "sort", - "rnaseq", - "genome", - "fastq", - "bam", - "sam", - "cram" - ], - "components": [ - "hisat2/align", - "samtools/stats", - "samtools/idxstats", - "samtools/flagstat", - "bam_sort_stats_samtools" - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" - } - }, - { - "index": { - "type": "file", - "description": "HISAT2 genome index file", - "pattern": "*.ht2" - } - }, - { - "splicesites": { - "type": "file", - "description": "Splices sites in gtf file", - "pattern": "*.{txt}" - } - }, - { - "fasta_fai": { - "type": "file", - "description": "Reference genome fasta file and index", - "pattern": "*.{fasta,fa,fai}" - } - }, - { - "save_unaligned": { - "type": "boolean", - "description": "Save unaligned reads to FastQ files" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "Output BAM file containing read alignments", - "pattern": "*.{bam}" - } - }, - { - "summary": { - "type": "file", - "description": "Alignment log", - "pattern": "*.log" - } - }, - { - "fastq": { - "type": "file", - "description": "Optional output FASTQ file containing unaligned reads", - "pattern": ".fastq.gz" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "bai": { - "type": "file", - "description": "BAM/CRAM/SAM index file", - "pattern": "*.{bai,crai,sai}" - } - }, - { - "crai": { - "type": "file", - "description": "BAM/CRAM/SAM index file", - "pattern": "*.{bai,crai,sai}" - } - }, - { - "stats": { - "type": "file", - "description": "File containing samtools stats output", - "pattern": "*.{stats}" - } - }, - { - "flagstat": { - "type": "file", - "description": "File containing samtools flagstat output", - "pattern": "*.{flagstat}" - } - }, - { - "idxstats": { - "type": "file", - "description": "File containing samtools idxstats output", - "pattern": "*.{idxstats}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@priyanka-surana" - ], - "maintainers": [ - "@priyanka-surana" - ] - }, - "pipelines": [ - { - "name": "lncpipe", - "version": "dev" - }, - { - "name": "nascent", - "version": "2.3.0" - }, - { - "name": "rnadnavar", - "version": "dev" - }, - { - "name": "rnaseq", - "version": "3.26.0" - } - ] - }, - { - "name": "fastq_align_mapad", - "path": "subworkflows/nf-core/fastq_align_mapad/meta.yml", - "type": "subworkflow", - "meta": { - "name": "fastq_align_mapad", - "description": "Align FASTQ files against reference genome with the mapAD aDNA short-read aligner producing a sorted and indexed BAM files", - "keywords": [ - "sort", - "fastq", - "bam", - "mapad", - "align", - "map" - ], - "components": [ - "mapad/map", - "samtools/sort", - "samtools/index", - "samtools/stats", - "samtools/idxstats", - "samtools/flagstat", - "bam_sort_stats_samtools" - ], - "input": [ - { - "ch_reads": { - "description": "List of input FASTQ file\nStructure: [ val(meta), path(reads) ]\n" - } - }, - { - "ch_index": { - "description": "mapAD genome index files\nStructure: [ val(meta), path(index) ]\n" - } - }, - { - "ch_fasta_fai": { - "type": "file", - "description": "Reference fasta file and index\nStructure: [ val(meta), path(fasta), path(fai) ]\n" - } - }, - { - "val_mismatch_parameter": { - "type": "float", - "description": "`bwa aln` compatible allowed-mismatches parameter\n" - } - }, - { - "val_double_stranded_library": { - "type": "boolean", - "description": "If true, `--library` is set to `double_stranded`\n", - "pattern": "true|false" - } - }, - { - "val_five_prime_overhang": { - "type": "float", - "description": "5' overhang parameter (global overhang parameter\nif `val_double_stranded_library` is set to `true`)\n" - } - }, - { - "val_three_prime_overhang": { - "type": "float", - "description": "3' overhang parameter (ignored if\n`val_double_stranded_library` is set to `true`)\n" - } - }, - { - "val_deam_rate_double_stranded": { - "type": "float", - "description": "`-d` parameter. Specifies the expected deamination\nrate in double-stranded stems of the reads.\n" - } - }, - { - "val_deam_rate_single_stranded": { - "type": "float", - "description": "`-s` parameter. Specifies the expected deamination\nrate in single-stranded overhangs of the reads.\n" - } - }, - { - "val_indel_rate": { - "type": "float", - "description": "`-i` parameter. Specifies the expected rate of InDels.\n" - } - } - ], - "output": [ - { - "bam_unsorted": { - "description": "BAM file produced by mapAD\nStructure: [ val(meta), path(bam) ]\n" - } - }, - { - "bam": { - "description": "BAM file sorted by samtools\nStructure: [ val(meta), path(bam) ]\n" - } - }, - { - "bai": { - "description": "BAI index of the sorted BAM file\nStructure: [ val(meta), path(bai) ]\n" - } - }, - { - "csi": { - "description": "CSI index of the sorted BAM file\nStructure: [ val(meta), path(csi) ]\n" - } - }, - { - "stats": { - "description": "File containing samtools stats output\nStructure: [ val(meta), path(stats) ]\n" - } - }, - { - "flagstat": { - "description": "File containing samtools flagstat output\nStructure: [ val(meta), path(flagstat) ]\n" - } - }, - { - "idxstats": { - "description": "File containing samtools idxstats output\nStructure: [ val(meta), path(idxstats) ]\n" - } - }, - { - "versions": { - "description": "Files containing software versions\nStructure: [ path(versions.yml) ]\n" - } - } - ], - "authors": [ - "@jch-13" - ] - } - }, - { - "name": "fastq_align_star", - "path": "subworkflows/nf-core/fastq_align_star/meta.yml", - "type": "subworkflow", - "meta": { - "name": "fastq_align_star", - "description": "Align reads to a reference genome using bowtie2 then sort with samtools", - "keywords": [ - "align", - "fasta", - "genome", - "reference" - ], - "components": [ - "star/align", - "samtools/sort", - "samtools/index", - "samtools/stats", - "samtools/idxstats", - "samtools/flagstat", - "bam_sort_stats_samtools" - ], - "input": [ - { - "ch_reads": { - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\nStructure: [ val(meta), [ path(reads) ] ]\n" - } - }, - { - "ch_index": { - "type": "directory", - "description": "STAR genome index", - "pattern": "star" - } - }, - { - "ch_gtf": { - "type": "file", - "description": "GTF file used to set the splice junctions with the --sjdbGTFfile flag\n", - "pattern": "*.gtf" - } - }, - { - "val_star_ignore_sjdbgtf": { - "type": "boolean", - "description": "If true the --sjdbGTFfile flag is set\n", - "pattern": "true|false" - } - }, - { - "ch_fasta_fai": { - "type": "file", - "description": "Reference genome fasta file and index", - "pattern": "*.{fasta,fa,fna,fai}" - } - }, - { - "ch_transcripts_fasta_fai": { - "type": "file", - "description": "Optional reference genome fasta file and index", - "pattern": "*.{fasta,fa,fna,fai}" - } - } - ], - "output": [ - { - "orig_bam": { - "description": "Output BAM file containing read alignments\nStructure: [ val(meta), path(bam) ]\n" - } - }, - { - "log_final": { - "description": "STAR final log file\nStructure: [ val(meta), path(log_final) ]\n" - } - }, - { - "log_out": { - "description": "STAR log out file\nStructure: [ val(meta), path(log_out) ]\n" - } - }, - { - "log_progress": { - "description": "STAR log progress file\nStructure: [ val(meta), path(log_progress) ]\n" - } - }, - { - "bam_sorted": { - "description": "Sorted BAM file of read alignments (optional)\nStructure: [ val(meta), path(bam) ]\n" - } - }, - { - "orig_bam_transcript": { - "description": "Output BAM file of transcriptome alignment (optional)\nStructure: [ val(meta), path(bam) ]\n" - } - }, - { - "fastq": { - "description": "Unmapped FastQ files (optional)\nStructure: [ val(meta), path(fastq) ]\n" - } - }, - { - "tab": { - "description": "STAR output tab file(s) (optional)\nStructure: [ val(meta), path(tab) ]\n" - } - }, - { - "bam": { - "description": "BAM file ordered by samtools\nStructure: [ val(meta), path(bam) ]\n" - } - }, - { - "bai": { - "description": "BAI index of the ordered BAM file\nStructure: [ val(meta), path(bai) ]\n" - } - }, - { - "stats": { - "description": "File containing samtools stats output\nStructure: [ val(meta), path(stats) ]\n" - } - }, - { - "flagstat": { - "description": "File containing samtools flagstat output\nStructure: [ val(meta), path(flagstat) ]\n" - } - }, - { - "idxstats": { - "description": "File containing samtools idxstats output\nStructure: [ val(meta), path(idxstats) ]\n" - } - }, - { - "bam_transcript": { - "description": "Transcriptome-level BAM file ordered by samtools (optional)\nStructure: [ val(meta), path(bam) ]\n" - } - }, - { - "bai_transcript": { - "description": "Transcriptome-level BAI index of the ordered BAM file (optional)\nStructure: [ val(meta), path(bai) ]\n" - } - }, - { - "stats_transcript": { - "description": "Transcriptome-level file containing samtools stats output (optional)\nStructure: [ val(meta), path(stats) ]\n" - } - }, - { - "flagstat_transcript": { - "description": "Transcriptome-level file containing samtools flagstat output (optional)\nStructure: [ val(meta), path(flagstat) ]\n" - } - }, - { - "idxstats_transcript": { - "description": "Transcriptome-level file containing samtools idxstats output (optional)\nStructure: [ val(meta), path(idxstats) ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@JoseEspinosa" - ], - "maintainers": [ - "@JoseEspinosa" - ] - }, - "pipelines": [ - { - "name": "lncpipe", - "version": "dev" - }, - { - "name": "nascent", - "version": "2.3.0" - }, - { - "name": "riboseq", - "version": "1.2.0" - }, - { - "name": "rnadnavar", - "version": "dev" - }, - { - "name": "rnafusion", - "version": "4.1.2" - }, - { - "name": "rnavar", - "version": "1.2.3" - } - ] - }, - { - "name": "fastq_complexity_filter", - "path": "subworkflows/nf-core/fastq_complexity_filter/meta.yml", - "type": "subworkflow", - "meta": { - "name": "fastq_complexity_filter", - "description": "Perform low-complexity filtering of FASTQ reads using a selectable tool.\nOne of PRINSEQ++, BBDuk, or fastp is executed based on the provided tool name.\nOnly complexity filtering is applied; no adapter trimming, read merging, or\nquality trimming is performed.\n", - "keywords": [ - "fastq", - "complexity filtering", - "low complexity", - "entropy", - "qc" - ], - "components": [ - "prinseqplusplus", - "bbmap/bbduk", - "fastp" - ], - "input": [ - { - "ch_reads": { - "type": "file", - "description": "Input channel containing sample metadata and FASTQ reads.\nStructure: [ val(meta), path(fastq) ]\n", - "pattern": "*.{fastq,fastq.gz}" - } - }, - { - "val_complexity_filter_tool": { - "type": "string", - "description": "Complexity filtering tool to use.\nMust be one of: 'prinseqplusplus', 'bbduk', or 'fastp'.\n" - } - } - ], - "output": [ - { - "filtered_reads": { - "type": "file", - "description": "Channel containing complexity-filtered FASTQ reads.\nStructure: [ val(meta), path(fastq) ]\n", - "pattern": "*.{fastq,fastq.gz}" - } - }, - { - "logfile": { - "type": "file", - "description": "Tool-specific log files, when available.\nStructure: [ val(meta), path(log) ]\n", - "pattern": "*.log" - } - }, - { - "report": { - "type": "file", - "description": "HTML report generated by fastp. Empty for other tools.\nStructure: [ val(meta), path(html) ]\n", - "pattern": "*.html" - } - }, - { - "multiqc_files": { - "type": "file", - "description": "Files emitted for MultiQC aggregation (e.g. fastp JSON reports,\nBBDuk logs).\nStructure: [ path(file) ]\n", - "pattern": "*.{json,log}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions\nStructure: [ path(versions.yml) ]\n", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@vagkaratzas" - ], - "maintainers": [ - "@vagkaratzas" - ] - } - }, - { - "name": "fastq_contam_seqtk_kraken", - "path": "subworkflows/nf-core/fastq_contam_seqtk_kraken/meta.yml", - "type": "subworkflow", - "meta": { - "name": "FASTQ_CONTAM_SEQTK_KRAKEN", - "description": "Produces a contamination report from FastQ input after subsampling", - "keywords": [ - "statistics", - "fastq", - "contamination" - ], - "components": [ - "kraken2/kraken2", - "seqtk/sample" - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively" - } - }, - { - "sample_size": { - "type": "string", - "description": "Number of reads to subsample for contamination detection." - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "report": { - "type": "file", - "description": "Kraken2 contamination report", - "pattern": "*.txt" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@apeltzer" - ], - "maintainers": [ - "@apeltzer" - ] - }, - "pipelines": [ - { - "name": "demultiplex", - "version": "1.7.1" - } - ] - }, - { - "name": "fastq_create_umi_consensus_fgbio", - "path": "subworkflows/nf-core/fastq_create_umi_consensus_fgbio/meta.yml", - "type": "subworkflow", - "meta": { - "name": "fastq_create_umi_consensus_fgbio", - "description": "This workflow uses the suite FGBIO to identify and remove UMI tags from FASTQ reads\nconvert them to unmapped BAM file, map them to the reference genome,\nand finally use the mapped information to group UMIs and generate consensus reads in each group\n", - "keywords": [ - "fgbio", - "umi", - "samblaster", - "samtools", - "bwa" - ], - "components": [ - "bwa/index", - "bwa/mem", - "bwamem2/mem", - "bwamem2/index", - "fgbio/fastqtobam", - "fgbio/groupreadsbyumi", - "fgbio/callmolecularconsensusreads", - "fgbio/callduplexconsensusreads", - "fgbio/filterconsensusreads", - "samblaster", - "samtools/bam2fq", - "samtools/sort", - "samtools/index", - "samtools/fastq", - "fgbio/zipperbams" - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "reads": { - "type": "list", - "description": "list umi-tagged reads", - "pattern": "[ *.{fastq.gz/fq.gz} ]" - } - }, - { - "fasta_fai_dict": { - "type": "file", - "description": "The reference fasta file, index and dictionary", - "pattern": "*.{fa,fasta,fna,fai,dict}" - } - }, - { - "bwa_index": { - "type": "file", - "description": "The reference genome bwa index files", - "pattern": "*.{fa,fasta,fna,amb,ann,bwt,pac,sa}" - } - }, - { - "groupreadsbyumi_strategy": { - "type": "string", - "description": "Defines the UMI assignment strategy.", - "Required argument": "defines the UMI assignment strategy.", - "enum": [ - "Identity", - "Edit", - "Adjacency", - "Paired" - ] - } - }, - { - "aligner": { - "type": "string", - "description": "The aligner to use for mapping the reads to the reference genome. Options are bwa-mem and bwamem2.", - "enum": [ - "bwa-mem", - "bwamem2" - ] - } - }, - { - "duplex": { - "type": "boolean", - "description": "Whether the library contains duplex UMIs." - } - }, - { - "min_reads": { - "type": "integer", - "description": "One integer (for non-duplex) or a string of up-to three space-separated numbers for duplex sequencing" - } - }, - { - "min_baseq": { - "type": "integer", - "description": "Minimum base quality for bases to be considered in consensus calling." - } - }, - { - "max_base_error_rate": { - "type": "integer", - "description": "Maximum base error rate for consensus building" - } - } - ], - "output": [ - { - "ubam": { - "type": "file", - "description": "unmapped bam file", - "pattern": "*.bam" - } - }, - { - "groupbam": { - "type": "file", - "description": "mapped bam file, where reads are grouped by UMI tag", - "pattern": "*.bam" - } - }, - { - "consensusbam": { - "type": "file", - "description": "mapped bam file, where reads are created as consensus of those\nbelonging to the same UMI group\n", - "pattern": "*.bam" - } - }, - { - "mappedconsensusbam": { - "type": "file", - "description": "mapped bam file, where reads are created as consensus of those\nbelonging to the same UMI group and filtered for minimum base quality and maximum error rate\n", - "pattern": "*.bam" - } - } - ], - "authors": [ - "@lescai" - ], - "maintainers": [ - "@lescai" - ] - } - }, - { - "name": "fastq_decontaminate_deacon", - "path": "subworkflows/nf-core/fastq_decontaminate_deacon/meta.yml", - "type": "subworkflow", - "meta": { - "name": "fastq_decontaminate_deacon", - "description": "Decontaminate FastQ files by filtering reads that match a reference genome using Deacon\n", - "keywords": [ - "filter", - "index", - "fasta", - "fastq", - "genome", - "reference", - "minimizer", - "decontamination" - ], - "components": [ - "deacon/index", - "deacon/filter" - ], - "input": [ - { - "ch_fasta_reads": { - "type": "file", - "description": "Input genome fasta file and a list of FastQ files of size 1 and 2 for single-end and paired-end data, respectively.\nStructure: [ val(meta), path(fasta), [ path(reads) ] ]\n" - } - } - ], - "output": [ - { - "index": { - "type": "file", - "description": "Deacon minimizer index file\nStructure: [ val(meta), path(index) ]\n", - "pattern": ".idx" - } - }, - { - "fastq_filtered": { - "type": "file", - "description": "List of output filtered FastQ files of size 1 and 2 for single-end and paired-end data, respectively.\nStructure: [ val(meta), path(${prefix}*.fq) ]\n", - "pattern": "*.fq" - } - }, - { - "summary": { - "type": "file", - "description": "JSON file containing summary of results.\nStructure: [ val(meta), path(${prefix}.json) ]\n", - "pattern": "*.json" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions\nStructure: [ path(versions.yml) ]\n", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@Baksic-Ivan", - "@Omer0191" - ], - "maintainers": [ - "@Baksic-Ivan", - "@Omer0191" - ] - } - }, - { - "name": "fastq_decontaminate_deacon_hostile", - "path": "subworkflows/nf-core/fastq_decontaminate_deacon_hostile/meta.yml", - "type": "subworkflow", - "meta": { - "name": "fastq_decontaminate_deacon_hostile", - "description": "Decontaminate FastQ files by filtering reads that match a reference genome using Deacon or Hostile", - "keywords": [ - "hostile", - "deacon", - "filter", - "index", - "fasta", - "fastq", - "genome", - "reference", - "minimizer", - "decontamination" - ], - "components": [ - "hostile/fetch", - "hostile/clean", - "deacon/index", - "deacon/filter", - "fastq_fetch_clean_hostile", - "fastq_index_filter_deacon" - ], - "input": [ - { - "ch_reads": { - "type": "file", - "description": "List of FastQ files of size 1 and 2 for single-end and paired-end data, respectively.\nStructure: [ val(meta), [ path(reads) ] ]\n" - } - }, - { - "ch_fasta": { - "type": "file", - "description": "Input genome fasta file used by Deacon. Meta must match the meta of ch_reads.\nStructure: [ val(meta), [ path(fasta) ] ]\n" - } - }, - { - "ch_reference": { - "type": "directory", - "description": "Directory containing index file(s) corresponding to the preferred aligner (bowtie2 short reads or minimap for long reads) used by Hostile.\nNote that single end data is assumed to be long reads. If you have single-end short read you must supply both the BowTie2\nindices AND explicitly specify `--aligner bowtie2`\n" - } - }, - { - "index_name": { - "type": "string", - "description": "Name of the reference genome index to download for Hostile fetch if the reference is not provided." - } - }, - { - "decontaminator": { - "type": "string", - "description": "Name of the deacontamination tool to use.", - "enum": [ - "deacon", - "hostile" - ] - } - } - ], - "output": [ - { - "fastq_filtered": { - "type": "file", - "description": "List of output filtered FastQ files of size 1 and 2 for single-end and paired-end data, respectively.\nStructure: [ val(meta), path(${prefix}*.fq.gz) ]\n", - "pattern": "*.fq.gz" - } - }, - { - "reference": { - "type": "channel", - "description": "Channel containing reference name and directory with index files for Hostile.\nStructure: [ val(reference_name), path(reference_dir) ]\n" - } - }, - { - "json": { - "type": "channel", - "description": "Channel containing sample metadata and Hostile cleaning log in JSON format.\nStructure: [ val(meta), path(*.json) ]\n", - "pattern": "*.json" - } - }, - { - "index": { - "type": "file", - "description": "Deacon minimizer index file.\nStructure: [ val(meta), path(index) ]\n", - "pattern": ".idx" - } - }, - { - "summary": { - "type": "file", - "description": "JSON file containing summary of results.\nStructure: [ val(meta), path(${prefix}.json) ]\n", - "pattern": "*.json" - } - } - ], - "authors": [ - "@Baksic-Ivan" - ], - "maintainers": [ - "@Baksic-Ivan" - ] - } - }, - { - "name": "fastq_download_prefetch_fasterqdump_sratools", - "path": "subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/meta.yml", - "type": "subworkflow", - "meta": { - "name": "fastq_download_prefetch_fasterqdump_sratools", - "description": "Download FASTQ sequencing reads from the NCBI's Sequence Read Archive (SRA).", - "keywords": [ - "SRA", - "NCBI", - "sequencing", - "fastq", - "prefetch", - "fasterq-dump" - ], - "components": [ - "custom/sratoolsncbisettings", - "sratools/prefetch", - "sratools/fasterqdump" - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]\n" - } - }, - { - "id": { - "type": "string", - "description": "SRA run identifier.\n" - } - }, - { - "certificate": { - "type": "file", - "description": "Path to a JWT cart file used to access protected dbGAP data on SRA using the sra-toolkit\n", - "pattern": "*.cart" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "Extracted FASTQ file or files if the sequencing reads are paired-end.", - "pattern": "*.fastq.gz" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@Midnighter", - "@drpatelh" - ], - "maintainers": [ - "@Midnighter", - "@drpatelh" - ] - }, - "pipelines": [ - { - "name": "fetchngs", - "version": "1.12.0" - } - ] - }, - { - "name": "fastq_extract_kraken_krakentools", - "path": "subworkflows/nf-core/fastq_extract_kraken_krakentools/meta.yml", - "type": "subworkflow", - "meta": { - "name": "fastq_extract_kraken_krakentools", - "description": "Extract classified Kraken2 reads by taxonomic id", - "keywords": [ - "classify", - "metagenomics", - "fastq", - "db", - "kraken2", - "krakentools", - "extract", - "extractreads" - ], - "components": [ - "kraken2/kraken2", - "krakentools/extractkrakenreads" - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "ch_reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" - } - }, - { - "ch_db": { - "type": "directory", - "description": "Kraken2 database" - } - }, - { - "val_taxid": { - "type": "string", - "description": "A string of one or more of taxonomic IDs (e.g. from NCBI Taxonomy) separated by spaces" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "report": { - "type": "file", - "description": "Kraken2 report containing stats about classified\nand not classified reads.\n" - } - }, - { - "extracted_kraken2_reads": { - "type": "file", - "description": "FASTQ or FASTA file of just reads assigned to the requested taxonomic IDs.\n", - "pattern": "*.{fastq.gz,fasta.gz}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions\nStructure: [ path(versions.yml) ]\n", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@MarieLataretu" - ], - "maintainers": [ - "@MarieLataretu" - ] - } - }, - { - "name": "fastq_fastqc_umitools_fastp", - "path": "subworkflows/nf-core/fastq_fastqc_umitools_fastp/meta.yml", - "type": "subworkflow", - "meta": { - "name": "fastq_fastqc_umitools_fastp", - "description": "Read QC, UMI extraction and trimming", - "keywords": [ - "fastq", - "fastqc", - "qc", - "UMI", - "trimming", - "fastp" - ], - "components": [ - "fastqc", - "umitools/extract", - "fastp" - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" - } - }, - { - "skip_fastqc": { - "type": "boolean", - "description": "Skip fastqc process\n" - } - }, - { - "with_umi": { - "type": "boolean", - "description": "With or without umi detection\n" - } - }, - { - "skip_umi_extract": { - "type": "boolean", - "description": "With or without umi extrection\n" - } - }, - { - "umi_discard_read": { - "type": "integer", - "description": "Discard R1 / R2 if required\n" - } - }, - { - "skip_trimming": { - "type": "boolean", - "description": "Allows to skip FastP execution\n" - } - }, - { - "adapter_fasta": { - "type": "file", - "description": "Fasta file of adapter sequences\n" - } - }, - { - "save_trimmed_fail": { - "type": "boolean", - "description": "Save trimmed fastqs of failed samples\n" - } - }, - { - "save_merged": { - "type": "boolean", - "description": "Save merged fastqs\n" - } - }, - { - "min_trimmed_reads": { - "type": "integer", - "description": "Inputs with fewer than this reads will be filtered out of the \"reads\" output channel\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "Extracted FASTQ files. | For single-end reads, pattern is \\${prefix}.umi_extract.fastq.gz. | For paired-end reads, pattern is \\${prefix}.umi_extract_{1,2}.fastq.gz.\n", - "pattern": "*.{fastq.gz}" - } - }, - { - "fastqc_html": { - "type": "file", - "description": "FastQC report", - "pattern": "*_{fastqc.html}" - } - }, - { - "fastqc_zip": { - "type": "file", - "description": "FastQC report archive", - "pattern": "*_{fastqc.zip}" - } - }, - { - "log": { - "type": "file", - "description": "Logfile for umi_tools", - "pattern": "*.{log}" - } - }, - { - "trim_json": { - "type": "file", - "description": "FastP Trimming report", - "pattern": "*.{fastp.json}" - } - }, - { - "trim_html": { - "type": "file", - "description": "FastP Trimming report", - "pattern": "*.{fastp.html}" - } - }, - { - "log": { - "type": "file", - "description": "Logfile FastP", - "pattern": "*.{fastp.log}" - } - }, - { - "trim_reads_fail": { - "type": "file", - "description": "Trimmed fastq files failing QC", - "pattern": "*.{fastq.gz}" - } - }, - { - "trim_reads_merged": { - "type": "file", - "description": "Trimmed and merged fastq files", - "pattern": "*.{fastq.gz}" - } - }, - { - "trim_read_count": { - "type": "integer", - "description": "Number of reads after trimming" - } - }, - { - "fastqc_trim_html": { - "type": "file", - "description": "FastQC report", - "pattern": "*_{fastqc.html}" - } - }, - { - "fastqc_trim_zip": { - "type": "file", - "description": "FastQC report archive", - "pattern": "*_{fastqc.zip}" - } - }, - { - "adapter_seq": { - "type": "string", - "description": "Adapter Sequence found in read1\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@robsyme" - ], - "maintainers": [ - "@robsyme" - ] - }, - "pipelines": [ - { - "name": "lncpipe", - "version": "dev" - }, - { - "name": "riboseq", - "version": "1.2.0" - }, - { - "name": "rnafusion", - "version": "4.1.2" - }, - { - "name": "rnaseq", - "version": "3.26.0" - }, - { - "name": "smrnaseq", - "version": "2.4.1" - }, - { - "name": "viralmetagenome", - "version": "1.1.1" - } - ] - }, - { - "name": "fastq_fastqc_umitools_trimgalore", - "path": "subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/meta.yml", - "type": "subworkflow", - "meta": { - "name": "fastq_fastqc_umitools_trimgalore", - "description": "Read QC, UMI extraction and trimming", - "keywords": [ - "fastq", - "fastqc", - "qc", - "UMI", - "trimming", - "trimgalore" - ], - "components": [ - "fastqc", - "umitools/extract", - "trimgalore" - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" - } - }, - { - "skip_fastqc": { - "type": "boolean", - "description": "Skip fastqc process\n" - } - }, - { - "with_umi": { - "type": "boolean", - "description": "With or without umi detection\n" - } - }, - { - "skip_umi_extract": { - "type": "boolean", - "description": "With or without umi extrection\n" - } - }, - { - "skip_trimming": { - "type": "boolean", - "description": "Allows to skip trimgalore execution\n" - } - }, - { - "umi_discard_read": { - "type": "integer", - "description": "Discard R1 / R2 if required\n" - } - }, - { - "min_trimmed_reads": { - "type": "integer", - "description": "Inputs with fewer than this reads will be filtered out of the \"reads\" output channel\n" - } - } - ], - "output": [ - { - "reads": { - "type": "file", - "description": "Extracted FASTQ files. | For single-end reads, pattern is \\${prefix}.umi_extract.fastq.gz. |\n\n\n\n For paired-end reads, pattern is \\${prefix}.umi_extract_{1,2}.fastq.gz.\n", - "pattern": "*.{fastq.gz}" - } - }, - { - "fastqc_html": { - "type": "file", - "description": "FastQC report", - "pattern": "*_{fastqc.html}" - } - }, - { - "fastqc_zip": { - "type": "file", - "description": "FastQC report archive", - "pattern": "*_{fastqc.zip}" - } - }, - { - "log": { - "type": "file", - "description": "Logfile for umi_tools", - "pattern": "*.{log}" - } - }, - { - "trim_unpaired": { - "type": "file", - "description": "FastQ files containing unpaired reads from read 1 or read 2\n", - "pattern": "*unpaired*.fq.gz" - } - }, - { - "trim_html": { - "type": "file", - "description": "FastQC report (optional)", - "pattern": "*_{fastqc.html}" - } - }, - { - "trim_zip": { - "type": "file", - "description": "FastQC report archive (optional)", - "pattern": "*_{fastqc.zip}" - } - }, - { - "trim_log": { - "type": "file", - "description": "Trim Galore! trimming report", - "pattern": "*_{report.txt}" - } - }, - { - "trim_read_count": { - "type": "integer", - "description": "Number of reads remaining after trimming for all input samples" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@drpatelh", - "@KamilMaliszArdigen" - ], - "maintainers": [ - "@drpatelh", - "@KamilMaliszArdigen" - ] - }, - "pipelines": [ - { - "name": "atacseq", - "version": "2.1.2" - }, - { - "name": "chipseq", - "version": "2.1.0" - }, - { - "name": "lncpipe", - "version": "dev" - }, - { - "name": "riboseq", - "version": "1.2.0" - }, - { - "name": "rnaseq", - "version": "3.26.0" - }, - { - "name": "rnasplice", - "version": "1.0.4" - } - ] - }, - { - "name": "fastq_fetch_clean_hostile", - "path": "subworkflows/nf-core/fastq_fetch_clean_hostile/meta.yml", - "type": "subworkflow", - "meta": { - "name": "fastq_fetch_clean_hostile", - "description": "Downloads required reference genomes for hostile and removes host reads from short-read FASTQ sequencing files", - "keywords": [ - "hostile", - "decontamination", - "human removal", - "download", - "host removal", - "clean" - ], - "components": [ - "hostile/fetch", - "hostile/clean" - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "reads": { - "type": "file", - "description": "Input FASTQ files for hostile cleaning", - "pattern": "*.{fastq,fastq.gz,fq,fq.gz}" - } - }, - { - "reference_name": { - "type": "string", - "description": "Name of the reference to align against and thus remove mapped reads to." - } - }, - { - "reference_dir": { - "type": "directory", - "description": "Directory containing index file(s) corresponding to the preferred aligner (bowtie2 short reads or minimap for long reads).\nNote that single end data is assumed to be long reads. If you have single-end short read you must supply both the BowTie2\nindices AND explicitly specify `--aligner bowtie2`\n" - } - }, - { - "index_name": { - "type": "string", - "description": "Name of the reference genome index to download for hostile fetch if the reference is not provided." - } - } - ], - "output": [ - { - "reference": { - "type": "channel", - "description": "Channel containing reference name and directory with index files for Hostile.\nStructure: [ val(reference_name), path(reference_dir) ]\n" - } - }, - { - "fastq": { - "type": "file", - "description": "Channel containing sample metadata and cleaned FASTQ files.\nStructure: [ val(meta), path(*.fastq.gz) ]\n", - "pattern": "*.{fastq,fq,fastq.gz,fq.gz}" - } - }, - { - "json": { - "type": "channel", - "description": "Channel containing sample metadata and Hostile cleaning log in JSON format.\nStructure: [ val(meta), path(*.json) ]\n", - "pattern": "*.json" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@maia-munteanu" - ], - "maintainers": [ - "@maia-munteanu", - "@vagkaratzas" - ] - } - }, - { - "name": "fastq_find_mirna_mirdeep2", - "path": "subworkflows/nf-core/fastq_find_mirna_mirdeep2/meta.yml", - "type": "subworkflow", - "meta": { - "name": "fastq_find_mirna_mirdeep2", - "description": "This subworkflow identifies miRNAs from FASTQ files using miRDeep2. The workflow converts FASTQ to FASTA, processes and replaces any whitespace in sequence IDs, builds a Bowtie index of the genome, and then maps reads using miRDeep2 mapper before identifying known and novel miRNAs.\n", - "keywords": [ - "miRNA", - "FASTQ", - "FASTA", - "Bowtie", - "miRDeep2" - ], - "components": [ - "seqkit/fq2fa", - "seqkit/replace", - "bowtie/build", - "mirdeep2/mapper", - "mirdeep2/mirdeep2" - ], - "input": [ - { - "ch_reads": { - "type": "file", - "description": "The input channel containing the FASTQ files to process and identify miRNAs.\nStructure: [ val(meta), path(fastq) ]\n", - "pattern": "*.fastq.gz" - } - }, - { - "ch_genome_fasta": { - "type": "file", - "description": "The input channel containing the genome FASTA files used to build the Bowtie index.\nStructure: [ val(meta), path(fasta) ]\n", - "pattern": "*.fa" - } - }, - { - "ch_mirna_mature_hairpin": { - "type": "file", - "description": "The input channel containing the mature and hairpin miRNA sequences for miRNA identification.\nStructure: [ val(meta), path(mature_fasta), path(hairpin_fasta) ]\n", - "pattern": "*.fa" - } - } - ], - "output": [ - { - "outputs": { - "type": "file", - "description": "The output channel containing the BED, CSV, and HTML files with the identified miRNAs.\nStructure: [ val(meta), path(bed), path(csv), path(html) ]\n", - "pattern": "*.{bed,csv,html}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions\nStructure: [ path(versions.yml) ]\n", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@atrigila" - ], - "maintainers": [ - "@atrigila" - ] - }, - "pipelines": [ - { - "name": "smrnaseq", - "version": "2.4.1" - } - ] - }, - { - "name": "fastq_index_filter_deacon", - "path": "subworkflows/nf-core/fastq_index_filter_deacon/meta.yml", - "type": "subworkflow", - "meta": { - "name": "fastq_index_filter_deacon", - "description": "Decontaminate FastQ files by filtering reads that match a reference genome using Deacon\n", - "keywords": [ - "filter", - "index", - "fasta", - "fastq", - "genome", - "reference", - "minimizer", - "decontamination" - ], - "components": [ - "deacon/index", - "deacon/filter" - ], - "input": [ - { - "ch_fasta_reads": { - "type": "file", - "description": "Input genome fasta file and a list of FastQ files of size 1 and 2 for single-end and paired-end data, respectively.\nStructure: [ val(meta), path(fasta), [ path(reads) ] ]\n" - } - } - ], - "output": [ - { - "index": { - "type": "file", - "description": "Deacon minimizer index file\nStructure: [ val(meta), path(index) ]\n", - "pattern": ".idx" - } - }, - { - "fastq_filtered": { - "type": "file", - "description": "List of output filtered FastQ files of size 1 and 2 for single-end and paired-end data, respectively.\nStructure: [ val(meta), path(${prefix}*.fq) ]\n", - "pattern": "*.fq.gz" - } - }, - { - "summary": { - "type": "file", - "description": "JSON file containing summary of results.\nStructure: [ val(meta), path(${prefix}.json) ]\n", - "pattern": "*.json" - } - } - ], - "authors": [ - "@Baksic-Ivan", - "@Omer0191" - ], - "maintainers": [ - "@Baksic-Ivan", - "@Omer0191" - ] - } - }, - { - "name": "fastq_ngscheckmate", - "path": "subworkflows/nf-core/fastq_ngscheckmate/meta.yml", - "type": "subworkflow", - "meta": { - "name": "fastq_ngscheckmate", - "description": "Take a set of fastq files and run NGSCheckMate to determine whether samples match with each other, using a set of SNPs.", - "keywords": [ - "ngscheckmate", - "qc", - "fastq", - "snp" - ], - "components": [ - "ngscheckmate/fastq", - "ngscheckmate/vafncm" - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "fastq": { - "type": "file", - "description": "Single or pair of fastq files", - "pattern": "*.{fastq.gz}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing snp_pt file information\ne.g. [ id:'sarscov2' ]\n" - } - }, - { - "snp_bed": { - "type": "file", - "description": "Binary PT file containing the SNPs to analyse. NGSCheckMate provides one for human samples.", - "pattern": "*.{bed}" - } - } - ], - "output": [ - { - "pdf": { - "type": "file", - "description": "A pdf containing a dendrogram showing how the samples match up", - "pattern": "*.{pdf}" - } - }, - { - "corr_matrix": { - "type": "file", - "description": "A text file containing the correlation matrix between each sample", - "pattern": "*corr_matrix.txt" - } - }, - { - "matched": { - "type": "file", - "description": "A txt file containing only the samples that match with each other", - "pattern": "*matched.txt" - } - }, - { - "all": { - "type": "file", - "description": "A txt file containing all the sample comparisons, whether they match or not", - "pattern": "*all.txt" - } - }, - { - "vcf": { - "type": "file", - "description": "vcf files for each sample giving the SNP calls", - "pattern": "*.vcf" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@SPPearce" - ], - "maintainers": [ - "@SPPearce" - ] - } - }, - { - "name": "fastq_preprocess", - "path": "subworkflows/nf-core/fastq_preprocess/meta.yml", - "type": "subworkflow", - "meta": { - "name": "fastq_preprocess", - "description": "Subworkflow that preprocesses FASTQ files", - "keywords": [ - "fasta", - "seqkit", - "preprocessing" - ], - "components": [ - "fastq_sanitise_seqkit", - "seqkit/sana", - "seqkit/pair", - "seqkit/seq", - "seqkit/replace", - "seqkit/rmdup" - ], - "input": [ - { - "ch_reads": { - "type": "channel", - "description": "Channel containing sample metadata and FASTQ files.\nStructure: [ val(meta), [ fastq ] ]\nWhere meta is a map containing at least:\n- id: sample identifier\n- single_end: boolean indicating if data is single-end (true) or paired-end (false)\n", - "pattern": "*.{fastq,fastq.gz,fq,fq.gz}" - } - }, - { - "skip_seqkit_sana_pair": { - "type": "boolean", - "description": "If true, skips the seqkit_sana_pair subworkflow.\n" - } - }, - { - "skip_seqkit_seq": { - "type": "boolean", - "description": "If true, skips the seqkit_seq process.\n" - } - }, - { - "skip_seqkit_replace": { - "type": "boolean", - "description": "If true, skips the seqkit_replace process.\n" - } - }, - { - "skip_seqkit_rmdup": { - "type": "boolean", - "description": "If true, skips the seqkit_rmdup process.\n" - } - } - ], - "output": [ - { - "reads": { - "type": "channel", - "description": "Channel containing filtered FASTQ files.\nStructure: [ val(meta), [ fastq ] ]\n", - "pattern": "*.{fastq,fastq.gz,fq,fq.gz}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions\nStructure: [ path(versions.yml) ]\n", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@maia-munteanu" - ], - "maintainers": [ - "@maia-munteanu", - "@vagkaratzas" - ] - } - }, - { - "name": "fastq_preprocess_seqkit", - "path": "subworkflows/nf-core/fastq_preprocess_seqkit/meta.yml", - "type": "subworkflow", - "meta": { - "name": "fastq_preprocess_seqkit", - "description": "Subworkflow that preprocesses FASTQ files", - "keywords": [ - "fastq", - "seqkit", - "preprocessing" - ], - "components": [ - "fastq_sanitise_seqkit", - "seqkit/sana", - "seqkit/pair", - "seqkit/seq", - "seqkit/replace", - "seqkit/rmdup" - ], - "input": [ - { - "ch_reads": { - "type": "channel", - "description": "Channel containing sample metadata and FASTQ files.\nStructure: [ val(meta), [ fastq ] ]\nWhere meta is a map containing at least:\n- id: sample identifier\n- single_end: boolean indicating if data is single-end (true) or paired-end (false)\n", - "pattern": "*.{fastq,fastq.gz,fq,fq.gz}" - } - }, - { - "skip_seqkit_sana_pair": { - "type": "boolean", - "description": "If true, skips the seqkit_sana_pair subworkflow.\n" - } - }, - { - "skip_seqkit_seq": { - "type": "boolean", - "description": "If true, skips the seqkit_seq process.\n" - } - }, - { - "skip_seqkit_replace": { - "type": "boolean", - "description": "If true, skips the seqkit_replace process.\n" - } - }, - { - "skip_seqkit_rmdup": { - "type": "boolean", - "description": "If true, skips the seqkit_rmdup process.\n" - } - } - ], - "output": [ - { - "reads": { - "type": "channel", - "description": "Channel containing filtered FASTQ files.\nStructure: [ val(meta), [ fastq ] ]\n", - "pattern": "*.{fastq,fastq.gz,fq,fq.gz}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions\nStructure: [ path(versions.yml) ]\n", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@maia-munteanu" - ], - "maintainers": [ - "@maia-munteanu", - "@vagkaratzas" - ] - } - }, - { - "name": "fastq_qc_stats", - "path": "subworkflows/nf-core/fastq_qc_stats/meta.yml", - "type": "subworkflow", - "meta": { - "name": "fastq_qc_stats", - "description": "Generate statistics for short read sequencing data using multiple tools", - "keywords": [ - "fastq", - "qc", - "fastqc", - "seqfu", - "seqkit", - "seqtk" - ], - "components": [ - "fastqc", - "seqfu/check", - "seqfu/stats", - "seqkit/stats", - "seqtk/comp" - ], - "input": [ - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" - } - }, - { - "skip_fastqc": { - "type": "boolean", - "description": "Skip fastqc process\n" - } - }, - { - "skip_seqfu_check": { - "type": "boolean", - "description": "Skip seqfu_check process\n" - } - }, - { - "skip_seqfu_stats": { - "type": "boolean", - "description": "Skip seqfu_stats process\n" - } - }, - { - "skip_seqkit_stats": { - "type": "boolean", - "description": "Skip seqkit_stats process\n" - } - }, - { - "skip_seqtk_comp": { - "type": "boolean", - "description": "Skip seqtk_comp process\n" - } - } - ], - "output": [ - { - "fastqc_html": { - "type": "file", - "description": "FastQC report", - "pattern": "*_fastqc.html" - } - }, - { - "fastqc_zip": { - "type": "file", - "description": "FastQC report archive", - "pattern": "*_fastqc.zip" - } - }, - { - "seqfu_check": { - "type": "file", - "description": "seqfu check tsv report", - "pattern": "*.tsv" - } - }, - { - "seqfu_stats": { - "type": "file", - "description": "seqfu stats tsv report", - "pattern": "*.tsv" - } - }, - { - "seqfu_multiqc": { - "type": "file", - "description": "seqfu stats MultiQC report", - "pattern": "*_mqc.txt" - } - }, - { - "seqkit_stats": { - "type": "file", - "description": "seqkit stats report", - "pattern": "*.tsv" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@pablo-scd" - ], - "maintainers": [ - "@pablo-scd", - "@vagkaratzas" - ] - } - }, - { - "name": "fastq_qc_trim_filter_setstrandedness", - "path": "subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/meta.yml", - "type": "subworkflow", - "meta": { - "name": "fastq_qc_trim_filter_setstrandedness", - "description": "Performs linting, quality control, trimming, filtering, and strandedness determination on RNA-seq FASTQ files, preparing them for downstream analysis.", - "keywords": [ - "fastq", - "rnaseq", - "rrna", - "trimming", - "subsample", - "strandedness" - ], - "components": [ - "bbmap/bbsplit", - "cat/fastq", - "fastqc", - "fq/lint", - "fastq_remove_rrna", - "fastq_subsample_fq_salmon", - "fastq_fastqc_umitools_trimgalore", - "fastq_fastqc_umitools_fastp" - ], - "input": [ - { - "ch_reads": { - "description": "Channel with input FastQ files", - "structure": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test' ]" - } - }, - { - "reads": { - "type": "file", - "description": "FastQ files", - "pattern": "*.{fq,fastq},{,.gz}" - } - } - ] - } - }, - { - "ch_fasta": { - "description": "Channel with genome sequence in fasta format", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata for the fasta file" - } - }, - { - "fasta": { - "type": "file", - "description": "Genome fasta file", - "pattern": "*.{fa,fasta}" - } - } - ] - } - }, - { - "ch_transcript_fasta": { - "description": "Channel with transcriptome sequence in fasta format", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata for the transcript fasta file" - } - }, - { - "fasta": { - "type": "file", - "description": "Transcript fasta file", - "pattern": "*.{fa,fasta}" - } - } - ] - } - }, - { - "ch_gtf": { - "description": "Channel with features in GTF format", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata for the GTF file" - } - }, - { - "gtf": { - "type": "file", - "description": "GTF file", - "pattern": "*.gtf" - } - } - ] - } - }, - { - "ch_salmon_index": { - "description": "Directory containing Salmon index", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata for the Salmon index" - } - }, - { - "index": { - "type": "directory", - "description": "Salmon index directory" - } - } - ] - } - }, - { - "ch_sortmerna_index": { - "description": "Directory containing sortmerna index", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata for the SortMeRNA index" - } - }, - { - "index": { - "type": "directory", - "description": "SortMeRNA index directory" - } - } - ] - } - }, - { - "ch_bowtie2_index": { - "description": "Directory containing bowtie2 index for rRNA removal", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata for the Bowtie2 index" - } - }, - { - "index": { - "type": "directory", - "description": "Bowtie2 index directory" - } - } - ] - } - }, - { - "ch_bbsplit_index": { - "description": "Path to directory or tar.gz archive for pre-built BBSplit index", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata for the BBSplit index" - } - }, - { - "index": { - "type": "file", - "description": "BBSplit index directory or tar.gz archive", - "pattern": "{*,*.tar.gz}" - } - } - ] - } - }, - { - "ch_rrna_fastas": { - "description": "Channel containing one or more FASTA files containing rRNA sequences for use with SortMeRNA or Bowtie2", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata for the rRNA fasta files" - } - }, - { - "fasta": { - "type": "file", - "description": "rRNA fasta files", - "pattern": "*.{fa,fasta}" - } - } - ] - } - }, - { - "skip_bbsplit": { - "type": "boolean", - "description": "Whether to skip BBSplit for removal of non-reference genome reads" - } - }, - { - "skip_fastqc": { - "type": "boolean", - "description": "Whether to skip FastQC" - } - }, - { - "skip_trimming": { - "type": "boolean", - "description": "Whether to skip trimming" - } - }, - { - "skip_umi_extract": { - "type": "boolean", - "description": "Skip the UMI extraction from the read in case the UMIs have been moved to the headers in advance of the pipeline run" - } - }, - { - "skip_linting": { - "type": "boolean", - "description": "Whether to skip linting of FastQ files" - } - }, - { - "make_salmon_index": { - "type": "boolean", - "description": "Whether to create salmon index before running salmon quant" - } - }, - { - "make_sortmerna_index": { - "type": "boolean", - "description": "Whether to create sortmerna index before running sortmerna" - } - }, - { - "make_bowtie2_index": { - "type": "boolean", - "description": "Whether to create bowtie2 index before running bowtie2 for rRNA removal" - } - }, - { - "trimmer": { - "type": "string", - "description": "Specifies the trimming tool to use", - "enum": [ - "trimgalore", - "fastp" - ] - } - }, - { - "min_trimmed_reads": { - "type": "integer", - "description": "Minimum number of trimmed reads below which samples are removed from further processing" - } - }, - { - "save_trimmed": { - "type": "boolean", - "description": "Save the trimmed FastQ files in the results directory?" - } - }, - { - "fastp_merge": { - "type": "boolean", - "description": "For FASTP, save merged fastqs stitching together read1 and read2 for paired end reads\n" - } - }, - { - "remove_ribo_rna": { - "type": "boolean", - "description": "Enable the removal of reads derived from ribosomal RNA" - } - }, - { - "ribo_removal_tool": { - "type": "string", - "description": "Specifies the rRNA removal tool to use", - "enum": [ - "sortmerna", - "ribodetector", - "bowtie2" - ] - } - }, - { - "with_umi": { - "type": "boolean", - "description": "Enable UMI-based read deduplication" - } - }, - { - "umi_discard_read": { - "type": "integer", - "description": "After UMI barcode extraction discard either R1 or R2 by setting this parameter to 1 or 2, respectively" - } - }, - { - "stranded_threshold": { - "type": "float", - "min": 0.5, - "description": "The fraction of stranded reads that must be assigned to a strandedness for confident assignment. Must be at least 0.5." - } - }, - { - "unstranded_threshold": { - "type": "float", - "description": "The difference in fraction of stranded reads assigned to 'forward' and 'reverse' below which a sample is classified as 'unstranded'." - } - } - ], - "output": [ - { - "reads": { - "description": "Preprocessed fastq reads", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata for the preprocessed reads" - } - }, - { - "reads": { - "type": "file", - "description": "Preprocessed FastQ files", - "pattern": "*.{fq,fastq},{,.gz}" - } - } - ] - } - }, - { - "multiqc_files": { - "description": "MultiQC-compatible output files from tools used in preprocessing", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata for the MultiQC files" - } - }, - { - "mqc": { - "type": "file", - "description": "MultiQC-compatible files", - "pattern": "*" - } - } - ] - } - }, - { - "trim_read_count": { - "description": "Number of reads remaining after trimming for all input samples", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata for the trim read count" - } - }, - { - "count": { - "type": "integer", - "description": "Number of reads after trimming" - } - } - ] - } - }, - { - "lint_log": { - "description": "Log files from FastQ linting", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata for the lint log" - } - }, - { - "log": { - "type": "file", - "description": "FastQ lint log file", - "pattern": "*.log" - } - } - ] - } - }, - { - "fastqc_filtered_html": { - "description": "FastQC report HTML files for filtered reads (after BBSplit and/or rRNA removal)", - "structure": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "html": { - "type": "file", - "description": "FastQC report HTML file", - "pattern": "*.html" - } - } - ] - } - }, - { - "fastqc_filtered_zip": { - "description": "FastQC report ZIP files for filtered reads (after BBSplit and/or rRNA removal)", - "structure": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "zip": { - "type": "file", - "description": "FastQC report ZIP file", - "pattern": "*.zip" - } - } - ] - } - }, - { - "per_sample_mqc_bundle": { - "description": "Per-sample MultiQC-feeding outputs (FastQC raw/trim/filtered zips,\ntrim log/JSON, UMI log, BBSplit stats, SortMeRNA log, RiboDetector\nlog, SeqKit stats, Bowtie2 log) joined on meta.\n", - "structure": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "files": { - "type": "file", - "description": "List of MultiQC-relevant files for the sample" - } - } - ] - } - } - ], - "authors": [ - "@pinin4fjords" - ], - "maintainers": [ - "@pinin4fjords" - ] - }, - "pipelines": [ - { - "name": "lncpipe", - "version": "dev" - }, - { - "name": "riboseq", - "version": "1.2.0" - }, - { - "name": "rnaseq", - "version": "3.26.0" - } - ] - }, - { - "name": "fastq_remove_rrna", - "path": "subworkflows/nf-core/fastq_remove_rrna/meta.yml", - "type": "subworkflow", - "meta": { - "name": "fastq_remove_rrna", - "description": "Remove ribosomal RNA reads from FASTQ files using SortMeRNA, RiboDetector, or Bowtie2", - "keywords": [ - "fastq", - "rrna", - "ribosomal", - "filter", - "sortmerna", - "ribodetector", - "bowtie2" - ], - "components": [ - "bowtie2/align", - "bowtie2/build", - "ribodetector", - "samtools/fastq", - "samtools/view", - "seqkit/replace", - "seqkit/stats", - "sortmerna" - ], - "input": [ - { - "ch_reads": { - "type": "file", - "description": "List of FastQ files of size 1 and 2 for single-end and paired-end data, respectively.\n", - "structure": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]" - } - }, - { - "reads": { - "type": "file", - "description": "FastQ files", - "pattern": "*.{fq,fastq}{,.gz}" - } - } - ] - } - }, - { - "ch_rrna_fastas": { - "type": "file", - "description": "Channel containing one or more FASTA files with rRNA sequences for use with SortMeRNA or Bowtie2.\nNot required for RiboDetector which uses built-in models.\n", - "structure": [ - { - "fasta": { - "type": "file", - "description": "rRNA reference fasta files", - "pattern": "*.{fa,fasta}{,.gz}" - } - } - ] - } - }, - { - "ch_sortmerna_index": { - "type": "directory", - "description": "Pre-built SortMeRNA index directory. Optional - can be built on-the-fly if make_sortmerna_index is true.\n", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata for the SortMeRNA index" - } - }, - { - "index": { - "type": "directory", - "description": "SortMeRNA index directory" - } - } - ] - } - }, - { - "ch_bowtie2_index": { - "type": "directory", - "description": "Pre-built Bowtie2 index directory. Optional - can be built on-the-fly if make_bowtie2_index is true.\n", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata for the Bowtie2 index" - } - }, - { - "index": { - "type": "directory", - "description": "Bowtie2 index directory" - } - } - ] - } - }, - { - "ribo_removal_tool": { - "type": "string", - "description": "Specifies the rRNA removal tool to use", - "enum": [ - "sortmerna", - "ribodetector", - "bowtie2" - ] - } - }, - { - "make_sortmerna_index": { - "type": "boolean", - "description": "Whether to create SortMeRNA index before running SortMeRNA" - } - }, - { - "make_bowtie2_index": { - "type": "boolean", - "description": "Whether to create Bowtie2 index before running Bowtie2 for rRNA removal" - } - } - ], - "output": [ - { - "reads": { - "type": "file", - "description": "FASTQ files with rRNA reads removed.\n", - "structure": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information" - } - }, - { - "reads": { - "type": "file", - "description": "Filtered FastQ files", - "pattern": "*.{fq,fastq}{,.gz}" - } - } - ] - } - }, - { - "multiqc_files": { - "type": "file", - "description": "Log files from the rRNA removal tool, compatible with MultiQC.\n", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata for the log files" - } - }, - { - "log": { - "type": "file", - "description": "Tool-specific log files", - "pattern": "*.log" - } - } - ] - } - } - ], - "authors": [ - "@pinin4fjords" - ], - "maintainers": [ - "@pinin4fjords" - ] - }, - "pipelines": [ - { - "name": "rnaseq", - "version": "3.26.0" - } - ] - }, - { - "name": "fastq_removeadapters_merge", - "path": "subworkflows/nf-core/fastq_removeadapters_merge/meta.yml", - "type": "subworkflow", - "meta": { - "name": "fastq_removeadapters_merge", - "description": "Remove adapters and merge reads based on various module choices", - "keywords": [ - "adapters", - "removal", - "short reads", - "merge", - "trim" - ], - "components": [ - "trimmomatic", - "cutadapt", - "trimgalore", - "bbmap/bbduk", - "leehom", - "fastp", - "adapterremoval", - "cat/fastq" - ], - "input": [ - { - "ch_input_reads": { - "type": "file", - "description": "List of FastQ files of size 1 and 2 for single-end and paired-end data, respectively.\nStructure: [ val(meta), [ path(reads) ] ]\n" - } - }, - { - "val_adapter_tool": { - "type": "string", - "description": "Choose one of the available adapter removal and/or merging tools\n", - "enum": [ - "trimmomatic", - "cutadapt", - "trimgalore", - "bbduk", - "leehom", - "fastp", - "adapterremoval" - ] - } - }, - { - "ch_custom_adapters_file": { - "type": "file", - "description": "Optional reference files, containing adapter and/or contaminant sequences for removal.\nIn fasta format for bbmap/bbduk and fastp, or in text format for AdapterRemoval (one adapter per line).\n" - } - }, - { - "val_save_merged": { - "type": "boolean", - "description": "Specify true to output merged reads instead\nUsed by fastp and adapterremoval\n" - } - }, - { - "val_fastp_discard_trimmed_pass": { - "type": "boolean", - "description": "Used only by fastp.\nSpecify true to not write any reads that pass trimming thresholds from the fastp process.\nThis can be used to use fastp for the output report only.\n" - } - }, - { - "val_fastp_save_trimmed_fail": { - "type": "boolean", - "description": "Used only by fastp.\nSpecify true to save files that failed to pass fastp trimming thresholds\n" - } - } - ], - "output": [ - { - "processed_reads": { - "type": "file", - "description": "Structure: [ val(meta), path(fastq.gz) ]\nThe trimmed/modified single or paired end or merged fastq reads\n", - "pattern": "*.fastq.gz" - } - }, - { - "discarded_reads": { - "type": "file", - "description": "Structure: [ val(meta), path(fastq.gz) ]\nThe discarded reads\n", - "pattern": "*.fastq.gz" - } - }, - { - "logfile": { - "type": "file", - "description": "Execution log file\n(trimmomatic {log}, trimgalore {txt}, fastp {log})\n", - "pattern": "*.{log,txt}" - } - }, - { - "report": { - "type": "file", - "description": "Execution report\n(trimmomatic {summary}, trimgalore {html,zip}, fastp {html})\n", - "pattern": "*.{summary,html,zip}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions\nStructure: [ path(versions.yml) ]\n", - "pattern": "versions.yml" - } - }, - { - "multiqc_files": { - "type": "file", - "description": "MultiQC-compatible output files from tools used in preprocessing\n(trimmomatic, cutadapt, bbduk, leehom, fastp, adapterremoval)\n" - } - } - ], - "authors": [ - "@kornkv", - "@vagkaratzas" - ], - "maintainers": [ - "@kornkv", - "@vagkaratzas" - ] - } - }, - { - "name": "fastq_sanitise_seqkit", - "path": "subworkflows/nf-core/fastq_sanitise_seqkit/meta.yml", - "type": "subworkflow", - "meta": { - "name": "fastq_sanitise_seqkit", - "description": "Filters and reports malformed FASTQ sequences with seqkit/sana,\nand then pairs any paired-end files using seqkit/pair\n", - "keywords": [ - "fastq", - "quality control", - "filtering", - "malformed", - "pairing", - "seqkit", - "preprocessing" - ], - "components": [ - "seqkit/sana", - "seqkit/pair" - ], - "input": [ - { - "ch_reads": { - "type": "channel", - "description": "Channel containing sample metadata and FASTQ files.\nStructure: [ val(meta), [ fastq ] ]\nWhere meta is a map containing at least:\n- id: sample identifier\n- single_end: boolean indicating if data is single-end (true) or paired-end (false)\n", - "pattern": "*.{fastq,fastq.gz,fq,fq.gz}" - } - } - ], - "output": [ - { - "reads": { - "type": "channel", - "description": "Channel containing filtered (i.e., non-malformed) and paired FASTQ files.\nFor single-end data: returns filtered reads\nFor paired-end data: returns properly paired reads and any unpaired reads\nStructure: [ val(meta), [ fastq ] ]\n", - "pattern": "*.{fastq,fastq.gz,fq,fq.gz}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions\nStructure: [ path(versions.yml) ]\n", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@vagkaratzas" - ], - "maintainers": [ - "@vagkaratzas" - ] - } - }, - { - "name": "fastq_shortreads_preprocess_qc", - "path": "subworkflows/nf-core/fastq_shortreads_preprocess_qc/meta.yml", - "type": "subworkflow", - "meta": { - "name": "fastq_shortreads_preprocess_qc", - "description": "Quality check and preprocessing subworkflow of Illumina short reads\nthat can do: quality check of input reads and generate statistics,\npreprocess and validate reads, barcode removal, remove adapters and merge reads,\nfilter by sequence complexity, deduplicate reads, remove host contamination,\nconcatenate reads and generate statistics for post-processing reads.\nWARNING: requires at least the process configurations from the nextflow.config\nto be added to the modules.config in the pipeline in order to work as intended.\n", - "keywords": [ - "fastq", - "illumina", - "short", - "reads", - "qc", - "stats", - "preprocessing", - "barcoding", - "adapters", - "merge", - "complexity", - "deduplication", - "host", - "decontamination" - ], - "components": [ - "fastq_qc_stats", - "fastqc", - "seqfu/check", - "seqfu/stats", - "seqkit/stats", - "seqtk/comp", - "fastq_preprocess_seqkit", - "fastq_sanitise_seqkit", - "seqkit/sana", - "seqkit/pair", - "seqkit/seq", - "seqkit/replace", - "seqkit/rmdup", - "umitools/extract", - "fastq_removeadapters_merge", - "trimmomatic", - "cutadapt", - "trimgalore", - "bbmap/bbduk", - "leehom", - "fastp", - "adapterremoval", - "cat/fastq", - "fastq_complexity_filter", - "prinseqplusplus", - "bbmap/clumpify", - "fastq_decontaminate_deacon_hostile", - "fastq_index_filter_deacon", - "fastq_fetch_clean_hostile", - "hostile/fetch", - "hostile/clean", - "bowtie2/build", - "deacon/filter", - "deacon/index" - ], - "input": [ - { - "ch_reads": { - "type": "file", - "description": "List of FastQ files of size 1 and 2 for single-end and paired-end data, respectively.\nStructure: [ val(meta), [ path(reads) ] ]\n", - "pattern": "*.fastq.gz" - } - }, - { - "skip_fastqc": { - "type": "boolean", - "description": "Skip FastQC quality control step\n" - } - }, - { - "skip_seqfu_check": { - "type": "boolean", - "description": "Skip SeqFu check step\n" - } - }, - { - "skip_seqfu_stats": { - "type": "boolean", - "description": "Skip SeqFu statistics step\n" - } - }, - { - "skip_seqkit_stats": { - "type": "boolean", - "description": "Skip SeqKit statistics step\n" - } - }, - { - "skip_seqtk_comp": { - "type": "boolean", - "description": "Skip SeqTk composition analysis step\n" - } - }, - { - "skip_seqkit_sana_pair": { - "type": "boolean", - "description": "Skip SeqKit sanitize and pair step\n" - } - }, - { - "skip_seqkit_seq": { - "type": "boolean", - "description": "Skip SeqKit sequence processing step\n" - } - }, - { - "skip_seqkit_replace": { - "type": "boolean", - "description": "Skip SeqKit replace step\n" - } - }, - { - "skip_seqkit_rmdup": { - "type": "boolean", - "description": "Skip SeqKit remove duplicates step\n" - } - }, - { - "skip_umitools_extract": { - "type": "boolean", - "description": "Skip UMI-tools extract barcoding step\n" - } - }, - { - "val_umi_discard_read": { - "type": "integer", - "description": "Discard R1 or R2 after UMI extraction (0 = keep both, 1 = discard R1, 2 = discard R2)\n" - } - }, - { - "skip_adapterremoval": { - "type": "boolean", - "description": "Skip the adapter removal and merge subworkflow completely\n" - } - }, - { - "val_adapter_tool": { - "type": "string", - "description": "Choose one of the available adapter removal and/or merging tools\n", - "enum": [ - "trimmomatic", - "cutadapt", - "trimgalore", - "bbduk", - "leehom", - "fastp", - "adapterremoval" - ] - } - }, - { - "ch_custom_adapters_file": { - "type": "file", - "description": "Optional reference files, containing adapter and/or contaminant sequences for removal.\nIn fasta format for bbmap/bbduk and fastp, or in text format for AdapterRemoval (one adapter per line).\n" - } - }, - { - "val_save_merged": { - "type": "boolean", - "description": "Specify true to output merged reads instead\nUsed by fastp and adapterremoval\n" - } - }, - { - "val_fastp_discard_trimmed_pass": { - "type": "boolean", - "description": "Used only by fastp.\nSpecify true to not write any reads that pass trimming thresholds from the fastp process.\nThis can be used to use fastp for the output report only.\n" - } - }, - { - "val_fastp_save_trimmed_fail": { - "type": "boolean", - "description": "Used only by fastp.\nSpecify true to save files that failed to pass fastp trimming thresholds\n" - } - }, - { - "skip_complexity_filtering": { - "type": "boolean", - "description": "Skip PRINSEQ++ complexity filtering step\n" - } - }, - { - "val_complexity_filter_tool": { - "type": "string", - "description": "Complexity filtering tool to use.\nMust be one of: 'prinseqplusplus', 'bbduk', or 'fastp'.\n" - } - }, - { - "skip_deduplication": { - "type": "boolean", - "description": "Skip BBMap Clumpify deduplication step\n" - } - }, - { - "skip_decontamination": { - "type": "boolean", - "description": "Skip host decontamination step\n" - } - }, - { - "ch_decontamination_fasta": { - "type": "file", - "description": "Reference genome FASTA file for decontamination (optional)\nStructure: [ val(meta), [ path(fasta) ] ]\n", - "pattern": "*.{fasta,fa,fna}" - } - }, - { - "ch_decontamination_reference": { - "type": "directory", - "description": "Pre-built reference index directory for decontamination (optional)\nStructure: [ val(reference_name), path(reference_dir) ]\n" - } - }, - { - "val_decontamination_index_name": { - "type": "string", - "description": "Name for the decontamination index (optional)\n" - } - }, - { - "val_decontamination_tool": { - "type": "string", - "description": "Decontamination tool to use ('hostile' or 'deacon')\n" - } - }, - { - "skip_final_concatenation": { - "type": "boolean", - "description": "Skip final FASTQ concatenation step\n" - } - } - ], - "output": [ - { - "reads": { - "type": "file", - "description": "Channel containing processed short reads\nStructure: [ val(meta), path(reads) ]\n", - "pattern": "*.fastq.gz" - } - }, - { - "pre_stats_fastqc_html": { - "type": "file", - "description": "FastQC HTML reports for pre-processing reads\nStructure: [ val(meta), path(html) ]\n", - "pattern": "*.html" - } - }, - { - "pre_stats_fastqc_zip": { - "type": "file", - "description": "FastQC ZIP archives for pre-processing reads\nStructure: [ val(meta), path(zip) ]\n", - "pattern": "*.zip" - } - }, - { - "pre_stats_seqfu_check": { - "type": "file", - "description": "SeqFu check results for pre-processing reads\nStructure: [ val(meta), path(check) ]\n" - } - }, - { - "pre_stats_seqfu_stats": { - "type": "file", - "description": "SeqFu statistics for pre-processing reads\nStructure: [ val(meta), path(stats) ]\n" - } - }, - { - "pre_stats_seqfu_multiqc": { - "type": "file", - "description": "SeqFu MultiQC-compatible stats for pre-processing reads\nStructure: [ val(meta), path(multiqc) ]\n" - } - }, - { - "pre_stats_seqkit_stats": { - "type": "file", - "description": "SeqKit statistics for pre-processing reads\nStructure: [ val(meta), path(stats) ]\n" - } - }, - { - "pre_stats_seqtk_stats": { - "type": "file", - "description": "SeqTk composition statistics for pre-processing reads\nStructure: [ val(meta), path(stats) ]\n" - } - }, - { - "post_stats_fastqc_html": { - "type": "file", - "description": "FastQC HTML reports for post-processing reads\nStructure: [ val(meta), path(html) ]\n", - "pattern": "*.html" - } - }, - { - "post_stats_fastqc_zip": { - "type": "file", - "description": "FastQC ZIP archives for post-processing reads\nStructure: [ val(meta), path(zip) ]\n", - "pattern": "*.zip" - } - }, - { - "post_stats_seqfu_check": { - "type": "file", - "description": "SeqFu check results for post-processing reads\nStructure: [ val(meta), path(check) ]\n" - } - }, - { - "post_stats_seqfu_stats": { - "type": "file", - "description": "SeqFu statistics for post-processing reads\nStructure: [ val(meta), path(stats) ]\n" - } - }, - { - "post_stats_seqfu_multiqc": { - "type": "file", - "description": "SeqFu MultiQC-compatible stats for post-processing reads\nStructure: [ val(meta), path(multiqc) ]\n" - } - }, - { - "post_stats_seqkit_stats": { - "type": "file", - "description": "SeqKit statistics for post-processing reads\nStructure: [ val(meta), path(stats) ]\n" - } - }, - { - "post_stats_seqtk_stats": { - "type": "file", - "description": "SeqTk composition statistics for post-processing reads\nStructure: [ val(meta), path(stats) ]\n" - } - }, - { - "umi_log": { - "type": "file", - "description": "UMI-tools extract log file\nStructure: [ val(meta), path(log) ]\n" - } - }, - { - "adapterremoval_discarded_reads": { - "type": "file", - "description": "Reads discarded during adapter removal or merging\nStructure: [ val(meta), path(fastq) ]\n", - "pattern": "*.fastq.gz" - } - }, - { - "adapterremoval_logfile": { - "type": "file", - "description": "Adapter removal execution log file\n(trimmomatic {log}, trimgalore {txt}, fastp {log})\nStructure: [ val(meta), path({log,txt}) ]\n" - } - }, - { - "adapterremoval_report": { - "type": "file", - "description": "Adapter removal report\n(trimmomatic {summary}, trimgalore {html,zip}, fastp {html})\nStructure: [ val(meta), path({summary,html,zip}) ]\n" - } - }, - { - "complexity_filter_log": { - "type": "file", - "description": "Log file from complexity filtering\nStructure: [ val(meta), path(log) ]\n" - } - }, - { - "complexity_filter_report": { - "type": "file", - "description": "Report generated by complexity filtering\nHTML report generated by fastp. Empty for other tools.\nStructure: [ val(meta), path(html) ]\n" - } - }, - { - "clumpify_log": { - "type": "file", - "description": "BBMap Clumpify log file\nStructure: [ val(meta), path(log) ]\n" - } - }, - { - "hostile_reference": { - "type": "file", - "description": "Hostile reference files used for decontamination\nStructure: [ val(reference_name), path(reference_dir) ]\n" - } - }, - { - "hostile_json": { - "type": "file", - "description": "Hostile JSON report\nStructure: [ val(meta), path(json) ]\n" - } - }, - { - "deacon_index": { - "type": "directory", - "description": "Deacon index directory\nStructure: [ val(meta), path(index) ]\n" - } - }, - { - "deacon_summary": { - "type": "file", - "description": "Deacon decontamination summary file\nStructure: [ val(meta), path(log) ]\n" - } - }, - { - "multiqc_files": { - "type": "file", - "description": "MultiQC compatible files for aggregated reporting\nStructure: [ path(files) ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions\nStructure: [ path(versions.yml) ]\n", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@vagkaratzas" - ], - "maintainers": [ - "@vagkaratzas" - ] - } - }, - { - "name": "fastq_subsample_fq_salmon", - "path": "subworkflows/nf-core/fastq_subsample_fq_salmon/meta.yml", - "type": "subworkflow", - "meta": { - "name": "fastq_subsample_fq_salmon", - "description": "Subsample fastq", - "keywords": [ - "fastq", - "subsample", - "strandedness" - ], - "components": [ - "fq/subsample", - "salmon/quant", - "salmon/index" - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "ch_reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" - } - }, - { - "ch_genome_fasta": { - "type": "file", - "description": "Genome fasta file", - "pattern": "Path to genome sequence in fasta format" - } - }, - { - "ch_transcript_fasta": { - "type": "file", - "description": "Transcript fasta file", - "pattern": "Path to transcript sequence in fasta format" - } - }, - { - "ch_gtf": { - "type": "file", - "description": "GTF features file", - "pattern": "Path features in GTF format" - } - }, - { - "ch_index": { - "type": "file", - "description": "Salmon index files", - "pattern": "Directory containing Salmon index" - } - }, - { - "make_index": { - "type": "boolean", - "description": "Whether to create salmon index before running salmon quant" - } - } - ], - "output": [ - { - "index": { - "type": "directory", - "description": "Directory containing salmon index", - "pattern": "salmon" - } - }, - { - "reads": { - "type": "file", - "description": "Subsampled fastq reads.", - "pattern": "*.{fq,fastq}{,.gz}" - } - }, - { - "results": { - "type": "directory", - "description": "Folder containing the quantification results for a specific sample", - "pattern": "${prefix}" - } - }, - { - "json_info": { - "type": "file", - "description": "File containing meta information from Salmon quant\nWhich could be used to infer strandedness among other things\n", - "pattern": "*info.json" - } - } - ], - "authors": [ - "@robsyme", - "@drpatelh" - ], - "maintainers": [ - "@robsyme", - "@drpatelh" - ] - }, - "pipelines": [ - { - "name": "lncpipe", - "version": "dev" - }, - { - "name": "riboseq", - "version": "1.2.0" - }, - { - "name": "rnaseq", - "version": "3.26.0" - } - ] - }, - { - "name": "fastq_taxonomic_profile_metaphlan", - "path": "subworkflows/nf-core/fastq_taxonomic_profile_metaphlan/meta.yml", - "type": "subworkflow", - "meta": { - "name": "fastq_taxonomic_profile_metaphlan", - "description": "Subworkflow to taxonomically classify metagenomic sequencing data using MetaPhlAn", - "keywords": [ - "metaphlan", - "metagenomics", - "database", - "classification", - "merge", - "profiles" - ], - "components": [ - "metaphlan/makedb", - "metaphlan/metaphlan", - "metaphlan/mergemetaphlantables" - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:‘test’, single_end:false ]\n" - } - }, - { - "ch_fastq": { - "type": "file", - "description": "The input channel containing the FASTQ files\nStructure: [ val(meta), path(fastqs) ]\n", - "pattern": "*.{fastq/fastq.gz}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:‘test’, single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions\nStructure: [ path(versions.yml) ]\n", - "pattern": "versions.yml" - } - }, - { - "txt": { - "type": "file", - "description": "Combined MetaPhlAn table\nStructure: [ val(meta), path(txt) ]\n", - "pattern": "*.txt" - } - } - ], - "authors": [ - "@LaurenGonsalves", - "@hhayden01", - "@ErikLHendrickson", - "@CarsonJM" - ], - "maintainers": [ - "@LaurenGonsalves", - "@CarsonJM" - ] - } - }, - { - "name": "fastq_trim_fastp_fastqc", - "path": "subworkflows/nf-core/fastq_trim_fastp_fastqc/meta.yml", - "type": "subworkflow", - "meta": { - "name": "fastq_trim_fastp_fastqc", - "description": "Read QC, fastp trimming and read qc", - "keywords": [ - "qc", - "quality_control", - "adapters", - "trimming", - "fastq" - ], - "components": [ - "fastqc", - "fastp" - ], - "input": [ - { - "ch_reads": { - "type": "file", - "description": "Structure: [ val(meta), path (reads) ]\nGroovy Map containing sample information\ne.g. [ id:'test', single_end:false ], List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively. If you wish to run interleaved paired-end data, supply as single-end data\nbut with `--interleaved_in` in your `modules.conf`'s `ext.args` for the module.\n" - } - }, - { - "ch_adapter_fasta": { - "type": "file", - "description": "Structure: path(adapter_fasta)\nFile in FASTA format containing possible adapters to remove.\n" - } - }, - { - "val_save_trimmed_fail": { - "type": "boolean", - "description": "Structure: val(save_trimmed_fail)\nSpecify true to save files that failed to pass trimming thresholds ending in `*.fail.fastq.gz`\n" - } - }, - { - "val_discard_trimmed_pass": { - "type": "boolean", - "description": "Structure: val(discard_trimmed)\nSpecify true to not write any reads that pass trimming thresholds.\nThis can be used to use fastp for the output report only.\n" - } - }, - { - "val_save_merged": { - "type": "boolean", - "description": "Structure: val(save_merged)\nSpecify true to save all merged reads to the a file ending in `*.merged.fastq.gz`\n" - } - }, - { - "val_skip_fastqc": { - "type": "boolean", - "description": "Structure: val(skip_fastqc)\nskip the fastqc process if true\n" - } - }, - { - "val_skip_fastp": { - "type": "boolean", - "description": "Structure: val(skip_fastp)\nskip the fastp process if true\n" - } - } - ], - "output": [ - { - "meta": { - "type": "string", - "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]" - } - }, - { - "reads": { - "type": "file", - "description": "Structure: [ val(meta), path(reads) ]\nThe trimmed/modified/unmerged fastq reads\n" - } - }, - { - "trim_json": { - "type": "file", - "description": "Structure: [ val(meta), path(trim_json) ]\nResults in JSON format\n" - } - }, - { - "trim_html": { - "type": "file", - "description": "Structure: [ val(meta), path(trim_html) ]\nResults in HTML format\n" - } - }, - { - "trim_log": { - "type": "file", - "description": "Structure: [ val(meta), path(trim_log) ]\nfastq log file\n" - } - }, - { - "trim_reads_fail": { - "type": "file", - "description": "Structure: [ val(meta), path(trim_reads_fail) ]\nReads the failed the preprocessing\n" - } - }, - { - "trim_reads_merged": { - "type": "file", - "description": "Structure: [ val(meta), path(trim_reads_merged) ]\nReads that were successfully merged\n" - } - }, - { - "fastqc_raw_html": { - "type": "file", - "description": "Structure: [ val(meta), path(fastqc_raw_html) ]\nRaw fastQC report\n" - } - }, - { - "fastqc_raw_zip": { - "type": "file", - "description": "Structure: [ val(meta), path(fastqc_raw_zip) ]\nRaw fastQC report archive\n" - } - }, - { - "fastqc_trim_html": { - "type": "file", - "description": "Structure: [ val(meta), path(fastqc_trim_html) ]\nTrimmed fastQC report\n" - } - }, - { - "fastqc_trim_zip": { - "type": "file", - "description": "Structure: [ val(meta), path(fastqc_trim_zip) ]\nTrimmed fastQC report archive\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@Joon-Klaps" - ], - "maintainers": [ - "@Joon-Klaps" - ] - }, - "pipelines": [ - { - "name": "bacass", - "version": "2.6.0" - }, - { - "name": "denovotranscript", - "version": "1.2.1" - } - ] - }, - { - "name": "gtf_hybridmerge_gffcompare", - "path": "subworkflows/nf-core/gtf_hybridmerge_gffcompare/meta.yml", - "type": "subworkflow", - "meta": { - "name": "gtf_hybridmerge_gffcompare", - "description": "Build a hybrid GTF by classifying a novel-transcript GTF against a reference\nannotation with gffcompare, filtering the resulting annotated GTF down to a\nuser-supplied set of class codes (e.g. \"u\" for novel intergenic), optionally\nsubtracting features that overlap a user-supplied blacklist BED, and merging\nthe survivors into an annotation backbone GTF. Gene rows missing from the\nbackbone for surviving novel transcripts are synthesised with coordinates\nspanning the union of their child transcripts so the output is a\nself-consistent GTF.\n\nInput format scope: standard GTF2 with `gene_id` / `transcript_id`\nattributes in column 9 and `gene` / `transcript` (and child `exon` etc.)\nfeature types in column 3. GFF3 dialects (Parent= / ID= attributes) and\nprokaryotic GTFs without transcript rows are out of scope.\n\nResource sizing: GAWK steps hold the full input in memory under\n`process_single`. Fine for annotation-scale GTFs; for >~500 MB inputs\noverride `memory` / `cpus` directly via `withName`.\n", - "keywords": [ - "gtf", - "annotation", - "novel-transcripts", - "gffcompare", - "merge", - "hybrid" - ], - "components": [ - "gffcompare", - "gawk", - "bedtools/intersect" - ], - "input": [ - { - "ch_novel_gtf": { - "type": "file", - "description": "Channel of novel-transcript GTFs (e.g. output of a StringTie merge or\na user-supplied annotation of unannotated transcribed regions) that\nwill be classified against the reference annotation. The subworkflow\nis designed for a single novel-vs-single-backbone build; if a caller\nhas multiple novel GTFs (one per sample, say) they should be merged\nbefore the call - the meta swap at the concat step adopts the\nbackbone meta and would collapse multiple emissions to the same id.\nStructure: [ val(meta), path(novel_gtf) ]\n", - "pattern": "*.{gtf,gff,gff3}" - } - }, - { - "ch_reference_gtf": { - "type": "file", - "description": "Channel containing the reference annotation GTF used by gffcompare to\ncompute class codes for every novel transcript. This drives which\ntranscripts survive the class-code filter, so callers usually want\nthe most complete annotation available here (not a subset such as a\ncanonical-only backbone).\nStructure: [ val(meta), path(reference_gtf) ]\n", - "pattern": "*.{gtf,gff,gff3}" - } - }, - { - "ch_backbone_gtf": { - "type": "file", - "description": "Channel containing the annotation GTF that surviving novel transcripts\nare merged into. The output is the concatenation of this backbone and\nthe filtered novel transcripts; missing gene rows are synthesised. For\ncallers that only have one annotation, pass the same channel as\nch_reference_gtf; callers that want the novel transcripts grafted onto\na reduced annotation (e.g. canonical-only) pass the reduced GTF here.\nStructure: [ val(meta), path(backbone_gtf) ]\n", - "pattern": "*.{gtf,gff,gff3}" - } - }, - { - "val_class_codes": { - "type": "string", - "description": "Single-element value channel carrying the gffcompare class codes to\nkeep, either as a comma-separated string (\"u\" or \"u,j,i\") or a List\n([\"u\", \"j\"]). Class codes describe how each novel transcript relates\nto the reference: \"u\" is intergenic (unknown), \"j\" is a multi-exon\nalternative splice junction, \"i\" is fully within a reference intron,\netc. See the gffcompare documentation for the full list.\n" - } - }, - { - "ch_blacklist_bed": { - "type": "file", - "description": "Optional channel containing a BED file of regions to exclude. Novel\ntranscripts overlapping these regions are dropped via `bedtools\nintersect -v` (the bundled `nextflow.config` sets `ext.args = '-v'`\non `BEDTOOLS_INTERSECT`; consumers can override in their own\n`modules.config` if they want strand-aware subtraction with `-v -s`,\nor positive overlap, etc.). Useful for rRNA loci, repeats, or any\nother interval set the caller wants kept out of the final hybrid GTF.\nPass `channel.empty()` to skip the intersect step entirely.\nStructure: [ val(meta), path(blacklist_bed) ]\n", - "pattern": "*.{bed}" - } - } - ], - "output": [ - { - "hybrid_gtf": { - "type": "file", - "description": "The hybrid GTF: the backbone annotation concatenated with surviving\nnovel transcripts, with synthesised gene rows for any novel gene_id\nnot already present in the backbone. Comment lines (`#`) are stripped.\nThe emitted meta is the backbone's meta (`ch_backbone_gtf`), not the\nnovel input's, so downstream channels keyed on the backbone's\nidentity can `.join()` against this output directly.\nStructure: [ val(meta), path(hybrid_gtf) ]\n", - "pattern": "*.gtf" - } - }, - { - "gffcompare_stats": { - "type": "file", - "description": "gffcompare summary statistics file. Useful for QC reporting of the\nclassification step.\nStructure: [ val(meta), path(stats) ]\n", - "pattern": "*.stats" - } - }, - { - "gffcompare_tracking": { - "type": "file", - "description": "gffcompare per-transcript tracking file, mapping every novel transcript\nto its best match in the reference annotation.\nStructure: [ val(meta), path(tracking) ]\n", - "pattern": "*.tracking" - } - }, - { - "gffcompare_loci": { - "type": "file", - "description": "gffcompare loci file, listing each locus covered by the novel and\nreference transcripts.\nStructure: [ val(meta), path(loci) ]\n", - "pattern": "*.loci" - } - }, - { - "versions": { - "type": "file", - "description": "Software versions are emitted via the `versions` topic channel by the\nupstream gffcompare, gawk, and bedtools modules; no separate output is\nemitted from this subworkflow.\n" - } - } - ], - "authors": [ - "@pinin4fjords" - ], - "maintainers": [ - "@pinin4fjords" - ] - } - }, - { - "name": "h5ad_removebackground_barcodes_cellbender_anndata", - "path": "subworkflows/nf-core/h5ad_removebackground_barcodes_cellbender_anndata/meta.yml", - "type": "subworkflow", - "meta": { - "name": "h5ad_removebackground_barcodes_cellbender_anndata", - "description": "Use cellbender for empty droplet removal", - "keywords": [ - "scdownstream", - "cellbender", - "anndata" - ], - "components": [ - "cellbender/removebackground", - "anndata/barcodes" - ], - "input": [ - { - "ch_unfiltered": { - "type": "file", - "description": "The input channel containing the unfiltered AnnData file to process\nand remove background noise and empty droplets\nStructure: [ val(meta), path(h5ad) ]\n", - "pattern": "*.h5ad" - } - } - ], - "output": [ - { - "h5ad": { - "description": "Background and empty droplet removed AnnData file containing cells with\nbarcodes exceeding 0.5 posterior cell probability determined by the\ncellbender's remove-background\nStructure: [ val(meta), path(h5ad) ]\n", - "pattern": "*.h5ad" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions\n", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@nictru", - "@chaochaowong" - ], - "maintainers": [ - "@nictru" - ] - }, - "pipelines": [ - { - "name": "scdownstream", - "version": "dev" - }, - { - "name": "scrnaseq", - "version": "4.1.0" - } - ] - }, - { - "name": "homer_groseq", - "path": "subworkflows/nf-core/homer_groseq/meta.yml", - "type": "subworkflow", - "meta": { - "name": "homer_groseq", - "description": "Basic process of trying to analyze GRO-Seq data with HOMER. From the [GRO-Seq Analysis Tutorial](http://homer.ucsd.edu/homer/ngs/groseq/groseq.html).", - "keywords": [ - "homer", - "groseq", - "nascent" - ], - "components": [ - "unzip", - "homer/maketagdirectory", - "homer/makeucscfile", - "homer/findpeaks", - "homer/pos2bed" - ], - "input": [ - { - "bam": { - "description": "list of BAM files, also able to take SAM and BED as input", - "pattern": "[ *.{bam/sam/bed} ]" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference fasta file", - "pattern": "*.fasta" - } - }, - { - "uniqmap": { - "type": "file", - "description": "Optional HOMER uniqmap", - "pattern": "*.zip" - } - } - ], - "output": [ - { - "tagdir": { - "type": "directory", - "description": "The \"Tag Directory\"", - "pattern": "*_tagdir" - } - }, - { - "bed_graph": { - "type": "file", - "description": "The UCSC bed graph", - "pattern": "*.bedGraph.gz" - } - }, - { - "peaks": { - "type": "file", - "description": "The found peaks", - "pattern": "*.peaks.txt" - } - }, - { - "bed": { - "type": "file", - "description": "A BED file of the found peaks", - "pattern": "*.bed" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@edmundmiller" - ], - "maintainers": [ - "@edmundmiller" - ] - }, - "pipelines": [ - { - "name": "nascent", - "version": "2.3.0" - } - ] - }, - { - "name": "mafft_align", - "path": "subworkflows/nf-core/mafft_align/meta.yml", - "type": "subworkflow", - "meta": { - "name": "mafft_align", - "description": "Prepare channels for running MAFFT/align", - "keywords": [ - "msa", - "mafft", - "align" - ], - "components": [ - "mafft/align" - ], - "input": [ - { - "ch_fasta": { - "type": "file", - "description": "The input channel containing the FASTA files\n", - "pattern": "*.{bam/cram/sam}", - "structure": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input sequences in FASTA format", - "pattern": "*.{fa,fasta}", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1929" - } - ] - } - } - ] - ] - } - } - ], - "output": [ - { - "alignment": { - "type": "file", - "description": "Channel containing the alignment file in fasta format.", - "structure": [ - [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" - } - }, - { - "*.aln.gz": { - "type": "file", - "description": "Alignment file, in FASTA format.", - "pattern": "*.aln.gz", - "ontologies": [ - { - "edam": "http://edamontology.org/format_1984" - } - ] - } - } - ] - ] - } - } - ], - "authors": [ - "@mirpedrol" - ], - "maintainers": [ - "@mirpedrol", - "@luisas", - "@JoseEspinosa" - ] - } - }, - { - "name": "mmseqs_contig_taxonomy", - "path": "subworkflows/nf-core/mmseqs_contig_taxonomy/meta.yml", - "type": "subworkflow", - "meta": { - "name": "mmseqs_contig_taxonomy", - "description": "Assign taxonomy to contigs using the MMseqs2 workflow.", - "keywords": [ - "metagenomics", - "database", - "contigs", - "mmsesq2", - "taxonomy" - ], - "components": [ - "mmseqs/databases", - "mmseqs/createdb", - "mmseqs/taxonomy", - "mmseqs/createtsv" - ], - "input": [ - { - "contigs": { - "type": "file", - "description": "Channel containing each fasta in nucleotide format as a distinct element with meta.\nStructure: [ val(meta), path(fasta) ]\n", - "pattern": "*.{fasta,fa,fna}" - } - }, - { - "mmseqs_databases": { - "type": "string", - "description": "Channel containing a database created by mmseqs2 databases.\nStructure: [ path(mmseqsdb) ]\n", - "pattern": "*/mmseqs/database" - } - }, - { - "databases_id": { - "type": "string", - "description": "Channel containing the ID of a database made available by developers of mmseqs2. Please refer to https://github.com/soedinglab/MMseqs2/wiki#downloading-databases for possible IDs to use.\nStructure: [ val(id) ]\n" - } - } - ], - "output": [ - { - "taxonomy": { - "type": "file", - "description": "Channel containing the tab separated file with all assigned taxonomy.\nStructure: [ val(meta), path(tsv) ]\n", - "pattern": "*.tsv" - } - }, - { - "db_mmseqs": { - "type": "directory", - "description": "Channel containing the mmseqs database directory. Useful for when the databases is downloaded in the pipeline.\nStructure: [ path(outputdir) ]\n", - "pattern": "*/mmseqs_database" - } - }, - { - "db_taxonomy": { - "type": "directory", - "description": "Channel containing the database containing the taxonomic classification for each input fasta file.\nStructure: [ path(outputdir) ]\n", - "pattern": "*/sample_taxonomy" - } - }, - { - "db_contig": { - "type": "directory", - "description": "Channel containing the database containing the mmseqs format of each input fasta file.\nStructure: [ path(outputdir) ]\n", - "pattern": "*/sample_db" - } - } - ], - "authors": [ - "@darcy220606" - ], - "maintainers": [ - "@darcy220606" - ] - } - }, - { - "name": "mmseqs_fasta_cluster", - "path": "subworkflows/nf-core/mmseqs_fasta_cluster/meta.yml", - "type": "subworkflow", - "meta": { - "name": "MMSEQS_FASTA_CLUSTER", - "description": "Subworkflow that generates a clustering TSV file from a set of amino acid sequence within a FASTA file.", - "keywords": [ - "fasta", - "sequences", - "cluster", - "linclust", - "mmseqs" - ], - "components": [ - "mmseqs/createdb", - "mmseqs/cluster", - "mmseqs/linclust", - "mmseqs/createtsv" - ], - "input": [ - { - "sequences": { - "type": "file", - "description": "Fasta file containing sequences for clustering.\n" - } - }, - { - "clustering_tool": { - "type": "string", - "description": "Clustering algorithm of MMSeqs to use for cluster generation. Options are 'linclust' or 'cluster'.\n" - } - } - ], - "output": [ - { - "versions": { - "type": "file", - "description": "Versions file containing the software versions used in the workflow.\n" - } - }, - { - "seqs": { - "type": "file", - "description": "The input FASTA file mapped to its corresponding clustering tsv, per input entry." - } - }, - { - "clusters": { - "type": "file", - "description": "Clustering file mapped to its corresponding input FASTA file." - } - } - ], - "authors": [ - "@vagkaratzas" - ], - "maintainers": [ - "@vagkaratzas" - ] - }, - "pipelines": [ - { - "name": "proteinfamilies", - "version": "2.3.0" - }, - { - "name": "viralmetagenome", - "version": "1.1.1" - } - ] - }, - { - "name": "multiple_impute_glimpse2", - "path": "subworkflows/nf-core/multiple_impute_glimpse2/meta.yml", - "type": "subworkflow", - "meta": { - "name": "multiple_impute_glimpse2", - "description": "Impute VCF/BCF files, but also CRAM and BAM files with Glimpse2", - "keywords": [ - "glimpse", - "chunk", - "phase", - "ligate", - "split_reference" - ], - "components": [ - "glimpse2/chunk", - "glimpse2/phase", - "glimpse2/ligate", - "glimpse2/splitreference", - "bcftools/index" - ], - "input": [ - { - "ch_input": { - "type": "file", - "description": "Target dataset in CRAM, BAM or VCF/BCF format.\nIndex file of the input file.\nFile with sample names and ploidy information.\nStructure: [ meta, file, index, txt ]\n" - } - }, - { - "ch_ref": { - "type": "file", - "description": "Reference panel of haplotypes in VCF/BCF format.\nIndex file of the Reference panel file.\nTarget region, usually a full chromosome (e.g. chr20:1000000-2000000 or chr20).\nThe file could possibly be without GT field (for efficiency reasons a file containing only the positions is recommended).\nStructure: [ meta, vcf, csi, region ]\n" - } - }, - { - "ch_map": { - "type": "file", - "description": "File containing the genetic map.\nStructure: [ meta, gmap ]\n" - } - }, - { - "ch_fasta": { - "type": "file", - "description": "Reference genome in fasta format.\nReference genome index in fai format\nStructure: [ meta, fasta, fai ]\n" - } - } - ], - "output": [ - { - "chunk_chr": { - "type": "file", - "description": "Tab delimited output txt file containing buffer and imputation regions.\nStructure: [meta, txt]\n" - } - }, - { - "merged_variants": { - "type": "file", - "description": "Output VCF/BCF file for the merged regions.\nPhased information (HS field) is updated accordingly for the full region.\nStructure: [ val(meta), bcf ]\n" - } - }, - { - "merged_variants_index": { - "type": "file", - "description": "Index file of the ligated phased variants files." - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@LouisLeNezet" - ], - "maintainers": [ - "@LouisLeNezet" - ] - } - }, - { - "name": "quant_tximport_summarizedexperiment", - "path": "subworkflows/nf-core/quant_tximport_summarizedexperiment/meta.yml", - "type": "subworkflow", - "meta": { - "name": "quant_tximport_summarizedexperiment", - "description": "Post-process transcript-level quantification results using tximport to produce count matrices and SummarizedExperiment objects", - "keywords": [ - "rnaseq", - "quantification", - "tximport", - "summarizedexperiment", - "salmon", - "kallisto", - "rsem" - ], - "components": [ - "custom/tx2gene", - "tximeta/tximport", - "summarizedexperiment/summarizedexperiment" - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing study-level sample sheet information. e.g. [\n id:'SRP1234' ].\n" - } - }, - { - "samplesheet": { - "type": "file", - "description": "Sample sheet, to be baked into the `colData` of SummarizedExperiment\nobjects.\n", - "pattern": "*.{csv,tsv}" - } - }, - { - "quant_results": { - "type": "file", - "description": "Per-sample quantification results. For Salmon these are result\ndirectories containing quant.sf, for Kallisto directories containing\nabundance.tsv, and for RSEM the .isoforms.results files. All samples\nmust have been quantified against the same transcriptome, as only a\nsingle sample is used for transcript-to-gene mapping discovery. If\nsupport for mixed transcriptomes is needed in future, tx2gene would\nneed to run independently per sample.\n" - } - }, - { - "gtf": { - "type": "file", - "description": "Channel with features in GTF format, used to generate transcript/gene\nmappings via tx2gene.\n" - } - }, - { - "gtf_id_attribute": { - "type": "string", - "description": "Attribute in GTF file corresponding to the gene identifier.\n" - } - }, - { - "gtf_extra_attribute": { - "type": "string", - "description": "GTF alternative gene attribute (e.g. gene_name)" - } - }, - { - "quant_type": { - "type": "string", - "description": "Quantification tool type. One of 'salmon', 'kallisto', or 'rsem'.\n" - } - }, - { - "skip_merge": { - "type": "boolean", - "description": "Skip cross-sample merging. When true, runs tximport per-sample\ninstead of collecting all samples, and skips SummarizedExperiment\ncreation. Useful for very large cohorts.\n" - } - } - ], - "output": [ - { - "tx2gene": { - "type": "file", - "description": "Transcript-to-gene mapping file generated from the GTF.\n", - "pattern": "*.tx2gene.tsv" - } - }, - { - "tpm_gene": { - "type": "file", - "description": "Gene-level matrix of abundance values in TPM.\n", - "pattern": "*.gene_tpm.tsv" - } - }, - { - "counts_gene": { - "type": "file", - "description": "Gene-level matrix of unadjusted estimated counts from tximport\n(`countsFromAbundance = 'no'`).\n", - "pattern": "*.gene_counts.tsv" - } - }, - { - "lengths_gene": { - "type": "file", - "description": "Gene-level matrix of effective length values.\n", - "pattern": "*.gene_lengths.tsv" - } - }, - { - "counts_gene_length_scaled": { - "type": "file", - "description": "Gene-level matrix of estimated counts, generated from abundance (TPM)\nvalues by scaling to library size, additionally scaled using the\naverage transcript length, using tximport\n`countsFromAbundance = 'lengthScaledTPM'`.\n", - "pattern": "*.gene_counts_length_scaled.tsv" - } - }, - { - "counts_gene_scaled": { - "type": "file", - "description": "Gene-level matrix of estimated counts, generated from abundance (TPM)\nvalues by scaling to library size with tximport\n`countsFromAbundance = 'scaledTPM'`.\n", - "pattern": "*.gene_counts_scaled.tsv" - } - }, - { - "tpm_transcript": { - "type": "file", - "description": "Transcript-level matrix of abundance values in TPM.\n", - "pattern": "*.transcript_tpm.tsv" - } - }, - { - "counts_transcript": { - "type": "file", - "description": "Transcript-level matrix of unadjusted estimated counts from tximport\n(`countsFromAbundance = 'no'`).\n", - "pattern": "*.transcript_counts.tsv" - } - }, - { - "lengths_transcript": { - "type": "file", - "description": "Transcript-level matrix of effective length values.\n", - "pattern": "*.transcript_lengths.tsv" - } - }, - { - "merged_gene_rds": { - "type": "file", - "description": "Serialised SummarizedExperiment object containing gene-level assays\n(counts, length-scaled counts, scaled counts, lengths, TPM).\n", - "pattern": "*.rds" - } - }, - { - "merged_transcript_rds": { - "type": "file", - "description": "Serialised SummarizedExperiment object containing transcript-level\nassays (counts, lengths, TPM).\n", - "pattern": "*.rds" - } - } - ], - "authors": [ - "@pinin4fjords" - ], - "maintainers": [ - "@pinin4fjords" - ] - }, - "pipelines": [ - { - "name": "rnaseq", - "version": "3.26.0" - } - ] - }, - { - "name": "quantify_pseudo_alignment", - "path": "subworkflows/nf-core/quantify_pseudo_alignment/meta.yml", - "type": "subworkflow", - "meta": { - "name": "quantify_pseudo_alignment", - "description": "Perform quantification with Salmon or Kallisto to produce count tables and SummarizedExperiment objects", - "keywords": [ - "rnaseq", - "quantification", - "kallisto", - "salmon" - ], - "components": [ - "kallisto/quant", - "quant_tximport_summarizedexperiment", - "salmon/quant" - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing study-level sample sheet information. e.g. [\n id:'SRP1234' ].\n" - } - }, - { - "samplesheet": { - "type": "file", - "description": "Sample sheet, to be baked into the `colData` of summarizedexperiment\nobjects.\n", - "pattern": "*.{csv,tsv}" - } - }, - { - "reads": { - "type": "file", - "description": "Channel with input FastQ files of size 1 and 2 for single-end and\npaired-end data, respectively. OR a transcriptome-level BAM file if\nrunning Salmon in alignment mode.\n" - } - }, - { - "index": { - "type": "path", - "description": "Path to Salmon or Kallisto index in the tool-appropriate form.\n" - } - }, - { - "gtf": { - "type": "file", - "description": "Channel with features in GTF format. Passed to pseudoaligners and used\nto generate transcript/ gene mappings.\n" - } - }, - { - "gtf_id_attribute": { - "type": "string", - "description": "Attribute in GTF file corresponding to the gene identifier.\n" - } - }, - { - "gtf_extra_attribute": { - "type": "string", - "description": "GTF alternative gene attribute (e.g. gene_name)" - } - }, - { - "pseudo_aligner": { - "type": "string", - "description": "Pseudoaligner, `kallisto` or `salmon`." - } - }, - { - "alignment_mode": { - "type": "boolean", - "description": "If running Salmon, run in alignment mode (`true` or `false`).\n" - } - }, - { - "lib_type": { - "type": "string", - "description": "String to override Salmon library type." - } - }, - { - "kallisto_quant_fraglen": { - "type": "integer", - "description": "Estimated fragment length. Required if running Kallisto with\nsingle-ended reads.\n" - } - }, - { - "kallisto_quant_fraglen_sd": { - "type": "integer", - "description": "Estimated standard error for fragment length required by Kallisto in\nsingle-end mode.\n" - } - }, - { - "skip_merge": { - "type": "boolean", - "description": "Skip cross-sample merging. When true, runs tximport per-sample\ninstead of collecting all samples, and skips SummarizedExperiment\ncreation. Useful for very large cohorts.\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing study-level sample sheet information. e.g. [\n id:'SRP1234' ].\n" - } - }, - { - "results": { - "type": "file", - "description": "Channel containing sample-wise results directories from the\npseudoaligner.\n" - } - }, - { - "multiqc": { - "type": "file", - "description": "Channel containing those pseudoaligner outputs readable by MultiQC for\npassing to workflow-level reporting.\n" - } - }, - { - "tpm_gene": { - "type": "file", - "description": "Gene-level matrix of abundance values in TPM.\n", - "pattern": "*.gene_tpm.tsv" - } - }, - { - "counts_gene": { - "type": "file", - "description": "Gene-level matrix of unadjusted estimated counts from tximport\n(`countsFromAbundance = 'no'`).\n", - "pattern": "*.gene_counts.tsv" - } - }, - { - "lengths_gene": { - "type": "file", - "description": "Gene-level matrix of length values for modelling in downstream\nanalysis.\n", - "pattern": "gene_lengths.tsv" - } - }, - { - "counts_gene_length_scaled": { - "type": "file", - "description": "Gene-level matrix of estimated counts, generated from abundance (TPM)\nvalues by scaling to library size, additionally scaled using the\naverage transcript length, averaged over samples and to library size,\nusing tximport `countsFromAbundance = 'lengthScaledTPM'`.\n", - "pattern": "*.gene_counts_length_scaled.tsv" - } - }, - { - "counts_gene_scaled": { - "type": "file", - "description": "Gene-level matrix of estimated counts, generated from abundance (TPM)\nvalues by scaling to library size with tximport `countsFromAbundance =\n'scaledTPM'`.\n", - "pattern": "*.gene_counts_length_scaled.tsv" - } - }, - { - "tpm_transcript": { - "type": "file", - "description": "Transcript-level matrix of abundance values in TPM.\n", - "pattern": "*.transcript_tpm.tsv" - } - }, - { - "counts_transcript": { - "type": "file", - "description": "Transcript-level matrix of unadjusted estimated counts from tximport\n(`countsFromAbundance = 'no'`).\n", - "pattern": "*.transcript_counts.tsv" - } - }, - { - "lengths_transcript": { - "type": "file", - "description": "Transcript-level matrix of length values for modelling in downstream\nanalysis.\n", - "pattern": "transcript_lengths.tsv" - } - }, - { - "merged_gene_rds_unified": { - "type": "file", - "description": "Serialised SummarizedExperiment object containing gene level\nabundance, count, and length matrices generated from tximport.\n", - "pattern": "*.rds" - } - }, - { - "merged_transcript_rds_unified": { - "type": "file", - "description": "Serialised SummarizedExperiment object containing transcript level\nabundance, count, and length matrices generated from tximport.\n", - "pattern": "*.rds" - } - } - ], - "authors": [ - "@pinin4fjords", - "@adamrtalbot" - ], - "maintainers": [ - "@pinin4fjords", - "@adamrtalbot" - ] - }, - "pipelines": [ - { - "name": "riboseq", - "version": "1.2.0" - }, - { - "name": "rnaseq", - "version": "3.26.0" - } - ] - }, - { - "name": "quantify_rsem", - "path": "subworkflows/nf-core/quantify_rsem/meta.yml", - "type": "subworkflow", - "meta": { - "name": "quantify_rsem", - "description": "Perform quantification with RSEM to produce count tables, legacy merge matrices, and SummarizedExperiment objects", - "keywords": [ - "rnaseq", - "quantification", - "rsem", - "tximport" - ], - "components": [ - "rsem/calculateexpression", - "sentieon/rsemcalculateexpression", - "custom/rsemmergecounts", - "quant_tximport_summarizedexperiment" - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing study-level sample sheet information. e.g. [\n id:'SRP1234' ].\n" - } - }, - { - "samplesheet": { - "type": "file", - "description": "Sample sheet, to be baked into the `colData` of summarizedexperiment\nobjects.\n", - "pattern": "*.{csv,tsv}" - } - }, - { - "reads": { - "type": "file", - "description": "Channel with input FastQ files of size 1 and 2 for single-end and\npaired-end data, respectively. OR a transcriptome-level BAM file if\nrunning RSEM in alignment mode.\n" - } - }, - { - "index": { - "type": "path", - "description": "Path to RSEM index directory.\n" - } - }, - { - "gtf": { - "type": "file", - "description": "Channel with features in GTF format. Used to generate transcript/gene\nmappings.\n" - } - }, - { - "gtf_id_attribute": { - "type": "string", - "description": "Attribute in GTF file corresponding to the gene identifier.\n" - } - }, - { - "gtf_extra_attribute": { - "type": "string", - "description": "GTF alternative gene attribute (e.g. gene_name)" - } - }, - { - "use_sentieon_star": { - "type": "boolean", - "description": "Use Sentieon-accelerated STAR for alignment within RSEM. Only\nmeaningful in FASTQ input mode; set to `false` for BAM-mode consumers.\n" - } - }, - { - "skip_merge": { - "type": "boolean", - "description": "Skip cross-sample merging. When true, runs tximport per-sample\ninstead of collecting all samples, skips RSEM merge counts, and\nskips SummarizedExperiment creation. Useful for very large cohorts.\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information. e.g. [ id:'test' ].\n" - } - }, - { - "raw_counts_gene": { - "type": "file", - "description": "Per-sample RSEM gene-level results files.\n", - "pattern": "*.genes.results" - } - }, - { - "raw_counts_transcript": { - "type": "file", - "description": "Per-sample RSEM transcript-level results files.\n", - "pattern": "*.isoforms.results" - } - }, - { - "stat": { - "type": "file", - "description": "Per-sample RSEM statistics files.\n", - "pattern": "*.stat" - } - }, - { - "logs": { - "type": "file", - "description": "Per-sample RSEM log files (optional, FASTQ mode only).\n", - "pattern": "*.log" - } - }, - { - "merged_counts_gene": { - "type": "file", - "description": "Wide-format gene-level count matrix from RSEM merge.\n", - "pattern": "*.gene_counts.tsv" - } - }, - { - "merged_tpm_gene": { - "type": "file", - "description": "Wide-format gene-level TPM matrix from RSEM merge.\n", - "pattern": "*.gene_tpm.tsv" - } - }, - { - "merged_counts_transcript": { - "type": "file", - "description": "Wide-format transcript-level count matrix from RSEM merge.\n", - "pattern": "*.transcript_counts.tsv" - } - }, - { - "merged_tpm_transcript": { - "type": "file", - "description": "Wide-format transcript-level TPM matrix from RSEM merge.\n", - "pattern": "*.transcript_tpm.tsv" - } - }, - { - "merged_genes_long": { - "type": "file", - "description": "Long-format gene-level results from RSEM merge.\n", - "pattern": "*.genes_long.tsv" - } - }, - { - "merged_isoforms_long": { - "type": "file", - "description": "Long-format isoform-level results from RSEM merge.\n", - "pattern": "*.isoforms_long.tsv" - } - }, - { - "tpm_gene": { - "type": "file", - "description": "Gene-level matrix of abundance values in TPM from tximport.\n", - "pattern": "*.gene_tpm.tsv" - } - }, - { - "counts_gene": { - "type": "file", - "description": "Gene-level matrix of unadjusted estimated counts from tximport\n(`countsFromAbundance = 'no'`).\n", - "pattern": "*.gene_counts.tsv" - } - }, - { - "counts_gene_length_scaled": { - "type": "file", - "description": "Gene-level matrix of estimated counts from tximport using\n`countsFromAbundance = 'lengthScaledTPM'`.\n", - "pattern": "*.gene_counts_length_scaled.tsv" - } - }, - { - "counts_gene_scaled": { - "type": "file", - "description": "Gene-level matrix of estimated counts from tximport using\n`countsFromAbundance = 'scaledTPM'`.\n", - "pattern": "*.gene_counts_scaled.tsv" - } - }, - { - "lengths_gene": { - "type": "file", - "description": "Gene-level matrix of length values from tximport.\n", - "pattern": "*.gene_lengths.tsv" - } - }, - { - "tpm_transcript": { - "type": "file", - "description": "Transcript-level matrix of abundance values in TPM from tximport.\n", - "pattern": "*.transcript_tpm.tsv" - } - }, - { - "counts_transcript": { - "type": "file", - "description": "Transcript-level matrix of unadjusted estimated counts from tximport\n(`countsFromAbundance = 'no'`).\n", - "pattern": "*.transcript_counts.tsv" - } - }, - { - "lengths_transcript": { - "type": "file", - "description": "Transcript-level matrix of length values from tximport.\n", - "pattern": "*.transcript_lengths.tsv" - } - }, - { - "merged_gene_rds_unified": { - "type": "file", - "description": "Serialised SummarizedExperiment object containing gene level\nabundance, count, and length matrices generated from tximport.\n", - "pattern": "*.rds" - } - }, - { - "merged_transcript_rds_unified": { - "type": "file", - "description": "Serialised SummarizedExperiment object containing transcript level\nabundance, count, and length matrices generated from tximport.\n", - "pattern": "*.rds" - } - }, - { - "tx2gene": { - "type": "file", - "description": "Transcript to gene mapping table.\n", - "pattern": "*.tx2gene.tsv" - } - } - ], - "authors": [ - "@pinin4fjords" - ], - "maintainers": [ - "@pinin4fjords" - ] - }, - "pipelines": [ - { - "name": "rnaseq", - "version": "3.26.0" - } - ] - }, - { - "name": "tif_registration_stainwarpy", - "path": "subworkflows/nf-core/tif_registration_stainwarpy/meta.yml", - "type": "subworkflow", - "meta": { - "name": "tif_registration_stainwarpy", - "description": "Register H&E stained and multiplexed tissue images and transform segmentation masks using stainwarpy", - "keywords": [ - "image registration", - "histology", - "hne", - "multiplexed", - "segmentation mask" - ], - "components": [ - "stainwarpy/extractchannel", - "stainwarpy/register", - "stainwarpy/transformsegmask" - ], - "input": [ - { - "ch_hne": { - "type": "file", - "description": "Channel containing H&E stained tissue image in TIF/OME-TIF format\nStructure: [ val(meta), path(ome.tif) ]\n", - "pattern": "*.{tif,ome.tif,tiff,ome.tiff}" - } - }, - { - "ch_multiplexed": { - "type": "file", - "description": "Channel containing multiplexed tissue image in TIF/OME-TIF format\nStructure: [ val(meta), path(ome.tif) ]\n", - "pattern": "*.{tif,ome.tif,tiff,ome.tiff}" - } - }, - { - "ch_segmask": { - "type": "file", - "description": "Channel containing segmentation mask in TIF/OME-TIF/npy format. (optional input)\nStructure: [ val(meta), path(ome.tif) ]\n", - "pattern": "*.{tif,ome.tif,tiff,ome.tiff,npy}" - } - }, - { - "val_fixed_img": { - "type": "string", - "description": "Fixed image to use for registration (\"multiplexed\" or \"hne\")\n" - } - }, - { - "val_final_img_sz": { - "type": "string", - "description": "Final image size to output registered image and segmentation mask (\"multiplexed\" or \"hne\")\n" - } - } - ], - "output": [ - { - "transformed_image": { - "type": "file", - "description": "Channel containing registered tissue image\nStructure: [ val(meta), path(ome.tif) ]\n", - "pattern": "*_transformed_image.ome.tif" - } - }, - { - "transformed_segmask": { - "type": "file", - "description": "Channel containing transformed segmentation mask (empty if 'ch_segmask' not provided)\nStructure: [ val(meta), path(ome.tif) ]\n", - "pattern": "*_transformed_segmentation_mask.ome.tif" - } - }, - { - "metrics": { - "type": "file", - "description": "Channel containing registration metrics and transformation map file\nStructure: [ val(meta), path(json) ]\n", - "pattern": "*_registration_metrics_tform_map.json" - } - } - ], - "authors": [ - "@tckumarasekara" - ], - "maintainers": [ - "@tckumarasekara" - ] - } - }, - { - "name": "tiff_segmentation_vpt", - "path": "subworkflows/nf-core/tiff_segmentation_vpt/meta.yml", - "type": "subworkflow", - "meta": { - "name": "tiff_segmentation_vpt", - "description": "Perform segmentation of MERSCOPE TIFF images using the vizgen-postprocessing tool", - "keywords": [ - "segmentation", - "imaging", - "merscope", - "vizgen", - "tiff", - "spatial" - ], - "components": [ - "vizgenpostprocessing/preparesegmentation", - "vizgenpostprocessing/runsegmentationontile", - "vizgenpostprocessing/compiletilesegmentation" - ], - "input": [ - { - "ch_input": { - "type": "channel", - "description": "The input channel containing image directory and transformation file\nStructure: [ val(meta), path(image_dir), path(micron_to_mosaic_pixel_transform.csv) ]\n", - "pattern": "*" - } - }, - { - "ch_algorithm_json": { - "type": "channel", - "description": "Channel containing algorithm configuration file\nStructure: [ path(algorithm.json) ]\n", - "pattern": "*.json" - } - }, - { - "ch_images_regex": { - "type": "channel", - "description": "Channel containing regex pattern for image matching\nStructure: [ val(regex) ]\n", - "pattern": "*" - } - }, - { - "ch_custom_weights": { - "type": "channel", - "description": "Channel containing custom weights for segmentation\nStructure: [ path(custom_weights) ]\n", - "pattern": "*" - } - } - ], - "output": [ - { - "micron_space_segmentation": { - "type": "file", - "description": "Channel containing micron space segmentation results\nStructure: [ val(meta), path(parquet) ]\n", - "pattern": "*.parquet" - } - }, - { - "mosaic_space_segmentation": { - "type": "file", - "description": "Channel containing mosaic space segmentation results\nStructure: [ val(meta), path(parquet) ]\n", - "pattern": "*.parquet" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions\nStructure: [ path(versions.yml) ]\n", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@mcmero" - ], - "maintainers": [ - "@mcmero" - ] - } - }, - { - "name": "utils_annotation_cache", - "path": "subworkflows/nf-core/utils_annotation_cache/meta.yml", - "type": "subworkflow", - "meta": { - "name": "utils_annotation_cache", - "description": "Check the path to the annotation cache depending if local or on the cloud, or using annotation-cache itself", - "keywords": [ - "snpeff", - "ensemblvep", - "annotation-cache", - "annotation", - "cache", - "verification" - ], - "components": [], - "input": [ - { - "ensemblvep_cache": { - "description": "Path to root cache\nStructure: [ path(cache) ]\n" - } - }, - { - "ensemblvep_cache_version": { - "description": "cache_version to use\nStructure: [ val(cache_version) ]\n" - } - }, - { - "ensemblvep_custom_args": { - "description": "custom args, to check if refseq or merged is needed\nStructure: [ val(custom args) ]\n" - } - }, - { - "ensemblvep_genome": { - "description": "genome to use\nStructure: [ val(genome) ]\n" - } - }, - { - "ensemblvep_species": { - "description": "species to use\nStructure: [ val(species) ]\n" - } - }, - { - "ensemblvep_enabled": { - "description": "Boolean to enable ensemblvep\nStructure: [ Boolean ]\n" - } - }, - { - "snpeff_cache": { - "description": "Path to root cache\nStructure: [ path(cache) ]\n" - } - }, - { - "snpeff_db": { - "description": "db to use\nStructure: [ val(db) ]\n" - } - }, - { - "snpeff_enabled": { - "description": "Boolean to enable snpeff\nStructure: [ Boolean ]\n" - } - }, - { - "help_message": { - "description": "Extra help message to display when error\nStructure: [ val(species) ]\n" - } - } - ], - "output": [ - { - "ensemblvep_cache": { - "description": "Path to ensemblvep cache\nStructure: [ val(meta), path(cache) ]\n" - } - }, - { - "snpeff_cache": { - "description": "Path to snpeff cache\nStructure: [ val(meta), path(cache) ]\n" - } - } - ], - "authors": [ - "@maxulysse" - ], - "maintainers": [ - "@maxulysse" - ] - } - }, - { - "name": "utils_nextflow_pipeline", - "path": "subworkflows/nf-core/utils_nextflow_pipeline/meta.yml", - "type": "subworkflow", - "meta": { - "name": "UTILS_NEXTFLOW_PIPELINE", - "description": "Subworkflow with functionality that may be useful for any Nextflow pipeline", - "keywords": [ - "utility", - "pipeline", - "initialise", - "version" - ], - "components": [], - "input": [ - { - "print_version": { - "type": "boolean", - "description": "Print the version of the pipeline and exit\n" - } - }, - { - "dump_parameters": { - "type": "boolean", - "description": "Dump the parameters of the pipeline to a JSON file\n" - } - }, - { - "output_directory": { - "type": "directory", - "description": "Path to output dir to write JSON file to.", - "pattern": "results/" - } - }, - { - "check_conda_channel": { - "type": "boolean", - "description": "Check if the conda channel priority is correct.\n" - } - } - ], - "output": [ - { - "dummy_emit": { - "type": "boolean", - "description": "Dummy emit to make nf-core subworkflows lint happy\n" - } - } - ], - "authors": [ - "@adamrtalbot", - "@drpatelh" - ], - "maintainers": [ - "@adamrtalbot", - "@drpatelh", - "@maxulysse" - ] - }, - "pipelines": [ - { - "name": "abotyper", - "version": "dev" - }, - { - "name": "airrflow", - "version": "5.0.0" - }, - { - "name": "ampliseq", - "version": "2.17.0" - }, - { - "name": "bacass", - "version": "2.6.0" - }, - { - "name": "bamtofastq", - "version": "2.2.1" - }, - { - "name": "cellpainting", - "version": "dev" - }, - { - "name": "chipseq", - "version": "2.1.0" - }, - { - "name": "circrna", - "version": "dev" - }, - { - "name": "coproid", - "version": "2.0.1" - }, - { - "name": "createpanelrefs", - "version": "dev" - }, - { - "name": "createtaxdb", - "version": "3.0.0" - }, - { - "name": "crisprseq", - "version": "2.3.0" - }, - { - "name": "dartseq", - "version": "dev" - }, - { - "name": "datasync", - "version": "dev" - }, - { - "name": "deepmodeloptim", - "version": "dev" - }, - { - "name": "deepmutscan", - "version": "dev" - }, - { - "name": "demo", - "version": "1.1.0" - }, - { - "name": "demultiplex", - "version": "1.7.1" - }, - { - "name": "denovotranscript", - "version": "1.2.1" - }, - { - "name": "detaxizer", - "version": "1.3.0" - }, - { - "name": "differentialabundance", - "version": "1.5.0" - }, - { - "name": "diseasemodulediscovery", - "version": "dev" - }, - { - "name": "drop", - "version": "1.0.0" - }, - { - "name": "drugresponseeval", - "version": "1.2.0" - }, - { - "name": "epigenomesegmentation", - "version": "dev" - }, - { - "name": "epitopeprediction", - "version": "3.1.0" - }, - { - "name": "evexplorer", - "version": "dev" - }, - { - "name": "fastqrepair", - "version": "1.0.0" - }, - { - "name": "fastquorum", - "version": "1.2.0" - }, - { - "name": "fetchngs", - "version": "1.12.0" - }, - { - "name": "funcprofiler", - "version": "dev" - }, - { - "name": "funcscan", - "version": "3.0.0" - }, - { - "name": "genephylomodeler", - "version": "dev" - }, - { - "name": "genomeassembler", - "version": "1.1.0" - }, - { - "name": "genomeqc", - "version": "dev" - }, - { - "name": "genomicrelatedness", - "version": "dev" - }, - { - "name": "gwas", - "version": "dev" - }, - { - "name": "hlatyping", - "version": "2.2.0" - }, - { - "name": "isoseq", - "version": "2.0.0" - }, - { - "name": "lncpipe", - "version": "dev" - }, - { - "name": "lsmquant", - "version": "1.0.0" - }, - { - "name": "mag", - "version": "5.4.2" - }, - { - "name": "magmap", - "version": "1.0.0" - }, - { - "name": "mcmicro", - "version": "dev" - }, - { - "name": "meerpipe", - "version": "dev" - }, - { - "name": "metaboigniter", - "version": "2.0.1" - }, - { - "name": "metapep", - "version": "1.0.0" - }, - { - "name": "metatdenovo", - "version": "1.3.0" - }, - { - "name": "methylarray", - "version": "dev" - }, - { - "name": "methylong", - "version": "2.0.0" - }, - { - "name": "methylseq", - "version": "4.2.0" - }, - { - "name": "mhcquant", - "version": "3.2.0" - }, - { - "name": "mitodetect", - "version": "dev" - }, - { - "name": "molkart", - "version": "1.2.0" - }, - { - "name": "mspepid", - "version": "dev" - }, - { - "name": "multiplesequencealign", - "version": "1.1.1" - }, - { - "name": "nanostring", - "version": "1.3.3" - }, - { - "name": "nascent", - "version": "2.3.0" - }, - { - "name": "ncrnannotator", - "version": "dev" - }, - { - "name": "oncoanalyser", - "version": "2.3.0" - }, - { - "name": "pacsomatic", - "version": "dev" - }, - { - "name": "pacvar", - "version": "1.0.1" - }, - { - "name": "pairgenomealign", - "version": "2.2.3" - }, - { - "name": "pangenome", - "version": "1.1.3" - }, - { - "name": "panoramaseq", - "version": "dev" - }, - { - "name": "pathogensurveillance", - "version": "1.1.0" - }, - { - "name": "phaseimpute", - "version": "1.1.0" - }, - { - "name": "phyloplace", - "version": "2.0.0" - }, - { - "name": "pixelator", - "version": "4.0.0" - }, - { - "name": "proteinannotator", - "version": "1.1.0" - }, - { - "name": "proteinfamilies", - "version": "2.3.0" - }, - { - "name": "proteinfold", - "version": "2.0.0" - }, - { - "name": "rangeland", - "version": "1.0.0" - }, - { - "name": "raredisease", - "version": "3.0.0" - }, - { - "name": "rarevariantburden", - "version": "dev" - }, - { - "name": "readsimulator", - "version": "1.0.1" - }, - { - "name": "references", - "version": "0.1" - }, - { - "name": "reportho", - "version": "1.1.0" - }, - { - "name": "ribomsqc", - "version": "1.0.0" - }, - { - "name": "riboseq", - "version": "1.2.0" - }, - { - "name": "rnadnavar", - "version": "dev" - }, - { - "name": "rnafusion", - "version": "4.1.2" - }, - { - "name": "rnaseq", - "version": "3.26.0" - }, - { - "name": "sammyseq", - "version": "dev" - }, - { - "name": "sarek", - "version": "3.8.1" - }, - { - "name": "scdownstream", - "version": "dev" - }, - { - "name": "scnanoseq", - "version": "1.2.2" - }, - { - "name": "scrnaseq", - "version": "4.1.0" - }, - { - "name": "seqinspector", - "version": "1.0.1" - }, - { - "name": "seqsubmit", - "version": "dev" - }, - { - "name": "smrnaseq", - "version": "2.4.1" - }, - { - "name": "sopa", - "version": "dev" - }, - { - "name": "spatialvi", - "version": "dev" - }, - { - "name": "spatialxe", - "version": "dev" - }, - { - "name": "stableexpression", - "version": "dev" - }, - { - "name": "taxprofiler", - "version": "2.0.0" - }, - { - "name": "tbanalyzer", - "version": "dev" - }, - { - "name": "tfactivity", - "version": "dev" - }, - { - "name": "troughgraph", - "version": "dev" - }, - { - "name": "variantbenchmarking", - "version": "1.5.0" - }, - { - "name": "variantprioritization", - "version": "1.0.0" - }, - { - "name": "viralmetagenome", - "version": "1.1.1" - }, - { - "name": "viralrecon", - "version": "3.0.0" - } - ] - }, - { - "name": "utils_nfcore_pipeline", - "path": "subworkflows/nf-core/utils_nfcore_pipeline/meta.yml", - "type": "subworkflow", - "meta": { - "name": "UTILS_NFCORE_PIPELINE", - "description": "Subworkflow with utility functions specific to the nf-core pipeline template", - "keywords": [ - "utility", - "pipeline", - "initialise", - "version" - ], - "components": [], - "input": [ - { - "nextflow_cli_args": { - "type": "list", - "description": "Nextflow CLI positional arguments\n" - } - } - ], - "output": [ - { - "success": { - "type": "boolean", - "description": "Dummy output to indicate success\n" - } - } - ], - "authors": [ - "@adamrtalbot" - ], - "maintainers": [ - "@adamrtalbot", - "@maxulysse" - ] - }, - "pipelines": [ - { - "name": "abotyper", - "version": "dev" - }, - { - "name": "airrflow", - "version": "5.0.0" - }, - { - "name": "ampliseq", - "version": "2.17.0" - }, - { - "name": "bacass", - "version": "2.6.0" - }, - { - "name": "bamtofastq", - "version": "2.2.1" - }, - { - "name": "cellpainting", - "version": "dev" - }, - { - "name": "chipseq", - "version": "2.1.0" - }, - { - "name": "circrna", - "version": "dev" - }, - { - "name": "coproid", - "version": "2.0.1" - }, - { - "name": "createpanelrefs", - "version": "dev" - }, - { - "name": "createtaxdb", - "version": "3.0.0" - }, - { - "name": "crisprseq", - "version": "2.3.0" - }, - { - "name": "dartseq", - "version": "dev" - }, - { - "name": "datasync", - "version": "dev" - }, - { - "name": "deepmodeloptim", - "version": "dev" - }, - { - "name": "deepmutscan", - "version": "dev" - }, - { - "name": "demo", - "version": "1.1.0" - }, - { - "name": "demultiplex", - "version": "1.7.1" - }, - { - "name": "denovotranscript", - "version": "1.2.1" - }, - { - "name": "detaxizer", - "version": "1.3.0" - }, - { - "name": "differentialabundance", - "version": "1.5.0" - }, - { - "name": "diseasemodulediscovery", - "version": "dev" - }, - { - "name": "drop", - "version": "1.0.0" - }, - { - "name": "drugresponseeval", - "version": "1.2.0" - }, - { - "name": "epigenomesegmentation", - "version": "dev" - }, - { - "name": "epitopeprediction", - "version": "3.1.0" - }, - { - "name": "evexplorer", - "version": "dev" - }, - { - "name": "fastqrepair", - "version": "1.0.0" - }, - { - "name": "fastquorum", - "version": "1.2.0" - }, - { - "name": "fetchngs", - "version": "1.12.0" - }, - { - "name": "funcprofiler", - "version": "dev" - }, - { - "name": "funcscan", - "version": "3.0.0" - }, - { - "name": "genephylomodeler", - "version": "dev" - }, - { - "name": "genomeassembler", - "version": "1.1.0" - }, - { - "name": "genomeqc", - "version": "dev" - }, - { - "name": "genomicrelatedness", - "version": "dev" - }, - { - "name": "gwas", - "version": "dev" - }, - { - "name": "hlatyping", - "version": "2.2.0" - }, - { - "name": "isoseq", - "version": "2.0.0" - }, - { - "name": "lncpipe", - "version": "dev" - }, - { - "name": "lsmquant", - "version": "1.0.0" - }, - { - "name": "mag", - "version": "5.4.2" - }, - { - "name": "magmap", - "version": "1.0.0" - }, - { - "name": "mcmicro", - "version": "dev" - }, - { - "name": "meerpipe", - "version": "dev" - }, - { - "name": "metaboigniter", - "version": "2.0.1" - }, - { - "name": "metapep", - "version": "1.0.0" - }, - { - "name": "metatdenovo", - "version": "1.3.0" - }, - { - "name": "methylarray", - "version": "dev" - }, - { - "name": "methylong", - "version": "2.0.0" - }, - { - "name": "methylseq", - "version": "4.2.0" - }, - { - "name": "mhcquant", - "version": "3.2.0" - }, - { - "name": "mitodetect", - "version": "dev" - }, - { - "name": "molkart", - "version": "1.2.0" - }, - { - "name": "mspepid", - "version": "dev" - }, - { - "name": "multiplesequencealign", - "version": "1.1.1" - }, - { - "name": "nanostring", - "version": "1.3.3" - }, - { - "name": "nascent", - "version": "2.3.0" - }, - { - "name": "ncrnannotator", - "version": "dev" - }, - { - "name": "oncoanalyser", - "version": "2.3.0" - }, - { - "name": "pacsomatic", - "version": "dev" - }, - { - "name": "pacvar", - "version": "1.0.1" - }, - { - "name": "pairgenomealign", - "version": "2.2.3" - }, - { - "name": "pangenome", - "version": "1.1.3" - }, - { - "name": "panoramaseq", - "version": "dev" - }, - { - "name": "pathogensurveillance", - "version": "1.1.0" - }, - { - "name": "phaseimpute", - "version": "1.1.0" - }, - { - "name": "phyloplace", - "version": "2.0.0" - }, - { - "name": "pixelator", - "version": "4.0.0" - }, - { - "name": "proteinannotator", - "version": "1.1.0" - }, - { - "name": "proteinfamilies", - "version": "2.3.0" - }, - { - "name": "proteinfold", - "version": "2.0.0" - }, - { - "name": "rangeland", - "version": "1.0.0" - }, - { - "name": "raredisease", - "version": "3.0.0" - }, - { - "name": "rarevariantburden", - "version": "dev" - }, - { - "name": "readsimulator", - "version": "1.0.1" - }, - { - "name": "references", - "version": "0.1" - }, - { - "name": "reportho", - "version": "1.1.0" - }, - { - "name": "ribomsqc", - "version": "1.0.0" - }, - { - "name": "riboseq", - "version": "1.2.0" - }, - { - "name": "rnadnavar", - "version": "dev" - }, - { - "name": "rnafusion", - "version": "4.1.2" - }, - { - "name": "rnaseq", - "version": "3.26.0" - }, - { - "name": "sammyseq", - "version": "dev" - }, - { - "name": "sarek", - "version": "3.8.1" - }, - { - "name": "scdownstream", - "version": "dev" - }, - { - "name": "scnanoseq", - "version": "1.2.2" - }, - { - "name": "scrnaseq", - "version": "4.1.0" - }, - { - "name": "seqinspector", - "version": "1.0.1" - }, - { - "name": "seqsubmit", - "version": "dev" - }, - { - "name": "smrnaseq", - "version": "2.4.1" - }, - { - "name": "sopa", - "version": "dev" - }, - { - "name": "spatialvi", - "version": "dev" - }, - { - "name": "spatialxe", - "version": "dev" - }, - { - "name": "stableexpression", - "version": "dev" - }, - { - "name": "taxprofiler", - "version": "2.0.0" - }, - { - "name": "tbanalyzer", - "version": "dev" - }, - { - "name": "tfactivity", - "version": "dev" - }, - { - "name": "troughgraph", - "version": "dev" - }, - { - "name": "tumourevo", - "version": "dev" - }, - { - "name": "variantbenchmarking", - "version": "1.5.0" - }, - { - "name": "variantprioritization", - "version": "1.0.0" - }, - { - "name": "viralmetagenome", - "version": "1.1.1" - }, - { - "name": "viralrecon", - "version": "3.0.0" - } - ] - }, - { - "name": "utils_nfschema_plugin", - "path": "subworkflows/nf-core/utils_nfschema_plugin/meta.yml", - "type": "subworkflow", - "meta": { - "name": "utils_nfschema_plugin", - "description": "Run nf-schema to validate parameters and create a summary of changed parameters", - "keywords": [ - "validation", - "JSON schema", - "plugin", - "parameters", - "summary" - ], - "components": [], - "input": [ - { - "input_workflow": { - "type": "object", - "description": "The workflow object of the used pipeline.\nThis object contains meta data used to create the params summary log\n" - } - }, - { - "validate_params": { - "type": "boolean", - "description": "Validate the parameters and error if invalid." - } - }, - { - "parameters_schema": { - "type": "string", - "description": "Path to the parameters JSON schema.\nThis has to be the same as the schema given to the `validation.parametersSchema` config\noption. When this input is empty it will automatically use the configured schema or\n\"${projectDir}/nextflow_schema.json\" as default. The schema should not be given in this way\nfor meta pipelines.\n" - } - }, - { - "help": { - "type": "boolean, string", - "description": "Show the help message and exit. When a parameter name is given, show the help message for that parameter instead of the general help message.\n" - } - }, - { - "help_full": { - "type": "boolean", - "description": "Show the full help message and exit." - } - }, - { - "show_hidden": { - "type": "boolean", - "description": "Show hidden parameters in the help message." - } - }, - { - "before_text": { - "type": "string", - "description": "Text to show before the parameters summary and help message." - } - }, - { - "after_text": { - "type": "string", - "description": "Text to show after the parameters summary and help message." - } - }, - { - "command": { - "type": "string", - "description": "An example command to run the pipeline, to show in the help message and the summary." - } - }, - { - "cli_typecast": { - "type": "boolean", - "description": "Whether to apply typecasting to the parameters given via the CLI before validation.\nSet this to `null` to use the default behavior.\n" - } - } - ], - "output": [ - { - "dummy_emit": { - "type": "boolean", - "description": "Dummy emit to make nf-core subworkflows lint happy" - } - } - ], - "authors": [ - "@nvnieuwk" - ], - "maintainers": [ - "@nvnieuwk" - ] - }, - "pipelines": [ - { - "name": "abotyper", - "version": "dev" - }, - { - "name": "airrflow", - "version": "5.0.0" - }, - { - "name": "ampliseq", - "version": "2.17.0" - }, - { - "name": "bacass", - "version": "2.6.0" - }, - { - "name": "bamtofastq", - "version": "2.2.1" - }, - { - "name": "cellpainting", - "version": "dev" - }, - { - "name": "circrna", - "version": "dev" - }, - { - "name": "coproid", - "version": "2.0.1" - }, - { - "name": "createpanelrefs", - "version": "dev" - }, - { - "name": "createtaxdb", - "version": "3.0.0" - }, - { - "name": "crisprseq", - "version": "2.3.0" - }, - { - "name": "dartseq", - "version": "dev" - }, - { - "name": "datasync", - "version": "dev" - }, - { - "name": "deepmodeloptim", - "version": "dev" - }, - { - "name": "deepmutscan", - "version": "dev" - }, - { - "name": "demo", - "version": "1.1.0" - }, - { - "name": "demultiplex", - "version": "1.7.1" - }, - { - "name": "denovotranscript", - "version": "1.2.1" - }, - { - "name": "detaxizer", - "version": "1.3.0" - }, - { - "name": "diseasemodulediscovery", - "version": "dev" - }, - { - "name": "drop", - "version": "1.0.0" - }, - { - "name": "drugresponseeval", - "version": "1.2.0" - }, - { - "name": "epigenomesegmentation", - "version": "dev" - }, - { - "name": "epitopeprediction", - "version": "3.1.0" - }, - { - "name": "evexplorer", - "version": "dev" - }, - { - "name": "fastqrepair", - "version": "1.0.0" - }, - { - "name": "fastquorum", - "version": "1.2.0" - }, - { - "name": "funcprofiler", - "version": "dev" - }, - { - "name": "funcscan", - "version": "3.0.0" - }, - { - "name": "genephylomodeler", - "version": "dev" - }, - { - "name": "genomeassembler", - "version": "1.1.0" - }, - { - "name": "genomeqc", - "version": "dev" - }, - { - "name": "genomicrelatedness", - "version": "dev" - }, - { - "name": "gwas", - "version": "dev" - }, - { - "name": "hlatyping", - "version": "2.2.0" - }, - { - "name": "lncpipe", - "version": "dev" - }, - { - "name": "lsmquant", - "version": "1.0.0" - }, - { - "name": "mag", - "version": "5.4.2" - }, - { - "name": "magmap", - "version": "1.0.0" - }, - { - "name": "mcmicro", - "version": "dev" - }, - { - "name": "metapep", - "version": "1.0.0" - }, - { - "name": "metatdenovo", - "version": "1.3.0" - }, - { - "name": "methylarray", - "version": "dev" - }, - { - "name": "methylong", - "version": "2.0.0" - }, - { - "name": "methylseq", - "version": "4.2.0" - }, - { - "name": "mhcquant", - "version": "3.2.0" - }, - { - "name": "mitodetect", - "version": "dev" - }, - { - "name": "molkart", - "version": "1.2.0" - }, - { - "name": "mspepid", - "version": "dev" - }, - { - "name": "multiplesequencealign", - "version": "1.1.1" - }, - { - "name": "nanostring", - "version": "1.3.3" - }, - { - "name": "nascent", - "version": "2.3.0" - }, - { - "name": "ncrnannotator", - "version": "dev" - }, - { - "name": "oncoanalyser", - "version": "2.3.0" - }, - { - "name": "pacsomatic", - "version": "dev" - }, - { - "name": "pacvar", - "version": "1.0.1" - }, - { - "name": "pairgenomealign", - "version": "2.2.3" - }, - { - "name": "pangenome", - "version": "1.1.3" - }, - { - "name": "panoramaseq", - "version": "dev" - }, - { - "name": "pathogensurveillance", - "version": "1.1.0" - }, - { - "name": "phaseimpute", - "version": "1.1.0" - }, - { - "name": "phyloplace", - "version": "2.0.0" - }, - { - "name": "pixelator", - "version": "4.0.0" - }, - { - "name": "proteinannotator", - "version": "1.1.0" - }, - { - "name": "proteinfamilies", - "version": "2.3.0" - }, - { - "name": "proteinfold", - "version": "2.0.0" - }, - { - "name": "rangeland", - "version": "1.0.0" - }, - { - "name": "raredisease", - "version": "3.0.0" - }, - { - "name": "rarevariantburden", - "version": "dev" - }, - { - "name": "references", - "version": "0.1" - }, - { - "name": "reportho", - "version": "1.1.0" - }, - { - "name": "ribomsqc", - "version": "1.0.0" - }, - { - "name": "riboseq", - "version": "1.2.0" - }, - { - "name": "rnadnavar", - "version": "dev" - }, - { - "name": "rnafusion", - "version": "4.1.2" - }, - { - "name": "rnaseq", - "version": "3.26.0" - }, - { - "name": "sammyseq", - "version": "dev" - }, - { - "name": "sarek", - "version": "3.8.1" - }, - { - "name": "scdownstream", - "version": "dev" - }, - { - "name": "scnanoseq", - "version": "1.2.2" - }, - { - "name": "scrnaseq", - "version": "4.1.0" - }, - { - "name": "seqinspector", - "version": "1.0.1" - }, - { - "name": "seqsubmit", - "version": "dev" - }, - { - "name": "smrnaseq", - "version": "2.4.1" - }, - { - "name": "sopa", - "version": "dev" - }, - { - "name": "spatialvi", - "version": "dev" - }, - { - "name": "spatialxe", - "version": "dev" - }, - { - "name": "stableexpression", - "version": "dev" - }, - { - "name": "taxprofiler", - "version": "2.0.0" - }, - { - "name": "tbanalyzer", - "version": "dev" - }, - { - "name": "tfactivity", - "version": "dev" - }, - { - "name": "troughgraph", - "version": "dev" - }, - { - "name": "tumourevo", - "version": "dev" - }, - { - "name": "variantbenchmarking", - "version": "1.5.0" - }, - { - "name": "variantprioritization", - "version": "1.0.0" - }, - { - "name": "viralmetagenome", - "version": "1.1.1" - }, - { - "name": "viralrecon", - "version": "3.0.0" - } - ] - }, - { - "name": "utils_nfvalidation_plugin", - "path": "subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml", - "type": "subworkflow", - "meta": { - "name": "UTILS_NFVALIDATION_PLUGIN", - "description": "Use nf-validation to initiate and validate a pipeline", - "keywords": [ - "utility", - "pipeline", - "initialise", - "validation" - ], - "components": [], - "input": [ - { - "print_help": { - "type": "boolean", - "description": "Print help message and exit\n" - } - }, - { - "workflow_command": { - "type": "string", - "description": "The command to run the workflow e.g. \"nextflow run main.nf\"\n" - } - }, - { - "pre_help_text": { - "type": "string", - "description": "Text to print before the help message\n" - } - }, - { - "post_help_text": { - "type": "string", - "description": "Text to print after the help message\n" - } - }, - { - "validate_params": { - "type": "boolean", - "description": "Validate the parameters and error if invalid.\n" - } - }, - { - "schema_filename": { - "type": "string", - "description": "The filename of the schema to validate against.\n" - } - } - ], - "output": [ - { - "dummy_emit": { - "type": "boolean", - "description": "Dummy emit to make nf-core subworkflows lint happy\n" - } - } - ], - "authors": [ - "@adamrtalbot" - ], - "maintainers": [ - "@adamrtalbot", - "@maxulysse" - ] - }, - "pipelines": [ - { - "name": "chipseq", - "version": "2.1.0" - }, - { - "name": "differentialabundance", - "version": "1.5.0" - }, - { - "name": "fetchngs", - "version": "1.12.0" - }, - { - "name": "isoseq", - "version": "2.0.0" - }, - { - "name": "meerpipe", - "version": "dev" - }, - { - "name": "metaboigniter", - "version": "2.0.1" - }, - { - "name": "readsimulator", - "version": "1.0.1" - } - ] - }, - { - "name": "utils_references", - "path": "subworkflows/nf-core/utils_references/meta.yml", - "type": "subworkflow", - "meta": { - "name": "utils_references", - "description": "Functionality for dealing with references that may be useful for any Nextflow pipeline", - "keywords": [ - "utility", - "pipeline", - "references" - ], - "components": [], - "input": [], - "output": [], - "authors": [ - "@maxulysse" - ], - "maintainers": [ - "@maxulysse" - ] - } - }, - { - "name": "vcf_annotate_ensemblvep", - "path": "subworkflows/nf-core/vcf_annotate_ensemblvep/meta.yml", - "type": "subworkflow", - "meta": { - "name": "vcf_annotate_ensemblvep", - "description": "Perform annotation with ensemblvep and bgzip + tabix index the resulting VCF file", - "keywords": [ - "vcf", - "annotation", - "ensemblvep" - ], - "components": [ - "ensemblvep/vep", - "tabix/tabix" - ], - "input": [ - { - "ch_vcf": { - "description": "vcf file to annotate\nStructure: [ val(meta), path(vcf), [path(custom_file1), path(custom_file2)... (optional)] ]\n" - } - }, - { - "ch_fasta": { - "description": "Reference genome fasta file (optional)\nStructure: [ val(meta2), path(fasta) ]\n" - } - }, - { - "val_genome": { - "type": "string", - "description": "genome to use" - } - }, - { - "val_species": { - "type": "string", - "description": "species to use" - } - }, - { - "val_cache_version": { - "type": "integer", - "description": "cache version to use" - } - }, - { - "ch_cache": { - "description": "the root cache folder for ensemblvep (optional)\nStructure: [ val(meta3), path(cache) ]\n" - } - }, - { - "ch_extra_files": { - "description": "any extra files needed by plugins for ensemblvep (optional)\nStructure: [ path(file1), path(file2)... ]\n" - } - } - ], - "output": [ - { - "vcf_tbi": { - "description": "Compressed vcf file + tabix index\nStructure: [ val(meta), path(vcf), path(tbi) ]\n" - } - }, - { - "json": { - "description": "json file\nStructure: [ val(meta), path(json) ]\n" - } - }, - { - "tab": { - "description": "tab file\nStructure: [ val(meta), path(tab) ]\n" - } - }, - { - "reports": { - "type": "file", - "description": "html reports", - "pattern": "*.html" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@maxulysse", - "@matthdsm", - "@nvnieuwk" - ], - "maintainers": [ - "@maxulysse", - "@matthdsm", - "@nvnieuwk" - ] - }, - "pipelines": [ - { - "name": "rnadnavar", - "version": "dev" - }, - { - "name": "rnavar", - "version": "1.2.3" - } - ] - }, - { - "name": "vcf_annotate_ensemblvep_snpeff", - "path": "subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/meta.yml", - "type": "subworkflow", - "meta": { - "name": "vcf_annotate_ensemblvep_snpeff", - "description": "Perform annotation with ensemblvep and/or snpeff and bgzip + tabix index the resulting VCF file. This subworkflow uses the scatter-gather method to run VEP/snpEff in parallel to increase throughput. The input VCF is split into multiple smaller VCFs of fixed size, which are annotated separately and concatenated back together to a single output file per sample. Only VCF/BCF outputs are currently supported.\n", - "keywords": [ - "vcf", - "annotation", - "ensemblvep", - "snpeff" - ], - "components": [ - "ensemblvep/download", - "ensemblvep/vep", - "snpeff/download", - "snpeff/snpeff", - "htslib/bgziptabix", - "bcftools/pluginscatter", - "bcftools/concat", - "bcftools/sort" - ], - "input": [ - { - "ch_vcf": { - "description": "vcf file to annotate\nStructure: [ val(meta), path(vcf), path(tbi) ]\n" - } - }, - { - "ch_fasta": { - "description": "Reference genome fasta file (optional)\nStructure: [ val(meta2), path(fasta) ]\n" - } - }, - { - "val_vep_genome": { - "type": "string", - "description": "genome to use for ensemblvep" - } - }, - { - "val_vep_species": { - "type": "string", - "description": "species to use for ensemblvep" - } - }, - { - "val_vep_cache_version": { - "type": "integer", - "description": "cache version to use for ensemblvep" - } - }, - { - "ch_vep_cache": { - "description": "the root cache folder for ensemblvep (optional)\nStructure: [ path(cache) ]\n" - } - }, - { - "ch_vep_extra_files": { - "description": "any extra files needed by plugins for ensemblvep (optional)\nStructure: [ path(file1), path(file2)... ]\n" - } - }, - { - "val_snpeff_db": { - "type": "string", - "description": "database to use for snpeff, usually consists of the genome and the database version\ne.g. WBcel235.99\n" - } - }, - { - "ch_snpeff_cache": { - "description": "the root cache folder for snpeff (optional)\nStructure: [ path(cache) ]\n" - } - }, - { - "val_tools_to_use": { - "type": "list", - "description": "The tools to use. Options => '[\"ensemblvep\", \"snpeff\"]'" - } - }, - { - "val_sites_per_chunk": { - "type": "integer", - "description": "The amount of variants per scattered VCF.\nSet this value to `null`, `[]` or `false` to disable scattering.\n" - } - } - ], - "output": [ - { - "vcf_tbi": { - "description": "Compressed vcf file + tabix index\nStructure: [ val(meta), path(vcf), path(tbi) ]\n" - } - }, - { - "vep_reports": { - "type": "file", - "description": "html reports generated by Ensembl VEP", - "pattern": "*.html" - } - }, - { - "snpeff_reports": { - "description": "csv reports generated by snpeff\nStructure: [ val(meta), path(csv) ]\n" - } - }, - { - "snpeff_html": { - "description": "html reports generated by snpeff\nStructure: [ val(meta), path(html) ]\n" - } - }, - { - "snpeff_genes": { - "description": "txt (tab separated) file having counts of the number of variants\naffecting each transcript and gene\nStructure: [ val(meta), path(txt) ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@maxulysse", - "@matthdsm", - "@nvnieuwk" - ], - "maintainers": [ - "@maxulysse", - "@matthdsm", - "@nvnieuwk" - ] - } - }, - { - "name": "vcf_annotate_snpeff", - "path": "subworkflows/nf-core/vcf_annotate_snpeff/meta.yml", - "type": "subworkflow", - "meta": { - "name": "vcf_annotate_snpeff", - "description": "Perform annotation with snpEff and bgzip + tabix index the resulting VCF file", - "keywords": [ - "vcf", - "annotation", - "snpeff" - ], - "components": [ - "snpeff", - "snpeff/snpeff", - "htslib/bgziptabix" - ], - "input": [ - { - "ch_vcf": { - "description": "vcf file\nStructure: [ val(meta), path(vcf) ]\n" - } - }, - { - "val_snpeff_db": { - "type": "string", - "description": "db version to use" - } - }, - { - "ch_snpeff_cache": { - "description": "path to root cache folder for snpEff (optional)\nStructure: [ path(cache) ]\n" - } - } - ], - "output": [ - { - "vcf_tbi": { - "description": "Compressed vcf file + tabix index\nStructure: [ val(meta), path(vcf), path(tbi) ]\n" - } - }, - { - "reports": { - "description": "html reports\nStructure: [ path(html) ]\n" - } - }, - { - "summary": { - "description": "html reports\nStructure: [ path(csv) ]\n" - } - }, - { - "genes_txt": { - "description": "html reports\nStructure: [ path(txt) ]\n" - } - }, - { - "versions": { - "description": "Files containing software versions\nStructure: [ path(versions.yml) ]\n" - } - } - ], - "authors": [ - "@maxulysse" - ], - "maintainers": [ - "@maxulysse" - ] - }, - "pipelines": [ - { - "name": "rnavar", - "version": "1.2.3" - }, - { - "name": "sarek", - "version": "3.8.1" - } - ] - }, - { - "name": "vcf_extract_relate_somalier", - "path": "subworkflows/nf-core/vcf_extract_relate_somalier/meta.yml", - "type": "subworkflow", - "meta": { - "name": "vcf_extract_relate_somalier", - "description": "Perform somalier extraction and relate stats on input VCFs", - "keywords": [ - "somalier", - "stats", - "vcf", - "ped", - "relatedness" - ], - "components": [ - "htslib/bgziptabix", - "somalier/extract", - "somalier/relate" - ], - "input": [ - { - "ch_vcfs": { - "description": "The input VCFs to perform the stats on, optionally with their indices.\nThis channel can also contain the number of samples in the same family/group\nto check relatedness. This is advised to add as it can improve the efficiency of your pipeline\nStructure: [ val(meta), path(vcf), path(tbi), val(count) ]\n" - } - }, - { - "ch_fasta": { - "description": "The reference FASTA used to create the VCF files\nStructure: [ path(fasta) ]\n" - } - }, - { - "ch_fasta_fai": { - "description": "The index of the reference FASTA\nStructure: [ path(fasta_fai) ]\n" - } - }, - { - "ch_somalier_sites": { - "description": "A VCF containing the common sites for Somalier\nStructure: [ path(somalier_sites_vcf) ]\n" - } - }, - { - "ch_peds": { - "description": "A channel containing an optional PED file for the corresponding families. This channel has to be given, but can be like `[meta, []]`.\nWhen you don't want to use a PED file, you must supply a channel\ncontaining the meta and an empty value (`[]`) instead of a PED\nStructure: [ val(meta), path(ped) ]\n" - } - }, - { - "ch_sample_groups": { - "description": "Optional - A text file describing how the samples should be grouped\nStructure: [ path(txt) ]\n" - } - }, - { - "val_common_id": { - "description": "Optional - A common identifier in the meta map.\nThis will be used to determine which VCFs should be used in somalier_relate.\nThis value should be given when using single sample VCFs\n" - } - } - ], - "output": [ - { - "extract": { - "description": "The extract file created with Somalier extract\nStructure: [ val(meta), path(extract) ]\n" - } - }, - { - "html": { - "description": "An HTML file containing an interactive graph on the relatedness of the samples\nStructure: [ val(meta), path(html) ]\n" - } - }, - { - "pairs_tsv": { - "description": "A TSV file detailing the relatedness between pairs of samples\nStructure: [ val(meta), path(tsv) ]\n" - } - }, - { - "samples_tsv": { - "description": "A TSV file detailing the relatedness between all samples with the same meta\nStructure: [ val(meta), path(tsv) ]\n" - } - } - ], - "authors": [ - "@nvnieuwk" - ], - "maintainers": [ - "@nvnieuwk" - ] - } - }, - { - "name": "vcf_filter_bcftools_ensemblvep", - "path": "subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/meta.yml", - "type": "subworkflow", - "meta": { - "name": "vcf_filter_bcftools_ensemblvep", - "description": "Filter VCF file with bcftools and filter_vep", - "keywords": [ - "filter", - "vcf", - "bcftools", - "filter_vep" - ], - "components": [ - "bcftools/view", - "ensemblvep/filtervep", - "htslib/bgziptabix" - ], - "input": [ - { - "ch_vcf": { - "type": "file", - "description": "The input channel containing the VCF files\nStructure: [ val(meta), path(vcf) ]\n", - "pattern": "*.{vcf/vcf.gz}" - } - }, - { - "ch_filter_vep_file": { - "type": "file", - "description": "File to pass to filter_vep, containing e.g. HGNC IDs to filter on\nStructure: [ val(meta), path(txt) ]\n" - } - }, - { - "filter_with_bcftools": { - "type": "boolean", - "description": "Whether to filter the VCF file with bcftools before passing it to filter_vep\n" - } - }, - { - "filter_with_filter_vep": { - "type": "boolean", - "description": "Whether to filter the VCF file with filter_vep\n" - } - } - ], - "output": [ - { - "vcf": { - "type": "file", - "description": "Channel containing VCF files\nStructure: [ val(meta), path(bam) ]\n", - "pattern": "*.vcf.gz" - } - }, - { - "bai": { - "type": "file", - "description": "Channel containing indexed VCF (TBI) files\nStructure: [ val(meta), path(bai) ]\n", - "pattern": "*.tbi" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions\nStructure: [ path(versions.yml) ]\n", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@fellen31" - ], - "maintainers": [ - "@fellen31", - "@ramprasadn" - ] - }, - "pipelines": [ - { - "name": "raredisease", - "version": "3.0.0" - } - ] - }, - { - "name": "vcf_gather_bcftools", - "path": "subworkflows/nf-core/vcf_gather_bcftools/meta.yml", - "type": "subworkflow", - "meta": { - "name": "vcf_gather_bcftools", - "description": "Concatenate several VCF files using bcftools concat.\nAn additional option can be given to sort the concatenated VCF.\n", - "keywords": [ - "concat", - "vcf", - "gather", - "sort", - "bcftools" - ], - "components": [ - "bcftools/sort", - "bcftools/concat", - "htslib/bgziptabix" - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing at least a common field for each VCF that needs to be merged\ne.g. [ id:'test.001', common_meta:'test' ]\n" - } - }, - { - "ch_vcfs": { - "type": "file(s)", - "description": "VCF files and their indices that should be concatenated as well as the expected number of vcf\nStructure: [ meta, vcf, tbi, count ]\n" - } - }, - { - "arr_common_meta": { - "type": "array", - "description": "OPTIONAL:\nA string array of the common meta keys to use to group the vcfs.\nPlease make sure all VCFs that need to be concatenated have the same value in the\nthe meta fields specified - the subworkflow will error if a required key is missing from a meta map.\n" - } - }, - { - "sort": { - "type": "boolean", - "description": "Whether or not to sort the output VCF,\nthis can be useful if this subworkflow isn't used in a scatter/gather workflow\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "The concatenated (and possible sorted) VCF file\nStructure: [ meta, vcf ]\n", - "pattern": "*.vcf.gz" - } - }, - { - "index": { - "type": "file", - "description": "The indices of the output VCFs\nStructure: [ meta, [tbi, csi] ]\n", - "pattern": "*.vcf.gz.{tbi,csi}" - } - }, - { - "vcf_index": { - "type": "file", - "description": "Aggregated channel with the vcf and indices\nStructure: [ meta, vcf, [tbi, csi] ]\n" - } - } - ], - "authors": [ - "@nvnieuwk" - ], - "maintainers": [ - "@nvnieuwk" - ] - } - }, - { - "name": "vcf_impute_beagle5", - "path": "subworkflows/nf-core/vcf_impute_beagle5/meta.yml", - "type": "subworkflow", - "meta": { - "name": "VCF_IMPUTE_BEAGLE5", - "description": "Subworkflow to impute VCF files using BEAGLE5 software. The subworkflow\ntakes VCF files, phased reference panel, genetic maps and chunks region to perform imputation\nand outputs phased and imputed VCF files.\nMeta map of all channels, except ch_input, will be used to perform joint operations.\n\"regionout\" and \"regionsize\" keys will be added to the meta map to distinguish the different\nfile before ligation and therefore should not be used.\n", - "keywords": [ - "VCF", - "imputation", - "beagle5", - "phasing" - ], - "components": [ - "beagle5/beagle", - "bcftools/index", - "bcftools/view", - "glimpse2/ligate" - ], - "input": [ - { - "ch_input": { - "description": "Channel with input data", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata map containing sample information\n" - } - }, - { - "vcf": { - "type": "file", - "description": "Input VCF files", - "pattern": "*.{vcf,bcf}{.gz}?" - } - }, - { - "index": { - "type": "file", - "description": "Input index file", - "pattern": "*.{tbi,csi}" - } - } - ] - } - }, - { - "ch_panel": { - "description": "Channel with phased reference panel data", - "structure": [ + "pipelines": [ + { + "name": "abotyper", + "version": "dev" + }, + { + "name": "airrflow", + "version": "5.0.0" + }, + { + "name": "ampliseq", + "version": "2.17.0" + }, + { + "name": "bacass", + "version": "2.6.0" + }, + { + "name": "bamtofastq", + "version": "2.2.1" + }, + { + "name": "cellpainting", + "version": "dev" + }, + { + "name": "circrna", + "version": "dev" + }, + { + "name": "coproid", + "version": "2.0.1" + }, + { + "name": "createpanelrefs", + "version": "dev" + }, + { + "name": "createtaxdb", + "version": "3.0.0" + }, + { + "name": "crisprseq", + "version": "2.3.0" + }, + { + "name": "dartseq", + "version": "dev" + }, + { + "name": "datasync", + "version": "dev" + }, + { + "name": "deepmodeloptim", + "version": "dev" + }, + { + "name": "deepmutscan", + "version": "dev" + }, + { + "name": "demo", + "version": "1.1.0" + }, { - "meta": { - "type": "map", - "description": "Metadata map that will be combined with the input data map\n" - } + "name": "demultiplex", + "version": "1.7.1" }, { - "vcf": { - "type": "file", - "description": "Reference panel VCF files by chromosomes", - "pattern": "*.{vcf,bcf,vcf.gz}" - } + "name": "denovotranscript", + "version": "1.2.1" }, { - "index": { - "type": "file", - "description": "Reference panel VCF index files", - "pattern": "*.{tbi,csi}" - } - } - ] - } - }, - { - "ch_chunks": { - "description": "Channel containing the region to impute", - "structure": [ + "name": "detaxizer", + "version": "1.3.0" + }, { - "meta": { - "type": "map", - "description": "Metadata map containing chromosome information\n" - } + "name": "diseasemodulediscovery", + "version": "dev" }, { - "regionout": null, - "type": "string", - "description": "Region to perform the phasing on", - "pattern": "[chr]+[0-9]+:[0-9]+-[0-9]+" - } - ] - } - }, - { - "ch_map": { - "description": "Channel with genetic map data", - "structure": [ + "name": "drop", + "version": "1.0.0" + }, { - "meta": { - "type": "map", - "description": "Metadata map containing chromosome information\n" - } + "name": "drugresponseeval", + "version": "1.2.0" }, { - "map": { - "type": "file", - "description": "Plink format genetic map files", - "pattern": "*.map" - } - } - ] - } - } - ], - "output": [ - { - "vcf_index": { - "description": "Channel with imputed and phased VCF files", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata map of the target input file combined with the reference panel map.\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF imputed and phased file by sample", - "pattern": "*.{vcf,bcf,vcf.gz}" - } - }, - { - "index": { - "type": "file", - "description": "VCF index file", - "pattern": "*.{tbi,csi}" - } - } - ] - } - } - ], - "authors": [ - "@LouisLeNezet", - "@gichas" - ], - "maintainers": [ - "@LouisLeNezet", - "@gichas" - ] - } - }, - { - "name": "vcf_impute_glimpse", - "path": "subworkflows/nf-core/vcf_impute_glimpse/meta.yml", - "type": "subworkflow", - "meta": { - "name": "vcf_impute_glimpse", - "description": "Impute VCF/BCF files with Glimpse", - "keywords": [ - "glimpse", - "chunk", - "phase", - "ligate" - ], - "components": [ - "glimpse/chunk", - "glimpse/phase", - "glimpse/ligate", - "bcftools/index" - ], - "input": [ - { - "ch_vcf": { - "description": "Channel with target VCF files", - "structure": [ - { - "meta": null, - "type": "map", - "description": "Metadata map" - }, - { - "vcf": null, - "type": "file", - "description": "VCF file", - "pattern": "*.{vcf,bcf,vcf.gz}" - }, - { - "index": null, - "type": "file", - "description": "VCF index file", - "pattern": "*.{tbi,csi}" - }, - { - "infos": null, - "type": "file", - "description": "File containing ploidy information of each sample\n", - "pattern": "*.{txt, tsv}" - } - ] - } - }, - { - "ch_ref": { - "description": "Channel with reference phased VCF files", - "structure": [ + "name": "epigenomesegmentation", + "version": "dev" + }, { - "meta": null, - "type": "map", - "description": "Metadata map" + "name": "epitopeprediction", + "version": "3.1.0" }, { - "vcf": null, - "type": "file", - "description": "VCF file", - "pattern": "*.{vcf,bcf,vcf.gz}" + "name": "evexplorer", + "version": "dev" }, { - "index": null, - "type": "file", - "description": "VCF index file", - "pattern": "*.{tbi,csi}" + "name": "fastqrepair", + "version": "1.0.0" }, { - "region": null, - "type": "string", - "description": "Region to perform chunking on", - "pattern": "[chr]+[0-9]+:[0-9]+-[0-9]+" - } - ] - } - }, - { - "ch_chunks": { - "description": "Channel with chunks data", - "structure": [ + "name": "fastquorum", + "version": "1.2.0" + }, { - "meta": null, - "type": "map", - "description": "Metadata map that will be combined with the input data map" + "name": "funcprofiler", + "version": "dev" }, { - "regionin": null, - "type": "string", - "description": "Chunk region without buffer", - "pattern": "[chr]+[0-9]+:[0-9]+-[0-9]+" + "name": "funcscan", + "version": "3.0.0" }, { - "regionout": null, - "type": "string", - "description": "Chunk region with buffer", - "pattern": "[chr]+[0-9]+:[0-9]+-[0-9]+" - } - ] - } - }, - { - "ch_map": { - "description": "Channel with genetic map data (optional)", - "structure": [ + "name": "genephylomodeler", + "version": "dev" + }, { - "meta": null, - "type": "map", - "description": "Metadata map" + "name": "genomeassembler", + "version": "1.1.0" }, { - "map": null, - "type": "file", - "description": "Map file in GLIMPSE format", - "pattern": "*.map" - } - ] - } - }, - { - "chunk": { - "type": "boolean", - "description": "Whether to perform chunking of the input data before imputation." - } - } - ], - "output": [ - { - "chunks": { - "type": "file", - "description": "Tab delimited output txt file containing buffer and imputation regions.\nStructure: [meta, txt]\n" - } - }, - { - "merged_variants": { - "type": "file", - "description": "Output phased VCF/BCF file for the merged regions.\nPhased information (HS field) is updated accordingly for the full region.\nStructure: [ val(meta), bcf ]\n" - } - }, - { - "merged_variants_index": { - "type": "file", - "description": "Index output of phased VCF/BCF file for the merged regions.\nStructure: [ val(meta), csi ]\n" - } - } - ], - "authors": [ - "@LouisLeNezet" - ], - "maintainers": [ - "@LouisLeNezet" - ] - } - }, - { - "name": "vcf_impute_minimac4", - "path": "subworkflows/nf-core/vcf_impute_minimac4/meta.yml", - "type": "subworkflow", - "meta": { - "name": "VCF_IMPUTE_MINIMAC4", - "description": "Subworkflow to impute VCF files using MINIMAC4 software. The subworkflow\ntakes VCF files, phased reference panel, and genetic maps to perform imputation\nand outputs phased and imputed VCF files.\nMeta map of all channels, except ch_input, will be used to perform joint operations.\n\"regionout\" key will be added to the meta map to distinguish the different file\nbefore ligation and therefore should not be used.\n", - "keywords": [ - "VCF", - "imputation", - "minimac4", - "phasing", - "MSAV" - ], - "components": [ - "minimac4/compressref", - "minimac4/impute", - "bcftools/index", - "glimpse2/ligate" - ], - "input": [ - { - "ch_input": { - "description": "Channel with input data", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata map containing sample information\n" - } - }, - { - "vcf": { - "type": "file", - "description": "Input VCF files", - "pattern": "*.{vcf,bcf,vcf.gz}" - } - }, - { - "index": { - "type": "file", - "description": "Input index file", - "pattern": "*.{tbi,csi}" - } - } - ] - } - }, - { - "ch_panel": { - "description": "Channel with phased reference panel data", - "structure": [ + "name": "genomeqc", + "version": "dev" + }, { - "meta": { - "type": "map", - "description": "Metadata map that will be combined with the input data map\n" - } + "name": "genomicrelatedness", + "version": "dev" }, { - "vcf": { - "type": "file", - "description": "Reference panel VCF files by chromosomes", - "pattern": "*.{vcf,bcf,vcf.gz}" - } + "name": "gwas", + "version": "dev" }, { - "index": { - "type": "file", - "description": "Reference panel VCF index files", - "pattern": "*.{tbi,csi}" - } - } - ] - } - }, - { - "ch_posfile": { - "description": "Channel with variants position to impute", - "structure": [ + "name": "hlatyping", + "version": "2.2.0" + }, { - "meta": { - "type": "map", - "description": "Metadata map containing chromosome information\n" - } + "name": "lncpipe", + "version": "dev" }, { - "sites_vcf": { - "type": "file", - "descrition": "VCF/BCF file containing position to impute\n" - } + "name": "lsmquant", + "version": "1.0.0" }, { - "sites_index": { - "type": "file", - "description": "CSI|TBI index file of the sites to impute\n" - } - } - ] - } - }, - { - "ch_chunks": { - "description": "Channel containing the region to impute", - "structure": [ + "name": "mag", + "version": "5.4.2" + }, { - "meta": { - "type": "map", - "description": "Metadata map containing chromosome information\n" - } + "name": "magmap", + "version": "1.0.0" }, { - "regionout": null, - "type": "string", - "description": "Region to perform the phasing on", - "pattern": "[chr]+[0-9]+:[0-9]+-[0-9]+" - } - ] - } - }, - { - "ch_map": { - "description": "Channel with genetic map data", - "structure": [ + "name": "mcmicro", + "version": "dev" + }, { - "meta": { - "type": "map", - "description": "Metadata map containing chromosome information\n" - } + "name": "metapep", + "version": "1.0.0" }, { - "map": { - "type": "file", - "description": "Minimac format genetic map files", - "pattern": "*.map" - } - } - ] - } - } - ], - "output": [ - { - "vcf_index": { - "description": "Channel with imputed and phased VCF files", - "structure": [ - { - "meta": { - "type": "map", - "description": "Metadata map of the target input file combined with the reference panel map.\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF imputed and phased file by sample", - "pattern": "*.{vcf,bcf,vcf.gz}" - } - }, - { - "index": { - "type": "file", - "description": "VCF index file", - "pattern": "*.{tbi,csi}" - } - } - ] - } - } - ], - "authors": [ - "@LouisLeNezet", - "@gichas" - ], - "maintainers": [ - "@LouisLeNezet", - "@gichas" - ] - } - }, - { - "name": "vcf_phase_shapeit5", - "path": "subworkflows/nf-core/vcf_phase_shapeit5/meta.yml", - "type": "subworkflow", - "meta": { - "name": "VCF_PHASE_SHAPEIT5", - "description": "Subworkflow to phase a reference panel VCF file using SHAPEIT5.\nThe panel is first chunked by chromosome by glimpse2/chunk,\nthen genotypes are phased with shapeit5/phasecommon and\nfinally the chunks are merged back together by shapeit5/ligate by chromosomes.\nMeta map of all channels will be used to perform joint operations.\n\"regionout\" key will be added to the meta map to distinguish the different file\nbefore ligation and therefore should not be used.\n", - "keywords": [ - "VCF", - "phase", - "shapeit5", - "haplotype" - ], - "components": [ - "glimpse2/chunk", - "shapeit5/phasecommon", - "shapeit5/ligate", - "bcftools/index" - ], - "input": [ - { - "ch_vcf": { - "description": "Channel with target VCF files", - "structure": [ - { - "meta": null, - "type": "map", - "description": "Metadata map" - }, - { - "vcf": null, - "type": "file", - "description": "VCF file", - "pattern": "*.{vcf,bcf,vcf.gz}" - }, - { - "index": null, - "type": "file", - "description": "VCF index file", - "pattern": "*.{tbi,csi}" - }, - { - "pedigree": null, - "type": "file", - "description": { - "Pedigree information in the following format": "offspring father mother." - }, - "pattern": "*.{txt, tsv}" - }, - { - "region": null, - "type": "string", - "description": "Region to perform the chunking on for GLIMPSE2_chunk", - "pattern": "[chr]+[0-9]+:[0-9]+-[0-9]+" - } - ] - } - }, - { - "ch_chunks": { - "description": "Channel with region data", - "structure": [ + "name": "metatdenovo", + "version": "1.3.0" + }, { - "meta": null, - "type": "map", - "description": "Metadata map that will be combined with the input data map" + "name": "methylarray", + "version": "dev" }, { - "regionout": null, - "type": "string", - "description": "Region to perform the phasing on", - "pattern": "[chr]+[0-9]+:[0-9]+-[0-9]+" - } - ] - } - }, - { - "ch_ref": { - "description": "Channel with reference phased VCF files", - "structure": [ + "name": "methylong", + "version": "2.0.0" + }, { - "meta": null, - "type": "map", - "description": "Metadata map" + "name": "methylseq", + "version": "4.2.0" }, { - "vcf": null, - "type": "file", - "description": "VCF file", - "pattern": "*.{vcf,bcf,vcf.gz}" + "name": "mhcquant", + "version": "3.2.0" }, { - "index": null, - "type": "file", - "description": "VCF index file", - "pattern": "*.{tbi,csi}" - } - ] - } - }, - { - "ch_scaffold": { - "description": "Channel with reference scaffold VCF files", - "structure": [ + "name": "mitodetect", + "version": "dev" + }, + { + "name": "molkart", + "version": "1.2.0" + }, + { + "name": "mspepid", + "version": "dev" + }, + { + "name": "multiplesequencealign", + "version": "1.1.1" + }, + { + "name": "nanostring", + "version": "1.3.3" + }, + { + "name": "nascent", + "version": "2.3.0" + }, + { + "name": "ncrnannotator", + "version": "dev" + }, + { + "name": "oncoanalyser", + "version": "2.3.0" + }, + { + "name": "pacsomatic", + "version": "dev" + }, + { + "name": "pacvar", + "version": "1.0.1" + }, + { + "name": "pairgenomealign", + "version": "2.2.3" + }, + { + "name": "pangenome", + "version": "1.1.3" + }, + { + "name": "panoramaseq", + "version": "dev" + }, + { + "name": "pathogensurveillance", + "version": "1.1.0" + }, + { + "name": "phaseimpute", + "version": "1.1.0" + }, + { + "name": "phyloplace", + "version": "2.0.0" + }, + { + "name": "pixelator", + "version": "4.0.0" + }, + { + "name": "proteinannotator", + "version": "1.1.0" + }, + { + "name": "proteinfamilies", + "version": "2.3.0" + }, + { + "name": "proteinfold", + "version": "2.0.0" + }, + { + "name": "rangeland", + "version": "1.0.0" + }, + { + "name": "raredisease", + "version": "3.0.0" + }, + { + "name": "rarevariantburden", + "version": "dev" + }, + { + "name": "references", + "version": "0.1" + }, + { + "name": "reportho", + "version": "1.1.0" + }, + { + "name": "ribomsqc", + "version": "1.0.0" + }, + { + "name": "riboseq", + "version": "1.2.0" + }, + { + "name": "rnadnavar", + "version": "dev" + }, + { + "name": "rnafusion", + "version": "4.1.2" + }, + { + "name": "rnaseq", + "version": "3.26.0" + }, + { + "name": "sammyseq", + "version": "dev" + }, + { + "name": "sarek", + "version": "3.8.1" + }, + { + "name": "scdownstream", + "version": "dev" + }, + { + "name": "scnanoseq", + "version": "1.2.2" + }, + { + "name": "scrnaseq", + "version": "4.1.0" + }, + { + "name": "seqinspector", + "version": "1.0.1" + }, + { + "name": "seqsubmit", + "version": "dev" + }, + { + "name": "smrnaseq", + "version": "2.4.1" + }, + { + "name": "sopa", + "version": "dev" + }, + { + "name": "spatialvi", + "version": "dev" + }, + { + "name": "spatialxe", + "version": "dev" + }, + { + "name": "stableexpression", + "version": "dev" + }, { - "meta": null, - "type": "map", - "description": "Metadata map" + "name": "taxprofiler", + "version": "2.0.0" }, { - "vcf": null, - "type": "file", - "description": "VCF file", - "pattern": "*.{vcf,bcf,vcf.gz}" + "name": "tbanalyzer", + "version": "dev" }, { - "index": null, - "type": "file", - "description": "VCF index file", - "pattern": "*.{tbi,csi}" + "name": "tfactivity", + "version": "dev" + }, + { + "name": "troughgraph", + "version": "dev" + }, + { + "name": "tumourevo", + "version": "dev" + }, + { + "name": "variantbenchmarking", + "version": "1.5.0" + }, + { + "name": "variantprioritization", + "version": "1.0.0" + }, + { + "name": "viralmetagenome", + "version": "1.1.1" + }, + { + "name": "viralrecon", + "version": "3.0.0" } - ] - } - }, - { - "ch_map": { - "description": "Channel with genetic map data (optional)", - "structure": [ + ] + }, + { + "name": "utils_nfvalidation_plugin", + "path": "subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml", + "type": "subworkflow", + "meta": { + "name": "UTILS_NFVALIDATION_PLUGIN", + "description": "Use nf-validation to initiate and validate a pipeline", + "keywords": ["utility", "pipeline", "initialise", "validation"], + "components": [], + "input": [ + { + "print_help": { + "type": "boolean", + "description": "Print help message and exit\n" + } + }, + { + "workflow_command": { + "type": "string", + "description": "The command to run the workflow e.g. \"nextflow run main.nf\"\n" + } + }, + { + "pre_help_text": { + "type": "string", + "description": "Text to print before the help message\n" + } + }, + { + "post_help_text": { + "type": "string", + "description": "Text to print after the help message\n" + } + }, + { + "validate_params": { + "type": "boolean", + "description": "Validate the parameters and error if invalid.\n" + } + }, + { + "schema_filename": { + "type": "string", + "description": "The filename of the schema to validate against.\n" + } + } + ], + "output": [ + { + "dummy_emit": { + "type": "boolean", + "description": "Dummy emit to make nf-core subworkflows lint happy\n" + } + } + ], + "authors": ["@adamrtalbot"], + "maintainers": ["@adamrtalbot", "@maxulysse"] + }, + "pipelines": [ + { + "name": "chipseq", + "version": "2.1.0" + }, + { + "name": "differentialabundance", + "version": "1.5.0" + }, + { + "name": "fetchngs", + "version": "1.12.0" + }, + { + "name": "isoseq", + "version": "2.0.0" + }, { - "meta": null, - "type": "map", - "description": "Metadata map" + "name": "meerpipe", + "version": "dev" }, { - "map": null, - "type": "file", - "description": "Map file in GLIMPSE format", - "pattern": "*.map" + "name": "metaboigniter", + "version": "2.0.1" + }, + { + "name": "readsimulator", + "version": "1.0.1" } - ] - } - }, - { - "chunk": { - "type": "boolean", - "description": "Whether to perform chunking of the input data before imputation." - } - }, - { - "chunk_model": { - "description": "Chunk model for GLIMPSE2_chunk", - "type": "string", - "enum": [ - "recursive", - "sequential" - ] + ] + }, + { + "name": "utils_references", + "path": "subworkflows/nf-core/utils_references/meta.yml", + "type": "subworkflow", + "meta": { + "name": "utils_references", + "description": "Functionality for dealing with references that may be useful for any Nextflow pipeline", + "keywords": ["utility", "pipeline", "references"], + "components": [], + "input": [], + "output": [], + "authors": ["@maxulysse"], + "maintainers": ["@maxulysse"] } - } - ], - "output": [ - { - "chunks": { - "description": "Channel with chunks regions", - "structure": [ + }, + { + "name": "vcf_annotate_ensemblvep", + "path": "subworkflows/nf-core/vcf_annotate_ensemblvep/meta.yml", + "type": "subworkflow", + "meta": { + "name": "vcf_annotate_ensemblvep", + "description": "Perform annotation with ensemblvep and bgzip + tabix index the resulting VCF file", + "keywords": ["vcf", "annotation", "ensemblvep"], + "components": ["ensemblvep/vep", "tabix/tabix"], + "input": [ + { + "ch_vcf": { + "description": "vcf file to annotate\nStructure: [ val(meta), path(vcf), [path(custom_file1), path(custom_file2)... (optional)] ]\n" + } + }, + { + "ch_fasta": { + "description": "Reference genome fasta file (optional)\nStructure: [ val(meta2), path(fasta) ]\n" + } + }, + { + "val_genome": { + "type": "string", + "description": "genome to use" + } + }, + { + "val_species": { + "type": "string", + "description": "species to use" + } + }, + { + "val_cache_version": { + "type": "integer", + "description": "cache version to use" + } + }, + { + "ch_cache": { + "description": "the root cache folder for ensemblvep (optional)\nStructure: [ val(meta3), path(cache) ]\n" + } + }, + { + "ch_extra_files": { + "description": "any extra files needed by plugins for ensemblvep (optional)\nStructure: [ path(file1), path(file2)... ]\n" + } + } + ], + "output": [ + { + "vcf_tbi": { + "description": "Compressed vcf file + tabix index\nStructure: [ val(meta), path(vcf), path(tbi) ]\n" + } + }, + { + "json": { + "description": "json file\nStructure: [ val(meta), path(json) ]\n" + } + }, + { + "tab": { + "description": "tab file\nStructure: [ val(meta), path(tab) ]\n" + } + }, + { + "reports": { + "type": "file", + "description": "html reports", + "pattern": "*.html" + } + }, + { + "versions": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ], + "authors": ["@maxulysse", "@matthdsm", "@nvnieuwk"], + "maintainers": ["@maxulysse", "@matthdsm", "@nvnieuwk"] + }, + "pipelines": [ { - "meta": null, - "type": "map", - "description": "Metadata map" + "name": "rnadnavar", + "version": "dev" }, { - "regionout": null, - "type": "string", - "description": "Region to perform the phasing on", - "pattern": "[chr]+[0-9]+:[0-9]+-[0-9]+" + "name": "rnavar", + "version": "1.2.3" } - ] + ] + }, + { + "name": "vcf_annotate_ensemblvep_snpeff", + "path": "subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/meta.yml", + "type": "subworkflow", + "meta": { + "name": "vcf_annotate_ensemblvep_snpeff", + "description": "Perform annotation with ensemblvep and/or snpeff and bgzip + tabix index the resulting VCF file. This subworkflow uses the scatter-gather method to run VEP/snpEff in parallel to increase throughput. The input VCF is split into multiple smaller VCFs of fixed size, which are annotated separately and concatenated back together to a single output file per sample. Only VCF/BCF outputs are currently supported.\n", + "keywords": ["vcf", "annotation", "ensemblvep", "snpeff"], + "components": [ + "ensemblvep/download", + "ensemblvep/vep", + "snpeff/download", + "snpeff/snpeff", + "htslib/bgziptabix", + "bcftools/pluginscatter", + "bcftools/concat", + "bcftools/sort" + ], + "input": [ + { + "ch_vcf": { + "description": "vcf file to annotate\nStructure: [ val(meta), path(vcf), path(tbi) ]\n" + } + }, + { + "ch_fasta": { + "description": "Reference genome fasta file (optional)\nStructure: [ val(meta2), path(fasta) ]\n" + } + }, + { + "val_vep_genome": { + "type": "string", + "description": "genome to use for ensemblvep" + } + }, + { + "val_vep_species": { + "type": "string", + "description": "species to use for ensemblvep" + } + }, + { + "val_vep_cache_version": { + "type": "integer", + "description": "cache version to use for ensemblvep" + } + }, + { + "ch_vep_cache": { + "description": "the root cache folder for ensemblvep (optional)\nStructure: [ path(cache) ]\n" + } + }, + { + "ch_vep_extra_files": { + "description": "any extra files needed by plugins for ensemblvep (optional)\nStructure: [ path(file1), path(file2)... ]\n" + } + }, + { + "val_snpeff_db": { + "type": "string", + "description": "database to use for snpeff, usually consists of the genome and the database version\ne.g. WBcel235.99\n" + } + }, + { + "ch_snpeff_cache": { + "description": "the root cache folder for snpeff (optional)\nStructure: [ path(cache) ]\n" + } + }, + { + "val_tools_to_use": { + "type": "list", + "description": "The tools to use. Options => '[\"ensemblvep\", \"snpeff\"]'" + } + }, + { + "val_sites_per_chunk": { + "type": "integer", + "description": "The amount of variants per scattered VCF.\nSet this value to `null`, `[]` or `false` to disable scattering.\n" + } + } + ], + "output": [ + { + "vcf_tbi": { + "description": "Compressed vcf file + tabix index\nStructure: [ val(meta), path(vcf), path(tbi) ]\n" + } + }, + { + "vep_reports": { + "type": "file", + "description": "html reports generated by Ensembl VEP", + "pattern": "*.html" + } + }, + { + "snpeff_reports": { + "description": "csv reports generated by snpeff\nStructure: [ val(meta), path(csv) ]\n" + } + }, + { + "snpeff_html": { + "description": "html reports generated by snpeff\nStructure: [ val(meta), path(html) ]\n" + } + }, + { + "snpeff_genes": { + "description": "txt (tab separated) file having counts of the number of variants\naffecting each transcript and gene\nStructure: [ val(meta), path(txt) ]\n" + } + }, + { + "versions": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ], + "authors": ["@maxulysse", "@matthdsm", "@nvnieuwk"], + "maintainers": ["@maxulysse", "@matthdsm", "@nvnieuwk"] } - }, - { - "vcf_index": { - "description": "Channel with phased VCF files", - "structure": [ + }, + { + "name": "vcf_annotate_snpeff", + "path": "subworkflows/nf-core/vcf_annotate_snpeff/meta.yml", + "type": "subworkflow", + "meta": { + "name": "vcf_annotate_snpeff", + "description": "Perform annotation with snpEff and bgzip + tabix index the resulting VCF file", + "keywords": ["vcf", "annotation", "snpeff"], + "components": ["snpeff", "snpeff/snpeff", "htslib/bgziptabix"], + "input": [ + { + "ch_vcf": { + "description": "vcf file\nStructure: [ val(meta), path(vcf) ]\n" + } + }, + { + "val_snpeff_db": { + "type": "string", + "description": "db version to use" + } + }, + { + "ch_snpeff_cache": { + "description": "path to root cache folder for snpEff (optional)\nStructure: [ path(cache) ]\n" + } + } + ], + "output": [ + { + "vcf_tbi": { + "description": "Compressed vcf file + tabix index\nStructure: [ val(meta), path(vcf), path(tbi) ]\n" + } + }, + { + "reports": { + "description": "html reports\nStructure: [ path(html) ]\n" + } + }, + { + "summary": { + "description": "html reports\nStructure: [ path(csv) ]\n" + } + }, + { + "genes_txt": { + "description": "html reports\nStructure: [ path(txt) ]\n" + } + }, + { + "versions": { + "description": "Files containing software versions\nStructure: [ path(versions.yml) ]\n" + } + } + ], + "authors": ["@maxulysse"], + "maintainers": ["@maxulysse"] + }, + "pipelines": [ { - "meta": null, - "type": "map", - "description": "Metadata map" + "name": "rnavar", + "version": "1.2.3" }, { - "vcf": null, - "type": "file", - "description": "VCF file", - "pattern": "*.{vcf,bcf,vcf.gz}" - }, + "name": "sarek", + "version": "3.8.1" + } + ] + }, + { + "name": "vcf_extract_relate_somalier", + "path": "subworkflows/nf-core/vcf_extract_relate_somalier/meta.yml", + "type": "subworkflow", + "meta": { + "name": "vcf_extract_relate_somalier", + "description": "Perform somalier extraction and relate stats on input VCFs", + "keywords": ["somalier", "stats", "vcf", "ped", "relatedness"], + "components": ["htslib/bgziptabix", "somalier/extract", "somalier/relate"], + "input": [ + { + "ch_vcfs": { + "description": "The input VCFs to perform the stats on, optionally with their indices.\nThis channel can also contain the number of samples in the same family/group\nto check relatedness. This is advised to add as it can improve the efficiency of your pipeline\nStructure: [ val(meta), path(vcf), path(tbi), val(count) ]\n" + } + }, + { + "ch_fasta": { + "description": "The reference FASTA used to create the VCF files\nStructure: [ path(fasta) ]\n" + } + }, + { + "ch_fasta_fai": { + "description": "The index of the reference FASTA\nStructure: [ path(fasta_fai) ]\n" + } + }, + { + "ch_somalier_sites": { + "description": "A VCF containing the common sites for Somalier\nStructure: [ path(somalier_sites_vcf) ]\n" + } + }, + { + "ch_peds": { + "description": "A channel containing an optional PED file for the corresponding families. This channel has to be given, but can be like `[meta, []]`.\nWhen you don't want to use a PED file, you must supply a channel\ncontaining the meta and an empty value (`[]`) instead of a PED\nStructure: [ val(meta), path(ped) ]\n" + } + }, + { + "ch_sample_groups": { + "description": "Optional - A text file describing how the samples should be grouped\nStructure: [ path(txt) ]\n" + } + }, + { + "val_common_id": { + "description": "Optional - A common identifier in the meta map.\nThis will be used to determine which VCFs should be used in somalier_relate.\nThis value should be given when using single sample VCFs\n" + } + } + ], + "output": [ + { + "extract": { + "description": "The extract file created with Somalier extract\nStructure: [ val(meta), path(extract) ]\n" + } + }, + { + "html": { + "description": "An HTML file containing an interactive graph on the relatedness of the samples\nStructure: [ val(meta), path(html) ]\n" + } + }, + { + "pairs_tsv": { + "description": "A TSV file detailing the relatedness between pairs of samples\nStructure: [ val(meta), path(tsv) ]\n" + } + }, + { + "samples_tsv": { + "description": "A TSV file detailing the relatedness between all samples with the same meta\nStructure: [ val(meta), path(tsv) ]\n" + } + } + ], + "authors": ["@nvnieuwk"], + "maintainers": ["@nvnieuwk"] + } + }, + { + "name": "vcf_filter_bcftools_ensemblvep", + "path": "subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/meta.yml", + "type": "subworkflow", + "meta": { + "name": "vcf_filter_bcftools_ensemblvep", + "description": "Filter VCF file with bcftools and filter_vep", + "keywords": ["filter", "vcf", "bcftools", "filter_vep"], + "components": ["bcftools/view", "ensemblvep/filtervep", "htslib/bgziptabix"], + "input": [ + { + "ch_vcf": { + "type": "file", + "description": "The input channel containing the VCF files\nStructure: [ val(meta), path(vcf) ]\n", + "pattern": "*.{vcf/vcf.gz}" + } + }, + { + "ch_filter_vep_file": { + "type": "file", + "description": "File to pass to filter_vep, containing e.g. HGNC IDs to filter on\nStructure: [ val(meta), path(txt) ]\n" + } + }, + { + "filter_with_bcftools": { + "type": "boolean", + "description": "Whether to filter the VCF file with bcftools before passing it to filter_vep\n" + } + }, + { + "filter_with_filter_vep": { + "type": "boolean", + "description": "Whether to filter the VCF file with filter_vep\n" + } + } + ], + "output": [ + { + "vcf": { + "type": "file", + "description": "Channel containing VCF files\nStructure: [ val(meta), path(bam) ]\n", + "pattern": "*.vcf.gz" + } + }, + { + "bai": { + "type": "file", + "description": "Channel containing indexed VCF (TBI) files\nStructure: [ val(meta), path(bai) ]\n", + "pattern": "*.tbi" + } + }, + { + "versions": { + "type": "file", + "description": "File containing software versions\nStructure: [ path(versions.yml) ]\n", + "pattern": "versions.yml" + } + } + ], + "authors": ["@fellen31"], + "maintainers": ["@fellen31", "@ramprasadn"] + }, + "pipelines": [ { - "index": null, - "type": "file", - "description": "VCF index file", - "pattern": "*.{tbi,csi}" + "name": "raredisease", + "version": "3.0.0" } - ] + ] + }, + { + "name": "vcf_gather_bcftools", + "path": "subworkflows/nf-core/vcf_gather_bcftools/meta.yml", + "type": "subworkflow", + "meta": { + "name": "vcf_gather_bcftools", + "description": "Concatenate several VCF files using bcftools concat.\nAn additional option can be given to sort the concatenated VCF.\n", + "keywords": ["concat", "vcf", "gather", "sort", "bcftools"], + "components": ["bcftools/sort", "bcftools/concat", "htslib/bgziptabix"], + "input": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing at least a common field for each VCF that needs to be merged\ne.g. [ id:'test.001', common_meta:'test' ]\n" + } + }, + { + "ch_vcfs": { + "type": "file(s)", + "description": "VCF files and their indices that should be concatenated as well as the expected number of vcf\nStructure: [ meta, vcf, tbi, count ]\n" + } + }, + { + "arr_common_meta": { + "type": "array", + "description": "OPTIONAL:\nA string array of the common meta keys to use to group the vcfs.\nPlease make sure all VCFs that need to be concatenated have the same value in the\nthe meta fields specified - the subworkflow will error if a required key is missing from a meta map.\n" + } + }, + { + "sort": { + "type": "boolean", + "description": "Whether or not to sort the output VCF,\nthis can be useful if this subworkflow isn't used in a scatter/gather workflow\n" + } + } + ], + "output": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "The concatenated (and possible sorted) VCF file\nStructure: [ meta, vcf ]\n", + "pattern": "*.vcf.gz" + } + }, + { + "index": { + "type": "file", + "description": "The indices of the output VCFs\nStructure: [ meta, [tbi, csi] ]\n", + "pattern": "*.vcf.gz.{tbi,csi}" + } + }, + { + "vcf_index": { + "type": "file", + "description": "Aggregated channel with the vcf and indices\nStructure: [ meta, vcf, [tbi, csi] ]\n" + } + } + ], + "authors": ["@nvnieuwk"], + "maintainers": ["@nvnieuwk"] + } + }, + { + "name": "vcf_impute_beagle5", + "path": "subworkflows/nf-core/vcf_impute_beagle5/meta.yml", + "type": "subworkflow", + "meta": { + "name": "VCF_IMPUTE_BEAGLE5", + "description": "Subworkflow to impute VCF files using BEAGLE5 software. The subworkflow\ntakes VCF files, phased reference panel, genetic maps and chunks region to perform imputation\nand outputs phased and imputed VCF files.\nMeta map of all channels, except ch_input, will be used to perform joint operations.\n\"regionout\" and \"regionsize\" keys will be added to the meta map to distinguish the different\nfile before ligation and therefore should not be used.\n", + "keywords": ["VCF", "imputation", "beagle5", "phasing"], + "components": ["beagle5/beagle", "bcftools/index", "bcftools/view", "glimpse2/ligate"], + "input": [ + { + "ch_input": { + "description": "Channel with input data", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata map containing sample information\n" + } + }, + { + "vcf": { + "type": "file", + "description": "Input VCF files", + "pattern": "*.{vcf,bcf}{.gz}?" + } + }, + { + "index": { + "type": "file", + "description": "Input index file", + "pattern": "*.{tbi,csi}" + } + } + ] + } + }, + { + "ch_panel": { + "description": "Channel with phased reference panel data", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata map that will be combined with the input data map\n" + } + }, + { + "vcf": { + "type": "file", + "description": "Reference panel VCF files by chromosomes", + "pattern": "*.{vcf,bcf,vcf.gz}" + } + }, + { + "index": { + "type": "file", + "description": "Reference panel VCF index files", + "pattern": "*.{tbi,csi}" + } + } + ] + } + }, + { + "ch_chunks": { + "description": "Channel containing the region to impute", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata map containing chromosome information\n" + } + }, + { + "regionout": null, + "type": "string", + "description": "Region to perform the phasing on", + "pattern": "[chr]+[0-9]+:[0-9]+-[0-9]+" + } + ] + } + }, + { + "ch_map": { + "description": "Channel with genetic map data", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata map containing chromosome information\n" + } + }, + { + "map": { + "type": "file", + "description": "Plink format genetic map files", + "pattern": "*.map" + } + } + ] + } + } + ], + "output": [ + { + "vcf_index": { + "description": "Channel with imputed and phased VCF files", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata map of the target input file combined with the reference panel map.\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF imputed and phased file by sample", + "pattern": "*.{vcf,bcf,vcf.gz}" + } + }, + { + "index": { + "type": "file", + "description": "VCF index file", + "pattern": "*.{tbi,csi}" + } + } + ] + } + } + ], + "authors": ["@LouisLeNezet", "@gichas"], + "maintainers": ["@LouisLeNezet", "@gichas"] + } + }, + { + "name": "vcf_impute_glimpse", + "path": "subworkflows/nf-core/vcf_impute_glimpse/meta.yml", + "type": "subworkflow", + "meta": { + "name": "vcf_impute_glimpse", + "description": "Impute VCF/BCF files with Glimpse", + "keywords": ["glimpse", "chunk", "phase", "ligate"], + "components": ["glimpse/chunk", "glimpse/phase", "glimpse/ligate", "bcftools/index"], + "input": [ + { + "ch_vcf": { + "description": "Channel with target VCF files", + "structure": [ + { + "meta": null, + "type": "map", + "description": "Metadata map" + }, + { + "vcf": null, + "type": "file", + "description": "VCF file", + "pattern": "*.{vcf,bcf,vcf.gz}" + }, + { + "index": null, + "type": "file", + "description": "VCF index file", + "pattern": "*.{tbi,csi}" + }, + { + "infos": null, + "type": "file", + "description": "File containing ploidy information of each sample\n", + "pattern": "*.{txt, tsv}" + } + ] + } + }, + { + "ch_ref": { + "description": "Channel with reference phased VCF files", + "structure": [ + { + "meta": null, + "type": "map", + "description": "Metadata map" + }, + { + "vcf": null, + "type": "file", + "description": "VCF file", + "pattern": "*.{vcf,bcf,vcf.gz}" + }, + { + "index": null, + "type": "file", + "description": "VCF index file", + "pattern": "*.{tbi,csi}" + }, + { + "region": null, + "type": "string", + "description": "Region to perform chunking on", + "pattern": "[chr]+[0-9]+:[0-9]+-[0-9]+" + } + ] + } + }, + { + "ch_chunks": { + "description": "Channel with chunks data", + "structure": [ + { + "meta": null, + "type": "map", + "description": "Metadata map that will be combined with the input data map" + }, + { + "regionin": null, + "type": "string", + "description": "Chunk region without buffer", + "pattern": "[chr]+[0-9]+:[0-9]+-[0-9]+" + }, + { + "regionout": null, + "type": "string", + "description": "Chunk region with buffer", + "pattern": "[chr]+[0-9]+:[0-9]+-[0-9]+" + } + ] + } + }, + { + "ch_map": { + "description": "Channel with genetic map data (optional)", + "structure": [ + { + "meta": null, + "type": "map", + "description": "Metadata map" + }, + { + "map": null, + "type": "file", + "description": "Map file in GLIMPSE format", + "pattern": "*.map" + } + ] + } + }, + { + "chunk": { + "type": "boolean", + "description": "Whether to perform chunking of the input data before imputation." + } + } + ], + "output": [ + { + "chunks": { + "type": "file", + "description": "Tab delimited output txt file containing buffer and imputation regions.\nStructure: [meta, txt]\n" + } + }, + { + "merged_variants": { + "type": "file", + "description": "Output phased VCF/BCF file for the merged regions.\nPhased information (HS field) is updated accordingly for the full region.\nStructure: [ val(meta), bcf ]\n" + } + }, + { + "merged_variants_index": { + "type": "file", + "description": "Index output of phased VCF/BCF file for the merged regions.\nStructure: [ val(meta), csi ]\n" + } + } + ], + "authors": ["@LouisLeNezet"], + "maintainers": ["@LouisLeNezet"] + } + }, + { + "name": "vcf_impute_minimac4", + "path": "subworkflows/nf-core/vcf_impute_minimac4/meta.yml", + "type": "subworkflow", + "meta": { + "name": "VCF_IMPUTE_MINIMAC4", + "description": "Subworkflow to impute VCF files using MINIMAC4 software. The subworkflow\ntakes VCF files, phased reference panel, and genetic maps to perform imputation\nand outputs phased and imputed VCF files.\nMeta map of all channels, except ch_input, will be used to perform joint operations.\n\"regionout\" key will be added to the meta map to distinguish the different file\nbefore ligation and therefore should not be used.\n", + "keywords": ["VCF", "imputation", "minimac4", "phasing", "MSAV"], + "components": ["minimac4/compressref", "minimac4/impute", "bcftools/index", "glimpse2/ligate"], + "input": [ + { + "ch_input": { + "description": "Channel with input data", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata map containing sample information\n" + } + }, + { + "vcf": { + "type": "file", + "description": "Input VCF files", + "pattern": "*.{vcf,bcf,vcf.gz}" + } + }, + { + "index": { + "type": "file", + "description": "Input index file", + "pattern": "*.{tbi,csi}" + } + } + ] + } + }, + { + "ch_panel": { + "description": "Channel with phased reference panel data", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata map that will be combined with the input data map\n" + } + }, + { + "vcf": { + "type": "file", + "description": "Reference panel VCF files by chromosomes", + "pattern": "*.{vcf,bcf,vcf.gz}" + } + }, + { + "index": { + "type": "file", + "description": "Reference panel VCF index files", + "pattern": "*.{tbi,csi}" + } + } + ] + } + }, + { + "ch_posfile": { + "description": "Channel with variants position to impute", + "structure": [ + { + "meta": { + "type": "map", + "description": "Metadata map containing chromosome information\n" + } + }, + { + "sites_vcf": { + "type": "file", + "descrition": "VCF/BCF file containing position to impute\n" + } + }, + { + "sites_index": { + "type": "file", + "description": "CSI|TBI index file of the sites to impute\n" + } + } + ] + } + }, + { + "ch_chunks": { + "description": "Channel containing the region to impute", + "structure": [ + 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"name": "pangenome", + "version": "1.1.3" + } + ] + } + ], + "wfmash_merge_segments": [ + { + "type": "boolean", + "pipelines": [ + { + "name": "pangenome", + "version": "1.1.3" + } + ] + } + ], + "wfmash_n_mappings": [ + { + "type": "integer", + "pipelines": [ + { + "name": "pangenome", + "version": "1.1.3" + } + ] + } + ], + "wfmash_no_splits": [ + { + "type": "boolean", + "pipelines": [ + { + "name": "pangenome", + "version": "1.1.3" + } + ] + } + ], + "wfmash_only": [ + { + "type": "boolean", + "pipelines": [ + { + "name": "pangenome", + "version": "1.1.3" + } + ] + } + ], + "wfmash_segment_length": [ + { + "type": "string", + "pipelines": [ + { + "name": "pangenome", + "version": "1.1.3" + } + ] + } + ], + "wfmash_sparse_map": [ + { + "type": "string", + "pipelines": [ + { + "name": "pangenome", + "version": "1.1.3" + } + ] + } + ], + "wfmash_temp_dir": [ + { + "type": "string", + "pipelines": [ + { + "name": "pangenome", + "version": "1.1.3" + } + ] + } + ], + "whitelist": [ + { + "type": "string", + "pipelines": [ + { + "name": "rnadnavar", + "version": "dev" + }, + { + "name": "rnafusion", + "version": "4.1.2" + }, + { + "name": "scnanoseq", + "version": "1.2.2" + } + ] + } + ], + "wholegenome": [ + { + "type": "boolean", + "pipelines": [ + { + "name": "readsimulator", + "version": "1.0.1" + } + ] + } + ], + "wholegenome_error_rate": [ + { + "type": "number", + "pipelines": [ + { + "name": "readsimulator", + "version": "1.0.1" + } + ] + } + ], + "wholegenome_indel_extended": [ + { + "type": "number", + "pipelines": [ + { + "name": "readsimulator", + "version": "1.0.1" + } + ] + } + ], + "wholegenome_indel_fraction": [ + { + "type": "number", + "pipelines": [ + { + "name": "readsimulator", + "version": "1.0.1" + } + ] + } + ], + "wholegenome_mutation_rate": [ + { + "type": "number", + "pipelines": [ + { + "name": "readsimulator", + "version": "1.0.1" + } + ] + } + ], + "wholegenome_n_reads": [ + { + "type": "integer", + "pipelines": [ + { + "name": "readsimulator", + "version": "1.0.1" + } + ] + } + ], + "wholegenome_outer_dist": [ + { + "type": "integer", + "pipelines": [ + { + "name": "readsimulator", + "version": "1.0.1" + } + ] + } + ], + "wholegenome_r1_length": [ + { + "type": "integer", + "pipelines": [ + { + "name": "readsimulator", + "version": "1.0.1" + } + ] + } + ], + "wholegenome_r2_length": [ + { + "type": "integer", + "pipelines": [ + { + "name": "readsimulator", + "version": "1.0.1" + } + ] + } + ], + "wholegenome_standard_dev": [ + { + "type": "integer", + "pipelines": [ + { + "name": "readsimulator", + "version": "1.0.1" + } + ] + } + ], + "wide_format_output": [ + { + "type": "boolean", + "pipelines": [ + { + "name": "epitopeprediction", + "version": "3.1.0" + } + ] + } + ], + "wild_type": [ + { + "type": "boolean", + "pipelines": [ + { + "name": "epitopeprediction", + "version": "3.1.0" + } + ] + } + ], + "winAnchorMultimapNmax": [ + { + "type": "integer", + "pipelines": [ + { + "name": "dualrnaseq", + "version": "1.0.0" + } + ] + } + ], + "window_size": [ + { + "type": "integer", + "pipelines": [ + { + "name": "tfactivity", + "version": "dev" + } + ] + } + ], + "winnowmap_kmers": [ + { + "type": "string", + "pipelines": [ + { + "name": "longraredisease", + "version": "dev" + } + ] + } + ], + "winnowmap_model": [ + { + "type": "string", + "pipelines": [ + { + "name": "longraredisease", + "version": "dev" + } + ] + } + ], + "with_control": [ + { + "type": "boolean", + "pipelines": [ + { + "name": "atacseq", + "version": "2.1.2" + } + ] + } + ], + "with_umi": [ + { + "type": "boolean", + "pipelines": [ + { + "name": "lncpipe", + "version": "dev" + }, + { + "name": "nascent", + "version": "2.3.0" + }, + { + "name": "riboseq", + "version": "1.2.0" + }, + { + "name": "rnaseq", + "version": "3.26.0" + }, + { + "name": "smrnaseq", + "version": "2.4.1" + }, + { + "name": "viralmetagenome", + "version": "1.1.1" + } + ] + } + ], + "workflow": [ + { + "type": "string", + "pipelines": [ + { + "name": "pacsomatic", + "version": "dev" + }, + { + "name": "pacvar", + "version": "1.0.1" + } + ] + } + ], + "writeMappings": [ + { + "type": "boolean", + "pipelines": [ + { + "name": "dualrnaseq", + "version": "1.0.0" + } + ] + } + ], + "writeUnmappedNames": [ + { + "type": "boolean", + "pipelines": [ + { + "name": "dualrnaseq", + "version": "1.0.0" + } + ] + } + ], + "write_allele_frequencies": [ + { + "type": "boolean", + "pipelines": [ + { + "name": "eager", + "version": "2.5.3" + } + ] + } + ], + "write_barcode_meta_csv": [ + { + "type": "string", + "pipelines": [ + { + "name": "kmermaid", + "version": "0.1.0-alpha" + } + ] + } + ], + "wvdb": [ + { + "type": "string", + "pipelines": [ + { + "name": "rangeland", + "version": "1.0.0" + } + ] + } + ], + "xeniumranger_only": [ + { + "type": "boolean", + "pipelines": [ + { + "name": "spatialxe", + "version": "dev" + } + ] + } + ], + "xreactive_chr_targets": [ + { + "type": "string", + "pipelines": [ + { + "name": "methylarray", + "version": "dev" + } + ] + } + ], + "zenodo_link": [ + { + "type": "string", + "pipelines": [ + { + "name": "drugresponseeval", + "version": "1.2.0" + } + ] + } + ], + "zymo": [ + { + "type": "boolean", + "pipelines": [ + { + "name": "methylseq", + "version": "4.2.0" + } + ] + } + ] +} diff --git a/public/pipeline_names.json b/public/pipeline_names.json index 3e6a90d63b..9357fd11f7 100644 --- a/public/pipeline_names.json +++ b/public/pipeline_names.json @@ -1 +1,141 @@ -{"pipeline":["abotyper","airrflow","alleleexpression","ampliseq","atacseq","bacass","bactmap","bamtofastq","cageseq","callingcards","cellpainting","chipseq","circdna","circrna","clipseq","coproid","createpanelrefs","createtaxdb","crisprseq","cutandrun","dartseq","datasync","deepmodeloptim","deepmutscan","demo","demultiplex","denovotranscript","detaxizer","diaproteomics","differentialabundance","diseasemodulediscovery","drop","drugresponseeval","dualrnaseq","eager","epigenomesegmentation","epitopeprediction","evexplorer","fastqrepair","fastquorum","fetchngs","funcprofiler","funcscan","genephylomodeler","genomeannotator","genomeassembler","genomeqc","genomeskim","genomicrelatedness","gwas","hadge","hgtseq","hic","hicar","hlatyping","imcyto","isoseq","kmermaid","lncpipe","longraredisease","lsmquant","mag","magmap","marsseq","mcmicro","meerpipe","metaboigniter","metapep","metatdenovo","methylarray","methylong","methylseq","mhcquant","mitodetect","mnaseseq","molkart","mspepid","multiplesequencealign","nanoseq","nanostring","nascent","ncrnannotator","omicsgenetraitassociation","oncoanalyser","pacsomatic","pacvar","pairgenomealign","pangenome","panoramaseq","pathogensurveillance","phageannotator","phaseimpute","phyloplace","pixelator","proteinannotator","proteinfamilies","proteinfold","proteogenomicsdb","radseq","rangeland","raredisease","rarevariantburden","readsimulator","references","reportho","ribomsqc","riboseq","rnadnavar","rnafusion","rnaseq","rnasplice","rnavar","sammyseq","sarek","scdownstream","scnanoseq","scrnaseq","seqinspector","seqsubmit","slamseq","smrnaseq","sopa","spatialvi","spatialxe","spinningjenny","stableexpression","taxprofiler","tbanalyzer","tfactivity","troughgraph","tumourevo","variantbenchmarking","variantcatalogue","variantprioritization","viralintegration","viralmetagenome","viralrecon"]} \ No newline at end of file +{ + "pipeline": [ + "abotyper", + "airrflow", + "alleleexpression", + "ampliseq", + "atacseq", + "bacass", + "bactmap", + "bamtofastq", + "cageseq", + "callingcards", + "cellpainting", + "chipseq", + "circdna", + "circrna", + "clipseq", + "coproid", + "createpanelrefs", + "createtaxdb", + "crisprseq", + "cutandrun", + "dartseq", + "datasync", + "deepmodeloptim", + "deepmutscan", + "demo", + "demultiplex", + "denovotranscript", + "detaxizer", + "diaproteomics", + "differentialabundance", + "diseasemodulediscovery", + "drop", + "drugresponseeval", + "dualrnaseq", + "eager", + "epigenomesegmentation", + "epitopeprediction", + "evexplorer", + "fastqrepair", + "fastquorum", + "fetchngs", + "funcprofiler", + "funcscan", + "genephylomodeler", + "genomeannotator", + "genomeassembler", + "genomeqc", + "genomeskim", + "genomicrelatedness", + "gwas", + "hadge", + "hgtseq", + "hic", + "hicar", + "hlatyping", + "imcyto", + "isoseq", + "kmermaid", + "lncpipe", + "longraredisease", + "lsmquant", + "mag", + "magmap", + "marsseq", + "mcmicro", + "meerpipe", + "metaboigniter", + "metapep", + "metatdenovo", + "methylarray", + "methylong", + "methylseq", + "mhcquant", + "mitodetect", + "mnaseseq", + "molkart", + "mspepid", + "multiplesequencealign", + "nanoseq", + "nanostring", + "nascent", + "ncrnannotator", + "omicsgenetraitassociation", + "oncoanalyser", + "pacsomatic", + "pacvar", + "pairgenomealign", + "pangenome", + "panoramaseq", + "pathogensurveillance", + "phageannotator", + "phaseimpute", + "phyloplace", + "pixelator", + "proteinannotator", + "proteinfamilies", + "proteinfold", + "proteogenomicsdb", + "radseq", + "rangeland", + "raredisease", + "rarevariantburden", + "readsimulator", + "references", + "reportho", + "ribomsqc", + "riboseq", + "rnadnavar", + "rnafusion", + "rnaseq", + "rnasplice", + "rnavar", + "sammyseq", + "sarek", + "scdownstream", + "scnanoseq", + "scrnaseq", + "seqinspector", + "seqsubmit", + "slamseq", + "smrnaseq", + "sopa", + "spatialvi", + "spatialxe", + "spinningjenny", + "stableexpression", + "taxprofiler", + "tbanalyzer", + "tfactivity", + "troughgraph", + "tumourevo", + "variantbenchmarking", + "variantcatalogue", + "variantprioritization", + "viralintegration", + "viralmetagenome", + "viralrecon" + ] +} diff --git a/public/pipelines.json b/public/pipelines.json index c9dd43afc5..8a8e01ee90 100644 --- a/public/pipelines.json +++ b/public/pipelines.json @@ -86,10 +86,7 @@ "master_branch_exists": false, "main_branch_exists": true, "main_branch_protection_up_to_date": true, - "main_branch_protection_status_checks": [ - "pre-commit", - "nf-core" - ], + "main_branch_protection_status_checks": ["pre-commit", "nf-core"], "main_branch_protection_required_reviews": 2, "main_branch_protection_require_codeowner_review": false, "main_branch_protection_require_non_stale_review": false, @@ -127,13 +124,9 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "main_nextflow_config_plugins": [ - "nf-schema@2.1.1" - ], + "main_nextflow_config_plugins": ["nf-schema@2.1.1"], "main_nextflow_config_manifest": {}, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -143,10 +136,7 @@ "published_at": "2026-04-29T05:57:00Z", "tag_sha": "2271ad2d77960cbf1c478fb902fc62a2f23c8381", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "fastqc", @@ -157,17 +147,11 @@ "samtools_mpileup", "samtools_stats" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": ">=25.10.4", "nf_core_version": "4.0.0", - "plugins": [ - "nf-schema@2.1.1" - ], + "plugins": ["nf-schema@2.1.1"], "co2footprint_files": null } ] @@ -204,13 +188,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "airr", - "b-cell", - "immcantation", - "immunorepertoire", - "repseq" - ], + "topics": ["airr", "b-cell", "immcantation", "immunorepertoire", "repseq"], "visibility": "public", "forks": 56, "open_issues": 43, @@ -263,10 +241,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": -1, - "master_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "master_branch_protection_status_checks": ["nf-core", "pre-commit"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -274,10 +249,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "dev_branch_protection_status_checks": ["nf-core", "pre-commit"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -366,15 +338,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "master_nextflow_config_plugins": ["nf-schema@2.5.1"], "master_nextflow_config_manifest": { "defaultBranch": "master" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -403,17 +371,11 @@ "multiqc", "trust4" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.04.0", "nf_core_version": "3.5.1", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null }, { @@ -443,11 +405,7 @@ "multiqc", "trust4" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.2.0" @@ -478,11 +436,7 @@ "multiqc", "trust4" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.2.0" @@ -492,10 +446,7 @@ "published_at": "2024-12-11T00:21:58Z", "tag_sha": "d91dd840f47e46c2fcffab88cc84e6d047b8d449", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "cat_fastq", @@ -506,11 +457,7 @@ "multiqc", "trust4" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.0.2" @@ -520,19 +467,9 @@ "published_at": "2024-06-01T01:18:23Z", "tag_sha": "0c0bcde09516df6dd5532e7eb88906673d00370b", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "cat_fastq", - "cellranger_mkvdjref", - "cellranger_vdj", - "fastp", - "fastqc", - "multiqc" - ], + "modules": ["cat_fastq", "cellranger_mkvdjref", "cellranger_vdj", "fastp", "fastqc", "multiqc"], "subworkflows": [ "utils_nextflow_pipeline", "utils_nfcore_pipeline", @@ -547,19 +484,9 @@ "published_at": "2024-04-23T15:53:52Z", "tag_sha": "2f492b0e7e668135ca65c0054add6fe0d9db8b27", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "cat_fastq", - "cellranger_mkvdjref", - "cellranger_vdj", - "fastp", - "fastqc", - "multiqc" - ], + "modules": ["cat_fastq", "cellranger_mkvdjref", "cellranger_vdj", "fastp", "fastqc", "multiqc"], "subworkflows": [ "utils_nextflow_pipeline", "utils_nfcore_pipeline", @@ -574,19 +501,9 @@ "published_at": "2024-04-01T00:00:21Z", "tag_sha": "5c9a30bd35565b08d998a2feab02e4a1ccf84d8a", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "cat_fastq", - "cellranger_mkvdjref", - "cellranger_vdj", - "fastp", - "fastqc", - "multiqc" - ], + "modules": ["cat_fastq", "cellranger_mkvdjref", "cellranger_vdj", "fastp", "fastqc", "multiqc"], "subworkflows": [ "utils_nextflow_pipeline", "utils_nfcore_pipeline", @@ -601,17 +518,9 @@ "published_at": "2023-10-27T13:24:04Z", "tag_sha": "333c8b521d62f6c61c658823d8831df93bc5b532", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "custom_dumpsoftwareversions", - "fastp", - "fastqc", - "multiqc" - ] + "modules": ["custom_dumpsoftwareversions", "fastp", "fastqc", "multiqc"] }, "nextflow_version": "!>=23.04.0", "nf_core_version": null @@ -621,17 +530,9 @@ "published_at": "2023-06-05T20:57:03Z", "tag_sha": "a2a6099a9e73cca504f3e33b566ddb997acdb7b5", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "custom_dumpsoftwareversions", - "fastp", - "fastqc", - "multiqc" - ] + "modules": ["custom_dumpsoftwareversions", "fastp", "fastqc", "multiqc"] }, "nextflow_version": "!>=22.10.1", "nf_core_version": null @@ -641,17 +542,9 @@ "published_at": "2023-03-20T11:45:08Z", "tag_sha": "f0debd6b83b1070118a67d2cfb9baf3508c5991b", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "custom_dumpsoftwareversions", - "fastp", - "fastqc", - "multiqc" - ] + "modules": ["custom_dumpsoftwareversions", "fastp", "fastqc", "multiqc"] }, "nextflow_version": "!>=22.10.1", "nf_core_version": null @@ -661,17 +554,9 @@ "published_at": "2022-12-06T08:30:54Z", "tag_sha": "a6fdad9f6a2408d7846789e549f8650c30485fe5", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "custom_dumpsoftwareversions", - "fastp", - "fastqc", - "multiqc" - ] + "modules": ["custom_dumpsoftwareversions", "fastp", "fastqc", "multiqc"] }, "nextflow_version": "!>=21.10.3", "nf_core_version": null @@ -681,16 +566,9 @@ "published_at": "2022-09-16T14:46:55Z", "tag_sha": "8c1185f7d659d7797a66b541bb27aa5861d34991", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "custom_dumpsoftwareversions", - "fastqc", - "multiqc" - ] + "modules": ["custom_dumpsoftwareversions", "fastqc", "multiqc"] }, "nextflow_version": "!>=21.10.3", "nf_core_version": null @@ -700,16 +578,9 @@ "published_at": "2022-06-03T14:03:24Z", "tag_sha": "5e30384d64921cc721edff43ed0f24d6c74566ef", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "custom_dumpsoftwareversions", - "fastqc", - "multiqc" - ] + "modules": ["custom_dumpsoftwareversions", "fastqc", "multiqc"] }, "nextflow_version": "!>=21.10.3", "nf_core_version": null @@ -719,16 +590,9 @@ "published_at": "2022-05-02T10:52:43Z", "tag_sha": "0bb3ca4c6763d56c612c8567cb8efb7e54923a5e", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "custom_dumpsoftwareversions", - "fastqc", - "multiqc" - ] + "modules": ["custom_dumpsoftwareversions", "fastqc", "multiqc"] }, "nextflow_version": "!>=21.10.3", "nf_core_version": null @@ -738,15 +602,9 @@ "published_at": "2021-07-19T10:58:30Z", "tag_sha": "cc29af5aeb19fb1a58ed6d627ac7aa5145d713fe", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "fastqc", - "multiqc" - ] + "modules": ["fastqc", "multiqc"] }, "nextflow_version": "!>=21.04.0", "nf_core_version": null @@ -756,10 +614,7 @@ "published_at": "2020-01-14T11:05:30Z", "tag_sha": "c3107f30e6c061fc5bb35a526199ed4297aa4eb7", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=19.04.0" }, { @@ -767,10 +622,7 @@ "published_at": "2019-11-08T13:12:45Z", "tag_sha": "11d19bc2c68633cca93c522736552691fff459da", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=19.04.0" }, { @@ -778,10 +630,7 @@ "published_at": "2019-04-16T12:00:43Z", "tag_sha": "df7e204ae7e15b3185ebbe1ffe529a86303bf9f1", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=0.32.0" }, { @@ -809,17 +658,11 @@ "multiqc", "trust4" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.04.0", "nf_core_version": "3.5.1", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null } ] @@ -910,10 +753,7 @@ "master_branch_exists": false, "main_branch_exists": true, "main_branch_protection_up_to_date": true, - "main_branch_protection_status_checks": [ - "pre-commit", - "nf-core" - ], + "main_branch_protection_status_checks": ["pre-commit", "nf-core"], "main_branch_protection_required_reviews": 2, "main_branch_protection_require_codeowner_review": false, "main_branch_protection_require_non_stale_review": false, @@ -946,13 +786,9 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "main_nextflow_config_plugins": [ - "nf-validation@1.1.3" - ], + "main_nextflow_config_plugins": ["nf-validation@1.1.3"], "main_nextflow_config_manifest": {}, - "dev_nextflow_config_plugins": [ - "nf-validation@1.1.3" - ], + "dev_nextflow_config_plugins": ["nf-validation@1.1.3"], "dev_nextflow_config_manifest": {}, "releases": [ { @@ -960,10 +796,7 @@ "published_at": "2026-01-13T11:20:47Z", "tag_sha": "862bd3453274865736c12ccbb78bf7247827174e", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bcftools_annotate", @@ -982,9 +815,7 @@ }, "nextflow_version": "!>=23.04.0", "nf_core_version": "3.3.1", - "plugins": [ - "nf-validation@1.1.3" - ], + "plugins": ["nf-validation@1.1.3"], "co2footprint_files": null } ] @@ -1091,10 +922,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": -1, - "master_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "master_branch_protection_status_checks": ["nf-core", "pre-commit"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -1102,11 +930,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "nf-core", - "pre-commit", - "confirm-pass" - ], + "dev_branch_protection_status_checks": ["nf-core", "pre-commit", "confirm-pass"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -1340,15 +1164,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "master_nextflow_config_plugins": ["nf-schema@2.5.1"], "master_nextflow_config_manifest": { "defaultBranch": "master" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.7.2" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.7.2"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -1358,10 +1178,7 @@ "published_at": "2026-04-15T16:22:40Z", "tag_sha": "d34664b0f57aeefc92a1dd5ea6e44c6955ec13a6", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "clustalo_align", @@ -1398,9 +1215,7 @@ }, "nextflow_version": "!>=25.04.8", "nf_core_version": "3.5.2", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null }, { @@ -1408,10 +1223,7 @@ "published_at": "2026-01-23T09:42:08Z", "tag_sha": "7cf7ed2b2a42f6144f607e7c7f511db12e398060", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "cutadapt", @@ -1443,9 +1255,7 @@ }, "nextflow_version": "!>=25.04.8", "nf_core_version": "3.5.1", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null }, { @@ -1453,10 +1263,7 @@ "published_at": "2026-01-16T09:35:40Z", "tag_sha": "3d5c7e5bec28de279337f3ffe3c312a45940b782", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "cutadapt", @@ -1488,9 +1295,7 @@ }, "nextflow_version": "!>=25.04.8", "nf_core_version": "3.5.1", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null }, { @@ -1498,10 +1303,7 @@ "published_at": "2025-10-06T13:32:44Z", "tag_sha": "d8dd15d5e7760752691357c177bed2e35a2e413f", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "cutadapt", @@ -1539,10 +1341,7 @@ "published_at": "2025-05-23T12:19:03Z", "tag_sha": "e7bcfdadc2cebfe3fd096b02d6379a630a9d17fb", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "cutadapt", @@ -1580,10 +1379,7 @@ "published_at": "2025-04-04T09:36:54Z", "tag_sha": "9c52c22f17179b9bd5cb2621c05ec3a931adcb02", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "cutadapt", @@ -1621,10 +1417,7 @@ "published_at": "2024-11-15T07:49:59Z", "tag_sha": "8f139cecd95a23920617f2c2b154733494ed4562", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "cutadapt", @@ -1662,10 +1455,7 @@ "published_at": "2024-08-05T13:56:21Z", "tag_sha": "0473e157ac9a7b1d36845ff9f8fa7ac843d3b234", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "cutadapt", @@ -1703,10 +1493,7 @@ "published_at": "2024-06-27T09:36:26Z", "tag_sha": "3f40a1b6a84c02ad1cdde7a60a2be15f09731508", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "cutadapt", @@ -1744,10 +1531,7 @@ "published_at": "2024-04-03T13:29:42Z", "tag_sha": "717abb8a0372c1821f5837ab3a902be90faf4cba", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "cutadapt", @@ -1785,10 +1569,7 @@ "published_at": "2024-01-16T14:55:31Z", "tag_sha": "f3c97e1b9088b229d4bcdeb2f9a25f21d6552f8b", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "custom_dumpsoftwareversions", @@ -1812,9 +1593,7 @@ "vsearch_sintax", "vsearch_usearchglobal" ], - "subworkflows": [ - "fasta_newick_epang_gappa" - ] + "subworkflows": ["fasta_newick_epang_gappa"] }, "nextflow_version": "!>=23.04.0", "nf_core_version": null @@ -1824,10 +1603,40 @@ "published_at": "2023-11-13T11:35:32Z", "tag_sha": "113e90bdff42a52807f5c8b3cbaafaa31c145b9d", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], + "components": { + "modules": [ + "custom_dumpsoftwareversions", + "cutadapt", + "epang_place", + "epang_split", + "fastqc", + "gappa_examineassign", + "gappa_examinegraft", + "gappa_examineheattree", + "hmmer_eslalimask", + "hmmer_eslreformat", + "hmmer_hmmalign", + "hmmer_hmmbuild", + "kraken2_kraken2", + "mafft", + "multiqc", + "untar", + "vsearch_cluster", + "vsearch_sintax", + "vsearch_usearchglobal" + ], + "subworkflows": ["fasta_newick_epang_gappa"] + }, + "nextflow_version": "!>=23.04.0", + "nf_core_version": null + }, + { + "tag_name": "2.7.0", + "published_at": "2023-10-19T14:33:25Z", + "tag_sha": "4e48b7100302e2576ac1be2ccc7d464253e9d20e", + "has_schema": true, + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "custom_dumpsoftwareversions", @@ -1850,47 +1659,7 @@ "vsearch_sintax", "vsearch_usearchglobal" ], - "subworkflows": [ - "fasta_newick_epang_gappa" - ] - }, - "nextflow_version": "!>=23.04.0", - "nf_core_version": null - }, - { - "tag_name": "2.7.0", - "published_at": "2023-10-19T14:33:25Z", - "tag_sha": "4e48b7100302e2576ac1be2ccc7d464253e9d20e", - "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], - "components": { - "modules": [ - "custom_dumpsoftwareversions", - "cutadapt", - "epang_place", - "epang_split", - "fastqc", - "gappa_examineassign", - "gappa_examinegraft", - "gappa_examineheattree", - "hmmer_eslalimask", - "hmmer_eslreformat", - "hmmer_hmmalign", - "hmmer_hmmbuild", - "kraken2_kraken2", - "mafft", - "multiqc", - "untar", - "vsearch_cluster", - "vsearch_sintax", - "vsearch_usearchglobal" - ], - "subworkflows": [ - "fasta_newick_epang_gappa" - ] + "subworkflows": ["fasta_newick_epang_gappa"] }, "nextflow_version": "!>=23.04.0", "nf_core_version": null @@ -1900,10 +1669,7 @@ "published_at": "2023-06-28T06:57:20Z", "tag_sha": "3b252d263d101879c7077eae94a7a3d714b051aa", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "custom_dumpsoftwareversions", @@ -1923,9 +1689,7 @@ "vsearch_sintax", "vsearch_usearchglobal" ], - "subworkflows": [ - "fasta_newick_epang_gappa" - ] + "subworkflows": ["fasta_newick_epang_gappa"] }, "nextflow_version": "!>=23.04.0", "nf_core_version": null @@ -1935,10 +1699,7 @@ "published_at": "2023-06-27T07:09:40Z", "tag_sha": "9ac22bac93ffdf859da6bda751112ec0932892eb", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "custom_dumpsoftwareversions", @@ -1958,9 +1719,7 @@ "vsearch_sintax", "vsearch_usearchglobal" ], - "subworkflows": [ - "fasta_newick_epang_gappa" - ] + "subworkflows": ["fasta_newick_epang_gappa"] }, "nextflow_version": "!>=22.10.1", "nf_core_version": null @@ -1970,10 +1729,7 @@ "published_at": "2023-03-02T18:34:15Z", "tag_sha": "78b7514ceeba80efb66b0e973e5321878cb9b0ba", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "custom_dumpsoftwareversions", @@ -1991,10 +1747,7 @@ "published_at": "2022-12-07T15:52:21Z", "tag_sha": "83877d2fe539293818be84dec3bd1f43238c9c3c", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "custom_dumpsoftwareversions", @@ -2012,10 +1765,7 @@ "published_at": "2022-09-07T15:16:58Z", "tag_sha": "708b8398d007d9a8c907ce6da478717e1ab5f5bc", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "custom_dumpsoftwareversions", @@ -2033,17 +1783,9 @@ "published_at": "2022-05-27T11:14:40Z", "tag_sha": "aed35e5b4bad907ed2bdf6587efb82ad2578e6b1", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "custom_dumpsoftwareversions", - "cutadapt", - "fastqc", - "multiqc" - ] + "modules": ["custom_dumpsoftwareversions", "cutadapt", "fastqc", "multiqc"] }, "nextflow_version": "!>=21.10.3", "nf_core_version": null @@ -2053,17 +1795,9 @@ "published_at": "2022-04-05T14:40:16Z", "tag_sha": "306ad5df8f0a3b7cd033d040ddd440c09eb9a361", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "custom_dumpsoftwareversions", - "cutadapt", - "fastqc", - "multiqc" - ] + "modules": ["custom_dumpsoftwareversions", "cutadapt", "fastqc", "multiqc"] }, "nextflow_version": "!>=21.10.3", "nf_core_version": null @@ -2073,17 +1807,9 @@ "published_at": "2022-04-04T11:37:58Z", "tag_sha": "680a7a15ba7cc9c850e2d3eeb99c886e45d72c7d", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "custom_dumpsoftwareversions", - "cutadapt", - "fastqc", - "multiqc" - ] + "modules": ["custom_dumpsoftwareversions", "cutadapt", "fastqc", "multiqc"] }, "nextflow_version": "!>=21.10.3", "nf_core_version": null @@ -2093,17 +1819,9 @@ "published_at": "2022-01-31T14:11:47Z", "tag_sha": "3beb2392044ad0575df76b54b0a5a26c6ce4b32a", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "custom_dumpsoftwareversions", - "cutadapt", - "fastqc", - "multiqc" - ] + "modules": ["custom_dumpsoftwareversions", "cutadapt", "fastqc", "multiqc"] }, "nextflow_version": "!>=21.10.3" }, @@ -2112,16 +1830,9 @@ "published_at": "2021-10-28T15:02:11Z", "tag_sha": "80b3cb8b05d3b596bd0a52866e7febe40ea497db", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "fastqc", - "multiqc", - "cutadapt" - ] + "modules": ["fastqc", "multiqc", "cutadapt"] }, "nextflow_version": "!>=21.04.0" }, @@ -2130,16 +1841,9 @@ "published_at": "2021-09-14T12:01:06Z", "tag_sha": "68e4b5ff9aef5e97c9f8b8a56c8b7a394a38e18f", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "fastqc", - "multiqc", - "cutadapt" - ] + "modules": ["fastqc", "multiqc", "cutadapt"] }, "nextflow_version": "!>=21.04.0" }, @@ -2148,10 +1852,7 @@ "published_at": "2021-06-29T10:52:51Z", "tag_sha": "ce4d7f4bbe876be0d942cd597614143bf1677030", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": "!>=21.04.0" }, { @@ -2159,10 +1860,7 @@ "published_at": "2021-02-04T15:44:03Z", "tag_sha": "1e76f1c0c6d270572573a6ad76aa40bfc185c3da", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=20.04.0" }, { @@ -2170,10 +1868,7 @@ "published_at": "2020-11-02T14:40:10Z", "tag_sha": "70b23f4710094df9299e5ab2d18a1d412bbd4d04", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=19.10.0" }, { @@ -2181,10 +1876,7 @@ "published_at": "2019-12-19T20:38:39Z", "tag_sha": "cd23988d881ebb5c9fc42d5f030e3673274983c3", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=19.10.0" }, { @@ -2192,10 +1884,7 @@ "published_at": "2019-12-09T15:06:10Z", "tag_sha": "4371681d2418516e692065374b05669d96868a02", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=19.10.0" }, { @@ -2203,10 +1892,7 @@ "published_at": "2019-07-15T15:21:51Z", "tag_sha": "57e1ee2f9028d0a8c5838ee8aa8cf4b383f61174", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=18.10.1" }, { @@ -2214,10 +1900,7 @@ "published_at": "2018-12-13T11:16:07Z", "tag_sha": "f0357d61cf1afb1f0df4f8c701c62609f9374bbb", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=18.10.1" }, { @@ -2225,10 +1908,7 @@ "published_at": "2026-05-21T12:50:17Z", "tag_sha": "907778bf4a4fce3a4baa5d3b4c7721aa10008600", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "clustalo_align", @@ -2265,9 +1945,7 @@ }, "nextflow_version": "!>=25.10.4", "nf_core_version": "4.0.2", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null } ] @@ -2304,10 +1982,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "atac-seq", - "chromatin-accessibiity" - ], + "topics": ["atac-seq", "chromatin-accessibiity"], "visibility": "public", "forks": 134, "open_issues": 49, @@ -2360,10 +2035,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": -1, - "master_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "master_branch_protection_status_checks": ["nf-core", "pre-commit"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -2371,9 +2043,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "nf-core" - ], + "dev_branch_protection_status_checks": ["nf-core"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -2467,13 +2137,9 @@ "is_DSL2": true, "has_nf_test": false, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-validation" - ], + "master_nextflow_config_plugins": ["nf-validation"], "master_nextflow_config_manifest": {}, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -2483,10 +2149,7 @@ "published_at": "2023-08-07T22:00:22Z", "tag_sha": "1a1dbe52ffbd82256c941a032b0e22abbd925b8a", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "ataqv_ataqv", @@ -2542,10 +2205,7 @@ "published_at": "2023-07-21T17:08:07Z", "tag_sha": "415795d3c14fb296c6418b427279ca34ab976844", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "ataqv_ataqv", @@ -2601,10 +2261,7 @@ "published_at": "2023-07-21T14:13:10Z", "tag_sha": "d5037cde121faa030bf066bf96bfc74b00e3318d", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "ataqv_ataqv", @@ -2660,10 +2317,7 @@ "published_at": "2022-11-30T20:17:57Z", "tag_sha": "0add18866a5f095e93b8ec345a12b76d675f4af9", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "ataqv_ataqv", @@ -2719,10 +2373,7 @@ "published_at": "2022-05-12T20:26:57Z", "tag_sha": "f327c86324427c64716be09c98634ae0bc8165f6", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=19.10.0" }, { @@ -2730,10 +2381,7 @@ "published_at": "2020-07-29T15:34:54Z", "tag_sha": "1b3a832db5a53c92c2c89a4d6d79455e860461ad", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=19.10.0" }, { @@ -2741,10 +2389,7 @@ "published_at": "2020-07-02T10:27:10Z", "tag_sha": "766424e3a3f55c28fa746da519e3e61362a78d68", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=19.10.0" }, { @@ -2752,10 +2397,7 @@ "published_at": "2019-11-05T12:38:28Z", "tag_sha": "fa1e3f8993cd20e249b9df09d29c5498eff311d2", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=19.10.0" }, { @@ -2763,10 +2405,7 @@ "published_at": "2019-04-09T13:15:17Z", "tag_sha": "c65bf6cd11c8a98807084d2d4039822a19f03969", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=0.32.0" }, { @@ -2774,10 +2413,7 @@ "published_at": "2026-05-20T17:23:30Z", "tag_sha": "487128bfe873ccd75c2f19563ddbb5ef63ad0e39", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "ataqv_ataqv", @@ -2831,9 +2467,7 @@ }, "nextflow_version": "!>=25.10.4", "nf_core_version": "4.0.2", - "plugins": [ - "nf-validation" - ], + "plugins": ["nf-validation"], "co2footprint_files": null } ] @@ -2932,10 +2566,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": -1, - "master_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "master_branch_protection_status_checks": ["nf-core", "pre-commit"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -2943,10 +2574,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "dev_branch_protection_status_checks": ["nf-core", "pre-commit"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -3085,15 +2713,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "master_nextflow_config_plugins": ["nf-schema@2.5.1"], "master_nextflow_config_manifest": { "defaultBranch": "main" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "main" }, @@ -3103,10 +2727,7 @@ "published_at": "2026-05-05T09:14:48Z", "tag_sha": "61b9413bc0531a79190806fde34538fdfbbe15f6", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "autocycler_cluster", @@ -3155,9 +2776,7 @@ }, "nextflow_version": "!>=25.04.0", "nf_core_version": "3.5.2", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null }, { @@ -3165,10 +2784,7 @@ "published_at": "2025-10-17T12:52:01Z", "tag_sha": "76e4b12cacdc242891ea57e723c5e273f4ac71b4", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bakta_bakta", @@ -3212,10 +2828,7 @@ "published_at": "2024-11-18T14:48:41Z", "tag_sha": "be9c064f571ada41692f9e98f99474f16bf5c04b", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bakta_bakta", @@ -3255,10 +2868,7 @@ "published_at": "2024-06-24T09:10:55Z", "tag_sha": "c81202b7702c67d0e829085685083847b9e59435", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bakta_bakta", @@ -3295,10 +2905,7 @@ "published_at": "2024-06-12T15:28:35Z", "tag_sha": "d230ebf3d77e030bdcd0d002ef082a3870c68d99", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bakta_bakta", @@ -3335,10 +2942,7 @@ "published_at": "2024-04-17T08:05:46Z", "tag_sha": "9f368d48575dd16794fa04f099262b83d33d8739", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bakta_bakta", @@ -3376,10 +2980,7 @@ "published_at": "2023-10-24T06:59:41Z", "tag_sha": "e94a17331129cff2b9e2558d7698209f0cc3fcac", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bakta_bakta", @@ -3402,9 +3003,7 @@ "samtools_sort", "untar" ], - "subworkflows": [ - "fastq_trim_fastp_fastqc" - ] + "subworkflows": ["fastq_trim_fastp_fastqc"] }, "nextflow_version": "!>=23.04.0", "nf_core_version": null @@ -3414,10 +3013,7 @@ "published_at": "2021-08-27T12:26:07Z", "tag_sha": "959967364c7c0105b5b271acf0441fa9290e0d4c", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "fastqc", @@ -3436,10 +3032,7 @@ "published_at": "2020-11-05T11:00:42Z", "tag_sha": "4500b3bf69c45c1b5a8d368f24048575b18588dd", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=19.10.0" }, { @@ -3447,10 +3040,7 @@ "published_at": "2019-12-13T13:07:30Z", "tag_sha": "c6d5c3a0f80099fa247bf8be1cdedcf5fce644fb", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=19.10.0" }, { @@ -3458,10 +3048,7 @@ "published_at": "2019-05-06T14:47:21Z", "tag_sha": "ae7f903ffae61fb86d7af52b0751ee5fce030479", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=18.10.1" }, { @@ -3469,10 +3056,7 @@ "published_at": "2026-05-11T15:10:30Z", "tag_sha": "92d5f6d208c5466b4a1963eacbbbffb0ebd3e6fb", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "autocycler_cluster", @@ -3521,9 +3105,7 @@ }, "nextflow_version": "!>=25.04.0", "nf_core_version": "3.5.2", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null } ] @@ -3621,10 +3203,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": -1, - "master_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "master_branch_protection_status_checks": ["nf-core", "pre-commit"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -3632,10 +3211,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "pre-commit", - "nf-core" - ], + "dev_branch_protection_status_checks": ["pre-commit", "nf-core"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -3694,15 +3270,11 @@ "is_DSL2": true, "has_nf_test": false, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-schema@2.4.2" - ], + "master_nextflow_config_plugins": ["nf-schema@2.4.2"], "master_nextflow_config_manifest": { "defaultBranch": "master" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -3712,10 +3284,7 @@ "published_at": "2021-06-18T12:11:08Z", "tag_sha": "834642d8ac150ca10d705833223e7bcf15efc210", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": "!>=21.04.0" }, { @@ -3723,10 +3292,7 @@ "published_at": "2021-05-10T21:33:05Z", "tag_sha": "0a087bf1162c734dc38ab5b274a2ce7eb3733077", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": "!>=20.11.0-edge" }, { @@ -3734,10 +3300,7 @@ "published_at": "2021-05-08T16:50:35Z", "tag_sha": "f5ad2bbb5cfd01d479fb7898a0584538fc4dfec1", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": "!>=20.11.0-edge" }, { @@ -3799,9 +3362,7 @@ }, "nextflow_version": "!>=25.10.0", "nf_core_version": "3.5.2", - "plugins": [ - "nf-schema@2.4.2" - ], + "plugins": ["nf-schema@2.4.2"], "co2footprint_files": null } ] @@ -3838,11 +3399,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "bamtofastq", - "conversion", - "cramtofastq" - ], + "topics": ["bamtofastq", "conversion", "cramtofastq"], "visibility": "public", "forks": 18, "open_issues": 8, @@ -3895,11 +3452,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": -1, - "master_branch_protection_status_checks": [ - "nf-core", - "pre-commit", - "nf-test-changes" - ], + "master_branch_protection_status_checks": ["nf-core", "pre-commit", "nf-test-changes"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -3907,10 +3460,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "dev_branch_protection_status_checks": ["nf-core", "pre-commit"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -3984,15 +3534,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-schema@2.6.1" - ], + "master_nextflow_config_plugins": ["nf-schema@2.6.1"], "master_nextflow_config_manifest": { "defaultBranch": "master" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.6.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.6.1"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -4002,10 +3548,7 @@ "published_at": "2026-05-13T11:16:10Z", "tag_sha": "8a295860c0c9221337dec7f2620709a47cea254d", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "cat_fastq", @@ -4021,17 +3564,11 @@ "samtools_stats", "samtools_view" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.10.4", "nf_core_version": "4.0.2", - "plugins": [ - "nf-schema@2.6.1" - ], + "plugins": ["nf-schema@2.6.1"], "co2footprint_files": null }, { @@ -4039,10 +3576,7 @@ "published_at": "2025-06-17T07:53:08Z", "tag_sha": "869832186b25d2ccbcd31d5f69edacc1ba32b718", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "cat_fastq", @@ -4058,11 +3592,7 @@ "samtools_stats", "samtools_view" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.3.1" @@ -4072,10 +3602,7 @@ "published_at": "2024-05-06T09:59:25Z", "tag_sha": "38fdb8becade1ac67dc733da62ddec0f188998dc", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "cat_fastq", @@ -4104,10 +3631,7 @@ "published_at": "2023-10-06T14:43:51Z", "tag_sha": "c70f49b20c83c72a0e6198e4b13edb5e2fb14725", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "cat_fastq", @@ -4132,10 +3656,7 @@ "published_at": "2023-05-31T14:11:18Z", "tag_sha": "ceae4d6d08356d22c3b8089292167d86d1ff7d15", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "cat_fastq", @@ -4160,10 +3681,7 @@ "published_at": "2022-01-13T08:19:00Z", "tag_sha": "b1fc8255cc5af1fd617de199a62408146c083f43", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=20.04.1" }, { @@ -4171,10 +3689,7 @@ "published_at": "2021-04-22T15:52:55Z", "tag_sha": "d6756dd74d3347d1fee6cd19052f536db7d9d0ab", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=20.04.1" }, { @@ -4182,10 +3697,7 @@ "published_at": "2020-09-10T08:25:53Z", "tag_sha": "1d9d14f341d544dad7136f5049921dc6da3700e4", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=20.04.1" }, { @@ -4193,10 +3705,7 @@ "published_at": "2026-05-13T12:19:23Z", "tag_sha": "665440cdcccfec66ceb8212589a3c6ee92920d49", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "cat_fastq", @@ -4212,17 +3721,11 @@ "samtools_stats", "samtools_view" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.10.4", "nf_core_version": "4.0.2", - "plugins": [ - "nf-schema@2.6.1" - ], + "plugins": ["nf-schema@2.6.1"], "co2footprint_files": null } ] @@ -4259,13 +3762,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "cage", - "cage-seq", - "cageseq-data", - "gene-expression", - "rna" - ], + "topics": ["cage", "cage-seq", "cageseq-data", "gene-expression", "rna"], "visibility": "public", "forks": 12, "open_issues": 13, @@ -4318,10 +3815,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": -1, - "master_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "master_branch_protection_status_checks": ["nf-core", "pre-commit"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -4385,9 +3879,7 @@ "has_nf_test_dev": true, "master_nextflow_config_plugins": [], "master_nextflow_config_manifest": {}, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "main" }, @@ -4397,10 +3889,7 @@ "published_at": "2021-01-14T07:56:52Z", "tag_sha": "838d2a5165edb86439d7ff0400bd385d6bcf6927", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=20.04.0" }, { @@ -4408,10 +3897,7 @@ "published_at": "2020-11-23T14:51:08Z", "tag_sha": "0e58db8cce0555684fb71ccaa8ced7c7a8fa4fdc", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=20.04.0" }, { @@ -4419,10 +3905,7 @@ "published_at": "2020-10-16T11:11:58Z", "tag_sha": "729fbcb775bfde5c2f2af731374fbdfcb697d5eb", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=19.10.0" }, { @@ -4430,10 +3913,7 @@ "published_at": "2026-05-20T10:01:50Z", "tag_sha": "f3ce0656b62b7a2b1622f1ff31b679114c5bf415", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bowtie2_align", @@ -4555,10 +4035,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": -1, - "master_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "master_branch_protection_status_checks": ["nf-core", "pre-commit"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -4566,11 +4043,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "nf-core", - "Run pipeline with test data", - "pre-commit" - ], + "dev_branch_protection_status_checks": ["nf-core", "Run pipeline with test data", "pre-commit"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -4604,13 +4077,9 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-validation@1.1.3" - ], + "master_nextflow_config_plugins": ["nf-validation@1.1.3"], "master_nextflow_config_manifest": {}, - "dev_nextflow_config_plugins": [ - "nf-schema@2.2.0" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.2.0"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -4620,10 +4089,7 @@ "published_at": "2024-05-24T13:20:28Z", "tag_sha": "20b66e785a822028eaa125583aad0747d55bba61", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bedtools_maskfasta", @@ -4662,11 +4128,7 @@ "trimmomatic", "umitools_extract" ], - "subworkflows": [ - "bam_rseqc", - "bam_stats_samtools", - "fastq_align_bwaaln" - ] + "subworkflows": ["bam_rseqc", "bam_stats_samtools", "fastq_align_bwaaln"] }, "nextflow_version": "!>=23.04.0", "nf_core_version": "2.14.1" @@ -4676,10 +4138,7 @@ "published_at": "2025-05-13T20:59:34Z", "tag_sha": "649f56c01b44fe26c174fd901a9c79be15e4be00", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bedtools_maskfasta", @@ -4718,17 +4177,11 @@ "trimmomatic", "umitools_extract" ], - "subworkflows": [ - "bam_rseqc", - "bam_stats_samtools", - "fastq_align_bwaaln" - ] + "subworkflows": ["bam_rseqc", "bam_stats_samtools", "fastq_align_bwaaln"] }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.2.1", - "plugins": [ - "nf-validation@1.1.3" - ], + "plugins": ["nf-validation@1.1.3"], "co2footprint_files": null } ] @@ -4818,10 +4271,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": true, - "master_branch_protection_status_checks": [ - "pre-commit", - "nf-core" - ], + "master_branch_protection_status_checks": ["pre-commit", "nf-core"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -4914,15 +4364,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-schema@2.2.0" - ], + "master_nextflow_config_plugins": ["nf-schema@2.2.0"], "master_nextflow_config_manifest": { "defaultBranch": "master" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -4932,25 +4378,14 @@ "published_at": "2026-04-30T21:29:41Z", "tag_sha": "eebfc70c4fc381335540854fefbc47c219cfa854", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "multiqc" - ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "modules": ["multiqc"], + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.04.0", "nf_core_version": "3.5.1", - "plugins": [ - "nf-schema@2.2.0" - ], + "plugins": ["nf-schema@2.2.0"], "co2footprint_files": null } ] @@ -4987,13 +4422,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "chip", - "chip-seq", - "chromatin-immunoprecipitation", - "macs2", - "peak-calling" - ], + "topics": ["chip", "chip-seq", "chromatin-immunoprecipitation", "macs2", "peak-calling"], "visibility": "public", "forks": 176, "open_issues": 31, @@ -5046,9 +4475,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": -1, - "master_branch_protection_status_checks": [ - "nf-core" - ], + "master_branch_protection_status_checks": ["nf-core"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -5056,9 +4483,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "nf-core" - ], + "dev_branch_protection_status_checks": ["nf-core"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -5177,13 +4602,9 @@ "is_DSL2": true, "has_nf_test": false, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-validation@1.1.3" - ], + "master_nextflow_config_plugins": ["nf-validation@1.1.3"], "master_nextflow_config_manifest": {}, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -5193,10 +4614,7 @@ "published_at": "2024-10-07T15:14:22Z", "tag_sha": "76e2382b6d443db4dc2396e6831d1243256d80b0", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bowtie2_align", @@ -5255,10 +4673,7 @@ "published_at": "2022-10-03T15:30:50Z", "tag_sha": "51eba00b32885c4d0bec60db3cb0a45eb61e34c5", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bowtie2_align", @@ -5303,10 +4718,7 @@ "published_at": "2021-04-22T19:29:04Z", "tag_sha": "6924b669422215f9021144b251e83fc9929be1fe", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=19.10.0" }, { @@ -5314,10 +4726,7 @@ "published_at": "2020-07-29T16:35:15Z", "tag_sha": "0f487ed76dc947793ab48527d8d3025f5f3060a5", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=19.10.0" }, { @@ -5325,10 +4734,7 @@ "published_at": "2020-07-02T11:20:41Z", "tag_sha": "048fd6854fcc85b355c61dfc2e21da0bcc6399ea", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=19.10.0" }, { @@ -5336,10 +4742,7 @@ "published_at": "2019-11-05T12:15:37Z", "tag_sha": "21be3149542cdc84431e12d1e092359058aed32a", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=19.10.0" }, { @@ -5347,10 +4750,7 @@ "published_at": "2019-06-06T15:14:45Z", "tag_sha": "5e95c969bae35a8a39d47dfe70f8ec18e990c979", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=0.32.0" }, { @@ -5358,10 +4758,7 @@ "published_at": "2026-05-20T17:23:03Z", "tag_sha": "cbfbdef2da846e7ddebf1d15e5b93626270e6353", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bedtools_genomecov", @@ -5415,9 +4812,7 @@ }, "nextflow_version": "!>=25.10.4", "nf_core_version": "4.0.2", - "plugins": [ - "nf-validation@1.1.3" - ], + "plugins": ["nf-validation@1.1.3"], "co2footprint_files": null } ] @@ -5517,9 +4912,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": -1, - "master_branch_protection_status_checks": [ - "nf-core" - ], + "master_branch_protection_status_checks": ["nf-core"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -5527,9 +4920,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "nf-core" - ], + "dev_branch_protection_status_checks": ["nf-core"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -5563,13 +4954,9 @@ "is_DSL2": true, "has_nf_test": false, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-validation@1.1.3" - ], + "master_nextflow_config_plugins": ["nf-validation@1.1.3"], "master_nextflow_config_manifest": {}, - "dev_nextflow_config_plugins": [ - "nf-schema@2.3.0" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.3.0"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -5579,10 +4966,7 @@ "published_at": "2024-02-10T09:02:00Z", "tag_sha": "8e0e14c84f90c94d975c2bac6bde8e5a1d5bc8ab", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bwa_index", @@ -5600,10 +4984,7 @@ "samtools_view", "trimgalore" ], - "subworkflows": [ - "bam_markduplicates_picard", - "bam_stats_samtools" - ] + "subworkflows": ["bam_markduplicates_picard", "bam_stats_samtools"] }, "nextflow_version": "!>=23.04.0", "nf_core_version": null @@ -5613,10 +4994,7 @@ "published_at": "2023-06-27T08:31:03Z", "tag_sha": "09a5015cf8d10b6f0fd6e96a3039f60e4a8b1670", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bwa_index", @@ -5635,10 +5013,7 @@ "samtools_view", "trimgalore" ], - "subworkflows": [ - "bam_markduplicates_picard", - "bam_stats_samtools" - ] + "subworkflows": ["bam_markduplicates_picard", "bam_stats_samtools"] }, "nextflow_version": "!>=22.10.1", "nf_core_version": null @@ -5648,10 +5023,7 @@ "published_at": "2023-06-05T11:36:20Z", "tag_sha": "09bdf9a4686fbef160c901096a1c2bb32b4ed39c", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bwa_index", @@ -5670,10 +5042,7 @@ "samtools_view", "trimgalore" ], - "subworkflows": [ - "bam_markduplicates_picard", - "bam_stats_samtools" - ] + "subworkflows": ["bam_markduplicates_picard", "bam_stats_samtools"] }, "nextflow_version": "!>=22.10.1", "nf_core_version": null @@ -5683,10 +5052,7 @@ "published_at": "2023-05-17T14:18:14Z", "tag_sha": "0ec8d8552c32831242e99549879aa8c4a0ab0a12", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bwa_index", @@ -5705,9 +5071,7 @@ "samtools_view", "trimgalore" ], - "subworkflows": [ - "bam_stats_samtools" - ] + "subworkflows": ["bam_stats_samtools"] }, "nextflow_version": "!>=22.10.1", "nf_core_version": null @@ -5717,10 +5081,7 @@ "published_at": "2023-05-17T06:52:28Z", "tag_sha": "41452bfef40b220d9138dfca16091f0c9db58f3a", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bwa_index", @@ -5739,9 +5100,7 @@ "samtools_view", "trimgalore" ], - "subworkflows": [ - "bam_stats_samtools" - ] + "subworkflows": ["bam_stats_samtools"] }, "nextflow_version": "!>=22.10.1", "nf_core_version": null @@ -5751,10 +5110,7 @@ "published_at": "2023-03-09T11:08:49Z", "tag_sha": "cce84734ef507c7ab039bdbc498ff31679a32fb4", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bwa_index", @@ -5773,9 +5129,7 @@ "samtools_view", "trimgalore" ], - "subworkflows": [ - "bam_stats_samtools" - ] + "subworkflows": ["bam_stats_samtools"] }, "nextflow_version": "!>=22.10.1", "nf_core_version": null @@ -5785,10 +5139,7 @@ "published_at": "2022-06-22T14:11:21Z", "tag_sha": "50681adaf7c089d51071ebbebee75e07c6650965", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bwa_index", @@ -5815,10 +5166,7 @@ "published_at": "2022-06-01T07:45:57Z", "tag_sha": "b0152a3629114ff0e1fb5db03403e0677783c8a6", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bwa_index", @@ -5846,10 +5194,7 @@ "published_at": "2026-04-28T14:06:54Z", "tag_sha": "b5e2fbe05c2892f963e7e02784efd657d429634d", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bwa_index", @@ -5884,9 +5229,7 @@ }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.3.1", - "plugins": [ - "nf-validation@1.1.3" - ], + "plugins": ["nf-validation@1.1.3"], "co2footprint_files": null } ] @@ -5986,10 +5329,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": -1, - "master_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "master_branch_protection_status_checks": ["nf-core", "pre-commit"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -5997,10 +5337,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "dev_branch_protection_status_checks": ["nf-core", "pre-commit"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -6071,9 +5408,7 @@ "has_nf_test_dev": true, "master_nextflow_config_plugins": [], "master_nextflow_config_manifest": {}, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -6083,10 +5418,7 @@ "published_at": "2026-05-11T05:05:16Z", "tag_sha": "bdba2f02bc819da073fc80b18ba9cc9d76292620", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "agat_convertbed2gff", @@ -6188,12 +5520,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "clip", - "clip-seq", - "peak-calling", - "rna-rbp-interactions" - ], + "topics": ["clip", "clip-seq", "peak-calling", "rna-rbp-interactions"], "visibility": "public", "forks": 42, "open_issues": 51, @@ -6319,10 +5646,7 @@ "published_at": "2021-04-27T10:40:00Z", "tag_sha": "45ae3c0b9b16206b687f4a645e1643c85b3f1ab4", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=20.04.0" }, { @@ -6330,10 +5654,7 @@ "published_at": "2023-03-15T21:35:41Z", "tag_sha": "ed1f64863be8cf400b65ffc767ce1e90275c0cea", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=20.04.0", "nf_core_version": null, "plugins": [], @@ -6373,12 +5694,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "adna", - "ancient-dna", - "coprolite", - "microbiome" - ], + "topics": ["adna", "ancient-dna", "coprolite", "microbiome"], "visibility": "public", "forks": 6, "open_issues": 3, @@ -6511,15 +5827,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "master_nextflow_config_plugins": ["nf-schema@2.5.1"], "master_nextflow_config_manifest": { "defaultBranch": "master" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -6529,10 +5841,7 @@ "published_at": "2026-02-17T06:31:12Z", "tag_sha": "045d569d5b01b2d1572220718e64a6d054ad57eb", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bowtie2_align", @@ -6552,17 +5861,11 @@ "untar", "xz_decompress" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.04.0", "nf_core_version": "3.5.2", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null }, { @@ -6570,10 +5873,7 @@ "published_at": "2025-05-22T10:27:06Z", "tag_sha": "56308278ce860c1e96e2b9d4d39f4eb5e1bb7638", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bowtie2_align", @@ -6593,11 +5893,7 @@ "untar", "xz_decompress" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.10.0", "nf_core_version": "3.2.0" @@ -6607,10 +5903,7 @@ "published_at": "2022-11-04T16:44:51Z", "tag_sha": "baab5d8ad1a4bf3aaf386166328cec81adb7aba2", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=19.10.0" }, { @@ -6618,10 +5911,7 @@ "published_at": "2020-04-29T11:07:03Z", "tag_sha": "7dc3362267bc89ce658651d47534455e01dc152b", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=19.10.0" }, { @@ -6629,10 +5919,7 @@ "published_at": "2019-04-29T14:55:26Z", "tag_sha": "e69aa3dd0e0d090e49f0c13208a15da9460b8427", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=0.32.0" }, { @@ -6640,10 +5927,7 @@ "published_at": "2026-02-15T22:49:15Z", "tag_sha": "1c63bc8fe75e3ee3c0b884e2bcb94d23dc3b281f", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bowtie2_align", @@ -6663,17 +5947,11 @@ "untar", "xz_decompress" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.04.0", "nf_core_version": "3.5.2", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null } ] @@ -6764,21 +6042,14 @@ "master_branch_exists": false, "main_branch_exists": true, "main_branch_protection_up_to_date": -1, - "main_branch_protection_status_checks": [ - "nf-core", - "Run pipeline with test data", - "pre-commit" - ], + "main_branch_protection_status_checks": ["nf-core", "Run pipeline with test data", "pre-commit"], "main_branch_protection_required_reviews": 2, "main_branch_protection_require_codeowner_review": false, "main_branch_protection_require_non_stale_review": false, "main_branch_protection_enforce_admins": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "nf-core", - "confirm-pass" - ], + "dev_branch_protection_status_checks": ["nf-core", "confirm-pass"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -6827,16 +6098,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "main_nextflow_config_plugins": [ - "nf-schema@2.3.0" - ], + "main_nextflow_config_plugins": ["nf-schema@2.3.0"], "main_nextflow_config_manifest": { "defaultBranch": "master" }, - "dev_nextflow_config_plugins": [ - "nf-core-utils@0.4.0", - "nf-schema@2.7.1" - ], + "dev_nextflow_config_plugins": ["nf-core-utils@0.4.0", "nf-schema@2.7.1"], "dev_nextflow_config_manifest": { "defaultBranch": "main" }, @@ -6846,10 +6112,7 @@ "published_at": "2026-05-19T15:15:08Z", "tag_sha": "8e82d2b5a0fa3cdf1c8ef0da536136d6584718dd", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "cnvkit_batch", @@ -6887,9 +6150,7 @@ }, "nextflow_version": "!>=25.10.4", "nf_core_version": "4.0.2", - "plugins": [ - "nf-schema@2.3.0" - ], + "plugins": ["nf-schema@2.3.0"], "co2footprint_files": null } ] @@ -6987,22 +6248,14 @@ "master_branch_exists": false, "main_branch_exists": true, "main_branch_protection_up_to_date": -1, - "main_branch_protection_status_checks": [ - "pre-commit", - "nf-core", - "confirm-pass" - ], + "main_branch_protection_status_checks": ["pre-commit", "nf-core", "confirm-pass"], "main_branch_protection_required_reviews": 2, "main_branch_protection_require_codeowner_review": false, "main_branch_protection_require_non_stale_review": false, "main_branch_protection_enforce_admins": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "nf-core", - "pre-commit", - "confirm-pass" - ], + "dev_branch_protection_status_checks": ["nf-core", "pre-commit", "confirm-pass"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -7076,15 +6329,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "main_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "main_nextflow_config_plugins": ["nf-schema@2.5.1"], "main_nextflow_config_manifest": { "defaultBranch": "main" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "main" }, @@ -7133,9 +6382,7 @@ }, "nextflow_version": "!>=25.10.4", "nf_core_version": "4.0.1", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null }, { @@ -7182,9 +6429,7 @@ }, "nextflow_version": "!>=25.04.2", "nf_core_version": "3.5.1", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null }, { @@ -7192,12 +6437,7 @@ "published_at": "2025-11-14T10:10:05Z", "tag_sha": "628ac51463a022a3678e7a42dd25869842b96c17", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md", - "docs/usage/dev.md", - "docs/usage/faq.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md", "docs/usage/dev.md", "docs/usage/faq.md"], "components": { "modules": [ "bracken_build", @@ -7229,9 +6469,7 @@ }, "nextflow_version": "!>=25.04.2", "nf_core_version": "3.4.1", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null }, { @@ -7239,11 +6477,7 @@ "published_at": "2025-06-19T07:45:45Z", "tag_sha": "08be5d25eb97f40f32a232e3ae12ef0d7f6c7fe5", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md", - "docs/usage/faq.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md", "docs/usage/faq.md"], "components": { "modules": [ "bracken_build", @@ -7318,9 +6552,7 @@ }, "nextflow_version": "!>=25.10.4", "nf_core_version": "4.0.2", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null } ] @@ -7357,12 +6589,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "crispr", - "crispr-analysis", - "crispr-cas", - "ngs" - ], + "topics": ["crispr", "crispr-analysis", "crispr-cas", "ngs"], "visibility": "public", "forks": 36, "open_issues": 30, @@ -7415,10 +6642,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": -1, - "master_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "master_branch_protection_status_checks": ["nf-core", "pre-commit"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -7490,14 +6714,9 @@ "is_DSL2": true, "has_nf_test": false, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-schema@2.1.1" - ], + "master_nextflow_config_plugins": ["nf-schema@2.1.1"], "master_nextflow_config_manifest": {}, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1", - "nf-gpt@0.4.0" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1", "nf-gpt@0.4.0"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -7539,11 +6758,7 @@ "vsearch_cluster", "vsearch_sort" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.0.2" @@ -7767,10 +6982,7 @@ "published_at": "2023-02-02T10:11:01Z", "tag_sha": "53572ae0879454115d778862e89614e6279856f8", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bowtie2_align", @@ -7829,17 +7041,11 @@ "vsearch_cluster", "vsearch_sort" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.04.0", "nf_core_version": "3.5.1", - "plugins": [ - "nf-schema@2.1.1" - ], + "plugins": ["nf-schema@2.1.1"], "co2footprint_files": null } ] @@ -7968,10 +7174,7 @@ "published_at": "2019-07-10T17:38:01Z", "tag_sha": "7d00851db258fcaa2ac668c5779d3ae576fbf5c2", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ] + "doc_files": ["docs/output.md", "docs/usage.md"] } ] }, @@ -8007,12 +7210,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "cutandrun", - "cutandrun-seq", - "cutandtag", - "cutandtag-seq" - ], + "topics": ["cutandrun", "cutandrun-seq", "cutandtag", "cutandtag-seq"], "visibility": "public", "forks": 71, "open_issues": 57, @@ -8065,9 +7263,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": -1, - "master_branch_protection_status_checks": [ - "nf-core" - ], + "master_branch_protection_status_checks": ["nf-core"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -8075,9 +7271,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "nf-core" - ], + "dev_branch_protection_status_checks": ["nf-core"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -8151,13 +7345,9 @@ "is_DSL2": true, "has_nf_test": false, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-validation@1.1.3" - ], + "master_nextflow_config_plugins": ["nf-validation@1.1.3"], "master_nextflow_config_manifest": {}, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -8167,10 +7357,7 @@ "published_at": "2024-02-01T16:38:34Z", "tag_sha": "6e1125d4fee4ea7c8b70ed836bb0e92a89e3305f", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bedtools_bamtobed", @@ -8206,10 +7393,7 @@ "ucsc_bedgraphtobigwig", "untar" ], - "subworkflows": [ - "bam_sort_stats_samtools", - "bam_stats_samtools" - ] + "subworkflows": ["bam_sort_stats_samtools", "bam_stats_samtools"] }, "nextflow_version": "!>=23.04.0", "nf_core_version": null @@ -8219,10 +7403,7 @@ "published_at": "2023-10-25T10:32:53Z", "tag_sha": "2727de382fb7df8f37fc4c6dbde99c979be04e77", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bedtools_bamtobed", @@ -8258,10 +7439,7 @@ "ucsc_bedgraphtobigwig", "untar" ], - "subworkflows": [ - "bam_sort_stats_samtools", - "bam_stats_samtools" - ] + "subworkflows": ["bam_sort_stats_samtools", "bam_stats_samtools"] }, "nextflow_version": "!>=23.04.0", "nf_core_version": null @@ -8271,10 +7449,7 @@ "published_at": "2023-08-31T16:16:52Z", "tag_sha": "506a325350fe1ac2d99d998adf8f1e2f010892f5", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bedtools_bamtobed", @@ -8310,10 +7485,7 @@ "ucsc_bedgraphtobigwig", "untar" ], - "subworkflows": [ - "bam_sort_stats_samtools", - "bam_stats_samtools" - ] + "subworkflows": ["bam_sort_stats_samtools", "bam_stats_samtools"] }, "nextflow_version": "!>=23.04.0", "nf_core_version": null @@ -8323,10 +7495,7 @@ "published_at": "2023-03-10T11:20:46Z", "tag_sha": "42502fb44975e930eec865353c5481f472bcf766", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bedtools_bamtobed", @@ -8360,10 +7529,7 @@ "ucsc_bedgraphtobigwig", "untar" ], - "subworkflows": [ - "bam_sort_stats_samtools", - "bam_stats_samtools" - ] + "subworkflows": ["bam_sort_stats_samtools", "bam_stats_samtools"] }, "nextflow_version": "!>=22.10.1", "nf_core_version": null @@ -8373,10 +7539,7 @@ "published_at": "2022-10-27T09:10:05Z", "tag_sha": "dcaa4423d783017996c30302d16d772facb0da7e", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bedtools_bamtobed", @@ -8416,10 +7579,7 @@ "published_at": "2022-06-08T13:11:07Z", "tag_sha": "971984a48ad4dc5b39fc20b56c5729f4ca20379a", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bedtools_bamtobed", @@ -8457,10 +7617,7 @@ "published_at": "2022-01-20T11:08:19Z", "tag_sha": "c30a37fd57dcd717870c1ce947bc157ca3a88838", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bedtools_bamtobed", @@ -8496,10 +7653,7 @@ "published_at": "2021-11-06T09:43:06Z", "tag_sha": "5b9f4fad41d11e98cbbfa30359a6e494f8f77694", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bedtools_bamtobed", @@ -8534,10 +7688,7 @@ "published_at": "2026-05-14T10:51:51Z", "tag_sha": "d59714a50c67486951b480febb726e47a7833187", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bedtools_bamtobed", @@ -8584,9 +7735,7 @@ }, "nextflow_version": "!>=25.04.0", "nf_core_version": "3.4.1", - "plugins": [ - "nf-validation@1.1.3" - ], + "plugins": ["nf-validation@1.1.3"], "co2footprint_files": null } ] @@ -8623,11 +7772,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "dartseq", - "rna-editing", - "rnaseq" - ], + "topics": ["dartseq", "rna-editing", "rnaseq"], "visibility": "public", "forks": 0, "open_issues": 0, @@ -8680,10 +7825,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": true, - "master_branch_protection_status_checks": [ - "pre-commit", - "nf-core" - ], + "master_branch_protection_status_checks": ["pre-commit", "nf-core"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -8717,15 +7859,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "master_nextflow_config_plugins": ["nf-schema@2.5.1"], "master_nextflow_config_manifest": { "defaultBranch": "master" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -8735,10 +7873,7 @@ "published_at": "2026-05-20T14:17:08Z", "tag_sha": "6d947beb5d825b0bdf63ec7815cff59ecfd118b2", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "fastp", @@ -8753,17 +7888,11 @@ "star_genomegenerate", "trimgalore" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.04.0", "nf_core_version": "3.5.2", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null } ] @@ -8853,10 +7982,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": -1, - "master_branch_protection_status_checks": [ - "pre-commit", - "nf-core" - ], + "master_branch_protection_status_checks": ["pre-commit", "nf-core"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -8864,10 +7990,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "pre-commit", - "nf-core" - ], + "dev_branch_protection_status_checks": ["pre-commit", "nf-core"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -8896,13 +8019,9 @@ "is_DSL2": true, "has_nf_test": false, "has_nf_test_dev": false, - "master_nextflow_config_plugins": [ - "nf-validation@1.1.3" - ], + "master_nextflow_config_plugins": ["nf-validation@1.1.3"], "master_nextflow_config_manifest": {}, - "dev_nextflow_config_plugins": [ - "nf-schema@2.1.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.1.1"], "dev_nextflow_config_manifest": {}, "releases": [ { @@ -8910,25 +8029,14 @@ "published_at": "2024-12-11T10:47:53Z", "tag_sha": "daa8765856886120b6fb98612a8afe3d2d48d239", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "multiqc" - ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "modules": ["multiqc"], + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.0.2", - "plugins": [ - "nf-validation@1.1.3" - ], + "plugins": ["nf-validation@1.1.3"], "co2footprint_files": null } ] @@ -8963,10 +8071,7 @@ "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, - "topics": [ - "proteomics", - "shotgun-ms" - ], + "topics": ["proteomics", "shotgun-ms"], "visibility": "public", "forks": 3, "open_issues": 7, @@ -9279,10 +8384,7 @@ "published_at": "2022-05-05T14:41:23Z", "tag_sha": "e1f270b8260d1795ac8cac1cdce47caf015162ad", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ] + "doc_files": ["docs/output.md", "docs/usage.md"] } ] }, @@ -9380,10 +8482,7 @@ "master_branch_exists": false, "main_branch_exists": true, "main_branch_protection_up_to_date": true, - "main_branch_protection_status_checks": [ - "pre-commit", - "nf-core" - ], + "main_branch_protection_status_checks": ["pre-commit", "nf-core"], "main_branch_protection_required_reviews": 2, "main_branch_protection_require_codeowner_review": false, "main_branch_protection_require_non_stale_review": false, @@ -9391,10 +8490,7 @@ "main_uses_ruleset": true, "dev_branch_exists": true, "dev_branch_protection_up_to_date": true, - "dev_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "dev_branch_protection_status_checks": ["nf-core", "pre-commit"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -9464,15 +8560,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "main_nextflow_config_plugins": [ - "nf-schema@2.4.2" - ], + "main_nextflow_config_plugins": ["nf-schema@2.4.2"], "main_nextflow_config_manifest": { "defaultBranch": "master" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.3.0" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.3.0"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -9482,10 +8574,7 @@ "published_at": "2025-06-26T12:43:52Z", "tag_sha": "151accd47c04e24cde6fdefc7aa0e371b9ab157a", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bedtools_getfasta", @@ -9497,17 +8586,11 @@ "custom_getchromsizes", "gawk" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.2.0", - "plugins": [ - "nf-schema@2.4.2" - ], + "plugins": ["nf-schema@2.4.2"], "co2footprint_files": null } ] @@ -9544,12 +8627,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "community-workflow", - "deep-mutational-scanning", - "genotype-phenotype", - "shotgun-sequencing" - ], + "topics": ["community-workflow", "deep-mutational-scanning", "genotype-phenotype", "shotgun-sequencing"], "visibility": "public", "forks": 4, "open_issues": 3, @@ -9602,10 +8680,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": true, - "master_branch_protection_status_checks": [ - "pre-commit", - "nf-core" - ], + "master_branch_protection_status_checks": ["pre-commit", "nf-core"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -9649,15 +8724,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-schema@2.3.0" - ], + "master_nextflow_config_plugins": ["nf-schema@2.3.0"], "master_nextflow_config_manifest": { "defaultBranch": "master" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -9667,28 +8738,14 @@ "published_at": "2026-05-19T13:40:22Z", "tag_sha": "ff38f7db7af65b768bc764bcdce30118769786bd", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "bwa_index", - "bwa_mem", - "fastqc", - "multiqc" - ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "modules": ["bwa_index", "bwa_mem", "fastqc", "multiqc"], + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.10.4", "nf_core_version": "4.0.2", - "plugins": [ - "nf-schema@2.3.0" - ], + "plugins": ["nf-schema@2.3.0"], "co2footprint_files": null } ] @@ -9723,12 +8780,7 @@ "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, - "topics": [ - "deep-variant", - "dna", - "google", - "variant-calling" - ], + "topics": ["deep-variant", "dna", "google", "variant-calling"], "visibility": "public", "forks": 21, "open_issues": 10, @@ -10061,20 +9113,14 @@ "published_at": "2018-11-19T14:44:51Z", "tag_sha": "2b5486356c4dbd4dcb598b611281997119c2e350", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ] + "doc_files": ["docs/output.md", "docs/usage.md"] }, { "tag_name": "dev", "published_at": "2019-01-03T10:02:01Z", "tag_sha": "a1ee13c06b1a1cd662afcdd1ea1194c8b0916bdb", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ] + "doc_files": ["docs/output.md", "docs/usage.md"] } ] }, @@ -10110,12 +9156,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "demo", - "minimal-example", - "training", - "tutorial" - ], + "topics": ["demo", "minimal-example", "training", "tutorial"], "visibility": "public", "forks": 26, "open_issues": 5, @@ -10230,15 +9271,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-schema@2.6.1" - ], + "master_nextflow_config_plugins": ["nf-schema@2.6.1"], "master_nextflow_config_manifest": { "defaultBranch": "master" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.6.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.6.1"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -10248,27 +9285,14 @@ "published_at": "2026-01-30T12:40:53Z", "tag_sha": "45904cb9d12db3d89900e6c479fe604ef71b297b", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "fastqc", - "multiqc", - "seqtk_trim" - ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "modules": ["fastqc", "multiqc", "seqtk_trim"], + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.10.2", "nf_core_version": "3.5.1", - "plugins": [ - "nf-schema@2.6.1" - ], + "plugins": ["nf-schema@2.6.1"], "co2footprint_files": null }, { @@ -10276,21 +9300,10 @@ "published_at": "2025-06-27T19:51:39Z", "tag_sha": "db7f526ce151cecde9c4497a4adb54f71c553ed2", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "fastqc", - "multiqc", - "seqtk_trim" - ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "modules": ["fastqc", "multiqc", "seqtk_trim"], + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.3.1" @@ -10300,21 +9313,10 @@ "published_at": "2024-10-18T11:18:34Z", "tag_sha": "04060b4644d68649180db796e89a3db2a466a8d8", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "fastqc", - "multiqc", - "seqtk_trim" - ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "modules": ["fastqc", "multiqc", "seqtk_trim"], + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.0.2" @@ -10324,16 +9326,9 @@ "published_at": "2024-06-20T18:22:30Z", "tag_sha": "705f18e4b1540f207cf8ffdc97ee5bd70a0b022c", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "fastqc", - "multiqc", - "seqtk_trim" - ], + "modules": ["fastqc", "multiqc", "seqtk_trim"], "subworkflows": [ "utils_nextflow_pipeline", "utils_nfcore_pipeline", @@ -10348,27 +9343,14 @@ "published_at": "2026-03-11T07:46:46Z", "tag_sha": "ed969ce783288a37eb9e98c12aca38176e19a485", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "fastqc", - "multiqc", - "seqtk_trim" - ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "modules": ["fastqc", "multiqc", "seqtk_trim"], + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.10.2", "nf_core_version": "3.5.1", - "plugins": [ - "nf-schema@2.6.1" - ], + "plugins": ["nf-schema@2.6.1"], "co2footprint_files": null } ] @@ -10405,13 +9387,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "bases2fastq", - "bcl2fastq", - "demultiplexing", - "elementbiosciences", - "illumina" - ], + "topics": ["bases2fastq", "bcl2fastq", "demultiplexing", "elementbiosciences", "illumina"], "visibility": "public", "forks": 56, "open_issues": 18, @@ -10464,10 +9440,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": true, - "master_branch_protection_status_checks": [ - "pre-commit", - "nf-core" - ], + "master_branch_protection_status_checks": ["pre-commit", "nf-core"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -10476,10 +9449,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": true, - "dev_branch_protection_status_checks": [ - "pre-commit", - "nf-core" - ], + "dev_branch_protection_status_checks": ["pre-commit", "nf-core"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -10659,15 +9629,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-schema@2.7.0" - ], + "master_nextflow_config_plugins": ["nf-schema@2.7.0"], "master_nextflow_config_manifest": { "defaultBranch": "master" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.7.0" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.7.0"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -10677,10 +9643,7 @@ "published_at": "2026-04-17T12:05:00Z", "tag_sha": "fbec8e442f0599f8b74876e62263af05b9a41d33", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bases2fastq", @@ -10712,9 +9675,7 @@ }, "nextflow_version": "!>=25.10.2", "nf_core_version": "3.5.2", - "plugins": [ - "nf-schema@2.7.0" - ], + "plugins": ["nf-schema@2.7.0"], "co2footprint_files": null }, { @@ -10722,10 +9683,7 @@ "published_at": "2025-10-28T15:27:36Z", "tag_sha": "1b94ed6c8d5e315e41cf58521a7671ff0da8b9b6", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bases2fastq", @@ -10762,10 +9720,7 @@ "published_at": "2025-04-24T20:35:10Z", "tag_sha": "2d9cb0582d9b8b56465eace57b500c39d3e1749c", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bases2fastq", @@ -10801,10 +9756,7 @@ "published_at": "2025-02-19T20:04:43Z", "tag_sha": "7c2040c5b999eff5a945fe8136a51b597a64ca2f", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bases2fastq", @@ -10840,10 +9792,7 @@ "published_at": "2024-12-10T12:50:47Z", "tag_sha": "ea061789470b19b04d39c7775bc55634ff60b38e", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bases2fastq", @@ -10879,10 +9828,7 @@ "published_at": "2024-11-06T09:14:45Z", "tag_sha": "2e648b585a5432b16ba87389dd4d876ad73db460", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bases2fastq", @@ -10918,10 +9864,7 @@ "published_at": "2024-10-07T19:12:23Z", "tag_sha": "ebefeef236f0e566e2c874f483535c70d198c862", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bases2fastq", @@ -10956,10 +9899,7 @@ "published_at": "2024-08-20T06:57:22Z", "tag_sha": "17cde5d8f22f5327beac9637e941e4775ada1b3f", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bases2fastq", @@ -10994,10 +9934,7 @@ "published_at": "2024-08-13T19:51:59Z", "tag_sha": "512ea7e7b0787140b7e51854553e78f936286e49", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bases2fastq", @@ -11033,10 +9970,7 @@ "published_at": "2024-02-27T15:35:34Z", "tag_sha": "aa4d93673a4e04b1daf7b4bd71269d6054275534", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bases2fastq", @@ -11051,9 +9985,7 @@ "sgdemux", "untar" ], - "subworkflows": [ - "bcl_demultiplex" - ] + "subworkflows": ["bcl_demultiplex"] }, "nextflow_version": "!>=23.04.0", "nf_core_version": null @@ -11063,10 +9995,7 @@ "published_at": "2023-12-15T07:37:17Z", "tag_sha": "aaaf54442ed1fc46378d60c1954dd599fc05cb3f", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bases2fastq", @@ -11081,9 +10010,7 @@ "sgdemux", "untar" ], - "subworkflows": [ - "bcl_demultiplex" - ] + "subworkflows": ["bcl_demultiplex"] }, "nextflow_version": "!>=23.04.0", "nf_core_version": null @@ -11093,10 +10020,7 @@ "published_at": "2023-06-07T18:42:22Z", "tag_sha": "67b846577346a9267e1f1292c0159cdf002e2186", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bases2fastq", @@ -11111,9 +10035,7 @@ "sgdemux", "untar" ], - "subworkflows": [ - "bcl_demultiplex" - ] + "subworkflows": ["bcl_demultiplex"] }, "nextflow_version": "!>=22.10.1", "nf_core_version": null @@ -11123,10 +10045,7 @@ "published_at": "2023-06-05T12:56:05Z", "tag_sha": "8f5d9bab6c40a0140ba48a7df4a01f16297418c5", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bases2fastq", @@ -11141,9 +10060,7 @@ "sgdemux", "untar" ], - "subworkflows": [ - "bcl_demultiplex" - ] + "subworkflows": ["bcl_demultiplex"] }, "nextflow_version": "!>=22.10.1", "nf_core_version": null @@ -11153,10 +10070,7 @@ "published_at": "2023-05-31T17:43:05Z", "tag_sha": "8709f05c1af86ddc12f86aaf108fa77935af1a96", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bases2fastq", @@ -11171,9 +10085,7 @@ "sgdemux", "untar" ], - "subworkflows": [ - "bcl_demultiplex" - ] + "subworkflows": ["bcl_demultiplex"] }, "nextflow_version": "!>=22.10.1", "nf_core_version": null @@ -11183,10 +10095,7 @@ "published_at": "2023-04-25T07:29:32Z", "tag_sha": "ee3f8d01b1a917b52a885da20de67b08a7a0b790", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bases2fastq", @@ -11201,9 +10110,7 @@ "sgdemux", "untar" ], - "subworkflows": [ - "bcl_demultiplex" - ] + "subworkflows": ["bcl_demultiplex"] }, "nextflow_version": "!>=22.10.1", "nf_core_version": null @@ -11213,10 +10120,7 @@ "published_at": "2023-01-23T21:52:34Z", "tag_sha": "8e42b6cb4e12bf00828fa8cb282e01bcb487fe6e", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bases2fastq", @@ -11229,9 +10133,7 @@ "multiqc", "untar" ], - "subworkflows": [ - "bcl_demultiplex" - ] + "subworkflows": ["bcl_demultiplex"] }, "nextflow_version": "!>=22.10.1", "nf_core_version": null @@ -11241,10 +10143,7 @@ "published_at": "2022-10-06T14:22:07Z", "tag_sha": "b0a004eb2e79f6fceb9b5d79b91b563b7724ed62", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bases2fastq", @@ -11266,10 +10165,7 @@ "published_at": "2026-04-16T15:02:06Z", "tag_sha": "257df49988d242fabb42b6d87fb1e3a69c39789f", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bases2fastq", @@ -11301,9 +10197,7 @@ }, "nextflow_version": "!>=25.10.2", "nf_core_version": "3.5.2", - "plugins": [ - "nf-schema@2.7.0" - ], + "plugins": ["nf-schema@2.7.0"], "co2footprint_files": null } ] @@ -11650,10 +10544,7 @@ "published_at": "2019-08-22T09:58:02Z", "tag_sha": "92996210dcbb9dededdefb9169527645afd24cde", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ] + "doc_files": ["docs/output.md", "docs/usage.md"] } ] }, @@ -11689,11 +10580,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "denovo-assembly", - "rna-seq", - "transcriptome" - ], + "topics": ["denovo-assembly", "rna-seq", "transcriptome"], "visibility": "public", "forks": 4, "open_issues": 10, @@ -11747,20 +10634,14 @@ "master_branch_exists": false, "main_branch_exists": true, "main_branch_protection_up_to_date": -1, - "main_branch_protection_status_checks": [ - "pre-commit", - "nf-core" - ], + "main_branch_protection_status_checks": ["pre-commit", "nf-core"], "main_branch_protection_required_reviews": 2, "main_branch_protection_require_codeowner_review": false, "main_branch_protection_require_non_stale_review": false, "main_branch_protection_enforce_admins": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "pre-commit", - "nf-core" - ], + "dev_branch_protection_status_checks": ["pre-commit", "nf-core"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -11804,15 +10685,11 @@ "is_DSL2": true, "has_nf_test": false, "has_nf_test_dev": false, - "main_nextflow_config_plugins": [ - "nf-schema@2.3.0" - ], + "main_nextflow_config_plugins": ["nf-schema@2.3.0"], "main_nextflow_config_manifest": { "defaultBranch": "master" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.2.0" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.2.0"], "dev_nextflow_config_manifest": { "defaultBranch": "main" }, @@ -11822,11 +10699,7 @@ "published_at": "2025-08-28T09:23:52Z", "tag_sha": "9ab0f57785c37f77e05a03c8c327e35c63c8432b", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md", - "docs/usage/example_workflow.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md", "docs/usage/example_workflow.md"], "components": { "modules": [ "busco_busco", @@ -11858,11 +10731,7 @@ "published_at": "2025-01-30T07:26:03Z", "tag_sha": "28487c6397c8f157b11ef65a373aa4469141040a", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md", - "docs/usage/example_workflow.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md", "docs/usage/example_workflow.md"], "components": { "modules": [ "busco_busco", @@ -11894,11 +10763,7 @@ "published_at": "2024-11-29T00:26:00Z", "tag_sha": "cb8abd344196e27ec10044505509229830d7c2fc", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md", - "docs/usage/example_workflow.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md", "docs/usage/example_workflow.md"], "components": { "modules": [ "busco_busco", @@ -11930,11 +10795,7 @@ "published_at": "2024-08-15T01:25:07Z", "tag_sha": "558ff4b639039ac8ec9bece3490841aa17eec971", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md", - "docs/usage/example_workflow.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md", "docs/usage/example_workflow.md"], "components": { "modules": [ "busco_busco", @@ -11966,11 +10827,7 @@ "published_at": "2025-05-27T08:03:22Z", "tag_sha": "c5f4e32a1c444762e45bc8a2d69d21af4d91dd54", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md", - "docs/usage/example_workflow.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md", "docs/usage/example_workflow.md"], "components": { "modules": [ "busco_busco", @@ -11996,9 +10853,7 @@ }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.2.1", - "plugins": [ - "nf-schema@2.3.0" - ], + "plugins": ["nf-schema@2.3.0"], "co2footprint_files": null } ] @@ -12103,10 +10958,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": -1, - "master_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "master_branch_protection_status_checks": ["nf-core", "pre-commit"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -12114,10 +10966,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "dev_branch_protection_status_checks": ["nf-core", "pre-commit"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -12181,15 +11030,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "master_nextflow_config_plugins": ["nf-schema@2.5.1"], "master_nextflow_config_manifest": { "defaultBranch": "master" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -12199,10 +11044,7 @@ "published_at": "2025-11-14T11:41:27Z", "tag_sha": "3586921aa3a4c49271f1b2082309bdc33c819749", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bbmap_bbduk", @@ -12214,17 +11056,11 @@ "kraken2_kraken2", "multiqc" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.04.8", "nf_core_version": "3.4.1", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null }, { @@ -12232,10 +11068,7 @@ "published_at": "2025-08-07T09:33:45Z", "tag_sha": "698eedc033cae71b8a478905823d42a8ef82fffa", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bbmap_bbduk", @@ -12246,11 +11079,7 @@ "kraken2_kraken2", "multiqc" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.10.5", "nf_core_version": "3.3.2" @@ -12260,10 +11089,7 @@ "published_at": "2024-11-08T15:28:07Z", "tag_sha": "69f308c6dd5681af2216e5315c9ffa8d03dea808", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bbmap_bbduk", @@ -12274,11 +11100,7 @@ "kraken2_kraken2", "multiqc" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.0.2" @@ -12288,10 +11110,7 @@ "published_at": "2024-03-26T11:30:03Z", "tag_sha": "9a3c7cbdf9b595734d3db2cc29a9d06b87a5e94f", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "blast_blastn", @@ -12315,10 +11134,7 @@ "published_at": "2025-11-17T09:24:30Z", "tag_sha": "e352a73bf1d8b3d0fb884aa2baf15dc29f43775e", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bbmap_bbduk", @@ -12330,17 +11146,11 @@ "kraken2_kraken2", "multiqc" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.04.8", "nf_core_version": "3.4.1", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null } ] @@ -12377,12 +11187,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "data-independent-proteomics", - "dia-proteomics", - "openms", - "proteomics" - ], + "topics": ["data-independent-proteomics", "dia-proteomics", "openms", "proteomics"], "visibility": "public", "forks": 12, "open_issues": 8, @@ -12511,10 +11316,7 @@ "published_at": "2021-04-29T06:40:55Z", "tag_sha": "58b18dd02583ad4288949aa31471bcec375705cc", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=20.04.0" }, { @@ -12522,10 +11324,7 @@ "published_at": "2021-04-26T09:40:12Z", "tag_sha": "47ac20ca5d6c4c788a7bea4c49644096b2c80b61", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=20.04.0" }, { @@ -12533,10 +11332,7 @@ "published_at": "2021-02-24T21:13:30Z", "tag_sha": "a219be9c33de0b0732cbab0282702f03d21432c8", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=20.04.0" }, { @@ -12544,10 +11340,7 @@ "published_at": "2021-02-18T12:27:18Z", "tag_sha": "e118578569e022406224dce3bda901d12a4a7c0c", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=20.04.0" }, { @@ -12555,10 +11348,7 @@ "published_at": "2021-02-17T13:12:38Z", "tag_sha": "6c4157d8454cbaf3897f982abb538aaa6f89cb27", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=20.04.0" }, { @@ -12566,10 +11356,7 @@ "published_at": "2020-12-03T08:58:23Z", "tag_sha": "77f51fdb56c1ae792aba1d780879130a9c44b5f6", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=20.04.0" }, { @@ -12577,10 +11364,7 @@ "published_at": "2020-11-13T11:45:28Z", "tag_sha": "39db11edcd318870329a5ab91518d4d076539de4", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=19.10.0" }, { @@ -12588,10 +11372,7 @@ "published_at": "2025-01-13T10:51:53Z", "tag_sha": "92314aba5cc590906a4e4616be55781a1dd4d530", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=20.04.0", "nf_core_version": null, "plugins": [], @@ -12695,10 +11476,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": -1, - "master_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "master_branch_protection_status_checks": ["nf-core", "pre-commit"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -12706,10 +11484,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "dev_branch_protection_status_checks": ["nf-core", "pre-commit"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -12778,13 +11553,9 @@ "is_DSL2": true, "has_nf_test": false, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-validation@1.1.3" - ], + "master_nextflow_config_plugins": ["nf-validation@1.1.3"], "master_nextflow_config_manifest": {}, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -12794,10 +11565,7 @@ "published_at": "2024-05-08T10:53:38Z", "tag_sha": "3dd360fed0dca1780db1bdf5dce85e5258fa2253", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "affy_justrma", @@ -12834,10 +11602,7 @@ "published_at": "2023-11-27T10:42:36Z", "tag_sha": "a3d664c12c4050bae2acc83b1c636dcc3546b9a5", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "affy_justrma", @@ -12870,10 +11635,7 @@ "published_at": "2023-10-27T07:43:17Z", "tag_sha": "44c449be0a703c64a7c323a2b431ec6627194f00", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "affy_justrma", @@ -12906,10 +11668,7 @@ "published_at": "2023-10-24T13:11:49Z", "tag_sha": "e2e26764a199f279a015f94b4f8329c16b6f79c8", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "affy_justrma", @@ -12942,10 +11701,7 @@ "published_at": "2023-04-19T17:47:26Z", "tag_sha": "3a849f046990707cad2a0df751c371ac7f1165ab", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "affy_justrma", @@ -12975,10 +11731,7 @@ "published_at": "2023-03-03T08:25:50Z", "tag_sha": "47e3d923bbf2311ace0b9dea12d756287798275e", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "affy_justrma", @@ -13007,10 +11760,7 @@ "published_at": "2023-02-24T10:33:25Z", "tag_sha": "c5de0561506f73887979909274b9f7155ef1cf90", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "affy_justrma", @@ -13039,10 +11789,7 @@ "published_at": "2023-01-25T10:16:33Z", "tag_sha": "f9bed37741dd5b9b67c9ef7b6d65af1122b69115", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "atlasgeneannotationmanipulation_gtf2featureannotation", @@ -13068,10 +11815,7 @@ "published_at": "2023-01-24T10:45:16Z", "tag_sha": "17aec4fd0ab2c84b1d384932187797aa7ea1e962", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "atlasgeneannotationmanipulation_gtf2featureannotation", @@ -13097,11 +11841,7 @@ "published_at": "2026-05-22T17:15:02Z", "tag_sha": "996a07d69d221fcf10f77f95656fa2b4e123cdb0", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md", - "docs/usage/contributing.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md", "docs/usage/contributing.md"], "components": { "modules": [ "affy_justrma", @@ -13141,9 +11881,7 @@ }, "nextflow_version": "!>=25.10.4", "nf_core_version": "4.0.2", - "plugins": [ - "nf-validation@1.1.3" - ], + "plugins": ["nf-validation@1.1.3"], "co2footprint_files": null } ] @@ -13248,10 +11986,7 @@ "master_branch_exists": false, "main_branch_exists": true, "main_branch_protection_up_to_date": true, - "main_branch_protection_status_checks": [ - "pre-commit", - "nf-core" - ], + "main_branch_protection_status_checks": ["pre-commit", "nf-core"], "main_branch_protection_required_reviews": 2, "main_branch_protection_require_codeowner_review": false, "main_branch_protection_require_non_stale_review": false, @@ -13267,12 +12002,7 @@ "dev_uses_ruleset": true, "TEMPLATE_branch_exists": true, "has_required_topics": false, - "missing_topics": [ - "nf-core", - "nextflow", - "workflow", - "pipeline" - ], + "missing_topics": ["nf-core", "nextflow", "workflow", "pipeline"], "open_pr_count": 9, "repository_url": "https://github.com/nf-core/diseasemodulediscovery", "contributors": [ @@ -13330,15 +12060,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "main_nextflow_config_plugins": [ - "nf-schema@2.3.0" - ], + "main_nextflow_config_plugins": ["nf-schema@2.3.0"], "main_nextflow_config_manifest": { "defaultBranch": "main" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "main" }, @@ -13348,26 +12074,14 @@ "published_at": "2026-05-18T09:01:33Z", "tag_sha": "4d35338c037b7fc01b731a41f1e060f94129bfcc", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "gprofiler2_gost", - "multiqc" - ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "modules": ["gprofiler2_gost", "multiqc"], + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.10.4", "nf_core_version": "4.0.2", - "plugins": [ - "nf-schema@2.3.0" - ], + "plugins": ["nf-schema@2.3.0"], "co2footprint_files": null } ] @@ -13457,11 +12171,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": true, - "master_branch_protection_status_checks": [ - "pre-commit", - "nf-core", - "confirm-pass" - ], + "master_branch_protection_status_checks": ["pre-commit", "nf-core", "confirm-pass"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -13470,11 +12180,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": true, - "dev_branch_protection_status_checks": [ - "nf-core", - "pre-commit", - "confirm-pass" - ], + "dev_branch_protection_status_checks": ["nf-core", "pre-commit", "confirm-pass"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -13529,15 +12235,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-schema@2.6.1" - ], + "master_nextflow_config_plugins": ["nf-schema@2.6.1"], "master_nextflow_config_manifest": { "defaultBranch": "master" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.6.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.6.1"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -13547,10 +12249,7 @@ "published_at": "2026-04-02T07:39:31Z", "tag_sha": "20388350d242746f8e799b28c3ae80421627b077", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "gatk4_createsequencedictionary", @@ -13561,17 +12260,11 @@ "tabix_tabix", "untar" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.10.0", "nf_core_version": "3.5.2", - "plugins": [ - "nf-schema@2.6.1" - ], + "plugins": ["nf-schema@2.6.1"], "co2footprint_files": null }, { @@ -13579,10 +12272,7 @@ "published_at": "2026-05-11T08:01:21Z", "tag_sha": "f1266ac313adb9eb5129eb761874eabe54629d87", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "gatk4_createsequencedictionary", @@ -13593,17 +12283,11 @@ "tabix_tabix", "untar" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.10.0", "nf_core_version": "3.5.2", - "plugins": [ - "nf-schema@2.6.1" - ], + "plugins": ["nf-schema@2.6.1"], "co2footprint_files": null } ] @@ -13714,20 +12398,14 @@ "master_branch_protection_enforce_admins": -1, "main_branch_exists": true, "main_branch_protection_up_to_date": -1, - "main_branch_protection_status_checks": [ - "pre-commit", - "nf-core" - ], + "main_branch_protection_status_checks": ["pre-commit", "nf-core"], "main_branch_protection_required_reviews": 2, "main_branch_protection_require_codeowner_review": false, "main_branch_protection_require_non_stale_review": false, "main_branch_protection_enforce_admins": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "dev_branch_protection_status_checks": ["nf-core", "pre-commit"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -13771,19 +12449,13 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-validation" - ], + "master_nextflow_config_plugins": ["nf-validation"], "master_nextflow_config_manifest": {}, - "main_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "main_nextflow_config_plugins": ["nf-schema@2.5.1"], "main_nextflow_config_manifest": { "defaultBranch": "main" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "main" }, @@ -13793,26 +12465,14 @@ "published_at": "2026-01-20T10:39:11Z", "tag_sha": "ac143eacd9aa4e6acd7b16e0f58aab678e92d111", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "custom_dumpsoftwareversions", - "unzip" - ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "modules": ["custom_dumpsoftwareversions", "unzip"], + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.10.0", "nf_core_version": "3.5.1", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null }, { @@ -13820,19 +12480,10 @@ "published_at": "2025-07-03T12:43:45Z", "tag_sha": "60890c6b5f9b9a20947b4b343280241800c7bc2a", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "custom_dumpsoftwareversions" - ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "modules": ["custom_dumpsoftwareversions"], + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.3.1" @@ -13842,17 +12493,10 @@ "published_at": "2025-01-31T13:21:49Z", "tag_sha": "b6d27d751c2e648045243e1826d502242dccf5fd", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.2.0" @@ -13862,26 +12506,14 @@ "published_at": "2026-01-22T11:15:18Z", "tag_sha": "cb4ee861ad61be17950b59608a96357d725eb78f", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "custom_dumpsoftwareversions", - "unzip" - ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "modules": ["custom_dumpsoftwareversions", "unzip"], + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.10.0", "nf_core_version": "3.5.1", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null } ] @@ -13918,13 +12550,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "dualrna-seq", - "host-pathogen", - "quantification", - "readmapping", - "rna-seq" - ], + "topics": ["dualrna-seq", "host-pathogen", "quantification", "readmapping", "rna-seq"], "visibility": "public", "forks": 36, "open_issues": 48, @@ -14036,9 +12662,7 @@ "has_nf_test_dev": false, "master_nextflow_config_plugins": [], "master_nextflow_config_manifest": {}, - "dev_nextflow_config_plugins": [ - "nf-schema@2.3.0" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.3.0"], "dev_nextflow_config_manifest": {}, "releases": [ { @@ -14046,10 +12670,7 @@ "published_at": "2021-02-14T19:46:40Z", "tag_sha": "d8dcd8acfa6f1c2de933294bc73344d6258ebb42", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=20.10.0" }, { @@ -14057,18 +12678,9 @@ "published_at": "2025-06-26T02:18:07Z", "tag_sha": "df992a7516a2018b7bffefd069c21b2ff956d404", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "custom_dumpsoftwareversions", - "cutadapt", - "fastqc", - "htseq_count", - "multiqc" - ], + "modules": ["custom_dumpsoftwareversions", "cutadapt", "fastqc", "htseq_count", "multiqc"], "subworkflows": [ "utils_nextflow_pipeline", "utils_nfcore_pipeline", @@ -14180,11 +12792,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": -1, - "master_branch_protection_status_checks": [ - "nf-core", - "pre-commit", - "confirm-pass" - ], + "master_branch_protection_status_checks": ["nf-core", "pre-commit", "confirm-pass"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -14192,11 +12800,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "nf-core", - "pre-commit", - "confirm-pass" - ], + "dev_branch_protection_status_checks": ["nf-core", "pre-commit", "confirm-pass"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -14327,9 +12931,7 @@ "has_nf_test_dev": true, "master_nextflow_config_plugins": [], "master_nextflow_config_manifest": {}, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -14339,10 +12941,7 @@ "published_at": "2025-03-18T09:25:10Z", "tag_sha": "3f9d64ced5e287391bcd5517a0c40153a01268e5", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=20.07.1" }, { @@ -14350,10 +12949,7 @@ 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true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=20.07.1" }, { @@ -14471,10 +13037,7 @@ "published_at": "2021-06-04T06:17:57Z", "tag_sha": "70e3d276d3a39859b8f067518added35ef616af7", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=20.07.1" }, { @@ -14482,10 +13045,7 @@ "published_at": "2021-05-05T11:23:15Z", "tag_sha": "10bfbdff86607f816c4e1819e8ede0f5f00ea2ac", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": "!>=20.07.1" }, { @@ -14493,10 +13053,7 @@ "published_at": "2021-04-08T11:37:08Z", "tag_sha": "ad8e41a20a49febb1814c530de5460a5d342df8c", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], 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"85e2e3288ae9e357bfa0e7bd55ea63bca6291c5c", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": "!>=20.04.0" }, { @@ -14548,10 +13093,7 @@ "published_at": "2020-10-29T18:27:54Z", "tag_sha": "7971d89e54621c44055b2062a569c76a36045723", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": "!>=20.04.0" }, { @@ -14559,10 +13101,7 @@ "published_at": "2020-10-21T08:14:21Z", "tag_sha": "b1ae5ad6c1aa54c11f3f571f25920506f9b92129", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": "!>=20.04.0" }, { @@ -14570,10 +13109,7 @@ "published_at": "2020-03-05T15:42:54Z", "tag_sha": "26ae7e945f738b47996cce32fe86ec37897087a9", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + 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"visibility": "public", "forks": 1, "open_issues": 2, @@ -14853,10 +13358,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": true, - "master_branch_protection_status_checks": [ - "pre-commit", - "nf-core" - ], + "master_branch_protection_status_checks": ["pre-commit", "nf-core"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -14895,15 +13397,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "master_nextflow_config_plugins": ["nf-schema@2.5.1"], "master_nextflow_config_manifest": { "defaultBranch": "master" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -14913,23 +13411,14 @@ "published_at": "2026-05-14T16:19:57Z", "tag_sha": "1ec638ada897f4ab00e105ad1561289bdea64b63", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.04.0", "nf_core_version": "3.5.2", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null } ] @@ -14966,11 +13455,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "epitope", - "epitope-prediction", - "mhc-binding-prediction" - ], + "topics": ["epitope", "epitope-prediction", "mhc-binding-prediction"], "visibility": "public", "forks": 34, "open_issues": 25, @@ -15023,9 +13508,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": -1, - "master_branch_protection_status_checks": [ - "nf-core" - ], + "master_branch_protection_status_checks": ["nf-core"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -15033,9 +13516,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "nf-core" - ], + "dev_branch_protection_status_checks": ["nf-core"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -15124,17 +13605,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-schema@2.5.1", - "nf-co2footprint@1.0.0" - ], + "master_nextflow_config_plugins": ["nf-schema@2.5.1", "nf-co2footprint@1.0.0"], "master_nextflow_config_manifest": { "defaultBranch": "master" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1", - "nf-co2footprint@1.0.0" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1", "nf-co2footprint@1.0.0"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -15144,30 +13619,14 @@ "published_at": "2025-11-21T10:25:11Z", "tag_sha": "4c13c15b46ec69e959faf2cf338e9ceb795a19d5", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "bcftools_stats", - "cat_cat", - "gunzip", - "multiqc", - "snpsift_split" - ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "modules": ["bcftools_stats", "cat_cat", "gunzip", "multiqc", "snpsift_split"], + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.04.0", "nf_core_version": "3.4.1", - "plugins": [ - "nf-schema@2.5.1", - "nf-co2footprint@1.0.0" - ], + "plugins": ["nf-schema@2.5.1", "nf-co2footprint@1.0.0"], "co2footprint_files": { "filename": "co2footprint_summary_2025-11-21_10-26-49.txt", "co2e_emissions": 10.51, @@ -15179,23 +13638,10 @@ "published_at": "2025-05-09T05:43:08Z", "tag_sha": "37c08f05dcb0444a859b656545e1ed15c1ea95d1", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "bcftools_stats", - "cat_cat", - "gunzip", - "multiqc", - "snpsift_split" - ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "modules": ["bcftools_stats", "cat_cat", "gunzip", "multiqc", "snpsift_split"], + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.2.1" @@ -15205,15 +13651,9 @@ "published_at": "2024-05-17T12:05:03Z", "tag_sha": "cfbfeb56b2224ae603539e88088ff4170a01dba6", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "gunzip", - "multiqc" - ], + "modules": ["gunzip", "multiqc"], "subworkflows": [ "utils_nextflow_pipeline", "utils_nfcore_pipeline", @@ -15228,16 +13668,9 @@ "published_at": "2024-02-26T11:52:24Z", "tag_sha": "e173620ac2a10fae8d0a47f597aa723684456deb", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "custom_dumpsoftwareversions", - "gunzip", - "multiqc" - ], + "modules": ["custom_dumpsoftwareversions", "gunzip", "multiqc"], "subworkflows": [ "utils_nextflow_pipeline", "utils_nfcore_pipeline", @@ -15252,16 +13685,9 @@ "published_at": "2023-03-17T10:16:26Z", "tag_sha": "b0f0d7a5b3cd352e548901e4cc19937c73add465", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "custom_dumpsoftwareversions", - "gunzip", - "multiqc" - ] + "modules": ["custom_dumpsoftwareversions", "gunzip", "multiqc"] }, "nextflow_version": "!>=22.10.1", "nf_core_version": null @@ -15271,16 +13697,9 @@ "published_at": "2023-03-03T10:20:50Z", "tag_sha": "7abf023b210803657760f5300f6a21d286ed167e", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "custom_dumpsoftwareversions", - "gunzip", - "multiqc" - ] + "modules": ["custom_dumpsoftwareversions", "gunzip", "multiqc"] }, "nextflow_version": "!>=22.10.1", "nf_core_version": null @@ -15290,16 +13709,9 @@ "published_at": "2022-08-04T11:05:07Z", "tag_sha": "1bd1df07058169d3965bdc5090a00e0e05050bcd", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "custom_dumpsoftwareversions", - "gunzip", - "multiqc" - ] + "modules": ["custom_dumpsoftwareversions", "gunzip", "multiqc"] }, "nextflow_version": "!>=21.10.3", "nf_core_version": null @@ -15309,15 +13721,9 @@ "published_at": "2021-12-21T12:32:47Z", "tag_sha": "1afbbf19ed6adca477451a3c42e2e0ac0c75af28", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "custom_dumpsoftwareversions", - "multiqc" - ] + "modules": ["custom_dumpsoftwareversions", "multiqc"] }, "nextflow_version": "!>=21.10.3" }, @@ -15326,10 +13732,7 @@ "published_at": "2020-10-20T18:29:47Z", "tag_sha": "ce15e440954f8e7c83c341261b82aacc8e3535ac", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=19.10.0" }, { @@ -15337,10 +13740,7 @@ "published_at": "2019-12-05T16:31:15Z", "tag_sha": "a4c32a0ad83f6d7b8e9f36829af6bb75379ab60d", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=19.10.0" }, { @@ -15348,10 +13748,7 @@ "published_at": "2026-05-25T08:03:29Z", "tag_sha": "2d0cf16db9f9e791438e06dc3a9ad7f246a35cf8", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bcftools_norm", @@ -15361,18 +13758,11 @@ "multiqc", "snpsift_split" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.10.4", "nf_core_version": "4.0.2", - "plugins": [ - "nf-schema@2.5.1", - "nf-co2footprint@1.0.0" - ], + "plugins": ["nf-schema@2.5.1", "nf-co2footprint@1.0.0"], "co2footprint_files": null } ] @@ -15409,10 +13799,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "extracellular-vesicles", - "ont" - ], + "topics": ["extracellular-vesicles", "ont"], "visibility": "public", "forks": 3, "open_issues": 1, @@ -15466,10 +13853,7 @@ "master_branch_exists": false, "main_branch_exists": true, "main_branch_protection_up_to_date": true, - "main_branch_protection_status_checks": [ - "pre-commit", - "nf-core" - ], + "main_branch_protection_status_checks": ["pre-commit", "nf-core"], "main_branch_protection_required_reviews": 2, "main_branch_protection_require_codeowner_review": false, "main_branch_protection_require_non_stale_review": false, @@ -15507,15 +13891,11 @@ "is_DSL2": true, "has_nf_test": false, "has_nf_test_dev": false, - "main_nextflow_config_plugins": [ - "nf-schema@2.3.0" - ], + "main_nextflow_config_plugins": ["nf-schema@2.3.0"], "main_nextflow_config_manifest": { "defaultBranch": "master" }, - "dev_nextflow_config_plugins": [ - "nf-validation@1.1.3" - ], + "dev_nextflow_config_plugins": ["nf-validation@1.1.3"], "dev_nextflow_config_manifest": {}, "releases": [ { @@ -15523,10 +13903,7 @@ "published_at": "2025-05-05T13:07:59Z", "tag_sha": "f446969e762a9f7398842d38952207e71991aaad", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "cutadapt", @@ -15541,17 +13918,11 @@ "star_align", "star_genomegenerate" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=23.04.0", "nf_core_version": "2.14.1", - "plugins": [ - "nf-schema@2.3.0" - ], + "plugins": ["nf-schema@2.3.0"], "co2footprint_files": null } ] @@ -15586,12 +13957,7 @@ "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, - "topics": [ - "exome", - "exome-sequencing", - "genomics", - "variant-calling" - ], + "topics": ["exome", "exome-sequencing", "genomics", "variant-calling"], "visibility": "public", "forks": 28, "open_issues": 14, @@ -15653,12 +14019,7 @@ "dev_branch_protection_enforce_admins": -1, "TEMPLATE_branch_exists": false, "has_required_topics": false, - "missing_topics": [ - "nf-core", - "nextflow", - "workflow", - "pipeline" - ], + "missing_topics": ["nf-core", "nextflow", "workflow", "pipeline"], "open_pr_count": 1, "repository_url": "https://github.com/nf-core/exoseq", "contributors": [ @@ -15706,10 +14067,7 @@ "published_at": "2018-11-29T10:24:10Z", "tag_sha": "819cbac792b76cf66c840b567ed0ee9a2f620db7", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ] + "doc_files": ["docs/output.md", "docs/usage.md"] } ] }, @@ -15809,10 +14167,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": -1, - "master_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "master_branch_protection_status_checks": ["nf-core", "pre-commit"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -15854,15 +14209,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-schema@2.3.0" - ], + "master_nextflow_config_plugins": ["nf-schema@2.3.0"], "master_nextflow_config_manifest": { "defaultBranch": "main" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.4.2" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.4.2"], "dev_nextflow_config_manifest": { "defaultBranch": "main" }, @@ -15872,10 +14223,7 @@ "published_at": "2025-02-03T18:33:35Z", "tag_sha": "5f102cae4cfaa1d9281b9702ccc3738d9974e388", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bbmap_repair", @@ -15887,11 +14235,7 @@ "wipertools_fastqwiper", "wipertools_reportgather" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.2.0" @@ -15901,10 +14245,7 @@ "published_at": "2025-08-20T15:20:05Z", "tag_sha": "7282b520275d81f6400b798059e6dea7621c1f1a", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bbmap_repair", @@ -15916,17 +14257,11 @@ "wipertools_fastqwiper", "wipertools_reportgather" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.10.5", "nf_core_version": "3.3.2", - "plugins": [ - "nf-schema@2.3.0" - ], + "plugins": ["nf-schema@2.3.0"], "co2footprint_files": null } ] @@ -15963,12 +14298,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "consensus", - "umi", - "umis", - "unique-molecular-identifier" - ], + "topics": ["consensus", "umi", "umis", "unique-molecular-identifier"], "visibility": "public", "forks": 16, "open_issues": 15, @@ -16022,18 +14352,14 @@ "master_branch_exists": false, "main_branch_exists": true, "main_branch_protection_up_to_date": -1, - "main_branch_protection_status_checks": [ - "nf-core" - ], + "main_branch_protection_status_checks": ["nf-core"], "main_branch_protection_required_reviews": 2, "main_branch_protection_require_codeowner_review": false, "main_branch_protection_require_non_stale_review": false, "main_branch_protection_enforce_admins": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "nf-core" - ], + "dev_branch_protection_status_checks": ["nf-core"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -16072,16 +14398,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "main_nextflow_config_plugins": [ - "nf-schema@2.1.1" - ], + "main_nextflow_config_plugins": ["nf-schema@2.1.1"], "main_nextflow_config_manifest": { "defaultBranch": "master" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1", - "nf-fgbio@1.0.0" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1", "nf-fgbio@1.0.0"], "dev_nextflow_config_manifest": { "defaultBranch": "main" }, @@ -16091,10 +14412,7 @@ "published_at": "2025-04-11T15:28:38Z", "tag_sha": "e6414c99ef5eef47a4ac3f124962e3dc5c21ab4b", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bwa_index", @@ -16104,11 +14422,7 @@ "samtools_faidx", "samtools_merge" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.2.0" @@ -16118,10 +14432,7 @@ "published_at": "2024-12-02T23:25:33Z", "tag_sha": "1f6d25fc9c0b30f2c756fd844bdaa7c352a82e07", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bwa_index", @@ -16132,11 +14443,7 @@ "samtools_faidx", "samtools_merge" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.0.2" @@ -16146,10 +14453,7 @@ "published_at": "2024-09-11T15:27:18Z", "tag_sha": "6d6395110984ff658748a4ee827fbe0d5cdb7530", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bwa_index", @@ -16174,10 +14478,7 @@ "published_at": "2024-05-23T21:00:01Z", "tag_sha": "ea307015cf134358883d48fcd7a86b365a0a8bb2", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bwa_index", @@ -16201,10 +14502,7 @@ "published_at": "2026-03-27T23:05:39Z", "tag_sha": "4d3d4ab08b313159d9792f3cc521696550b8069d", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bwa_index", @@ -16214,17 +14512,11 @@ "samtools_faidx", "samtools_merge" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.04.0", "nf_core_version": "3.5.2", - "plugins": [ - "nf-schema@2.1.1" - ], + "plugins": ["nf-schema@2.1.1"], "co2footprint_files": null } ] @@ -16261,15 +14553,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "ddbj", - "download", - "ena", - "fastq", - "geo", - "sra", - "synapse" - ], + "topics": ["ddbj", "download", "ena", "fastq", "geo", "sra", "synapse"], "visibility": "public", "forks": 92, "open_issues": 49, @@ -16322,11 +14606,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": -1, - "master_branch_protection_status_checks": [ - "nf-core", - "confirm-pass", - "pre-commit" - ], + "master_branch_protection_status_checks": ["nf-core", "confirm-pass", "pre-commit"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -16334,11 +14614,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "nf-core", - "confirm-pass", - "pre-commit" - ], + "dev_branch_protection_status_checks": ["nf-core", "confirm-pass", "pre-commit"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -16462,13 +14738,9 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-validation@1.1.3" - ], + "master_nextflow_config_plugins": ["nf-validation@1.1.3"], "master_nextflow_config_manifest": {}, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -16478,10 +14750,7 @@ "published_at": "2024-02-29T16:18:23Z", "tag_sha": "8ec2d934f9301c818d961b1e4fdf7fc79610bdc5", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "custom_sratoolsncbisettings", @@ -16504,10 +14773,7 @@ "published_at": "2023-10-18T10:50:07Z", "tag_sha": "04ee5031a4941b5fc52c158847cf797b45977965", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "custom_sratoolsncbisettings", @@ -16530,10 +14796,7 @@ "published_at": "2023-10-08T18:31:31Z", "tag_sha": "b774d8df22b8958acc78ee5de40f73aa9fba0def", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "custom_dumpsoftwareversions", @@ -16541,9 +14804,7 @@ "sratools_fasterqdump", "sratools_prefetch" ], - "subworkflows": [ - "fastq_download_prefetch_fasterqdump_sratools" - ] + "subworkflows": ["fastq_download_prefetch_fasterqdump_sratools"] }, "nextflow_version": "!>=23.04.0", "nf_core_version": null @@ -16553,10 +14814,7 @@ "published_at": "2023-05-16T16:12:51Z", "tag_sha": "27067828746a19484d40d4d175f7e14044e5beb3", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "custom_dumpsoftwareversions", @@ -16564,9 +14822,7 @@ "sratools_fasterqdump", "sratools_prefetch" ], - "subworkflows": [ - "fastq_download_prefetch_fasterqdump_sratools" - ] + "subworkflows": ["fastq_download_prefetch_fasterqdump_sratools"] }, "nextflow_version": "!>=22.10.1", "nf_core_version": null @@ -16576,10 +14832,7 @@ "published_at": "2022-12-21T13:50:31Z", "tag_sha": "084e5ef3038b3210efaf203ce57d0ba21a6ece0b", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "custom_dumpsoftwareversions", @@ -16587,9 +14840,7 @@ "sratools_fasterqdump", "sratools_prefetch" ], - "subworkflows": [ - "fastq_download_prefetch_fasterqdump_sratools" - ] + "subworkflows": ["fastq_download_prefetch_fasterqdump_sratools"] }, "nextflow_version": "!>=22.10.1", "nf_core_version": null @@ -16599,10 +14850,7 @@ "published_at": "2022-11-08T09:48:55Z", "tag_sha": "249210f1856edaf4713430ebc42d6bdf60561d7a", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "custom_dumpsoftwareversions", @@ -16610,9 +14858,7 @@ "sratools_fasterqdump", "sratools_prefetch" ], - "subworkflows": [ - "fastq_download_prefetch_fasterqdump_sratools" - ] + "subworkflows": ["fastq_download_prefetch_fasterqdump_sratools"] }, "nextflow_version": "!>=21.10.3", "nf_core_version": null @@ -16622,10 +14868,7 @@ "published_at": "2022-07-01T16:12:49Z", "tag_sha": "b79cde2fb58ec3bee3ef20124c6ade0c2f263d7d", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "custom_dumpsoftwareversions", @@ -16642,10 +14885,7 @@ "published_at": "2022-05-17T11:58:37Z", "tag_sha": "7b7ab2f818d8202b0bc71b7eb901c1329216ddd9", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "custom_dumpsoftwareversions", @@ -16662,14 +14902,9 @@ "published_at": "2021-12-01T09:29:32Z", "tag_sha": "c318ae12fcb972ff28f6d38edd3165c88b6d0b3f", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "custom_dumpsoftwareversions" - ] + "modules": ["custom_dumpsoftwareversions"] }, "nextflow_version": "!>=21.10.3", "nf_core_version": null @@ -16679,10 +14914,7 @@ "published_at": "2021-11-09T15:28:52Z", "tag_sha": "0c43cc787290d88c9127af8281bb69554d905012", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": "!>=21.04.0", "nf_core_version": null }, @@ -16691,10 +14923,7 @@ "published_at": "2021-09-15T16:31:18Z", "tag_sha": "2d593fb504caf65301c78b8076272f895e364cd7", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": "!>=21.04.0", "nf_core_version": null }, @@ -16703,10 +14932,7 @@ "published_at": "2021-07-28T08:25:36Z", "tag_sha": "8c00805705b66587167a1f166935506413225260", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": "!>=21.04.0", "nf_core_version": null }, @@ -16715,10 +14941,7 @@ "published_at": "2021-06-22T10:14:46Z", "tag_sha": "3bd6ea5f0e657dde934ac4c8f7cb28ad19d14df7", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": "!>=21.04.0" }, { @@ -16726,10 +14949,7 @@ "published_at": "2021-06-08T15:04:52Z", "tag_sha": "4611da4046667c74ad3bb943e88fcd6f5e60287a", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": "!>=21.04.0" }, { @@ -16737,10 +14957,7 @@ "published_at": "2026-04-29T08:51:02Z", "tag_sha": "918395bc8c8c018e8f531b89f88c058d052c0395", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "custom_sratoolsncbisettings", @@ -16758,9 +14975,7 @@ }, "nextflow_version": "!>=25.04.0", "nf_core_version": "3.5.2", - "plugins": [ - "nf-validation@1.1.3" - ], + "plugins": ["nf-validation@1.1.3"], "co2footprint_files": null } ] @@ -16851,10 +15066,7 @@ "master_branch_exists": false, "main_branch_exists": true, "main_branch_protection_up_to_date": true, - "main_branch_protection_status_checks": [ - "pre-commit", - "nf-core" - ], + "main_branch_protection_status_checks": ["pre-commit", "nf-core"], "main_branch_protection_required_reviews": 2, "main_branch_protection_require_codeowner_review": false, "main_branch_protection_require_non_stale_review": false, @@ -16902,15 +15114,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "main_nextflow_config_plugins": [ - "nf-schema@2.4.2" - ], + "main_nextflow_config_plugins": ["nf-schema@2.4.2"], "main_nextflow_config_manifest": { "defaultBranch": "main" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "main" }, @@ -16920,10 +15128,7 @@ "published_at": "2026-05-23T06:08:01Z", "tag_sha": "646f37cd1d47cde795fca5c470ff5ca7fed1189b", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "cat_fastq", @@ -16941,17 +15146,11 @@ "seqkit_fq2fa", "untar" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.10.4", "nf_core_version": "4.0.2", - "plugins": [ - "nf-schema@2.4.2" - ], + "plugins": ["nf-schema@2.4.2"], "co2footprint_files": null } ] @@ -17058,22 +15257,14 @@ "master_branch_exists": false, "main_branch_exists": true, "main_branch_protection_up_to_date": -1, - "main_branch_protection_status_checks": [ - "nf-core", - "download", - "pre-commit", - "confirm-pass" - ], + "main_branch_protection_status_checks": ["nf-core", "download", "pre-commit", "confirm-pass"], "main_branch_protection_required_reviews": 2, "main_branch_protection_require_codeowner_review": false, "main_branch_protection_require_non_stale_review": false, "main_branch_protection_enforce_admins": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "nf-core", - "confirm-pass" - ], + "dev_branch_protection_status_checks": ["nf-core", "confirm-pass"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -17152,15 +15343,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "main_nextflow_config_plugins": [ - "nf-schema@2.4.2" - ], + "main_nextflow_config_plugins": ["nf-schema@2.4.2"], "main_nextflow_config_manifest": { "defaultBranch": "master" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "main" }, @@ -17170,10 +15357,7 @@ "published_at": "2025-10-04T19:03:00Z", "tag_sha": "fa9db018e528ffb5149cdde928e2fa24e7c546fe", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "abricate_run", @@ -17219,11 +15403,7 @@ "tabix_bgzip", "untar" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.10.5", "nf_core_version": "3.3.2" @@ -17233,10 +15413,7 @@ "published_at": "2025-03-05T12:58:17Z", "tag_sha": "ed9af9dfc43d86c97ded359747a1b4feef6811ef", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "abricate_run", @@ -17282,11 +15459,7 @@ "tabix_bgzip", "untar" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.2.0" @@ -17296,10 +15469,7 @@ "published_at": "2024-09-05T10:50:02Z", "tag_sha": "66e7a337def880472b06eaf0a2b2dc09e32ce399", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "abricate_run", @@ -17358,10 +15528,7 @@ "published_at": "2024-07-08T12:12:15Z", "tag_sha": "2a5c32a4dd72ed18b53a797af7bd8e11694af9e1", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "abricate_run", @@ -17408,10 +15575,7 @@ "published_at": "2024-03-20T22:40:21Z", "tag_sha": "ec1f1b61515d1e6b458fbb17bd087da0b75e0085", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "abricate_run", @@ -17458,10 +15622,7 @@ "published_at": "2023-11-07T14:10:28Z", "tag_sha": "274042b24d5267f85fb375aef4245c73035e8c63", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "abricate_run", @@ -17508,10 +15669,7 @@ "published_at": "2023-08-11T12:36:40Z", "tag_sha": "eb8f79ce5a966f5a01b398dfe7d881c04b697192", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "abricate_run", @@ -17559,10 +15717,7 @@ "published_at": "2023-06-30T06:43:37Z", "tag_sha": "7105f4a398a4b07207432d9e572a41babdcbcc21", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "abricate_run", @@ -17610,112 +15765,103 @@ "published_at": "2023-05-24T21:32:40Z", "tag_sha": "34063c49cb46f429241b7d3744ab839fa3ccddf6", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], - "components": { - "modules": [ - "abricate_run", - "ampcombi", - "ampir", - "amplify_predict", - "amrfinderplus_run", - "amrfinderplus_update", - "antismash_antismashlite", - "antismash_antismashlitedownloaddatabases", - "bakta_bakta", - "bakta_baktadbdownload", - "bioawk", - "custom_dumpsoftwareversions", - "deeparg_downloaddata", - "deeparg_predict", - "deepbgc_download", - "deepbgc_pipeline", - "fargene", - "fastqc", - "gecco_run", - "gunzip", - "hamronization_abricate", - "hamronization_amrfinderplus", - "hamronization_deeparg", - "hamronization_fargene", - "hamronization_rgi", - "hamronization_summarize", - "hmmer_hmmsearch", - "macrel_contigs", - "multiqc", - "prodigal", - "prokka", - "pyrodigal", - "rgi_main", - "tabix_bgzip", - "untar" - ] - }, - "nextflow_version": "!>=22.10.1", - "nf_core_version": null - }, - { - "tag_name": "1.1.0", - "published_at": "2023-04-27T21:46:23Z", - "tag_sha": "1c1c9ae408ba78b8ec74ed33da5ba1ef0bf57eb1", - "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], - "components": { - "modules": [ - "abricate_run", - "ampcombi", - "ampir", - "amplify_predict", - "amrfinderplus_run", - "amrfinderplus_update", - "antismash_antismashlite", - "antismash_antismashlitedownloaddatabases", - "bakta_bakta", - "bakta_baktadbdownload", - "bioawk", - "custom_dumpsoftwareversions", - "deeparg_downloaddata", - "deeparg_predict", - "deepbgc_download", - "deepbgc_pipeline", - "fargene", - "fastqc", - "gecco_run", - "gunzip", - "hamronization_abricate", - "hamronization_amrfinderplus", - "hamronization_deeparg", - "hamronization_fargene", - "hamronization_rgi", - "hamronization_summarize", - "hmmer_hmmsearch", - "macrel_contigs", - "multiqc", - "prodigal", - "prokka", - "pyrodigal", - "rgi_main", - "tabix_bgzip", - "untar" - ] - }, - "nextflow_version": "!>=22.10.1", - "nf_core_version": null - }, - { - "tag_name": "1.0.1", - "published_at": "2023-02-27T12:01:01Z", - "tag_sha": "98a08153aa3308d6a0f374fc21dbf9790eba0819", - "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], + "components": { + "modules": [ + "abricate_run", + "ampcombi", + "ampir", + "amplify_predict", + "amrfinderplus_run", + "amrfinderplus_update", + "antismash_antismashlite", + "antismash_antismashlitedownloaddatabases", + "bakta_bakta", + "bakta_baktadbdownload", + "bioawk", + "custom_dumpsoftwareversions", + "deeparg_downloaddata", + "deeparg_predict", + "deepbgc_download", + "deepbgc_pipeline", + "fargene", + "fastqc", + "gecco_run", + "gunzip", + "hamronization_abricate", + "hamronization_amrfinderplus", + "hamronization_deeparg", + "hamronization_fargene", + "hamronization_rgi", + "hamronization_summarize", + "hmmer_hmmsearch", + "macrel_contigs", + "multiqc", + "prodigal", + "prokka", + "pyrodigal", + "rgi_main", + "tabix_bgzip", + "untar" + ] + }, + "nextflow_version": "!>=22.10.1", + "nf_core_version": null + }, + { + "tag_name": "1.1.0", + "published_at": "2023-04-27T21:46:23Z", + "tag_sha": "1c1c9ae408ba78b8ec74ed33da5ba1ef0bf57eb1", + "has_schema": false, + "doc_files": ["docs/output.md", "docs/usage.md"], + "components": { + "modules": [ + "abricate_run", + "ampcombi", + "ampir", + "amplify_predict", + "amrfinderplus_run", + "amrfinderplus_update", + "antismash_antismashlite", + "antismash_antismashlitedownloaddatabases", + "bakta_bakta", + "bakta_baktadbdownload", + "bioawk", + "custom_dumpsoftwareversions", + "deeparg_downloaddata", + "deeparg_predict", + "deepbgc_download", + "deepbgc_pipeline", + "fargene", + "fastqc", + "gecco_run", + "gunzip", + "hamronization_abricate", + "hamronization_amrfinderplus", + "hamronization_deeparg", + "hamronization_fargene", + "hamronization_rgi", + "hamronization_summarize", + "hmmer_hmmsearch", + "macrel_contigs", + "multiqc", + "prodigal", + "prokka", + "pyrodigal", + "rgi_main", + "tabix_bgzip", + "untar" + ] + }, + "nextflow_version": "!>=22.10.1", + "nf_core_version": null + }, + { + "tag_name": "1.0.1", + "published_at": "2023-02-27T12:01:01Z", + "tag_sha": "98a08153aa3308d6a0f374fc21dbf9790eba0819", + "has_schema": true, + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "abricate_run", @@ -17761,10 +15907,7 @@ "published_at": "2023-02-15T11:41:14Z", "tag_sha": "d6773ca1902569c89da607d578eab70a1ff590b9", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "abricate_run", @@ -17810,11 +15953,7 @@ "published_at": "2026-05-21T15:42:26Z", "tag_sha": "753f349104c8f261c3fd78a6d489129cb69e8245", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md", - "docs/usage/developing.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md", "docs/usage/developing.md"], "components": { "modules": [ "abricate_run", @@ -17865,17 +16004,11 @@ "tabix_bgzip", "untar" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.10.4", "nf_core_version": "4.0.2", - "plugins": [ - "nf-schema@2.4.2" - ], + "plugins": ["nf-schema@2.4.2"], "co2footprint_files": null } ] @@ -17912,13 +16045,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "evolutionary-models", - "msa", - "natural-selection", - "phylogenetics", - "positive-selection" - ], + "topics": ["evolutionary-models", "msa", "natural-selection", "phylogenetics", "positive-selection"], "visibility": "public", "forks": 0, "open_issues": 6, @@ -17972,10 +16099,7 @@ "master_branch_exists": false, "main_branch_exists": true, "main_branch_protection_up_to_date": true, - "main_branch_protection_status_checks": [ - "pre-commit", - "nf-core" - ], + "main_branch_protection_status_checks": ["pre-commit", "nf-core"], "main_branch_protection_required_reviews": 2, "main_branch_protection_require_codeowner_review": false, "main_branch_protection_require_non_stale_review": false, @@ -18013,15 +16137,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "main_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "main_nextflow_config_plugins": ["nf-schema@2.5.1"], "main_nextflow_config_manifest": { "defaultBranch": "master" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -18031,23 +16151,14 @@ "published_at": "2026-04-29T20:31:37Z", "tag_sha": "c812faefe0574c87ceab07bee654cb0052225872", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.04.0", "nf_core_version": "3.4.1", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null } ] @@ -18196,18 +16307,9 @@ "published_at": "2022-03-29T14:33:51Z", "tag_sha": "cbd878f7997d367ccbe952648e114ad25962963f", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "cat_fastq", - "custom_dumpsoftwareversions", - "fastqc", - "gunzip", - "multiqc" - ] + "modules": ["cat_fastq", "custom_dumpsoftwareversions", "fastqc", "gunzip", "multiqc"] }, "nextflow_version": "!>=21.10.3", "nf_core_version": null, @@ -18248,9 +16350,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "genome-assembly" - ], + "topics": ["genome-assembly"], "visibility": "public", "forks": 22, "open_issues": 11, @@ -18303,10 +16403,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": -1, - "master_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "master_branch_protection_status_checks": ["nf-core", "pre-commit"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -18314,10 +16411,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "dev_branch_protection_status_checks": ["nf-core", "pre-commit"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -18376,15 +16470,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-schema@2.4.2" - ], + "master_nextflow_config_plugins": ["nf-schema@2.4.2"], "master_nextflow_config_manifest": { "defaultBranch": "master" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -18394,10 +16484,7 @@ "published_at": "2025-07-21T10:58:15Z", "tag_sha": "ccf1b89898cb720f46a966029c3a60dbcc25b012", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "busco_busco", @@ -18439,10 +16526,7 @@ "published_at": "2025-03-19T08:19:37Z", "tag_sha": "3f1f59ddfbf92836cea735aff5a67b6212fed9f9", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "busco_busco", @@ -18481,10 +16565,7 @@ "published_at": "2025-03-07T08:16:54Z", "tag_sha": "e7636a6fd1f2aadd25a2c0b00a5dca1e98b548b5", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "busco_busco", @@ -18523,10 +16604,7 @@ "published_at": "2025-11-20T15:54:07Z", "tag_sha": "b017207723b90730c53a0c2b17a4a62170a2cfff", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "busco_busco", @@ -18562,9 +16640,7 @@ }, "nextflow_version": "!>=25.04.0", "nf_core_version": "3.5.1", - "plugins": [ - "nf-schema@2.4.2" - ], + "plugins": ["nf-schema@2.4.2"], "co2footprint_files": null } ] @@ -18601,12 +16677,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "genome-assembly-evaluation", - "genomics", - "phylogenetic-trees", - "quality-control" - ], + "topics": ["genome-assembly-evaluation", "genomics", "phylogenetic-trees", "quality-control"], "visibility": "public", "forks": 24, "open_issues": 78, @@ -18660,10 +16731,7 @@ "master_branch_exists": false, "main_branch_exists": true, "main_branch_protection_up_to_date": true, - "main_branch_protection_status_checks": [ - "pre-commit", - "nf-core" - ], + "main_branch_protection_status_checks": ["pre-commit", "nf-core"], "main_branch_protection_required_reviews": 2, "main_branch_protection_require_codeowner_review": false, "main_branch_protection_require_non_stale_review": false, @@ -18679,12 +16747,7 @@ "dev_uses_ruleset": true, "TEMPLATE_branch_exists": true, "has_required_topics": false, - "missing_topics": [ - "nf-core", - "nextflow", - "workflow", - "pipeline" - ], + "missing_topics": ["nf-core", "nextflow", "workflow", "pipeline"], "open_pr_count": 6, "repository_url": "https://github.com/nf-core/genomeqc", "contributors": [ @@ -18737,13 +16800,9 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "main_nextflow_config_plugins": [ - "nf-validation@1.1.3" - ], + "main_nextflow_config_plugins": ["nf-validation@1.1.3"], "main_nextflow_config_manifest": {}, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -18753,10 +16812,7 @@ "published_at": "2026-05-07T14:09:44Z", "tag_sha": "a946e6c32014b44d25d0d9621a591b869103c126", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "agat_convertspgxf2gxf", @@ -18794,9 +16850,7 @@ }, "nextflow_version": "!>=25.10.4", "nf_core_version": "4.0.2", - "plugins": [ - "nf-validation@1.1.3" - ], + "plugins": ["nf-validation@1.1.3"], "co2footprint_files": null } ] @@ -18833,13 +16887,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "chloroplast-genome", - "genome", - "genome-skimming", - "mitochondrial-genomes", - "organelle" - ], + "topics": ["chloroplast-genome", "genome", "genome-skimming", "mitochondrial-genomes", "organelle"], "visibility": "public", "forks": 3, "open_issues": 2, @@ -18934,16 +16982,9 @@ "published_at": "2022-08-09T10:34:34Z", "tag_sha": "0c969583df4a65daf62c2bfb6e2dcd9ead4e850a", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "custom_dumpsoftwareversions", - "fastqc", - "multiqc" - ] + "modules": ["custom_dumpsoftwareversions", "fastqc", "multiqc"] }, "nextflow_version": "!>=21.10.3", "nf_core_version": null, @@ -18984,9 +17025,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "wgs" - ], + "topics": ["wgs"], "visibility": "public", "forks": 5, "open_issues": 0, @@ -19040,10 +17079,7 @@ "master_branch_exists": false, "main_branch_exists": true, "main_branch_protection_up_to_date": true, - "main_branch_protection_status_checks": [ - "pre-commit", - "nf-core" - ], + "main_branch_protection_status_checks": ["pre-commit", "nf-core"], "main_branch_protection_required_reviews": 2, "main_branch_protection_require_codeowner_review": false, "main_branch_protection_require_non_stale_review": false, @@ -19086,15 +17122,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "main_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "main_nextflow_config_plugins": ["nf-schema@2.5.1"], "main_nextflow_config_manifest": { "defaultBranch": "master" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "dev" }, @@ -19104,10 +17136,7 @@ "published_at": "2026-05-13T05:47:10Z", "tag_sha": "14c1035344db22683551b3455e42fddaed9ea60c", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bcftools_concat", @@ -19146,17 +17175,11 @@ "spring_decompress", "vcftools" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.10.4", "nf_core_version": "4.0.2", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null } ] @@ -19193,9 +17216,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "gwas" - ], + "topics": ["gwas"], "visibility": "public", "forks": 28, "open_issues": 23, @@ -19248,9 +17269,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": -1, - "master_branch_protection_status_checks": [ - "nf-core" - ], + "master_branch_protection_status_checks": ["nf-core"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -19264,9 +17283,7 @@ "main_branch_protection_enforce_admins": -1, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "nf-core" - ], + "dev_branch_protection_status_checks": ["nf-core"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -19342,15 +17359,11 @@ "has_nf_test_dev": true, "master_nextflow_config_plugins": [], "master_nextflow_config_manifest": {}, - "main_nextflow_config_plugins": [ - "nf-schema@2.2.0" - ], + "main_nextflow_config_plugins": ["nf-schema@2.2.0"], "main_nextflow_config_manifest": { "defaultBranch": "main" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -19360,27 +17373,14 @@ "published_at": "2026-03-16T20:01:55Z", "tag_sha": "2e6660aa8db59c674df4a70a25449cf2aedc630c", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "multiqc", - "plink_gwas", - "plink_vcf" - ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "modules": ["multiqc", "plink_gwas", "plink_vcf"], + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.04.0", "nf_core_version": "3.5.2", - "plugins": [ - "nf-schema@2.2.0" - ], + "plugins": ["nf-schema@2.2.0"], "co2footprint_files": null } ] @@ -19483,10 +17483,7 @@ "master_branch_exists": false, "main_branch_exists": true, "main_branch_protection_up_to_date": true, - "main_branch_protection_status_checks": [ - "pre-commit", - "nf-core" - ], + "main_branch_protection_status_checks": ["pre-commit", "nf-core"], "main_branch_protection_required_reviews": 2, "main_branch_protection_require_codeowner_review": false, "main_branch_protection_require_non_stale_review": false, @@ -19494,10 +17491,7 @@ "main_uses_ruleset": true, "dev_branch_exists": true, "dev_branch_protection_up_to_date": true, - "dev_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "dev_branch_protection_status_checks": ["nf-core", "pre-commit"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -19527,15 +17521,11 @@ "is_DSL2": true, "has_nf_test": false, "has_nf_test_dev": true, - "main_nextflow_config_plugins": [ - "nf-schema@2.4.2" - ], + "main_nextflow_config_plugins": ["nf-schema@2.4.2"], "main_nextflow_config_manifest": { "defaultBranch": "master" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "main" }, @@ -19567,10 +17557,7 @@ "published_at": "2026-02-22T11:08:17Z", "tag_sha": "067f0a18b0bc6422c7665ac6b1e83b36a3bfb5de", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bff", @@ -19594,17 +17581,11 @@ "untar", "vireo" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.04.0", "nf_core_version": "3.5.2", - "plugins": [ - "nf-schema@2.4.2" - ], + "plugins": ["nf-schema@2.4.2"], "co2footprint_files": null } ] @@ -19708,11 +17689,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": -1, - "master_branch_protection_status_checks": [ - "nf-core", - "Prettier", - "EditorConfig" - ], + "master_branch_protection_status_checks": ["nf-core", "Prettier", "EditorConfig"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -19720,11 +17697,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "nf-core", - "Prettier", - "EditorConfig" - ], + "dev_branch_protection_status_checks": ["nf-core", "Prettier", "EditorConfig"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -19765,9 +17738,7 @@ "has_nf_test_dev": true, "master_nextflow_config_plugins": [], "master_nextflow_config_manifest": {}, - "dev_nextflow_config_plugins": [ - "nf-schema@2.4.2" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.4.2"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -19777,10 +17748,7 @@ "published_at": "2023-05-16T12:15:32Z", "tag_sha": "683daaf41bb396839445e603152b45daa141ced4", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bamtools_stats", @@ -19814,10 +17782,7 @@ "published_at": "2022-10-24T13:09:05Z", "tag_sha": "4cd916f0c15e2c1a6a4a09228981cfd919b33222", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bamtools_stats", @@ -19851,10 +17816,7 @@ "published_at": "2025-11-14T11:35:20Z", "tag_sha": "b2b144902c2ec92cfb2c898777b293093f0d4be5", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bamtools_stats", @@ -19879,11 +17841,7 @@ "trimgalore", "untar" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.3.2", @@ -19924,10 +17882,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "chromosome-conformation-capture", - "hi-c" - ], + "topics": ["chromosome-conformation-capture", "hi-c"], "visibility": "public", "forks": 67, "open_issues": 48, @@ -19980,10 +17935,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": true, - "master_branch_protection_status_checks": [ - "pre-commit", - "nf-core" - ], + "master_branch_protection_status_checks": ["pre-commit", "nf-core"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -19992,10 +17944,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": true, - "dev_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "dev_branch_protection_status_checks": ["nf-core", "pre-commit"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -20067,9 +18016,7 @@ "has_nf_test_dev": true, "master_nextflow_config_plugins": [], "master_nextflow_config_manifest": {}, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -20079,10 +18026,7 @@ "published_at": "2023-06-01T13:44:15Z", "tag_sha": "fe4ac656317d24c37e81e7940a526ed9ea812f8e", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bowtie2_align", @@ -20106,10 +18050,7 @@ "published_at": "2023-01-21T11:45:05Z", "tag_sha": "b4d89cfacf97a5835fba804887cf0fc7e0449e8d", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bowtie2_align", @@ -20133,10 +18074,7 @@ "published_at": "2021-05-25T08:28:06Z", "tag_sha": "ac74763a91961ef7b274a651608c76be05be15e4", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=20.04.0" }, { @@ -20144,10 +18082,7 @@ "published_at": "2020-09-03T08:07:23Z", "tag_sha": "52e5f048a66541a4d33d4b721ff4a0a05ba1745e", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=19.10.0" }, { @@ -20155,10 +18090,7 @@ "published_at": "2020-07-09T13:37:53Z", "tag_sha": "ae2352c5b864a5e11d1220137d631a7c98b9ad14", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=19.10.0" }, { @@ -20166,10 +18098,7 @@ "published_at": "2020-07-09T06:54:37Z", "tag_sha": "b84069e1f2f1d51414341a992200c339cdce711b", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=19.10.0" }, { @@ -20177,10 +18106,7 @@ "published_at": "2019-10-23T12:19:03Z", "tag_sha": "481964d91cd3c4ab1d4b3afcba0f8a639911d97e", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=19.04.0" }, { @@ -20188,10 +18114,7 @@ "published_at": "2019-05-06T17:02:29Z", "tag_sha": "f7a827eeda4e5b8fd30f1724d1ae1f21ec65b3dd", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=0.32.0" }, { @@ -20199,10 +18122,7 @@ "published_at": "2026-05-06T07:49:40Z", "tag_sha": "e0084aec16e0b5c6ce5f11e00a0a995585fde3ed", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bowtie2_align", @@ -20231,11 +18151,7 @@ "samtools_sort", "trimgalore" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.04.0", "nf_core_version": "3.5.1", @@ -20276,14 +18192,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "atac", - "atac-seq", - "hic", - "hicar", - "multi-omics", - "transcriptome" - ], + "topics": ["atac", "atac-seq", "hic", "hicar", "multi-omics", "transcriptome"], "visibility": "public", "forks": 7, "open_issues": 9, @@ -20336,9 +18245,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": -1, - "master_branch_protection_status_checks": [ - "nf-core" - ], + "master_branch_protection_status_checks": ["nf-core"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -20346,11 +18253,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "nf-core", - "Prettier", - "EditorConfig" - ], + "dev_branch_protection_status_checks": ["nf-core", "Prettier", "EditorConfig"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -20411,9 +18314,7 @@ "has_nf_test_dev": false, "master_nextflow_config_plugins": [], "master_nextflow_config_manifest": {}, - "dev_nextflow_config_plugins": [ - "nf-validation" - ], + "dev_nextflow_config_plugins": ["nf-validation"], "dev_nextflow_config_manifest": {}, "releases": [ { @@ -20421,10 +18322,7 @@ "published_at": "2022-05-03T18:45:18Z", "tag_sha": "429087d2b13e59c3edd2e71b8005c1adc5bbb7bb", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bedtools_genomecov", @@ -20470,10 +18368,7 @@ "published_at": "2023-07-19T11:36:34Z", "tag_sha": "d2d17a924e42d6f88640b79d48d8b332f33a953f", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bedtools_genomecov", @@ -20556,15 +18451,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "dna", - "hla", - "hla-typing", - "immunology", - "optitype", - "personalized-medicine", - "rna" - ], + "topics": ["dna", "hla", "hla-typing", "immunology", "optitype", "personalized-medicine", "rna"], "visibility": "public", "forks": 37, "open_issues": 10, @@ -20617,10 +18504,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": -1, - "master_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "master_branch_protection_status_checks": ["nf-core", "pre-commit"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -20628,10 +18512,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "dev_branch_protection_status_checks": ["nf-core", "pre-commit"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -20725,15 +18606,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "master_nextflow_config_plugins": ["nf-schema@2.5.1"], "master_nextflow_config_manifest": { "defaultBranch": "master" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -20743,10 +18620,7 @@ "published_at": "2026-02-02T07:06:35Z", "tag_sha": "3237d20e7e611d8bbf8c37e637202dfe8a23e996", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "cat_fastq", @@ -20759,17 +18633,11 @@ "yara_index", "yara_mapper" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.04.2", "nf_core_version": "3.5.1", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null }, { @@ -20777,10 +18645,7 @@ "published_at": "2025-04-14T15:11:21Z", "tag_sha": "7d27f7ea1c64ddcb93f70db05bc263e89a67299f", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "cat_fastq", @@ -20793,11 +18658,7 @@ "yara_index", "yara_mapper" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.2.0" @@ -20807,10 +18668,7 @@ "published_at": "2022-10-18T12:12:03Z", "tag_sha": "7c9a2fbd404fae653d12e14db823b378512fbb40", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "custom_dumpsoftwareversions", @@ -20832,10 +18690,7 @@ "published_at": "2020-08-21T11:26:05Z", "tag_sha": "69987947952ec3f188356a3043cce724d72125e3", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=19.10.0" }, { @@ -20843,10 +18698,7 @@ "published_at": "2019-06-27T09:13:32Z", "tag_sha": "bf5d0c2d4646df8ce240230b1a15c0a241658a07", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=18.10.1" }, { @@ -20854,10 +18706,7 @@ "published_at": "2019-03-07T10:06:43Z", "tag_sha": "4bcced898ee23600bd8c249ff085f8f88db90e7c", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=18.10.1" }, { @@ -20865,10 +18714,7 @@ "published_at": "2019-02-04T13:28:33Z", "tag_sha": "18740c24175eb82cb1e206e8d471c2899e59ab7e", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=18.10.1" }, { @@ -20876,10 +18722,7 @@ "published_at": "2018-12-12T14:33:18Z", "tag_sha": "5a5687958004e2d8e9c2625f0bde558deffdda99", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=0.31.0" }, { @@ -20887,10 +18730,7 @@ "published_at": "2018-08-21T07:22:23Z", "tag_sha": "af1f68457c50060dcae8ed7e53b780e7f6203e60", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=0.31.0" }, { @@ -20898,10 +18738,7 @@ "published_at": "2018-08-15T13:56:31Z", "tag_sha": "17826e8340be96fd9def2fad4d7bb778294ca9b1", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=0.31.0" }, { @@ -20909,10 +18746,7 @@ "published_at": "2018-07-18T15:28:12Z", "tag_sha": "41d7b6baf787cb1f29ba44c5bc864b3eddfcfe3c", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": null }, { @@ -20920,10 +18754,7 @@ "published_at": "2018-07-18T13:27:40Z", "tag_sha": "41d7b6baf787cb1f29ba44c5bc864b3eddfcfe3c", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": null }, { @@ -20931,10 +18762,7 @@ "published_at": "2026-05-21T14:33:45Z", "tag_sha": "3d9231c02103f1cc8125134e50c89e7d18bffcde", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "cat_fastq", @@ -20951,17 +18779,11 @@ "yara_index", "yara_mapper" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.10.4", "nf_core_version": "4.0.2", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null } ] @@ -20998,12 +18820,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "cytometry", - "image-analysis", - "image-processing", - "image-segmentation" - ], + "topics": ["cytometry", "image-analysis", "image-processing", "image-segmentation"], "visibility": "public", "forks": 18, "open_issues": 6, @@ -21070,9 +18887,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "nf-core" - ], + "dev_branch_protection_status_checks": ["nf-core"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -21121,10 +18936,7 @@ "published_at": "2020-05-29T12:38:02Z", "tag_sha": "5d6631332b43c78f12b853594e91a7f7356d87ae", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=19.10.0" }, { @@ -21132,14 +18944,9 @@ "published_at": "2022-07-20T09:25:59Z", "tag_sha": "fac968e589a298cd5087cde684c46a1c1c292d0d", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "custom_dumpsoftwareversions" - ] + "modules": ["custom_dumpsoftwareversions"] }, "nextflow_version": "!>=21.10.3", "nf_core_version": null, @@ -21180,13 +18987,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "isoseq", - "isoseq-3", - "rna", - "tama", - "ultra" - ], + "topics": ["isoseq", "isoseq-3", "rna", "tama", "ultra"], "visibility": "public", "forks": 20, "open_issues": 13, @@ -21239,10 +19040,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": -1, - "master_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "master_branch_protection_status_checks": ["nf-core", "pre-commit"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -21250,10 +19048,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "dev_branch_protection_status_checks": ["nf-core", "pre-commit"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -21277,13 +19072,9 @@ "is_DSL2": true, "has_nf_test": false, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-validation@1.1.3" - ], + "master_nextflow_config_plugins": ["nf-validation@1.1.3"], "master_nextflow_config_manifest": {}, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -21293,10 +19084,7 @@ "published_at": "2024-09-05T16:17:25Z", "tag_sha": "c7536ab0e18a27460476d4e8557845950292f070", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bamtools_convert", @@ -21328,10 +19116,7 @@ "published_at": "2023-09-04T08:32:50Z", "tag_sha": "1d5244a14713bad7e76c4807f1179b9017d07ee9", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bamtools_convert", @@ -21358,10 +19143,7 @@ "published_at": "2023-03-13T13:35:16Z", "tag_sha": "977b9bb18393474dfea31923cd479e005e8976db", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bamtools_convert", @@ -21387,10 +19169,7 @@ "published_at": "2023-03-09T09:19:11Z", "tag_sha": "26153d74898361e5e08b80885f9f67c6a2c881c9", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bamtools_convert", @@ -21416,10 +19195,7 @@ "published_at": "2023-01-12T19:29:02Z", "tag_sha": "a568a758220204c0baa4a0ea74496d37811a205f", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bamtools_convert", @@ -21445,10 +19221,7 @@ "published_at": "2022-09-27T15:28:41Z", "tag_sha": "322f3a2f4b22855c03f59d29802fe35c5ddaafbc", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bamtools_convert", @@ -21474,10 +19247,7 @@ "published_at": "2022-07-12T06:52:05Z", "tag_sha": "f191d29c552e236fb66b0ce9b80ffd7a70dc0f58", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bamtools_convert", @@ -21503,10 +19273,7 @@ "published_at": "2022-06-28T08:56:05Z", "tag_sha": "af7d5049a60fed0838249c65039386f1b551ef5f", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bamtools_convert", @@ -21532,10 +19299,7 @@ "published_at": "2026-04-09T06:23:57Z", "tag_sha": "6f7705489a38e6152d1ea9f9d11c484b2356f440", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bamtools_convert", @@ -21552,17 +19316,11 @@ "ultra_align", "ultra_index" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.04.0", "nf_core_version": "3.4.1", - "plugins": [ - "nf-validation@1.1.3" - ], + "plugins": ["nf-validation@1.1.3"], "co2footprint_files": null } ] @@ -21599,12 +19357,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "k-mer", - "kmer", - "kmer-counting", - "kmer-frequency-count" - ], + "topics": ["k-mer", "kmer", "kmer-counting", "kmer-frequency-count"], "visibility": "public", "forks": 15, "open_issues": 23, @@ -21670,10 +19423,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "dev_branch_protection_status_checks": ["nf-core", "pre-commit"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -21734,9 +19484,7 @@ "has_nf_test_dev": false, "master_nextflow_config_plugins": [], "master_nextflow_config_manifest": {}, - "dev_nextflow_config_plugins": [ - "nf-schema@2.1.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.1.1"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -21746,10 +19494,7 @@ "published_at": "2020-10-27T22:54:41Z", "tag_sha": "e1f736c5c694037d548af53e8d1d1cacf120327f", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=20.07.1" }, { @@ -21757,20 +19502,10 @@ "published_at": "2025-01-13T10:51:02Z", "tag_sha": "bc622c3e53831555fe5aaf83199a859fa445c510", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "fastqc", - "multiqc" - ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "modules": ["fastqc", "multiqc"], + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.1.1", @@ -22112,15 +19847,9 @@ "published_at": "2021-08-12T08:56:11Z", "tag_sha": "800d619c28b8647b9be443d2e0dd6e8b76b2a680", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "fastqc", - "multiqc" - ] + "modules": ["fastqc", "multiqc"] } } ] @@ -22286,11 +20015,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "lncrnas", - "nextflow", - "pipeline" - ], + "topics": ["lncrnas", "nextflow", "pipeline"], "visibility": "public", "forks": 50, "open_issues": 6, @@ -22399,11 +20124,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "lncrnas", - "nextflow", - "pipeline" - ], + "topics": ["lncrnas", "nextflow", "pipeline"], "visibility": "public", "forks": 50, "open_issues": 6, @@ -22444,10 +20165,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": -1, - "master_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "master_branch_protection_status_checks": ["nf-core", "pre-commit"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -22455,10 +20173,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "dev_branch_protection_status_checks": ["nf-core", "pre-commit"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -22507,15 +20222,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-schema@2.3.0" - ], + "master_nextflow_config_plugins": ["nf-schema@2.3.0"], "master_nextflow_config_manifest": { "defaultBranch": "master" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.3.0" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.3.0"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -22525,10 +20236,7 @@ "published_at": "2025-04-04T10:55:14Z", "tag_sha": "39e1e236c8a6624912f8e74bbf3e817bd94b987c", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bbmap_bbsplit", @@ -22588,9 +20296,7 @@ }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.2.0", - "plugins": [ - "nf-schema@2.3.0" - ], + "plugins": ["nf-schema@2.3.0"], "co2footprint_files": null } ] @@ -22680,10 +20386,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": true, - "master_branch_protection_status_checks": [ - "pre-commit", - "nf-core" - ], + "master_branch_protection_status_checks": ["pre-commit", "nf-core"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -22692,10 +20395,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": true, - "dev_branch_protection_status_checks": [ - "pre-commit", - "nf-core" - ], + "dev_branch_protection_status_checks": ["pre-commit", "nf-core"], "dev_branch_protection_required_reviews": -1, "dev_branch_protection_require_codeowner_review": -1, "dev_branch_protection_require_non_stale_review": -1, @@ -22720,15 +20420,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "master_nextflow_config_plugins": ["nf-schema@2.5.1"], "master_nextflow_config_manifest": { "defaultBranch": "master" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -22747,10 +20443,7 @@ "published_at": "2026-03-25T13:20:43Z", "tag_sha": "d6e1a120a696d2de5b5b3bef5ca93210131d2002", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "annotsv_annotsv", @@ -22812,9 +20505,7 @@ }, "nextflow_version": "!>=25.04.6", "nf_core_version": "3.5.1", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null } ] @@ -22911,10 +20602,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": true, - "master_branch_protection_status_checks": [ - "pre-commit", - "nf-core" - ], + "master_branch_protection_status_checks": ["pre-commit", "nf-core"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -22923,10 +20611,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": true, - "dev_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "dev_branch_protection_status_checks": ["nf-core", "pre-commit"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -22934,12 +20619,7 @@ "dev_uses_ruleset": true, "TEMPLATE_branch_exists": true, "has_required_topics": false, - "missing_topics": [ - "nf-core", - "nextflow", - "workflow", - "pipeline" - ], + "missing_topics": ["nf-core", "nextflow", "workflow", "pipeline"], "open_pr_count": 5, "repository_url": "https://github.com/nf-core/lsmquant", "contributors": [ @@ -22967,15 +20647,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "master_nextflow_config_plugins": ["nf-schema@2.5.1"], "master_nextflow_config_manifest": { "defaultBranch": "master" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -22985,29 +20661,14 @@ "published_at": "2026-04-14T16:20:35Z", "tag_sha": "ee07d1c1f0ebc8f99cc3c9b30517396ad6204f0d", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "mat2json", - "multiqc", - "numorph_intensity", - "numorph_resample", - "unzip" - ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "modules": ["mat2json", "multiqc", "numorph_intensity", "numorph_resample", "unzip"], + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.04.0", "nf_core_version": "3.5.1", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null }, { @@ -23015,29 +20676,14 @@ "published_at": "2026-05-19T12:24:01Z", "tag_sha": "4c85347ab70b510882cd0164215d0c626f5650cd", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "mat2json", - "multiqc", - "numorph_intensity", - "numorph_resample", - "unzip" - ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "modules": ["mat2json", "multiqc", "numorph_intensity", "numorph_resample", "unzip"], + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.04.0", "nf_core_version": "3.5.2", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null } ] @@ -23137,22 +20783,14 @@ "master_branch_exists": false, "main_branch_exists": true, "main_branch_protection_up_to_date": -1, - "main_branch_protection_status_checks": [ - "nf-core", - "pre-commit", - "confirm-pass" - ], + "main_branch_protection_status_checks": ["nf-core", "pre-commit", "confirm-pass"], "main_branch_protection_required_reviews": 2, "main_branch_protection_require_codeowner_review": false, "main_branch_protection_require_non_stale_review": false, "main_branch_protection_enforce_admins": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "nf-core", - "pre-commit", - "confirm-pass" - ], + "dev_branch_protection_status_checks": ["nf-core", "pre-commit", "confirm-pass"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -23391,15 +21029,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "main_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "main_nextflow_config_plugins": ["nf-schema@2.5.1"], "main_nextflow_config_manifest": { "defaultBranch": "main" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "main" }, @@ -23409,10 +21043,7 @@ "published_at": "2026-03-31T08:57:49Z", "tag_sha": "5dabb0159ac0104885e09f301db22126e8fcb394", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "adapterremoval", @@ -23494,9 +21125,7 @@ }, "nextflow_version": "!>=25.04.2", "nf_core_version": "3.5.2", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null }, { @@ -23504,10 +21133,7 @@ "published_at": "2026-03-12T11:00:06Z", "tag_sha": "0c370baf735c9b42b95ed9933bae5a11919e010f", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "adapterremoval", @@ -23589,9 +21215,7 @@ }, "nextflow_version": "!>=25.04.2", "nf_core_version": "3.5.2", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null }, { @@ -23599,10 +21223,7 @@ "published_at": "2026-02-02T14:08:54Z", "tag_sha": "b52fa53592ac9de93d3764ce69a05a711ae9f498", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "adapterremoval", @@ -23684,9 +21305,7 @@ }, "nextflow_version": "!>=25.04.2", "nf_core_version": "3.5.1", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null }, { @@ -23694,10 +21313,7 @@ "published_at": "2025-12-05T12:02:56Z", "tag_sha": "ccfb744aab0c00a805a2dfbf7d9c9d8729c30805", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "adapterremoval", @@ -23778,9 +21394,7 @@ }, "nextflow_version": "!>=25.04.2", "nf_core_version": "3.5.1", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null }, { @@ -23788,10 +21402,7 @@ "published_at": "2025-11-07T14:21:43Z", "tag_sha": "99859fc04cfba21dde02a2d88dc0be684c3d98ae", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "adapterremoval", @@ -23871,9 +21482,7 @@ }, "nextflow_version": "!>=25.04.2", "nf_core_version": "3.4.1", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null }, { @@ -23881,10 +21490,7 @@ "published_at": "2025-10-27T20:09:33Z", "tag_sha": "b0bc5cae64fdd7fa6aec76f270b2daf7882ed84b", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "adapterremoval", @@ -23970,10 +21576,7 @@ "published_at": "2025-09-30T07:37:43Z", "tag_sha": "3d41222776d2ed7a78dd3fd4dd643690c49f6bd2", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "adapterremoval", @@ -24058,10 +21661,7 @@ "published_at": "2025-05-22T13:14:16Z", "tag_sha": "7ffd8b8c65b5c41534d8d7daf1cf8b23d92c8f22", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "adapterremoval", @@ -24140,10 +21740,7 @@ "published_at": "2025-04-04T07:47:54Z", "tag_sha": "4717d3d466402c9ceefecae2ceb549c7cbe27e62", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "adapterremoval", @@ -24219,10 +21816,7 @@ "published_at": "2025-02-13T13:08:21Z", "tag_sha": "b2377f1629a0345276b16281642ed432d95b2c71", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "adapterremoval", @@ -24297,10 +21891,7 @@ "published_at": "2024-12-19T13:10:22Z", "tag_sha": "049ea0a819e8c404580a0260002cf2331aa0e7d0", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "adapterremoval", @@ -24375,10 +21966,7 @@ "published_at": "2024-10-30T09:17:52Z", "tag_sha": "b582aae7d64816e08d6efae7c82ed55ea20ee7b2", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "adapterremoval", @@ -24449,10 +22037,7 @@ "published_at": "2024-10-27T15:10:28Z", "tag_sha": "74b5c92b9226d3ae19c20ed9f1d107e9273c0d00", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "adapterremoval", @@ -24523,10 +22108,7 @@ "published_at": "2024-10-04T07:32:41Z", "tag_sha": "cf931af514a7606d82e98b38260147a7cddbdbee", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "adapterremoval", @@ -24593,10 +22175,7 @@ "published_at": "2024-08-27T08:29:46Z", "tag_sha": "8e3f760f23daed13777a0ca1895ef78429618ab8", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "adapterremoval", @@ -24663,10 +22242,7 @@ "published_at": "2024-07-04T06:37:27Z", "tag_sha": "bb74c4695d7767c7094fc5411bf5c49b1caf137d", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "adapterremoval", @@ -24734,10 +22310,7 @@ "published_at": "2024-06-10T14:25:45Z", "tag_sha": "aac4962a09b1815c27ca88bb8bf6f64e7b78505f", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "adapterremoval", @@ -24802,10 +22375,7 @@ "published_at": "2024-05-13T13:38:53Z", "tag_sha": "a50117e4ddc681b8ec5535fc265c66df45e38d30", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "adapterremoval", @@ -24863,10 +22433,7 @@ "published_at": "2024-02-12T19:22:52Z", "tag_sha": "e486bb23b9012ecf649061f1eb448bb853e0aad8", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "adapterremoval", @@ -24910,9 +22477,7 @@ "seqtk_mergepe", "tiara_tiara" ], - "subworkflows": [ - "fasta_binning_concoct" - ] + "subworkflows": ["fasta_binning_concoct"] }, "nextflow_version": "!>=23.04.0", "nf_core_version": null @@ -24922,10 +22487,7 @@ "published_at": "2024-02-05T14:46:11Z", "tag_sha": "7bd5dc6007aa15beb63ec827f50bc0e982beb8e2", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "adapterremoval", @@ -24969,9 +22531,7 @@ "seqtk_mergepe", "tiara_tiara" ], - "subworkflows": [ - "fasta_binning_concoct" - ] + "subworkflows": ["fasta_binning_concoct"] }, "nextflow_version": "!>=23.04.0", "nf_core_version": null @@ -24981,10 +22541,7 @@ "published_at": "2024-02-02T14:30:07Z", "tag_sha": "274412afa54f477dccf4d6230506ec7de3dfaa4d", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "adapterremoval", @@ -25028,9 +22585,7 @@ "seqtk_mergepe", "tiara_tiara" ], - "subworkflows": [ - "fasta_binning_concoct" - ] + "subworkflows": ["fasta_binning_concoct"] }, "nextflow_version": "!>=23.04.0", "nf_core_version": null @@ -25040,10 +22595,7 @@ "published_at": "2023-11-17T04:37:45Z", "tag_sha": "e72890089a1fb69d32f2cf0762739c824412bf2b", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "adapterremoval", @@ -25087,9 +22639,7 @@ "seqtk_mergepe", "tiara_tiara" ], - "subworkflows": [ - "fasta_binning_concoct" - ] + "subworkflows": ["fasta_binning_concoct"] }, "nextflow_version": "!>=23.04.0", "nf_core_version": null @@ -25099,10 +22649,7 @@ "published_at": "2023-10-10T11:37:47Z", "tag_sha": "ba7234959405b7a6df253d6d03158a7cde030c96", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "adapterremoval", @@ -25146,9 +22693,7 @@ "seqtk_mergepe", "tiara_tiara" ], - "subworkflows": [ - "fasta_binning_concoct" - ] + "subworkflows": ["fasta_binning_concoct"] }, "nextflow_version": "!>=23.04.0", "nf_core_version": null @@ -25158,10 +22703,7 @@ "published_at": "2023-09-26T09:01:35Z", "tag_sha": "18a1645fa3e0cc6ea417f009d592f82bbe7b57f2", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "adapterremoval", @@ -25205,9 +22747,7 @@ "seqtk_mergepe", "tiara_tiara" ], - "subworkflows": [ - "fasta_binning_concoct" - ] + "subworkflows": ["fasta_binning_concoct"] }, "nextflow_version": "!>=23.04.0", "nf_core_version": null @@ -25217,10 +22757,7 @@ "published_at": "2023-06-23T11:40:26Z", "tag_sha": "66cf53aff834d2a254b78b94fc54cd656b8b7b57", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "adapterremoval", @@ -25255,9 +22792,7 @@ "pydamage_filter", "samtools_faidx" ], - "subworkflows": [ - "fasta_binning_concoct" - ] + "subworkflows": ["fasta_binning_concoct"] }, "nextflow_version": "!>=22.10.1", "nf_core_version": null @@ -25267,10 +22802,7 @@ "published_at": "2023-06-19T20:37:43Z", "tag_sha": "61deef81c74b3c4c3bc0bce265e1d2e181d2260d", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "adapterremoval", @@ -25305,9 +22837,7 @@ "pydamage_filter", "samtools_faidx" ], - "subworkflows": [ - "fasta_binning_concoct" - ] + "subworkflows": ["fasta_binning_concoct"] }, "nextflow_version": "!>=22.10.1", "nf_core_version": null @@ -25317,10 +22847,7 @@ "published_at": "2023-03-02T10:12:03Z", "tag_sha": "c9468cb9154402c4a4cab78664ee50c24a91f6c3", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "adapterremoval", @@ -25355,9 +22882,7 @@ "pydamage_filter", "samtools_faidx" ], - "subworkflows": [ - "fasta_binning_concoct" - ] + "subworkflows": ["fasta_binning_concoct"] }, "nextflow_version": "!>=22.10.1", "nf_core_version": null @@ -25367,10 +22892,7 @@ "published_at": "2022-08-25T10:35:57Z", "tag_sha": "a8e92af70eca59a92b72262e6cdde11e69375801", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "adapterremoval", @@ -25402,10 +22924,7 @@ "published_at": "2022-06-14T07:41:48Z", "tag_sha": "3b4dd3469725654d67e06b3853ba460d64c80788", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "adapterremoval", @@ -25437,17 +22956,9 @@ "published_at": "2021-11-26T10:56:44Z", "tag_sha": "e065754c46eedc85d46cd8a71b32ad73b3b741cb", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "fastp", - "fastqc", - "prodigal", - "prokka" - ] + "modules": ["fastp", "fastqc", "prodigal", "prokka"] }, "nextflow_version": "!>=21.04.0", "nf_core_version": null @@ -25457,15 +22968,9 @@ "published_at": "2021-07-29T07:07:34Z", "tag_sha": "d4f00bc2d178c1c8dc25b576c9e77e70511d5d21", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "fastp", - "fastqc" - ] + "modules": ["fastp", "fastqc"] }, "nextflow_version": "!>=21.04.0", "nf_core_version": null @@ -25475,10 +22980,7 @@ "published_at": "2021-06-01T11:54:01Z", "tag_sha": "0b4f0ef116481a346e3e5ffebafb811872db2ba9", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": "!>=21.04.0" }, { @@ -25486,10 +22988,7 @@ "published_at": "2021-02-10T10:36:52Z", "tag_sha": "485c3fa0ba7345ac124bef04d08391d5e7cdcb42", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=20.04.0" }, { @@ -25497,10 +22996,7 @@ "published_at": "2020-11-24T18:07:18Z", "tag_sha": "8c0f1fedf2d86ad17032c45add7851578022972a", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=20.04.0" }, { @@ -25508,10 +23004,7 @@ "published_at": "2020-11-10T17:38:23Z", "tag_sha": "a3122b1743bc483f04f33eff846dab2f2460e62c", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=19.10.0" }, { @@ -25519,10 +23012,7 @@ "published_at": "2020-10-06T15:26:21Z", "tag_sha": "7384cef0313583bc1c1277ba8f139f9783f0619e", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=19.10.0" }, { @@ -25530,10 +23020,7 @@ "published_at": "2019-12-21T10:21:58Z", "tag_sha": "4c2f61cbbb2be56d9a176947a758cdb4d7941910", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=19.01.0" }, { @@ -25541,10 +23028,7 @@ "published_at": "2026-05-25T14:04:51Z", "tag_sha": "c5bc88fd8f4f0a47362a2e843df0991a430b0c84", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "adapterremoval", @@ -25627,9 +23111,7 @@ }, "nextflow_version": "!>=25.10.4", "nf_core_version": "4.0.2", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null } ] @@ -25776,15 +23258,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "master_nextflow_config_plugins": ["nf-schema@2.5.1"], "master_nextflow_config_manifest": { "defaultBranch": "master" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -25794,10 +23272,7 @@ "published_at": "2025-11-28T16:11:54Z", "tag_sha": "a7c0869580dbd3c68c5a78227fa2684c8c5e7b66", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bbmap_align", @@ -25832,9 +23307,7 @@ }, "nextflow_version": "!>=25.04.0", "nf_core_version": "3.5.1", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null }, { @@ -25842,10 +23315,7 @@ "published_at": "2026-05-08T10:59:43Z", "tag_sha": "eb710a0721d6e532edb81ec96c86544dc438f424", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bbmap_align", @@ -25880,9 +23350,7 @@ }, "nextflow_version": "!>=25.04.0", "nf_core_version": "3.5.2", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null } ] @@ -25979,10 +23447,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": -1, - "master_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "master_branch_protection_status_checks": ["nf-core", "pre-commit"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -25990,10 +23455,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "dev_branch_protection_status_checks": ["nf-core", "pre-commit"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -26022,13 +23484,9 @@ "is_DSL2": true, "has_nf_test": false, "has_nf_test_dev": false, - "master_nextflow_config_plugins": [ - "nf-validation" - ], + "master_nextflow_config_plugins": ["nf-validation"], "master_nextflow_config_manifest": {}, - "dev_nextflow_config_plugins": [ - "nf-schema@2.1.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.1.1"], "dev_nextflow_config_manifest": {}, "releases": [ { @@ -26036,10 +23494,7 @@ "published_at": "2023-07-18T10:55:05Z", "tag_sha": "b02ede773092f8a8a5999400acda6894d51b4d26", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bowtie2_align", @@ -26062,10 +23517,7 @@ "published_at": "2023-07-11T12:17:51Z", "tag_sha": "87ea6e2b1f96d5af1854d0cbdff27af1bcde7ba2", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bowtie2_align", @@ -26088,10 +23540,7 @@ "published_at": "2023-06-26T07:09:56Z", "tag_sha": "0ca38c3bd5a35e7abcf2e83dc1ff7c1e73e50856", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bowtie2_align", @@ -26114,10 +23563,7 @@ "published_at": "2023-06-21T09:30:19Z", "tag_sha": "dda9122454b0d9e5bcdd481008c216eb52da16b2", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bowtie2_align", @@ -26140,17 +23586,9 @@ "published_at": "2023-05-18T07:39:37Z", "tag_sha": "6d1265f89f826513e9f1208dcd7b65ca77a7ab79", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "fastqc", - "multiqc", - "bowtie2_build", - "gunzip" - ] + "modules": ["fastqc", "multiqc", "bowtie2_build", "gunzip"] }, "nextflow_version": "!>=21.04.0" }, @@ -26159,10 +23597,7 @@ "published_at": "2025-06-02T12:09:16Z", "tag_sha": "c9a702eb7f4b8d25a6fe7a115078dd3ac211f346", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bowtie2_align", @@ -26177,17 +23612,11 @@ "star_genomegenerate", "star_starsolo" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.0.2", - "plugins": [ - "nf-validation" - ], + "plugins": ["nf-validation"], "co2footprint_files": null } ] @@ -26290,10 +23719,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": -1, - "master_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "master_branch_protection_status_checks": ["nf-core", "pre-commit"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -26301,10 +23727,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "dev_branch_protection_status_checks": ["nf-core", "pre-commit"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -26365,9 +23788,7 @@ "has_nf_test_dev": true, "master_nextflow_config_plugins": [], "master_nextflow_config_manifest": {}, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -26377,10 +23798,7 @@ "published_at": "2026-02-28T00:11:43Z", "tag_sha": "811df80beffe0731d9b32d65a116c875d1f6e82f", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "ashlar", @@ -26396,11 +23814,7 @@ "multiqc", "scimap_mcmicro" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.04.0", "nf_core_version": "3.5.1", @@ -26494,10 +23908,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": -1, - "master_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "master_branch_protection_status_checks": ["nf-core", "pre-commit"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -26505,10 +23916,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "pre-commit", - "nf-core" - ], + "dev_branch_protection_status_checks": ["pre-commit", "nf-core"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -26544,9 +23952,7 @@ "has_nf_test_dev": true, "master_nextflow_config_plugins": [], "master_nextflow_config_manifest": {}, - "dev_nextflow_config_plugins": [ - "nf-validation@1.1.3" - ], + "dev_nextflow_config_plugins": ["nf-validation@1.1.3"], "dev_nextflow_config_manifest": { "defaultBranch": "main" }, @@ -26556,14 +23962,9 @@ "published_at": "2026-01-28T04:09:54Z", "tag_sha": "76b676212bdf0a9de91ac1497d237211a492f153", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "custom_dumpsoftwareversions" - ], + "modules": ["custom_dumpsoftwareversions"], "subworkflows": [ "utils_nextflow_pipeline", "utils_nfcore_pipeline", @@ -26609,14 +24010,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "identification", - "mass-spectrometry", - "metabolomics", - "ms1", - "ms2", - "quantification" - ], + "topics": ["identification", "mass-spectrometry", "metabolomics", "ms1", "ms2", "quantification"], "visibility": "public", "forks": 17, "open_issues": 7, @@ -26669,10 +24063,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": -1, - "master_branch_protection_status_checks": [ - "nf-core", - "Run pipeline with test data (latest-everything)" - ], + "master_branch_protection_status_checks": ["nf-core", "Run pipeline with test data (latest-everything)"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -26680,10 +24071,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "nf-core", - "Run pipeline with test data (latest-everything)" - ], + "dev_branch_protection_status_checks": ["nf-core", "Run pipeline with test data (latest-everything)"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -26732,13 +24120,9 @@ "is_DSL2": true, "has_nf_test": false, "has_nf_test_dev": false, - "master_nextflow_config_plugins": [ - "nf-validation@1.1.3" - ], + "master_nextflow_config_plugins": ["nf-validation@1.1.3"], "master_nextflow_config_manifest": {}, - "dev_nextflow_config_plugins": [ - "nf-validation@1.1.3" - ], + "dev_nextflow_config_plugins": ["nf-validation@1.1.3"], "dev_nextflow_config_manifest": {}, "releases": [ { @@ -26746,15 +24130,9 @@ "published_at": "2024-04-15T14:40:14Z", "tag_sha": "55d82547604fcae3b6557fe7a3c442b623184f34", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "fastqc", - "multiqc" - ], + "modules": ["fastqc", "multiqc"], "subworkflows": [ "utils_nextflow_pipeline", "utils_nfcore_pipeline", @@ -26769,14 +24147,9 @@ "published_at": "2023-12-19T13:53:54Z", "tag_sha": "2f8f077d38fcacd2caef9590dc557ddcc17c78c6", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "custom_dumpsoftwareversions" - ] + "modules": ["custom_dumpsoftwareversions"] }, "nextflow_version": "!>=23.04.0", "nf_core_version": null @@ -26786,10 +24159,7 @@ "published_at": "2021-05-18T08:14:57Z", "tag_sha": "fca2ab5c508fc8179380ff747eab68b6db8aa93f", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=20.04.0" }, { @@ -26797,10 +24167,7 @@ "published_at": "2021-05-08T16:43:56Z", "tag_sha": "43d491841e7e4ac21fff73e72ec79762c3b5276e", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=19.10.0" }, { @@ -26808,15 +24175,9 @@ "published_at": "2024-05-22T08:19:41Z", "tag_sha": "6239953247efcf1d7c69ed6986227584470bd8db", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "fastqc", - "multiqc" - ], + "modules": ["fastqc", "multiqc"], "subworkflows": [ "utils_nextflow_pipeline", "utils_nfcore_pipeline", @@ -26825,9 +24186,7 @@ }, "nextflow_version": "!>=23.04.0", "nf_core_version": "2.14.1", - "plugins": [ - "nf-validation@1.1.3" - ], + "plugins": ["nf-validation@1.1.3"], "co2footprint_files": null } ] @@ -26917,10 +24276,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": -1, - "master_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "master_branch_protection_status_checks": ["nf-core", "pre-commit"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -26928,10 +24284,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "dev_branch_protection_status_checks": ["nf-core", "pre-commit"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -26975,13 +24328,9 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-schema@2.1.1" - ], + "master_nextflow_config_plugins": ["nf-schema@2.1.1"], "master_nextflow_config_manifest": {}, - "dev_nextflow_config_plugins": [ - "nf-schema@2.4.2" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.4.2"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -26991,20 +24340,10 @@ "published_at": "2024-11-22T09:20:10Z", "tag_sha": "84feafc9476978c2a1b84849871a553cffd9762a", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "multiqc", - "prodigal" - ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "modules": ["multiqc", "prodigal"], + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.0.2" @@ -27014,26 +24353,14 @@ "published_at": "2026-04-15T10:44:22Z", "tag_sha": "034ac0e8afd267c78cabef85b96dc6c8d3952098", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "multiqc", - "prodigal" - ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "modules": ["multiqc", "prodigal"], + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.10.5", "nf_core_version": "3.3.2", - "plugins": [ - "nf-schema@2.1.1" - ], + "plugins": ["nf-schema@2.1.1"], "co2footprint_files": null } ] @@ -27070,13 +24397,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "eukaryotes", - "metagenomics", - "metatranscriptomics", - "prokaryotes", - "viruses" - ], + "topics": ["eukaryotes", "metagenomics", "metatranscriptomics", "prokaryotes", "viruses"], "visibility": "public", "forks": 19, "open_issues": 22, @@ -27129,10 +24450,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": -1, - "master_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "master_branch_protection_status_checks": ["nf-core", "pre-commit"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -27140,9 +24458,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "nf-core" - ], + "dev_branch_protection_status_checks": ["nf-core"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -27211,15 +24527,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-schema@2.4.2" - ], + "master_nextflow_config_plugins": ["nf-schema@2.4.2"], "master_nextflow_config_manifest": { "defaultBranch": "master" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -27229,10 +24541,7 @@ "published_at": "2025-08-29T08:21:28Z", "tag_sha": "2a51399ef548164750563a4bf581fa25a39770f8", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bbmap_align", @@ -27276,10 +24585,7 @@ "published_at": "2025-06-18T05:33:31Z", "tag_sha": "c58c01c45738664d6e57fd1bb0faa30d3ba9cbcf", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bbmap_align", @@ -27323,10 +24629,7 @@ "published_at": "2025-03-13T09:43:04Z", "tag_sha": "c42a8d4a0c9eacb1f4605bae4ed824b91d345089", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bbmap_align", @@ -27354,11 +24657,7 @@ "trimgalore", "untar" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.2.0" @@ -27368,10 +24667,7 @@ "published_at": "2025-02-26T01:19:20Z", "tag_sha": "b7eab0b7068464dbff5de2ff8e0663709b003a39", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bbmap_align", @@ -27399,11 +24695,7 @@ "trimgalore", "untar" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.2.0" @@ -27413,10 +24705,7 @@ "published_at": "2024-04-03T11:13:13Z", "tag_sha": "10eab6d7ac6a05cc9a4b9bebfa99fae7c3f64a4b", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bbmap_align", @@ -27445,10 +24734,7 @@ "transdecoder_predict", "trimgalore" ], - "subworkflows": [ - "bam_sort_stats_samtools", - "bam_stats_samtools" - ] + "subworkflows": ["bam_sort_stats_samtools", "bam_stats_samtools"] }, "nextflow_version": "!>=23.04.0", "nf_core_version": null @@ -27458,10 +24744,7 @@ "published_at": "2024-02-15T15:12:46Z", "tag_sha": "766abe90b6798d8eaa3a3700da1fd6c70b53a2a5", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bbmap_align", @@ -27489,10 +24772,7 @@ "transdecoder_predict", "trimgalore" ], - "subworkflows": [ - "bam_sort_stats_samtools", - "bam_stats_samtools" - ] + "subworkflows": ["bam_sort_stats_samtools", "bam_stats_samtools"] }, "nextflow_version": "!>=23.04.0", "nf_core_version": null @@ -27502,10 +24782,7 @@ "published_at": "2026-04-06T05:07:14Z", "tag_sha": "53618bf411392c9ef6c0d07ad063f984bf4cc227", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bbmap_align", @@ -27543,9 +24820,7 @@ }, "nextflow_version": "!>=25.04.0", "nf_core_version": "3.5.2", - "plugins": [ - "nf-schema@2.4.2" - ], + "plugins": ["nf-schema@2.4.2"], "co2footprint_files": null } ] @@ -27672,13 +24947,9 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "main_nextflow_config_plugins": [ - "nf-validation@1.1.3" - ], + "main_nextflow_config_plugins": ["nf-validation@1.1.3"], "main_nextflow_config_manifest": {}, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -27688,26 +24959,14 @@ "published_at": "2026-02-17T06:31:38Z", "tag_sha": "eb5fb7db5015069030bc6c0cf0d2f0985b93cefb", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "fastqc", - "multiqc" - ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "modules": ["fastqc", "multiqc"], + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.04.0", "nf_core_version": "3.5.1", - "plugins": [ - "nf-validation@1.1.3" - ], + "plugins": ["nf-validation@1.1.3"], "co2footprint_files": null } ] @@ -27744,13 +25003,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "dna-methylation", - "fiber-seq", - "long-read", - "ont", - "pacbio" - ], + "topics": ["dna-methylation", "fiber-seq", "long-read", "ont", "pacbio"], "visibility": "public", "forks": 7, "open_issues": 7, @@ -27803,10 +25056,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": true, - "master_branch_protection_status_checks": [ - "pre-commit", - "nf-core" - ], + "master_branch_protection_status_checks": ["pre-commit", "nf-core"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -27814,10 +25064,7 @@ "master_uses_ruleset": true, "main_branch_exists": true, "main_branch_protection_up_to_date": true, - "main_branch_protection_status_checks": [ - "pre-commit", - "nf-core" - ], + "main_branch_protection_status_checks": ["pre-commit", "nf-core"], "main_branch_protection_required_reviews": 2, "main_branch_protection_require_codeowner_review": false, "main_branch_protection_require_non_stale_review": false, @@ -27825,10 +25072,7 @@ "main_uses_ruleset": true, "dev_branch_exists": true, "dev_branch_protection_up_to_date": true, - "dev_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "dev_branch_protection_status_checks": ["nf-core", "pre-commit"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -27863,17 +25107,13 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "master_nextflow_config_plugins": ["nf-schema@2.5.1"], "master_nextflow_config_manifest": { "defaultBranch": "master" }, "main_nextflow_config_plugins": [], "main_nextflow_config_manifest": {}, - "dev_nextflow_config_plugins": [ - "nf-schema@2.7.0" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.7.0"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -27883,10 +25123,7 @@ "published_at": "2025-11-21T02:26:23Z", "tag_sha": "3513e80df682ad20f42d6429a2ee142b606949b5", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "clair3", @@ -27913,11 +25150,7 @@ "samtools_sort", "tabix_bgziptabix" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.04.0", "nf_core_version": "3.5.1", @@ -27929,10 +25162,7 @@ "published_at": "2025-05-08T15:15:53Z", "tag_sha": "597317b1c9f9749b1bf834eb6df6721499aec2e6", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "fastqc", @@ -27950,11 +25180,7 @@ "samtools_index", "samtools_sort" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.2.1" @@ -27964,10 +25190,7 @@ "published_at": "2026-04-07T11:37:04Z", "tag_sha": "7b03e9a9821d8ea9a137dc4b1bde7856d4e7ae1e", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "clair3", @@ -27995,11 +25218,7 @@ "tabix_bgziptabix", "tabix_tabix" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.10.4", "nf_core_version": "3.5.2", @@ -28112,9 +25331,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "nf-core" - ], + "dev_branch_protection_status_checks": ["nf-core"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -28318,15 +25535,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "master_nextflow_config_plugins": ["nf-schema@2.5.1"], "master_nextflow_config_manifest": { "defaultBranch": "master" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -28336,11 +25549,7 @@ "published_at": "2025-12-12T10:48:18Z", "tag_sha": "5aa56467a85a5e2d6795ea72dfa5a5f0c9babc23", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md", - "docs/usage/bs-seq-primer.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md", "docs/usage/bs-seq-primer.md"], "components": { "modules": [ "bedtools_intersect", @@ -28401,9 +25610,7 @@ }, "nextflow_version": "!>=25.04.0", "nf_core_version": "3.5.1", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null }, { @@ -28411,11 +25618,7 @@ "published_at": "2025-08-10T14:28:48Z", "tag_sha": "db60bfe1f0d0409244a02c6b046301ebfd697db7", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md", - "docs/usage/bs-seq-primer.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md", "docs/usage/bs-seq-primer.md"], "components": { "modules": [ "bedtools_intersect", @@ -28467,10 +25670,7 @@ "published_at": "2025-07-04T06:51:51Z", "tag_sha": "f3e4b1bf58f5da9a2788426bfb320d8ed81ead15", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bedtools_intersect", @@ -28522,10 +25722,7 @@ "published_at": "2024-12-16T17:05:29Z", "tag_sha": "4415e90a60faba40ccefd4c847666d28688a86ee", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bismark_align", @@ -28573,10 +25770,7 @@ "published_at": "2024-10-27T07:45:50Z", "tag_sha": "d16f8f81e812d86f4d297e69de3f001628dfd5b4", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bismark_align", @@ -28606,11 +25800,7 @@ "trimgalore", "untar" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.0.2" @@ -28620,10 +25810,7 @@ "published_at": "2024-10-25T05:04:00Z", "tag_sha": "aac172df2c1c6558683885d3d52157bed3b6bbab", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bismark_align", @@ -28653,11 +25840,7 @@ "trimgalore", "untar" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.0.2" @@ -28667,10 +25850,7 @@ "published_at": "2024-01-06T00:37:05Z", "tag_sha": "54f823e102ef3d04077cc091a5ae435519f9923a", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bismark_align", @@ -28709,10 +25889,7 @@ "published_at": "2023-10-18T10:15:06Z", "tag_sha": "66c6138322ec5cc87738219e24d65240299dcc10", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bismark_align", @@ -28750,10 +25927,7 @@ "published_at": "2023-06-12T18:26:50Z", "tag_sha": "81f989c93e866a9b0bd0d9584e077b9b8f78affe", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bismark_align", @@ -28791,10 +25965,7 @@ "published_at": "2022-12-17T00:40:12Z", "tag_sha": "93bc5811603c287c766a0ff7e03b5b41f4483895", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bismark_align", @@ -28832,10 +26003,7 @@ "published_at": "2022-11-28T23:34:26Z", "tag_sha": "a1aaa924eeeaf6526d69af3a625bcc61676b150a", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bismark_align", @@ -28873,10 +26041,7 @@ "published_at": "2022-11-10T12:51:16Z", "tag_sha": "44b80aa2bf6e8f11e23d506227bbd7293c108cb1", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bismark_align", @@ -28913,10 +26078,7 @@ "published_at": "2022-11-09T10:15:37Z", "tag_sha": "04025de523dd111c9f86101255ed3d6f4c16fb5a", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bismark_align", @@ -28952,10 +26114,7 @@ "published_at": "2021-05-09T20:06:01Z", "tag_sha": "03972a686bedeb2920803cd575f4d671e9135af0", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=20.07.1" }, { @@ -28963,10 +26122,7 @@ "published_at": "2021-03-26T16:07:01Z", "tag_sha": "b3e5e3b95aaf01d98391a62a10a3990c0a4de395", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=20.07.1" }, { @@ -28974,10 +26130,7 @@ "published_at": "2020-04-09T15:06:38Z", "tag_sha": "4f31ed1792e3cc8ce0ea648b6ee8f541f70102f7", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=19.10.0" }, { @@ -28985,10 +26138,7 @@ "published_at": "2019-11-20T12:42:31Z", "tag_sha": "40760ecffbf1d3ce8659712f692454ed88e59324", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=19.04.0" }, { @@ -28996,10 +26146,7 @@ "published_at": "2019-02-01T22:32:13Z", "tag_sha": "1d3f5cc5898c973832722a7e76538eab0933b3f5", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=0.32.0" }, { @@ -29007,10 +26154,7 @@ "published_at": "2019-01-02T12:18:44Z", "tag_sha": "1f0eaa6f1a8342e98c87b639553f54c47536f9c3", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=0.32.0" }, { @@ -29018,10 +26162,7 @@ "published_at": "2018-08-10T10:24:19Z", "tag_sha": "feafff3436760a2f35a63973ed6652c00fe7ccc0", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": null }, { @@ -29029,10 +26170,7 @@ "published_at": "2018-04-17T15:49:27Z", "tag_sha": "e9106e500a4a0d7685b30e6a79dfb278490d99f6", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": null }, { @@ -29040,11 +26178,7 @@ "published_at": "2026-04-10T14:18:02Z", "tag_sha": "d39c3deb67e65f0f93f83b0096a54278339731be", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md", - "docs/usage/bs-seq-primer.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md", "docs/usage/bs-seq-primer.md"], "components": { "modules": [ "bedtools_intersect", @@ -29105,9 +26239,7 @@ }, "nextflow_version": "!>=25.04.0", "nf_core_version": "3.5.1", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null } ] @@ -29144,14 +26276,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "dda", - "immunopeptidomics", - "mass-spectrometry", - "mhc", - "openms", - "peptides" - ], + "topics": ["dda", "immunopeptidomics", "mass-spectrometry", "mhc", "openms", "peptides"], "visibility": "public", "forks": 34, "open_issues": 12, @@ -29204,9 +26329,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": -1, - "master_branch_protection_status_checks": [ - "nf-core" - ], + "master_branch_protection_status_checks": ["nf-core"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -29214,9 +26337,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "nf-core" - ], + "dev_branch_protection_status_checks": ["nf-core"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -29335,15 +26456,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "master_nextflow_config_plugins": ["nf-schema@2.5.1"], "master_nextflow_config_manifest": { "defaultBranch": "master" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -29353,10 +26470,7 @@ 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"gunzip", @@ -29414,17 +26519,11 @@ "openmsthirdparty_cometadapter", "thermorawfileparser" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.04.0", "nf_core_version": "3.4.1", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null }, { @@ -29432,10 +26531,7 @@ "published_at": "2025-05-22T20:10:53Z", "tag_sha": "4e0dd557a9e4dfdc52b249d16caffcd47e7fafe5", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "gunzip", @@ -29452,11 +26548,7 @@ "openmsthirdparty_cometadapter", "thermorawfileparser" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.2.1" @@ -29466,10 +26558,7 @@ "published_at": "2024-06-17T16:31:13Z", "tag_sha": "1b3069246d10ec305ec2f478f490ec05aa734ce5", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "gunzip", @@ -29496,15 +26585,9 @@ "published_at": "2023-10-10T14:42:08Z", "tag_sha": "b80a5a4fbf1ff4d409885d08ab09f6ceeb7fe4c9", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "custom_dumpsoftwareversions", - "multiqc" - ] + "modules": ["custom_dumpsoftwareversions", "multiqc"] }, "nextflow_version": "!>=23.04.0", "nf_core_version": null @@ -29514,15 +26597,9 @@ "published_at": "2023-04-06T08:59:15Z", "tag_sha": "3feaf7c2c8e05fb5b6f256e218dae3fa0c108878", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "custom_dumpsoftwareversions", - "multiqc" - ] + "modules": ["custom_dumpsoftwareversions", "multiqc"] }, "nextflow_version": "!>=22.10.1", "nf_core_version": null @@ -29532,15 +26609,9 @@ "published_at": "2022-12-02T09:08:13Z", "tag_sha": "a2235d555c1bc6618ded2d922176d7401eccdd50", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "custom_dumpsoftwareversions", - "multiqc" - ] + "modules": ["custom_dumpsoftwareversions", "multiqc"] }, "nextflow_version": "!>=21.10.3", "nf_core_version": null @@ -29550,15 +26621,9 @@ "published_at": "2022-05-10T09:15:58Z", "tag_sha": "bc0a2dd30bae440c86e0953feabcb1d971a96b52", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "custom_dumpsoftwareversions", - "multiqc" - ] + "modules": ["custom_dumpsoftwareversions", "multiqc"] }, "nextflow_version": "!>=21.10.3", "nf_core_version": null @@ -29568,15 +26633,9 @@ "published_at": "2022-04-05T19:21:31Z", "tag_sha": "b24db1e0fd9e63ac2dd41eb70355ef0ee6a211cd", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "custom_dumpsoftwareversions", - "multiqc" - ] + "modules": ["custom_dumpsoftwareversions", "multiqc"] }, "nextflow_version": "!>=21.10.3", "nf_core_version": null @@ -29586,15 +26645,9 @@ "published_at": "2022-01-14T16:23:42Z", "tag_sha": "8447c4d8073fd939febbd2935eb64baf76e5e02a", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "custom_dumpsoftwareversions", - "multiqc" - ] + "modules": ["custom_dumpsoftwareversions", "multiqc"] }, "nextflow_version": "!>=21.10.3", "nf_core_version": null @@ -29604,15 +26657,9 @@ "published_at": "2021-12-09T14:06:07Z", "tag_sha": "3dd74fb6845395f091713db97e1ed62c634a84ca", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "custom_dumpsoftwareversions", - "multiqc" - ] + "modules": ["custom_dumpsoftwareversions", "multiqc"] }, "nextflow_version": "!>=21.10.3", "nf_core_version": null @@ -29622,10 +26669,7 @@ "published_at": "2021-09-03T06:45:53Z", "tag_sha": "c95201d5a57b45e97491664641be3506ef6f1d7c", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=21.04.0", "nf_core_version": null }, @@ -29634,10 +26678,7 @@ "published_at": "2020-10-06T17:04:17Z", "tag_sha": "3437540db07a1b51e6b88bcb41a5c8c6844bf283", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=19.10.0" }, { @@ -29645,10 +26686,7 @@ "published_at": "2020-04-24T09:26:02Z", "tag_sha": "22e1bd6e04fb8b42d0b2ca59f336fca1d6b250f8", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=19.10.0" }, { @@ -29656,10 +26694,7 @@ "published_at": "2020-04-21T15:10:57Z", "tag_sha": "09a40054d3fe408a3d2bd6ef65aff854d50a74fb", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=19.10.0" }, { @@ -29667,10 +26702,7 @@ "published_at": "2020-03-23T19:23:04Z", "tag_sha": "d6b79571f7f3708dc5b4b91198824839db6aafba", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=19.10.0" }, { @@ -29678,10 +26710,7 @@ "published_at": "2019-08-03T15:58:22Z", "tag_sha": "2dca3219b5deb3a0747a9d8b6387f89c3b9eb514", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=0.32.0" }, { @@ -29689,10 +26718,7 @@ "published_at": "2019-03-05T21:54:04Z", "tag_sha": "124cbbe5a070e1ee1dec25da1f65c9baea179b91", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=0.32.0" }, { @@ -29700,10 +26726,7 @@ "published_at": "2019-03-04T21:25:25Z", "tag_sha": "455c20cd8a2331ae854adf1d10cfcac518bc59b9", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=0.32.0" }, { @@ -29711,10 +26734,7 @@ "published_at": "2019-02-06T10:17:43Z", "tag_sha": "16dcb86088627f19fcca68030eb28e864a4935ba", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=0.32.0" }, { @@ -29722,10 +26742,7 @@ "published_at": "2019-02-04T13:27:11Z", "tag_sha": "213936032889fd8e5f9f9b43002879cfea9ea0d3", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=0.32.0" }, { @@ -29733,10 +26750,7 @@ "published_at": "2019-01-28T11:45:37Z", "tag_sha": "9e0235edefc5e5e1748e716c267bc0760a329a58", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=0.32.0" }, { @@ -29744,10 +26758,7 @@ "published_at": "2019-01-25T09:19:43Z", "tag_sha": "3bed2d2e86c841c99af7ae0339b6b2a17a0f28df", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=0.32.0" }, { @@ -29755,10 +26766,7 @@ "published_at": "2019-01-21T12:02:08Z", "tag_sha": "8f2b0ae8e055a0b2a84ea16cb442196c47566d4c", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=0.32.0" }, { @@ -29766,10 +26774,7 @@ "published_at": "2019-01-04T13:34:28Z", "tag_sha": "84967b1ad3e7b552990d9498815237b1393419b3", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=0.32.0" }, { @@ -29777,10 +26782,7 @@ "published_at": "2018-11-27T12:26:49Z", "tag_sha": "6bd8137849407565e36f2c26f688a209a3c141b9", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=0.32.0" }, { @@ -29788,10 +26790,7 @@ "published_at": "2026-05-22T09:51:09Z", "tag_sha": "5b6d0d5270c141d3985c4285a5f6776ac2f10c61", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "gunzip", @@ -29811,17 +26810,11 @@ "pridepy_fetchsdrf", "thermorawfileparser" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.10.4", "nf_core_version": "4.0.2", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null } ] @@ -29911,10 +26904,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": true, - "master_branch_protection_status_checks": [ - "pre-commit", - "nf-core" - ], + "master_branch_protection_status_checks": ["pre-commit", "nf-core"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -29923,10 +26913,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": true, - "dev_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "dev_branch_protection_status_checks": ["nf-core", "pre-commit"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -29951,15 +26938,11 @@ "is_DSL2": true, "has_nf_test": false, "has_nf_test_dev": false, - "master_nextflow_config_plugins": [ - "nf-schema@2.3.0" - ], + "master_nextflow_config_plugins": ["nf-schema@2.3.0"], "master_nextflow_config_manifest": { "defaultBranch": "master" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.3.0" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.3.0"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -29969,26 +26952,14 @@ "published_at": "2025-02-11T12:50:03Z", "tag_sha": "15a56a5f137e4c9094a9ab5a667199cd545a68ea", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "fastqc", - "multiqc" - ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "modules": ["fastqc", "multiqc"], + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.2.0", - "plugins": [ - "nf-schema@2.3.0" - ], + "plugins": ["nf-schema@2.3.0"], "co2footprint_files": null } ] @@ -30025,12 +26996,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "mnase-seq", - "nucleosome", - "nucleosome-maps", - "nucleosome-positioning" - ], + "topics": ["mnase-seq", "nucleosome", "nucleosome-maps", "nucleosome-positioning"], "visibility": "public", "forks": 13, "open_issues": 8, @@ -30140,10 +27106,7 @@ "published_at": "2022-05-25T15:44:07Z", "tag_sha": "eb5ea5c9b122f2cc29810e6a040187838bda6702", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=19.10.0" }, { @@ -30151,10 +27114,7 @@ "published_at": "2022-05-25T15:50:57Z", "tag_sha": "b7c0d8a13111bebc995186f3217bd7d1b768594f", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=19.10.0", "nf_core_version": null, "plugins": [], @@ -30264,9 +27224,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "nf-core" - ], + "dev_branch_protection_status_checks": ["nf-core"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -30310,15 +27268,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "master_nextflow_config_plugins": ["nf-schema@2.5.1"], "master_nextflow_config_manifest": { "defaultBranch": "master" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -30328,10 +27282,7 @@ "published_at": "2025-10-27T08:35:43Z", "tag_sha": "4ec0790d80cf77f2428d33b1a8571ccb498e2170", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "cellpose", @@ -30343,11 +27294,7 @@ "multiqc", "stardist" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.04.0", "nf_core_version": "3.4.1" @@ -30357,10 +27304,7 @@ "published_at": "2025-03-06T17:32:19Z", "tag_sha": "d33d298b06ad8b4463a635bf02bb9f4f351e724b", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "cellpose", @@ -30372,11 +27316,7 @@ "multiqc", "stardist" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.2.0" @@ -30386,10 +27326,7 @@ "published_at": "2024-02-12T14:34:20Z", "tag_sha": "7605a53092930a0b65509c64f79834a6c8449e9b", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "cellpose", @@ -30410,10 +27347,7 @@ "published_at": "2026-02-17T18:59:44Z", "tag_sha": "fdbb5802a4de87ada9c7aa4b85423726c461db41", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "cellpose", @@ -30425,17 +27359,11 @@ "multiqc", "stardist" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.04.0", "nf_core_version": "3.5.1", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null } ] @@ -30472,10 +27400,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "mass-spectrometry", - "proteomics" - ], + "topics": ["mass-spectrometry", "proteomics"], "visibility": "public", "forks": 1, "open_issues": 4, @@ -30566,15 +27491,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "main_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "main_nextflow_config_plugins": ["nf-schema@2.5.1"], "main_nextflow_config_manifest": { "defaultBranch": "main" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "main" }, @@ -30584,10 +27505,7 @@ "published_at": "2026-05-15T14:55:38Z", "tag_sha": "3296f7535f4f2e6aa3863416db542460bc3d222f", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "comet", @@ -30599,17 +27517,11 @@ "unzip", "unzipfiles" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.10.4", "nf_core_version": "4.0.2", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null } ] @@ -30714,10 +27626,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "dev_branch_protection_status_checks": ["nf-core", "pre-commit"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -30771,19 +27680,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-schema@2.2.0", - "nf-co2footprint@1.0.0-beta", - "nf-prov@1.2.2" - ], + "master_nextflow_config_plugins": ["nf-schema@2.2.0", "nf-co2footprint@1.0.0-beta", "nf-prov@1.2.2"], "master_nextflow_config_manifest": { "defaultBranch": "master" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.2.0", - "nf-co2footprint@1.0.0", - "nf-prov@1.2.2" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.2.0", "nf-co2footprint@1.0.0", "nf-prov@1.2.2"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -30834,19 +27735,11 @@ "untar", "upp_align" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.04.2", "nf_core_version": "3.2.1", - "plugins": [ - "nf-schema@2.2.0", - "nf-co2footprint@1.0.0-beta", - "nf-prov@1.2.2" - ], + "plugins": ["nf-schema@2.2.0", "nf-co2footprint@1.0.0-beta", "nf-prov@1.2.2"], "co2footprint_files": { "filename": "co2footprint_summary_2025-05-28_13-38-21.txt", "co2e_emissions": 169.72, @@ -30899,19 +27792,11 @@ "untar", "upp_align" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.10.4", "nf_core_version": "3.2.0", - "plugins": [ - "nf-schema@2.2.0", - "nf-co2footprint@1.0.0-beta", - "nf-prov@1.2.2" - ], + "plugins": ["nf-schema@2.2.0", "nf-co2footprint@1.0.0-beta", "nf-prov@1.2.2"], "co2footprint_files": { "filename": "co2footprint_summary_2025-04-23_13-14-22.txt", "co2e_emissions": 8.38, @@ -30923,10 +27808,7 @@ "published_at": "2024-10-04T08:43:04Z", "tag_sha": "9e83630c5a40fe48694db80bd855d1dac429ee87", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "clustalo_align", @@ -30963,11 +27845,7 @@ }, "nextflow_version": "!>=24.04.1", "nf_core_version": "2.14.1", - "plugins": [ - "nf-schema@2.2.0", - "nf-co2footprint@1.0.0-beta", - "nf-prov@1.2.2" - ], + "plugins": ["nf-schema@2.2.0", "nf-co2footprint@1.0.0-beta", "nf-prov@1.2.2"], "co2footprint_files": null }, { @@ -31016,19 +27894,11 @@ "untar", "upp_align" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.04.2", "nf_core_version": "3.2.1", - "plugins": [ - "nf-schema@2.2.0", - "nf-co2footprint@1.0.0-beta", - "nf-prov@1.2.2" - ], + "plugins": ["nf-schema@2.2.0", "nf-co2footprint@1.0.0-beta", "nf-prov@1.2.2"], "co2footprint_files": null } ] @@ -31065,12 +27935,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "alignment", - "demultiplexing", - "nanopore", - "qc" - ], + "topics": ["alignment", "demultiplexing", "nanopore", "qc"], "visibility": "public", "forks": 105, "open_issues": 60, @@ -31123,11 +27988,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": -1, - "master_branch_protection_status_checks": [ - "nf-core", - "Prettier", - "EditorConfig" - ], + "master_branch_protection_status_checks": ["nf-core", "Prettier", "EditorConfig"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -31223,9 +28084,7 @@ "has_nf_test_dev": false, "master_nextflow_config_plugins": [], "master_nextflow_config_manifest": {}, - "dev_nextflow_config_plugins": [ - "nf-schema@2.2.0" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.2.0"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -31235,10 +28094,7 @@ "published_at": "2023-03-10T11:40:53Z", "tag_sha": "6e563e54362cddb8e48d15c156251708c22d0e8d", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bcftools_sort", @@ -31269,10 +28125,7 @@ "published_at": "2022-06-20T10:44:41Z", "tag_sha": "1e60482a2c4621234393a6eef8e9a104309c20ae", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "custom_dumpsoftwareversions", @@ -31300,10 +28153,7 @@ "published_at": "2021-11-30T07:39:03Z", "tag_sha": "a93c84624e59ed07062c334afa9bc03aebfe4737", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "custom_dumpsoftwareversions", @@ -31327,10 +28177,7 @@ "published_at": "2021-11-26T15:53:44Z", "tag_sha": "73cbe193e9cd19610daa0fa0b00db603acd76750", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "custom_dumpsoftwareversions", @@ -31354,10 +28201,7 @@ "published_at": "2020-11-06T12:12:51Z", "tag_sha": "ad5b2bb7a37a6edb9f61603636bd26e43259f58b", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=19.10.0" }, { @@ -31365,10 +28209,7 @@ "published_at": "2020-03-05T13:58:13Z", "tag_sha": "05669df8a8e42837c8a16cc2985d9c8a19e48c4f", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=19.10.0" }, { @@ -31376,10 +28217,7 @@ "published_at": "2025-05-28T01:14:35Z", "tag_sha": "b175040bc1bb03d675c982e15668ee073f241933", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bedtools_bamtobed", @@ -31455,10 +28293,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "nanostring", - "nanostringnorm" - ], + "topics": ["nanostring", "nanostringnorm"], "visibility": "public", "forks": 15, "open_issues": 6, @@ -31511,9 +28346,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": -1, - "master_branch_protection_status_checks": [ - "nf-core" - ], + "master_branch_protection_status_checks": ["nf-core"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -31521,9 +28354,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "nf-core" - ], + "dev_branch_protection_status_checks": ["nf-core"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -31597,15 +28428,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-schema@2.6.1" - ], + "master_nextflow_config_plugins": ["nf-schema@2.6.1"], "master_nextflow_config_manifest": { "defaultBranch": "master" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.6.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.6.1"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -31615,27 +28442,14 @@ "published_at": "2026-01-30T15:24:34Z", "tag_sha": "6f0b2d537a1f06e8fe1d6c63d7c409009141aa62", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "multiqc", - "nacho_normalize", - "nacho_qc" - ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "modules": ["multiqc", "nacho_normalize", "nacho_qc"], + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.10.2", "nf_core_version": "3.5.1", - "plugins": [ - "nf-schema@2.6.1" - ], + "plugins": ["nf-schema@2.6.1"], "co2footprint_files": null }, { @@ -31643,27 +28457,14 @@ "published_at": "2026-01-15T14:54:52Z", "tag_sha": "4b4f5fd15514f38d7735420b3edcfcac953bc942", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "multiqc", - "nacho_normalize", - "nacho_qc" - ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "modules": ["multiqc", "nacho_normalize", "nacho_qc"], + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.10.2", "nf_core_version": "3.5.1", - "plugins": [ - "nf-schema@2.6.1" - ], + "plugins": ["nf-schema@2.6.1"], "co2footprint_files": null }, { @@ -31671,21 +28472,10 @@ "published_at": "2025-01-27T11:40:59Z", "tag_sha": "4402218a2b8a76f9b22007bab35d44e76282c137", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "multiqc", - "nacho_normalize", - "nacho_qc" - ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "modules": ["multiqc", "nacho_normalize", "nacho_qc"], + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.1.2" @@ -31695,14 +28485,9 @@ "published_at": "2024-08-27T08:54:21Z", "tag_sha": "e765843c16d2bfe90c72e31a7a3719466d1bdfb0", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "multiqc" - ], + "modules": ["multiqc"], "subworkflows": [ "utils_nextflow_pipeline", "utils_nfcore_pipeline", @@ -31717,15 +28502,9 @@ "published_at": "2024-01-18T10:53:29Z", "tag_sha": "b79564a85be0b86a9555de1b95183546b01fc51e", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "custom_dumpsoftwareversions", - "multiqc" - ], + "modules": ["custom_dumpsoftwareversions", "multiqc"], "subworkflows": [] }, "nextflow_version": "!>=23.04.0", @@ -31736,16 +28515,9 @@ "published_at": "2023-09-04T09:52:03Z", "tag_sha": "415bc686f6d3c2f4df98fdf019a0c1e22fb40ccf", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "custom_dumpsoftwareversions", - "fastqc", - "multiqc" - ] + "modules": ["custom_dumpsoftwareversions", "fastqc", "multiqc"] }, "nextflow_version": "!>=23.04.0", "nf_core_version": null @@ -31755,15 +28527,9 @@ "published_at": "2023-06-23T14:02:16Z", "tag_sha": "7451087e71bd653b7341a5e5485d91af387923a9", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "custom_dumpsoftwareversions", - "multiqc" - ] + "modules": ["custom_dumpsoftwareversions", "multiqc"] }, "nextflow_version": "!>=23.04.0", "nf_core_version": null @@ -31773,15 +28539,9 @@ "published_at": "2023-06-22T14:05:02Z", "tag_sha": "b13f05af2c57037c0b34a2098d18e2fd07fad481", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "custom_dumpsoftwareversions", - "multiqc" - ] + "modules": ["custom_dumpsoftwareversions", "multiqc"] }, "nextflow_version": "!>=23.04.0", "nf_core_version": null @@ -31791,15 +28551,9 @@ "published_at": "2023-06-12T14:06:04Z", "tag_sha": "baf7623e6854724f62eaa82e40f91905d210ca2d", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "custom_dumpsoftwareversions", - "multiqc" - ] + "modules": ["custom_dumpsoftwareversions", "multiqc"] }, "nextflow_version": "!>=23.04.0", "nf_core_version": null @@ -31809,27 +28563,14 @@ "published_at": "2026-01-30T16:32:15Z", "tag_sha": "915f51d2d8892f3c702cdc59e9ab997372375a40", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "multiqc", - "nacho_normalize", - "nacho_qc" - ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "modules": ["multiqc", "nacho_normalize", "nacho_qc"], + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.10.2", "nf_core_version": "3.5.1", - "plugins": [ - "nf-schema@2.6.1" - ], + "plugins": ["nf-schema@2.6.1"], "co2footprint_files": null } ] @@ -31866,14 +28607,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "gro-seq", - "nascent", - "pro-seq", - "rna", - "transcription", - "tss" - ], + "topics": ["gro-seq", "nascent", "pro-seq", "rna", "transcription", "tss"], "visibility": "public", "forks": 11, "open_issues": 59, @@ -31927,20 +28661,14 @@ "master_branch_exists": false, "main_branch_exists": true, "main_branch_protection_up_to_date": -1, - "main_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "main_branch_protection_status_checks": ["nf-core", "pre-commit"], "main_branch_protection_required_reviews": 2, "main_branch_protection_require_codeowner_review": false, "main_branch_protection_require_non_stale_review": false, "main_branch_protection_enforce_admins": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": true, - "dev_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "dev_branch_protection_status_checks": ["nf-core", "pre-commit"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -31995,15 +28723,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "main_nextflow_config_plugins": [ - "nf-schema@2.2.0" - ], + "main_nextflow_config_plugins": ["nf-schema@2.2.0"], "main_nextflow_config_manifest": { "defaultBranch": "master" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.2.0" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.2.0"], "dev_nextflow_config_manifest": { "defaultBranch": "main" }, @@ -32013,10 +28737,7 @@ "published_at": "2025-05-08T00:44:26Z", "tag_sha": "7d4fe61975015f652c271886e661764b05cfd3bf", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bbmap_pileup", @@ -32094,10 +28815,7 @@ "published_at": "2024-03-05T17:18:29Z", "tag_sha": "02bbefb701598dc96d29da23d90d60a9ffadd18d", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bbmap_pileup", @@ -32159,10 +28877,7 @@ "published_at": "2023-02-17T15:45:10Z", "tag_sha": "9ff33c78968717b2cee89d7b5be2b5110facf928", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bbmap_pileup", @@ -32221,10 +28936,7 @@ "published_at": "2023-02-15T15:42:56Z", "tag_sha": "12e9ba628540fbf63e7dfc888bb23325218a3ee0", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bbmap_pileup", @@ -32283,10 +28995,7 @@ "published_at": "2022-10-24T14:49:33Z", "tag_sha": "985f37e1030e838d692a742f45fb67aa94cb1d76", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bbmap_pileup", @@ -32345,10 +29054,7 @@ "published_at": "2019-04-16T08:36:18Z", "tag_sha": "ada9b280c9f94f6d5e493715605257bc8a30b2b6", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=0.32.0" }, { @@ -32356,10 +29062,7 @@ "published_at": "2025-07-13T15:36:00Z", "tag_sha": "8d094841b348aca2e857c9d40b4e0c8f5f8320ec", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bbmap_pileup", @@ -32430,9 +29133,7 @@ }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.2.1", - "plugins": [ - "nf-schema@2.2.0" - ], + "plugins": ["nf-schema@2.2.0"], "co2footprint_files": null } ] @@ -32469,11 +29170,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "infernal", - "ncrna", - "rfam" - ], + "topics": ["infernal", "ncrna", "rfam"], "visibility": "public", "forks": 1, "open_issues": 4, @@ -32541,12 +29238,7 @@ "dev_branch_protection_enforce_admins": -1, "TEMPLATE_branch_exists": true, "has_required_topics": false, - "missing_topics": [ - "nf-core", - "nextflow", - "workflow", - "pipeline" - ], + "missing_topics": ["nf-core", "nextflow", "workflow", "pipeline"], "open_pr_count": 2, "repository_url": "https://github.com/nf-core/ncrnannotator", "contributors": [ @@ -32569,15 +29261,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "master_nextflow_config_plugins": ["nf-schema@2.5.1"], "master_nextflow_config_manifest": { "defaultBranch": "master" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -32587,25 +29275,14 @@ "published_at": "2026-03-23T22:26:24Z", "tag_sha": "1a57ac306827ace09b52473a1e8f64dcb33c55a5", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "multiqc" - ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "modules": ["multiqc"], + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.04.0", "nf_core_version": "3.5.2", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null } ] @@ -32741,20 +29418,14 @@ "published_at": "2019-12-12T08:41:29Z", "tag_sha": "71f6e3f0377dfb0b4c8324a9cb965d8140869d76", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ] + "doc_files": ["docs/output.md", "docs/usage.md"] }, { "tag_name": "dev", "published_at": "2020-03-30T13:12:31Z", "tag_sha": "e9378b0828f5592154d950021bb2f4b0f36b03ec", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ] + "doc_files": ["docs/output.md", "docs/usage.md"] } ] }, @@ -32851,10 +29522,7 @@ "main_branch_protection_enforce_admins": true, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "pre-commit", - "nf-core" - ], + "dev_branch_protection_status_checks": ["pre-commit", "nf-core"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -32885,9 +29553,7 @@ "has_nf_test_dev": false, "main_nextflow_config_plugins": [], "main_nextflow_config_manifest": {}, - "dev_nextflow_config_plugins": [ - "nf-validation@1.1.3" - ], + "dev_nextflow_config_plugins": ["nf-validation@1.1.3"], "dev_nextflow_config_manifest": {}, "releases": [ { @@ -32895,16 +29561,9 @@ "published_at": "2024-02-22T00:13:23Z", "tag_sha": "f64a3c7867ffe159a0f347d3b07d11c99ade49fb", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "custom_dumpsoftwareversions", - "fastqc", - "multiqc" - ] + "modules": ["custom_dumpsoftwareversions", "fastqc", "multiqc"] }, "nextflow_version": "!>=23.04.0", "nf_core_version": null, @@ -33012,10 +29671,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": -1, - "master_branch_protection_status_checks": [ - "pre-commit", - "nf-core" - ], + "master_branch_protection_status_checks": ["pre-commit", "nf-core"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -33023,10 +29679,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "pre-commit", - "nf-core" - ], + "dev_branch_protection_status_checks": ["pre-commit", "nf-core"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -33110,15 +29763,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "master_nextflow_config_plugins": ["nf-schema@2.5.1"], "master_nextflow_config_manifest": { "defaultBranch": "master" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -33145,17 +29794,11 @@ "samtools_sort", "star_genomegenerate" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.04.0", "nf_core_version": "3.5.1", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null }, { @@ -33179,11 +29822,7 @@ "samtools_sort", "star_genomegenerate" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.10.5", "nf_core_version": "3.3.2" @@ -33209,11 +29848,7 @@ "samtools_sort", "star_genomegenerate" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.3.1" @@ -33239,11 +29874,7 @@ "samtools_sort", "star_genomegenerate" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.0.2" @@ -33253,10 +29884,7 @@ "published_at": "2024-08-26T01:59:09Z", "tag_sha": "4227bc1083209d79c8735d32e6c75f762a640006", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bwa_index", @@ -33299,17 +29927,11 @@ "samtools_sort", "star_genomegenerate" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.04.0", "nf_core_version": "3.5.1", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null } ] @@ -33400,10 +30022,7 @@ "master_branch_exists": false, "main_branch_exists": true, "main_branch_protection_up_to_date": true, - "main_branch_protection_status_checks": [ - "pre-commit", - "nf-core" - ], + "main_branch_protection_status_checks": ["pre-commit", "nf-core"], "main_branch_protection_required_reviews": 2, "main_branch_protection_require_codeowner_review": false, "main_branch_protection_require_non_stale_review": false, @@ -33411,10 +30030,7 @@ "main_uses_ruleset": true, "dev_branch_exists": true, "dev_branch_protection_up_to_date": true, - "dev_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "dev_branch_protection_status_checks": ["nf-core", "pre-commit"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -33422,12 +30038,7 @@ "dev_uses_ruleset": true, "TEMPLATE_branch_exists": true, "has_required_topics": false, - "missing_topics": [ - "nf-core", - "nextflow", - "workflow", - "pipeline" - ], + "missing_topics": ["nf-core", "nextflow", "workflow", "pipeline"], "open_pr_count": 0, "repository_url": "https://github.com/nf-core/pacsomatic", "contributors": [ @@ -33450,15 +30061,11 @@ "is_DSL2": true, "has_nf_test": false, "has_nf_test_dev": true, - "main_nextflow_config_plugins": [ - "nf-schema@2.3.0" - ], + "main_nextflow_config_plugins": ["nf-schema@2.3.0"], "main_nextflow_config_manifest": { "defaultBranch": "main" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.3.0" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.3.0"], "dev_nextflow_config_manifest": { "defaultBranch": "main" }, @@ -33468,10 +30075,7 @@ "published_at": "2026-01-26T21:43:30Z", "tag_sha": "24c84cb371b0339c1d65a4de9451671945e19772", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "annotsv_annotsv", @@ -33517,9 +30121,7 @@ }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.1.2", - "plugins": [ - "nf-schema@2.3.0" - ], + "plugins": ["nf-schema@2.3.0"], "co2footprint_files": null } ] @@ -33556,14 +30158,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "alignment", - "long-read", - "pacbio", - "puretarget", - "variant-calling", - "wgs" - ], + "topics": ["alignment", "long-read", "pacbio", "puretarget", "variant-calling", "wgs"], "visibility": "public", "forks": 13, "open_issues": 10, @@ -33616,10 +30211,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": true, - "master_branch_protection_status_checks": [ - "pre-commit", - "nf-core" - ], + "master_branch_protection_status_checks": ["pre-commit", "nf-core"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -33628,10 +30220,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": true, - "dev_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "dev_branch_protection_status_checks": ["nf-core", "pre-commit"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -33671,15 +30260,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-schema@2.3.0" - ], + "master_nextflow_config_plugins": ["nf-schema@2.3.0"], "master_nextflow_config_manifest": { "defaultBranch": "master" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -33689,10 +30274,7 @@ "published_at": "2025-03-06T21:30:45Z", "tag_sha": "73596e1d271d6afbc9d1c41b4227fc80f9e0bf13", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bcftools_index", @@ -33717,11 +30299,7 @@ "trgt_genotype", "trgt_plot" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.2.0" @@ -33731,10 +30309,7 @@ "published_at": "2025-02-05T18:52:06Z", "tag_sha": "2812f8a10499338c30cdae1451e8446520351929", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bcftools_index", @@ -33759,11 +30334,7 @@ "trgt_genotype", "trgt_plot" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.2.0" @@ -33773,10 +30344,7 @@ "published_at": "2026-05-05T18:45:41Z", "tag_sha": "c025c42297718ded01a6626a93cb826b5b18aa02", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bcftools_index", @@ -33818,9 +30386,7 @@ }, "nextflow_version": "!>=25.10.2", "nf_core_version": "3.5.2", - "plugins": [ - "nf-schema@2.3.0" - ], + "plugins": ["nf-schema@2.3.0"], "co2footprint_files": null } ] @@ -33918,10 +30484,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": -1, - "master_branch_protection_status_checks": [ - "pre-commit", - "nf-core" - ], + "master_branch_protection_status_checks": ["pre-commit", "nf-core"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -33929,10 +30492,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "pre-commit", - "nf-core" - ], + "dev_branch_protection_status_checks": ["pre-commit", "nf-core"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -33971,15 +30531,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "master_nextflow_config_plugins": ["nf-schema@2.5.1"], "master_nextflow_config_manifest": { "defaultBranch": "master" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -33989,10 +30545,7 @@ "published_at": "2026-05-23T00:09:41Z", "tag_sha": "4a3649d1133f2fa5bb23acb05cbc970f04ad65a3", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "assemblyscan", @@ -34008,17 +30561,11 @@ "samtools_faidx", "seqtk_cutn" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.10.4", "nf_core_version": "4.0.2", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null }, { @@ -34026,10 +30573,7 @@ "published_at": "2026-01-30T05:07:36Z", "tag_sha": "c17c98b49780cd94a04093dec0fa0ac9156161df", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "assemblyscan", @@ -34045,17 +30589,11 @@ "samtools_faidx", "seqtk_cutn" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.04.0", "nf_core_version": "3.5.1", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null }, { @@ -34063,10 +30601,7 @@ "published_at": "2025-08-18T16:08:08Z", "tag_sha": "86a011b8505d196a1d79737fea2b837d997afb6c", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "assemblyscan", @@ -34082,11 +30617,7 @@ "samtools_faidx", "seqtk_cutn" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.10.5", "nf_core_version": "3.3.2" @@ -34096,10 +30627,7 @@ "published_at": "2025-07-10T12:58:46Z", "tag_sha": "f4e1715bf4580191a80fba70b62ea8a51033b5f4", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "assemblyscan", @@ -34115,11 +30643,7 @@ "samtools_faidx", "seqtk_cutn" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.10.1", "nf_core_version": "3.2.1" @@ -34129,10 +30653,7 @@ "published_at": "2025-05-16T07:13:50Z", "tag_sha": "9b5fd10e78014d55697d5fa1b32b8c728cd2373f", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "assemblyscan", @@ -34146,11 +30667,7 @@ "multiqc", "seqtk_cutn" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.10.1", "nf_core_version": "3.2.1" @@ -34160,10 +30677,7 @@ "published_at": "2025-02-05T11:59:58Z", "tag_sha": "9ed7c7bd3247b39ffacad59d1aeb2ac3d294416d", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "assemblyscan", @@ -34178,11 +30692,7 @@ "multiqc", "seqtk_cutn" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.10.1", "nf_core_version": "3.2.0" @@ -34192,10 +30702,7 @@ "published_at": "2024-12-18T23:50:50Z", "tag_sha": "0c1a6b9d22b14a6acc82ba9e5866da63aa742d82", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "assemblyscan", @@ -34209,11 +30716,7 @@ "multiqc", "seqtk_cutn" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.10.1", "nf_core_version": "3.1.0" @@ -34223,10 +30726,7 @@ "published_at": "2024-10-10T01:07:14Z", "tag_sha": "65e829836a2510ac3fcc5e5a75e9f91ff7604512", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "assemblyscan", @@ -34254,10 +30754,7 @@ "published_at": "2024-08-27T23:41:16Z", "tag_sha": "c493be3ba884299576f4f91c2064b1aa8c7aa8f6", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "assemblyscan", @@ -34285,10 +30782,7 @@ "published_at": "2026-05-26T00:44:28Z", "tag_sha": "715fd61fc11561b1624b47b812aad24843c44ea9", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "assemblyscan", @@ -34304,17 +30798,11 @@ "samtools_faidx", "seqtk_cutn" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.10.4", "nf_core_version": "4.0.2", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null } ] @@ -34351,9 +30839,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "pangenome" - ], + "topics": ["pangenome"], "visibility": "public", "forks": 23, "open_issues": 16, @@ -34418,10 +30904,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "dev_branch_protection_status_checks": ["nf-core", "pre-commit"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -34490,15 +30973,11 @@ "is_DSL2": true, "has_nf_test": false, "has_nf_test_dev": false, - "master_nextflow_config_plugins": [ - "nf-schema@2.3.0" - ], + "master_nextflow_config_plugins": ["nf-schema@2.3.0"], "master_nextflow_config_manifest": { "defaultBranch": "master" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.2.0" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.2.0"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -34508,10 +30987,7 @@ "published_at": "2025-02-09T10:51:43Z", "tag_sha": "3d02bd1df79f48b4bfdb4ad95d4ca0d7f6aeb337", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "gfaffix", @@ -34531,11 +31007,7 @@ "tabix_bgzip", "wfmash" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.2.0" @@ -34545,10 +31017,7 @@ "published_at": "2024-03-25T15:07:58Z", "tag_sha": "0e8a38734ea3c0397f94416a0146a2972fe2db8b", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "gfaffix", @@ -34582,10 +31051,7 @@ "published_at": "2024-03-15T08:58:44Z", "tag_sha": "7fb3047d972143a0fe2d00b2f80d19d9df1703eb", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "gfaffix", @@ -34619,10 +31085,7 @@ "published_at": "2024-02-28T13:37:10Z", "tag_sha": "9740ffc4d0a00d6dc89e1c8f9579e628598d43a5", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "gfaffix", @@ -34656,10 +31119,7 @@ "published_at": "2023-08-01T08:54:03Z", "tag_sha": "9fc8ccd2eebb78ad93d14b52744d2e20967494dc", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "custom_dumpsoftwareversions", @@ -34689,10 +31149,7 @@ "published_at": "2026-04-29T18:01:37Z", "tag_sha": "e8e7ced9efc1484b3189bb2e2a1f137fec6642ec", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "gfaffix", @@ -34712,17 +31169,11 @@ "tabix_bgzip", "wfmash" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.2.1", - "plugins": [ - "nf-schema@2.3.0" - ], + "plugins": ["nf-schema@2.3.0"], "co2footprint_files": null } ] @@ -34812,10 +31263,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": true, - "master_branch_protection_status_checks": [ - "pre-commit", - "nf-core" - ], + "master_branch_protection_status_checks": ["pre-commit", "nf-core"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -34824,10 +31272,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": true, - "dev_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "dev_branch_protection_status_checks": ["nf-core", "pre-commit"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -34852,15 +31297,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-schema@2.2.0" - ], + "master_nextflow_config_plugins": ["nf-schema@2.2.0"], "master_nextflow_config_manifest": { "defaultBranch": "master" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.2.0" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.2.0"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -34870,10 +31311,7 @@ "published_at": "2026-04-08T14:31:58Z", "tag_sha": "6ae42ff41da173277612264afb4482667ff91cde", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "cutadapt", @@ -34888,17 +31326,11 @@ "subread_featurecounts", "umitools_extract" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.5.2", - "plugins": [ - "nf-schema@2.2.0" - ], + "plugins": ["nf-schema@2.2.0"], "co2footprint_files": null } ] @@ -34935,10 +31367,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "biosurveillance", - "pathogen-identification" - ], + "topics": ["biosurveillance", "pathogen-identification"], "visibility": "public", "forks": 8, "open_issues": 74, @@ -34991,10 +31420,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": -1, - "master_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "master_branch_protection_status_checks": ["nf-core", "pre-commit"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -35002,10 +31428,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "dev_branch_protection_status_checks": ["nf-core", "pre-commit"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -35079,15 +31502,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "master_nextflow_config_plugins": ["nf-schema@2.5.1"], "master_nextflow_config_manifest": { "defaultBranch": "main" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "main" }, @@ -35097,10 +31516,7 @@ "published_at": "2026-02-13T22:26:31Z", "tag_sha": "13547eaa7345dab4ac97db49775ae8284af4113d", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bakta_bakta", @@ -35141,17 +31557,11 @@ "untar", "vcflib_vcffilter" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.04.6", "nf_core_version": "3.5.1", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null }, { @@ -35159,10 +31569,7 @@ "published_at": "2025-06-27T17:50:17Z", "tag_sha": "a83b789a7b61e96bee4d5e72a2681876c7289883", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bakta_bakta", @@ -35204,11 +31611,7 @@ "untar", "vcflib_vcffilter" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.3.1" @@ -35218,10 +31621,7 @@ "published_at": "2026-02-13T21:34:40Z", "tag_sha": "f9a0d73b990e050f13545c071f9eb7d16ca683e1", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bakta_bakta", @@ -35262,17 +31662,11 @@ "untar", "vcflib_vcffilter" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.04.6", "nf_core_version": "3.5.1", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null } ] @@ -35414,13 +31808,9 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-validation" - ], + "master_nextflow_config_plugins": ["nf-validation"], "master_nextflow_config_manifest": {}, - "dev_nextflow_config_plugins": [ - "nf-validation@1.1.3" - ], + "dev_nextflow_config_plugins": ["nf-validation@1.1.3"], "dev_nextflow_config_manifest": {}, "releases": [ { @@ -35428,10 +31818,7 @@ "published_at": "2024-04-18T18:11:47Z", "tag_sha": "129a138b32e88c3e9e43a46d8146f70d2061f67f", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bacphlip", @@ -35472,9 +31859,7 @@ }, "nextflow_version": "!>=23.04.0", "nf_core_version": null, - "plugins": [ - "nf-validation" - ], + "plugins": ["nf-validation"], "co2footprint_files": null } ] @@ -35511,13 +31896,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "genomics", - "genotype", - "imputation", - "low-pass-sequencing", - "phasing" - ], + "topics": ["genomics", "genotype", "imputation", "low-pass-sequencing", "phasing"], "visibility": "public", "forks": 23, "open_issues": 13, @@ -35571,20 +31950,14 @@ "master_branch_exists": false, "main_branch_exists": true, "main_branch_protection_up_to_date": -1, - "main_branch_protection_status_checks": [ - "pre-commit", - "nf-core" - ], + "main_branch_protection_status_checks": ["pre-commit", "nf-core"], "main_branch_protection_required_reviews": 2, "main_branch_protection_require_codeowner_review": false, "main_branch_protection_require_non_stale_review": false, "main_branch_protection_enforce_admins": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "pre-commit", - "nf-core" - ], + "dev_branch_protection_status_checks": ["pre-commit", "nf-core"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -35648,18 +32021,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "main_nextflow_config_plugins": [ - "nf-schema@2.5.1", - "nf-co2footprint@1.0.0-beta" - ], + "main_nextflow_config_plugins": ["nf-schema@2.5.1", "nf-co2footprint@1.0.0-beta"], "main_nextflow_config_manifest": { "defaultBranch": "master" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1", - "nf-co2footprint@1.0.0-beta", - "nf-core-utils@0.4.0" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1", "nf-co2footprint@1.0.0-beta", "nf-core-utils@0.4.0"], "dev_nextflow_config_manifest": { "defaultBranch": "main" }, @@ -35669,10 +32035,7 @@ "published_at": "2025-12-01T18:33:30Z", "tag_sha": "452783d960ebd2b4d337a649e9c8eb3859611916", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bcftools_annotate", @@ -35715,18 +32078,11 @@ "tabix_tabix", "vcflib_vcffixup" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.04.0", "nf_core_version": "3.5.1", - "plugins": [ - "nf-schema@2.5.1", - "nf-co2footprint@1.0.0-beta" - ], + "plugins": ["nf-schema@2.5.1", "nf-co2footprint@1.0.0-beta"], "co2footprint_files": { "filename": "co2footprint_summary_2025-12-01_18-35-20.txt", "co2e_emissions": 528.62, @@ -35738,10 +32094,7 @@ "published_at": "2024-12-09T09:19:04Z", "tag_sha": "ac730dc42d5b967f18c3f10900db7378bbd0fd9a", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bcftools_annotate", @@ -35781,11 +32134,7 @@ "tabix_tabix", "vcflib_vcffixup" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.0.2" @@ -35795,10 +32144,7 @@ "published_at": "2026-05-25T13:23:06Z", "tag_sha": "0b54a875b93964872ce17d5c9ed7ff5e9d6f7915", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bcftools_annotate", @@ -35863,10 +32209,7 @@ }, "nextflow_version": "!>=25.10.4", "nf_core_version": "4.0.2", - "plugins": [ - "nf-schema@2.5.1", - "nf-co2footprint@1.0.0-beta" - ], + "plugins": ["nf-schema@2.5.1", "nf-co2footprint@1.0.0-beta"], "co2footprint_files": null } ] @@ -35963,10 +32306,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": -1, - "master_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "master_branch_protection_status_checks": ["nf-core", "pre-commit"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -35974,10 +32314,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "dev_branch_protection_status_checks": ["nf-core", "pre-commit"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -36006,15 +32343,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-schema@2.3.0" - ], + "master_nextflow_config_plugins": ["nf-schema@2.3.0"], "master_nextflow_config_manifest": { "defaultBranch": "master" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.3.0" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.3.0"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -36024,10 +32357,7 @@ "published_at": "2025-02-21T12:52:52Z", "tag_sha": "827b85d4c6718f23937d317b6f84fe828d73aecb", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "clustalo_align", @@ -36062,10 +32392,7 @@ "published_at": "2023-02-15T16:57:26Z", "tag_sha": "665a4c2d3c39e8684ef6c3fdef680817ee876498", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "custom_dumpsoftwareversions", @@ -36081,9 +32408,7 @@ "mafft", "multiqc" ], - "subworkflows": [ - "fasta_newick_epang_gappa" - ] + "subworkflows": ["fasta_newick_epang_gappa"] }, "nextflow_version": "!>=22.10.1", "nf_core_version": null @@ -36093,10 +32418,7 @@ "published_at": "2025-02-21T15:38:17Z", "tag_sha": "374dcf211e508f749a56bf70639283b2fc2b0de2", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "clustalo_align", @@ -36125,9 +32447,7 @@ }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.2.0", - "plugins": [ - "nf-schema@2.3.0" - ], + "plugins": ["nf-schema@2.3.0"], "co2footprint_files": null } ] @@ -36224,9 +32544,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": -1, - "master_branch_protection_status_checks": [ - "nf-core" - ], + "master_branch_protection_status_checks": ["nf-core"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -36234,9 +32552,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "nf-core" - ], + "dev_branch_protection_status_checks": ["nf-core"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -36300,17 +32616,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-schema@2.5.1", - "nf-slack@0.5.1" - ], + "master_nextflow_config_plugins": ["nf-schema@2.5.1", "nf-slack@0.5.1"], "master_nextflow_config_manifest": { "defaultBranch": "master" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1", - "nf-slack@0.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1", "nf-slack@0.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -36320,26 +32630,14 @@ "published_at": "2026-05-25T06:25:51Z", "tag_sha": "2f6ec18dc7820e75d6880ad7a9d0033f53f732fc", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "cat_fastq" - ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "modules": ["cat_fastq"], + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.10.4", "nf_core_version": "4.0.2", - "plugins": [ - "nf-schema@2.5.1", - "nf-slack@0.5.1" - ], + "plugins": ["nf-schema@2.5.1", "nf-slack@0.5.1"], "co2footprint_files": null }, { @@ -36347,25 +32645,14 @@ "published_at": "2026-03-09T12:33:51Z", "tag_sha": "9c79407885cd09caafa55be564508754d83e11b2", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "cat_fastq" - ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "modules": ["cat_fastq"], + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.04.0", "nf_core_version": "3.5.2", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null }, { @@ -36373,25 +32660,14 @@ "published_at": "2026-03-04T09:16:37Z", "tag_sha": "71a224c44a3a95dc51801cb89939c8097ec32627", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "cat_fastq" - ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "modules": ["cat_fastq"], + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.04.0", "nf_core_version": "3.5.2", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null }, { @@ -36399,25 +32675,14 @@ "published_at": "2026-01-19T07:41:23Z", "tag_sha": "9d1d575fd6967324b1d211da42022133158622ba", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "cat_fastq" - ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "modules": ["cat_fastq"], + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.04.0", "nf_core_version": "3.5.1", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null }, { @@ -36425,25 +32690,14 @@ "published_at": "2025-12-15T10:31:04Z", "tag_sha": "79fa5005b1b7d600bb1f0ab4a6f1645177c9c21e", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "cat_fastq" - ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "modules": ["cat_fastq"], + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.04.0", "nf_core_version": "3.5.1", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null }, { @@ -36451,25 +32705,14 @@ "published_at": "2025-11-05T08:18:40Z", "tag_sha": "1affbf6a29e608424038d17baf69cac37e2fa477", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "cat_fastq" - ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "modules": ["cat_fastq"], + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.04.0", "nf_core_version": "3.4.1", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null }, { @@ -36477,19 +32720,10 @@ "published_at": "2025-09-17T15:34:52Z", "tag_sha": "24337872a846c734e211fb6026701d781b9e8bc3", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "cat_fastq" - ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "modules": ["cat_fastq"], + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.10.5", "nf_core_version": "3.3.2" @@ -36499,19 +32733,10 @@ "published_at": "2025-06-24T08:10:53Z", "tag_sha": "9c976359dc9e9ad40835a378723b5a52d498d2de", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "cat_fastq" - ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "modules": ["cat_fastq"], + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.2.1" @@ -36521,19 +32746,10 @@ "published_at": "2025-01-22T11:37:01Z", "tag_sha": "42424bb2977d73babba67a6766f2a1c8334b958b", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "cat_fastq" - ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "modules": ["cat_fastq"], + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.1.1" @@ -36543,14 +32759,9 @@ "published_at": "2024-07-31T14:40:43Z", "tag_sha": "511dd17fc4bf61e773584b879afde194f14fbdf2", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "cat_fastq" - ], + "modules": ["cat_fastq"], "subworkflows": [ "utils_nextflow_pipeline", "utils_nfcore_pipeline", @@ -36565,14 +32776,9 @@ "published_at": "2024-07-17T09:16:56Z", "tag_sha": "bf492303a94d145d16ece9c91ce35a4705741654", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "cat_fastq" - ], + "modules": ["cat_fastq"], "subworkflows": [ "utils_nextflow_pipeline", "utils_nfcore_pipeline", @@ -36587,14 +32793,9 @@ "published_at": "2024-05-28T11:55:30Z", "tag_sha": "35c594fe090df301b634011314e8d018906eb4f2", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "cat_fastq" - ], + "modules": ["cat_fastq"], "subworkflows": [ "utils_nextflow_pipeline", "utils_nfcore_pipeline", @@ -36609,15 +32810,9 @@ "published_at": "2024-03-29T16:06:05Z", "tag_sha": "e0ab35d82e03999a6925a4a358851c0146e6abbb", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "cat_fastq", - "custom_dumpsoftwareversions" - ], + "modules": ["cat_fastq", "custom_dumpsoftwareversions"], "subworkflows": [ "utils_nextflow_pipeline", "utils_nfcore_pipeline", @@ -36632,15 +32827,9 @@ "published_at": "2024-01-22T08:48:41Z", "tag_sha": "c8e57efae70d49e1bdfcca6d006bfdd669ea2a40", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "cat_fastq", - "custom_dumpsoftwareversions" - ] + "modules": ["cat_fastq", "custom_dumpsoftwareversions"] }, "nextflow_version": "!>=23.04.0", "nf_core_version": null @@ -36650,15 +32839,9 @@ "published_at": "2023-11-20T12:11:40Z", "tag_sha": "436f974c6cd8543b6a3db9fda6aa3e6ae142427a", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "cat_fastq", - "custom_dumpsoftwareversions" - ] + "modules": ["cat_fastq", "custom_dumpsoftwareversions"] }, "nextflow_version": "!>=23.04.0", "nf_core_version": null @@ -36668,15 +32851,9 @@ "published_at": "2023-10-27T11:00:20Z", "tag_sha": "cf8bc130370b07cf3765fd8294d161fc639cec44", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "cat_fastq", - "custom_dumpsoftwareversions" - ] + "modules": ["cat_fastq", "custom_dumpsoftwareversions"] }, "nextflow_version": "!>=23.04.0", "nf_core_version": null @@ -36686,15 +32863,9 @@ "published_at": "2023-10-17T16:57:46Z", "tag_sha": "1cde7e8a47d7af6c2198ded58d751f311ee1dccf", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "cat_fastq", - "custom_dumpsoftwareversions" - ] + "modules": ["cat_fastq", "custom_dumpsoftwareversions"] }, "nextflow_version": "!>=23.04.0", "nf_core_version": null @@ -36704,26 +32875,14 @@ "published_at": "2026-05-25T07:04:39Z", "tag_sha": "b98f6bcbf0f2c535938b7e21d72ec19df2d8ae37", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "cat_fastq" - ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "modules": ["cat_fastq"], + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.10.4", "nf_core_version": "4.0.2", - "plugins": [ - "nf-schema@2.5.1", - "nf-slack@0.5.1" - ], + "plugins": ["nf-schema@2.5.1", "nf-slack@0.5.1"], "co2footprint_files": null } ] @@ -36760,10 +32919,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "annotation", - "proteomics" - ], + "topics": ["annotation", "proteomics"], "visibility": "public", "forks": 13, "open_issues": 27, @@ -36817,10 +32973,7 @@ "master_branch_exists": false, "main_branch_exists": true, "main_branch_protection_up_to_date": true, - "main_branch_protection_status_checks": [ - "pre-commit", - "nf-core" - ], + "main_branch_protection_status_checks": ["pre-commit", "nf-core"], "main_branch_protection_required_reviews": 2, "main_branch_protection_require_codeowner_review": false, "main_branch_protection_require_non_stale_review": false, @@ -36898,15 +33051,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "main_nextflow_config_plugins": [ - "nf-schema@2.6.1" - ], + "main_nextflow_config_plugins": ["nf-schema@2.6.1"], "main_nextflow_config_manifest": { "defaultBranch": "master" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.6.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.6.1"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -36916,10 +33065,7 @@ "published_at": "2026-05-07T16:35:02Z", "tag_sha": "cbf78d471f62d91af666e8c77bcd580b4743c6be", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "aria2", @@ -36942,9 +33088,7 @@ }, "nextflow_version": "!>=25.10.4", "nf_core_version": "4.0.2", - "plugins": [ - "nf-schema@2.6.1" - ], + "plugins": ["nf-schema@2.6.1"], "co2footprint_files": null }, { @@ -36952,10 +33096,7 @@ "published_at": "2026-02-09T12:58:57Z", "tag_sha": "382d936447460baf5d9938250f385ec86e773fde", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "aria2", @@ -36979,9 +33120,7 @@ }, "nextflow_version": "!>=25.10.0", "nf_core_version": "3.5.1", - "plugins": [ - "nf-schema@2.6.1" - ], + "plugins": ["nf-schema@2.6.1"], "co2footprint_files": null }, { @@ -36989,10 +33128,7 @@ "published_at": "2026-05-08T12:26:54Z", "tag_sha": "6bcb8b0e40b8368e864d929cde63aa446020ee62", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "aria2", @@ -37015,9 +33151,7 @@ }, "nextflow_version": "!>=25.10.4", "nf_core_version": "4.0.2", - "plugins": [ - "nf-schema@2.6.1" - ], + "plugins": ["nf-schema@2.6.1"], "co2footprint_files": null } ] @@ -37054,10 +33188,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "metagenomics", - "protein-families" - ], + "topics": ["metagenomics", "protein-families"], "visibility": "public", "forks": 4, "open_issues": 7, @@ -37111,22 +33242,14 @@ "master_branch_exists": false, "main_branch_exists": true, "main_branch_protection_up_to_date": -1, - "main_branch_protection_status_checks": [ - "nf-core", - "pre-commit", - "confirm-pass" - ], + "main_branch_protection_status_checks": ["nf-core", "pre-commit", "confirm-pass"], "main_branch_protection_required_reviews": 2, "main_branch_protection_require_codeowner_review": false, "main_branch_protection_require_non_stale_review": false, "main_branch_protection_enforce_admins": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "confirm-pass", - "nf-core", - "pre-commit" - ], + "dev_branch_protection_status_checks": ["confirm-pass", "nf-core", "pre-commit"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -37200,15 +33323,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "main_nextflow_config_plugins": [ - "nf-schema@2.6.1" - ], + "main_nextflow_config_plugins": ["nf-schema@2.6.1"], "main_nextflow_config_manifest": { "defaultBranch": "main" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.6.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.6.1"], "dev_nextflow_config_manifest": { "defaultBranch": "main" }, @@ -37218,10 +33337,7 @@ "published_at": "2026-05-06T06:44:17Z", "tag_sha": "db4b0aab636c47a3a8e5c769149d9a9fdfd670c2", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "clipkit", @@ -37254,9 +33370,7 @@ }, "nextflow_version": "!>=25.10.4", "nf_core_version": "4.0.2", - "plugins": [ - "nf-schema@2.6.1" - ], + "plugins": ["nf-schema@2.6.1"], "co2footprint_files": null }, { @@ -37264,10 +33378,7 @@ "published_at": "2025-12-19T09:59:12Z", "tag_sha": "4517bf0900a864da5ec0ab0eddfb23ccb57a0d14", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "clipkit", @@ -37300,9 +33411,7 @@ }, "nextflow_version": "!>=25.10.0", "nf_core_version": "3.5.1", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null }, { @@ -37310,10 +33419,7 @@ "published_at": "2025-11-25T10:48:27Z", "tag_sha": "f398731e665c8f36034af0fb32d88187880aef0e", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "clipkit", @@ -37345,9 +33451,7 @@ }, "nextflow_version": "!>=25.10.0", "nf_core_version": "3.5.1", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null }, { @@ -37355,10 +33459,7 @@ "published_at": "2025-10-17T13:39:12Z", "tag_sha": "eff3e0822b92ab6a7b6f252d8b0f76589d0d7d53", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "clipkit", @@ -37396,10 +33497,7 @@ "published_at": "2025-09-23T15:20:46Z", "tag_sha": "8f76f5a807984c3d667f6ba3c9a87f63048cc765", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "clipkit", @@ -37434,10 +33532,7 @@ "published_at": "2025-08-06T14:33:49Z", "tag_sha": "4b8c2c06c37b1aa87c7f696b2d94980af2346ef6", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "clipkit", @@ -37457,11 +33552,7 @@ "seqkit_stats", "untar" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.10.5", "nf_core_version": "3.3.2" @@ -37471,10 +33562,7 @@ "published_at": "2025-06-16T08:06:14Z", "tag_sha": "58e15747237c4d921094f8c94be143889666ec89", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "cat_cat", @@ -37493,11 +33581,7 @@ "seqkit_seq", "untar" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.3.1" @@ -37507,10 +33591,7 @@ "published_at": "2025-05-20T10:20:36Z", "tag_sha": "f862501bb49cdc94137ffe1e24b66507df64d3d8", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "cat_cat", @@ -37529,11 +33610,7 @@ "seqkit_seq", "untar" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.2.1" @@ -37543,10 +33620,7 @@ "published_at": "2025-05-09T11:15:17Z", "tag_sha": "c671acfa8f3ec5998103ea1ec0a77e325c217cbf", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "cat_cat", @@ -37565,11 +33639,7 @@ "seqkit_seq", "untar" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.2.1" @@ -37579,10 +33649,7 @@ "published_at": "2025-02-17T09:22:48Z", "tag_sha": "dcb933865d64a8acadd7c7b97dd8bc7cf83eec09", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "cat_cat", @@ -37600,11 +33667,7 @@ "seqkit_seq", "untar" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.2.0" @@ -37614,10 +33677,7 @@ "published_at": "2026-05-06T08:16:17Z", "tag_sha": "86be6d21e8c30fcb70e4fe54af1b27c3da2888a3", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "clipkit", @@ -37650,9 +33710,7 @@ }, "nextflow_version": "!>=25.10.4", "nf_core_version": "4.0.2", - "plugins": [ - "nf-schema@2.6.1" - ], + "plugins": ["nf-schema@2.6.1"], "co2footprint_files": null } ] @@ -37750,10 +33808,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": -1, - "master_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "master_branch_protection_status_checks": ["nf-core", "pre-commit"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -37761,10 +33816,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "dev_branch_protection_status_checks": ["nf-core", "pre-commit"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -37913,15 +33965,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-schema@2.6.1" - ], + "master_nextflow_config_plugins": ["nf-schema@2.6.1"], "master_nextflow_config_manifest": { "defaultBranch": "master" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.7.2" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.7.2"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -37955,17 +34003,11 @@ "untar", "unzip" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.10.2", "nf_core_version": "3.5.1", - "plugins": [ - "nf-schema@2.6.1" - ], + "plugins": ["nf-schema@2.6.1"], "co2footprint_files": null }, { @@ -37973,10 +34015,7 @@ "published_at": "2024-07-30T15:15:30Z", "tag_sha": "9bea0dc4ebb26358142afbcab3d7efd962d3a820", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "aria2", @@ -38000,10 +34039,7 @@ "published_at": "2024-06-25T12:37:58Z", "tag_sha": "d75ade173c8429876f90739ed830d62193271bae", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "aria2", @@ -38027,10 +34063,7 @@ "published_at": "2023-02-10T17:23:25Z", "tag_sha": "94bd58250591c29e23d9afbb9deedf95800fe3fc", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "aria2", @@ -38074,17 +34107,11 @@ "untar", "unzip" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.10.4", "nf_core_version": "4.0.2", - "plugins": [ - "nf-schema@2.6.1" - ], + "plugins": ["nf-schema@2.6.1"], "co2footprint_files": null } ] @@ -38121,14 +34148,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "cosmic", - "gnomad", - "protein-databases", - "proteogenomics", - "proteomics", - "pypgatk" - ], + "topics": ["cosmic", "gnomad", "protein-databases", "proteogenomics", "proteomics", "pypgatk"], "visibility": "public", "forks": 12, "open_issues": 9, @@ -38258,10 +34278,7 @@ "published_at": "2021-04-27T08:11:42Z", "tag_sha": "4eda7a827f83a9be0470de16331f7105ab48bdd1", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=20.04.0" }, { @@ -38269,10 +34286,7 @@ "published_at": "2021-04-27T11:53:35Z", "tag_sha": "e700d967253c5c80985fdcdc48e482dace2bb2d0", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=20.04.0", "nf_core_version": null, "plugins": [], @@ -38312,11 +34326,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "label-free-quantification", - "openms", - "proteomics" - ], + "topics": ["label-free-quantification", "openms", "proteomics"], "visibility": "public", "forks": 20, "open_issues": 28, @@ -38449,10 +34459,7 @@ "published_at": "2020-10-19T07:55:34Z", "tag_sha": "43c77e50c955d7e62899e7d31e0d6f6a87ac2316", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": "!>=20.01.0" }, { @@ -38460,10 +34467,7 @@ "published_at": "2022-03-24T15:14:36Z", "tag_sha": "69a0b9fc99bdc82faaae36f5e830dbfef52927b5", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": "!>=20.04.0", "nf_core_version": null, "plugins": [], @@ -38501,16 +34505,7 @@ "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, - "topics": [ - "dia", - "lfq", - "mass-spec", - "mass-spectrometry", - "openms", - "proteogenomics", - "proteomics", - "tmt" - ], + "topics": ["dia", "lfq", "mass-spec", "mass-spectrometry", "openms", "proteogenomics", "proteomics", "tmt"], "visibility": "public", "forks": 1, "open_issues": 5, @@ -38629,13 +34624,7 @@ "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, - "topics": [ - "lfq", - "mass-spectrometry", - "proteogenomics", - "proteomics", - "tmt" - ], + "topics": ["lfq", "mass-spectrometry", "proteogenomics", "proteomics", "tmt"], "visibility": "public", "forks": 43, "open_issues": 61, @@ -38742,13 +34731,7 @@ "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, - "topics": [ - "lfq", - "mass-spectrometry", - "proteogenomics", - "proteomics", - "tmt" - ], + "topics": ["lfq", "mass-spectrometry", "proteogenomics", "proteomics", "tmt"], "visibility": "public", "forks": 43, "open_issues": 61, @@ -38855,13 +34838,9 @@ "is_DSL2": true, "has_nf_test": false, "has_nf_test_dev": false, - "master_nextflow_config_plugins": [ - "nf-validation" - ], + "master_nextflow_config_plugins": ["nf-validation"], "master_nextflow_config_manifest": {}, - "dev_nextflow_config_plugins": [ - "nf-validation@1.1.3" - ], + "dev_nextflow_config_plugins": ["nf-validation@1.1.3"], "dev_nextflow_config_manifest": {}, "releases": [ { @@ -38869,15 +34848,9 @@ "published_at": "2023-11-02T18:25:42Z", "tag_sha": "fa34d79f5071ae064d1438ad59c53b0093622ae5", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "custom_dumpsoftwareversions", - "multiqc" - ] + "modules": ["custom_dumpsoftwareversions", "multiqc"] } }, { @@ -38885,15 +34858,9 @@ "published_at": "2023-03-27T10:25:29Z", "tag_sha": "600505011027ab196bb18b1320607468bdae951a", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "custom_dumpsoftwareversions", - "multiqc" - ] + "modules": ["custom_dumpsoftwareversions", "multiqc"] } }, { @@ -38901,15 +34868,9 @@ "published_at": "2023-03-20T20:57:57Z", "tag_sha": "ee011ba94fb8986c63386ddd15dd33f53ce4004b", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "custom_dumpsoftwareversions", - "multiqc" - ] + "modules": ["custom_dumpsoftwareversions", "multiqc"] } }, { @@ -38917,15 +34878,9 @@ "published_at": "2022-05-02T14:59:37Z", "tag_sha": "6ffb0c92964cb70e212e18225c769b9e26cb1c11", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "custom_dumpsoftwareversions", - "multiqc" - ] + "modules": ["custom_dumpsoftwareversions", "multiqc"] } }, { @@ -38933,15 +34888,9 @@ "published_at": "2024-04-08T13:03:14Z", "tag_sha": "1ba58086c4c77ae8c148b7dcb20002959ec9e26d", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "custom_dumpsoftwareversions", - "multiqc" - ], + "modules": ["custom_dumpsoftwareversions", "multiqc"], "subworkflows": [ "utils_nextflow_pipeline", "utils_nfcore_pipeline", @@ -39037,10 +34986,7 @@ "master_branch_exists": false, "main_branch_exists": true, "main_branch_protection_up_to_date": true, - "main_branch_protection_status_checks": [ - "pre-commit", - "nf-core" - ], + "main_branch_protection_status_checks": ["pre-commit", "nf-core"], "main_branch_protection_required_reviews": 2, "main_branch_protection_require_codeowner_review": false, "main_branch_protection_require_non_stale_review": false, @@ -39048,10 +34994,7 @@ "main_uses_ruleset": true, "dev_branch_exists": true, "dev_branch_protection_up_to_date": true, - "dev_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "dev_branch_protection_status_checks": ["nf-core", "pre-commit"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -39091,10 +35034,7 @@ "published_at": "2024-11-19T19:05:09Z", "tag_sha": "26ff6763ac5d6e5d9306ed262efc8e002c08bb7f", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bcftools_concat", @@ -39241,9 +35181,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": -1, - "master_branch_protection_status_checks": [ - "nf-core" - ], + "master_branch_protection_status_checks": ["nf-core"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -39251,9 +35189,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "nf-core" - ], + "dev_branch_protection_status_checks": ["nf-core"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -39282,15 +35218,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-schema@2.1.1" - ], + "master_nextflow_config_plugins": ["nf-schema@2.1.1"], "master_nextflow_config_manifest": { "defaultBranch": "master" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -39300,20 +35232,10 @@ "published_at": "2025-01-17T13:41:23Z", "tag_sha": "7c5cb9593b80d2a3cdc8bcb14137722351644435", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "multiqc", - "untar" - ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "modules": ["multiqc", "untar"], + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.1.1" @@ -39323,26 +35245,14 @@ "published_at": "2026-03-24T12:38:27Z", "tag_sha": "21003c9efe984e91f7e43eea8de2c1466005105e", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "multiqc", - "untar" - ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "modules": ["multiqc", "untar"], + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.04.0", "nf_core_version": "3.5.1", - "plugins": [ - "nf-schema@2.1.1" - ], + "plugins": ["nf-schema@2.1.1"], "co2footprint_files": null } ] @@ -39441,11 +35351,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": -1, - "master_branch_protection_status_checks": [ - "nf-core", - "pre-commit", - "confirm-pass" - ], + "master_branch_protection_status_checks": ["nf-core", "pre-commit", "confirm-pass"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -39453,11 +35359,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "nf-core", - "pre-commit", - "confirm-pass" - ], + "dev_branch_protection_status_checks": ["nf-core", "pre-commit", "confirm-pass"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -39651,15 +35553,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "master_nextflow_config_plugins": ["nf-schema@2.5.1"], "master_nextflow_config_manifest": { "defaultBranch": "master" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -39669,10 +35567,7 @@ "published_at": "2026-05-11T22:35:28Z", "tag_sha": "12eafba3db40d76ed2f7bd27414e169ce89d3e01", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bcftools_annotate", @@ -39796,9 +35691,7 @@ }, "nextflow_version": "!>=25.10.4", "nf_core_version": "3.5.1", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null }, { @@ -39806,10 +35699,7 @@ "published_at": "2025-06-25T10:03:02Z", "tag_sha": "dc7219d70971ccac454ed04c2239c288e32be903", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bcftools_annotate", @@ -39917,11 +35807,7 @@ "vcfanno", "verifybamid_verifybamid2" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.3.1" @@ -39931,10 +35817,7 @@ "published_at": "2025-05-22T11:05:09Z", "tag_sha": "46afe31a3601fa282ca9869d780ebae28bfd6db1", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bcftools_annotate", @@ -40041,11 +35924,7 @@ "vcfanno", "verifybamid_verifybamid2" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.2.1" @@ -40055,10 +35934,7 @@ "published_at": "2025-02-24T13:58:38Z", "tag_sha": "8d40fe2838a52d299ed691fb6dada8687a1a0073", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bcftools_annotate", @@ -40164,11 +36040,7 @@ "vcf2cytosure", "vcfanno" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.2.0" @@ -40178,10 +36050,7 @@ "published_at": "2025-02-13T09:22:46Z", "tag_sha": "fe9f0ad4db94ac8d3560254724d59e601ed3d90b", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bcftools_annotate", @@ -40287,11 +36156,7 @@ "vcf2cytosure", "vcfanno" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.2.0" @@ -40301,10 +36166,7 @@ "published_at": "2024-09-13T14:44:59Z", "tag_sha": "fa61a657257a14a6433e3d751c577ab4c9d2eda4", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bcftools_annotate", @@ -40423,10 +36285,7 @@ "published_at": "2024-05-29T10:28:20Z", "tag_sha": "c7a6f389c9b958bf5099c1f48c9b8145d755510f", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bcftools_annotate", @@ -40546,10 +36405,7 @@ "published_at": "2024-03-25T12:56:58Z", "tag_sha": "1489b71cc0e15ade7e98a834df0170b650aa932c", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bcftools_annotate", @@ -40667,10 +36523,7 @@ "published_at": "2024-03-18T09:52:08Z", "tag_sha": "30e27813a8980fbf54438dcdd73733f7c1369c99", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bcftools_annotate", @@ -40788,10 +36641,7 @@ "published_at": "2023-07-26T08:56:58Z", "tag_sha": "c371602095ff83064f51747fe90dfc405ca7a864", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bcftools_annotate", @@ -40882,10 +36732,7 @@ "published_at": "2023-07-21T10:22:06Z", "tag_sha": "1a664228169de771dd4e5957546f887a4f888653", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bcftools_annotate", @@ -40976,10 +36823,7 @@ "published_at": "2023-06-01T15:59:15Z", "tag_sha": "03b5d37d54f160ea682547be41819a738eaf2116", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bcftools_concat", @@ -41058,10 +36902,7 @@ "published_at": "2026-05-21T07:52:06Z", "tag_sha": "3d2ad4f251582b57910a7bf2d1de19d4431fbe8e", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bcftools_annotate", @@ -41186,9 +37027,7 @@ }, "nextflow_version": "!>=25.10.4", "nf_core_version": "4.0.2", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null } ] @@ -41225,12 +37064,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "burden-test", - "cocorv", - "public-data-as-controlset", - "rarevariant" - ], + "topics": ["burden-test", "cocorv", "public-data-as-controlset", "rarevariant"], "visibility": "public", "forks": 4, "open_issues": 4, @@ -41283,10 +37117,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": true, - "master_branch_protection_status_checks": [ - "pre-commit", - "nf-core" - ], + "master_branch_protection_status_checks": ["pre-commit", "nf-core"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -41319,15 +37150,11 @@ "is_DSL2": true, "has_nf_test": false, "has_nf_test_dev": false, - "master_nextflow_config_plugins": [ - "nf-schema@2.3.0" - ], + "master_nextflow_config_plugins": ["nf-schema@2.3.0"], "master_nextflow_config_manifest": { "defaultBranch": "master" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.3.0" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.3.0"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -41337,23 +37164,14 @@ "published_at": "2026-05-11T17:01:26Z", "tag_sha": "e9392c4294ecdd4f6f984b9c235eb220306455be", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.2.0", - "plugins": [ - "nf-schema@2.3.0" - ], + "plugins": ["nf-schema@2.3.0"], "co2footprint_files": null } ] @@ -41443,9 +37261,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": -1, - "master_branch_protection_status_checks": [ - "nf-core" - ], + "master_branch_protection_status_checks": ["nf-core"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -41453,9 +37269,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "nf-core" - ], + "dev_branch_protection_status_checks": ["nf-core"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -41494,13 +37308,9 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-validation@1.1.3" - ], + "master_nextflow_config_plugins": ["nf-validation@1.1.3"], "master_nextflow_config_manifest": {}, - "dev_nextflow_config_plugins": [ - "nf-validation@1.1.3" - ], + "dev_nextflow_config_plugins": ["nf-validation@1.1.3"], "dev_nextflow_config_manifest": {}, "releases": [ { @@ -41508,10 +37318,7 @@ "published_at": "2024-04-26T23:37:16Z", "tag_sha": "0e8805ddbcd0e0fdcdc62105d59c3f29dd985a64", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "art_illumina", @@ -41538,10 +37345,7 @@ "published_at": "2024-02-06T01:06:44Z", "tag_sha": "82facc6eeb399dc8fff921fe5126370154327980", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "art_illumina", @@ -41563,10 +37367,7 @@ "published_at": "2024-04-26T23:24:25Z", "tag_sha": "0594160e22d147aed283553c4fc06839914fa036", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "art_illumina", @@ -41587,9 +37388,7 @@ }, "nextflow_version": "!>=23.04.0", "nf_core_version": null, - "plugins": [ - "nf-validation@1.1.3" - ], + "plugins": ["nf-validation@1.1.3"], "co2footprint_files": null } ] @@ -41626,11 +37425,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "genome", - "references", - "reproducibility" - ], + "topics": ["genome", "references", "reproducibility"], "visibility": "public", "forks": 7, "open_issues": 28, @@ -41683,10 +37478,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": true, - "master_branch_protection_status_checks": [ - "pre-commit", - "nf-core" - ], + "master_branch_protection_status_checks": ["pre-commit", "nf-core"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -41694,10 +37486,7 @@ "master_uses_ruleset": true, "main_branch_exists": true, "main_branch_protection_up_to_date": true, - "main_branch_protection_status_checks": [ - "pre-commit", - "nf-core" - ], + "main_branch_protection_status_checks": ["pre-commit", "nf-core"], "main_branch_protection_required_reviews": 2, "main_branch_protection_require_codeowner_review": false, "main_branch_protection_require_non_stale_review": false, @@ -41740,18 +37529,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-validation@1.1.3" - ], + "master_nextflow_config_plugins": ["nf-validation@1.1.3"], "master_nextflow_config_manifest": {}, - "main_nextflow_config_plugins": [ - "nf-schema@2.1.1" - ], + "main_nextflow_config_plugins": ["nf-schema@2.1.1"], "main_nextflow_config_manifest": {}, - "dev_nextflow_config_plugins": [ - "nf-core-utils@0.4.0", - "nf-schema@2.7.2" - ], + "dev_nextflow_config_plugins": ["nf-core-utils@0.4.0", "nf-schema@2.7.2"], "dev_nextflow_config_manifest": { "defaultBranch": "main" }, @@ -41761,10 +37543,7 @@ "published_at": "2024-12-30T10:55:12Z", "tag_sha": "3ab25b0cdadc6a5440405ef20118e09e5f82dfa4", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bbmap_bbsplit", @@ -41790,11 +37569,7 @@ "star_genomegenerate", "tabix_tabix" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.10.1", "nf_core_version": "3.0.2" @@ -41804,26 +37579,14 @@ "published_at": "2026-05-04T14:51:25Z", "tag_sha": "8969df350de17a4f0e8382aa260e5d8683daeb83", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "gunzip", - "multiqc", - "untar", - "unzip" - ], - "subworkflows": [ - "archive_extract" - ] + "modules": ["gunzip", "multiqc", "untar", "unzip"], + "subworkflows": ["archive_extract"] }, "nextflow_version": "!>=26.04.0", "nf_core_version": "4.0.1", - "plugins": [ - "nf-schema@2.1.1" - ], + "plugins": ["nf-schema@2.1.1"], "co2footprint_files": null } ] @@ -41860,9 +37623,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "ortholog" - ], + "topics": ["ortholog"], "visibility": "public", "forks": 6, "open_issues": 14, @@ -41915,10 +37676,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": -1, - "master_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "master_branch_protection_status_checks": ["nf-core", "pre-commit"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -41932,10 +37690,7 @@ "main_branch_protection_enforce_admins": -1, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "pre-commit", - "nf-core" - ], + "dev_branch_protection_status_checks": ["pre-commit", "nf-core"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -41974,21 +37729,15 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "master_nextflow_config_plugins": ["nf-schema@2.5.1"], "master_nextflow_config_manifest": { "defaultBranch": "master" }, - "main_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "main_nextflow_config_plugins": ["nf-schema@2.5.1"], "main_nextflow_config_manifest": { "defaultBranch": "master" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -41998,24 +37747,10 @@ "published_at": "2025-10-21T14:54:11Z", "tag_sha": "9e8ae5a07ddb5ccd34bb01c72e70e390d97d1cb7", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "cat_cat", - "csvtk_concat", - "csvtk_join", - "diamond_cluster", - "gawk", - "multiqc" - ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "modules": ["cat_cat", "csvtk_concat", "csvtk_join", "diamond_cluster", "gawk", "multiqc"], + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.04.0", "nf_core_version": "3.4.1" @@ -42025,19 +37760,9 @@ "published_at": "2024-07-18T12:48:38Z", "tag_sha": "42b305199b903365b71e7a8554cfcc6a822da8a8", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "csvtk_concat", - "csvtk_join", - "fastme", - "iqtree", - "multiqc", - "tcoffee_align" - ], + "modules": ["csvtk_concat", "csvtk_join", "fastme", "iqtree", "multiqc", "tcoffee_align"], "subworkflows": [ "utils_nextflow_pipeline", "utils_nfcore_pipeline", @@ -42052,19 +37777,9 @@ "published_at": "2024-06-11T11:57:53Z", "tag_sha": "dd05afebd1e19739b7fa6002bf0c10ce42b33821", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "csvtk_concat", - "csvtk_join", - "fastme", - "iqtree", - "multiqc", - "tcoffee_align" - ], + "modules": ["csvtk_concat", "csvtk_join", "fastme", "iqtree", "multiqc", "tcoffee_align"], "subworkflows": [ "utils_nextflow_pipeline", "utils_nfcore_pipeline", @@ -42079,30 +37794,14 @@ "published_at": "2025-10-21T15:16:26Z", "tag_sha": "de4ba462df58d43eb438ea529074519edbb9058f", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "cat_cat", - "csvtk_concat", - "csvtk_join", - "diamond_cluster", - "gawk", - "multiqc" - ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "modules": ["cat_cat", "csvtk_concat", "csvtk_join", "diamond_cluster", "gawk", "multiqc"], + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.04.0", "nf_core_version": "3.4.1", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null } ] @@ -42192,10 +37891,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": true, - "master_branch_protection_status_checks": [ - "pre-commit", - "nf-core" - ], + "master_branch_protection_status_checks": ["pre-commit", "nf-core"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -42234,15 +37930,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "master_nextflow_config_plugins": ["nf-schema@2.5.1"], "master_nextflow_config_manifest": { "defaultBranch": "master" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -42252,26 +37944,14 @@ "published_at": "2026-03-13T08:34:01Z", "tag_sha": "79916e8dea42d7d60b139607ca8eacfaf68e0e19", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "multiqc", - "thermorawfileparser" - ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "modules": ["multiqc", "thermorawfileparser"], + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.04.0", "nf_core_version": "3.4.1", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null }, { @@ -42279,26 +37959,14 @@ "published_at": "2026-03-13T15:09:22Z", "tag_sha": "8a0e1ed486cbeade43845c428c9ef939bd0379a9", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "multiqc", - "thermorawfileparser" - ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "modules": ["multiqc", "thermorawfileparser"], + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.04.0", "nf_core_version": "3.5.1", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null } ] @@ -42388,10 +38056,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": -1, - "master_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "master_branch_protection_status_checks": ["nf-core", "pre-commit"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -42399,11 +38064,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "nf-core", - "pre-commit", - "confirm-pass" - ], + "dev_branch_protection_status_checks": ["nf-core", "pre-commit", "confirm-pass"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -42462,15 +38123,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "master_nextflow_config_plugins": ["nf-schema@2.5.1"], "master_nextflow_config_manifest": { "defaultBranch": "master" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -42480,10 +38137,7 @@ "published_at": "2025-12-03T14:58:05Z", "tag_sha": "74ab1ea2668ee9a221a5c96c86b2a6ee1b2d2f2f", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "anota2seq_anota2seqrun", @@ -42546,9 +38200,7 @@ }, "nextflow_version": "!>=25.04.8", "nf_core_version": "3.5.1", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null }, { @@ -42556,10 +38208,7 @@ "published_at": "2025-02-03T10:06:21Z", "tag_sha": "235e008eda637ff7827db31669148824e9dd1ede", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "anota2seq_anota2seqrun", @@ -42627,10 +38276,7 @@ "published_at": "2024-04-17T12:18:06Z", "tag_sha": "3d3e57978c5e0a418e56728496b6cc12700e6443", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "anota2seq_anota2seqrun", @@ -42694,10 +38340,7 @@ "published_at": "2024-04-12T16:02:08Z", "tag_sha": "58e7265af89163e7accf77f799b03c56b82966a0", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "anota2seq_anota2seqrun", @@ -42761,10 +38404,7 @@ "published_at": "2026-05-05T08:04:08Z", "tag_sha": "bbcd3aef5937b936fdf811611774e339036e1dc3", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "anota2seq_anota2seqrun", @@ -42846,9 +38486,7 @@ }, "nextflow_version": "!>=25.04.8", "nf_core_version": "3.5.1", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null } ] @@ -42951,9 +38589,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "nf-core" - ], + "dev_branch_protection_status_checks": ["nf-core"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -42994,9 +38630,7 @@ "has_nf_test_dev": true, "master_nextflow_config_plugins": [], "master_nextflow_config_manifest": {}, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -43006,10 +38640,7 @@ "published_at": "2025-12-08T15:56:13Z", "tag_sha": "26df4e3c87388298a607231049cf8f59433c97c9", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bcftools_sort", @@ -43129,13 +38760,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "fusion", - "fusion-genes", - "gene-fusion", - "rna", - "rna-seq" - ], + "topics": ["fusion", "fusion-genes", "gene-fusion", "rna", "rna-seq"], "visibility": "public", "forks": 122, "open_issues": 29, @@ -43188,9 +38813,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": -1, - "master_branch_protection_status_checks": [ - "nf-core" - ], + "master_branch_protection_status_checks": ["nf-core"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": true, "master_branch_protection_require_non_stale_review": false, @@ -43198,9 +38821,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "nf-core" - ], + "dev_branch_protection_status_checks": ["nf-core"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": true, "dev_branch_protection_require_non_stale_review": false, @@ -43374,15 +38995,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "master_nextflow_config_plugins": ["nf-schema@2.5.1"], "master_nextflow_config_manifest": { "defaultBranch": "master" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -43392,10 +39009,7 @@ "published_at": "2026-05-20T12:27:06Z", "tag_sha": "d34cf3b6d4e6948f7ef745799e5dc6762f76df0d", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "agat_convertgff2bed", @@ -43453,9 +39067,7 @@ }, "nextflow_version": "!>=25.10.4", "nf_core_version": "4.0.2", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null }, { @@ -43463,10 +39075,7 @@ "published_at": "2026-05-20T08:44:00Z", "tag_sha": "f783a7d237d56ce2ca2187f742188473fb294833", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "agat_convertgff2bed", @@ -43524,9 +39133,7 @@ }, "nextflow_version": "!>=25.10.4", "nf_core_version": "4.0.2", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null }, { @@ -43534,10 +39141,7 @@ "published_at": "2026-03-18T08:12:47Z", "tag_sha": "eabd3f2d60d3e70d5e80d6c62b81d7d3473c36d1", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "agat_convertgff2bed", @@ -43595,9 +39199,7 @@ }, "nextflow_version": "!>=24.10.5", "nf_core_version": "3.3.2", - "plugins": [ - "nf-schema@2.4.2" - ], + "plugins": ["nf-schema@2.4.2"], "co2footprint_files": null }, { @@ -43605,10 +39207,7 @@ "published_at": "2025-11-14T12:34:44Z", "tag_sha": "9fcbad93adbe26f14acc80d7d0257891604fd60d", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "agat_convertspgff2tsv", @@ -43636,9 +39235,7 @@ }, "nextflow_version": "!>=23.04.0", "nf_core_version": null, - "plugins": [ - "nf-schema@2.4.2" - ], + "plugins": ["nf-schema@2.4.2"], "co2footprint_files": null }, { @@ -43646,10 +39243,7 @@ "published_at": "2025-09-19T13:18:29Z", "tag_sha": "4e5de7da9c9768545b484235d2a12c65441acada", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "agat_convertgff2bed", @@ -43712,10 +39306,7 @@ "published_at": "2024-04-10T08:29:46Z", "tag_sha": "42eb8d6322abdad8cd65037a4a2ce447450e9af9", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "agat_convertspgff2tsv", @@ -43753,10 +39344,7 @@ "published_at": "2023-11-29T17:25:02Z", "tag_sha": "98f02be34cf1f6787af9cfc4fb09e93dff74dad4", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "agat_convertspgff2tsv", @@ -43790,10 +39378,7 @@ "published_at": "2023-11-27T15:50:26Z", "tag_sha": "f5ecf8dbd593fd844ff6648e3727332ce26cc20d", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "agat_convertspgff2tsv", @@ -43827,10 +39412,7 @@ "published_at": "2023-09-25T08:31:34Z", "tag_sha": "c3b0f9fb047a6c3c72e02a8b580995e6f975aa10", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "arriba", @@ -43864,10 +39446,7 @@ "published_at": "2023-04-26T10:54:21Z", "tag_sha": "fb5af65466730cf9d4d6c204b2ed8db0739245c8", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "arriba", @@ -43901,10 +39480,7 @@ "published_at": "2023-04-26T09:51:45Z", "tag_sha": "d4de338fc709199e6bec6cde8abfb545d560ed75", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "arriba", @@ -43938,10 +39514,7 @@ "published_at": "2023-04-26T08:36:11Z", "tag_sha": "13cf83db3583d5513766015b84e1b6b1d392fcc7", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "arriba", @@ -43975,10 +39548,7 @@ "published_at": "2023-04-26T06:47:14Z", "tag_sha": "bbdcb3bf53421a3875f9bd52b4c961f28deda157", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "arriba", @@ -44012,10 +39582,7 @@ "published_at": "2023-04-24T11:02:18Z", "tag_sha": "c45b22c1745ea2ecbd0c0dbde73e00920a4284b8", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "arriba", @@ -44049,10 +39616,7 @@ "published_at": "2023-03-13T17:57:43Z", "tag_sha": "58afbbc208a6548aaa2f909fdff185d533b2025a", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "arriba", @@ -44086,10 +39650,7 @@ "published_at": "2022-07-12T14:15:36Z", "tag_sha": "6ffe30435b611339999145e4b71ac59158cf1182", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "arriba", @@ -44117,10 +39678,7 @@ "published_at": "2022-05-19T11:22:37Z", "tag_sha": "c47ce6fdbfbbb249b23613f4713dde27e9ca2853", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "arriba", @@ -44148,10 +39706,7 @@ "published_at": "2020-07-15T13:34:32Z", "tag_sha": "2e3d5de9dc718bd23eaa2f6f693cd9c311a459cf", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=19.10.0" }, { @@ -44159,10 +39714,7 @@ "published_at": "2020-02-10T10:43:06Z", "tag_sha": "505a0fb784771fdb5d2e9c3e28fccb490430727d", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=19.10.0" }, { @@ -44170,10 +39722,7 @@ "published_at": "2019-05-16T12:19:36Z", "tag_sha": "d4a622c2e24148c568994f3d019b2a3b5a014e17", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=0.32.0" }, { @@ -44181,10 +39730,7 @@ "published_at": "2019-04-06T20:10:24Z", "tag_sha": "d32090720b79a2e43d36977753ea5102750c8727", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=0.32.0" }, { @@ -44192,10 +39738,7 @@ "published_at": "2019-02-14T21:43:04Z", "tag_sha": "12e5cb28cc05197e00cd900d4fc92e36a66be772", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=0.32.0" }, { @@ -44203,10 +39746,7 @@ "published_at": 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"master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -44372,11 +39904,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "nf-core", - "pre-commit", - "confirm-pass" - ], + "dev_branch_protection_status_checks": ["nf-core", "pre-commit", "confirm-pass"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -44890,15 +40418,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "master_nextflow_config_plugins": ["nf-schema@2.5.1"], "master_nextflow_config_manifest": { "defaultBranch": "master" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.6.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.6.1"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -45022,9 +40546,7 @@ }, "nextflow_version": "!>=25.04.3", "nf_core_version": "4.0.2", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null }, { @@ -45146,9 +40668,7 @@ }, "nextflow_version": "!>=25.04.3", "nf_core_version": "3.5.2", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null }, { @@ -45264,9 +40784,7 @@ }, "nextflow_version": "!>=25.04.3", "nf_core_version": "3.5.2", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null }, { @@ -45381,9 +40899,7 @@ }, "nextflow_version": "!>=25.04.3", "nf_core_version": "3.5.1", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null }, { @@ -45484,9 +41000,7 @@ }, "nextflow_version": "!>=25.04.0", "nf_core_version": "3.5.1", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null }, { @@ -45587,9 +41101,7 @@ }, "nextflow_version": "!>=25.04.0", "nf_core_version": "3.5.1", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null }, { @@ -45690,9 +41202,7 @@ }, "nextflow_version": "!>=25.04.0", "nf_core_version": "3.5.1", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null }, { @@ -46090,10 +41600,7 @@ "published_at": "2024-10-24T11:32:08Z", "tag_sha": "00f924cf92a986a842bb352b3c4ae379c773c989", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bbmap_bbsplit", @@ -46177,10 +41684,7 @@ "published_at": "2024-10-16T12:53:09Z", "tag_sha": "1f3f64dac72d5ae8c15f19246fa5f564c9e063d7", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bbmap_bbsplit", @@ -46264,10 +41768,7 @@ "published_at": "2024-10-02T15:08:26Z", "tag_sha": "33df0c05ef99d1d9af97d1d74681ab0452612abb", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bbmap_bbsplit", @@ -46351,10 +41852,7 @@ "published_at": "2024-09-16T16:31:30Z", "tag_sha": "4053b2ec173fc0cfdd13ff2b51cfaceb59f783cb", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bbmap_bbsplit", @@ -46436,10 +41934,7 @@ "published_at": "2024-09-05T08:47:06Z", "tag_sha": "4e34945f6ca86621a08e7d573cd6b4fbb7fb1f0e", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bbmap_bbsplit", @@ -46521,10 +42016,7 @@ "published_at": 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"doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bbmap_bbsplit", @@ -46813,10 +42296,7 @@ "published_at": "2023-06-02T15:39:54Z", "tag_sha": "3bec2331cac2b5ff88a1dc71a21fab6529b57a0f", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bbmap_bbsplit", @@ -46884,10 +42364,7 @@ "published_at": "2023-04-25T10:56:51Z", "tag_sha": "5671b65af97fe78a2f9b4d05d850304918b1b86e", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bbmap_bbsplit", @@ -46955,10 +42432,7 @@ "published_at": "2023-03-31T16:06:30Z", "tag_sha": "287afcfe30a93de77e9b7cf70a1085f58c9525d8", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bbmap_bbsplit", @@ -47026,10 +42500,7 @@ "published_at": "2023-03-30T13:52:38Z", "tag_sha": "48fb9b4ea640f029f48c79283217d0f20661d38e", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bbmap_bbsplit", @@ -47097,10 +42568,7 @@ "published_at": "2023-01-05T12:14:44Z", "tag_sha": "6e1e448f535ccf34d11cc691bb241cfd6e60a647", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bbmap_bbsplit", @@ -47166,10 +42634,7 @@ "published_at": "2022-12-21T13:49:31Z", "tag_sha": "adce7ce9abc8f6b338b4f53d0d988ff9a0fd52ff", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bbmap_bbsplit", @@ -47235,10 +42700,7 @@ "published_at": 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"doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bbmap_bbsplit", @@ -47459,10 +42912,7 @@ "published_at": "2022-03-04T13:46:29Z", "tag_sha": "7106bd792b3fb04f9f09b4e737165fa4e736ea81", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bbmap_bbsplit", @@ -47514,10 +42964,7 @@ "published_at": "2021-12-17T16:08:03Z", "tag_sha": "646723c70f04ee6d66391758b02822d4f0fe2966", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bbmap_bbsplit", @@ -47568,10 +43015,7 @@ "published_at": "2021-10-05T13:46:22Z", "tag_sha": "964425e3fd8bfc3dc7bce43279a98d17a874d3f7", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bbmap_bbsplit", @@ -47621,10 +43065,7 @@ "published_at": "2021-07-29T13:24:52Z", "tag_sha": "8094c42add6dcdf69ce54dfdec957789c37ae903", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "cat_fastq", @@ -47674,10 +43115,7 @@ "published_at": "2021-06-18T13:59:37Z", "tag_sha": "b3ff92bc54363faf17d820689a8e9074ffd99045", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": "!>=21.04.0" }, { @@ -47685,10 +43123,7 @@ "published_at": "2021-05-13T13:02:56Z", "tag_sha": "0fcbb0ac491ecb8a80ef879c4f3dad5f869021f9", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": "!>=21.04.0" }, { @@ -47696,10 +43131,7 @@ "published_at": "2020-12-15T16:22:27Z", "tag_sha": "3643a94411b65f42bce5357c5015603099556ad9", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": "!>=20.11.0-edge" }, { @@ -47707,10 +43139,7 @@ "published_at": "2020-11-12T20:01:34Z", "tag_sha": "bc5fc76f40b2da6082a854927184c9d6e5060393", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=20.07.1" }, { @@ -47718,10 +43147,7 @@ "published_at": "2019-10-18T10:51:00Z", "tag_sha": "3b6df9bd104927298fcdf69e97cca7ff1f80527c", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=19.04.0" }, { @@ -47729,10 +43155,7 @@ "published_at": "2019-10-17T17:40:46Z", "tag_sha": "f213557a0851d3f897efb1faeb3e54e8eee1424c", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=19.04.0" }, { @@ -47854,9 +43277,7 @@ }, "nextflow_version": "!>=25.10.4", "nf_core_version": "4.0.2", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null } ] @@ -47893,12 +43314,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "alternative-splicing", - "rna", - "rna-seq", - "splicing" - ], + "topics": ["alternative-splicing", "rna", "rna-seq", "splicing"], "visibility": "public", "forks": 39, "open_issues": 26, @@ -47951,10 +43367,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": -1, - "master_branch_protection_status_checks": [ - "Prettier", - "nf-core" - ], + "master_branch_protection_status_checks": ["Prettier", "nf-core"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -47962,10 +43375,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "dev_branch_protection_status_checks": ["nf-core", "pre-commit"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -48024,13 +43434,9 @@ "is_DSL2": true, "has_nf_test": false, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-validation@1.1.3" - ], + "master_nextflow_config_plugins": ["nf-validation@1.1.3"], "master_nextflow_config_manifest": {}, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -48040,10 +43446,7 @@ "published_at": "2024-05-09T09:07:10Z", "tag_sha": "1d0494ae3402d1a46e0adadad24f81a0ff855c77", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "cat_fastq", @@ -48085,10 +43488,7 @@ "published_at": "2024-02-23T13:51:13Z", "tag_sha": "2b7adfa697f8c2f34bd39f3dfb8ddfdb83fc390e", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "cat_fastq", @@ -48130,10 +43530,7 @@ "published_at": "2024-01-08T17:05:38Z", "tag_sha": "f70bbce27cbade36f993a7e39fa6e574fc4c6d3a", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "cat_fastq", @@ -48175,10 +43572,7 @@ "published_at": "2023-11-16T13:39:28Z", "tag_sha": "907c293ad60edee7c9d37702ca93efce15801837", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "cat_fastq", @@ -48220,10 +43614,7 @@ "published_at": "2023-10-10T08:09:08Z", "tag_sha": "8fb78b2329622d4d2f3983a2e7f007ebad13392c", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "cat_fastq", @@ -48265,10 +43656,7 @@ "published_at": "2026-05-25T09:16:47Z", "tag_sha": "68b6d5e28217e9a53f6f367ba4c703806da2808d", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "cat_fastq", @@ -48309,9 +43697,7 @@ }, "nextflow_version": "!>=25.10.4", "nf_core_version": "4.0.2", - "plugins": [ - "nf-validation@1.1.3" - ], + "plugins": ["nf-validation@1.1.3"], "co2footprint_files": null } ] @@ -48348,13 +43734,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "gatk4", - "rna", - "rnaseq", - "variant-calling", - "worflow" - ], + "topics": ["gatk4", "rna", "rnaseq", "variant-calling", "worflow"], "visibility": "public", "forks": 48, "open_issues": 25, @@ -48407,10 +43787,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": -1, - "master_branch_protection_status_checks": [ - "nf-core", - "nf-test-changes" - ], + "master_branch_protection_status_checks": ["nf-core", "nf-test-changes"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -48418,10 +43795,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "nf-core", - "confirm-pass" - ], + "dev_branch_protection_status_checks": ["nf-core", "confirm-pass"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -48510,17 +43884,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-core-utils@0.4.0", - "nf-schema@2.6.1" - ], + "master_nextflow_config_plugins": ["nf-core-utils@0.4.0", "nf-schema@2.6.1"], "master_nextflow_config_manifest": { "defaultBranch": "master" }, - "dev_nextflow_config_plugins": [ - "nf-core-utils@0.4.0", - "nf-schema@2.6.1" - ], + "dev_nextflow_config_plugins": ["nf-core-utils@0.4.0", "nf-schema@2.6.1"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -48530,10 +43898,7 @@ "published_at": "2026-02-10T13:22:58Z", "tag_sha": "9db0282668a2c66d23f220bba2c720e0b8a78008", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bcftools_annotate", @@ -48589,10 +43954,7 @@ }, "nextflow_version": "!>=25.10.2", "nf_core_version": "3.5.2", - "plugins": [ - "nf-core-utils@0.4.0", - "nf-schema@2.6.1" - ], + "plugins": ["nf-core-utils@0.4.0", "nf-schema@2.6.1"], "co2footprint_files": null }, { @@ -48600,10 +43962,7 @@ "published_at": "2025-12-05T10:10:31Z", "tag_sha": "ea2c7b6286f5ae18f5b51dc0af6b5330ecd6a13a", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bcftools_annotate", @@ -48659,10 +44018,7 @@ }, "nextflow_version": "!>=25.10.2", "nf_core_version": "3.5.1", - "plugins": [ - "nf-schema@2.6.1", - "nf-core-utils@0.4.0" - ], + "plugins": ["nf-schema@2.6.1", "nf-core-utils@0.4.0"], "co2footprint_files": null }, { @@ -48670,10 +44026,7 @@ "published_at": "2025-09-23T09:18:19Z", "tag_sha": "2cbf0469363ca72cc98218e7ae0886bc1bd1fd8f", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bcftools_annotate", @@ -48738,10 +44091,7 @@ "published_at": "2025-08-27T08:15:10Z", "tag_sha": "0a9036c82b6a596015793a18ab089552140e3965", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bcftools_annotate", @@ -48806,10 +44156,7 @@ "published_at": "2025-08-14T06:27:38Z", "tag_sha": "564a754458622cf4b564b2515b6a6d29160fc190", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bcftools_annotate", @@ -48876,10 +44223,7 @@ "published_at": "2025-04-10T09:35:38Z", "tag_sha": "6a5ca7896f12ffc3b8a8c97c21cd0abcd7bf2e36", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bcftools_annotate", @@ -48946,10 +44290,7 @@ "published_at": "2022-06-20T09:25:11Z", "tag_sha": "85b98d51c6bdcbbe9780490d6484c4e50c3c182c", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "cat_fastq", @@ -48993,10 +44334,7 @@ "published_at": "2026-05-04T09:35:36Z", "tag_sha": "99700e73fc95e7a8f7bd6d8bdba67ff987774690", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bcftools_annotate", @@ -49050,10 +44388,7 @@ }, "nextflow_version": "!>=25.10.4", "nf_core_version": "4.0.2", - "plugins": [ - "nf-core-utils@0.4.0", - "nf-schema@2.6.1" - ], + "plugins": ["nf-core-utils@0.4.0", "nf-schema@2.6.1"], "co2footprint_files": null } ] @@ -49154,10 +44489,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": -1, - "master_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "master_branch_protection_status_checks": ["nf-core", "pre-commit"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -49165,10 +44497,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "dev_branch_protection_status_checks": ["nf-core", "pre-commit"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -49237,13 +44566,9 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-validation" - ], + "master_nextflow_config_plugins": ["nf-validation"], "master_nextflow_config_manifest": {}, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -49253,10 +44578,7 @@ "published_at": "2025-11-06T11:39:40Z", "tag_sha": "ff3da4b7c7e312e117427761cc388b694eca3ef5", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bedtools_intersect", @@ -49312,9 +44634,7 @@ }, "nextflow_version": "!>=25.04.0", "nf_core_version": "3.4.1", - "plugins": [ - "nf-validation" - ], + "plugins": ["nf-validation"], "co2footprint_files": null } ] @@ -49418,9 +44738,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": -1, - "master_branch_protection_status_checks": [ - "nf-core" - ], + "master_branch_protection_status_checks": ["nf-core"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -49428,9 +44746,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": true, - "dev_branch_protection_status_checks": [ - "nf-core" - ], + "dev_branch_protection_status_checks": ["nf-core"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -49974,12 +45290,7 @@ }, "nextflow_version": "!>=25.10.2", "nf_core_version": "3.5.1", - "plugins": [ - "nf-core-utils@0.4.0", - "nf-fgbio@1.0.0", - "nf-prov@1.2.2", - "nf-schema@2.6.1" - ], + "plugins": ["nf-core-utils@0.4.0", "nf-fgbio@1.0.0", "nf-prov@1.2.2", "nf-schema@2.6.1"], "co2footprint_files": null }, { @@ -50127,12 +45438,7 @@ }, "nextflow_version": "!>=25.10.2", "nf_core_version": "3.5.1", - "plugins": [ - "nf-core-utils@0.4.0", - "nf-fgbio@1.0.0", - "nf-prov@1.2.2", - "nf-schema@2.6.1" - ], + "plugins": ["nf-core-utils@0.4.0", "nf-fgbio@1.0.0", "nf-prov@1.2.2", "nf-schema@2.6.1"], "co2footprint_files": null }, { @@ -50279,11 +45585,7 @@ }, "nextflow_version": "!>=25.10.2", "nf_core_version": "3.5.1", - "plugins": [ - "nf-schema@2.6.1", - "nf-prov@1.2.2", - "nf-fgbio@1.0.0" - ], + "plugins": ["nf-schema@2.6.1", "nf-prov@1.2.2", "nf-fgbio@1.0.0"], "co2footprint_files": null }, { @@ -50430,11 +45732,7 @@ }, "nextflow_version": "!>=25.10.2", "nf_core_version": "3.5.1", - "plugins": [ - "nf-schema@2.6.1", - "nf-prov@1.2.2", - "nf-fgbio@1.0.0" - ], + "plugins": ["nf-schema@2.6.1", "nf-prov@1.2.2", "nf-fgbio@1.0.0"], "co2footprint_files": null }, { @@ -50984,10 +46282,7 @@ "published_at": "2024-09-03T12:06:04Z", "tag_sha": "5cc30494a6b8e7e53be64d308b582190ca7d2585", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "ascat", @@ -51106,10 +46401,7 @@ "published_at": "2024-08-07T13:44:10Z", "tag_sha": "e92242ead3dff8e24e13adbbd81bfbc0b6862e4c", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "ascat", @@ -51228,10 +46520,7 @@ "published_at": "2024-05-07T11:49:33Z", "tag_sha": "b5b766d3b4ac89864f2fa07441cdc8844e70a79e", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "ascat", @@ -51347,10 +46636,7 @@ "published_at": "2024-04-22T10:44:06Z", "tag_sha": "ea88402912c329b4fd234ad07294ce05bbd2590c", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "ascat", @@ -51466,10 +46752,7 @@ "published_at": "2023-11-15T17:02:23Z", "tag_sha": "6aeac929c924ba382baa42a0fe969b4e0e753ca9", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "ascat", @@ -51568,11 +46851,7 @@ "unzip", "vcftools" ], - "subworkflows": [ - "bam_ngscheckmate", - "vcf_annotate_ensemblvep", - "vcf_annotate_snpeff" - ] + "subworkflows": ["bam_ngscheckmate", "vcf_annotate_ensemblvep", "vcf_annotate_snpeff"] }, "nextflow_version": "!>=23.04.0", "nf_core_version": null @@ -51582,10 +46861,7 @@ "published_at": "2023-10-04T08:21:38Z", "tag_sha": "f034b737630972e90aeae851e236f9d4292b9a4f", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "ascat", @@ -51679,10 +46955,7 @@ "unzip", "vcftools" ], - "subworkflows": [ - "vcf_annotate_ensemblvep", - "vcf_annotate_snpeff" - ] + "subworkflows": ["vcf_annotate_ensemblvep", "vcf_annotate_snpeff"] }, "nextflow_version": "!>=23.04.0", "nf_core_version": null @@ -51692,10 +46965,7 @@ "published_at": "2023-09-18T17:46:45Z", "tag_sha": "59026dc07633edb83aab3bfb2f65f79db38437a1", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "ascat", @@ -51789,10 +47059,7 @@ "unzip", "vcftools" ], - "subworkflows": [ - "vcf_annotate_ensemblvep", - "vcf_annotate_snpeff" - ] + "subworkflows": ["vcf_annotate_ensemblvep", "vcf_annotate_snpeff"] }, "nextflow_version": "!>=23.04.0", "nf_core_version": null @@ -51802,10 +47069,7 @@ "published_at": "2023-09-13T20:35:40Z", "tag_sha": "1a263a2bac181199317217afc8d2fafba9c3e0df", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "ascat", @@ -51899,10 +47163,7 @@ "unzip", "vcftools" ], - "subworkflows": [ - "vcf_annotate_ensemblvep", - "vcf_annotate_snpeff" - ] + "subworkflows": ["vcf_annotate_ensemblvep", "vcf_annotate_snpeff"] }, "nextflow_version": "!>=23.04.0", "nf_core_version": null @@ -51912,10 +47173,7 @@ "published_at": "2023-06-22T12:09:53Z", "tag_sha": "ed1cc8499366dcefea216fe37e36c6189537d57b", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "ascat", @@ -52003,10 +47261,7 @@ "unzip", "vcftools" ], - "subworkflows": [ - "vcf_annotate_ensemblvep", - "vcf_annotate_snpeff" - ] + "subworkflows": ["vcf_annotate_ensemblvep", "vcf_annotate_snpeff"] }, "nextflow_version": "!>=23.04.0", "nf_core_version": null @@ -52016,10 +47271,7 @@ "published_at": "2023-06-15T14:24:30Z", "tag_sha": "6ec8c1c945fb132adf152e196053bd7f72f1dfdc", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "ascat", @@ -52107,10 +47359,7 @@ "unzip", "vcftools" ], - "subworkflows": [ - "vcf_annotate_ensemblvep", - "vcf_annotate_snpeff" - ] + "subworkflows": ["vcf_annotate_ensemblvep", "vcf_annotate_snpeff"] }, "nextflow_version": "!>=23.04.0", "nf_core_version": null @@ -52120,10 +47369,7 @@ "published_at": "2023-06-08T12:53:16Z", "tag_sha": "6c0d335e17fb4406f527540631da7b26a5fe1464", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "ascat", @@ -52211,10 +47457,7 @@ "unzip", "vcftools" ], - "subworkflows": [ - "vcf_annotate_ensemblvep", - "vcf_annotate_snpeff" - ] + "subworkflows": ["vcf_annotate_ensemblvep", "vcf_annotate_snpeff"] }, "nextflow_version": "!>=23.04.0", "nf_core_version": null @@ -52224,10 +47467,7 @@ "published_at": "2023-06-05T11:31:25Z", "tag_sha": "71fac185a93e7f31213ca77610a05b7f1489a31e", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "ascat", @@ -52315,10 +47555,7 @@ "unzip", "vcftools" ], - "subworkflows": [ - "vcf_annotate_ensemblvep", - "vcf_annotate_snpeff" - ] + "subworkflows": ["vcf_annotate_ensemblvep", "vcf_annotate_snpeff"] }, "nextflow_version": "!>=22.10.1", "nf_core_version": null @@ -52328,10 +47565,7 @@ "published_at": "2023-01-05T18:06:40Z", "tag_sha": "c87f4eb694a7183e4f99c70fca0f1d4e91750b33", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "ascat", @@ -52424,10 +47658,7 @@ "published_at": "2022-11-21T13:32:22Z", "tag_sha": "96749f742197e828f4632cc2a7481190e7f642ac", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "ascat", @@ -52520,10 +47751,7 @@ "published_at": "2022-11-16T13:30:46Z", "tag_sha": "0b7f0e2b6f0be7053838ba1884b2eb03e9f83f9e", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "ascat", @@ -52616,10 +47844,7 @@ "published_at": "2022-09-26T19:07:10Z", "tag_sha": "bcd7bf9cb98cddec27bb54fb47ee122c09388c02", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "ascat", @@ -52712,10 +47937,7 @@ "published_at": "2022-08-18T11:48:05Z", "tag_sha": "ad2b34f39fead34d7a09051e67506229e827e892", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "ascat", @@ -52808,10 +48030,7 @@ "published_at": "2022-07-21T11:34:21Z", "tag_sha": "5bb160ddb2cee50c811585e450b16cba13c95a02", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "ascat", @@ -52904,10 +48123,7 @@ "published_at": "2022-06-10T09:45:49Z", "tag_sha": "e8f56e5bbb6f8a34793a6b5a2945981eb43090aa", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=20.04.0" }, { @@ -52915,10 +48131,7 @@ "published_at": "2021-06-14T12:50:00Z", "tag_sha": "68b9930a74962f3c42eee71f51e6dd2646269199", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=20.04.0" }, { @@ -52926,10 +48139,7 @@ "published_at": "2021-01-26T14:46:44Z", "tag_sha": "7ccfb36509d8380946c048065129b29d69c8443b", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=20.04.0" }, { @@ -52937,10 +48147,7 @@ "published_at": "2020-06-23T09:15:28Z", "tag_sha": "bce378e09de25bb26c388b917f93f84806d3ba27", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=19.10.0" }, { @@ -52948,10 +48155,7 @@ "published_at": "2020-05-24T09:40:37Z", "tag_sha": "75fe254f0b5d93d1f3f0173f2163afa83686f6fd", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=19.10.0" }, { @@ -52959,10 +48163,7 @@ "published_at": "2019-12-16T14:48:20Z", "tag_sha": "5c30fd821ab7cdf27fd4105464a1fba5eabdfcd5", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=19.10.0" }, { @@ -52970,10 +48171,7 @@ "published_at": "2019-10-22T13:29:47Z", "tag_sha": "05c6e0b63251af83b9e7d5b259cec9e679fccf57", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=19.04.0" }, { @@ -52981,10 +48179,7 @@ "published_at": "2019-10-08T13:26:37Z", "tag_sha": "c5fc54788bdd5b8a0d39dba9d93a039a564f0e4b", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=19.04.0" }, { @@ -53132,12 +48327,7 @@ }, "nextflow_version": "!>=25.10.2", "nf_core_version": "3.5.1", - "plugins": [ - "nf-core-utils@0.4.0", - "nf-fgbio@1.0.0", - "nf-prov@1.2.2", - "nf-schema@2.6.1" - ], + "plugins": ["nf-core-utils@0.4.0", "nf-fgbio@1.0.0", "nf-prov@1.2.2", "nf-schema@2.6.1"], "co2footprint_files": null } ] @@ -53234,10 +48424,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": -1, - "master_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "master_branch_protection_status_checks": ["nf-core", "pre-commit"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -53245,10 +48432,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "dev_branch_protection_status_checks": ["nf-core", "pre-commit"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": true, "dev_branch_protection_require_non_stale_review": false, @@ -53387,14 +48571,9 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-validation@1.1.3" - ], + "master_nextflow_config_plugins": ["nf-validation@1.1.3"], "master_nextflow_config_manifest": {}, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1", - "nf-anndata@0.3.2" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1", "nf-anndata@0.3.2"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -53404,10 +48583,7 @@ "published_at": "2026-05-21T07:37:34Z", "tag_sha": "ccf015590114d56f29fb39ff48d2d1bedfc78b4d", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "anndata_barcodes", @@ -53431,9 +48607,7 @@ }, "nextflow_version": "!>=25.10.4", "nf_core_version": "4.0.2", - "plugins": [ - "nf-validation@1.1.3" - ], + "plugins": ["nf-validation@1.1.3"], "co2footprint_files": null } ] @@ -53468,12 +48642,7 @@ "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, - "topics": [ - "rnaseq", - "single-cell", - "single-nuclei", - "single-nuclei-rna-sequencing" - ], + "topics": ["rnaseq", "single-cell", "single-nuclei", "single-nuclei-rna-sequencing"], "visibility": "public", "forks": 11, "open_issues": 12, @@ 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"dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -53962,15 +49122,11 @@ "is_DSL2": true, "has_nf_test": false, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-schema@2.2.0" - ], + "master_nextflow_config_plugins": ["nf-schema@2.2.0"], "master_nextflow_config_manifest": { "defaultBranch": "master" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -53980,10 +49136,7 @@ "published_at": "2026-03-09T14:58:58Z", "tag_sha": "54005c66344e1402c489108a3620a1ee234a7c09", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bamtools_split", @@ -54022,9 +49175,7 @@ }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.2.1", - "plugins": [ - "nf-schema@2.2.0" - ], + "plugins": ["nf-schema@2.2.0"], "co2footprint_files": null }, { @@ -54032,10 +49183,7 @@ "published_at": "2025-09-02T18:45:00Z", "tag_sha": "4a6aade735c742d5c3d9ce73a5dfbc1902fbd0c1", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bamtools_split", @@ -54080,10 +49228,7 @@ "published_at": "2025-06-09T15:52:07Z", "tag_sha": "05d705a301a262669c2252c890106e31a28a120e", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bamtools_split", @@ -54128,10 +49273,7 @@ "published_at": "2025-03-18T17:39:22Z", "tag_sha": "500954ec86615baee2ee45a72483c7ff220f6fdb", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bamtools_split", @@ -54175,10 +49317,7 @@ "published_at": "2024-10-07T14:53:15Z", "tag_sha": "35da74af5daae60ade2920c84a48f833a4c3c2a1", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bamtools_split", @@ -54221,10 +49360,7 @@ "published_at": "2026-05-23T02:21:58Z", "tag_sha": "d385704a43db49159c8ed2adc0869cc7dec59918", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bamtools_split", @@ -54263,9 +49399,7 @@ }, "nextflow_version": "!>=25.04.2", "nf_core_version": "3.5.1", - "plugins": [ - "nf-schema@2.2.0" - ], + "plugins": ["nf-schema@2.2.0"], "co2footprint_files": null } ] @@ -54365,10 +49499,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": -1, - "master_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "master_branch_protection_status_checks": ["nf-core", "pre-commit"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -54376,10 +49507,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "dev_branch_protection_status_checks": ["nf-core", "pre-commit"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -54618,15 +49746,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "master_nextflow_config_plugins": ["nf-schema@2.5.1"], "master_nextflow_config_manifest": { "defaultBranch": "master" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -54636,10 +49760,7 @@ "published_at": "2025-10-30T19:52:05Z", "tag_sha": "f7bf36d7c7e4bddc5302c3facd8d19ca83e22226", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "anndata_barcodes", @@ -54678,10 +49799,7 @@ "published_at": "2025-03-11T08:05:42Z", "tag_sha": "e0ddddbff9d8b8c2421c67ff07449a06f9ca02d2", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "anndata_barcodes", @@ -54720,10 +49838,7 @@ "published_at": "2024-12-10T13:33:27Z", "tag_sha": "89a7986916703f7e4fb1961ce78351bae50bf2ba", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "cellbender_removebackground", @@ -54744,11 +49859,7 @@ "star_genomegenerate", "unzip" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.0.2" @@ -54758,10 +49869,7 @@ "published_at": "2024-08-15T06:27:11Z", "tag_sha": "4171377f40d629d43d4ca71654a7ea06e5619a09", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "cellranger_count", @@ -54796,10 +49904,7 @@ "published_at": "2024-06-25T14:06:24Z", "tag_sha": "c8f02f515d014ee2c98b401950e2cf7141a82b42", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "cellranger_count", @@ -54834,10 +49939,7 @@ "published_at": "2024-05-07T14:17:50Z", "tag_sha": "c5a64459fec1506304f7064639f3f8e12d971269", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "cellranger_count", @@ -54870,10 +49972,7 @@ "published_at": "2024-01-23T08:11:32Z", "tag_sha": "90cb6a48155248286c85395c53a201c3a31b2258", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "cellranger_count", @@ -54902,10 +50001,7 @@ "published_at": "2024-01-10T07:15:52Z", "tag_sha": "e03cd46fc9fb54cac63c7c4f0f542d229394787d", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "cellranger_count", @@ -54931,10 +50027,7 @@ "published_at": "2023-10-02T12:18:13Z", "tag_sha": "ca7c05afdd5c41dc31a5a32bb207d19767836ca5", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "cellranger_count", @@ -54959,10 +50052,7 @@ "published_at": "2023-08-24T08:10:26Z", "tag_sha": "61d1919aa96a4d82517aeb6d04943262a42a055e", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "cellranger_count", @@ -54987,10 +50077,7 @@ "published_at": "2023-06-07T18:50:18Z", "tag_sha": "06a85e8e543c006aec6720ee079a00f7085a1635", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "cellranger_count", @@ -55015,10 +50102,7 @@ "published_at": "2023-06-02T08:31:07Z", "tag_sha": "6cccb9d37afa873b6799cd09f8589b5b129c8ac1", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "cellranger_count", @@ -55043,10 +50127,7 @@ "published_at": "2023-05-03T20:46:50Z", "tag_sha": "cfada12a6f5d773a76d5f1793d70661e95852c53", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "cellranger_count", @@ -55071,10 +50152,7 @@ "published_at": "2023-03-20T08:10:47Z", "tag_sha": "c6ec2175a8f5d593c00136835c45c6291821fe11", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "cellranger_count", @@ -55099,10 +50177,7 @@ "published_at": "2022-10-06T09:45:36Z", "tag_sha": "c86646e4a818397f4bddfffd641b34240423f3ea", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "cellranger_count", @@ -55126,10 +50201,7 @@ "published_at": "2022-06-17T11:48:54Z", "tag_sha": "27f37ab827b3f72e8e305256a9c59a37bb85ef83", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "cellranger_count", @@ -55154,10 +50226,7 @@ "published_at": "2021-03-29T07:56:00Z", "tag_sha": "f31b12f79097ed5775fba925c3b2832d701b21f4", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=20.10.0" }, { @@ -55165,10 +50234,7 @@ "published_at": "2019-12-09T16:26:13Z", "tag_sha": "884e541285330e1ef4771ff9267ce27e42dfb2e3", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=19.10.0" }, { @@ -55176,10 +50242,7 @@ "published_at": "2026-05-20T17:00:31Z", "tag_sha": "aaf72401afa70a86e1ac75c112ca7ec09f8f76f6", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "anndata_barcodes", @@ -55213,9 +50276,7 @@ }, "nextflow_version": "!>=25.10.4", "nf_core_version": "4.0.2", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null } ] @@ -55252,10 +50313,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "genomics", - "quality-control" - ], + "topics": ["genomics", "quality-control"], "visibility": "public", "forks": 41, "open_issues": 31, @@ -55308,11 +50366,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": -1, - "master_branch_protection_status_checks": [ - "nf-core", - "pre-commit", - "nf-test-changes" - ], + "master_branch_protection_status_checks": ["nf-core", "pre-commit", "nf-test-changes"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -55320,11 +50374,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "pre-commit", - "nf-core", - "nf-test-changes" - ], + "dev_branch_protection_status_checks": ["pre-commit", "nf-core", "nf-test-changes"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -55448,17 +50498,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-core-utils@0.4.0", - "nf-schema@2.6.1" - ], + "master_nextflow_config_plugins": ["nf-core-utils@0.4.0", "nf-schema@2.6.1"], "master_nextflow_config_manifest": { "defaultBranch": "master" }, - "dev_nextflow_config_plugins": [ - "nf-core-utils@0.4.0", - "nf-schema@2.6.1" - ], + "dev_nextflow_config_plugins": ["nf-core-utils@0.4.0", "nf-schema@2.6.1"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -55468,10 +50512,7 @@ "published_at": "2026-03-02T14:59:12Z", "tag_sha": "14106c0a25537c2224d76cde5f0f610a2cf2fd4f", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bwamem2_index", @@ -55487,18 +50528,11 @@ "seqfu_stats", "seqtk_sample" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.10.2", "nf_core_version": "3.5.2", - "plugins": [ - "nf-core-utils@0.4.0", - "nf-schema@2.6.1" - ], + "plugins": ["nf-core-utils@0.4.0", "nf-schema@2.6.1"], "co2footprint_files": null }, { @@ -55506,10 +50540,7 @@ "published_at": "2026-02-24T12:11:02Z", "tag_sha": "98965867965c91bdc98f68819924fb0ef439ec12", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bwamem2_index", @@ -55525,18 +50556,11 @@ "seqfu_stats", "seqtk_sample" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.10.2", "nf_core_version": "3.5.2", - "plugins": [ - "nf-core-utils@0.4.0", - "nf-schema@2.6.1" - ], + "plugins": ["nf-core-utils@0.4.0", "nf-schema@2.6.1"], "co2footprint_files": null }, { @@ -55544,10 +50568,7 @@ "published_at": "2026-05-04T11:33:01Z", "tag_sha": "cf6432f7a35f651b32daa42b8c255cbcd5f37c8c", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bwamem2_index", @@ -55574,18 +50595,11 @@ "toulligqc", "untar" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.10.4", "nf_core_version": "4.0.2", - "plugins": [ - "nf-core-utils@0.4.0", - "nf-schema@2.6.1" - ], + "plugins": ["nf-core-utils@0.4.0", "nf-schema@2.6.1"], "co2footprint_files": null } ] @@ -55676,10 +50690,7 @@ "master_branch_exists": false, "main_branch_exists": true, "main_branch_protection_up_to_date": true, - "main_branch_protection_status_checks": [ - "pre-commit", - "nf-core" - ], + "main_branch_protection_status_checks": ["pre-commit", "nf-core"], "main_branch_protection_required_reviews": 2, "main_branch_protection_require_codeowner_review": false, "main_branch_protection_require_non_stale_review": false, @@ -55687,10 +50698,7 @@ "main_uses_ruleset": true, "dev_branch_exists": true, "dev_branch_protection_up_to_date": true, - "dev_branch_protection_status_checks": [ - "pre-commit", - "nf-core" - ], + "dev_branch_protection_status_checks": ["pre-commit", "nf-core"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -55750,15 +50758,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "main_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "main_nextflow_config_plugins": ["nf-schema@2.5.1"], "main_nextflow_config_manifest": { "defaultBranch": "main" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "main" }, @@ -55768,10 +50772,7 @@ "published_at": "2026-05-14T10:22:14Z", "tag_sha": "f3c1546fe9df586d93e667d6ea5ffaef7f7ec9c5", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "barrnap", @@ -55800,9 +50801,7 @@ }, "nextflow_version": "!>=25.10.4", "nf_core_version": "4.0.2", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null } ] @@ -55839,12 +50838,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "differential-expression", - "quantseq", - "slamseq", - "transcriptomics" - ], + "topics": ["differential-expression", "quantseq", "slamseq", "transcriptomics"], "visibility": "public", "forks": 10, "open_issues": 11, @@ -56177,10 +51171,7 @@ "published_at": "2020-05-14T12:40:04Z", "tag_sha": "855583252166ca5ff739b40a6762837534a99c36", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=19.10.0" }, { @@ -56188,10 +51179,7 @@ "published_at": "2021-04-26T13:04:00Z", "tag_sha": "c21d0faee30707ffe134f77e0b37887a1610503f", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=19.10.0", "nf_core_version": null, "plugins": [], @@ -56547,10 +51535,7 @@ "published_at": "2021-04-26T13:02:40Z", "tag_sha": "6d474839a0f5cf03a266e3314ba1d2c062d96285", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ] + "doc_files": ["docs/output.md", "docs/usage.md"] } ] }, @@ -56586,10 +51571,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "small-rna", - "smrna-seq" - ], + "topics": ["small-rna", "smrna-seq"], "visibility": "public", "forks": 134, "open_issues": 21, @@ -56642,9 +51624,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": -1, - "master_branch_protection_status_checks": [ - "nf-core" - ], + "master_branch_protection_status_checks": ["nf-core"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -56652,9 +51632,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "nf-core" - ], + "dev_branch_protection_status_checks": ["nf-core"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -56863,15 +51841,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "master_nextflow_config_plugins": ["nf-schema@2.5.1"], "master_nextflow_config_manifest": { "defaultBranch": "master" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -56881,10 +51855,7 @@ "published_at": "2026-01-07T13:41:35Z", "tag_sha": "cb0af579b24cb8d5a3accd87b2f14ea93fe04832", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bioawk", @@ -56931,9 +51902,7 @@ }, "nextflow_version": "!>=25.04.2", "nf_core_version": "3.5.1", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null }, { @@ -56941,10 +51910,7 @@ "published_at": "2024-10-14T09:59:05Z", "tag_sha": "72c4c4cf83e1f534319493f9de8344854f59736f", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bioawk", @@ -56998,10 +51964,7 @@ "published_at": "2024-04-18T15:16:15Z", "tag_sha": "5901bea438cb719c186f883bb6e6a11f1de70a5b", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "cat_cat", @@ -57035,10 +51998,7 @@ "published_at": "2024-02-23T11:00:51Z", "tag_sha": "c611b15e973999368a6d44dcee3f26c3e392358f", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "cat_cat", @@ -57072,10 +52032,7 @@ "published_at": "2023-11-03T19:29:45Z", "tag_sha": "87f2b3e27deb914a3657e1067bbfbde3c2c50785", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "cat_fastq", @@ -57089,10 +52046,7 @@ "samtools_sort", "samtools_stats" ], - "subworkflows": [ - "bam_sort_stats_samtools", - "bam_stats_samtools" - ] + "subworkflows": ["bam_sort_stats_samtools", "bam_stats_samtools"] }, "nextflow_version": "!>=23.04.0", "nf_core_version": null @@ -57102,10 +52056,7 @@ "published_at": "2023-09-06T11:01:31Z", "tag_sha": "18d6c84926a3c983d4d9518a53020a7791746c98", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "cat_fastq", @@ -57119,10 +52070,7 @@ "samtools_sort", "samtools_stats" ], - "subworkflows": [ - "bam_sort_stats_samtools", - "bam_stats_samtools" - ] + "subworkflows": ["bam_sort_stats_samtools", "bam_stats_samtools"] }, "nextflow_version": "!>=23.04.0", "nf_core_version": null @@ -57132,10 +52080,7 @@ "published_at": "2023-09-05T09:16:17Z", "tag_sha": "e6b6e5a06eef96d1dd2ecb207f401308748d8902", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "cat_fastq", @@ -57149,10 +52094,7 @@ "samtools_sort", "samtools_stats" ], - "subworkflows": [ - "bam_sort_stats_samtools", - "bam_stats_samtools" - ] + "subworkflows": ["bam_sort_stats_samtools", "bam_stats_samtools"] }, "nextflow_version": "!>=23.04.0", "nf_core_version": null @@ -57162,10 +52104,7 @@ "published_at": "2023-05-12T13:15:42Z", "tag_sha": "f7022abd9fc1a6db6f4ca114c17368dbbe8ca4f8", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "cat_fastq", @@ -57188,10 +52127,7 @@ "published_at": "2023-04-26T13:12:31Z", "tag_sha": "5ce052d93d4363c3d16667cc757948fa5ce2c763", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "cat_fastq", @@ -57214,10 +52150,7 @@ "published_at": "2022-10-24T22:41:27Z", "tag_sha": "27514c40c08d1eab8249521096f4f2f7be875104", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "cat_fastq", @@ -57240,10 +52173,7 @@ "published_at": "2022-05-31T19:24:06Z", "tag_sha": "d1299b132a910d8adb38a5445d0c223051e14264", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "cat_fastq", @@ -57266,10 +52196,7 @@ "published_at": "2021-06-15T12:46:55Z", "tag_sha": "03333bfa17adc8d829a400012ed9f13c5abf4cc3", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=20.04.0" }, { @@ -57277,10 +52204,7 @@ "published_at": "2019-09-21T09:10:21Z", "tag_sha": "28f3418bc80e9af23766b445a7ab5c20caa24deb", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=0.32.0" }, { @@ -57288,10 +52212,7 @@ "published_at": "2026-05-08T18:16:01Z", "tag_sha": "8a9a96e469caa25f56b74c6abb742c327ff4fb7f", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bioawk", @@ -57338,9 +52259,7 @@ }, "nextflow_version": "!>=25.04.2", "nf_core_version": "3.5.1", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null } ] @@ -57377,13 +52296,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "segmentation", - "spatial-omics", - "spatial-proteomics", - "spatial-transcriptomics", - "spatialdata" - ], + "topics": ["segmentation", "spatial-omics", "spatial-proteomics", "spatial-transcriptomics", "spatialdata"], "visibility": "public", "forks": 8, "open_issues": 6, @@ -57436,10 +52349,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": true, - "master_branch_protection_status_checks": [ - "pre-commit", - "nf-core" - ], + "master_branch_protection_status_checks": ["pre-commit", "nf-core"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -57483,15 +52393,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-schema@2.4.2" - ], + "master_nextflow_config_plugins": ["nf-schema@2.4.2"], "master_nextflow_config_manifest": { "defaultBranch": "master" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -57501,26 +52407,14 @@ "published_at": "2026-04-13T12:24:15Z", "tag_sha": "60b77214078bcfa789cfe6cf84aecf914138e266", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "spaceranger_count", - "untar" - ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "modules": ["spaceranger_count", "untar"], + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.04.0", "nf_core_version": "3.5.1", - "plugins": [ - "nf-schema@2.4.2" - ], + "plugins": ["nf-schema@2.4.2"], "co2footprint_files": null } ] @@ -57635,9 +52529,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "nf-core" - ], + "dev_branch_protection_status_checks": ["nf-core"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -57698,9 +52590,7 @@ "has_nf_test_dev": true, "master_nextflow_config_plugins": [], "master_nextflow_config_manifest": {}, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -57710,23 +52600,10 @@ "published_at": "2026-05-07T05:22:04Z", "tag_sha": "d0fd35d9a985b30db9895c8b4b08f291a700f722", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "fastqc", - "multiqc", - "quartonotebook", - "spaceranger_count", - "untar" - ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "modules": ["fastqc", "multiqc", "quartonotebook", "spaceranger_count", "untar"], + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.10.4", "nf_core_version": "4.0.2", @@ -57828,10 +52705,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": -1, - "master_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "master_branch_protection_status_checks": ["nf-core", "pre-commit"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -57839,10 +52713,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "dev_branch_protection_status_checks": ["nf-core", "pre-commit"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -57873,9 +52744,7 @@ "has_nf_test_dev": true, "master_nextflow_config_plugins": [], "master_nextflow_config_manifest": {}, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -57885,10 +52754,7 @@ "published_at": "2026-05-21T08:01:30Z", "tag_sha": "2af78b179cc4aed3524e2feae90c12a81feb1b9e", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "cellpose", @@ -57903,11 +52769,7 @@ "xeniumranger_relabel", "xeniumranger_resegment" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.04.0", "nf_core_version": "3.5.2", @@ -58014,10 +52876,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "dev_branch_protection_status_checks": ["nf-core", "pre-commit"], "dev_branch_protection_required_reviews": -1, "dev_branch_protection_require_codeowner_review": -1, "dev_branch_protection_require_non_stale_review": -1, @@ -58048,9 +52907,7 @@ "has_nf_test_dev": false, "master_nextflow_config_plugins": [], "master_nextflow_config_manifest": {}, - "dev_nextflow_config_plugins": [ - "nf-validation@1.1.3" - ], + "dev_nextflow_config_plugins": ["nf-validation@1.1.3"], "dev_nextflow_config_manifest": {}, "releases": [ { @@ -58058,10 +52915,7 @@ "published_at": "2024-04-03T09:34:48Z", "tag_sha": "9bb174383c4abda8f432548a34d69cb7f587bb4c", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": "!>=23.04.0", "nf_core_version": null, "plugins": [], @@ -58197,10 +53051,7 @@ "published_at": "2021-12-23T20:17:08Z", "tag_sha": "0cc3ee6ac2d3d8ed309b74e4ae61bad4006362cc", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bedtools_bamtobed", @@ -58257,11 +53108,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "expression", - "housekeeping-genes", - "qpcr-analysis" - ], + "topics": ["expression", "housekeeping-genes", "qpcr-analysis"], "visibility": "public", "forks": 2, "open_issues": 4, @@ -58314,10 +53161,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": true, - "master_branch_protection_status_checks": [ - "pre-commit", - "nf-core" - ], + "master_branch_protection_status_checks": ["pre-commit", "nf-core"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -58326,10 +53170,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": true, - "dev_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "dev_branch_protection_status_checks": ["nf-core", "pre-commit"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -58364,13 +53205,9 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-schema@2.0.0" - ], + "master_nextflow_config_plugins": ["nf-schema@2.0.0"], "master_nextflow_config_manifest": {}, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "main" }, @@ -58380,25 +53217,14 @@ "published_at": "2026-04-17T13:55:52Z", "tag_sha": "3c5669a174e0490923b094c1a72cd0523f71acf2", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "multiqc" - ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "modules": ["multiqc"], + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.04.0", "nf_core_version": "3.5.2", - "plugins": [ - "nf-schema@2.0.0" - ], + "plugins": ["nf-schema@2.0.0"], "co2footprint_files": null } ] @@ -58501,22 +53327,14 @@ "master_branch_exists": false, "main_branch_exists": true, "main_branch_protection_up_to_date": -1, - "main_branch_protection_status_checks": [ - "nf-core", - "download", - "confirm-pass" - ], + "main_branch_protection_status_checks": ["nf-core", "download", "confirm-pass"], "main_branch_protection_required_reviews": 2, "main_branch_protection_require_codeowner_review": false, "main_branch_protection_require_non_stale_review": false, "main_branch_protection_enforce_admins": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "nf-core", - "pre-commit", - "confirm-pass" - ], + "dev_branch_protection_status_checks": ["nf-core", "pre-commit", "confirm-pass"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -58655,15 +53473,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "main_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "main_nextflow_config_plugins": ["nf-schema@2.5.1"], "main_nextflow_config_manifest": { "defaultBranch": "main" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "main" }, @@ -58742,17 +53556,11 @@ "taxpasta_standardise", "untar" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.04.2", "nf_core_version": "3.5.2", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null }, { @@ -58822,17 +53630,11 @@ "taxpasta_standardise", "untar" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.04.2", "nf_core_version": "3.5.2", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null }, { @@ -58902,17 +53704,11 @@ "taxpasta_standardise", "untar" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.04.2", "nf_core_version": "3.5.1", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null }, { @@ -58982,11 +53778,7 @@ "taxpasta_standardise", "untar" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.04.2", "nf_core_version": "3.3.2" @@ -59058,11 +53850,7 @@ "taxpasta_standardise", "untar" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.2.0" @@ -59134,11 +53922,7 @@ "taxpasta_standardise", "untar" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.1.1" @@ -59210,11 +53994,7 @@ "taxpasta_standardise", "untar" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.0.2" @@ -59906,10 +54686,7 @@ "published_at": "2023-05-15T09:07:32Z", "tag_sha": "07b926a89e68bc1b0720170c0996a48b7eed618d", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "adapterremoval", @@ -59964,10 +54741,7 @@ "published_at": "2023-03-13T11:09:32Z", "tag_sha": "eaef6ac9bcfef0ae173919e45178415b9d3526fa", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "adapterremoval", @@ -60091,17 +54865,11 @@ "taxpasta_standardise", "untar" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.04.2", "nf_core_version": "3.5.2", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null } ] @@ -60138,10 +54906,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "mycobacterium-tuberculosis", - "mycobacterium-tuberculosis-complex" - ], + "topics": ["mycobacterium-tuberculosis", "mycobacterium-tuberculosis-complex"], "visibility": "public", "forks": 3, "open_issues": 4, @@ -60194,10 +54959,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": -1, - "master_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "master_branch_protection_status_checks": ["nf-core", "pre-commit"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -60205,10 +54967,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "dev_branch_protection_status_checks": ["nf-core", "pre-commit"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -60242,13 +55001,9 @@ "is_DSL2": true, "has_nf_test": false, "has_nf_test_dev": false, - "master_nextflow_config_plugins": [ - "nf-validation@1.1.3" - ], + "master_nextflow_config_plugins": ["nf-validation@1.1.3"], "master_nextflow_config_manifest": {}, - "dev_nextflow_config_plugins": [ - "nf-schema@2.1.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.1.1"], "dev_nextflow_config_manifest": {}, "releases": [ { @@ -60256,10 +55011,7 @@ "published_at": "2024-10-30T09:48:53Z", "tag_sha": "47670645b33e632772efefb02423537212b4e016", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bcftools_merge", @@ -60291,17 +55043,11 @@ "tabix_bgzip", "tbprofiler_profile" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.0.2", - "plugins": [ - "nf-validation@1.1.3" - ], + "plugins": ["nf-validation@1.1.3"], "co2footprint_files": null } ] @@ -60338,11 +55084,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "open-chromatin-regions", - "transcription-factors", - "transcriptomics" - ], + "topics": ["open-chromatin-regions", "transcription-factors", "transcriptomics"], "visibility": "public", "forks": 6, "open_issues": 0, @@ -60408,10 +55150,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "dev_branch_protection_status_checks": ["nf-core", "pre-commit"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -60450,13 +55189,9 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-validation@1.1.3" - ], + "master_nextflow_config_plugins": ["nf-validation@1.1.3"], "master_nextflow_config_manifest": {}, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -60466,10 +55201,7 @@ "published_at": "2026-05-09T20:16:36Z", "tag_sha": "4ac627e7439087a4a8be3dfe7bcb6f6ed55a3d1d", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bedtools_complement", @@ -60491,17 +55223,11 @@ "untar", "zip" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.10.4", "nf_core_version": "4.0.2", - "plugins": [ - "nf-validation@1.1.3" - ], + "plugins": ["nf-validation@1.1.3"], "co2footprint_files": null } ] @@ -60538,9 +55264,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "permafrost" - ], + "topics": ["permafrost"], "visibility": "public", "forks": 1, "open_issues": 3, @@ -60593,10 +55317,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": -1, - "master_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "master_branch_protection_status_checks": ["nf-core", "pre-commit"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -60604,10 +55325,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "dev_branch_protection_status_checks": ["nf-core", "pre-commit"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -60636,13 +55354,9 @@ "is_DSL2": true, "has_nf_test": false, "has_nf_test_dev": false, - "master_nextflow_config_plugins": [ - "nf-validation@1.1.3" - ], + "master_nextflow_config_plugins": ["nf-validation@1.1.3"], "master_nextflow_config_manifest": {}, - "dev_nextflow_config_plugins": [ - "nf-schema@2.3.0" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.3.0"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -60652,26 +55366,14 @@ "published_at": "2025-01-31T11:34:37Z", "tag_sha": "01dcf009af22e83b4581ade40941480fc6abcb4d", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { - "modules": [ - "fastqc", - "multiqc" - ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "modules": ["fastqc", "multiqc"], + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.2.0", - "plugins": [ - "nf-validation@1.1.3" - ], + "plugins": ["nf-validation@1.1.3"], "co2footprint_files": null } ] @@ -60771,10 +55473,7 @@ "master_branch_exists": false, "main_branch_exists": true, "main_branch_protection_up_to_date": true, - "main_branch_protection_status_checks": [ - "pre-commit", - "nf-core" - ], + "main_branch_protection_status_checks": ["pre-commit", "nf-core"], "main_branch_protection_required_reviews": 2, "main_branch_protection_require_codeowner_review": false, "main_branch_protection_require_non_stale_review": false, @@ -60854,9 +55553,7 @@ "has_nf_test_dev": true, "main_nextflow_config_plugins": [], "main_nextflow_config_manifest": {}, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -60866,10 +55563,7 @@ "published_at": "2026-05-25T16:01:46Z", "tag_sha": "f143dd2a3d1b8815dec80fa511ab6d5e9073e263", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bcftools_mpileup", @@ -60887,10 +55581,7 @@ "vcf2maf", "viber" ], - "subworkflows": [ - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.04.0", "nf_core_version": "3.5.1", @@ -60931,12 +55622,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "benchmark", - "small-variants", - "structural-variants", - "variant-calling" - ], + "topics": ["benchmark", "small-variants", "structural-variants", "variant-calling"], "visibility": "public", "forks": 29, "open_issues": 27, @@ -60989,10 +55675,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": -1, - "master_branch_protection_status_checks": [ - "pre-commit", - "nf-core" - ], + "master_branch_protection_status_checks": ["pre-commit", "nf-core"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -61000,10 +55683,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "pre-commit", - "nf-core" - ], + "dev_branch_protection_status_checks": ["pre-commit", "nf-core"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -61072,17 +55752,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-schema@2.5.1", - "nf-prov@1.2.2" - ], + "master_nextflow_config_plugins": ["nf-schema@2.5.1", "nf-prov@1.2.2"], "master_nextflow_config_manifest": { "defaultBranch": "master" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1", - "nf-prov@1.2.2" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1", "nf-prov@1.2.2"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -61092,10 +55766,7 @@ "published_at": "2026-04-22T09:39:33Z", "tag_sha": "8b21c01749c4447b285d242a198127736f3ffe51", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bcftools_annotate", @@ -61139,18 +55810,11 @@ "variantextractor", "wittyer" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.04.0", "nf_core_version": "3.5.1", - "plugins": [ - "nf-schema@2.5.1", - "nf-prov@1.2.2" - ], + "plugins": ["nf-schema@2.5.1", "nf-prov@1.2.2"], "co2footprint_files": null }, { @@ -61158,10 +55822,7 @@ "published_at": "2025-12-03T15:23:07Z", "tag_sha": "68a3209895196664b42b5ea0bbf434b30ec33848", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bcftools_annotate", @@ -61201,18 +55862,11 @@ "ucsc_liftover", "wittyer" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.04.0", "nf_core_version": "3.5.1", - "plugins": [ - "nf-schema@2.5.1", - "nf-prov@1.2.2" - ], + "plugins": ["nf-schema@2.5.1", "nf-prov@1.2.2"], "co2footprint_files": null }, { @@ -61220,10 +55874,7 @@ "published_at": "2025-07-31T15:05:59Z", "tag_sha": "55e33f4c03e478f79f46f7c268c707640519ab70", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bcftools_annotate", @@ -61260,11 +55911,7 @@ "ucsc_liftover", "wittyer" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.10.5", "nf_core_version": "3.3.2" @@ -61274,10 +55921,7 @@ "published_at": "2025-03-31T21:09:05Z", "tag_sha": "4cce9e45a7f4735ba8da116e7a4c63b4ea574aaa", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bcftools_annotate", @@ -61312,11 +55956,7 @@ "ucsc_liftover", "wittyer" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.2.0" @@ -61326,10 +55966,7 @@ "published_at": "2025-03-07T16:55:58Z", "tag_sha": "2e34d50d377049c7616aa2d96ec3030efa56656d", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bcftools_annotate", @@ -61365,11 +56002,7 @@ "ucsc_liftover", "wittyer" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.2.0" @@ -61379,10 +56012,7 @@ "published_at": "2025-02-24T10:00:45Z", "tag_sha": "7c6e4a7139b3621deb04e99a0c611cfb92558297", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bcftools_annotate", @@ -61416,11 +56046,7 @@ "ucsc_liftover", "wittyer" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=24.04.2", "nf_core_version": "3.2.0" @@ -61430,10 +56056,7 @@ "published_at": "2026-05-21T14:19:57Z", "tag_sha": "4d07dcda08ddcce51933018df2c9daec8479bbc1", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bcftools_annotate", @@ -61477,18 +56100,11 @@ "variantextractor", "wittyer" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.10.4", "nf_core_version": "4.0.2", - "plugins": [ - "nf-schema@2.5.1", - "nf-prov@1.2.2" - ], + "plugins": ["nf-schema@2.5.1", "nf-prov@1.2.2"], "co2footprint_files": null } ] @@ -61578,10 +56194,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": -1, - "master_branch_protection_status_checks": [ - "nf-core", - "Run pipeline with test data" - ], + "master_branch_protection_status_checks": ["nf-core", "Run pipeline with test data"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -61628,10 +56241,7 @@ "published_at": "2023-03-29T06:46:39Z", "tag_sha": "46154522d37b22694edce7b2e75af11e1c28ca26", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bcftools_annotate", @@ -61755,10 +56365,7 @@ "master_branch_exists": false, "main_branch_exists": true, "main_branch_protection_up_to_date": true, - "main_branch_protection_status_checks": [ - "pre-commit", - "nf-core" - ], + "main_branch_protection_status_checks": ["pre-commit", "nf-core"], "main_branch_protection_required_reviews": 2, "main_branch_protection_require_codeowner_review": false, "main_branch_protection_require_non_stale_review": false, @@ -61766,10 +56373,7 @@ "main_uses_ruleset": true, "dev_branch_exists": true, "dev_branch_protection_up_to_date": true, - "dev_branch_protection_status_checks": [ - "pre-commit", - "nf-core" - ], + "dev_branch_protection_status_checks": ["pre-commit", "nf-core"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -61819,15 +56423,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "main_nextflow_config_plugins": [ - "nf-schema@2.6.1" - ], + "main_nextflow_config_plugins": ["nf-schema@2.6.1"], "main_nextflow_config_manifest": { "defaultBranch": "master" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.6.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.6.1"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -61837,10 +56437,7 @@ "published_at": "2026-04-09T08:42:30Z", "tag_sha": "8ba629c53dbdb65057c85a3b0a76a7eb2e8688ef", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bcftools_filter", @@ -61851,17 +56448,11 @@ "tabix_tabix", "untar" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.10.0", "nf_core_version": "3.5.2", - "plugins": [ - "nf-schema@2.6.1" - ], + "plugins": ["nf-schema@2.6.1"], "co2footprint_files": null }, { @@ -61869,10 +56460,7 @@ "published_at": "2026-05-12T09:19:23Z", "tag_sha": "3313b3abff8d6b0d3eb324e434ee4debee9f2bbf", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bcftools_filter", @@ -61883,17 +56471,11 @@ "tabix_tabix", "untar" ], - "subworkflows": [ - "utils_nextflow_pipeline", - "utils_nfcore_pipeline", - "utils_nfschema_plugin" - ] + "subworkflows": ["utils_nextflow_pipeline", "utils_nfcore_pipeline", "utils_nfschema_plugin"] }, "nextflow_version": "!>=25.10.4", "nf_core_version": "4.0.2", - "plugins": [ - "nf-schema@2.6.1" - ], + "plugins": ["nf-schema@2.6.1"], "co2footprint_files": null } ] @@ -62042,10 +56624,7 @@ "published_at": "2018-09-25T07:17:26Z", "tag_sha": "af06171c860f8b63b41df86b6e4a3e15e46ec554", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ] + "doc_files": ["docs/output.md", "docs/usage.md"] } ] }, @@ -62081,13 +56660,7 @@ "web_commit_signoff_required": false, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "chimeric-alignment", - "ctat", - "viral-integration", - "virus", - "virusintegrationfinder" - ], + "topics": ["chimeric-alignment", "ctat", "viral-integration", "virus", "virusintegrationfinder"], "visibility": "public", "forks": 10, "open_issues": 23, @@ -62140,11 +56713,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": -1, - "master_branch_protection_status_checks": [ - "nf-core", - "nf-test docker-latest-everything", - "pre-commit" - ], + "master_branch_protection_status_checks": ["nf-core", "nf-test docker-latest-everything", "pre-commit"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -62152,10 +56721,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "dev_branch_protection_status_checks": ["nf-core", "pre-commit"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -62199,13 +56765,9 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-validation" - ], + "master_nextflow_config_plugins": ["nf-validation"], "master_nextflow_config_manifest": {}, - "dev_nextflow_config_plugins": [ - "nf-validation@1.1.3" - ], + "dev_nextflow_config_plugins": ["nf-validation@1.1.3"], "dev_nextflow_config_manifest": {}, "releases": [ { @@ -62213,10 +56775,7 @@ "published_at": "2023-07-19T17:24:36Z", "tag_sha": "70e558aaff836d43f5d662bf9c28414f4e6db642", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "custom_dumpsoftwareversions", @@ -62237,10 +56796,7 @@ "published_at": "2023-03-29T23:14:38Z", "tag_sha": "88a9d1708a2a8494f4994402440adedd7c527964", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "custom_dumpsoftwareversions", @@ -62261,10 +56817,7 @@ "published_at": "2025-06-02T16:18:05Z", "tag_sha": "46ee6bf894a622d09d3799aa388bc590afda69fb", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "fastqc", @@ -62283,9 +56836,7 @@ }, "nextflow_version": "!>=23.04.0", "nf_core_version": "2.14.1", - "plugins": [ - "nf-validation" - ], + "plugins": ["nf-validation"], "co2footprint_files": null } ] @@ -62322,14 +56873,7 @@ "web_commit_signoff_required": true, "has_pull_requests": true, "pull_request_creation_policy": "all", - "topics": [ - "epidemiology", - "fastq", - "ngs", - "viral-metagenomics", - "virology", - "virus-genomes" - ], + "topics": ["epidemiology", "fastq", "ngs", "viral-metagenomics", "virology", "virus-genomes"], "visibility": "public", "forks": 11, "open_issues": 16, @@ -62383,10 +56927,7 @@ "master_branch_exists": false, "main_branch_exists": true, "main_branch_protection_up_to_date": true, - "main_branch_protection_status_checks": [ - "pre-commit", - "nf-core" - ], + "main_branch_protection_status_checks": ["pre-commit", "nf-core"], "main_branch_protection_required_reviews": 2, "main_branch_protection_require_codeowner_review": false, "main_branch_protection_require_non_stale_review": false, @@ -62394,10 +56935,7 @@ "main_uses_ruleset": true, "dev_branch_exists": true, "dev_branch_protection_up_to_date": true, - "dev_branch_protection_status_checks": [ - "nf-core", - "pre-commit" - ], + "dev_branch_protection_status_checks": ["nf-core", "pre-commit"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -62442,15 +56980,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "main_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "main_nextflow_config_plugins": ["nf-schema@2.5.1"], "main_nextflow_config_manifest": { "defaultBranch": "master" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.5.1"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -62554,9 +57088,7 @@ }, "nextflow_version": "!>=25.04.0", "nf_core_version": "3.5.2", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null }, { @@ -62657,9 +57189,7 @@ }, "nextflow_version": "!>=25.04.0", "nf_core_version": "3.5.1", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null }, { @@ -62759,9 +57289,7 @@ }, "nextflow_version": "!>=25.04.0", "nf_core_version": "3.5.1", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null }, { @@ -62862,9 +57390,7 @@ }, "nextflow_version": "!>=25.04.0", "nf_core_version": "3.4.1", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null }, { @@ -62872,10 +57398,7 @@ "published_at": "2025-02-28T14:53:46Z", "tag_sha": "c882656699bb80541753242b3a797253946edc5c", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bbmap_bbduk", @@ -62966,10 +57489,7 @@ "published_at": "2024-05-08T12:37:29Z", "tag_sha": "1277bd403b270a14949dcb2f4066b12fdb70337e", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "bbmap_bbduk", @@ -63043,10 +57563,7 @@ "vrhyme_vrhyme", "vsearch_cluster" ], - "subworkflows": [ - "bam_stats_samtools", - "fastq_fastqc_umitools_fastp" - ] + "subworkflows": ["bam_stats_samtools", "fastq_fastqc_umitools_fastp"] }, "nextflow_version": "!>=23.04.0", "nf_core_version": null @@ -63150,9 +57667,7 @@ }, "nextflow_version": "!>=25.10.4", "nf_core_version": "4.0.2", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null } ] @@ -63258,9 +57773,7 @@ "team_core_permission_admin": true, "master_branch_exists": true, "master_branch_protection_up_to_date": -1, - "master_branch_protection_status_checks": [ - "nf-core" - ], + "master_branch_protection_status_checks": ["nf-core"], "master_branch_protection_required_reviews": 2, "master_branch_protection_require_codeowner_review": false, "master_branch_protection_require_non_stale_review": false, @@ -63268,9 +57781,7 @@ "main_branch_exists": false, "dev_branch_exists": true, "dev_branch_protection_up_to_date": -1, - "dev_branch_protection_status_checks": [ - "nf-core" - ], + "dev_branch_protection_status_checks": ["nf-core"], "dev_branch_protection_required_reviews": 1, "dev_branch_protection_require_codeowner_review": false, "dev_branch_protection_require_non_stale_review": false, @@ -63419,15 +57930,11 @@ "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, - "master_nextflow_config_plugins": [ - "nf-schema@2.5.1" - ], + "master_nextflow_config_plugins": ["nf-schema@2.5.1"], "master_nextflow_config_manifest": { "defaultBranch": "master" }, - "dev_nextflow_config_plugins": [ - "nf-schema@2.7.2" - ], + "dev_nextflow_config_plugins": ["nf-schema@2.7.2"], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, @@ -63437,10 +57944,7 @@ "published_at": "2025-10-28T14:52:12Z", "tag_sha": "395079f1d24dce731ac22e03d7a5e71f110103fc", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "abacas", @@ -63520,10 +58024,7 @@ "published_at": "2023-03-23T19:29:45Z", "tag_sha": "3731dd3a32a67a2648ea22c2bd980c224abdaee2", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "abacas", @@ -63593,10 +58094,7 @@ "published_at": "2022-07-13T15:42:23Z", "tag_sha": "3ee1fe98fdf17a80922aa8cf4da4afaf483f3429", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "abacas", @@ -63660,10 +58158,7 @@ "published_at": "2022-03-01T18:56:44Z", "tag_sha": "42e38bba3da80484bc480f53d2130642a349e8c6", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "abacas", @@ -63727,10 +58222,7 @@ "published_at": "2022-02-22T08:45:08Z", "tag_sha": "fbcb2ce94c9abded00d9fcb5181daa17b9ecd55e", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "abacas", @@ -63794,10 +58286,7 @@ "published_at": "2022-02-15T16:30:07Z", "tag_sha": "97bebf8fe12e0e802d4468e133f3a2277ceb843c", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "abacas", @@ -63861,10 +58350,7 @@ "published_at": "2022-02-04T17:59:26Z", "tag_sha": "fc9fece226061594208a25c8acdc05b0bf7c14d1", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "abacas", @@ -63928,10 +58414,7 @@ "published_at": "2021-07-29T15:45:45Z", "tag_sha": "2ebae61442598302c64916bd5127cf23c8ab5611", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "abacas", @@ -63989,10 +58472,7 @@ "published_at": "2021-06-15T14:58:31Z", "tag_sha": "f0171324a60d1759ca7f5d02351372d97d22cc12", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": "!>=21.04.0" }, { @@ -64000,10 +58480,7 @@ "published_at": "2021-05-13T15:11:46Z", "tag_sha": "a85d5969f9025409e3618d6c280ef15ce417df65", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": "!>=21.04.0" }, { @@ -64011,10 +58488,7 @@ "published_at": "2020-06-23T16:58:09Z", "tag_sha": "75a2f9763e9b4c1aa20ad342ae3ce148c33cc65a", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=19.10.0" }, { @@ -64022,10 +58496,7 @@ "published_at": "2020-06-01T13:30:31Z", "tag_sha": "7422b0d353b1a295fb7cda47f2f7750c3bd890d1", "has_schema": false, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "nextflow_version": ">=19.10.0" }, { @@ -64033,10 +58504,7 @@ "published_at": "2026-05-13T15:07:01Z", "tag_sha": "687bca385020f33126071d9f57018b613497d3a6", "has_schema": true, - "doc_files": [ - "docs/output.md", - "docs/usage.md" - ], + "doc_files": ["docs/output.md", "docs/usage.md"], "components": { "modules": [ "abacas", @@ -64111,12 +58579,10 @@ }, "nextflow_version": "!>=25.10.4", "nf_core_version": "4.0.2", - "plugins": [ - "nf-schema@2.5.1" - ], + "plugins": ["nf-schema@2.5.1"], "co2footprint_files": null } ] } ] -} \ No newline at end of file +} diff --git a/sites/configs/tsconfig.json b/sites/configs/tsconfig.json index 017f81bf0a..15b848d59f 100644 --- a/sites/configs/tsconfig.json +++ b/sites/configs/tsconfig.json @@ -16,8 +16,5 @@ "strictNullChecks": true }, "include": [".astro/types.d.ts", "**/*"], - "exclude": [ - "node_modules", - "dist", - ] + "exclude": ["node_modules", "dist"] } diff --git a/sites/docs/tsconfig.json b/sites/docs/tsconfig.json index 017f81bf0a..15b848d59f 100644 --- a/sites/docs/tsconfig.json +++ b/sites/docs/tsconfig.json @@ -16,8 +16,5 @@ "strictNullChecks": true }, "include": [".astro/types.d.ts", "**/*"], - "exclude": [ - "node_modules", - "dist", - ] + "exclude": ["node_modules", "dist"] } diff --git a/sites/main-site/public/params.json b/sites/main-site/public/params.json new file mode 120000 index 0000000000..5000dd24ae --- /dev/null +++ b/sites/main-site/public/params.json @@ -0,0 +1 @@ +../../../public/params.json \ No newline at end of file diff --git a/sites/main-site/src/components/BaseHead.astro b/sites/main-site/src/components/BaseHead.astro index 2a22866524..de7cda81ba 100644 --- a/sites/main-site/src/components/BaseHead.astro +++ b/sites/main-site/src/components/BaseHead.astro @@ -100,6 +100,10 @@ description = description?.replaceAll(/<[^>]*>?/g, ""); + +{#if loading} +
+ + Loading params data… +
+{:else if error} +
Failed to load params.json: {error}
+{:else} +
+
+ + +
+ +
+ + +
+ +
+ + +
+ +
+ +
+ + + {filteredParams.length} params and {sortedPipelines.length} pipelines + +
+ +
+ + + + + {#each sortedPipelines as pipeline} + {@const usedCount = pipelineCounts.get(pipeline) ?? 0} + {@const version = pipelineVersions.get(pipeline)} + {@const isDev = version === "dev"} + + {/each} + + + + {#each filteredParams as param} + + + {#each sortedPipelines as pipeline} + + {/each} + + {/each} + +
+
+ {pipeline} + {#if isDev} + + {/if} +
+
{@html param.label}
+
+{/if} + + diff --git a/sites/main-site/src/components/SpecialInterestGroupsListing.svelte b/sites/main-site/src/components/SpecialInterestGroupsListing.svelte index 52dc50ffd5..de7f8428e6 100644 --- a/sites/main-site/src/components/SpecialInterestGroupsListing.svelte +++ b/sites/main-site/src/components/SpecialInterestGroupsListing.svelte @@ -2,6 +2,7 @@ import ListingTableHeader from "@components/ListingTableHeader.svelte"; import ListingCard from "./ListingCard.svelte"; import { DisplayStyle, SearchQuery } from "@components/store"; + import { bsTooltip } from "@components/actions"; import type { CollectionEntry } from "astro:content"; @@ -75,7 +76,7 @@ target="_blank" rel="noopener noreferrer" class="badge text-bg-dark text-decoration-none" - data-bs-toggle="tooltip" + use:bsTooltip title={getLeadName(lead)} > @{getLeadName(lead)} @@ -128,7 +129,7 @@ target="_blank" rel="noopener noreferrer" class="badge text-bg-dark text-decoration-none" - data-bs-toggle="tooltip" + use:bsTooltip title={getLeadName(lead)} > @{getLeadName(lead)} diff --git a/sites/main-site/src/components/TagSection.svelte b/sites/main-site/src/components/TagSection.svelte index 11343dced0..417dac20fb 100644 --- a/sites/main-site/src/components/TagSection.svelte +++ b/sites/main-site/src/components/TagSection.svelte @@ -8,6 +8,8 @@ inline?: boolean; } + import { bsTooltip } from "@components/actions"; + let { tags, maxShown = 0, type, inline = false, includes = false, included = false }: Props = $props(); let expanded = $state(false); @@ -52,7 +54,7 @@ onkeydown={onclick} tabindex="0" role="button" - data-bs-toggle="tooltip" + use:bsTooltip data-bs-delay="500" > {#if expanded} diff --git a/sites/main-site/src/components/ThemeSwitch.svelte b/sites/main-site/src/components/ThemeSwitch.svelte index 058fb96f73..f9fcfba1dd 100644 --- a/sites/main-site/src/components/ThemeSwitch.svelte +++ b/sites/main-site/src/components/ThemeSwitch.svelte @@ -1,5 +1,6 @@ -
+